From d446ef2f771c275aa40f7baecc22c2c1d1af4621 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Thu, 21 Sep 2017 11:35:14 -0500 Subject: [PATCH 01/46] cleanup markdown --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 6bb2742..5e26adb 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ JSON files are generated by Swagger editor. ## Development Guidelines -** Git Structure +### Git Structure * This project uses the Git Flow methodology for code management and development: . @@ -25,17 +25,17 @@ JSON files are generated by Swagger editor. double-check your branches and merge operations so the two versions do not get mixed up. - * The *v1-master* branch is the master branch for ongoing V1 API - work, with *v1-develop* as its develop branch. + * The **v1-master** branch is the master branch for ongoing V1 API + work, with **v1-develop** as its develop branch. - * The *master* branch is for ongoing V2 API work, with *develop* as + * The **master** branch is for ongoing V2 API work, with **develop** as its develop branch. * New development and features should be done on branches that are - cloned from the *develop* (for V2) or *v1-develop* (for V1) branch, + cloned from the **develop** (for V2) or **v1-develop** (for V1) branch, and then merged into this branch when completed. - * Releases should merge *develop* into *master* (for V2) or - *v1-develop* into *v1-master* (for V1). Tag *master* or *v1-master* - *with the appropriate version. + * Releases should merge **develop** into **master** (for V2) or + **v1-develop** into **v1-master** (for V1). Tag **master** or **v1-master** + with the appropriate version. From 6eacbc441dab05504a7d8781bca204e1bc3e1052 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Sat, 23 Sep 2017 14:03:45 +1200 Subject: [PATCH 02/46] Move to version 2.0.5, with addition of a large number of AIRR fields (with correct AIRR names and descriptions in the response model). Added: - All of study fields - All of subject fields - All of sample fields - Those processing and diagnostic fields that exist in our current model YAML code works in editor, but the AIRR fields are only used in the model elements of the responses. Parameters part of the samples call are not AIRR compliant and the field names are wrong. --- iReceptor_Data_Service_API_V2.json | 507 +++++++++++++++++------------ iReceptor_Data_Service_API_V2.yaml | 502 ++++++++++++++++------------ 2 files changed, 599 insertions(+), 410 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 1481731..f998dff 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -2,7 +2,7 @@ "swagger": "2.0", "info": { "title": "iReceptor Data Source API", - "version": "2.0.4", + "version": "2.0.5", "contact": { "name": "iReceptor Project", "url": "http://www.ireceptor.org/", @@ -13,7 +13,6 @@ "host": "ipa.ireceptor.org", "basePath": "/v2", "schemes": [ - "http", "https" ], "produces": [ @@ -154,99 +153,143 @@ "properties": { "sequence_count": { "type": "integer", - "description": "e.g. 0\n" + "description": "The number of sequences that match the filter for this sample.\n" + }, + "study_id": { + "type": "string", + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" + }, + "study_title": { + "type": "string", + "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" }, - "subject_code": { + "study_type": { "type": "string", - "description": "e.g. Subject One\n" + "description": "Type of project/study (e.g. Cancer) (AIRR)\n" + }, + "inclusion_exclusion_criteria": { + "type": "string", + "description": "Study inclusion/exclusion criteria (AIRR)\n" + }, + "grants": { + "type": "string", + "description": "Grant funding agency (AIRR)\n" + }, + "lab_name": { + "type": "string", + "description": "Lab name (AIRR) \n" + }, + "collected_by": { + "type": "string", + "description": "Contact information (data collection) (AIRR)\n" + }, + "uploaded_by": { + "type": "string", + "description": "Contact information (data deposition) (AIRR)\n" + }, + "lab_address": { + "type": "string", + "description": "Lab address (AIRR)\n" + }, + "pubs_ids": { + "type": "string", + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" }, "subject_id": { - "type": "integer", - "description": "e.g. 1\n" + "type": "string", + "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" }, - "subject_gender": { + "organism": { "type": "string", - "description": "e.g. Male\n" + "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" }, - "subject_ethnicity": { + "sex": { "type": "string", - "description": "e.g. Eth1\n" + "description": "Sex (e.g. M/F) (AIRR)\n" }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" + "age": { + "type": "string", + "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" }, - "project_id": { - "type": "integer", - "description": "e.g. 0\n" + "age_event": { + "type": "string", + "description": "Age event (e.g. Enrollment) (AIRR)\n" }, - "study_title": { + "ancestry_population": { "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name)\n" + "description": "Ancestry population (AIRR)\n" }, - "study_type": { + "ethnicity": { "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type)\n" + "description": "Ethnicity (e.g. Tamil) (AIRR)\n" }, - "project_parent_id": { - "type": "integer", - "description": "e.g. null\n" + "race": { + "type": "string", + "description": "Race (e.g. South Indian) (AIRR)\n" }, - "lab_id": { - "type": "integer", - "description": "e.g. 0\n" + "species_name": { + "type": "string", + "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" }, - "lab_name": { + "strain_name": { "type": "string", - "description": "Name of the Laboratory running the study (AIRR)\n" + "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" }, - "case_control_id": { - "type": "integer", - "description": "e.g. 0\n" + "linked_subjects": { + "type": "string", + "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" }, - "case_control_name": { + "link_type": { "type": "string", - "description": "e.g. Control\n" + "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" }, "sample_id": { - "type": "integer", - "description": "e.g. 0\n" + "type": "string", + "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" }, - "sample_name": { + "sample_type": { "type": "string", - "description": "e.g. Blood Sample 01\n" + "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 0\n" + "tissue": { + "type": "string", + "description": "Anatomic site (e.g. spleen) (AIRR)\n" }, - "sample_subject_id": { - "type": "integer", - "description": "e.g. 0\n" + "disease_state_sample": { + "type": "string", + "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" }, - "dna_id": { - "type": "integer", - "description": "e.g. 0\n" + "collection_date": { + "type": "string", + "description": "Sample collection time (e.g. 10 days) (AIRR)\n" }, - "dna_type": { + "collection_time_event": { "type": "string", - "description": "e.g. cDNA\n" + "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" }, - "sample_source_id": { - "type": "integer", - "description": "e.g. 0\n" + "source_commercial": { + "type": "string", + "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" + }, + "cell_subset": { + "type": "string", + "description": "Cell subset (Controlled vocabulary) (AIRR)\n" }, - "sample_source_name": { + "cell_phenotype": { "type": "string", - "description": "e.g. Blood (PBMC)\n" + "description": "Cell subset phenotype (lab specific description) (AIRR)\n" }, - "lab_cell_subset_name": { + "study_group_description": { "type": "string", - "description": "e.g. Naive B Alpha\n" + "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" }, - "ireceptor_cell_subset_name": { + "library_source": { "type": "string", - "description": "e.g. Naive B\n" + "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" + }, + "subject_age": { + "type": "integer", + "description": "e.g. 1\n" }, "marker_1": { "type": "string", @@ -271,46 +314,49 @@ "marker_6": { "type": "string", "description": "e.g. null\n" + }, + "subject_db_id": { + "type": "integer", + "description": "Identifier used by repository to identify a subject.\n" + }, + "project_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "project_parent_db_id": { + "type": "integer", + "description": "e.g. null\n" + }, + "lab_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "case_control_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "sample_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "project_sample_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "sample_subject_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "dna_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "sample_source_db_id": { + "type": "integer", + "description": "e.g. 0\n" } } } - }, - "examples": { - "application/json": [ - { - "sequence_count": 1234567, - "subject_code": "Subject One", - "subject_id": 1, - "subject_gender": "Male", - "subject_ethnicity": "Caucasian", - "subject_species": "Human", - "project_id": 0, - "study_title": "First Project", - "study_type": "Cancer", - "project_parent_id": null, - "lab_id": 0, - "lab_name": "First Lab", - "case_control_id": 0, - "case_control_name": "Control", - "sample_id": 1, - "project_sample_id": 1, - "sample_name": "Blood Sample 01", - "subject_age": 22, - "sample_subject_id": 1, - "dna_id": 1, - "dna_type": "cDNA", - "sample_source_id": 2, - "sample_source_name": "Blood (PBMC)", - "lab_cell_subset_name": "Naive B Alpha", - "ireceptor_cell_subset_name": "Naive B", - "marker_1": "CR19", - "marker_2": "CR20", - "marker_3": "CR21", - "marker_4": null, - "marker_5": null, - "marker_6": null - } - ] } }, "400": { @@ -427,105 +473,145 @@ "items": { "type": "object", "properties": { - "subject_code": { + "sequence_count": { + "type": "integer", + "description": "The number of sequences that match the filter for this sample.\n" + }, + "study_id": { "type": "string", - "description": "e.g. Subject One\n" + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" }, - "subject_id": { - "type": "integer", - "description": "e.g. 1\n" + "study_title": { + "type": "string", + "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" }, - "subject_gender": { + "study_type": { "type": "string", - "description": "e.g. Male\n" + "description": "Type of project/study (e.g. Cancer) (AIRR)\n" }, - "subject_ethnicity": { + "inclusion_exclusion_criteria": { "type": "string", - "description": "e.g. Caucasian\n" + "description": "Study inclusion/exclusion criteria (AIRR)\n" }, - "subject_species": { + "grants": { "type": "string", - "description": "e.g. Human\n" + "description": "Grant funding agency (AIRR)\n" }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" + "lab_name": { + "type": "string", + "description": "Lab name (AIRR) \n" }, - "project_id": { - "type": "integer", - "description": "e.g. 0\n" + "collected_by": { + "type": "string", + "description": "Contact information (data collection) (AIRR)\n" }, - "study_title": { + "uploaded_by": { "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name)\n" + "description": "Contact information (data deposition) (AIRR)\n" }, - "study_type": { + "lab_address": { "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type)\n" + "description": "Lab address (AIRR)\n" }, - "project_parent_id": { - "type": "integer", - "description": "e.g. null\n" + "pubs_ids": { + "type": "string", + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" }, - "lab_id": { - "type": "integer", - "description": "e.g. 0\n" + "subject_id": { + "type": "string", + "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" }, - "lab_name": { + "organism": { "type": "string", - "description": "Name of the Laboratory running the study (AIRR)\n" + "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" }, - "case_control_id": { - "type": "integer", - "description": "e.g. 0\n" + "sex": { + "type": "string", + "description": "Sex (e.g. M/F) (AIRR)\n" }, - "case_control_name": { + "age": { "type": "string", - "description": "e.g. Control\n" + "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" + }, + "age_event": { + "type": "string", + "description": "Age event (e.g. Enrollment) (AIRR)\n" + }, + "ancestry_population": { + "type": "string", + "description": "Ancestry population (AIRR)\n" + }, + "ethnicity": { + "type": "string", + "description": "Ethnicity (e.g. Tamil) (AIRR)\n" + }, + "race": { + "type": "string", + "description": "Race (e.g. South Indian) (AIRR)\n" + }, + "species_name": { + "type": "string", + "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" + }, + "strain_name": { + "type": "string", + "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" + }, + "linked_subjects": { + "type": "string", + "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" + }, + "link_type": { + "type": "string", + "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" }, "sample_id": { - "type": "integer", - "description": "e.g. 0\n" + "type": "string", + "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" }, - "sample_name": { + "sample_type": { "type": "string", - "description": "e.g. Blood Sample 01\n" + "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 0\n" + "tissue": { + "type": "string", + "description": "Anatomic site (e.g. spleen) (AIRR)\n" }, - "sample_subject_id": { - "type": "integer", - "description": "e.g. 0\n" + "disease_state_sample": { + "type": "string", + "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" }, - "sequence_count": { - "type": "integer", - "description": "e.g. 0\n" + "collection_date": { + "type": "string", + "description": "Sample collection time (e.g. 10 days) (AIRR)\n" }, - "dna_id": { - "type": "integer", - "description": "e.g. 0\n" + "collection_time_event": { + "type": "string", + "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" }, - "dna_type": { + "source_commercial": { "type": "string", - "description": "e.g. cDNA\n" + "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" }, - "sample_source_id": { - "type": "integer", - "description": "e.g. 0\n" + "cell_subset": { + "type": "string", + "description": "Cell subset (Controlled vocabulary) (AIRR)\n" }, - "sample_source_name": { + "cell_phenotype": { "type": "string", - "description": "e.g. Blood (PBMC)\n" + "description": "Cell subset phenotype (lab specific description) (AIRR)\n" }, - "lab_cell_subset_name": { + "study_group_description": { "type": "string", - "description": "e.g. Naive B Alpha\n" + "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" }, - "ireceptor_cell_subset_name": { + "library_source": { "type": "string", - "description": "e.g. Naive B\n" + "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" + }, + "subject_age": { + "type": "integer", + "description": "e.g. 1\n" }, "marker_1": { "type": "string", @@ -550,46 +636,49 @@ "marker_6": { "type": "string", "description": "e.g. null\n" + }, + "subject_db_id": { + "type": "integer", + "description": "Identifier used by repository to identify a subject.\n" + }, + "project_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "project_parent_db_id": { + "type": "integer", + "description": "e.g. null\n" + }, + "lab_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "case_control_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "sample_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "project_sample_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "sample_subject_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "dna_db_id": { + "type": "integer", + "description": "e.g. 0\n" + }, + "sample_source_db_id": { + "type": "integer", + "description": "e.g. 0\n" } } } - }, - "examples": { - "application/json": [ - { - "sequence_count": 1234567, - "subject_code": "Subject One", - "subject_id": 1, - "subject_gender": "Male", - "subject_ethnicity": "Caucasian", - "subject_species": "Human", - "project_id": 0, - "study_title": "First Project", - "study_type": "Cancer", - "project_parent_id": null, - "lab_id": 0, - "lab_name": "First Lab", - "case_control_id": 0, - "case_control_name": "Control", - "sample_id": 1, - "project_sample_id": 1, - "sample_name": "Blood Sample 01", - "subject_age": 22, - "sample_subject_id": 1, - "dna_id": 1, - "dna_type": "cDNA", - "sample_source_id": 2, - "sample_source_name": "Blood (PBMC)", - "lab_cell_subset_name": "Naive B Alpha", - "ireceptor_cell_subset_name": "Naive B", - "marker_1": "CR19", - "marker_2": "CR20", - "marker_3": "CR21", - "marker_4": null, - "marker_5": null, - "marker_6": null - } - ] } }, "400": { @@ -665,6 +754,22 @@ "items": { "type": "object", "properties": { + "sequence_count": { + "type": "integer", + "description": "e.g. 0\n" + }, + "study_title": { + "type": "string", + "description": "Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name)\n" + }, + "study_type": { + "type": "string", + "description": "Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type)\n" + }, + "study": { + "type": "string", + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)(sra_accession)\n" + }, "subject_code": { "type": "string", "description": "e.g. Subject One\n" @@ -693,22 +798,10 @@ "type": "integer", "description": "e.g. 0\n" }, - "study_title": { - "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name)\n" - }, - "study_type": { - "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type)\n" - }, "project_parent_id": { "type": "integer", "description": "e.g. null\n" }, - "study": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)(sra_accession)\n" - }, "lab_id": { "type": "integer", "description": "e.g. 0\n" @@ -749,10 +842,6 @@ "type": "integer", "description": "e.g. 0\n" }, - "sequence_count": { - "type": "integer", - "description": "e.g. 0\n" - }, "dna_id": { "type": "integer", "description": "e.g. 0\n" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index eed031d..a53afcd 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -1,7 +1,7 @@ swagger: '2.0' info: title: iReceptor Data Source API - version: 2.0.4 + version: 2.0.5 contact: name: iReceptor Project url: 'http://www.ireceptor.org/' @@ -15,7 +15,6 @@ info: host: ipa.ireceptor.org basePath: /v2 schemes: - - http - https produces: - application/json @@ -142,99 +141,143 @@ paths: sequence_count: type: integer description: | - e.g. 0 - subject_code: + The number of sequences that match the filter for this sample. + study_id: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + study_title: + type: string + description: | + Publication or Protocol Title (e.g. My Study) (AIRR) + study_type: + type: string + description: | + Type of project/study (e.g. Cancer) (AIRR) + inclusion_exclusion_criteria: + type: string + description: | + Study inclusion/exclusion criteria (AIRR) + grants: + type: string + description: | + Grant funding agency (AIRR) + lab_name: + type: string + description: | + Lab name (AIRR) + collected_by: + type: string + description: | + Contact information (data collection) (AIRR) + uploaded_by: + type: string + description: | + Contact information (data deposition) (AIRR) + lab_address: + type: string + description: | + Lab address (AIRR) + pubs_ids: type: string description: | - e.g. Subject One + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) subject_id: - type: integer + type: string description: | - e.g. 1 - subject_gender: + UID assigned by submitter (e.g. SUB856413) (AIRR) + organism: type: string description: | - e.g. Male - subject_ethnicity: + Organism-based (human, mouse) or synthetic (AIRR) + sex: type: string description: | - e.g. Eth1 - subject_age: - type: integer + Sex (e.g. M/F) (AIRR) + age: + type: string description: | - e.g. 1 - project_id: - type: integer + Age - Time duration and unit (e.g. 200 days) (AIRR) + age_event: + type: string description: | - e.g. 0 - study_title: + Age event (e.g. Enrollment) (AIRR) + ancestry_population: type: string description: | - Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name) - study_type: + Ancestry population (AIRR) + ethnicity: type: string description: | - Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type) - project_parent_id: - type: integer + Ethnicity (e.g. Tamil) (AIRR) + race: + type: string description: | - e.g. null - lab_id: - type: integer + Race (e.g. South Indian) (AIRR) + species_name: + type: string description: | - e.g. 0 - lab_name: + Species name (e.g. Homo Sapiens) (AIRR) + strain_name: type: string description: | - Name of the Laboratory running the study (AIRR) - case_control_id: - type: integer + Strain name (e.g. C57BL/6J) (AIRR) + linked_subjects: + type: string description: | - e.g. 0 - case_control_name: + Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) + link_type: type: string description: | - e.g. Control + Relation type (.e.g sister, father, daughter) (AIRR) sample_id: - type: integer + type: string description: | - e.g. 0 - sample_name: + Biological sample ID - UID assigned by submitter (AIRR) + sample_type: type: string description: | - e.g. Blood Sample 01 - project_sample_id: - type: integer + Sample type (e.g. Tissue, body fluid) (AIRR) + tissue: + type: string description: | - e.g. 0 - sample_subject_id: - type: integer + Anatomic site (e.g. spleen) (AIRR) + disease_state_sample: + type: string description: | - e.g. 0 - dna_id: - type: integer + Disease state of sample (e.g. tumor vs margin) (AIRR) + collection_date: + type: string description: | - e.g. 0 - dna_type: + Sample collection time (e.g. 10 days) (AIRR) + collection_time_event: type: string description: | - e.g. cDNA - sample_source_id: - type: integer + Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) + source_commercial: + type: string description: | - e.g. 0 - sample_source_name: + Commercial source of sample (e.g. XYZ Pharma) (AIRR) + cell_subset: + type: string + description: | + Cell subset (Controlled vocabulary) (AIRR) + cell_phenotype: type: string description: | - e.g. Blood (PBMC) - lab_cell_subset_name: + Cell subset phenotype (lab specific description) (AIRR) + study_group_description: type: string description: | - e.g. Naive B Alpha - ireceptor_cell_subset_name: + Study group description (e.g. Case vs. Control) (AIRR) + library_source: type: string description: | - e.g. Naive B + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) + subject_age: + type: integer + description: | + e.g. 1 marker_1: type: string description: | @@ -259,39 +302,46 @@ paths: type: string description: | e.g. null - examples: - application/json: - - sequence_count: 1234567 - subject_code: Subject One - subject_id: 1 - subject_gender: Male - subject_ethnicity: Caucasian - subject_species: Human - project_id: 0 - study_title: First Project - study_type: Cancer - project_parent_id: null - lab_id: 0 - lab_name: First Lab - case_control_id: 0 - case_control_name: Control - sample_id: 1 - project_sample_id: 1 - sample_name: Blood Sample 01 - subject_age: 22 - sample_subject_id: 1 - dna_id: 1 - dna_type: cDNA - sample_source_id: 2 - sample_source_name: Blood (PBMC) - lab_cell_subset_name: Naive B Alpha - ireceptor_cell_subset_name: Naive B - marker_1: CR19 - marker_2: CR20 - marker_3: CR21 - marker_4: null - marker_5: null - marker_6: null + subject_db_id: + type: integer + description: | + Identifier used by repository to identify a subject. + project_db_id: + type: integer + description: | + e.g. 0 + project_parent_db_id: + type: integer + description: | + e.g. null + lab_db_id: + type: integer + description: | + e.g. 0 + case_control_db_id: + type: integer + description: | + e.g. 0 + sample_db_id: + type: integer + description: | + e.g. 0 + project_sample_db_id: + type: integer + description: | + e.g. 0 + sample_subject_db_id: + type: integer + description: | + e.g. 0 + dna_db_id: + type: integer + description: | + e.g. 0 + sample_source_db_id: + type: integer + description: | + e.g. 0 '400': description: malformed request '401': @@ -399,106 +449,146 @@ paths: items: type: object properties: - subject_code: + sequence_count: + type: integer + description: | + The number of sequences that match the filter for this sample. + study_id: type: string description: | - e.g. Subject One - subject_id: - type: integer + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + study_title: + type: string description: | - e.g. 1 - subject_gender: + Publication or Protocol Title (e.g. My Study) (AIRR) + study_type: type: string description: | - e.g. Male - subject_ethnicity: + Type of project/study (e.g. Cancer) (AIRR) + inclusion_exclusion_criteria: type: string description: | - e.g. Caucasian - subject_species: + Study inclusion/exclusion criteria (AIRR) + grants: type: string description: | - e.g. Human - subject_age: - type: integer + Grant funding agency (AIRR) + lab_name: + type: string description: | - e.g. 1 - project_id: - type: integer + Lab name (AIRR) + collected_by: + type: string description: | - e.g. 0 - study_title: + Contact information (data collection) (AIRR) + uploaded_by: type: string description: | - Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name) - study_type: + Contact information (data deposition) (AIRR) + lab_address: type: string description: | - Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type) - project_parent_id: - type: integer + Lab address (AIRR) + pubs_ids: + type: string description: | - e.g. null - lab_id: - type: integer + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + subject_id: + type: string description: | - e.g. 0 - lab_name: + UID assigned by submitter (e.g. SUB856413) (AIRR) + organism: type: string description: | - Name of the Laboratory running the study (AIRR) - case_control_id: - type: integer + Organism-based (human, mouse) or synthetic (AIRR) + sex: + type: string description: | - e.g. 0 - case_control_name: + Sex (e.g. M/F) (AIRR) + age: + type: string + description: | + Age - Time duration and unit (e.g. 200 days) (AIRR) + age_event: type: string description: | - e.g. Control + Age event (e.g. Enrollment) (AIRR) + ancestry_population: + type: string + description: | + Ancestry population (AIRR) + ethnicity: + type: string + description: | + Ethnicity (e.g. Tamil) (AIRR) + race: + type: string + description: | + Race (e.g. South Indian) (AIRR) + species_name: + type: string + description: | + Species name (e.g. Homo Sapiens) (AIRR) + strain_name: + type: string + description: | + Strain name (e.g. C57BL/6J) (AIRR) + linked_subjects: + type: string + description: | + Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) + link_type: + type: string + description: | + Relation type (.e.g sister, father, daughter) (AIRR) sample_id: - type: integer + type: string description: | - e.g. 0 - sample_name: + Biological sample ID - UID assigned by submitter (AIRR) + sample_type: type: string description: | - e.g. Blood Sample 01 - project_sample_id: - type: integer + Sample type (e.g. Tissue, body fluid) (AIRR) + tissue: + type: string description: | - e.g. 0 - sample_subject_id: - type: integer + Anatomic site (e.g. spleen) (AIRR) + disease_state_sample: + type: string description: | - e.g. 0 - sequence_count: - type: integer + Disease state of sample (e.g. tumor vs margin) (AIRR) + collection_date: + type: string description: | - e.g. 0 - dna_id: - type: integer + Sample collection time (e.g. 10 days) (AIRR) + collection_time_event: + type: string description: | - e.g. 0 - dna_type: + Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) + source_commercial: type: string description: | - e.g. cDNA - sample_source_id: - type: integer + Commercial source of sample (e.g. XYZ Pharma) (AIRR) + cell_subset: + type: string description: | - e.g. 0 - sample_source_name: + Cell subset (Controlled vocabulary) (AIRR) + cell_phenotype: type: string description: | - e.g. Blood (PBMC) - lab_cell_subset_name: + Cell subset phenotype (lab specific description) (AIRR) + study_group_description: type: string description: | - e.g. Naive B Alpha - ireceptor_cell_subset_name: + Study group description (e.g. Case vs. Control) (AIRR) + library_source: type: string description: | - e.g. Naive B + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) + subject_age: + type: integer + description: | + e.g. 1 marker_1: type: string description: | @@ -523,39 +613,46 @@ paths: type: string description: | e.g. null - examples: - application/json: - - sequence_count: 1234567 - subject_code: Subject One - subject_id: 1 - subject_gender: Male - subject_ethnicity: Caucasian - subject_species: Human - project_id: 0 - study_title: First Project - study_type: Cancer - project_parent_id: null - lab_id: 0 - lab_name: First Lab - case_control_id: 0 - case_control_name: Control - sample_id: 1 - project_sample_id: 1 - sample_name: Blood Sample 01 - subject_age: 22 - sample_subject_id: 1 - dna_id: 1 - dna_type: cDNA - sample_source_id: 2 - sample_source_name: Blood (PBMC) - lab_cell_subset_name: Naive B Alpha - ireceptor_cell_subset_name: Naive B - marker_1: CR19 - marker_2: CR20 - marker_3: CR21 - marker_4: null - marker_5: null - marker_6: null + subject_db_id: + type: integer + description: | + Identifier used by repository to identify a subject. + project_db_id: + type: integer + description: | + e.g. 0 + project_parent_db_id: + type: integer + description: | + e.g. null + lab_db_id: + type: integer + description: | + e.g. 0 + case_control_db_id: + type: integer + description: | + e.g. 0 + sample_db_id: + type: integer + description: | + e.g. 0 + project_sample_db_id: + type: integer + description: | + e.g. 0 + sample_subject_db_id: + type: integer + description: | + e.g. 0 + dna_db_id: + type: integer + description: | + e.g. 0 + sample_source_db_id: + type: integer + description: | + e.g. 0 '400': description: malformed request '401': @@ -617,6 +714,22 @@ paths: items: type: object properties: + sequence_count: + type: integer + description: | + e.g. 0 + study_title: + type: string + description: | + Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name) + study_type: + type: string + description: | + Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type) + study: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)(sra_accession) subject_code: type: string description: | @@ -645,22 +758,12 @@ paths: type: integer description: | e.g. 0 - study_title: - type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name) - study_type: - type: string - description: | - Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type) + project_parent_id: type: integer description: | e.g. null - study: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)(sra_accession) + lab_id: type: integer description: | @@ -701,10 +804,7 @@ paths: type: integer description: | e.g. 0 - sequence_count: - type: integer - description: | - e.g. 0 + dna_id: type: integer description: | From 2ab6df75e004c855eda23ac1e915eb541870164e Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Sat, 23 Sep 2017 14:30:11 +1200 Subject: [PATCH 03/46] Updated a few desciptions for the non AIRR fields in the response. --- iReceptor_Data_Service_API_V2.json | 52 +++++++++++++------------- iReceptor_Data_Service_API_V2.yaml | 60 +++++++++++++++++------------- 2 files changed, 60 insertions(+), 52 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index f998dff..434465d 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -317,43 +317,43 @@ }, "subject_db_id": { "type": "integer", - "description": "Identifier used by repository to identify a subject.\n" + "description": "Identifier used internally by the repository to identify a subject.\n" }, "project_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a project.\n" }, "project_parent_db_id": { "type": "integer", - "description": "e.g. null\n" + "description": "Identifier used internally by the repository to identify a parent/child\nrelationship between this project and its parent project.\n" }, "lab_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a lab.\n" }, "case_control_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" }, "sample_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a sample.\n" }, - "project_sample_db_id": { + "dna_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a DNA type.\n" }, - "sample_subject_db_id": { + "project_sample_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an association\na project with a sample.\n" }, - "dna_db_id": { + "sample_subject_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a subject.\n" }, "sample_source_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a sample source.\n" } } } @@ -639,43 +639,43 @@ }, "subject_db_id": { "type": "integer", - "description": "Identifier used by repository to identify a subject.\n" + "description": "Identifier used internally by the repository to identify a subject.\n" }, "project_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a project.\n" }, "project_parent_db_id": { "type": "integer", - "description": "e.g. null\n" + "description": "Identifier used internally by the repository to identify a parent/child\nrelationship between this project and its parent project.\n" }, "lab_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a lab.\n" }, "case_control_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" }, "sample_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a sample.\n" }, - "project_sample_db_id": { + "dna_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify a DNA type.\n" }, - "sample_subject_db_id": { + "project_sample_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an association\na project with a sample.\n" }, - "dna_db_id": { + "sample_subject_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a subject.\n" }, "sample_source_db_id": { "type": "integer", - "description": "e.g. 0\n" + "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a sample source.\n" } } } diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index a53afcd..ca3ae69 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -305,43 +305,47 @@ paths: subject_db_id: type: integer description: | - Identifier used by repository to identify a subject. + Identifier used internally by the repository to identify a subject. project_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify a project. project_parent_db_id: type: integer description: | - e.g. null + Identifier used internally by the repository to identify a parent/child + relationship between this project and its parent project. lab_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify a lab. case_control_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify an element in the case_control table. sample_db_id: type: integer description: | - e.g. 0 - project_sample_db_id: + Identifier used internally by the repository to identify a sample. + dna_db_id: type: integer description: | - e.g. 0 - sample_subject_db_id: + Identifier used internally by the repository to identify a DNA type. + project_sample_db_id: type: integer description: | - e.g. 0 - dna_db_id: + Identifier used internally by the repository to identify an association + a project with a sample. + sample_subject_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify an association + between a sample and a subject. sample_source_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify an association + between a sample and a sample source. '400': description: malformed request '401': @@ -616,43 +620,47 @@ paths: subject_db_id: type: integer description: | - Identifier used by repository to identify a subject. + Identifier used internally by the repository to identify a subject. project_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify a project. project_parent_db_id: type: integer description: | - e.g. null + Identifier used internally by the repository to identify a parent/child + relationship between this project and its parent project. lab_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify a lab. case_control_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify an element in the case_control table. sample_db_id: type: integer description: | - e.g. 0 - project_sample_db_id: + Identifier used internally by the repository to identify a sample. + dna_db_id: type: integer description: | - e.g. 0 - sample_subject_db_id: + Identifier used internally by the repository to identify a DNA type. + project_sample_db_id: type: integer description: | - e.g. 0 - dna_db_id: + Identifier used internally by the repository to identify an association + a project with a sample. + sample_subject_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify an association + between a sample and a subject. sample_source_db_id: type: integer description: | - e.g. 0 + Identifier used internally by the repository to identify an association + between a sample and a sample source. '400': description: malformed request '401': From 33c5e7ecba55a078c12a2933cc1a66a4eb620b51 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Tue, 26 Sep 2017 03:40:08 -0500 Subject: [PATCH 04/46] add default, info and swagger endpoints, add middleware hooks --- iReceptor_Data_Service_API_V2.json | 58 +++++++ iReceptor_Data_Service_API_V2.yaml | 244 +++++++++++++++++++---------- 2 files changed, 219 insertions(+), 83 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 434465d..9ddea73 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -19,6 +19,10 @@ "application/json" ], "tags": [ + { + "name": "info", + "description": "Service information" + }, { "name": "samples", "description": "Queries for samples" @@ -33,7 +37,57 @@ } ], "paths": { + "/": { + "x-swagger-router-controller": "status", + "get": { + "description": "Service heartbeat.\n", + "operationId": "getStatus", + "responses": { + "200": { + "description": "Success.\n", + "schema": { + "type": "object", + "properties": { + "result": { + "type": "string" + } + } + } + } + } + } + }, + "/info": { + "x-swagger-router-controller": "status", + "get": { + "description": "Service information.\n", + "tags": [ + "info" + ], + "operationId": "getInfo", + "responses": { + "200": { + "description": "Success.\n", + "schema": { + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "version": { + "type": "string" + } + } + } + } + } + } + }, + "/swagger": { + "x-swagger-pipe": "swagger_raw" + }, "/samples": { + "x-swagger-router-controller": "samples", "get": { "description": "This service returns metadata about samples, including higher-level meta-data around the study, subject, diagnosis, and sample processing (data relevant to MiAIRR data classes 1 through 3). The data returned is filtered based on the parameters provided.\nA successful call returns a json list with a sample level summary of each sample including a summary count of the number of sequences found for that sample.\n", "tags": [ @@ -700,6 +754,7 @@ } }, "/sequences_summary": { + "x-swagger-router-controller": "sequences", "get": { "description": "This service returns a summary of sequences that matches the GET provided filter. \"username\" parameter refers to external_users table.\n", "tags": [ @@ -1564,6 +1619,7 @@ } }, "/sequence_data": { + "x-swagger-router-controller": "sequences", "get": { "description": "This service returns the annotation data that matches the GET provided filter. \"username\" parameter refers to external_users table, and it requires the array of \"project_sample_id\", which limits which samples the sequences will be taken from. Other parameters are optional, and refer to the sequence_md_view view in iReceptor database.\n", "tags": [ @@ -2702,6 +2758,7 @@ } }, "/clones_summary": { + "x-swagger-router-controller": "clones", "get": { "description": "This service returns a summary of sequence clones that match the GET provided filter. \"username\" parameter refers to external_users table.\n", "tags": [ @@ -2784,6 +2841,7 @@ } }, "/clones_data": { + "x-swagger-router-controller": "clones", "get": { "description": "This service returns a list of clones that matches the GET provided filter. \"username\" parameter refers to external_users table.\n", "tags": [ diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index ca3ae69..f549bd8 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -8,10 +8,11 @@ info: email: breden@sfu.ca description: > Documentation of Major Version 2 of the iReceptor Adaptive Immune Receptor - Repertoire (AIRR) data source web service application programming interface (API). - V2 of the API implements an increased level of compliance with the [Minimal - Information for AIRR (MiAIRR) standard](https://github.com/airr-community/airr-standards). - Learn more about [iReceptor](http://www.ireceptor.org/) + Repertoire (AIRR) data source web service application programming interface + (API). V2 of the API implements an increased level of compliance with the + [Minimal Information for AIRR (MiAIRR) + standard](https://github.com/airr-community/airr-standards). Learn more + about [iReceptor](http://www.ireceptor.org/) host: ipa.ireceptor.org basePath: /v2 schemes: @@ -19,6 +20,8 @@ schemes: produces: - application/json tags: + - name: info + description: Service information - name: samples description: Queries for samples - name: sequences @@ -26,17 +29,54 @@ tags: - name: clones description: Queries for clones paths: + /: + x-swagger-router-controller: status + get: + description: | + Service heartbeat. + operationId: getStatus + responses: + '200': + description: | + Success. + schema: + type: object + properties: + result: + type: string + /info: + x-swagger-router-controller: status + get: + description: | + Service information. + tags: + - info + operationId: getInfo + responses: + '200': + description: | + Success. + schema: + type: object + properties: + name: + type: string + version: + type: string + /swagger: + x-swagger-pipe: swagger_raw /samples: + x-swagger-router-controller: samples get: description: > This service returns metadata about samples, including higher-level meta-data around the study, subject, diagnosis, and sample processing - (data relevant to MiAIRR data classes 1 through 3). The data - returned is filtered based on the parameters provided. + (data relevant to MiAIRR data classes 1 through 3). The data returned is + filtered based on the parameters provided. A successful call returns a json list with a sample level summary of - each sample including a summary count of the number of sequences found for - that sample. + each sample including a summary count of the number of sequences found + for that sample. tags: - samples parameters: @@ -140,8 +180,9 @@ paths: properties: sequence_count: type: integer - description: | - The number of sequences that match the filter for this sample. + description: > + The number of sequences that match the filter for this + sample. study_id: type: string description: | @@ -184,8 +225,7 @@ paths: Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) subject_id: type: string - description: | - UID assigned by submitter (e.g. SUB856413) (AIRR) + description: "UID assigned by submitter (e.g.\_SUB856413) (AIRR)\n" organism: type: string description: | @@ -224,12 +264,13 @@ paths: Strain name (e.g. C57BL/6J) (AIRR) linked_subjects: type: string - description: | - Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) + description: > + Relation to other subjects (SubjectID e.g. SUB1355648) + (AIRR) link_type: type: string description: | - Relation type (.e.g sister, father, daughter) (AIRR) + Relation type (.e.g sister, father, daughter) (AIRR) sample_id: type: string description: | @@ -252,8 +293,9 @@ paths: Sample collection time (e.g. 10 days) (AIRR) collection_time_event: type: string - description: | - Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) + description: > + Collection time event (T0) (e.g. vaccination, recruitment, + etc) (AIRR) source_commercial: type: string description: | @@ -272,8 +314,9 @@ paths: Study group description (e.g. Case vs. Control) (AIRR) library_source: type: string - description: | - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) + description: > + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) + (AIRR) subject_age: type: integer description: | @@ -304,47 +347,61 @@ paths: e.g. null subject_db_id: type: integer - description: | - Identifier used internally by the repository to identify a subject. + description: > + Identifier used internally by the repository to identify a + subject. project_db_id: type: integer - description: | - Identifier used internally by the repository to identify a project. + description: > + Identifier used internally by the repository to identify a + project. project_parent_db_id: type: integer - description: | - Identifier used internally by the repository to identify a parent/child + description: > + Identifier used internally by the repository to identify a + parent/child + relationship between this project and its parent project. lab_db_id: type: integer - description: | - Identifier used internally by the repository to identify a lab. + description: > + Identifier used internally by the repository to identify a + lab. case_control_db_id: type: integer - description: | - Identifier used internally by the repository to identify an element in the case_control table. + description: > + Identifier used internally by the repository to identify an + element in the case_control table. sample_db_id: type: integer - description: | - Identifier used internally by the repository to identify a sample. + description: > + Identifier used internally by the repository to identify a + sample. dna_db_id: type: integer - description: | - Identifier used internally by the repository to identify a DNA type. + description: > + Identifier used internally by the repository to identify a + DNA type. project_sample_db_id: type: integer - description: | - Identifier used internally by the repository to identify an association + description: > + Identifier used internally by the repository to identify an + association + a project with a sample. sample_subject_db_id: type: integer - description: | - Identifier used internally by the repository to identify an association + description: > + Identifier used internally by the repository to identify an + association + between a sample and a subject. sample_source_db_id: type: integer - description: | - Identifier used internally by the repository to identify an association + description: > + Identifier used internally by the repository to identify an + association + between a sample and a sample source. '400': description: malformed request @@ -360,12 +417,12 @@ paths: description: > This service returns metadata about samples, including higher-level meta-data around the study, subject, diagnosis, and sample processing - (data relevant to MiAIRR data classes 1 through 3). The data - returned is filtered based on the parameters provided. + (data relevant to MiAIRR data classes 1 through 3). The data returned is + filtered based on the parameters provided. A successful call returns a json list with a sample level summary of - each sample including a summary count of the number of sequences found for - that sample. + each sample including a summary count of the number of sequences found + for that sample. tags: - samples parameters: @@ -455,8 +512,9 @@ paths: properties: sequence_count: type: integer - description: | - The number of sequences that match the filter for this sample. + description: > + The number of sequences that match the filter for this + sample. study_id: type: string description: | @@ -499,8 +557,7 @@ paths: Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) subject_id: type: string - description: | - UID assigned by submitter (e.g. SUB856413) (AIRR) + description: "UID assigned by submitter (e.g.\_SUB856413) (AIRR)\n" organism: type: string description: | @@ -539,12 +596,13 @@ paths: Strain name (e.g. C57BL/6J) (AIRR) linked_subjects: type: string - description: | - Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) + description: > + Relation to other subjects (SubjectID e.g. SUB1355648) + (AIRR) link_type: type: string description: | - Relation type (.e.g sister, father, daughter) (AIRR) + Relation type (.e.g sister, father, daughter) (AIRR) sample_id: type: string description: | @@ -567,8 +625,9 @@ paths: Sample collection time (e.g. 10 days) (AIRR) collection_time_event: type: string - description: | - Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) + description: > + Collection time event (T0) (e.g. vaccination, recruitment, + etc) (AIRR) source_commercial: type: string description: | @@ -587,8 +646,9 @@ paths: Study group description (e.g. Case vs. Control) (AIRR) library_source: type: string - description: | - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) + description: > + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) + (AIRR) subject_age: type: integer description: | @@ -619,47 +679,61 @@ paths: e.g. null subject_db_id: type: integer - description: | - Identifier used internally by the repository to identify a subject. + description: > + Identifier used internally by the repository to identify a + subject. project_db_id: type: integer - description: | - Identifier used internally by the repository to identify a project. + description: > + Identifier used internally by the repository to identify a + project. project_parent_db_id: type: integer - description: | - Identifier used internally by the repository to identify a parent/child + description: > + Identifier used internally by the repository to identify a + parent/child + relationship between this project and its parent project. lab_db_id: type: integer - description: | - Identifier used internally by the repository to identify a lab. + description: > + Identifier used internally by the repository to identify a + lab. case_control_db_id: type: integer - description: | - Identifier used internally by the repository to identify an element in the case_control table. + description: > + Identifier used internally by the repository to identify an + element in the case_control table. sample_db_id: type: integer - description: | - Identifier used internally by the repository to identify a sample. + description: > + Identifier used internally by the repository to identify a + sample. dna_db_id: type: integer - description: | - Identifier used internally by the repository to identify a DNA type. + description: > + Identifier used internally by the repository to identify a + DNA type. project_sample_db_id: type: integer - description: | - Identifier used internally by the repository to identify an association + description: > + Identifier used internally by the repository to identify an + association + a project with a sample. sample_subject_db_id: type: integer - description: | - Identifier used internally by the repository to identify an association + description: > + Identifier used internally by the repository to identify an + association + between a sample and a subject. sample_source_db_id: type: integer - description: | - Identifier used internally by the repository to identify an association + description: > + Identifier used internally by the repository to identify an + association + between a sample and a sample source. '400': description: malformed request @@ -672,6 +746,7 @@ paths: '405': description: method not allowed /sequences_summary: + x-swagger-router-controller: sequences get: description: > This service returns a summary of sequences that matches the GET @@ -728,16 +803,19 @@ paths: e.g. 0 study_title: type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name) + description: > + Publication or Protocol Title (e.g. My Study) (AIRR)(v1 + = project_name) study_type: type: string - description: | - Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type) + description: > + Type of project/study (e.g. Cancer) (AIRR)(v1 = + project_type) study: type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)(sra_accession) + description: > + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) + (AIRR)(sra_accession) subject_code: type: string description: | @@ -766,12 +844,10 @@ paths: type: integer description: | e.g. 0 - project_parent_id: type: integer description: | e.g. null - lab_id: type: integer description: | @@ -812,7 +888,6 @@ paths: type: integer description: | e.g. 0 - dna_id: type: integer description: | @@ -1533,6 +1608,7 @@ paths: '405': description: method not allowed /sequence_data: + x-swagger-router-controller: sequences get: description: > This service returns the annotation data that matches the GET provided @@ -2672,6 +2748,7 @@ paths: '405': description: method not allowed /clones_summary: + x-swagger-router-controller: clones get: description: > This service returns a summary of sequence clones that match the GET @@ -2738,6 +2815,7 @@ paths: '405': description: method not allowed /clones_data: + x-swagger-router-controller: clones get: description: > This service returns a list of clones that matches the GET provided From 9a7b2c345febb1befab489dc8f2ce98a38aba233 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 27 Sep 2017 10:22:42 +1300 Subject: [PATCH 05/46] Added AIRR fields to /sequences and /clones API entry points Changed /sequence_data to /sequences_data for consistency with other entry points Changed some of the internal field names to provide consistency across API calls As of this commit, the response models should mostly be consistent in the sense that they all should return AIRR compliant fields in their responeses. Lots to still do, as parameters are not yet mapped correctly and examples are not coordinated with the models. --- iReceptor_Data_Service_API_V2.yaml | 1374 ++++++++++++++++++++++------ 1 file changed, 1115 insertions(+), 259 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index ca3ae69..9ce5b05 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -711,13 +711,19 @@ paths: responses: '200': description: > - A successful call returns an summary of sequence data as an array of - 'category' = count pairs in which the 'category' are string tags of - parameters of interest from a controlled vocabulary term set. + A successful call returns two components, an aggregated summary of the data + that satisfies the query and an example subset of the annotated sequence data + that meets the query criteria. The aggreated data returns a summary similar + to that returned by the /samples API entry point, returning the number of + sequences and the study/subject/sample meta-data for each sample. The example + subset of sequence data that is returned is a small subset of annotated sequences + that met the search criteria. The number of sequences returned is given in the + "num_sequences" paramter to the query and the format in which the sequences are + returned is provided by the "sequence_format" parameter to the query. schema: type: object properties: - aggregation_summary: + summary: type: array items: type: object @@ -725,118 +731,143 @@ paths: sequence_count: type: integer description: | - e.g. 0 + The number of sequences that match the filter for this sample. + study_id: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) study_title: type: string description: | - Publication or Protocol Title (e.g. My Study) (AIRR)(v1 = project_name) + Publication or Protocol Title (e.g. My Study) (AIRR) study_type: type: string description: | - Type of project/study (e.g. Cancer) (AIRR)(v1 = project_type) - study: + Type of project/study (e.g. Cancer) (AIRR) + inclusion_exclusion_criteria: type: string description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)(sra_accession) - subject_code: + Study inclusion/exclusion criteria (AIRR) + grants: type: string description: | - e.g. Subject One - subject_id: - type: integer + Grant funding agency (AIRR) + lab_name: + type: string description: | - e.g. 1 - subject_gender: + Lab name (AIRR) + collected_by: type: string description: | - e.g. Male - subject_species: + Contact information (data collection) (AIRR) + uploaded_by: type: string description: | - e.g. Mouse - subject_ethnicity: + Contact information (data deposition) (AIRR) + lab_address: type: string description: | - e.g. Eth1 - subject_age: - type: integer + Lab address (AIRR) + pubs_ids: + type: string description: | - e.g. 1 - project_id: - type: integer + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + subject_id: + type: string description: | - e.g. 0 - - project_parent_id: - type: integer + UID assigned by submitter (e.g. SUB856413) (AIRR) + organism: + type: string description: | - e.g. null - - lab_id: - type: integer + Organism-based (human, mouse) or synthetic (AIRR) + sex: + type: string description: | - e.g. 0 - lab_name: + Sex (e.g. M/F) (AIRR) + age: type: string description: | - Name of the Laboratory running the study (AIRR) - disease_state_id: - type: integer + Age - Time duration and unit (e.g. 200 days) (AIRR) + age_event: + type: string description: | - e.g. 1 - disease_state_name: + Age event (e.g. Enrollment) (AIRR) + ancestry_population: type: string description: | - e.g. HIV-1 infected - case_control_id: - type: integer + Ancestry population (AIRR) + ethnicity: + type: string description: | - e.g. 0 - case_control_name: + Ethnicity (e.g. Tamil) (AIRR) + race: + type: string + description: | + Race (e.g. South Indian) (AIRR) + species_name: + type: string + description: | + Species name (e.g. Homo Sapiens) (AIRR) + strain_name: + type: string + description: | + Strain name (e.g. C57BL/6J) (AIRR) + linked_subjects: + type: string + description: | + Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) + link_type: type: string description: | - e.g. Control + Relation type (.e.g sister, father, daughter) (AIRR) sample_id: - type: integer + type: string description: | - e.g. 0 - sample_name: + Biological sample ID - UID assigned by submitter (AIRR) + sample_type: type: string description: | - e.g. Blood Sample 01 - project_sample_id: - type: integer + Sample type (e.g. Tissue, body fluid) (AIRR) + tissue: + type: string description: | - e.g. 0 - sample_subject_id: - type: integer + Anatomic site (e.g. spleen) (AIRR) + disease_state_sample: + type: string description: | - e.g. 0 - - dna_id: - type: integer + Disease state of sample (e.g. tumor vs margin) (AIRR) + collection_date: + type: string description: | - e.g. 0 - dna_type: + Sample collection time (e.g. 10 days) (AIRR) + collection_time_event: type: string description: | - e.g. cDNA - sample_source_id: - type: integer + Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) + source_commercial: + type: string description: | - e.g. 0 - sample_source_name: + Commercial source of sample (e.g. XYZ Pharma) (AIRR) + cell_subset: + type: string + description: | + Cell subset (Controlled vocabulary) (AIRR) + cell_phenotype: type: string description: | - e.g. Blood (PBMC) - lab_cell_subset_name: + Cell subset phenotype (lab specific description) (AIRR) + study_group_description: type: string description: | - e.g. Naive B Alpha - ireceptor_cell_subset_name: + Study group description (e.g. Case vs. Control) (AIRR) + library_source: type: string description: | - e.g. Naive B + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) + subject_age: + type: integer + description: | + e.g. 1 marker_1: type: string description: | @@ -861,15 +892,94 @@ paths: type: string description: | e.g. null - sequences: + subject_db_id: type: integer description: | - e.g. 167793 - sequences: + Identifier used internally by the repository to identify a subject. + project_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a project. + project_parent_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a parent/child + relationship between this project and its parent project. + lab_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a lab. + case_control_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an element in the case_control table. + sample_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a sample. + dna_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a DNA type. + project_sample_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an association + a project with a sample. + sample_subject_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an association + between a sample and a subject. + sample_source_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an association + between a sample and a sample source. + items: type: array items: type: object properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) seq_id: type: integer description: | @@ -900,10 +1010,6 @@ paths: type: string description: | e.g. IGHV4-59 - vgene_allele: - type: string - description: | - e.g. IGHV4-59*01 or IGHV4-59*07 dgene_string: type: string description: | @@ -916,10 +1022,6 @@ paths: type: string description: | e.g. IGHD3-10 - dgene_allele: - type: string - description: | - e.g. IGHD3-10*01 jgene_string: type: string description: | @@ -932,10 +1034,6 @@ paths: type: string description: | e.g. IGHJ4 - jgene_allele: - type: string - description: | - e.g. IGHJ4*02 functionality: type: string description: | @@ -1024,10 +1122,6 @@ paths: type: string description: | cdr3 region nucleotide sequence - junction_sequence_nt: - type: string - description: | - junction nucleotide sequence vdjregion_sequence_nt_gapped: type: string description: | @@ -1136,10 +1230,6 @@ paths: type: string description: | cdr3 region amino acid sequence - junction_sequence_aa: - type: string - description: | - junction amino acid sequence vdjregion_sequence_aa_gapped: type: string description: | @@ -1346,7 +1436,7 @@ paths: e.g. VQuest examples: application/json: - aggregation_summary: + summary: - subject_code: IAVI 84 subject_id: 1 subject_gender: null @@ -1390,7 +1480,7 @@ paths: marker_5: ' CD14' marker_6: ' CD16, IgM, IgA, IgD ' sequences: 167793 - sequences: + items: - seq_id: 2 seq_name: SRR654169.17_G912ZWU01EPN4E_length=379 project_sample_id: 1 @@ -1398,15 +1488,15 @@ paths: vgene_string: Homsap IGHV1-24*01 F vgene_family: IGHV1 vgene_gene: IGHV1-24 - vgene_allele: ' IGHV1-24*01 ' + v_allele: ' IGHV1-24*01 ' jgene_string: Homsap IGHJ3*02 F jgene_family: IGHJ3 jgene_gene: IGHJ3 - jgene_allele: ' IGHJ3*02 ' + j_allele: ' IGHJ3*02 ' dgene_string: Homsap IGHD3-22*01 F dgene_family: IGHD3 dgene_gene: IGHD3-22 - dgene_allele: ' IGHD3-22*01 ' + d_allele: ' IGHD3-22*01 ' functionality: productive vgene_score: 1417 vgene_probablity: null @@ -1432,7 +1522,7 @@ paths: cdr1region_sequence_nt: ggatacaccctcactgaattatcc cdr2region_sequence_nt: tttgatcctgaagatggtgaaaca cdr3region_sequence_nt: gcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatc - junction_sequence_nt: tgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctgg + junction_nt: tgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctgg vdjregion_sequence_nt_gapped: >- caggtccagctggtagagtctggggct...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctc............actgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaa......gatggtgaaacaatctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag vjregion_sequence_nt_gapped: '' @@ -1468,7 +1558,7 @@ paths: cdr1region_sequence_aa: GYTLTELS cdr2region_sequence_aa: FDPEDGET cdr3region_sequence_aa: ATRSPPIVVIMDDGFDI - junction_sequence_aa: CATRSPPIVVIMDDGFDIW + junction_aa: CATRSPPIVVIMDDGFDIW vdjregion_sequence_aa_gapped: >- QVQLVESGA.EVKKPGASVKVSCKVSGYTL....TELSMHWVRQAPGKGLEWMGGFDPE..DGETIYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYCATRSPPIVVIMDDGFDIWGQGTMVTVSS vjregion_sequence_aa_gapped: '' @@ -1532,7 +1622,7 @@ paths: description: data not found '405': description: method not allowed - /sequence_data: + /sequences_data: get: description: > This service returns the annotation data that matches the GET provided @@ -1595,6 +1685,45 @@ paths: items: type: object properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) seq_id: type: integer description: | @@ -1623,10 +1752,6 @@ paths: type: string description: | e.g. IGHV4-59 - vgene_allele: - type: string - description: | - e.g. IGHV4-59*01 or IGHV4-59*07 dgene_string: type: string description: | @@ -1639,10 +1764,6 @@ paths: type: string description: | e.g. IGHD3-10 - dgene_allele: - type: string - description: | - e.g. IGHD3-10*01 jgene_string: type: string description: | @@ -1655,10 +1776,6 @@ paths: type: string description: | e.g. IGHJ4 - jgene_allele: - type: string - description: | - e.g. IGHJ4*02 functionality: type: string description: | @@ -1747,10 +1864,6 @@ paths: type: string description: | cdr3 region nucleotide sequence - junction_sequence_nt: - type: string - description: | - junction nucleotide sequence vdjregion_sequence_nt_gapped: type: string description: | @@ -1859,10 +1972,6 @@ paths: type: string description: | cdr3 region amino acid sequence - junction_sequence_aa: - type: string - description: | - junction amino acid sequence vdjregion_sequence_aa_gapped: type: string description: | @@ -2076,7 +2185,7 @@ paths: M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 vgene_gene: | IGHV4-59 - vgene_allele: | + v_allele: | IGHV4-59*01 or IGHV4-59*07 dgene_string: | Homsap IGHD3-10*01 F @@ -2084,7 +2193,7 @@ paths: IGHD3 dgene_gene: | IGHD3-10 - dgene_allele: | + d_allele: | IGHD3-10*01 jgene_string: | Homsap IGHJ4*02 F @@ -2092,7 +2201,7 @@ paths: IGHJ4 jgene_gene: | IGHJ4 - jgene_allele: | + j_allele: | IGHJ4*02 functionality: | productive @@ -2183,6 +2292,45 @@ paths: items: type: object properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) seq_id: type: integer description: | @@ -2207,24 +2355,18 @@ paths: type: string vgene_gene: type: string - vgene_allele: - type: string dgene_string: type: string dgene_family: type: string dgene_gene: type: string - dgene_allele: - type: string jgene_string: type: string jgene_family: type: string jgene_gene: type: string - jgene_allele: - type: string functionality: type: string functionality_comment: @@ -2311,10 +2453,6 @@ paths: type: string description: | cdr3 region nucleotide sequence - junction_sequence_nt: - type: string - description: | - junction nucleotide sequence vdjregion_sequence_nt_gapped: type: string description: | @@ -2423,10 +2561,6 @@ paths: type: string description: | cdr3 region amino acid sequence - junction_sequence_aa: - type: string - description: | - junction amino acid sequence vdjregion_sequence_aa_gapped: type: string description: | @@ -2622,7 +2756,7 @@ paths: M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 vgene_gene: | IGHV4-59 - vgene_allele: | + v_allele: | IGHV4-59*01 or IGHV4-59*07 dgene_string: | Homsap IGHD3-10*01 F @@ -2630,7 +2764,7 @@ paths: IGHD3 dgene_gene: | IGHD3-10 - dgene_allele: | + d_allele: | IGHD3-10*01 jgene_string: | Homsap IGHJ4*02 F @@ -2638,7 +2772,7 @@ paths: IGHJ4 jgene_gene: | IGHJ4 - jgene_allele: | + j_allele: | IGHJ4*02 functionality: | productive @@ -2715,111 +2849,849 @@ paths: 'category' = count pairs in which the 'category' are string tags of parameters of interest from a controlled vocabulary term set. schema: - type: array - items: - type: object - properties: - category: - type: string - description: | - e.g. samples - count: - type: integer - description: | - e.g. 100 - '400': - description: malformed request - '401': - description: authentication error - '403': - description: authorization error - '404': - description: data not found - '405': - description: method not allowed - /clones_data: - get: - description: > - This service returns a list of clones that matches the GET provided - filter. "username" parameter refers to external_users table. - tags: - - clones - parameters: - - name: username - in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true - type: string - - name: project_sample_id_list - in: query - required: true - type: array - items: - type: integer - - name: cdr3_length - in: query - description: >- - length of complementarity determining region in nucleotide base - pairs - required: false - type: integer - - name: vgene_string - in: query - required: false - type: string - - name: jgene_string - in: query - required: false - type: string - operationId: getCloneData - responses: - '200': - description: > - A successful call returns an array of sequence data. Optional - "output" parameter determines the output format. Default is a JSON - response, limited to top 50 results. If "output" is set to "csv", it - will return all the matching sequence annotations, in addition to - sample information and annotation tool information, in a - comma-separated format. - schema: - type: array - items: - type: object - properties: - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - vgene_family: - type: string + type: object + properties: + summary: + type: array + items: + type: object + properties: + sequence_count: + type: integer + description: | + The number of sequences that match the filter for this sample. + study_id: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + study_title: + type: string + description: | + Publication or Protocol Title (e.g. My Study) (AIRR) + study_type: + type: string + description: | + Type of project/study (e.g. Cancer) (AIRR) + inclusion_exclusion_criteria: + type: string + description: | + Study inclusion/exclusion criteria (AIRR) + grants: + type: string + description: | + Grant funding agency (AIRR) + lab_name: + type: string + description: | + Lab name (AIRR) + collected_by: + type: string + description: | + Contact information (data collection) (AIRR) + uploaded_by: + type: string + description: | + Contact information (data deposition) (AIRR) + lab_address: + type: string + description: | + Lab address (AIRR) + pubs_ids: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + subject_id: + type: string + description: | + UID assigned by submitter (e.g. SUB856413) (AIRR) + organism: + type: string + description: | + Organism-based (human, mouse) or synthetic (AIRR) + sex: + type: string + description: | + Sex (e.g. M/F) (AIRR) + age: + type: string + description: | + Age - Time duration and unit (e.g. 200 days) (AIRR) + age_event: + type: string + description: | + Age event (e.g. Enrollment) (AIRR) + ancestry_population: + type: string + description: | + Ancestry population (AIRR) + ethnicity: + type: string + description: | + Ethnicity (e.g. Tamil) (AIRR) + race: + type: string + description: | + Race (e.g. South Indian) (AIRR) + species_name: + type: string + description: | + Species name (e.g. Homo Sapiens) (AIRR) + strain_name: + type: string + description: | + Strain name (e.g. C57BL/6J) (AIRR) + linked_subjects: + type: string + description: | + Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) + link_type: + type: string + description: | + Relation type (.e.g sister, father, daughter) (AIRR) + sample_id: + type: string + description: | + Biological sample ID - UID assigned by submitter (AIRR) + sample_type: + type: string + description: | + Sample type (e.g. Tissue, body fluid) (AIRR) + tissue: + type: string + description: | + Anatomic site (e.g. spleen) (AIRR) + disease_state_sample: + type: string + description: | + Disease state of sample (e.g. tumor vs margin) (AIRR) + collection_date: + type: string + description: | + Sample collection time (e.g. 10 days) (AIRR) + collection_time_event: + type: string + description: | + Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) + source_commercial: + type: string + description: | + Commercial source of sample (e.g. XYZ Pharma) (AIRR) + cell_subset: + type: string + description: | + Cell subset (Controlled vocabulary) (AIRR) + cell_phenotype: + type: string + description: | + Cell subset phenotype (lab specific description) (AIRR) + study_group_description: + type: string + description: | + Study group description (e.g. Case vs. Control) (AIRR) + library_source: + type: string + description: | + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) + subject_age: + type: integer + description: | + e.g. 1 + marker_1: + type: string + description: | + e.g. CR19 + marker_2: + type: string + description: | + e.g. CR20 + marker_3: + type: string + description: | + e.g. CR21 + marker_4: + type: string + description: | + e.g. null + marker_5: + type: string + description: | + e.g. null + marker_6: + type: string + description: | + e.g. null + subject_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a subject. + project_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a project. + project_parent_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a parent/child + relationship between this project and its parent project. + lab_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a lab. + case_control_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an element in the case_control table. + sample_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a sample. + dna_db_id: + type: integer + description: | + Identifier used internally by the repository to identify a DNA type. + project_sample_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an association + a project with a sample. + sample_subject_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an association + between a sample and a subject. + sample_source_db_id: + type: integer + description: | + Identifier used internally by the repository to identify an association + between a sample and a sample source. + items: + type: array + items: + type: object + properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) + seq_id: + type: integer + description: | + e.g. 1 + seq_name: + type: string + project_sample_id: + type: integer + description: | + e.g. 6 + id: + type: integer + description: | + e.g. 1 + sequence_id: + type: integer + description: | + e.g. 1 + vgene_string: + type: string + description: | + e.g IGHV4-59*01 or IGHV4-59*07 + vgene_family: + type: string + description: | + e.g. IGHV4 + vgene_gene: + type: string + description: | + e.g. IGHV4-59 + dgene_string: + type: string + description: | + e.g. Homsap IGHD3-10*01 F + dgene_family: + type: string + description: | + e.g. IGHD3 + dgene_gene: + type: string + description: | + e.g. IGHD3-10 + jgene_string: + type: string + description: | + e.g. Homsap IGHJ4*02 F + jgene_family: + type: string + description: | + e.g. IGHJ4 + jgene_gene: + type: string + description: | + e.g. IGHJ4 + functionality: + type: string + description: | + e.g. productive + functionality_comment: + type: string + description: | + e.g. "" + orientation: + type: string + description: | + e.g. + + vgene_score: + type: integer + description: | + e.g. 1127 + vgene_probability: + type: integer + description: | + e.g. 95 + dregion_reading_frame: + type: integer + description: | + e.g. 2 + cdr1_length: + type: integer + description: | + e.g. 8 + cdr2_length: + type: integer + description: | + e.g. 7 + cdr3_length: + type: integer + description: | + e.g. 13 + vdjregion_sequence_nt: + type: string + description: | + vdj region nucleotide sequence + vjregion_sequence_nt: + type: string + description: | + vj region nucleotide sequence + djregion_sequence_nt: + type: string + description: | + dj region nucleotide sequence + vregion_sequence_nt: + type: string + description: | + v region nucleotide sequence + dregion_sequence_nt: + type: string + description: | + d region nucleotide sequence + jregion_sequence_nt: + type: string + description: | + j region nucleotide sequence + fr1region_sequence_nt: + type: string + description: | + fr1 region nucleotide sequence + fr2region_sequence_nt: + type: string + description: | + fr2 region nucleotide sequence + fr3region_sequence_nt: + type: string + description: | + fr3 region nucleotide sequence + fr4region_sequence_nt: + type: string + description: | + fr4 region nucleotide sequence + cdr1region_sequence_nt: + type: string + description: | + cdr1 region nucleotide sequence + cdr2region_sequence_nt: + type: string + description: | + cdr2 region nucleotide sequence + cdr3region_sequence_nt: + type: string + description: | + cdr3 region nucleotide sequence + vdjregion_sequence_nt_gapped: + type: string + description: | + gapped vdj region nucleotide sequence + vjregion_sequence_nt_gapped: + type: string + description: | + gapped vj region nucleotide sequence + djregion_sequence_nt_gapped: + type: string + description: | + gapped dj region nucleotide sequence + vregion_sequence_nt_gapped: + type: string + description: | + gapped v region nucleotide sequence + dregion_sequence_nt_gapped: + type: string + description: | + gapped d region nucleotide sequence + jregion_sequence_nt_gapped: + type: string + description: | + gapped j region nucleotide sequence + fr1region_sequence_nt_gapped: + type: string + description: | + gapped fr1 region nucleotide sequence + fr2region_sequence_nt_gapped: + type: string + description: | + gapped fr2 region nucleotide sequence + fr3region_sequence_nt_gapped: + type: string + description: | + gapped fr3 region nucleotide sequence + fr4region_sequence_nt_gapped: + type: string + description: | + gapped fr4 region nucleotide sequence + cdr1region_sequence_nt_gapped: + type: string + description: | + gapped cdr1 region nucleotide sequence + cdr2region_sequence_nt_gapped: + type: string + description: | + gapped cdr2 region nucleotide sequence + cdr3region_sequence_nt_gapped: + type: string + description: | + gapped cdr3 region nucleotide sequence + junction_sequence_nt_gapped: + type: string + description: | + gapped junction nucleotide sequence + vdjregion_sequence_aa: + type: string + description: | + vdj region amino acid sequence + vjregion_sequence_aa: + type: string + description: | + vj region amino acid sequence + djregion_sequence_aa: + type: string + description: | + dj region amino acid sequence + vregion_sequence_aa: + type: string + description: | + v region amino acid sequence + dregion_sequence_aa: + type: string + description: | + d region amino acid sequence + jregion_sequence_aa: + type: string + description: | + j region amino acid sequence + fr1region_sequence_aa: + type: string + description: | + fr1 region amino acid sequence + fr2region_sequence_aa: + type: string + description: | + fr2 region amino acid sequence + fr3region_sequence_aa: + type: string + description: | + fr3 region amino acid sequence + fr4region_sequence_aa: + type: string + description: | + fr4 region amino acid sequence + cdr1region_sequence_aa: + type: string + description: | + cdr1 region amino acid sequence + cdr2region_sequence_aa: + type: string + description: | + cdr2 region amino acid sequence + cdr3region_sequence_aa: + type: string + description: | + cdr3 region amino acid sequence + vdjregion_sequence_aa_gapped: + type: string + description: | + gapped vdj region amino acid sequence + vjregion_sequence_aa_gapped: + type: string + description: | + gapped vj region amino acid sequence + djregion_sequence_aa_gapped: + type: string + description: | + gapped dj region amino acid sequence + vregion_sequence_aa_gapped: + type: string + description: | + gapped v region amino acid sequence + dregion_sequence_aa_gapped: + type: string + description: | + gapped d region amino acid sequence + jregion_sequence_aa_gapped: + type: string + description: | + gapped j region amino acid sequence + fr1region_sequence_aa_gapped: + type: string + description: | + gapped fr1 region amino acid sequence + fr2region_sequence_aa_gapped: + type: string + description: | + gapped fr2 region amino acid sequence + fr3region_sequence_aa_gapped: + type: string + description: | + gapped fr3 region amino acid sequence + fr4region_sequence_aa_gapped: + type: string + description: | + gapped fr4 region amino acid sequence + cdr1region_sequence_aa_gapped: + type: string + description: | + gapped cdr1 region amino acid sequence + cdr2region_sequence_aa_gapped: + type: string + description: | + gapped cdr2 region amino acid sequence + cdr3region_sequence_aa_gapped: + type: string + description: | + gapped cdr3 region amino acid sequence + junction_sequence_aa_gapped: + type: string + description: | + gapped junction amino acid sequence + vdjregion_start: + type: integer + description: | + e.g. 1 + vdjregion_end: + type: integer + description: | + e.g. 321 + vjregion_start: + type: integer + description: | + e.g. 0 + vjregion_end: + type: integer + description: | + e.g. 0 + djregion_start: + type: integer + description: | + e.g. 254 + djregion_end: + type: integer + description: | + e.g. 321 + vregion_start: + type: integer + description: | + e.g. 286 + vregion_end: + type: integer + description: | + e.g. 252 + dregion_start: + type: integer + description: | + e.g. 254 + dregion_end: + type: integer + description: | + e.g. 321 + jregion_start: + type: integer + description: | + e.g. 286 + jregion_end: + type: integer + description: | + e.g. 321 + fr1region_start: + type: integer + description: | + e.g. 1 + fr1region_end: + type: integer + description: | + e.g. 38 + fr2region_start: + type: integer + description: | + e.g. 63 + fr2region_end: + type: integer + description: | + e.g. 113 + fr3region_start: + type: integer + description: | + e.g. 135 + fr3region_end: + type: integer + description: | + e.g. 248 + fr4region_start: + type: integer + description: | + e.g. 288 + fr4region_end: + type: integer + description: | + e.g. 321 + cdr1region_start: + type: integer + description: | + e.g. 39 + cdr1region_end: + type: integer + description: | + e.g. 321 + cdr2region_start: + type: integer + description: | + e.g. 62 + cdr2region_end: + type: integer + description: | + e.g. 134 + cdr3region_start: + type: integer + description: | + e.g. 249 + cdr3region_end: + type: integer + description: | + e.g. 287 + junction_start: + type: integer + description: | + e.g. 246 + junction_end: + type: integer + description: | + e.g. 290 + vregion_mutation_string: + type: string + description: > + e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - + +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - + -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| + fr1region_mutation_string: + type: string + description: | + e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| + fr2region_mutation_string: + type: string + description: | + e.g. + fr3region_mutation_string: + type: string + description: > + e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" + cdr1region_mutation_string: + type: string + description: | + e.g. + cdr2region_mutation_string: + type: string + description: | + e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" + cdr3region_mutation_string: + type: string + description: | + e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t + annotation_tool: + type: string + description: | + e.g. VQuest + + + '400': + description: malformed request + '401': + description: authentication error + '403': + description: authorization error + '404': + description: data not found + '405': + description: method not allowed + /clones_data: + get: + description: > + This service returns a list of clones that matches the GET provided + filter. "username" parameter refers to external_users table. + tags: + - clones + parameters: + - name: username + in: query + description: > + Username of the individual requesting access to the iReceptor + repository node. + required: true + type: string + - name: project_sample_id_list + in: query + required: true + type: array + items: + type: integer + - name: cdr3_length + in: query + description: >- + length of complementarity determining region in nucleotide base + pairs + required: false + type: integer + - name: vgene_string + in: query + required: false + type: string + - name: jgene_string + in: query + required: false + type: string + operationId: getCloneData + responses: + '200': + description: > + A successful call returns an array of sequence data. Optional + "output" parameter determines the output format. Default is a JSON + response, limited to top 50 results. If "output" is set to "csv", it + will return all the matching sequence annotations, in addition to + sample information and annotation tool information, in a + comma-separated format. + schema: + type: array + items: + type: object + properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) + seq_id: + type: integer + description: | + e.g. 1 + seq_name: + type: string + project_sample_id: + type: integer + description: | + e.g. 6 + id: + type: integer + description: | + e.g. 1 + sequence_id: + type: integer + description: | + e.g. 1 + vgene_string: + type: string + vgene_family: + type: string description: | e.g. IGHV4 vgene_gene: type: string description: | e.g. IGHV4-59 - vgene_allele: - type: string - description: | - e.g. IGHV4-59*01 or IGHV4-59*07 dgene_string: type: string description: | @@ -2832,10 +3704,6 @@ paths: type: string description: | e.g. IGHD3-10 - dgene_allele: - type: string - description: | - e.g. IGHD3-10*01 jgene_string: type: string description: | @@ -2848,10 +3716,6 @@ paths: type: string description: | e.g. IGHJ4 - jgene_allele: - type: string - description: | - e.g. IGHJ4*02 functionality: type: string description: | @@ -2940,10 +3804,6 @@ paths: type: string description: | cdr3 region nucleotide sequence - junction_sequence_nt: - type: string - description: | - junction nucleotide sequence vdjregion_sequence_nt_gapped: type: string description: | @@ -3052,10 +3912,6 @@ paths: type: string description: | cdr3 region amino acid sequence - junction_sequence_aa: - type: string - description: | - junction amino acid sequence vdjregion_sequence_aa_gapped: type: string description: | @@ -3269,7 +4125,7 @@ paths: M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 vgene_gene: | IGHV4-59 - vgene_allele: | + v_allele: | IGHV4-59*01 or IGHV4-59*07 dgene_string: | Homsap IGHD3-10*01 F @@ -3277,7 +4133,7 @@ paths: IGHD3 dgene_gene: | IGHD3-10 - dgene_allele: | + d_allele: | IGHD3-10*01 jgene_string: | Homsap IGHJ4*02 F From 08bb3d49fa949b1983f6c8e0d6365844286cb129 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 27 Sep 2017 15:10:05 +1300 Subject: [PATCH 06/46] Created data models for API responses using Swagger 2.0 supported "definitions". Created models for: - airr_sequence_model (AIRR defined VDJ annotation fields) - airr_and_ireceptor_sequence_model (Full model for AIRR and other iReceptor annotation fields - e.g. the vquest fields) - summary_model (Model for what the response is for the summary metadata) Used above models in all of the API response definitions. All response information is now centrally defined in a single location through the models and reused through the API spec (whew)... First steps to abstracting out the AIRR meta-data from other repository specific meta-data. Oddly enough I can't get the model extension mechanism to work (see the ErrorModel example here - https://github.com/OAI/OpenAPI-Specification/blob/master/versions/2.0.md). Parameters and examples are still very messy. I deleted most of the examples, which causes Swagger to use the model as the example (with not very useful example data). --- iReceptor_Data_Service_API_V2.json | 4322 +++++------------------ iReceptor_Data_Service_API_V2.yaml | 5142 +++++++--------------------- 2 files changed, 1931 insertions(+), 7533 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index fbe830d..3964b80 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -8,10 +8,779 @@ "url": "http://www.ireceptor.org/", "email": "breden@sfu.ca" }, - "description": "Documentation of Major Version 2 of the iReceptor Adaptive Immune Receptor Repertoire (AIRR) data source web service application programming interface (API). V2 of the API implements an increased level of compliance with the [Minimal Information for AIRR (MiAIRR) standard](https://github.com/airr-community/airr-standards). Learn more about [iReceptor](http://www.ireceptor.org/)\n" + "description": "Documentation of Major Version 2 of the iReceptor Adaptive Immune Receptor Repertoire (AIRR) data repsoitory web service application programming interface (API). V2 of the API implements an increased level of compliance with the [Minimal Information for AIRR (MiAIRR) standard](https://github.com/airr-community/airr-standards). Learn more about [iReceptor](http://www.ireceptor.org/)\n" }, "host": "ipa.ireceptor.org", "basePath": "/v2", + "definitions": { + "airr_sequence_model": { + "type": "array", + "items": { + "type": "object", + "properties": { + "germline_database": { + "type": "string", + "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" + }, + "cell_index": { + "type": "integer", + "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" + }, + "v_allele": { + "type": "string", + "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" + }, + "d_allele": { + "type": "string", + "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" + }, + "j_allele": { + "type": "string", + "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" + }, + "c_allele": { + "type": "string", + "description": "C region with allele (AIRR) \n" + }, + "junction_nt": { + "type": "string", + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" + }, + "junction_aa": { + "type": "string", + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" + }, + "duplicate_count": { + "type": "integer", + "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" + } + } + } + }, + "extended_sequence_model": { + "allOf": [ + { + "$ref": "#/definitions/airr_sequence_model" + }, + { + "type": "object", + "properties": { + "an_extended_model_element": { + "type": "string", + "description": "This does not seem to extend the model, it replaces it!" + } + } + } + ] + }, + "airr_and_ireceptor_sequence_model": { + "type": "array", + "items": { + "type": "object", + "properties": { + "germline_database": { + "type": "string", + "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" + }, + "cell_index": { + "type": "integer", + "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" + }, + "v_allele": { + "type": "string", + "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" + }, + "d_allele": { + "type": "string", + "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" + }, + "j_allele": { + "type": "string", + "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" + }, + "c_allele": { + "type": "string", + "description": "C region with allele (AIRR) \n" + }, + "junction_nt": { + "type": "string", + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" + }, + "junction_aa": { + "type": "string", + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" + }, + "duplicate_count": { + "type": "integer", + "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" + }, + "seq_id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "seq_name": { + "type": "string" + }, + "project_sample_id": { + "type": "integer", + "description": "e.g. 6\n" + }, + "id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "sequence_id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "vgene_string": { + "type": "string", + "description": "e.g IGHV4-59*01 or IGHV4-59*07\n" + }, + "vgene_family": { + "type": "string", + "description": "e.g. IGHV4\n" + }, + "vgene_gene": { + "type": "string", + "description": "e.g. IGHV4-59\n" + }, + "dgene_string": { + "type": "string", + "description": "e.g. Homsap IGHD3-10*01 F\n" + }, + "dgene_family": { + "type": "string", + "description": "e.g. IGHD3\n" + }, + "dgene_gene": { + "type": "string", + "description": "e.g. IGHD3-10\n" + }, + "jgene_string": { + "type": "string", + "description": "e.g. Homsap IGHJ4*02 F\n" + }, + "jgene_family": { + "type": "string", + "description": "e.g. IGHJ4\n" + }, + "jgene_gene": { + "type": "string", + "description": "e.g. IGHJ4\n" + }, + "functionality": { + "type": "string", + "description": "e.g. productive\n" + }, + "functionality_comment": { + "type": "string", + "description": "e.g. \"\"\n" + }, + "orientation": { + "type": "string", + "description": "e.g. +\n" + }, + "vgene_score": { + "type": "integer", + "description": "e.g. 1127\n" + }, + "vgene_probability": { + "type": "integer", + "description": "e.g. 95\n" + }, + "dregion_reading_frame": { + "type": "integer", + "description": "e.g. 2\n" + }, + "cdr1_length": { + "type": "integer", + "description": "e.g. 8\n" + }, + "cdr2_length": { + "type": "integer", + "description": "e.g. 7\n" + }, + "cdr3_length": { + "type": "integer", + "description": "e.g. 13\n" + }, + "vdjregion_sequence_nt": { + "type": "string", + "description": "vdj region nucleotide sequence\n" + }, + "vjregion_sequence_nt": { + "type": "string", + "description": "vj region nucleotide sequence\n" + }, + "djregion_sequence_nt": { + "type": "string", + "description": "dj region nucleotide sequence\n" + }, + "vregion_sequence_nt": { + "type": "string", + "description": "v region nucleotide sequence\n" + }, + "dregion_sequence_nt": { + "type": "string", + "description": "d region nucleotide sequence\n" + }, + "jregion_sequence_nt": { + "type": "string", + "description": "j region nucleotide sequence\n" + }, + "fr1region_sequence_nt": { + "type": "string", + "description": "fr1 region nucleotide sequence\n" + }, + "fr2region_sequence_nt": { + "type": "string", + "description": "fr2 region nucleotide sequence\n" + }, + "fr3region_sequence_nt": { + "type": "string", + "description": "fr3 region nucleotide sequence\n" + }, + "fr4region_sequence_nt": { + "type": "string", + "description": "fr4 region nucleotide sequence\n" + }, + "cdr1region_sequence_nt": { + "type": "string", + "description": "cdr1 region nucleotide sequence\n" + }, + "cdr2region_sequence_nt": { + "type": "string", + "description": "cdr2 region nucleotide sequence\n" + }, + "cdr3region_sequence_nt": { + "type": "string", + "description": "cdr3 region nucleotide sequence\n" + }, + "vdjregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped vdj region nucleotide sequence\n" + }, + "vjregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped vj region nucleotide sequence\n" + }, + "djregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped dj region nucleotide sequence\n" + }, + "vregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped v region nucleotide sequence\n" + }, + "dregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped d region nucleotide sequence\n" + }, + "jregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped j region nucleotide sequence\n" + }, + "fr1region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr1 region nucleotide sequence\n" + }, + "fr2region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr2 region nucleotide sequence\n" + }, + "fr3region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr3 region nucleotide sequence\n" + }, + "fr4region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr4 region nucleotide sequence\n" + }, + "cdr1region_sequence_nt_gapped": { + "type": "string", + "description": "gapped cdr1 region nucleotide sequence\n" + }, + "cdr2region_sequence_nt_gapped": { + "type": "string", + "description": "gapped cdr2 region nucleotide sequence\n" + }, + "cdr3region_sequence_nt_gapped": { + "type": "string", + "description": "gapped cdr3 region nucleotide sequence\n" + }, + "junction_sequence_nt_gapped": { + "type": "string", + "description": "gapped junction nucleotide sequence\n" + }, + "vdjregion_sequence_aa": { + "type": "string", + "description": "vdj region amino acid sequence\n" + }, + "vjregion_sequence_aa": { + "type": "string", + "description": "vj region amino acid sequence\n" + }, + "djregion_sequence_aa": { + "type": "string", + "description": "dj region amino acid sequence\n" + }, + "vregion_sequence_aa": { + "type": "string", + "description": "v region amino acid sequence\n" + }, + "dregion_sequence_aa": { + "type": "string", + "description": "d region amino acid sequence\n" + }, + "jregion_sequence_aa": { + "type": "string", + "description": "j region amino acid sequence\n" + }, + "fr1region_sequence_aa": { + "type": "string", + "description": "fr1 region amino acid sequence\n" + }, + "fr2region_sequence_aa": { + "type": "string", + "description": "fr2 region amino acid sequence\n" + }, + "fr3region_sequence_aa": { + "type": "string", + "description": "fr3 region amino acid sequence\n" + }, + "fr4region_sequence_aa": { + "type": "string", + "description": "fr4 region amino acid sequence\n" + }, + "cdr1region_sequence_aa": { + "type": "string", + "description": "cdr1 region amino acid sequence\n" + }, + "cdr2region_sequence_aa": { + "type": "string", + "description": "cdr2 region amino acid sequence\n" + }, + "cdr3region_sequence_aa": { + "type": "string", + "description": "cdr3 region amino acid sequence\n" + }, + "vdjregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped vdj region amino acid sequence\n" + }, + "vjregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped vj region amino acid sequence\n" + }, + "djregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped dj region amino acid sequence\n" + }, + "vregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped v region amino acid sequence\n" + }, + "dregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped d region amino acid sequence\n" + }, + "jregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped j region amino acid sequence\n" + }, + "fr1region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr1 region amino acid sequence\n" + }, + "fr2region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr2 region amino acid sequence\n" + }, + "fr3region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr3 region amino acid sequence\n" + }, + "fr4region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr4 region amino acid sequence\n" + }, + "cdr1region_sequence_aa_gapped": { + "type": "string", + "description": "gapped cdr1 region amino acid sequence\n" + }, + "cdr2region_sequence_aa_gapped": { + "type": "string", + "description": "gapped cdr2 region amino acid sequence\n" + }, + "cdr3region_sequence_aa_gapped": { + "type": "string", + "description": "gapped cdr3 region amino acid sequence\n" + }, + "junction_sequence_aa_gapped": { + "type": "string", + "description": "gapped junction amino acid sequence\n" + }, + "vdjregion_start": { + "type": "integer", + "description": "e.g. 1\n" + }, + "vdjregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "vjregion_start": { + "type": "integer", + "description": "e.g. 0\n" + }, + "vjregion_end": { + "type": "integer", + "description": "e.g. 0\n" + }, + "djregion_start": { + "type": "integer", + "description": "e.g. 254\n" + }, + "djregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "vregion_start": { + "type": "integer", + "description": "e.g. 286\n" + }, + "vregion_end": { + "type": "integer", + "description": "e.g. 252\n" + }, + "dregion_start": { + "type": "integer", + "description": "e.g. 254\n" + }, + "dregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "jregion_start": { + "type": "integer", + "description": "e.g. 286\n" + }, + "jregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "fr1region_start": { + "type": "integer", + "description": "e.g. 1\n" + }, + "fr1region_end": { + "type": "integer", + "description": "e.g. 38\n" + }, + "fr2region_start": { + "type": "integer", + "description": "e.g. 63\n" + }, + "fr2region_end": { + "type": "integer", + "description": "e.g. 113\n" + }, + "fr3region_start": { + "type": "integer", + "description": "e.g. 135\n" + }, + "fr3region_end": { + "type": "integer", + "description": "e.g. 248\n" + }, + "fr4region_start": { + "type": "integer", + "description": "e.g. 288\n" + }, + "fr4region_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "cdr1region_start": { + "type": "integer", + "description": "e.g. 39\n" + }, + "cdr1region_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "cdr2region_start": { + "type": "integer", + "description": "e.g. 62\n" + }, + "cdr2region_end": { + "type": "integer", + "description": "e.g. 134\n" + }, + "cdr3region_start": { + "type": "integer", + "description": "e.g. 249\n" + }, + "cdr3region_end": { + "type": "integer", + "description": "e.g. 287\n" + }, + "junction_start": { + "type": "integer", + "description": "e.g. 246\n" + }, + "junction_end": { + "type": "integer", + "description": "e.g. 290\n" + }, + "vregion_mutation_string": { + "type": "string", + "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" + }, + "fr1region_mutation_string": { + "type": "string", + "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" + }, + "fr2region_mutation_string": { + "type": "string", + "description": "e.g. \n" + }, + "fr3region_mutation_string": { + "type": "string", + "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" + }, + "cdr1region_mutation_string": { + "type": "string", + "description": "e.g.\n" + }, + "cdr2region_mutation_string": { + "type": "string", + "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" + }, + "cdr3region_mutation_string": { + "type": "string", + "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" + }, + "annotation_tool": { + "type": "string", + "description": "e.g. VQuest\n" + } + } + } + }, + "summary_model": { + "type": "array", + "items": { + "type": "object", + "properties": { + "sequence_count": { + "type": "integer", + "description": "The number of sequences that match the filter for this sample.\n" + }, + "study_id": { + "type": "string", + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" + }, + "study_title": { + "type": "string", + "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" + }, + "study_type": { + "type": "string", + "description": "Type of project/study (e.g. Cancer) (AIRR)\n" + }, + "inclusion_exclusion_criteria": { + "type": "string", + "description": "Study inclusion/exclusion criteria (AIRR)\n" + }, + "grants": { + "type": "string", + "description": "Grant funding agency (AIRR)\n" + }, + "lab_name": { + "type": "string", + "description": "Lab name (AIRR) \n" + }, + "collected_by": { + "type": "string", + "description": "Contact information (data collection) (AIRR)\n" + }, + "uploaded_by": { + "type": "string", + "description": "Contact information (data deposition) (AIRR)\n" + }, + "lab_address": { + "type": "string", + "description": "Lab address (AIRR)\n" + }, + "pubs_ids": { + "type": "string", + "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" + }, + "subject_id": { + "type": "string", + "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" + }, + "organism": { + "type": "string", + "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" + }, + "sex": { + "type": "string", + "description": "Sex (e.g. M/F) (AIRR)\n" + }, + "age": { + "type": "string", + "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" + }, + "age_event": { + "type": "string", + "description": "Age event (e.g. Enrollment) (AIRR)\n" + }, + "ancestry_population": { + "type": "string", + "description": "Ancestry population (AIRR)\n" + }, + "ethnicity": { + "type": "string", + "description": "Ethnicity (e.g. Tamil) (AIRR)\n" + }, + "race": { + "type": "string", + "description": "Race (e.g. South Indian) (AIRR)\n" + }, + "species_name": { + "type": "string", + "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" + }, + "strain_name": { + "type": "string", + "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" + }, + "linked_subjects": { + "type": "string", + "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" + }, + "link_type": { + "type": "string", + "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" + }, + "sample_id": { + "type": "string", + "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" + }, + "sample_type": { + "type": "string", + "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" + }, + "tissue": { + "type": "string", + "description": "Anatomic site (e.g. spleen) (AIRR)\n" + }, + "disease_state_sample": { + "type": "string", + "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" + }, + "collection_date": { + "type": "string", + "description": "Sample collection time (e.g. 10 days) (AIRR)\n" + }, + "collection_time_event": { + "type": "string", + "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" + }, + "source_commercial": { + "type": "string", + "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" + }, + "cell_subset": { + "type": "string", + "description": "Cell subset (Controlled vocabulary) (AIRR)\n" + }, + "cell_phenotype": { + "type": "string", + "description": "Cell subset phenotype (lab specific description) (AIRR)\n" + }, + "study_group_description": { + "type": "string", + "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" + }, + "library_source": { + "type": "string", + "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" + }, + "subject_age": { + "type": "integer", + "description": "e.g. 1\n" + }, + "marker_1": { + "type": "string", + "description": "e.g. CR19\n" + }, + "marker_2": { + "type": "string", + "description": "e.g. CR20\n" + }, + "marker_3": { + "type": "string", + "description": "e.g. CR21\n" + }, + "marker_4": { + "type": "string", + "description": "e.g. null\n" + }, + "marker_5": { + "type": "string", + "description": "e.g. null\n" + }, + "marker_6": { + "type": "string", + "description": "e.g. null\n" + }, + "subject_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a subject.\n" + }, + "project_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a project.\n" + }, + "project_parent_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a parent/child relationship between this project and its parent project.\n" + }, + "lab_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a lab.\n" + }, + "case_control_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" + }, + "sample_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a sample.\n" + }, + "dna_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a DNA type.\n" + }, + "project_sample_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an association a project with a sample.\n" + }, + "sample_subject_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an association between a sample and a subject.\n" + }, + "sample_source_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an association between a sample and a sample source.\n" + } + } + } + } + }, "schemes": [ "https" ], @@ -199,218 +968,9 @@ "operationId": "getSamples", "responses": { "200": { - "description": "A successful call returns the metadata for each sample, including\nthe number of sequences found for that sample.\n", + "description": "A successful call returns an array of sample summary metadata for\neach sample that meets the search criteria. The metadata returned\nfor each sample includes the number of sequences found for that sample\nas well as the study/subject/sample data for that sample. The metadata\nfor each sample in the response contains a set of AIRR compliant data\nas well as repository specific data that is required to query the\nrepository about those types of elements. \n", "schema": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sequence_count": { - "type": "integer", - "description": "The number of sequences that match the filter for this sample.\n" - }, - "study_id": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "study_title": { - "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" - }, - "study_type": { - "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)\n" - }, - "inclusion_exclusion_criteria": { - "type": "string", - "description": "Study inclusion/exclusion criteria (AIRR)\n" - }, - "grants": { - "type": "string", - "description": "Grant funding agency (AIRR)\n" - }, - "lab_name": { - "type": "string", - "description": "Lab name (AIRR) \n" - }, - "collected_by": { - "type": "string", - "description": "Contact information (data collection) (AIRR)\n" - }, - "uploaded_by": { - "type": "string", - "description": "Contact information (data deposition) (AIRR)\n" - }, - "lab_address": { - "type": "string", - "description": "Lab address (AIRR)\n" - }, - "pubs_ids": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "subject_id": { - "type": "string", - "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" - }, - "organism": { - "type": "string", - "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" - }, - "sex": { - "type": "string", - "description": "Sex (e.g. M/F) (AIRR)\n" - }, - "age": { - "type": "string", - "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" - }, - "age_event": { - "type": "string", - "description": "Age event (e.g. Enrollment) (AIRR)\n" - }, - "ancestry_population": { - "type": "string", - "description": "Ancestry population (AIRR)\n" - }, - "ethnicity": { - "type": "string", - "description": "Ethnicity (e.g. Tamil) (AIRR)\n" - }, - "race": { - "type": "string", - "description": "Race (e.g. South Indian) (AIRR)\n" - }, - "species_name": { - "type": "string", - "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" - }, - "strain_name": { - "type": "string", - "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" - }, - "linked_subjects": { - "type": "string", - "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" - }, - "link_type": { - "type": "string", - "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" - }, - "sample_id": { - "type": "string", - "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" - }, - "sample_type": { - "type": "string", - "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" - }, - "tissue": { - "type": "string", - "description": "Anatomic site (e.g. spleen) (AIRR)\n" - }, - "disease_state_sample": { - "type": "string", - "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" - }, - "collection_date": { - "type": "string", - "description": "Sample collection time (e.g. 10 days) (AIRR)\n" - }, - "collection_time_event": { - "type": "string", - "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" - }, - "source_commercial": { - "type": "string", - "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" - }, - "cell_subset": { - "type": "string", - "description": "Cell subset (Controlled vocabulary) (AIRR)\n" - }, - "cell_phenotype": { - "type": "string", - "description": "Cell subset phenotype (lab specific description) (AIRR)\n" - }, - "study_group_description": { - "type": "string", - "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" - }, - "library_source": { - "type": "string", - "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" - }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" - }, - "marker_1": { - "type": "string", - "description": "e.g. CR19\n" - }, - "marker_2": { - "type": "string", - "description": "e.g. CR20\n" - }, - "marker_3": { - "type": "string", - "description": "e.g. CR21\n" - }, - "marker_4": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_5": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_6": { - "type": "string", - "description": "e.g. null\n" - }, - "subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a subject.\n" - }, - "project_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a project.\n" - }, - "project_parent_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a parent/child\nrelationship between this project and its parent project.\n" - }, - "lab_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a lab.\n" - }, - "case_control_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" - }, - "sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a sample.\n" - }, - "dna_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a DNA type.\n" - }, - "project_sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\na project with a sample.\n" - }, - "sample_subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a subject.\n" - }, - "sample_source_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a sample source.\n" - } - } - } + "$ref": "#/definitions/summary_model" } }, "400": { @@ -521,218 +1081,9 @@ "operationId": "postSamples", "responses": { "200": { - "description": "A successful call returns the metadata for each sample, including\nthe number of sequences found for that sample.\n", + "description": "A successful call returns the metadata for each sample, including the number of sequences found for that sample.\n", "schema": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sequence_count": { - "type": "integer", - "description": "The number of sequences that match the filter for this sample.\n" - }, - "study_id": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "study_title": { - "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" - }, - "study_type": { - "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)\n" - }, - "inclusion_exclusion_criteria": { - "type": "string", - "description": "Study inclusion/exclusion criteria (AIRR)\n" - }, - "grants": { - "type": "string", - "description": "Grant funding agency (AIRR)\n" - }, - "lab_name": { - "type": "string", - "description": "Lab name (AIRR) \n" - }, - "collected_by": { - "type": "string", - "description": "Contact information (data collection) (AIRR)\n" - }, - "uploaded_by": { - "type": "string", - "description": "Contact information (data deposition) (AIRR)\n" - }, - "lab_address": { - "type": "string", - "description": "Lab address (AIRR)\n" - }, - "pubs_ids": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "subject_id": { - "type": "string", - "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" - }, - "organism": { - "type": "string", - "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" - }, - "sex": { - "type": "string", - "description": "Sex (e.g. M/F) (AIRR)\n" - }, - "age": { - "type": "string", - "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" - }, - "age_event": { - "type": "string", - "description": "Age event (e.g. Enrollment) (AIRR)\n" - }, - "ancestry_population": { - "type": "string", - "description": "Ancestry population (AIRR)\n" - }, - "ethnicity": { - "type": "string", - "description": "Ethnicity (e.g. Tamil) (AIRR)\n" - }, - "race": { - "type": "string", - "description": "Race (e.g. South Indian) (AIRR)\n" - }, - "species_name": { - "type": "string", - "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" - }, - "strain_name": { - "type": "string", - "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" - }, - "linked_subjects": { - "type": "string", - "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" - }, - "link_type": { - "type": "string", - "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" - }, - "sample_id": { - "type": "string", - "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" - }, - "sample_type": { - "type": "string", - "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" - }, - "tissue": { - "type": "string", - "description": "Anatomic site (e.g. spleen) (AIRR)\n" - }, - "disease_state_sample": { - "type": "string", - "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" - }, - "collection_date": { - "type": "string", - "description": "Sample collection time (e.g. 10 days) (AIRR)\n" - }, - "collection_time_event": { - "type": "string", - "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" - }, - "source_commercial": { - "type": "string", - "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" - }, - "cell_subset": { - "type": "string", - "description": "Cell subset (Controlled vocabulary) (AIRR)\n" - }, - "cell_phenotype": { - "type": "string", - "description": "Cell subset phenotype (lab specific description) (AIRR)\n" - }, - "study_group_description": { - "type": "string", - "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" - }, - "library_source": { - "type": "string", - "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" - }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" - }, - "marker_1": { - "type": "string", - "description": "e.g. CR19\n" - }, - "marker_2": { - "type": "string", - "description": "e.g. CR20\n" - }, - "marker_3": { - "type": "string", - "description": "e.g. CR21\n" - }, - "marker_4": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_5": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_6": { - "type": "string", - "description": "e.g. null\n" - }, - "subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a subject.\n" - }, - "project_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a project.\n" - }, - "project_parent_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a parent/child\nrelationship between this project and its parent project.\n" - }, - "lab_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a lab.\n" - }, - "case_control_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" - }, - "sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a sample.\n" - }, - "dna_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a DNA type.\n" - }, - "project_sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\na project with a sample.\n" - }, - "sample_subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a subject.\n" - }, - "sample_source_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a sample source.\n" - } - } - } + "$ref": "#/definitions/summary_model" } }, "400": { @@ -805,879 +1156,12 @@ "type": "object", "properties": { "summary": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sequence_count": { - "type": "integer", - "description": "The number of sequences that match the filter for this sample.\n" - }, - "study_id": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "study_title": { - "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" - }, - "study_type": { - "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)\n" - }, - "inclusion_exclusion_criteria": { - "type": "string", - "description": "Study inclusion/exclusion criteria (AIRR)\n" - }, - "grants": { - "type": "string", - "description": "Grant funding agency (AIRR)\n" - }, - "lab_name": { - "type": "string", - "description": "Lab name (AIRR) \n" - }, - "collected_by": { - "type": "string", - "description": "Contact information (data collection) (AIRR)\n" - }, - "uploaded_by": { - "type": "string", - "description": "Contact information (data deposition) (AIRR)\n" - }, - "lab_address": { - "type": "string", - "description": "Lab address (AIRR)\n" - }, - "pubs_ids": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "subject_id": { - "type": "string", - "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" - }, - "organism": { - "type": "string", - "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" - }, - "sex": { - "type": "string", - "description": "Sex (e.g. M/F) (AIRR)\n" - }, - "age": { - "type": "string", - "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" - }, - "age_event": { - "type": "string", - "description": "Age event (e.g. Enrollment) (AIRR)\n" - }, - "ancestry_population": { - "type": "string", - "description": "Ancestry population (AIRR)\n" - }, - "ethnicity": { - "type": "string", - "description": "Ethnicity (e.g. Tamil) (AIRR)\n" - }, - "race": { - "type": "string", - "description": "Race (e.g. South Indian) (AIRR)\n" - }, - "species_name": { - "type": "string", - "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" - }, - "strain_name": { - "type": "string", - "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" - }, - "linked_subjects": { - "type": "string", - "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" - }, - "link_type": { - "type": "string", - "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" - }, - "sample_id": { - "type": "string", - "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" - }, - "sample_type": { - "type": "string", - "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" - }, - "tissue": { - "type": "string", - "description": "Anatomic site (e.g. spleen) (AIRR)\n" - }, - "disease_state_sample": { - "type": "string", - "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" - }, - "collection_date": { - "type": "string", - "description": "Sample collection time (e.g. 10 days) (AIRR)\n" - }, - "collection_time_event": { - "type": "string", - "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" - }, - "source_commercial": { - "type": "string", - "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" - }, - "cell_subset": { - "type": "string", - "description": "Cell subset (Controlled vocabulary) (AIRR)\n" - }, - "cell_phenotype": { - "type": "string", - "description": "Cell subset phenotype (lab specific description) (AIRR)\n" - }, - "study_group_description": { - "type": "string", - "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" - }, - "library_source": { - "type": "string", - "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" - }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" - }, - "marker_1": { - "type": "string", - "description": "e.g. CR19\n" - }, - "marker_2": { - "type": "string", - "description": "e.g. CR20\n" - }, - "marker_3": { - "type": "string", - "description": "e.g. CR21\n" - }, - "marker_4": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_5": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_6": { - "type": "string", - "description": "e.g. null\n" - }, - "subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a subject.\n" - }, - "project_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a project.\n" - }, - "project_parent_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a parent/child\nrelationship between this project and its parent project.\n" - }, - "lab_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a lab.\n" - }, - "case_control_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" - }, - "sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a sample.\n" - }, - "dna_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a DNA type.\n" - }, - "project_sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\na project with a sample.\n" - }, - "sample_subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a subject.\n" - }, - "sample_source_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a sample source.\n" - } - } - } + "$ref": "#/definitions/summary_model" }, "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - }, - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string", - "description": "e.g IGHV4-59*01 or IGHV4-59*07\n" - }, - "vgene_family": { - "type": "string", - "description": "e.g. IGHV4\n" - }, - "vgene_gene": { - "type": "string", - "description": "e.g. IGHV4-59\n" - }, - "dgene_string": { - "type": "string", - "description": "e.g. Homsap IGHD3-10*01 F\n" - }, - "dgene_family": { - "type": "string", - "description": "e.g. IGHD3\n" - }, - "dgene_gene": { - "type": "string", - "description": "e.g. IGHD3-10\n" - }, - "jgene_string": { - "type": "string", - "description": "e.g. Homsap IGHJ4*02 F\n" - }, - "jgene_family": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "jgene_gene": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "functionality": { - "type": "string", - "description": "e.g. productive\n" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" - }, - "fr1region_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" - }, - "fr2region_mutation_string": { - "type": "string", - "description": "e.g. \n" - }, - "fr3region_mutation_string": { - "type": "string", - "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" - }, - "cdr1region_mutation_string": { - "type": "string", - "description": "e.g.\n" - }, - "cdr2region_mutation_string": { - "type": "string", - "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" - }, - "cdr3region_mutation_string": { - "type": "string", - "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" - }, - "annotation_tool": { - "type": "string", - "description": "e.g. VQuest\n" - } - } - } + "$ref": "#/definitions/airr_and_ireceptor_sequence_model" } } - }, - "examples": { - "application/json": { - "summary": [ - { - "subject_code": "IAVI 84", - "subject_id": 1, - "subject_gender": null, - "subject_ethnicity": "NA", - "subject_species": "Homo Sapiens", - "project_id": 1, - "study_title": "Mining the antibodyome for HIV-1 neutralizing antibodies with next generation sequencing and phylogenetic pairing of heavy/light chains", - "study_type": "HIV", - "project_parent_id": -1, - "study": "SRP018335", - "lab_id": 1, - "lab_name": "National Institute of Allergy and Infectious -DiseaseVaccine", - "Research Center": "Kwong Lab", - "disease_state_id": 7, - "disease_state_name": "HIV-1 infected for at least 3 years, not receiving antiretroviral treatment", - "case_control_id": 1, - "case_control_name": "Case", - "sample_id": 1, - "project_sample_id": 1, - "sequence_count": 253684, - "project_sample_note": null, - "sra_run_id": "SRR654169", - "sample_name": "SRS388604", - "subject_age": null, - "sample_subject_id": 1, - "dna_id": 1, - "dna_type": "cDNA", - "sample_source_id": 1, - "sample_source_name": "PBMCs", - "lab_cell_subset_name": "B cell memory", - "ireceptor_cell_subset_name": "Memory B Cell", - "marker_1": "IgG+", - "marker_2": "CD19+", - "marker_3": "sIgG+", - "marker_4": " negative depletion to CD3", - "marker_5": " CD14", - "marker_6": " CD16, IgM, IgA, IgD ", - "sequences": 167793 - } - ], - "items": [ - { - "seq_id": 2, - "seq_name": "SRR654169.17_G912ZWU01EPN4E_length=379", - "project_sample_id": 1, - "id": 37, - "vgene_string": "Homsap IGHV1-24*01 F", - "vgene_family": "IGHV1", - "vgene_gene": "IGHV1-24", - "v_allele": " IGHV1-24*01 ", - "jgene_string": "Homsap IGHJ3*02 F", - "jgene_family": "IGHJ3", - "jgene_gene": "IGHJ3", - "j_allele": " IGHJ3*02 ", - "dgene_string": "Homsap IGHD3-22*01 F", - "dgene_family": "IGHD3", - "dgene_gene": "IGHD3-22", - "d_allele": " IGHD3-22*01 ", - "functionality": "productive", - "vgene_score": 1417, - "vgene_probablity": null, - "dregion_reading_frame": "3", - "cdr1_length": 8, - "cdr2_length": 8, - "cdr3_length": 17, - "vdjregion_sequence_nt": "caggtccagctggtagagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaagtttccggatacaccctcactgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgatggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag", - "vjregion_sequence_nt": "", - "djregion_sequence_nt": "gatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag", - "vregion_sequence_nt": "caggtccagctggtagagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctcactgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaaca", - "jregion_sequence_nt": "gatggttttgatatctggggccaagggacaatggtcaccgtctcttcag", - "dregion_sequence_nt": "gatagttgtgattat", - "fr1region_sequence_nt": "caggtccagctggtagagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttcc", - "fr2region_sequence_nt": "atgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggt", - "fr3region_sequence_nt": "atctacgcacagaagttccagggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgt", - "fr4region_sequence_nt": "tggggccaagggacaatggtcaccgtctcttcag", - "cdr1region_sequence_nt": "ggatacaccctcactgaattatcc", - "cdr2region_sequence_nt": "tttgatcctgaagatggtgaaaca", - "cdr3region_sequence_nt": "gcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatc", - "junction_nt": "tgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctgg", - "vdjregion_sequence_nt_gapped": "caggtccagctggtagagtctggggct...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctc............actgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaa......gatggtgaaacaatctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag", - "vjregion_sequence_nt_gapped": "", - "djregion_sequence_nt_gapped": null, - "vregion_sequence_nt_gapped": "caggtccagctggtagagtctggggct...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctc............actgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaa......gatggtgaaacaatctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaaca", - "jregion_sequence_nt_gapped": "gatggttttgatatctggggccaagggacaatggtcaccgtctcttcag", - "dregion_sequence_nt_gapped": "gatggttttgatatctggggccaagggacaatggtcaccgtctcttcag", - "fr1region_sequence_nt_gapped": "caggtccagctggtagagtctggggct ...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttcc", - "fr2region_sequence_nt_gapped": "atgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggt", - "fr3region_sequence_nt_gapped": "atctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgt", - "fr4region_sequence_nt_gapped": "tggggccaagggacaatggtcaccgtctcttcag", - "cdr1region_sequence_nt_gapped": "ggatacaccctc............actgaattatcc", - "cdr2region_sequence_nt_gapped": "tttgatcctgaa......gatggtgaaaca", - "cdr3region_sequence_nt_gapped": "gcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatc", - "junction_sequence_nt_gapped": "tgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctgg", - "vdjregion_sequence_aa": "QVQLVESGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLEWMGGFDPEDGETIYAQKFQGR ITMTEDTSTDTAYMELSSLRSEDTAVYYCATRSPPIVVIMDDGFDIWGQGTMVTVSS", - "vjregion_sequence_aa": "", - "djregion_sequence_aa": null, - "vregion_sequence_aa": "QVQLVESGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLEWMGGFDPEDGETIYAQKFQGRITMTEDTSTDTAYMELSSLRSEDTAVYYCAT", - "jregion_sequence_aa": "DGFDIWGQGTMVTVSS", - "dregion_sequence_aa": null, - "fr1region_sequence_aa": "QVQLVESGAEVKKPGASVKVSCKVS", - "fr2region_sequence_aa": "MHWVRQAPGKGLEWMGG", - "fr3region_sequence_aa": "IYAQKFQGRITMTEDTSTDTAYMELSSLRSEDTAVYYC", - "fr4region_sequence_aa": "WGQGTMVTVSS", - "cdr1region_sequence_aa": "GYTLTELS", - "cdr2region_sequence_aa": "FDPEDGET", - "cdr3region_sequence_aa": "ATRSPPIVVIMDDGFDI", - "junction_aa": "CATRSPPIVVIMDDGFDIW", - "vdjregion_sequence_aa_gapped": "QVQLVESGA.EVKKPGASVKVSCKVSGYTL....TELSMHWVRQAPGKGLEWMGGFDPE..DGETIYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYCATRSPPIVVIMDDGFDIWGQGTMVTVSS", - "vjregion_sequence_aa_gapped": "", - "djregion_sequence_aa_gapped": null, - "vregion_sequence_aa_gapped": "QVQLVESGA.EVKKPGASVKVSCKVSGYTL....TELSMHWVRQAPGKGLEWMGGFDPE..DGETIYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYCAT", - "jregion_sequence_aa_gapped": "DGFDIWGQGTMVTVSS", - "dregion_sequence_aa_gapped": null, - "fr1region_sequence_aa_gapped": "QVQLVESGA.EVKKPGASVKVSCKVS", - "fr2region_sequence_aa_gapped": "MHWVRQAPGKGLEWMGG", - "fr3region_sequence_aa_gapped": "IYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYC", - "fr4region_sequence_aa_gapped": "WGQGTMVTVSS", - "cdr1region_sequence_aa_gapped": "GYTL....TELS", - "cdr2region_sequence_aa_gapped": "FDPE..DGET", - "cdr3region_sequence_aa_gapped": "ATRSPPIVVIMDDGFDI", - "junction_sequence_aa_gapped": "CATRSPPIVVIMDDGFDIW", - "vdjregion_start": 2, - "vdjregion_end": 374, - "vjregion_start": null, - "vjregion_end": null, - "vregion_start": 2, - "vregion_end": 295, - "jregion_start": 326, - "jregion_end": 374, - "dregion_start": 307, - "dregion_end": 374, - "fr1region_start": 2, - "fr1region_end": 76, - "fr2region_start": 101, - "fr2region_end": 151, - "fr3region_start": 176, - "fr3region_end": 289, - "fr4region_start": 341, - "fr4region_end": 374, - "cdr1region_start": 77, - "cdr1region_end": 100, - "cdr2region_start": 152, - "cdr2region_end": 175, - "cdr3region_start": 290, - "cdr3region_end": 340, - "junction_start": 287, - "junction_end": 343, - "vregion_mutation_string": "c16>g,Q6>E(++ -)|g226>a,V76>I(+ - +)|", - "fr1region_mutation_string": "c16>g,Q6>E(+ + -)|", - "fr2region_mutation_string": "", - "fr3region_mutation_string": "g226>a,V76>I(+ - +)|", - "cdr1region_mutation_string": "", - "cdr2region_mutation_string": "", - "cdr3region_mutation_string": "g319>a|a320>g|", - "vgene_probability": "99", - "djregion_start": 307, - "djregion_end": 374, - "annotation_tool": "VQuest" - } - ] - } } }, "400": { @@ -1754,530 +1238,7 @@ "200": { "description": "A successful call returns an array of sequence data. Optional \"format\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"format\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format; \"tsv\" returns a tab-delimited outputs; \"airr\" returns AIRR minimal standards encoded tab-delimited outputs.\n", "schema": { - "type": "array", - "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - }, - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string" - }, - "vgene_family": { - "type": "string", - "description": "e.g. IGHV4\n" - }, - "vgene_gene": { - "type": "string", - "description": "e.g. IGHV4-59\n" - }, - "dgene_string": { - "type": "string", - "description": "e.g. Homsap IGHD3-10*01 F\n" - }, - "dgene_family": { - "type": "string", - "description": "e.g. IGHD3\n" - }, - "dgene_gene": { - "type": "string", - "description": "e.g. IGHD3-10\n" - }, - "jgene_string": { - "type": "string", - "description": "e.g. Homsap IGHJ4*02 F\n" - }, - "jgene_family": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "jgene_gene": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "functionality": { - "type": "string", - "description": "e.g. productive\n" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" - }, - "fr1region_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" - }, - "fr2region_mutation_string": { - "type": "string", - "description": "e.g. \n" - }, - "fr3region_mutation_string": { - "type": "string", - "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" - }, - "cdr1region_mutation_string": { - "type": "string", - "description": "e.g.\n" - }, - "cdr2region_mutation_string": { - "type": "string", - "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" - }, - "cdr3region_mutation_string": { - "type": "string", - "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" - }, - "citation": { - "type": "object", - "properties": { - "doi": { - "type": "string" - }, - "title": { - "type": "string" - } - } - } - } - } - }, - "examples": { - "application/json": { - "seq_name": "M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0\n", - "vgene_gene": "IGHV4-59\n", - "v_allele": "IGHV4-59*01 or IGHV4-59*07\n", - "dgene_string": "Homsap IGHD3-10*01 F\n", - "dgene_family": "IGHD3\n", - "dgene_gene": "IGHD3-10\n", - "d_allele": "IGHD3-10*01\n", - "jgene_string": "Homsap IGHJ4*02 F\n", - "jgene_family": "IGHJ4\n", - "jgene_gene": "IGHJ4\n", - "j_allele": "IGHJ4*02\n", - "functionality": "productive\n", - "vregion_mutation_string": "a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ -\n+)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- -\n-)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ +\n-)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n", - "fr1region_mutation_string": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n", - "fr3region_mutation_string": "c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+\n- +)|g275>c,S92>T(+ - +)|t279>c|\"\n", - "cdr2region_mutation_string": "a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n", - "cdr3region_mutation_string": "g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n", - "citation": { - "doi": "10.1093/cid/ciw767", - "title": "RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.\n" - } - } + "$ref": "#/definitions/airr_and_ireceptor_sequence_model" } }, "400": { @@ -2344,514 +1305,7 @@ "200": { "description": "A successful call returns an array of sequence data. Optional \"format\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"format\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format; \"tsv\" returns a tab-delimited outputs; \"airr\" returns AIRR minimal standards encoded tab-delimited outputs.\n", "schema": { - "type": "array", - "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - }, - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string" - }, - "vgene_family": { - "type": "string" - }, - "vgene_gene": { - "type": "string" - }, - "dgene_string": { - "type": "string" - }, - "dgene_family": { - "type": "string" - }, - "dgene_gene": { - "type": "string" - }, - "jgene_string": { - "type": "string" - }, - "jgene_family": { - "type": "string" - }, - "jgene_gene": { - "type": "string" - }, - "functionality": { - "type": "string" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string" - }, - "fr1region_mutation_string": { - "type": "string" - }, - "fr2region_mutation_string": { - "type": "string" - }, - "fr3region_mutation_string": { - "type": "string" - }, - "cdr1region_mutation_string": { - "type": "string" - }, - "cdr2region_mutation_string": { - "type": "string" - }, - "cdr3region_mutation_string": { - "type": "string" - }, - "citation": { - "type": "object", - "properties": { - "doi": { - "type": "string" - }, - "title": { - "type": "string" - } - } - } - } - } - }, - "examples": { - "application/json": { - "seq_name": "M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0\n", - "vgene_gene": "IGHV4-59\n", - "v_allele": "IGHV4-59*01 or IGHV4-59*07\n", - "dgene_string": "Homsap IGHD3-10*01 F\n", - "dgene_family": "IGHD3\n", - "dgene_gene": "IGHD3-10\n", - "d_allele": "IGHD3-10*01\n", - "jgene_string": "Homsap IGHJ4*02 F\n", - "jgene_family": "IGHJ4\n", - "jgene_gene": "IGHJ4\n", - "j_allele": "IGHJ4*02\n", - "functionality": "productive\n", - "vregion_mutation_string": "a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ -\n+)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- -\n-)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ +\n-)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n", - "fr1region_mutation_string": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n", - "fr3region_mutation_string": "c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+\n- +)|g275>c,S92>T(+ - +)|t279>c|\"\n", - "cdr2region_mutation_string": "a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n", - "cdr3region_mutation_string": "g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n", - "citation": { - "doi": "10.1093/cid/ciw767", - "title": "RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.\n" - } - } + "$ref": "#/definitions/airr_and_ireceptor_sequence_model" } }, "400": { @@ -2924,711 +1378,10 @@ "type": "object", "properties": { "summary": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sequence_count": { - "type": "integer", - "description": "The number of sequences that match the filter for this sample.\n" - }, - "study_id": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "study_title": { - "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" - }, - "study_type": { - "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)\n" - }, - "inclusion_exclusion_criteria": { - "type": "string", - "description": "Study inclusion/exclusion criteria (AIRR)\n" - }, - "grants": { - "type": "string", - "description": "Grant funding agency (AIRR)\n" - }, - "lab_name": { - "type": "string", - "description": "Lab name (AIRR) \n" - }, - "collected_by": { - "type": "string", - "description": "Contact information (data collection) (AIRR)\n" - }, - "uploaded_by": { - "type": "string", - "description": "Contact information (data deposition) (AIRR)\n" - }, - "lab_address": { - "type": "string", - "description": "Lab address (AIRR)\n" - }, - "pubs_ids": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "subject_id": { - "type": "string", - "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" - }, - "organism": { - "type": "string", - "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" - }, - "sex": { - "type": "string", - "description": "Sex (e.g. M/F) (AIRR)\n" - }, - "age": { - "type": "string", - "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" - }, - "age_event": { - "type": "string", - "description": "Age event (e.g. Enrollment) (AIRR)\n" - }, - "ancestry_population": { - "type": "string", - "description": "Ancestry population (AIRR)\n" - }, - "ethnicity": { - "type": "string", - "description": "Ethnicity (e.g. Tamil) (AIRR)\n" - }, - "race": { - "type": "string", - "description": "Race (e.g. South Indian) (AIRR)\n" - }, - "species_name": { - "type": "string", - "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" - }, - "strain_name": { - "type": "string", - "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" - }, - "linked_subjects": { - "type": "string", - "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" - }, - "link_type": { - "type": "string", - "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" - }, - "sample_id": { - "type": "string", - "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" - }, - "sample_type": { - "type": "string", - "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" - }, - "tissue": { - "type": "string", - "description": "Anatomic site (e.g. spleen) (AIRR)\n" - }, - "disease_state_sample": { - "type": "string", - "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" - }, - "collection_date": { - "type": "string", - "description": "Sample collection time (e.g. 10 days) (AIRR)\n" - }, - "collection_time_event": { - "type": "string", - "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" - }, - "source_commercial": { - "type": "string", - "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" - }, - "cell_subset": { - "type": "string", - "description": "Cell subset (Controlled vocabulary) (AIRR)\n" - }, - "cell_phenotype": { - "type": "string", - "description": "Cell subset phenotype (lab specific description) (AIRR)\n" - }, - "study_group_description": { - "type": "string", - "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" - }, - "library_source": { - "type": "string", - "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" - }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" - }, - "marker_1": { - "type": "string", - "description": "e.g. CR19\n" - }, - "marker_2": { - "type": "string", - "description": "e.g. CR20\n" - }, - "marker_3": { - "type": "string", - "description": "e.g. CR21\n" - }, - "marker_4": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_5": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_6": { - "type": "string", - "description": "e.g. null\n" - }, - "subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a subject.\n" - }, - "project_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a project.\n" - }, - "project_parent_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a parent/child\nrelationship between this project and its parent project.\n" - }, - "lab_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a lab.\n" - }, - "case_control_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" - }, - "sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a sample.\n" - }, - "dna_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a DNA type.\n" - }, - "project_sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\na project with a sample.\n" - }, - "sample_subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a subject.\n" - }, - "sample_source_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association\nbetween a sample and a sample source.\n" - } - } - } + "$ref": "#/definitions/summary_model" }, "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - }, - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string", - "description": "e.g IGHV4-59*01 or IGHV4-59*07\n" - }, - "vgene_family": { - "type": "string", - "description": "e.g. IGHV4\n" - }, - "vgene_gene": { - "type": "string", - "description": "e.g. IGHV4-59\n" - }, - "dgene_string": { - "type": "string", - "description": "e.g. Homsap IGHD3-10*01 F\n" - }, - "dgene_family": { - "type": "string", - "description": "e.g. IGHD3\n" - }, - "dgene_gene": { - "type": "string", - "description": "e.g. IGHD3-10\n" - }, - "jgene_string": { - "type": "string", - "description": "e.g. Homsap IGHJ4*02 F\n" - }, - "jgene_family": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "jgene_gene": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "functionality": { - "type": "string", - "description": "e.g. productive\n" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" - }, - "fr1region_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" - }, - "fr2region_mutation_string": { - "type": "string", - "description": "e.g. \n" - }, - "fr3region_mutation_string": { - "type": "string", - "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" - }, - "cdr1region_mutation_string": { - "type": "string", - "description": "e.g.\n" - }, - "cdr2region_mutation_string": { - "type": "string", - "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" - }, - "cdr3region_mutation_string": { - "type": "string", - "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" - }, - "annotation_tool": { - "type": "string", - "description": "e.g. VQuest\n" - } - } - } + "$ref": "#/definitions/airr_and_ireceptor_sequence_model" } } } @@ -3700,525 +1453,14 @@ "200": { "description": "A successful call returns an array of sequence data. Optional \"output\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"output\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format. \n", "schema": { - "type": "array", - "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - }, - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string" - }, - "vgene_family": { - "type": "string", - "description": "e.g. IGHV4\n" - }, - "vgene_gene": { - "type": "string", - "description": "e.g. IGHV4-59\n" - }, - "dgene_string": { - "type": "string", - "description": "e.g. Homsap IGHD3-10*01 F\n" - }, - "dgene_family": { - "type": "string", - "description": "e.g. IGHD3\n" - }, - "dgene_gene": { - "type": "string", - "description": "e.g. IGHD3-10\n" - }, - "jgene_string": { - "type": "string", - "description": "e.g. Homsap IGHJ4*02 F\n" - }, - "jgene_family": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "jgene_gene": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "functionality": { - "type": "string", - "description": "e.g. productive\n" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" - }, - "fr1region_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" - }, - "fr2region_mutation_string": { - "type": "string", - "description": "e.g. \n" - }, - "fr3region_mutation_string": { - "type": "string", - "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" - }, - "cdr1region_mutation_string": { - "type": "string", - "description": "e.g.\n" - }, - "cdr2region_mutation_string": { - "type": "string", - "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" - }, - "cdr3region_mutation_string": { - "type": "string", - "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" - }, - "citation": { - "type": "object", - "properties": { - "doi": { - "type": "string" - }, - "title": { - "type": "string" - } - } - } - } - } + "$ref": "#/definitions/airr_and_ireceptor_sequence_model" }, "examples": { "application/json": { "seq_name": "M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0\n", - "vgene_gene": "IGHV4-59\n", "v_allele": "IGHV4-59*01 or IGHV4-59*07\n", - "dgene_string": "Homsap IGHD3-10*01 F\n", - "dgene_family": "IGHD3\n", - "dgene_gene": "IGHD3-10\n", "d_allele": "IGHD3-10*01\n", - "jgene_string": "Homsap IGHJ4*02 F\n", - "jgene_family": "IGHJ4\n", - "jgene_gene": "IGHJ4\n", - "jgene_allele": "IGHJ4*02\n", - "functionality": "productive\n", - "vregion_mutation_string": "a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ -\n+)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- -\n-)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ +\n-)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n", - "fr1region_mutation_string": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n", - "fr3region_mutation_string": "c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+\n- +)|g275>c,S92>T(+ - +)|t279>c|\"\n", - "cdr2region_mutation_string": "a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n", - "cdr3region_mutation_string": "g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n", + "j_allele": "IGHJ4*02\n", "citation": { "doi": "10.1093/cid/ciw767", "title": "RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.\n" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index b3a9bb8..1f4c7b5 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -8,412 +8,840 @@ info: email: breden@sfu.ca description: > Documentation of Major Version 2 of the iReceptor Adaptive Immune Receptor - Repertoire (AIRR) data source web service application programming interface + Repertoire (AIRR) data repsoitory web service application programming interface (API). V2 of the API implements an increased level of compliance with the [Minimal Information for AIRR (MiAIRR) standard](https://github.com/airr-community/airr-standards). Learn more about [iReceptor](http://www.ireceptor.org/) host: ipa.ireceptor.org basePath: /v2 -schemes: - - https -produces: - - application/json -tags: - - name: info - description: Service information - - name: samples - description: Queries for samples - - name: sequences - description: Queries for sequences - - name: clones - description: Queries for clones -paths: - /: - x-swagger-router-controller: status - get: - description: | - Service heartbeat. - operationId: getStatus - responses: - '200': +definitions: + airr_sequence_model: + type: array + items: + type: object + properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer description: | - Success. - schema: - type: object - properties: - result: - type: string - /info: - x-swagger-router-controller: status - get: - description: | - Service information. - tags: - - info - operationId: getInfo - responses: - '200': + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string description: | - Success. - schema: - type: object - properties: - name: - type: string - version: - type: string - /swagger: - x-swagger-pipe: swagger_raw - /samples: - x-swagger-router-controller: samples - get: - description: > - This service returns metadata about samples, including higher-level - meta-data around the study, subject, diagnosis, and sample processing - (data relevant to MiAIRR data classes 1 through 3). The data returned is - filtered based on the parameters provided. - - A successful call returns a json list with a sample level summary of - each sample including a summary count of the number of sequences found - for that sample. - tags: - - samples - parameters: - - name: username - in: query + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) + extended_sequence_model: + allOf: + - $ref: '#/definitions/airr_sequence_model' + - type: object + properties: + an_extended_model_element: + type: string + description: This does not seem to extend the model, it replaces it! + airr_and_ireceptor_sequence_model: + type: array + items: + type: object + properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: type: string - - name: lab_id - in: query + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) + seq_id: + type: integer description: | e.g. 1 - required: false + seq_name: + type: string + project_sample_id: + type: integer + description: | + e.g. 6 + id: type: integer - - name: project_id - in: query description: | e.g. 1 - required: false - type: array - items: - type: integer - - name: subject_code - in: query + sequence_id: + type: integer description: | - e.g. test - required: false + e.g. 1 + vgene_string: type: string - - name: subject_gender - in: query description: | - e.g. Male or Female - required: false + e.g IGHV4-59*01 or IGHV4-59*07 + vgene_family: type: string - - name: subject_species - in: query description: | - e.g. Human - required: false + e.g. IGHV4 + vgene_gene: type: string - - name: subject_ethnicity - in: query description: | - e.g. Caucasian - required: false + e.g. IGHV4-59 + dgene_string: type: string - - name: subject_age_min - in: query description: | - e.g. 10 - required: false + e.g. Homsap IGHD3-10*01 F + dgene_family: + type: string + description: | + e.g. IGHD3 + dgene_gene: + type: string + description: | + e.g. IGHD3-10 + jgene_string: + type: string + description: | + e.g. Homsap IGHJ4*02 F + jgene_family: + type: string + description: | + e.g. IGHJ4 + jgene_gene: + type: string + description: | + e.g. IGHJ4 + functionality: + type: string + description: | + e.g. productive + functionality_comment: + type: string + description: | + e.g. "" + orientation: + type: string + description: | + e.g. + + vgene_score: type: integer - - name: subject_age_max - in: query description: | - e.g. 12 - required: false + e.g. 1127 + vgene_probability: type: integer - - name: case_control_name - in: query description: | - e.g. Control - required: false + e.g. 95 + dregion_reading_frame: + type: integer + description: | + e.g. 2 + cdr1_length: + type: integer + description: | + e.g. 8 + cdr2_length: + type: integer + description: | + e.g. 7 + cdr3_length: + type: integer + description: | + e.g. 13 + vdjregion_sequence_nt: type: string - - name: sample_name - in: query description: | - e.g. test2 - required: false + vdj region nucleotide sequence + vjregion_sequence_nt: type: string - - name: sample_source_name - in: query description: | - e.g. Blood (PBMC) - required: false + vj region nucleotide sequence + djregion_sequence_nt: type: string - - name: ireceptor_cell_subset_name - in: query description: | - e.g. NaiveB - required: false + dj region nucleotide sequence + vregion_sequence_nt: type: string - - name: dna_type - in: query description: | - e.g. cDNA, gDNA - required: false + v region nucleotide sequence + dregion_sequence_nt: type: string - operationId: getSamples - responses: - '200': description: | - A successful call returns the metadata for each sample, including - the number of sequences found for that sample. - schema: - type: array - items: - type: object - properties: - sequence_count: - type: integer - description: > - The number of sequences that match the filter for this - sample. - study_id: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - study_title: - type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR) - study_type: - type: string - description: | - Type of project/study (e.g. Cancer) (AIRR) - inclusion_exclusion_criteria: - type: string - description: | - Study inclusion/exclusion criteria (AIRR) - grants: - type: string - description: | - Grant funding agency (AIRR) - lab_name: - type: string - description: | - Lab name (AIRR) - collected_by: - type: string - description: | - Contact information (data collection) (AIRR) - uploaded_by: - type: string - description: | - Contact information (data deposition) (AIRR) - lab_address: - type: string - description: | - Lab address (AIRR) - pubs_ids: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - subject_id: - type: string - description: "UID assigned by submitter (e.g.\_SUB856413) (AIRR)\n" - organism: - type: string - description: | - Organism-based (human, mouse) or synthetic (AIRR) - sex: - type: string - description: | - Sex (e.g. M/F) (AIRR) - age: - type: string - description: | - Age - Time duration and unit (e.g. 200 days) (AIRR) - age_event: - type: string - description: | - Age event (e.g. Enrollment) (AIRR) - ancestry_population: - type: string - description: | - Ancestry population (AIRR) - ethnicity: - type: string - description: | - Ethnicity (e.g. Tamil) (AIRR) - race: - type: string - description: | - Race (e.g. South Indian) (AIRR) - species_name: - type: string - description: | - Species name (e.g. Homo Sapiens) (AIRR) - strain_name: - type: string - description: | - Strain name (e.g. C57BL/6J) (AIRR) - linked_subjects: - type: string - description: > - Relation to other subjects (SubjectID e.g. SUB1355648) - (AIRR) - link_type: - type: string - description: | - Relation type (.e.g sister, father, daughter) (AIRR) - sample_id: - type: string - description: | - Biological sample ID - UID assigned by submitter (AIRR) - sample_type: - type: string - description: | - Sample type (e.g. Tissue, body fluid) (AIRR) - tissue: - type: string - description: | - Anatomic site (e.g. spleen) (AIRR) - disease_state_sample: - type: string - description: | - Disease state of sample (e.g. tumor vs margin) (AIRR) - collection_date: - type: string - description: | - Sample collection time (e.g. 10 days) (AIRR) - collection_time_event: - type: string - description: > - Collection time event (T0) (e.g. vaccination, recruitment, - etc) (AIRR) - source_commercial: - type: string - description: | - Commercial source of sample (e.g. XYZ Pharma) (AIRR) - cell_subset: - type: string - description: | - Cell subset (Controlled vocabulary) (AIRR) - cell_phenotype: - type: string - description: | - Cell subset phenotype (lab specific description) (AIRR) - study_group_description: - type: string - description: | - Study group description (e.g. Case vs. Control) (AIRR) - library_source: - type: string - description: > - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) - (AIRR) - subject_age: - type: integer - description: | - e.g. 1 - marker_1: - type: string - description: | - e.g. CR19 - marker_2: - type: string - description: | - e.g. CR20 - marker_3: - type: string - description: | - e.g. CR21 - marker_4: - type: string - description: | - e.g. null - marker_5: - type: string - description: | - e.g. null - marker_6: - type: string - description: | - e.g. null - subject_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - subject. - project_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - project. - project_parent_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - parent/child - - relationship between this project and its parent project. - lab_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - lab. - case_control_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - element in the case_control table. - sample_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - sample. - dna_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - DNA type. - project_sample_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association - - a project with a sample. - sample_subject_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association - - between a sample and a subject. - sample_source_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association - - between a sample and a sample source. - '400': - description: malformed request - '401': - description: authentication error - '403': - description: authorization error - '404': - description: data not found - '405': - description: method not allowed - post: + d region nucleotide sequence + jregion_sequence_nt: + type: string + description: | + j region nucleotide sequence + fr1region_sequence_nt: + type: string + description: | + fr1 region nucleotide sequence + fr2region_sequence_nt: + type: string + description: | + fr2 region nucleotide sequence + fr3region_sequence_nt: + type: string + description: | + fr3 region nucleotide sequence + fr4region_sequence_nt: + type: string + description: | + fr4 region nucleotide sequence + cdr1region_sequence_nt: + type: string + description: | + cdr1 region nucleotide sequence + cdr2region_sequence_nt: + type: string + description: | + cdr2 region nucleotide sequence + cdr3region_sequence_nt: + type: string + description: | + cdr3 region nucleotide sequence + vdjregion_sequence_nt_gapped: + type: string + description: | + gapped vdj region nucleotide sequence + vjregion_sequence_nt_gapped: + type: string + description: | + gapped vj region nucleotide sequence + djregion_sequence_nt_gapped: + type: string + description: | + gapped dj region nucleotide sequence + vregion_sequence_nt_gapped: + type: string + description: | + gapped v region nucleotide sequence + dregion_sequence_nt_gapped: + type: string + description: | + gapped d region nucleotide sequence + jregion_sequence_nt_gapped: + type: string + description: | + gapped j region nucleotide sequence + fr1region_sequence_nt_gapped: + type: string + description: | + gapped fr1 region nucleotide sequence + fr2region_sequence_nt_gapped: + type: string + description: | + gapped fr2 region nucleotide sequence + fr3region_sequence_nt_gapped: + type: string + description: | + gapped fr3 region nucleotide sequence + fr4region_sequence_nt_gapped: + type: string + description: | + gapped fr4 region nucleotide sequence + cdr1region_sequence_nt_gapped: + type: string + description: | + gapped cdr1 region nucleotide sequence + cdr2region_sequence_nt_gapped: + type: string + description: | + gapped cdr2 region nucleotide sequence + cdr3region_sequence_nt_gapped: + type: string + description: | + gapped cdr3 region nucleotide sequence + junction_sequence_nt_gapped: + type: string + description: | + gapped junction nucleotide sequence + vdjregion_sequence_aa: + type: string + description: | + vdj region amino acid sequence + vjregion_sequence_aa: + type: string + description: | + vj region amino acid sequence + djregion_sequence_aa: + type: string + description: | + dj region amino acid sequence + vregion_sequence_aa: + type: string + description: | + v region amino acid sequence + dregion_sequence_aa: + type: string + description: | + d region amino acid sequence + jregion_sequence_aa: + type: string + description: | + j region amino acid sequence + fr1region_sequence_aa: + type: string + description: | + fr1 region amino acid sequence + fr2region_sequence_aa: + type: string + description: | + fr2 region amino acid sequence + fr3region_sequence_aa: + type: string + description: | + fr3 region amino acid sequence + fr4region_sequence_aa: + type: string + description: | + fr4 region amino acid sequence + cdr1region_sequence_aa: + type: string + description: | + cdr1 region amino acid sequence + cdr2region_sequence_aa: + type: string + description: | + cdr2 region amino acid sequence + cdr3region_sequence_aa: + type: string + description: | + cdr3 region amino acid sequence + vdjregion_sequence_aa_gapped: + type: string + description: | + gapped vdj region amino acid sequence + vjregion_sequence_aa_gapped: + type: string + description: | + gapped vj region amino acid sequence + djregion_sequence_aa_gapped: + type: string + description: | + gapped dj region amino acid sequence + vregion_sequence_aa_gapped: + type: string + description: | + gapped v region amino acid sequence + dregion_sequence_aa_gapped: + type: string + description: | + gapped d region amino acid sequence + jregion_sequence_aa_gapped: + type: string + description: | + gapped j region amino acid sequence + fr1region_sequence_aa_gapped: + type: string + description: | + gapped fr1 region amino acid sequence + fr2region_sequence_aa_gapped: + type: string + description: | + gapped fr2 region amino acid sequence + fr3region_sequence_aa_gapped: + type: string + description: | + gapped fr3 region amino acid sequence + fr4region_sequence_aa_gapped: + type: string + description: | + gapped fr4 region amino acid sequence + cdr1region_sequence_aa_gapped: + type: string + description: | + gapped cdr1 region amino acid sequence + cdr2region_sequence_aa_gapped: + type: string + description: | + gapped cdr2 region amino acid sequence + cdr3region_sequence_aa_gapped: + type: string + description: | + gapped cdr3 region amino acid sequence + junction_sequence_aa_gapped: + type: string + description: | + gapped junction amino acid sequence + vdjregion_start: + type: integer + description: | + e.g. 1 + vdjregion_end: + type: integer + description: | + e.g. 321 + vjregion_start: + type: integer + description: | + e.g. 0 + vjregion_end: + type: integer + description: | + e.g. 0 + djregion_start: + type: integer + description: | + e.g. 254 + djregion_end: + type: integer + description: | + e.g. 321 + vregion_start: + type: integer + description: | + e.g. 286 + vregion_end: + type: integer + description: | + e.g. 252 + dregion_start: + type: integer + description: | + e.g. 254 + dregion_end: + type: integer + description: | + e.g. 321 + jregion_start: + type: integer + description: | + e.g. 286 + jregion_end: + type: integer + description: | + e.g. 321 + fr1region_start: + type: integer + description: | + e.g. 1 + fr1region_end: + type: integer + description: | + e.g. 38 + fr2region_start: + type: integer + description: | + e.g. 63 + fr2region_end: + type: integer + description: | + e.g. 113 + fr3region_start: + type: integer + description: | + e.g. 135 + fr3region_end: + type: integer + description: | + e.g. 248 + fr4region_start: + type: integer + description: | + e.g. 288 + fr4region_end: + type: integer + description: | + e.g. 321 + cdr1region_start: + type: integer + description: | + e.g. 39 + cdr1region_end: + type: integer + description: | + e.g. 321 + cdr2region_start: + type: integer + description: | + e.g. 62 + cdr2region_end: + type: integer + description: | + e.g. 134 + cdr3region_start: + type: integer + description: | + e.g. 249 + cdr3region_end: + type: integer + description: | + e.g. 287 + junction_start: + type: integer + description: | + e.g. 246 + junction_end: + type: integer + description: | + e.g. 290 + vregion_mutation_string: + type: string + description: > + e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - + +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - + -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| + fr1region_mutation_string: + type: string + description: | + e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| + fr2region_mutation_string: + type: string + description: | + e.g. + fr3region_mutation_string: + type: string + description: > + e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" + cdr1region_mutation_string: + type: string + description: | + e.g. + cdr2region_mutation_string: + type: string + description: | + e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" + cdr3region_mutation_string: + type: string + description: | + e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t + annotation_tool: + type: string + description: | + e.g. VQuest + summary_model: + type: array + items: + type: object + properties: + sequence_count: + type: integer + description: > + The number of sequences that match the filter for this + sample. + study_id: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + study_title: + type: string + description: | + Publication or Protocol Title (e.g. My Study) (AIRR) + study_type: + type: string + description: | + Type of project/study (e.g. Cancer) (AIRR) + inclusion_exclusion_criteria: + type: string + description: | + Study inclusion/exclusion criteria (AIRR) + grants: + type: string + description: | + Grant funding agency (AIRR) + lab_name: + type: string + description: | + Lab name (AIRR) + collected_by: + type: string + description: | + Contact information (data collection) (AIRR) + uploaded_by: + type: string + description: | + Contact information (data deposition) (AIRR) + lab_address: + type: string + description: | + Lab address (AIRR) + pubs_ids: + type: string + description: | + Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) + subject_id: + type: string + description: "UID assigned by submitter (e.g.\_SUB856413) (AIRR)\n" + organism: + type: string + description: | + Organism-based (human, mouse) or synthetic (AIRR) + sex: + type: string + description: | + Sex (e.g. M/F) (AIRR) + age: + type: string + description: | + Age - Time duration and unit (e.g. 200 days) (AIRR) + age_event: + type: string + description: | + Age event (e.g. Enrollment) (AIRR) + ancestry_population: + type: string + description: | + Ancestry population (AIRR) + ethnicity: + type: string + description: | + Ethnicity (e.g. Tamil) (AIRR) + race: + type: string + description: | + Race (e.g. South Indian) (AIRR) + species_name: + type: string + description: | + Species name (e.g. Homo Sapiens) (AIRR) + strain_name: + type: string + description: | + Strain name (e.g. C57BL/6J) (AIRR) + linked_subjects: + type: string + description: > + Relation to other subjects (SubjectID e.g. SUB1355648) + (AIRR) + link_type: + type: string + description: | + Relation type (.e.g sister, father, daughter) (AIRR) + sample_id: + type: string + description: | + Biological sample ID - UID assigned by submitter (AIRR) + sample_type: + type: string + description: | + Sample type (e.g. Tissue, body fluid) (AIRR) + tissue: + type: string + description: | + Anatomic site (e.g. spleen) (AIRR) + disease_state_sample: + type: string + description: | + Disease state of sample (e.g. tumor vs margin) (AIRR) + collection_date: + type: string + description: | + Sample collection time (e.g. 10 days) (AIRR) + collection_time_event: + type: string + description: > + Collection time event (T0) (e.g. vaccination, recruitment, + etc) (AIRR) + source_commercial: + type: string + description: | + Commercial source of sample (e.g. XYZ Pharma) (AIRR) + cell_subset: + type: string + description: | + Cell subset (Controlled vocabulary) (AIRR) + cell_phenotype: + type: string + description: | + Cell subset phenotype (lab specific description) (AIRR) + study_group_description: + type: string + description: | + Study group description (e.g. Case vs. Control) (AIRR) + library_source: + type: string + description: > + Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) + (AIRR) + subject_age: + type: integer + description: | + e.g. 1 + marker_1: + type: string + description: | + e.g. CR19 + marker_2: + type: string + description: | + e.g. CR20 + marker_3: + type: string + description: | + e.g. CR21 + marker_4: + type: string + description: | + e.g. null + marker_5: + type: string + description: | + e.g. null + marker_6: + type: string + description: | + e.g. null + subject_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + subject. + project_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + project. + project_parent_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + parent/child + relationship between this project and its parent project. + lab_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + lab. + case_control_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + element in the case_control table. + sample_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + sample. + dna_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + DNA type. + project_sample_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association a project with a sample. + sample_subject_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association between a sample and a subject. + sample_source_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association between a sample and a sample source. +schemes: + - https +produces: + - application/json +tags: + - name: info + description: Service information + - name: samples + description: Queries for samples + - name: sequences + description: Queries for sequences + - name: clones + description: Queries for clones +paths: + /: + x-swagger-router-controller: status + get: + description: | + Service heartbeat. + operationId: getStatus + responses: + '200': + description: | + Success. + schema: + type: object + properties: + result: + type: string + /info: + x-swagger-router-controller: status + get: + description: | + Service information. + tags: + - info + operationId: getInfo + responses: + '200': + description: | + Success. + schema: + type: object + properties: + name: + type: string + version: + type: string + /swagger: + x-swagger-pipe: swagger_raw + /samples: + x-swagger-router-controller: samples + get: description: > This service returns metadata about samples, including higher-level meta-data around the study, subject, diagnosis, and sample processing @@ -425,334 +853,6 @@ paths: for that sample. tags: - samples - parameters: - - name: query - in: body - required: true - schema: - type: object - required: - - username - properties: - username: - type: string - description: > - Username of the individual requesting access to the iReceptor - repository node. - lab_id: - type: integer - description: | - e.g. 1 - project_id: - type: array - items: - type: integer - description: | - e.g. 1 - subject_code: - type: string - description: | - e.g. test - subject_gender: - type: string - description: | - e.g. Male - subject_ethnicity: - type: string - description: | - e.g. Caucasian - subject_species: - type: string - description: | - e.g. Human - subject_age_min: - type: integer - description: | - e.g. 10 - subject_age_max: - type: integer - description: | - e.g. 12 - case_control_name: - type: string - description: | - e.g. Control - sample_name: - type: string - description: | - e.g. test2 - sample_source_name: - type: array - items: - type: string - description: | - e.g. Blood (PBMC) - ireceptor_cell_subset_name: - type: array - items: - type: string - description: | - e.g. NaiveB - dna_type: - type: array - items: - type: string - description: | - e.g. cDNA - operationId: postSamples - responses: - '200': - description: | - A successful call returns the metadata for each sample, including - the number of sequences found for that sample. - schema: - type: array - items: - type: object - properties: - sequence_count: - type: integer - description: > - The number of sequences that match the filter for this - sample. - study_id: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - study_title: - type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR) - study_type: - type: string - description: | - Type of project/study (e.g. Cancer) (AIRR) - inclusion_exclusion_criteria: - type: string - description: | - Study inclusion/exclusion criteria (AIRR) - grants: - type: string - description: | - Grant funding agency (AIRR) - lab_name: - type: string - description: | - Lab name (AIRR) - collected_by: - type: string - description: | - Contact information (data collection) (AIRR) - uploaded_by: - type: string - description: | - Contact information (data deposition) (AIRR) - lab_address: - type: string - description: | - Lab address (AIRR) - pubs_ids: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - subject_id: - type: string - description: "UID assigned by submitter (e.g.\_SUB856413) (AIRR)\n" - organism: - type: string - description: | - Organism-based (human, mouse) or synthetic (AIRR) - sex: - type: string - description: | - Sex (e.g. M/F) (AIRR) - age: - type: string - description: | - Age - Time duration and unit (e.g. 200 days) (AIRR) - age_event: - type: string - description: | - Age event (e.g. Enrollment) (AIRR) - ancestry_population: - type: string - description: | - Ancestry population (AIRR) - ethnicity: - type: string - description: | - Ethnicity (e.g. Tamil) (AIRR) - race: - type: string - description: | - Race (e.g. South Indian) (AIRR) - species_name: - type: string - description: | - Species name (e.g. Homo Sapiens) (AIRR) - strain_name: - type: string - description: | - Strain name (e.g. C57BL/6J) (AIRR) - linked_subjects: - type: string - description: > - Relation to other subjects (SubjectID e.g. SUB1355648) - (AIRR) - link_type: - type: string - description: | - Relation type (.e.g sister, father, daughter) (AIRR) - sample_id: - type: string - description: | - Biological sample ID - UID assigned by submitter (AIRR) - sample_type: - type: string - description: | - Sample type (e.g. Tissue, body fluid) (AIRR) - tissue: - type: string - description: | - Anatomic site (e.g. spleen) (AIRR) - disease_state_sample: - type: string - description: | - Disease state of sample (e.g. tumor vs margin) (AIRR) - collection_date: - type: string - description: | - Sample collection time (e.g. 10 days) (AIRR) - collection_time_event: - type: string - description: > - Collection time event (T0) (e.g. vaccination, recruitment, - etc) (AIRR) - source_commercial: - type: string - description: | - Commercial source of sample (e.g. XYZ Pharma) (AIRR) - cell_subset: - type: string - description: | - Cell subset (Controlled vocabulary) (AIRR) - cell_phenotype: - type: string - description: | - Cell subset phenotype (lab specific description) (AIRR) - study_group_description: - type: string - description: | - Study group description (e.g. Case vs. Control) (AIRR) - library_source: - type: string - description: > - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) - (AIRR) - subject_age: - type: integer - description: | - e.g. 1 - marker_1: - type: string - description: | - e.g. CR19 - marker_2: - type: string - description: | - e.g. CR20 - marker_3: - type: string - description: | - e.g. CR21 - marker_4: - type: string - description: | - e.g. null - marker_5: - type: string - description: | - e.g. null - marker_6: - type: string - description: | - e.g. null - subject_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - subject. - project_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - project. - project_parent_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - parent/child - - relationship between this project and its parent project. - lab_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - lab. - case_control_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - element in the case_control table. - sample_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - sample. - dna_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - DNA type. - project_sample_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association - - a project with a sample. - sample_subject_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association - - between a sample and a subject. - sample_source_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association - - between a sample and a sample source. - '400': - description: malformed request - '401': - description: authentication error - '403': - description: authorization error - '404': - description: data not found - '405': - description: method not allowed - /sequences_summary: - x-swagger-router-controller: sequences - get: - description: > - This service returns a summary of sequences that matches the GET - provided filter. "username" parameter refers to external_users table. - tags: - - sequences parameters: - name: username in: query @@ -761,1545 +861,203 @@ paths: repository node. required: true type: string - - name: project_sample_id_list + - name: lab_id in: query - required: true + description: | + e.g. 1 + required: false + type: integer + - name: project_id + in: query + description: | + e.g. 1 + required: false type: array items: type: integer - - name: cdr3_length + - name: subject_code in: query - description: >- - length of complementarity determining region in nucleotide base - pairs + description: | + e.g. test required: false - type: integer - - name: vgene_string + type: string + - name: subject_gender in: query + description: | + e.g. Male or Female required: false type: string - - name: jgene_string + - name: subject_species in: query + description: | + e.g. Human required: false type: string - operationId: getSequenceSummary - responses: - '200': - description: > - A successful call returns two components, an aggregated summary of the data - that satisfies the query and an example subset of the annotated sequence data - that meets the query criteria. The aggreated data returns a summary similar - to that returned by the /samples API entry point, returning the number of - sequences and the study/subject/sample meta-data for each sample. The example - subset of sequence data that is returned is a small subset of annotated sequences - that met the search criteria. The number of sequences returned is given in the - "num_sequences" paramter to the query and the format in which the sequences are - returned is provided by the "sequence_format" parameter to the query. - schema: - type: object - properties: - summary: - type: array - items: - type: object - properties: - sequence_count: - type: integer - description: | - The number of sequences that match the filter for this sample. - study_id: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - study_title: - type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR) - study_type: - type: string - description: | - Type of project/study (e.g. Cancer) (AIRR) - inclusion_exclusion_criteria: - type: string - description: | - Study inclusion/exclusion criteria (AIRR) - grants: - type: string - description: | - Grant funding agency (AIRR) - lab_name: - type: string - description: | - Lab name (AIRR) - collected_by: - type: string - description: | - Contact information (data collection) (AIRR) - uploaded_by: - type: string - description: | - Contact information (data deposition) (AIRR) - lab_address: - type: string - description: | - Lab address (AIRR) - pubs_ids: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - subject_id: - type: string - description: | - UID assigned by submitter (e.g. SUB856413) (AIRR) - organism: - type: string - description: | - Organism-based (human, mouse) or synthetic (AIRR) - sex: - type: string - description: | - Sex (e.g. M/F) (AIRR) - age: - type: string - description: | - Age - Time duration and unit (e.g. 200 days) (AIRR) - age_event: - type: string - description: | - Age event (e.g. Enrollment) (AIRR) - ancestry_population: - type: string - description: | - Ancestry population (AIRR) - ethnicity: - type: string - description: | - Ethnicity (e.g. Tamil) (AIRR) - race: - type: string - description: | - Race (e.g. South Indian) (AIRR) - species_name: - type: string - description: | - Species name (e.g. Homo Sapiens) (AIRR) - strain_name: - type: string - description: | - Strain name (e.g. C57BL/6J) (AIRR) - linked_subjects: - type: string - description: | - Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) - link_type: - type: string - description: | - Relation type (.e.g sister, father, daughter) (AIRR) - sample_id: - type: string - description: | - Biological sample ID - UID assigned by submitter (AIRR) - sample_type: - type: string - description: | - Sample type (e.g. Tissue, body fluid) (AIRR) - tissue: - type: string - description: | - Anatomic site (e.g. spleen) (AIRR) - disease_state_sample: - type: string - description: | - Disease state of sample (e.g. tumor vs margin) (AIRR) - collection_date: - type: string - description: | - Sample collection time (e.g. 10 days) (AIRR) - collection_time_event: - type: string - description: | - Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) - source_commercial: - type: string - description: | - Commercial source of sample (e.g. XYZ Pharma) (AIRR) - cell_subset: - type: string - description: | - Cell subset (Controlled vocabulary) (AIRR) - cell_phenotype: - type: string - description: | - Cell subset phenotype (lab specific description) (AIRR) - study_group_description: - type: string - description: | - Study group description (e.g. Case vs. Control) (AIRR) - library_source: - type: string - description: | - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) - subject_age: - type: integer - description: | - e.g. 1 - marker_1: - type: string - description: | - e.g. CR19 - marker_2: - type: string - description: | - e.g. CR20 - marker_3: - type: string - description: | - e.g. CR21 - marker_4: - type: string - description: | - e.g. null - marker_5: - type: string - description: | - e.g. null - marker_6: - type: string - description: | - e.g. null - subject_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a subject. - project_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a project. - project_parent_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a parent/child - relationship between this project and its parent project. - lab_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a lab. - case_control_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an element in the case_control table. - sample_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a sample. - dna_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a DNA type. - project_sample_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an association - a project with a sample. - sample_subject_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an association - between a sample and a subject. - sample_source_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an association - between a sample and a sample source. - items: - type: array - items: - type: object - properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: - type: integer - description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - type: string - description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - type: string - description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - type: string - description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - type: string - description: | - C region with allele (AIRR) - junction_nt: - type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: - type: string - description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: - type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - description: | - e.g IGHV4-59*01 or IGHV4-59*07 - vgene_family: - type: string - description: | - e.g. IGHV4 - vgene_gene: - type: string - description: | - e.g. IGHV4-59 - dgene_string: - type: string - description: | - e.g. Homsap IGHD3-10*01 F - dgene_family: - type: string - description: | - e.g. IGHD3 - dgene_gene: - type: string - description: | - e.g. IGHD3-10 - jgene_string: - type: string - description: | - e.g. Homsap IGHJ4*02 F - jgene_family: - type: string - description: | - e.g. IGHJ4 - jgene_gene: - type: string - description: | - e.g. IGHJ4 - functionality: - type: string - description: | - e.g. productive - functionality_comment: - type: string - description: | - e.g. "" - orientation: - type: string - description: | - e.g. + - vgene_score: - type: integer - description: | - e.g. 1127 - vgene_probability: - type: integer - description: | - e.g. 95 - dregion_reading_frame: - type: integer - description: | - e.g. 2 - cdr1_length: - type: integer - description: | - e.g. 8 - cdr2_length: - type: integer - description: | - e.g. 7 - cdr3_length: - type: integer - description: | - e.g. 13 - vdjregion_sequence_nt: - type: string - description: | - vdj region nucleotide sequence - vjregion_sequence_nt: - type: string - description: | - vj region nucleotide sequence - djregion_sequence_nt: - type: string - description: | - dj region nucleotide sequence - vregion_sequence_nt: - type: string - description: | - v region nucleotide sequence - dregion_sequence_nt: - type: string - description: | - d region nucleotide sequence - jregion_sequence_nt: - type: string - description: | - j region nucleotide sequence - fr1region_sequence_nt: - type: string - description: | - fr1 region nucleotide sequence - fr2region_sequence_nt: - type: string - description: | - fr2 region nucleotide sequence - fr3region_sequence_nt: - type: string - description: | - fr3 region nucleotide sequence - fr4region_sequence_nt: - type: string - description: | - fr4 region nucleotide sequence - cdr1region_sequence_nt: - type: string - description: | - cdr1 region nucleotide sequence - cdr2region_sequence_nt: - type: string - description: | - cdr2 region nucleotide sequence - cdr3region_sequence_nt: - type: string - description: | - cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: - type: string - description: | - gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: - type: string - description: | - gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: - type: string - description: | - gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: - type: string - description: | - gapped v region nucleotide sequence - dregion_sequence_nt_gapped: - type: string - description: | - gapped d region nucleotide sequence - jregion_sequence_nt_gapped: - type: string - description: | - gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: - type: string - description: | - gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: - type: string - description: | - gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: - type: string - description: | - gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: - type: string - description: | - gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: - type: string - description: | - gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: - type: string - description: | - gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: - type: string - description: | - gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: - type: string - description: | - gapped junction nucleotide sequence - vdjregion_sequence_aa: - type: string - description: | - vdj region amino acid sequence - vjregion_sequence_aa: - type: string - description: | - vj region amino acid sequence - djregion_sequence_aa: - type: string - description: | - dj region amino acid sequence - vregion_sequence_aa: - type: string - description: | - v region amino acid sequence - dregion_sequence_aa: - type: string - description: | - d region amino acid sequence - jregion_sequence_aa: - type: string - description: | - j region amino acid sequence - fr1region_sequence_aa: - type: string - description: | - fr1 region amino acid sequence - fr2region_sequence_aa: - type: string - description: | - fr2 region amino acid sequence - fr3region_sequence_aa: - type: string - description: | - fr3 region amino acid sequence - fr4region_sequence_aa: - type: string - description: | - fr4 region amino acid sequence - cdr1region_sequence_aa: - type: string - description: | - cdr1 region amino acid sequence - cdr2region_sequence_aa: - type: string - description: | - cdr2 region amino acid sequence - cdr3region_sequence_aa: - type: string - description: | - cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: - type: string - description: | - gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: - type: string - description: | - gapped vj region amino acid sequence - djregion_sequence_aa_gapped: - type: string - description: | - gapped dj region amino acid sequence - vregion_sequence_aa_gapped: - type: string - description: | - gapped v region amino acid sequence - dregion_sequence_aa_gapped: - type: string - description: | - gapped d region amino acid sequence - jregion_sequence_aa_gapped: - type: string - description: | - gapped j region amino acid sequence - fr1region_sequence_aa_gapped: - type: string - description: | - gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: - type: string - description: | - gapped fr2 region amino acid sequence - fr3region_sequence_aa_gapped: - type: string - description: | - gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: - type: string - description: | - gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: - type: string - description: | - gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: - type: string - description: | - gapped cdr2 region amino acid sequence - cdr3region_sequence_aa_gapped: - type: string - description: | - gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: - type: string - description: | - gapped junction amino acid sequence - vdjregion_start: - type: integer - description: | - e.g. 1 - vdjregion_end: - type: integer - description: | - e.g. 321 - vjregion_start: - type: integer - description: | - e.g. 0 - vjregion_end: - type: integer - description: | - e.g. 0 - djregion_start: - type: integer - description: | - e.g. 254 - djregion_end: - type: integer - description: | - e.g. 321 - vregion_start: - type: integer - description: | - e.g. 286 - vregion_end: - type: integer - description: | - e.g. 252 - dregion_start: - type: integer - description: | - e.g. 254 - dregion_end: - type: integer - description: | - e.g. 321 - jregion_start: - type: integer - description: | - e.g. 286 - jregion_end: - type: integer - description: | - e.g. 321 - fr1region_start: - type: integer - description: | - e.g. 1 - fr1region_end: - type: integer - description: | - e.g. 38 - fr2region_start: - type: integer - description: | - e.g. 63 - fr2region_end: - type: integer - description: | - e.g. 113 - fr3region_start: - type: integer - description: | - e.g. 135 - fr3region_end: - type: integer - description: | - e.g. 248 - fr4region_start: - type: integer - description: | - e.g. 288 - fr4region_end: - type: integer - description: | - e.g. 321 - cdr1region_start: - type: integer - description: | - e.g. 39 - cdr1region_end: - type: integer - description: | - e.g. 321 - cdr2region_start: - type: integer - description: | - e.g. 62 - cdr2region_end: - type: integer - description: | - e.g. 134 - cdr3region_start: - type: integer - description: | - e.g. 249 - cdr3region_end: - type: integer - description: | - e.g. 287 - junction_start: - type: integer - description: | - e.g. 246 - junction_end: - type: integer - description: | - e.g. 290 - vregion_mutation_string: - type: string - description: > - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: - type: string - description: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr2region_mutation_string: - type: string - description: | - e.g. - fr3region_mutation_string: - type: string - description: > - e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr1region_mutation_string: - type: string - description: | - e.g. - cdr2region_mutation_string: - type: string - description: | - e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: - type: string - description: | - e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - annotation_tool: - type: string - description: | - e.g. VQuest - examples: - application/json: - summary: - - subject_code: IAVI 84 - subject_id: 1 - subject_gender: null - subject_ethnicity: NA - subject_species: Homo Sapiens - project_id: 1 - study_title: >- - Mining the antibodyome for HIV-1 neutralizing antibodies - with next generation sequencing and phylogenetic pairing of - heavy/light chains - study_type: HIV - project_parent_id: -1 - study: SRP018335 - lab_id: 1 - lab_name: National Institute of Allergy and Infectious -DiseaseVaccine - Research Center: Kwong Lab - disease_state_id: 7 - disease_state_name: >- - HIV-1 infected for at least 3 years, not receiving - antiretroviral treatment - case_control_id: 1 - case_control_name: Case - sample_id: 1 - project_sample_id: 1 - sequence_count: 253684 - project_sample_note: null - sra_run_id: SRR654169 - sample_name: SRS388604 - subject_age: null - sample_subject_id: 1 - dna_id: 1 - dna_type: cDNA - sample_source_id: 1 - sample_source_name: PBMCs - lab_cell_subset_name: B cell memory - ireceptor_cell_subset_name: Memory B Cell - marker_1: IgG+ - marker_2: CD19+ - marker_3: sIgG+ - marker_4: ' negative depletion to CD3' - marker_5: ' CD14' - marker_6: ' CD16, IgM, IgA, IgD ' - sequences: 167793 - items: - - seq_id: 2 - seq_name: SRR654169.17_G912ZWU01EPN4E_length=379 - project_sample_id: 1 - id: 37 - vgene_string: Homsap IGHV1-24*01 F - vgene_family: IGHV1 - vgene_gene: IGHV1-24 - v_allele: ' IGHV1-24*01 ' - jgene_string: Homsap IGHJ3*02 F - jgene_family: IGHJ3 - jgene_gene: IGHJ3 - j_allele: ' IGHJ3*02 ' - dgene_string: Homsap IGHD3-22*01 F - dgene_family: IGHD3 - dgene_gene: IGHD3-22 - d_allele: ' IGHD3-22*01 ' - functionality: productive - vgene_score: 1417 - vgene_probablity: null - dregion_reading_frame: '3' - cdr1_length: 8 - cdr2_length: 8 - cdr3_length: 17 - vdjregion_sequence_nt: >- - caggtccagctggtagagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaagtttccggatacaccctcactgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgatggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag - vjregion_sequence_nt: '' - djregion_sequence_nt: >- - gatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag - vregion_sequence_nt: >- - caggtccagctggtagagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctcactgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaaca - jregion_sequence_nt: gatggttttgatatctggggccaagggacaatggtcaccgtctcttcag - dregion_sequence_nt: gatagttgtgattat - fr1region_sequence_nt: >- - caggtccagctggtagagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttcc - fr2region_sequence_nt: atgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggt - fr3region_sequence_nt: >- - atctacgcacagaagttccagggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgt - fr4region_sequence_nt: tggggccaagggacaatggtcaccgtctcttcag - cdr1region_sequence_nt: ggatacaccctcactgaattatcc - cdr2region_sequence_nt: tttgatcctgaagatggtgaaaca - cdr3region_sequence_nt: gcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatc - junction_nt: tgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctgg - vdjregion_sequence_nt_gapped: >- - caggtccagctggtagagtctggggct...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctc............actgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaa......gatggtgaaacaatctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctggggccaagggacaatggtcaccgtctcttcag - vjregion_sequence_nt_gapped: '' - djregion_sequence_nt_gapped: null - vregion_sequence_nt_gapped: >- - caggtccagctggtagagtctggggct...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctc............actgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaa......gatggtgaaacaatctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaaca - jregion_sequence_nt_gapped: gatggttttgatatctggggccaagggacaatggtcaccgtctcttcag - dregion_sequence_nt_gapped: gatggttttgatatctggggccaagggacaatggtcaccgtctcttcag - fr1region_sequence_nt_gapped: >- - caggtccagctggtagagtctggggct - ...gaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttcc - fr2region_sequence_nt_gapped: atgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggt - fr3region_sequence_nt_gapped: >- - atctacgcacagaagttccag...ggcagaatcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgt - fr4region_sequence_nt_gapped: tggggccaagggacaatggtcaccgtctcttcag - cdr1region_sequence_nt_gapped: ggatacaccctc............actgaattatcc - cdr2region_sequence_nt_gapped: tttgatcctgaa......gatggtgaaaca - cdr3region_sequence_nt_gapped: gcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatc - junction_sequence_nt_gapped: tgtgcaacaaggagtcctccgatagttgtgattatggacgatggttttgatatctgg - vdjregion_sequence_aa: >- - QVQLVESGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLEWMGGFDPEDGETIYAQKFQGR - ITMTEDTSTDTAYMELSSLRSEDTAVYYCATRSPPIVVIMDDGFDIWGQGTMVTVSS - vjregion_sequence_aa: '' - djregion_sequence_aa: null - vregion_sequence_aa: >- - QVQLVESGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLEWMGGFDPEDGETIYAQKFQGRITMTEDTSTDTAYMELSSLRSEDTAVYYCAT - jregion_sequence_aa: DGFDIWGQGTMVTVSS - dregion_sequence_aa: null - fr1region_sequence_aa: QVQLVESGAEVKKPGASVKVSCKVS - fr2region_sequence_aa: MHWVRQAPGKGLEWMGG - fr3region_sequence_aa: IYAQKFQGRITMTEDTSTDTAYMELSSLRSEDTAVYYC - fr4region_sequence_aa: WGQGTMVTVSS - cdr1region_sequence_aa: GYTLTELS - cdr2region_sequence_aa: FDPEDGET - cdr3region_sequence_aa: ATRSPPIVVIMDDGFDI - junction_aa: CATRSPPIVVIMDDGFDIW - vdjregion_sequence_aa_gapped: >- - QVQLVESGA.EVKKPGASVKVSCKVSGYTL....TELSMHWVRQAPGKGLEWMGGFDPE..DGETIYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYCATRSPPIVVIMDDGFDIWGQGTMVTVSS - vjregion_sequence_aa_gapped: '' - djregion_sequence_aa_gapped: null - vregion_sequence_aa_gapped: >- - QVQLVESGA.EVKKPGASVKVSCKVSGYTL....TELSMHWVRQAPGKGLEWMGGFDPE..DGETIYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYCAT - jregion_sequence_aa_gapped: DGFDIWGQGTMVTVSS - dregion_sequence_aa_gapped: null - fr1region_sequence_aa_gapped: QVQLVESGA.EVKKPGASVKVSCKVS - fr2region_sequence_aa_gapped: MHWVRQAPGKGLEWMGG - fr3region_sequence_aa_gapped: IYAQKFQ.GRITMTEDTSTDTAYMELSSLRSEDTAVYYC - fr4region_sequence_aa_gapped: WGQGTMVTVSS - cdr1region_sequence_aa_gapped: GYTL....TELS - cdr2region_sequence_aa_gapped: FDPE..DGET - cdr3region_sequence_aa_gapped: ATRSPPIVVIMDDGFDI - junction_sequence_aa_gapped: CATRSPPIVVIMDDGFDIW - vdjregion_start: 2 - vdjregion_end: 374 - vjregion_start: null - vjregion_end: null - vregion_start: 2 - vregion_end: 295 - jregion_start: 326 - jregion_end: 374 - dregion_start: 307 - dregion_end: 374 - fr1region_start: 2 - fr1region_end: 76 - fr2region_start: 101 - fr2region_end: 151 - fr3region_start: 176 - fr3region_end: 289 - fr4region_start: 341 - fr4region_end: 374 - cdr1region_start: 77 - cdr1region_end: 100 - cdr2region_start: 152 - cdr2region_end: 175 - cdr3region_start: 290 - cdr3region_end: 340 - junction_start: 287 - junction_end: 343 - vregion_mutation_string: 'c16>g,Q6>E(++ -)|g226>a,V76>I(+ - +)|' - fr1region_mutation_string: 'c16>g,Q6>E(+ + -)|' - fr2region_mutation_string: '' - fr3region_mutation_string: 'g226>a,V76>I(+ - +)|' - cdr1region_mutation_string: '' - cdr2region_mutation_string: '' - cdr3region_mutation_string: g319>a|a320>g| - vgene_probability: '99' - djregion_start: 307 - djregion_end: 374 - annotation_tool: VQuest - '400': - description: malformed request - '401': - description: authentication error - '403': - description: authorization error - '404': - description: data not found - '405': - description: method not allowed - /sequences_data: - x-swagger-router-controller: sequences - get: - description: > - This service returns the annotation data that matches the GET provided - filter. "username" parameter refers to external_users table, and it - requires the array of "project_sample_id", which limits which samples - the sequences will be taken from. Other parameters are optional, and - refer to the sequence_md_view view in iReceptor database. - tags: - - sequences - parameters: - - name: username + - name: subject_ethnicity + in: query + description: | + e.g. Caucasian + required: false + type: string + - name: subject_age_min + in: query + description: | + e.g. 10 + required: false + type: integer + - name: subject_age_max + in: query + description: | + e.g. 12 + required: false + type: integer + - name: case_control_name in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true + description: | + e.g. Control + required: false type: string - - name: project_sample_id_list - in: query - required: true - type: array - items: - type: integer - - name: cdr3_length + - name: sample_name in: query - description: >- - length of complementarity determining region in nucleotide base - pairs + description: | + e.g. test2 required: false - type: integer - - name: vgene_string + type: string + - name: sample_source_name in: query + description: | + e.g. Blood (PBMC) required: false type: string - - name: jgene_string + - name: ireceptor_cell_subset_name in: query + description: | + e.g. NaiveB required: false type: string - - name: format + - name: dna_type in: query - description: >- - 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as - per /v1 with tab delimiters instead of commas); 'airr' - AIRR - Formats rearrangements TSV (as per AIRR formats rearrangements spec) + description: | + e.g. cDNA, gDNA required: false type: string - operationId: getSequenceData + operationId: getSamples responses: '200': - description: > - A successful call returns an array of sequence data. Optional - "format" parameter determines the output format. Default is a JSON - response, limited to top 50 results. If "format" is set to "csv", it - will return all the matching sequence annotations, in addition to - sample information and annotation tool information, in a - comma-separated format; "tsv" returns a tab-delimited outputs; - "airr" returns AIRR minimal standards encoded tab-delimited outputs. + description: | + A successful call returns an array of sample summary metadata for + each sample that meets the search criteria. The metadata returned + for each sample includes the number of sequences found for that sample + as well as the study/subject/sample data for that sample. The metadata + for each sample in the response contains a set of AIRR compliant data + as well as repository specific data that is required to query the + repository about those types of elements. schema: - type: array - items: - type: object - properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: - type: integer - description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - type: string - description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - type: string - description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - type: string - description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - type: string - description: | - C region with allele (AIRR) - junction_nt: - type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: - type: string - description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: - type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - vgene_family: - type: string - description: | - e.g. IGHV4 - vgene_gene: - type: string - description: | - e.g. IGHV4-59 - dgene_string: - type: string - description: | - e.g. Homsap IGHD3-10*01 F - dgene_family: - type: string - description: | - e.g. IGHD3 - dgene_gene: - type: string - description: | - e.g. IGHD3-10 - jgene_string: - type: string - description: | - e.g. Homsap IGHJ4*02 F - jgene_family: - type: string - description: | - e.g. IGHJ4 - jgene_gene: - type: string - description: | - e.g. IGHJ4 - functionality: - type: string - description: | - e.g. productive - functionality_comment: - type: string - description: | - e.g. "" - orientation: - type: string - description: | - e.g. + - vgene_score: - type: integer - description: | - e.g. 1127 - vgene_probability: - type: integer - description: | - e.g. 95 - dregion_reading_frame: - type: integer - description: | - e.g. 2 - cdr1_length: - type: integer - description: | - e.g. 8 - cdr2_length: - type: integer - description: | - e.g. 7 - cdr3_length: - type: integer - description: | - e.g. 13 - vdjregion_sequence_nt: - type: string - description: | - vdj region nucleotide sequence - vjregion_sequence_nt: - type: string - description: | - vj region nucleotide sequence - djregion_sequence_nt: - type: string - description: | - dj region nucleotide sequence - vregion_sequence_nt: - type: string - description: | - v region nucleotide sequence - dregion_sequence_nt: - type: string - description: | - d region nucleotide sequence - jregion_sequence_nt: - type: string - description: | - j region nucleotide sequence - fr1region_sequence_nt: - type: string - description: | - fr1 region nucleotide sequence - fr2region_sequence_nt: - type: string - description: | - fr2 region nucleotide sequence - fr3region_sequence_nt: - type: string - description: | - fr3 region nucleotide sequence - fr4region_sequence_nt: - type: string - description: | - fr4 region nucleotide sequence - cdr1region_sequence_nt: - type: string - description: | - cdr1 region nucleotide sequence - cdr2region_sequence_nt: - type: string - description: | - cdr2 region nucleotide sequence - cdr3region_sequence_nt: - type: string - description: | - cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: - type: string - description: | - gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: - type: string - description: | - gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: - type: string - description: | - gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: - type: string - description: | - gapped v region nucleotide sequence - dregion_sequence_nt_gapped: - type: string - description: | - gapped d region nucleotide sequence - jregion_sequence_nt_gapped: - type: string - description: | - gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: - type: string - description: | - gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: - type: string - description: | - gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: - type: string - description: | - gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: - type: string - description: | - gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: - type: string - description: | - gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: - type: string - description: | - gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: - type: string - description: | - gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: - type: string - description: | - gapped junction nucleotide sequence - vdjregion_sequence_aa: - type: string - description: | - vdj region amino acid sequence - vjregion_sequence_aa: - type: string - description: | - vj region amino acid sequence - djregion_sequence_aa: - type: string - description: | - dj region amino acid sequence - vregion_sequence_aa: - type: string - description: | - v region amino acid sequence - dregion_sequence_aa: - type: string - description: | - d region amino acid sequence - jregion_sequence_aa: - type: string - description: | - j region amino acid sequence - fr1region_sequence_aa: - type: string - description: | - fr1 region amino acid sequence - fr2region_sequence_aa: - type: string - description: | - fr2 region amino acid sequence - fr3region_sequence_aa: - type: string - description: | - fr3 region amino acid sequence - fr4region_sequence_aa: - type: string - description: | - fr4 region amino acid sequence - cdr1region_sequence_aa: - type: string - description: | - cdr1 region amino acid sequence - cdr2region_sequence_aa: - type: string - description: | - cdr2 region amino acid sequence - cdr3region_sequence_aa: - type: string - description: | - cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: - type: string - description: | - gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: - type: string - description: | - gapped vj region amino acid sequence - djregion_sequence_aa_gapped: - type: string - description: | - gapped dj region amino acid sequence - vregion_sequence_aa_gapped: - type: string - description: | - gapped v region amino acid sequence - dregion_sequence_aa_gapped: - type: string - description: | - gapped d region amino acid sequence - jregion_sequence_aa_gapped: - type: string - description: | - gapped j region amino acid sequence - fr1region_sequence_aa_gapped: - type: string - description: | - gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: - type: string - description: | - gapped fr2 region amino acid sequence - fr3region_sequence_aa_gapped: - type: string - description: | - gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: - type: string - description: | - gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: - type: string - description: | - gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: - type: string - description: | - gapped cdr2 region amino acid sequence - cdr3region_sequence_aa_gapped: - type: string - description: | - gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: - type: string - description: | - gapped junction amino acid sequence - vdjregion_start: - type: integer - description: | - e.g. 1 - vdjregion_end: - type: integer - description: | - e.g. 321 - vjregion_start: - type: integer - description: | - e.g. 0 - vjregion_end: - type: integer - description: | - e.g. 0 - djregion_start: - type: integer - description: | - e.g. 254 - djregion_end: - type: integer - description: | - e.g. 321 - vregion_start: - type: integer - description: | - e.g. 286 - vregion_end: - type: integer - description: | - e.g. 252 - dregion_start: - type: integer - description: | - e.g. 254 - dregion_end: - type: integer - description: | - e.g. 321 - jregion_start: - type: integer - description: | - e.g. 286 - jregion_end: - type: integer - description: | - e.g. 321 - fr1region_start: - type: integer - description: | - e.g. 1 - fr1region_end: - type: integer - description: | - e.g. 38 - fr2region_start: - type: integer - description: | - e.g. 63 - fr2region_end: - type: integer - description: | - e.g. 113 - fr3region_start: - type: integer - description: | - e.g. 135 - fr3region_end: - type: integer - description: | - e.g. 248 - fr4region_start: - type: integer - description: | - e.g. 288 - fr4region_end: - type: integer - description: | - e.g. 321 - cdr1region_start: - type: integer - description: | - e.g. 39 - cdr1region_end: - type: integer - description: | - e.g. 321 - cdr2region_start: - type: integer - description: | - e.g. 62 - cdr2region_end: - type: integer - description: | - e.g. 134 - cdr3region_start: - type: integer - description: | - e.g. 249 - cdr3region_end: - type: integer - description: | - e.g. 287 - junction_start: - type: integer - description: | - e.g. 246 - junction_end: + $ref: '#/definitions/summary_model' + '400': + description: malformed request + '401': + description: authentication error + '403': + description: authorization error + '404': + description: data not found + '405': + description: method not allowed + post: + description: > + This service returns metadata about samples, including higher-level + meta-data around the study, subject, diagnosis, and sample processing + (data relevant to MiAIRR data classes 1 through 3). The data returned is + filtered based on the parameters provided. + + A successful call returns a json list with a sample level summary of + each sample including a summary count of the number of sequences found + for that sample. + tags: + - samples + parameters: + - name: query + in: body + required: true + schema: + type: object + required: + - username + properties: + username: + type: string + description: > + Username of the individual requesting access to the iReceptor + repository node. + lab_id: + type: integer + description: | + e.g. 1 + project_id: + type: array + items: type: integer - description: | - e.g. 290 - vregion_mutation_string: - type: string - description: > - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: - type: string - description: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr2region_mutation_string: - type: string - description: | - e.g. - fr3region_mutation_string: - type: string - description: > - e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr1region_mutation_string: + description: | + e.g. 1 + subject_code: + type: string + description: | + e.g. test + subject_gender: + type: string + description: | + e.g. Male + subject_ethnicity: + type: string + description: | + e.g. Caucasian + subject_species: + type: string + description: | + e.g. Human + subject_age_min: + type: integer + description: | + e.g. 10 + subject_age_max: + type: integer + description: | + e.g. 12 + case_control_name: + type: string + description: | + e.g. Control + sample_name: + type: string + description: | + e.g. test2 + sample_source_name: + type: array + items: type: string - description: | - e.g. - cdr2region_mutation_string: + description: | + e.g. Blood (PBMC) + ireceptor_cell_subset_name: + type: array + items: type: string - description: | - e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: + description: | + e.g. NaiveB + dna_type: + type: array + items: type: string - description: | - e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - citation: - type: object - properties: - doi: - type: string - title: - type: string - examples: - application/json: - seq_name: | - M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 - vgene_gene: | - IGHV4-59 - v_allele: | - IGHV4-59*01 or IGHV4-59*07 - dgene_string: | - Homsap IGHD3-10*01 F - dgene_family: | - IGHD3 - dgene_gene: | - IGHD3-10 - d_allele: | - IGHD3-10*01 - jgene_string: | - Homsap IGHJ4*02 F - jgene_family: | - IGHJ4 - jgene_gene: | - IGHJ4 - j_allele: | - IGHJ4*02 - functionality: | - productive - vregion_mutation_string: | - a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr3region_mutation_string: | - c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr2region_mutation_string: | - a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: | - g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - citation: - doi: 10.1093/cid/ciw767 - title: > - RNA-Seq Analysis of Gene Expression, Viral Pathogen, and - B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. + description: | + e.g. cDNA + operationId: postSamples + responses: + '200': + description: > + A successful call returns the metadata for each sample, including + the number of sequences found for that sample. + schema: + $ref: '#/definitions/summary_model' '400': description: malformed request '401': @@ -2310,567 +1068,199 @@ paths: description: data not found '405': description: method not allowed - post: + /sequences_summary: + x-swagger-router-controller: sequences + get: description: > - This service returns the annotation data that matches the POST provided - filter. "username" parameter refers to external_users table, and it - requires the array of "project_sample_id", which limits which samples - the sequences will be taken from. Other parameters are optional, and - refer to the sequence_md_view view in iReceptor database. A full list of - possible parameters is in the iReceptorAPI-sequenceMetadata file + This service returns a summary of sequences that matches the GET + provided filter. "username" parameter refers to external_users table. tags: - sequences parameters: - - name: query - in: body - schema: - type: object - required: - - username - properties: - username: - type: string - description: > - Username of the individual requesting access to the iReceptor - repository node. - project_sample_id_list: - type: array - items: - type: integer - cdr3_length: - description: > - length of complementarity determining region in nucleotide - base pairs - type: integer - vgene_string: - type: string - jgene_string: - type: string - format: - description: >- - 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based - TSV (as per /v1 with tab delimiters instead of commas); 'airr' - - AIRR Formats rearrangements TSV (as per AIRR formats - rearrangements spec) - operationId: postSequenceData + - name: username + in: query + description: > + Username of the individual requesting access to the iReceptor + repository node. + required: true + type: string + - name: project_sample_id_list + in: query + required: true + type: array + items: + type: integer + - name: cdr3_length + in: query + description: >- + length of complementarity determining region in nucleotide base + pairs + required: false + type: integer + - name: vgene_string + in: query + required: false + type: string + - name: jgene_string + in: query + required: false + type: string + operationId: getSequenceSummary responses: '200': description: > - A successful call returns an array of sequence data. Optional - "format" parameter determines the output format. Default is a JSON - response, limited to top 50 results. If "format" is set to "csv", it - will return all the matching sequence annotations, in addition to - sample information and annotation tool information, in a - comma-separated format; "tsv" returns a tab-delimited outputs; - "airr" returns AIRR minimal standards encoded tab-delimited outputs. + A successful call returns two components, an aggregated summary of the data + that satisfies the query and an example subset of the annotated sequence data + that meets the query criteria. The aggreated data returns a summary similar + to that returned by the /samples API entry point, returning the number of + sequences and the study/subject/sample meta-data for each sample. The example + subset of sequence data that is returned is a small subset of annotated sequences + that met the search criteria. The number of sequences returned is given in the + "num_sequences" paramter to the query and the format in which the sequences are + returned is provided by the "sequence_format" parameter to the query. schema: - type: array - items: - type: object - properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: - type: integer - description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - type: string - description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - type: string - description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - type: string - description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - type: string - description: | - C region with allele (AIRR) - junction_nt: - type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: - type: string - description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: - type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - vgene_family: - type: string - vgene_gene: - type: string - dgene_string: - type: string - dgene_family: - type: string - dgene_gene: - type: string - jgene_string: - type: string - jgene_family: - type: string - jgene_gene: - type: string - functionality: - type: string - functionality_comment: - type: string - description: | - e.g. "" - orientation: - type: string - description: | - e.g. + - vgene_score: - type: integer - description: | - e.g. 1127 - vgene_probability: - type: integer - description: | - e.g. 95 - dregion_reading_frame: - type: integer - description: | - e.g. 2 - cdr1_length: - type: integer - description: | - e.g. 8 - cdr2_length: - type: integer - description: | - e.g. 7 - cdr3_length: - type: integer - description: | - e.g. 13 - vdjregion_sequence_nt: - type: string - description: | - vdj region nucleotide sequence - vjregion_sequence_nt: - type: string - description: | - vj region nucleotide sequence - djregion_sequence_nt: - type: string - description: | - dj region nucleotide sequence - vregion_sequence_nt: - type: string - description: | - v region nucleotide sequence - dregion_sequence_nt: - type: string - description: | - d region nucleotide sequence - jregion_sequence_nt: - type: string - description: | - j region nucleotide sequence - fr1region_sequence_nt: - type: string - description: | - fr1 region nucleotide sequence - fr2region_sequence_nt: - type: string - description: | - fr2 region nucleotide sequence - fr3region_sequence_nt: - type: string - description: | - fr3 region nucleotide sequence - fr4region_sequence_nt: - type: string - description: | - fr4 region nucleotide sequence - cdr1region_sequence_nt: - type: string - description: | - cdr1 region nucleotide sequence - cdr2region_sequence_nt: - type: string - description: | - cdr2 region nucleotide sequence - cdr3region_sequence_nt: - type: string - description: | - cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: - type: string - description: | - gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: - type: string - description: | - gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: - type: string - description: | - gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: - type: string - description: | - gapped v region nucleotide sequence - dregion_sequence_nt_gapped: - type: string - description: | - gapped d region nucleotide sequence - jregion_sequence_nt_gapped: - type: string - description: | - gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: - type: string - description: | - gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: - type: string - description: | - gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: - type: string - description: | - gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: - type: string - description: | - gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: - type: string - description: | - gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: - type: string - description: | - gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: - type: string - description: | - gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: - type: string - description: | - gapped junction nucleotide sequence - vdjregion_sequence_aa: - type: string - description: | - vdj region amino acid sequence - vjregion_sequence_aa: - type: string - description: | - vj region amino acid sequence - djregion_sequence_aa: - type: string - description: | - dj region amino acid sequence - vregion_sequence_aa: - type: string - description: | - v region amino acid sequence - dregion_sequence_aa: - type: string - description: | - d region amino acid sequence - jregion_sequence_aa: - type: string - description: | - j region amino acid sequence - fr1region_sequence_aa: - type: string - description: | - fr1 region amino acid sequence - fr2region_sequence_aa: - type: string - description: | - fr2 region amino acid sequence - fr3region_sequence_aa: - type: string - description: | - fr3 region amino acid sequence - fr4region_sequence_aa: - type: string - description: | - fr4 region amino acid sequence - cdr1region_sequence_aa: - type: string - description: | - cdr1 region amino acid sequence - cdr2region_sequence_aa: - type: string - description: | - cdr2 region amino acid sequence - cdr3region_sequence_aa: - type: string - description: | - cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: - type: string - description: | - gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: - type: string - description: | - gapped vj region amino acid sequence - djregion_sequence_aa_gapped: - type: string - description: | - gapped dj region amino acid sequence - vregion_sequence_aa_gapped: - type: string - description: | - gapped v region amino acid sequence - dregion_sequence_aa_gapped: - type: string - description: | - gapped d region amino acid sequence - jregion_sequence_aa_gapped: - type: string - description: | - gapped j region amino acid sequence - fr1region_sequence_aa_gapped: - type: string - description: | - gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: - type: string - description: | - gapped fr2 region amino acid sequence - fr3region_sequence_aa_gapped: - type: string - description: | - gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: - type: string - description: | - gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: - type: string - description: | - gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: - type: string - description: | - gapped cdr2 region amino acid sequence - cdr3region_sequence_aa_gapped: - type: string - description: | - gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: - type: string - description: | - gapped junction amino acid sequence - vdjregion_start: - type: integer - description: | - e.g. 1 - vdjregion_end: - type: integer - description: | - e.g. 321 - vjregion_start: - type: integer - description: | - e.g. 0 - vjregion_end: - type: integer - description: | - e.g. 0 - djregion_start: - type: integer - description: | - e.g. 254 - djregion_end: - type: integer - description: | - e.g. 321 - vregion_start: - type: integer - description: | - e.g. 286 - vregion_end: - type: integer - description: | - e.g. 252 - dregion_start: - type: integer - description: | - e.g. 254 - dregion_end: - type: integer - description: | - e.g. 321 - jregion_start: - type: integer - description: | - e.g. 286 - jregion_end: - type: integer - description: | - e.g. 321 - fr1region_start: - type: integer - description: | - e.g. 1 - fr1region_end: - type: integer - description: | - e.g. 38 - fr2region_start: - type: integer - description: | - e.g. 63 - fr2region_end: - type: integer - description: | - e.g. 113 - fr3region_start: - type: integer - description: | - e.g. 135 - fr3region_end: - type: integer - description: | - e.g. 248 - fr4region_start: - type: integer - description: | - e.g. 288 - fr4region_end: - type: integer - description: | - e.g. 321 - cdr1region_start: - type: integer - description: | - e.g. 39 - cdr1region_end: - type: integer - description: | - e.g. 321 - cdr2region_start: - type: integer - description: | - e.g. 62 - cdr2region_end: - type: integer - description: | - e.g. 134 - cdr3region_start: - type: integer - description: | - e.g. 249 - cdr3region_end: - type: integer - description: | - e.g. 287 - junction_start: - type: integer - description: | - e.g. 246 - junction_end: + type: object + properties: + summary: + $ref: '#/definitions/summary_model' + items: + $ref: '#/definitions/airr_and_ireceptor_sequence_model' + '400': + description: malformed request + '401': + description: authentication error + '403': + description: authorization error + '404': + description: data not found + '405': + description: method not allowed + /sequences_data: + x-swagger-router-controller: sequences + get: + description: > + This service returns the annotation data that matches the GET provided + filter. "username" parameter refers to external_users table, and it + requires the array of "project_sample_id", which limits which samples + the sequences will be taken from. Other parameters are optional, and + refer to the sequence_md_view view in iReceptor database. + tags: + - sequences + parameters: + - name: username + in: query + description: > + Username of the individual requesting access to the iReceptor + repository node. + required: true + type: string + - name: project_sample_id_list + in: query + required: true + type: array + items: + type: integer + - name: cdr3_length + in: query + description: >- + length of complementarity determining region in nucleotide base + pairs + required: false + type: integer + - name: vgene_string + in: query + required: false + type: string + - name: jgene_string + in: query + required: false + type: string + - name: format + in: query + description: >- + 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as + per /v1 with tab delimiters instead of commas); 'airr' - AIRR + Formats rearrangements TSV (as per AIRR formats rearrangements spec) + required: false + type: string + operationId: getSequenceData + responses: + '200': + description: > + A successful call returns an array of sequence data. Optional + "format" parameter determines the output format. Default is a JSON + response, limited to top 50 results. If "format" is set to "csv", it + will return all the matching sequence annotations, in addition to + sample information and annotation tool information, in a + comma-separated format; "tsv" returns a tab-delimited outputs; + "airr" returns AIRR minimal standards encoded tab-delimited outputs. + schema: + $ref: '#/definitions/airr_and_ireceptor_sequence_model' + '400': + description: malformed request + '401': + description: authentication error + '403': + description: authorization error + '404': + description: data not found + '405': + description: method not allowed + post: + description: > + This service returns the annotation data that matches the POST provided + filter. "username" parameter refers to external_users table, and it + requires the array of "project_sample_id", which limits which samples + the sequences will be taken from. Other parameters are optional, and + refer to the sequence_md_view view in iReceptor database. A full list of + possible parameters is in the iReceptorAPI-sequenceMetadata file + tags: + - sequences + parameters: + - name: query + in: body + schema: + type: object + required: + - username + properties: + username: + type: string + description: > + Username of the individual requesting access to the iReceptor + repository node. + project_sample_id_list: + type: array + items: type: integer - description: | - e.g. 290 - vregion_mutation_string: - type: string - fr1region_mutation_string: - type: string - fr2region_mutation_string: - type: string - fr3region_mutation_string: - type: string - cdr1region_mutation_string: - type: string - cdr2region_mutation_string: - type: string - cdr3region_mutation_string: - type: string - citation: - type: object - properties: - doi: - type: string - title: - type: string - examples: - application/json: - seq_name: | - M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 - vgene_gene: | - IGHV4-59 - v_allele: | - IGHV4-59*01 or IGHV4-59*07 - dgene_string: | - Homsap IGHD3-10*01 F - dgene_family: | - IGHD3 - dgene_gene: | - IGHD3-10 - d_allele: | - IGHD3-10*01 - jgene_string: | - Homsap IGHJ4*02 F - jgene_family: | - IGHJ4 - jgene_gene: | - IGHJ4 - j_allele: | - IGHJ4*02 - functionality: | - productive - vregion_mutation_string: | - a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr3region_mutation_string: | - c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr2region_mutation_string: | - a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: | - g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - citation: - doi: 10.1093/cid/ciw767 - title: > - RNA-Seq Analysis of Gene Expression, Viral Pathogen, and - B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. + cdr3_length: + description: > + length of complementarity determining region in nucleotide + base pairs + type: integer + vgene_string: + type: string + jgene_string: + type: string + format: + description: >- + 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based + TSV (as per /v1 with tab delimiters instead of commas); 'airr' + - AIRR Formats rearrangements TSV (as per AIRR formats + rearrangements spec) + operationId: postSequenceData + responses: + '200': + description: > + A successful call returns an array of sequence data. Optional + "format" parameter determines the output format. Default is a JSON + response, limited to top 50 results. If "format" is set to "csv", it + will return all the matching sequence annotations, in addition to + sample information and annotation tool information, in a + comma-separated format; "tsv" returns a tab-delimited outputs; + "airr" returns AIRR minimal standards encoded tab-delimited outputs. + schema: + $ref: '#/definitions/airr_and_ireceptor_sequence_model' '400': description: malformed request '401': @@ -2929,716 +1319,9 @@ paths: type: object properties: summary: - type: array - items: - type: object - properties: - sequence_count: - type: integer - description: | - The number of sequences that match the filter for this sample. - study_id: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - study_title: - type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR) - study_type: - type: string - description: | - Type of project/study (e.g. Cancer) (AIRR) - inclusion_exclusion_criteria: - type: string - description: | - Study inclusion/exclusion criteria (AIRR) - grants: - type: string - description: | - Grant funding agency (AIRR) - lab_name: - type: string - description: | - Lab name (AIRR) - collected_by: - type: string - description: | - Contact information (data collection) (AIRR) - uploaded_by: - type: string - description: | - Contact information (data deposition) (AIRR) - lab_address: - type: string - description: | - Lab address (AIRR) - pubs_ids: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - subject_id: - type: string - description: | - UID assigned by submitter (e.g. SUB856413) (AIRR) - organism: - type: string - description: | - Organism-based (human, mouse) or synthetic (AIRR) - sex: - type: string - description: | - Sex (e.g. M/F) (AIRR) - age: - type: string - description: | - Age - Time duration and unit (e.g. 200 days) (AIRR) - age_event: - type: string - description: | - Age event (e.g. Enrollment) (AIRR) - ancestry_population: - type: string - description: | - Ancestry population (AIRR) - ethnicity: - type: string - description: | - Ethnicity (e.g. Tamil) (AIRR) - race: - type: string - description: | - Race (e.g. South Indian) (AIRR) - species_name: - type: string - description: | - Species name (e.g. Homo Sapiens) (AIRR) - strain_name: - type: string - description: | - Strain name (e.g. C57BL/6J) (AIRR) - linked_subjects: - type: string - description: | - Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR) - link_type: - type: string - description: | - Relation type (.e.g sister, father, daughter) (AIRR) - sample_id: - type: string - description: | - Biological sample ID - UID assigned by submitter (AIRR) - sample_type: - type: string - description: | - Sample type (e.g. Tissue, body fluid) (AIRR) - tissue: - type: string - description: | - Anatomic site (e.g. spleen) (AIRR) - disease_state_sample: - type: string - description: | - Disease state of sample (e.g. tumor vs margin) (AIRR) - collection_date: - type: string - description: | - Sample collection time (e.g. 10 days) (AIRR) - collection_time_event: - type: string - description: | - Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR) - source_commercial: - type: string - description: | - Commercial source of sample (e.g. XYZ Pharma) (AIRR) - cell_subset: - type: string - description: | - Cell subset (Controlled vocabulary) (AIRR) - cell_phenotype: - type: string - description: | - Cell subset phenotype (lab specific description) (AIRR) - study_group_description: - type: string - description: | - Study group description (e.g. Case vs. Control) (AIRR) - library_source: - type: string - description: | - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR) - subject_age: - type: integer - description: | - e.g. 1 - marker_1: - type: string - description: | - e.g. CR19 - marker_2: - type: string - description: | - e.g. CR20 - marker_3: - type: string - description: | - e.g. CR21 - marker_4: - type: string - description: | - e.g. null - marker_5: - type: string - description: | - e.g. null - marker_6: - type: string - description: | - e.g. null - subject_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a subject. - project_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a project. - project_parent_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a parent/child - relationship between this project and its parent project. - lab_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a lab. - case_control_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an element in the case_control table. - sample_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a sample. - dna_db_id: - type: integer - description: | - Identifier used internally by the repository to identify a DNA type. - project_sample_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an association - a project with a sample. - sample_subject_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an association - between a sample and a subject. - sample_source_db_id: - type: integer - description: | - Identifier used internally by the repository to identify an association - between a sample and a sample source. + $ref: '#/definitions/summary_model' items: - type: array - items: - type: object - properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: - type: integer - description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - type: string - description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - type: string - description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - type: string - description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - type: string - description: | - C region with allele (AIRR) - junction_nt: - type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: - type: string - description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: - type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - description: | - e.g IGHV4-59*01 or IGHV4-59*07 - vgene_family: - type: string - description: | - e.g. IGHV4 - vgene_gene: - type: string - description: | - e.g. IGHV4-59 - dgene_string: - type: string - description: | - e.g. Homsap IGHD3-10*01 F - dgene_family: - type: string - description: | - e.g. IGHD3 - dgene_gene: - type: string - description: | - e.g. IGHD3-10 - jgene_string: - type: string - description: | - e.g. Homsap IGHJ4*02 F - jgene_family: - type: string - description: | - e.g. IGHJ4 - jgene_gene: - type: string - description: | - e.g. IGHJ4 - functionality: - type: string - description: | - e.g. productive - functionality_comment: - type: string - description: | - e.g. "" - orientation: - type: string - description: | - e.g. + - vgene_score: - type: integer - description: | - e.g. 1127 - vgene_probability: - type: integer - description: | - e.g. 95 - dregion_reading_frame: - type: integer - description: | - e.g. 2 - cdr1_length: - type: integer - description: | - e.g. 8 - cdr2_length: - type: integer - description: | - e.g. 7 - cdr3_length: - type: integer - description: | - e.g. 13 - vdjregion_sequence_nt: - type: string - description: | - vdj region nucleotide sequence - vjregion_sequence_nt: - type: string - description: | - vj region nucleotide sequence - djregion_sequence_nt: - type: string - description: | - dj region nucleotide sequence - vregion_sequence_nt: - type: string - description: | - v region nucleotide sequence - dregion_sequence_nt: - type: string - description: | - d region nucleotide sequence - jregion_sequence_nt: - type: string - description: | - j region nucleotide sequence - fr1region_sequence_nt: - type: string - description: | - fr1 region nucleotide sequence - fr2region_sequence_nt: - type: string - description: | - fr2 region nucleotide sequence - fr3region_sequence_nt: - type: string - description: | - fr3 region nucleotide sequence - fr4region_sequence_nt: - type: string - description: | - fr4 region nucleotide sequence - cdr1region_sequence_nt: - type: string - description: | - cdr1 region nucleotide sequence - cdr2region_sequence_nt: - type: string - description: | - cdr2 region nucleotide sequence - cdr3region_sequence_nt: - type: string - description: | - cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: - type: string - description: | - gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: - type: string - description: | - gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: - type: string - description: | - gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: - type: string - description: | - gapped v region nucleotide sequence - dregion_sequence_nt_gapped: - type: string - description: | - gapped d region nucleotide sequence - jregion_sequence_nt_gapped: - type: string - description: | - gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: - type: string - description: | - gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: - type: string - description: | - gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: - type: string - description: | - gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: - type: string - description: | - gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: - type: string - description: | - gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: - type: string - description: | - gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: - type: string - description: | - gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: - type: string - description: | - gapped junction nucleotide sequence - vdjregion_sequence_aa: - type: string - description: | - vdj region amino acid sequence - vjregion_sequence_aa: - type: string - description: | - vj region amino acid sequence - djregion_sequence_aa: - type: string - description: | - dj region amino acid sequence - vregion_sequence_aa: - type: string - description: | - v region amino acid sequence - dregion_sequence_aa: - type: string - description: | - d region amino acid sequence - jregion_sequence_aa: - type: string - description: | - j region amino acid sequence - fr1region_sequence_aa: - type: string - description: | - fr1 region amino acid sequence - fr2region_sequence_aa: - type: string - description: | - fr2 region amino acid sequence - fr3region_sequence_aa: - type: string - description: | - fr3 region amino acid sequence - fr4region_sequence_aa: - type: string - description: | - fr4 region amino acid sequence - cdr1region_sequence_aa: - type: string - description: | - cdr1 region amino acid sequence - cdr2region_sequence_aa: - type: string - description: | - cdr2 region amino acid sequence - cdr3region_sequence_aa: - type: string - description: | - cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: - type: string - description: | - gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: - type: string - description: | - gapped vj region amino acid sequence - djregion_sequence_aa_gapped: - type: string - description: | - gapped dj region amino acid sequence - vregion_sequence_aa_gapped: - type: string - description: | - gapped v region amino acid sequence - dregion_sequence_aa_gapped: - type: string - description: | - gapped d region amino acid sequence - jregion_sequence_aa_gapped: - type: string - description: | - gapped j region amino acid sequence - fr1region_sequence_aa_gapped: - type: string - description: | - gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: - type: string - description: | - gapped fr2 region amino acid sequence - fr3region_sequence_aa_gapped: - type: string - description: | - gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: - type: string - description: | - gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: - type: string - description: | - gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: - type: string - description: | - gapped cdr2 region amino acid sequence - cdr3region_sequence_aa_gapped: - type: string - description: | - gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: - type: string - description: | - gapped junction amino acid sequence - vdjregion_start: - type: integer - description: | - e.g. 1 - vdjregion_end: - type: integer - description: | - e.g. 321 - vjregion_start: - type: integer - description: | - e.g. 0 - vjregion_end: - type: integer - description: | - e.g. 0 - djregion_start: - type: integer - description: | - e.g. 254 - djregion_end: - type: integer - description: | - e.g. 321 - vregion_start: - type: integer - description: | - e.g. 286 - vregion_end: - type: integer - description: | - e.g. 252 - dregion_start: - type: integer - description: | - e.g. 254 - dregion_end: - type: integer - description: | - e.g. 321 - jregion_start: - type: integer - description: | - e.g. 286 - jregion_end: - type: integer - description: | - e.g. 321 - fr1region_start: - type: integer - description: | - e.g. 1 - fr1region_end: - type: integer - description: | - e.g. 38 - fr2region_start: - type: integer - description: | - e.g. 63 - fr2region_end: - type: integer - description: | - e.g. 113 - fr3region_start: - type: integer - description: | - e.g. 135 - fr3region_end: - type: integer - description: | - e.g. 248 - fr4region_start: - type: integer - description: | - e.g. 288 - fr4region_end: - type: integer - description: | - e.g. 321 - cdr1region_start: - type: integer - description: | - e.g. 39 - cdr1region_end: - type: integer - description: | - e.g. 321 - cdr2region_start: - type: integer - description: | - e.g. 62 - cdr2region_end: - type: integer - description: | - e.g. 134 - cdr3region_start: - type: integer - description: | - e.g. 249 - cdr3region_end: - type: integer - description: | - e.g. 287 - junction_start: - type: integer - description: | - e.g. 246 - junction_end: - type: integer - description: | - e.g. 290 - vregion_mutation_string: - type: string - description: > - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: - type: string - description: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr2region_mutation_string: - type: string - description: | - e.g. - fr3region_mutation_string: - type: string - description: > - e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr1region_mutation_string: - type: string - description: | - e.g. - cdr2region_mutation_string: - type: string - description: | - e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: - type: string - description: | - e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - annotation_tool: - type: string - description: | - e.g. VQuest + $ref: '#/definitions/airr_and_ireceptor_sequence_model' '400': description: malformed request '401': @@ -3697,544 +1380,17 @@ paths: sample information and annotation tool information, in a comma-separated format. schema: - type: array - items: - type: object - properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: - type: integer - description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - type: string - description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - type: string - description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - type: string - description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - type: string - description: | - C region with allele (AIRR) - junction_nt: - type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: - type: string - description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: - type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - vgene_family: - type: string - description: | - e.g. IGHV4 - vgene_gene: - type: string - description: | - e.g. IGHV4-59 - dgene_string: - type: string - description: | - e.g. Homsap IGHD3-10*01 F - dgene_family: - type: string - description: | - e.g. IGHD3 - dgene_gene: - type: string - description: | - e.g. IGHD3-10 - jgene_string: - type: string - description: | - e.g. Homsap IGHJ4*02 F - jgene_family: - type: string - description: | - e.g. IGHJ4 - jgene_gene: - type: string - description: | - e.g. IGHJ4 - functionality: - type: string - description: | - e.g. productive - functionality_comment: - type: string - description: | - e.g. "" - orientation: - type: string - description: | - e.g. + - vgene_score: - type: integer - description: | - e.g. 1127 - vgene_probability: - type: integer - description: | - e.g. 95 - dregion_reading_frame: - type: integer - description: | - e.g. 2 - cdr1_length: - type: integer - description: | - e.g. 8 - cdr2_length: - type: integer - description: | - e.g. 7 - cdr3_length: - type: integer - description: | - e.g. 13 - vdjregion_sequence_nt: - type: string - description: | - vdj region nucleotide sequence - vjregion_sequence_nt: - type: string - description: | - vj region nucleotide sequence - djregion_sequence_nt: - type: string - description: | - dj region nucleotide sequence - vregion_sequence_nt: - type: string - description: | - v region nucleotide sequence - dregion_sequence_nt: - type: string - description: | - d region nucleotide sequence - jregion_sequence_nt: - type: string - description: | - j region nucleotide sequence - fr1region_sequence_nt: - type: string - description: | - fr1 region nucleotide sequence - fr2region_sequence_nt: - type: string - description: | - fr2 region nucleotide sequence - fr3region_sequence_nt: - type: string - description: | - fr3 region nucleotide sequence - fr4region_sequence_nt: - type: string - description: | - fr4 region nucleotide sequence - cdr1region_sequence_nt: - type: string - description: | - cdr1 region nucleotide sequence - cdr2region_sequence_nt: - type: string - description: | - cdr2 region nucleotide sequence - cdr3region_sequence_nt: - type: string - description: | - cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: - type: string - description: | - gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: - type: string - description: | - gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: - type: string - description: | - gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: - type: string - description: | - gapped v region nucleotide sequence - dregion_sequence_nt_gapped: - type: string - description: | - gapped d region nucleotide sequence - jregion_sequence_nt_gapped: - type: string - description: | - gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: - type: string - description: | - gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: - type: string - description: | - gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: - type: string - description: | - gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: - type: string - description: | - gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: - type: string - description: | - gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: - type: string - description: | - gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: - type: string - description: | - gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: - type: string - description: | - gapped junction nucleotide sequence - vdjregion_sequence_aa: - type: string - description: | - vdj region amino acid sequence - vjregion_sequence_aa: - type: string - description: | - vj region amino acid sequence - djregion_sequence_aa: - type: string - description: | - dj region amino acid sequence - vregion_sequence_aa: - type: string - description: | - v region amino acid sequence - dregion_sequence_aa: - type: string - description: | - d region amino acid sequence - jregion_sequence_aa: - type: string - description: | - j region amino acid sequence - fr1region_sequence_aa: - type: string - description: | - fr1 region amino acid sequence - fr2region_sequence_aa: - type: string - description: | - fr2 region amino acid sequence - fr3region_sequence_aa: - type: string - description: | - fr3 region amino acid sequence - fr4region_sequence_aa: - type: string - description: | - fr4 region amino acid sequence - cdr1region_sequence_aa: - type: string - description: | - cdr1 region amino acid sequence - cdr2region_sequence_aa: - type: string - description: | - cdr2 region amino acid sequence - cdr3region_sequence_aa: - type: string - description: | - cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: - type: string - description: | - gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: - type: string - description: | - gapped vj region amino acid sequence - djregion_sequence_aa_gapped: - type: string - description: | - gapped dj region amino acid sequence - vregion_sequence_aa_gapped: - type: string - description: | - gapped v region amino acid sequence - dregion_sequence_aa_gapped: - type: string - description: | - gapped d region amino acid sequence - jregion_sequence_aa_gapped: - type: string - description: | - gapped j region amino acid sequence - fr1region_sequence_aa_gapped: - type: string - description: | - gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: - type: string - description: | - gapped fr2 region amino acid sequence - fr3region_sequence_aa_gapped: - type: string - description: | - gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: - type: string - description: | - gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: - type: string - description: | - gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: - type: string - description: | - gapped cdr2 region amino acid sequence - cdr3region_sequence_aa_gapped: - type: string - description: | - gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: - type: string - description: | - gapped junction amino acid sequence - vdjregion_start: - type: integer - description: | - e.g. 1 - vdjregion_end: - type: integer - description: | - e.g. 321 - vjregion_start: - type: integer - description: | - e.g. 0 - vjregion_end: - type: integer - description: | - e.g. 0 - djregion_start: - type: integer - description: | - e.g. 254 - djregion_end: - type: integer - description: | - e.g. 321 - vregion_start: - type: integer - description: | - e.g. 286 - vregion_end: - type: integer - description: | - e.g. 252 - dregion_start: - type: integer - description: | - e.g. 254 - dregion_end: - type: integer - description: | - e.g. 321 - jregion_start: - type: integer - description: | - e.g. 286 - jregion_end: - type: integer - description: | - e.g. 321 - fr1region_start: - type: integer - description: | - e.g. 1 - fr1region_end: - type: integer - description: | - e.g. 38 - fr2region_start: - type: integer - description: | - e.g. 63 - fr2region_end: - type: integer - description: | - e.g. 113 - fr3region_start: - type: integer - description: | - e.g. 135 - fr3region_end: - type: integer - description: | - e.g. 248 - fr4region_start: - type: integer - description: | - e.g. 288 - fr4region_end: - type: integer - description: | - e.g. 321 - cdr1region_start: - type: integer - description: | - e.g. 39 - cdr1region_end: - type: integer - description: | - e.g. 321 - cdr2region_start: - type: integer - description: | - e.g. 62 - cdr2region_end: - type: integer - description: | - e.g. 134 - cdr3region_start: - type: integer - description: | - e.g. 249 - cdr3region_end: - type: integer - description: | - e.g. 287 - junction_start: - type: integer - description: | - e.g. 246 - junction_end: - type: integer - description: | - e.g. 290 - vregion_mutation_string: - type: string - description: > - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: - type: string - description: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr2region_mutation_string: - type: string - description: | - e.g. - fr3region_mutation_string: - type: string - description: > - e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr1region_mutation_string: - type: string - description: | - e.g. - cdr2region_mutation_string: - type: string - description: | - e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: - type: string - description: | - e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - citation: - type: object - properties: - doi: - type: string - title: - type: string + $ref: '#/definitions/airr_and_ireceptor_sequence_model' examples: application/json: seq_name: | M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 - vgene_gene: | - IGHV4-59 v_allele: | IGHV4-59*01 or IGHV4-59*07 - dgene_string: | - Homsap IGHD3-10*01 F - dgene_family: | - IGHD3 - dgene_gene: | - IGHD3-10 d_allele: | IGHD3-10*01 - jgene_string: | - Homsap IGHJ4*02 F - jgene_family: | - IGHJ4 - jgene_gene: | - IGHJ4 - jgene_allele: | + j_allele: | IGHJ4*02 - functionality: | - productive - vregion_mutation_string: | - a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr3region_mutation_string: | - c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr2region_mutation_string: | - a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: | - g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t citation: doi: 10.1093/cid/ciw767 title: > From 5b98ec30a9cdfee3bbb4fc7ef614a9f76216bd18 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 29 Sep 2017 16:26:33 +1300 Subject: [PATCH 07/46] Changed the models so they use the externally defined AIRR model. This is still a bit of an experiment, but this looks very promising. By using the AIRR Minimal Standards YAML file we externalize the definitions of the AIRR fields. As long as we can be sure that this exists and is robust (there is a consitent version) then this should work quite well. The response models for the URLs are now abstracted to using an AIRR model and an iReceptor model in aggregate form as required by the response... --- iReceptor_Data_Service_API_V2.json | 1173 +++++++++++++++------------- iReceptor_Data_Service_API_V2.yaml | 170 ++-- 2 files changed, 758 insertions(+), 585 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 3964b80..c2b94ed 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -13,54 +13,190 @@ "host": "ipa.ireceptor.org", "basePath": "/v2", "definitions": { - "airr_sequence_model": { + "ireceptor_summary_response": { "type": "array", "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" + "allOf": [ + { + "$ref": "#/definitions/ireceptor_sequence_count_model" }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" + { + "$ref": "#/definitions/airr_summary_model" }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" + { + "$ref": "#/definitions/ireceptor_summary_model" + } + ] + } + }, + "ireceptor_sequence_response": { + "type": "array", + "items": { + "allOf": [ + { + "$ref": "#/definitions/airr_sequence_annotation_model" }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" + { + "$ref": "#/definitions/ireceptor_sequence_annotation_model" } + ] + } + }, + "airr_summary_model": { + "allOf": [ + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Study" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Subject" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Diagnosis" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Sample" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/CellProcessing" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/NucleicAcidProcessing" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/RawSequenceData" + }, + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/SoftwareProcessing" + } + ] + }, + "ireceptor_sequence_count_model": { + "type": "object", + "properties": { + "sequence_count": { + "type": "integer", + "example": 123456 + } + } + }, + "ireceptor_summary_model": { + "type": "object", + "properties": { + "subject_age": { + "type": "integer", + "description": "e.g. 1\n" + }, + "marker_1": { + "type": "string", + "description": "e.g. CR19\n" + }, + "marker_2": { + "type": "string", + "description": "e.g. CR20\n" + }, + "marker_3": { + "type": "string", + "description": "e.g. CR21\n" + }, + "marker_4": { + "type": "string", + "description": "e.g. null\n" + }, + "marker_5": { + "type": "string", + "description": "e.g. null\n" + }, + "marker_6": { + "type": "string", + "description": "e.g. null\n" + }, + "subject_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a subject.\n" + }, + "project_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a project.\n" + }, + "project_parent_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a parent/child relationship between this project and its parent project.\n" + }, + "lab_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a lab.\n" + }, + "case_control_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" + }, + "sample_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a sample.\n" + }, + "dna_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a DNA type.\n" + }, + "project_sample_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an association a project with a sample.\n" + }, + "sample_subject_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an association between a sample and a subject.\n" + }, + "sample_source_db_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify an association between a sample and a sample source.\n" + } + } + }, + "airr_sequence_annotation_model": { + "type": "object", + "properties": { + "germline_database": { + "type": "string", + "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" + }, + "cell_index": { + "type": "integer", + "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" + }, + "v_allele": { + "type": "string", + "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" + }, + "d_allele": { + "type": "string", + "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" + }, + "j_allele": { + "type": "string", + "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" + }, + "c_allele": { + "type": "string", + "description": "C region with allele (AIRR) \n" + }, + "junction_nt": { + "type": "string", + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" + }, + "junction_aa": { + "type": "string", + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" + }, + "duplicate_count": { + "type": "integer", + "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" } } }, "extended_sequence_model": { "allOf": [ { - "$ref": "#/definitions/airr_sequence_model" + "$ref": "#/definitions/airr_sequence_annotation_model" }, { "type": "object", @@ -73,498 +209,459 @@ } ] }, - "airr_and_ireceptor_sequence_model": { - "type": "array", - "items": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - }, - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string", - "description": "e.g IGHV4-59*01 or IGHV4-59*07\n" - }, - "vgene_family": { - "type": "string", - "description": "e.g. IGHV4\n" - }, - "vgene_gene": { - "type": "string", - "description": "e.g. IGHV4-59\n" - }, - "dgene_string": { - "type": "string", - "description": "e.g. Homsap IGHD3-10*01 F\n" - }, - "dgene_family": { - "type": "string", - "description": "e.g. IGHD3\n" - }, - "dgene_gene": { - "type": "string", - "description": "e.g. IGHD3-10\n" - }, - "jgene_string": { - "type": "string", - "description": "e.g. Homsap IGHJ4*02 F\n" - }, - "jgene_family": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "jgene_gene": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "functionality": { - "type": "string", - "description": "e.g. productive\n" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" - }, - "fr1region_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" - }, - "fr2region_mutation_string": { - "type": "string", - "description": "e.g. \n" - }, - "fr3region_mutation_string": { - "type": "string", - "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" - }, - "cdr1region_mutation_string": { - "type": "string", - "description": "e.g.\n" - }, - "cdr2region_mutation_string": { - "type": "string", - "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" - }, - "cdr3region_mutation_string": { - "type": "string", - "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" - }, - "annotation_tool": { - "type": "string", - "description": "e.g. VQuest\n" - } + "ireceptor_sequence_annotation_model": { + "type": "object", + "properties": { + "seq_id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "seq_name": { + "type": "string" + }, + "project_sample_id": { + "type": "integer", + "description": "e.g. 6\n" + }, + "id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "sequence_id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "vgene_string": { + "type": "string", + "description": "e.g IGHV4-59*01 or IGHV4-59*07\n" + }, + "vgene_family": { + "type": "string", + "description": "e.g. IGHV4\n" + }, + "vgene_gene": { + "type": "string", + "description": "e.g. IGHV4-59\n" + }, + "dgene_string": { + "type": "string", + "description": "e.g. Homsap IGHD3-10*01 F\n" + }, + "dgene_family": { + "type": "string", + "description": "e.g. IGHD3\n" + }, + "dgene_gene": { + "type": "string", + "description": "e.g. IGHD3-10\n" + }, + "jgene_string": { + "type": "string", + "description": "e.g. Homsap IGHJ4*02 F\n" + }, + "jgene_family": { + "type": "string", + "description": "e.g. IGHJ4\n" + }, + "jgene_gene": { + "type": "string", + "description": "e.g. IGHJ4\n" + }, + "functionality": { + "type": "string", + "description": "e.g. productive\n" + }, + "functionality_comment": { + "type": "string", + "description": "e.g. \"\"\n" + }, + "orientation": { + "type": "string", + "description": "e.g. +\n" + }, + "vgene_score": { + "type": "integer", + "description": "e.g. 1127\n" + }, + "vgene_probability": { + "type": "integer", + "description": "e.g. 95\n" + }, + "dregion_reading_frame": { + "type": "integer", + "description": "e.g. 2\n" + }, + "cdr1_length": { + "type": "integer", + "description": "e.g. 8\n" + }, + "cdr2_length": { + "type": "integer", + "description": "e.g. 7\n" + }, + "cdr3_length": { + "type": "integer", + "description": "e.g. 13\n" + }, + "vdjregion_sequence_nt": { + "type": "string", + "description": "vdj region nucleotide sequence\n" + }, + "vjregion_sequence_nt": { + "type": "string", + "description": "vj region nucleotide sequence\n" + }, + "djregion_sequence_nt": { + "type": "string", + "description": "dj region nucleotide sequence\n" + }, + "vregion_sequence_nt": { + "type": "string", + "description": "v region nucleotide sequence\n" + }, + "dregion_sequence_nt": { + "type": "string", + "description": "d region nucleotide sequence\n" + }, + "jregion_sequence_nt": { + "type": "string", + "description": "j region nucleotide sequence\n" + }, + "fr1region_sequence_nt": { + "type": "string", + "description": "fr1 region nucleotide sequence\n" + }, + "fr2region_sequence_nt": { + "type": "string", + "description": "fr2 region nucleotide sequence\n" + }, + "fr3region_sequence_nt": { + "type": "string", + "description": "fr3 region nucleotide sequence\n" + }, + "fr4region_sequence_nt": { + "type": "string", + "description": "fr4 region nucleotide sequence\n" + }, + "cdr1region_sequence_nt": { + "type": "string", + "description": "cdr1 region nucleotide sequence\n" + }, + "cdr2region_sequence_nt": { + "type": "string", + "description": "cdr2 region nucleotide sequence\n" + }, + "cdr3region_sequence_nt": { + "type": "string", + "description": "cdr3 region nucleotide sequence\n" + }, + "vdjregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped vdj region nucleotide sequence\n" + }, + "vjregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped vj region nucleotide sequence\n" + }, + "djregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped dj region nucleotide sequence\n" + }, + "vregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped v region nucleotide sequence\n" + }, + "dregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped d region nucleotide sequence\n" + }, + "jregion_sequence_nt_gapped": { + "type": "string", + "description": "gapped j region nucleotide sequence\n" + }, + "fr1region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr1 region nucleotide sequence\n" + }, + "fr2region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr2 region nucleotide sequence\n" + }, + "fr3region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr3 region nucleotide sequence\n" + }, + "fr4region_sequence_nt_gapped": { + "type": "string", + "description": "gapped fr4 region nucleotide sequence\n" + }, + "cdr1region_sequence_nt_gapped": { + "type": "string", + "description": "gapped cdr1 region nucleotide sequence\n" + }, + "cdr2region_sequence_nt_gapped": { + "type": "string", + "description": "gapped cdr2 region nucleotide sequence\n" + }, + "cdr3region_sequence_nt_gapped": { + "type": "string", + "description": "gapped cdr3 region nucleotide sequence\n" + }, + "junction_sequence_nt_gapped": { + "type": "string", + "description": "gapped junction nucleotide sequence\n" + }, + "vdjregion_sequence_aa": { + "type": "string", + "description": "vdj region amino acid sequence\n" + }, + "vjregion_sequence_aa": { + "type": "string", + "description": "vj region amino acid sequence\n" + }, + "djregion_sequence_aa": { + "type": "string", + "description": "dj region amino acid sequence\n" + }, + "vregion_sequence_aa": { + "type": "string", + "description": "v region amino acid sequence\n" + }, + "dregion_sequence_aa": { + "type": "string", + "description": "d region amino acid sequence\n" + }, + "jregion_sequence_aa": { + "type": "string", + "description": "j region amino acid sequence\n" + }, + "fr1region_sequence_aa": { + "type": "string", + "description": "fr1 region amino acid sequence\n" + }, + "fr2region_sequence_aa": { + "type": "string", + "description": "fr2 region amino acid sequence\n" + }, + "fr3region_sequence_aa": { + "type": "string", + "description": "fr3 region amino acid sequence\n" + }, + "fr4region_sequence_aa": { + "type": "string", + "description": "fr4 region amino acid sequence\n" + }, + "cdr1region_sequence_aa": { + "type": "string", + "description": "cdr1 region amino acid sequence\n" + }, + "cdr2region_sequence_aa": { + "type": "string", + "description": "cdr2 region amino acid sequence\n" + }, + "cdr3region_sequence_aa": { + "type": "string", + "description": "cdr3 region amino acid sequence\n" + }, + "vdjregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped vdj region amino acid sequence\n" + }, + "vjregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped vj region amino acid sequence\n" + }, + "djregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped dj region amino acid sequence\n" + }, + "vregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped v region amino acid sequence\n" + }, + "dregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped d region amino acid sequence\n" + }, + "jregion_sequence_aa_gapped": { + "type": "string", + "description": "gapped j region amino acid sequence\n" + }, + "fr1region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr1 region amino acid sequence\n" + }, + "fr2region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr2 region amino acid sequence\n" + }, + "fr3region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr3 region amino acid sequence\n" + }, + "fr4region_sequence_aa_gapped": { + "type": "string", + "description": "gapped fr4 region amino acid sequence\n" + }, + "cdr1region_sequence_aa_gapped": { + "type": "string", + "description": "gapped cdr1 region amino acid sequence\n" + }, + "cdr2region_sequence_aa_gapped": { + "type": "string", + "description": "gapped cdr2 region amino acid sequence\n" + }, + "cdr3region_sequence_aa_gapped": { + "type": "string", + "description": "gapped cdr3 region amino acid sequence\n" + }, + "junction_sequence_aa_gapped": { + "type": "string", + "description": "gapped junction amino acid sequence\n" + }, + "vdjregion_start": { + "type": "integer", + "description": "e.g. 1\n" + }, + "vdjregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "vjregion_start": { + "type": "integer", + "description": "e.g. 0\n" + }, + "vjregion_end": { + "type": "integer", + "description": "e.g. 0\n" + }, + "djregion_start": { + "type": "integer", + "description": "e.g. 254\n" + }, + "djregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "vregion_start": { + "type": "integer", + "description": "e.g. 286\n" + }, + "vregion_end": { + "type": "integer", + "description": "e.g. 252\n" + }, + "dregion_start": { + "type": "integer", + "description": "e.g. 254\n" + }, + "dregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "jregion_start": { + "type": "integer", + "description": "e.g. 286\n" + }, + "jregion_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "fr1region_start": { + "type": "integer", + "description": "e.g. 1\n" + }, + "fr1region_end": { + "type": "integer", + "description": "e.g. 38\n" + }, + "fr2region_start": { + "type": "integer", + "description": "e.g. 63\n" + }, + "fr2region_end": { + "type": "integer", + "description": "e.g. 113\n" + }, + "fr3region_start": { + "type": "integer", + "description": "e.g. 135\n" + }, + "fr3region_end": { + "type": "integer", + "description": "e.g. 248\n" + }, + "fr4region_start": { + "type": "integer", + "description": "e.g. 288\n" + }, + "fr4region_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "cdr1region_start": { + "type": "integer", + "description": "e.g. 39\n" + }, + "cdr1region_end": { + "type": "integer", + "description": "e.g. 321\n" + }, + "cdr2region_start": { + "type": "integer", + "description": "e.g. 62\n" + }, + "cdr2region_end": { + "type": "integer", + "description": "e.g. 134\n" + }, + "cdr3region_start": { + "type": "integer", + "description": "e.g. 249\n" + }, + "cdr3region_end": { + "type": "integer", + "description": "e.g. 287\n" + }, + "junction_start": { + "type": "integer", + "description": "e.g. 246\n" + }, + "junction_end": { + "type": "integer", + "description": "e.g. 290\n" + }, + "vregion_mutation_string": { + "type": "string", + "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" + }, + "fr1region_mutation_string": { + "type": "string", + "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" + }, + "fr2region_mutation_string": { + "type": "string", + "description": "e.g. \n" + }, + "fr3region_mutation_string": { + "type": "string", + "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" + }, + "cdr1region_mutation_string": { + "type": "string", + "description": "e.g.\n" + }, + "cdr2region_mutation_string": { + "type": "string", + "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" + }, + "cdr3region_mutation_string": { + "type": "string", + "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" + }, + "annotation_tool": { + "type": "string", + "description": "e.g. VQuest\n" } } }, @@ -605,7 +702,7 @@ "type": "string", "description": "Contact information (data collection) (AIRR)\n" }, - "uploaded_by": { + "submitted_by": { "type": "string", "description": "Contact information (data deposition) (AIRR)\n" }, @@ -970,7 +1067,7 @@ "200": { "description": "A successful call returns an array of sample summary metadata for\neach sample that meets the search criteria. The metadata returned\nfor each sample includes the number of sequences found for that sample\nas well as the study/subject/sample data for that sample. The metadata\nfor each sample in the response contains a set of AIRR compliant data\nas well as repository specific data that is required to query the\nrepository about those types of elements. \n", "schema": { - "$ref": "#/definitions/summary_model" + "$ref": "#/definitions/ireceptor_summary_response" } }, "400": { @@ -1083,7 +1180,7 @@ "200": { "description": "A successful call returns the metadata for each sample, including the number of sequences found for that sample.\n", "schema": { - "$ref": "#/definitions/summary_model" + "$ref": "#/definitions/ireceptor_summary_response" } }, "400": { @@ -1156,10 +1253,10 @@ "type": "object", "properties": { "summary": { - "$ref": "#/definitions/summary_model" + "$ref": "#/definitions/ireceptor_summary_response" }, "items": { - "$ref": "#/definitions/airr_and_ireceptor_sequence_model" + "$ref": "#/definitions/ireceptor_sequence_response" } } } @@ -1238,7 +1335,7 @@ "200": { "description": "A successful call returns an array of sequence data. Optional \"format\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"format\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format; \"tsv\" returns a tab-delimited outputs; \"airr\" returns AIRR minimal standards encoded tab-delimited outputs.\n", "schema": { - "$ref": "#/definitions/airr_and_ireceptor_sequence_model" + "$ref": "#/definitions/ireceptor_sequence_response" } }, "400": { @@ -1305,7 +1402,7 @@ "200": { "description": "A successful call returns an array of sequence data. Optional \"format\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"format\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format; \"tsv\" returns a tab-delimited outputs; \"airr\" returns AIRR minimal standards encoded tab-delimited outputs.\n", "schema": { - "$ref": "#/definitions/airr_and_ireceptor_sequence_model" + "$ref": "#/definitions/ireceptor_sequence_response" } }, "400": { @@ -1378,10 +1475,10 @@ "type": "object", "properties": { "summary": { - "$ref": "#/definitions/summary_model" + "$ref": "#/definitions/ireceptor_summary_response" }, "items": { - "$ref": "#/definitions/airr_and_ireceptor_sequence_model" + "$ref": "#/definitions/ireceptor_sequence_response" } } } @@ -1453,7 +1550,7 @@ "200": { "description": "A successful call returns an array of sequence data. Optional \"output\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"output\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format. \n", "schema": { - "$ref": "#/definitions/airr_and_ireceptor_sequence_model" + "$ref": "#/definitions/ireceptor_sequence_response" }, "examples": { "application/json": { diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 1f4c7b5..40d58c0 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -16,61 +16,126 @@ info: host: ipa.ireceptor.org basePath: /v2 definitions: - airr_sequence_model: + # A definition of the summary response for an iReceptor API call. This + # response is used wherever summary data at the sample level is provided + # by an API call. + ireceptor_summary_response: type: array items: + allOf: + - $ref: '#/definitions/ireceptor_sequence_count_model' + - $ref: '#/definitions/airr_summary_model' + - $ref: '#/definitions/ireceptor_summary_model' + ireceptor_sequence_response: + type: array + items: + allOf: + - $ref: '#/definitions/airr_sequence_annotation_model' + - $ref: '#/definitions/ireceptor_sequence_annotation_model' + # The AIRR Minimal Standards model for metadata above the sequence annotation level. + airr_summary_model: + allOf: + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Study' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Subject' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Diagnosis' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Sample' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/CellProcessing' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/NucleicAcidProcessing' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/RawSequenceData' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/SoftwareProcessing' + # A simple model to represent a sequence count, used to make the + # composite responses clean in that they all refer to models. + ireceptor_sequence_count_model: type: object properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: + sequence_count: + type: integer + example: 123456 + # This model defines ancillary information returned by iReceptor + # on top of that provided by the AIRR standard. + ireceptor_summary_model: + type: object + properties: + subject_age: type: integer description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: + e.g. 1 + marker_1: type: string description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: + e.g. CR19 + marker_2: type: string description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: + e.g. CR20 + marker_3: type: string description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: + e.g. CR21 + marker_4: type: string description: | - C region with allele (AIRR) - junction_nt: + e.g. null + marker_5: type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: + description: | + e.g. null + marker_6: type: string + description: | + e.g. null + subject_db_id: + type: integer description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: + Identifier used internally by the repository to identify a + subject. + project_db_id: type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - extended_sequence_model: - allOf: - - $ref: '#/definitions/airr_sequence_model' - - type: object - properties: - an_extended_model_element: - type: string - description: This does not seem to extend the model, it replaces it! - airr_and_ireceptor_sequence_model: - type: array - items: + description: > + Identifier used internally by the repository to identify a + project. + project_parent_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + parent/child + relationship between this project and its parent project. + lab_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + lab. + case_control_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + element in the case_control table. + sample_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + sample. + dna_db_id: + type: integer + description: > + Identifier used internally by the repository to identify a + DNA type. + project_sample_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association a project with a sample. + sample_subject_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association between a sample and a subject. + sample_source_db_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association between a sample and a sample source. + airr_sequence_annotation_model: type: object properties: germline_database: @@ -112,6 +177,17 @@ definitions: type: integer description: | Number of times the sequence has been duplicated in a file (AIRR) + extended_sequence_model: + allOf: + - $ref: '#/definitions/airr_sequence_annotation_model' + - type: object + properties: + an_extended_model_element: + type: string + description: This does not seem to extend the model, it replaces it! + ireceptor_sequence_annotation_model: + type: object + properties: seq_id: type: integer description: | @@ -604,7 +680,7 @@ definitions: type: string description: | Contact information (data collection) (AIRR) - uploaded_by: + submitted_by: type: string description: | Contact information (data deposition) (AIRR) @@ -953,7 +1029,7 @@ paths: as well as repository specific data that is required to query the repository about those types of elements. schema: - $ref: '#/definitions/summary_model' + $ref: '#/definitions/ireceptor_summary_response' '400': description: malformed request '401': @@ -1057,7 +1133,7 @@ paths: A successful call returns the metadata for each sample, including the number of sequences found for that sample. schema: - $ref: '#/definitions/summary_model' + $ref: '#/definitions/ireceptor_summary_response' '400': description: malformed request '401': @@ -1122,9 +1198,9 @@ paths: type: object properties: summary: - $ref: '#/definitions/summary_model' + $ref: '#/definitions/ireceptor_summary_response' items: - $ref: '#/definitions/airr_and_ireceptor_sequence_model' + $ref: '#/definitions/ireceptor_sequence_response' '400': description: malformed request '401': @@ -1195,7 +1271,7 @@ paths: comma-separated format; "tsv" returns a tab-delimited outputs; "airr" returns AIRR minimal standards encoded tab-delimited outputs. schema: - $ref: '#/definitions/airr_and_ireceptor_sequence_model' + $ref: '#/definitions/ireceptor_sequence_response' '400': description: malformed request '401': @@ -1260,7 +1336,7 @@ paths: comma-separated format; "tsv" returns a tab-delimited outputs; "airr" returns AIRR minimal standards encoded tab-delimited outputs. schema: - $ref: '#/definitions/airr_and_ireceptor_sequence_model' + $ref: '#/definitions/ireceptor_sequence_response' '400': description: malformed request '401': @@ -1319,9 +1395,9 @@ paths: type: object properties: summary: - $ref: '#/definitions/summary_model' + $ref: '#/definitions/ireceptor_summary_response' items: - $ref: '#/definitions/airr_and_ireceptor_sequence_model' + $ref: '#/definitions/ireceptor_sequence_response' '400': description: malformed request '401': @@ -1380,7 +1456,7 @@ paths: sample information and annotation tool information, in a comma-separated format. schema: - $ref: '#/definitions/airr_and_ireceptor_sequence_model' + $ref: '#/definitions/ireceptor_sequence_response' examples: application/json: seq_name: | From cc291022d5a5e5dc675df66d676f140f7b62b94b Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 13 Oct 2017 15:45:06 +1300 Subject: [PATCH 08/46] Made iReceptor extensions to MiAIRR fields consistent with mapping file - essentially include an ir_ tag to each field that existed in the iReceptor API that does not exist in the MiAIRR API. --- iReceptor_Data_Service_API_V2.json | 38 +++++++++++++++++------------- iReceptor_Data_Service_API_V2.yaml | 38 +++++++++++++++++------------- 2 files changed, 42 insertions(+), 34 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index c2b94ed..c6411f1 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -82,71 +82,75 @@ "ireceptor_summary_model": { "type": "object", "properties": { - "subject_age": { + "ir_subject_age": { "type": "integer", "description": "e.g. 1\n" }, - "marker_1": { + "ir_sra_run_id": { + "type": "string", + "description": "" + }, + "ir_marker_1": { "type": "string", "description": "e.g. CR19\n" }, - "marker_2": { + "ir_marker_2": { "type": "string", "description": "e.g. CR20\n" }, - "marker_3": { + "ir_marker_3": { "type": "string", "description": "e.g. CR21\n" }, - "marker_4": { + "ir_marker_4": { "type": "string", "description": "e.g. null\n" }, - "marker_5": { + "ir_marker_5": { "type": "string", "description": "e.g. null\n" }, - "marker_6": { + "ir_marker_6": { "type": "string", "description": "e.g. null\n" }, - "subject_db_id": { + "ir_subject_id": { "type": "integer", "description": "Identifier used internally by the repository to identify a subject.\n" }, - "project_db_id": { + "ir_project_id": { "type": "integer", "description": "Identifier used internally by the repository to identify a project.\n" }, - "project_parent_db_id": { + "ir_project_parent_id": { "type": "integer", "description": "Identifier used internally by the repository to identify a parent/child relationship between this project and its parent project.\n" }, - "lab_db_id": { + "ir_lab_id": { "type": "integer", "description": "Identifier used internally by the repository to identify a lab.\n" }, - "case_control_db_id": { + "ir_case_control_id": { "type": "integer", "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" }, - "sample_db_id": { + "ir_sample_id": { "type": "integer", "description": "Identifier used internally by the repository to identify a sample.\n" }, - "dna_db_id": { + "ir_dna_id": { "type": "integer", "description": "Identifier used internally by the repository to identify a DNA type.\n" }, - "project_sample_db_id": { + "ir_project_sample_id": { "type": "integer", "description": "Identifier used internally by the repository to identify an association a project with a sample.\n" }, - "sample_subject_db_id": { + "ir_sample_subject_id": { "type": "integer", "description": "Identifier used internally by the repository to identify an association between a sample and a subject.\n" }, - "sample_source_db_id": { + "ir_sample_source_id": { "type": "integer", "description": "Identifier used internally by the repository to identify an association between a sample and a sample source.\n" } diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 40d58c0..fc0e60a 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -56,81 +56,85 @@ definitions: ireceptor_summary_model: type: object properties: - subject_age: + ir_subject_age: type: integer description: | e.g. 1 - marker_1: + ir_sra_run_id: + type: string + description: | + + ir_marker_1: type: string description: | e.g. CR19 - marker_2: + ir_marker_2: type: string description: | e.g. CR20 - marker_3: + ir_marker_3: type: string description: | e.g. CR21 - marker_4: + ir_marker_4: type: string description: | e.g. null - marker_5: + ir_marker_5: type: string description: | e.g. null - marker_6: + ir_marker_6: type: string description: | e.g. null - subject_db_id: + ir_subject_id: type: integer description: > Identifier used internally by the repository to identify a subject. - project_db_id: + ir_project_id: type: integer description: > Identifier used internally by the repository to identify a project. - project_parent_db_id: + ir_project_parent_id: type: integer description: > Identifier used internally by the repository to identify a parent/child relationship between this project and its parent project. - lab_db_id: + ir_lab_id: type: integer description: > Identifier used internally by the repository to identify a lab. - case_control_db_id: + ir_case_control_id: type: integer description: > Identifier used internally by the repository to identify an element in the case_control table. - sample_db_id: + ir_sample_id: type: integer description: > Identifier used internally by the repository to identify a sample. - dna_db_id: + ir_dna_id: type: integer description: > Identifier used internally by the repository to identify a DNA type. - project_sample_db_id: + ir_project_sample_id: type: integer description: > Identifier used internally by the repository to identify an association a project with a sample. - sample_subject_db_id: + ir_sample_subject_id: type: integer description: > Identifier used internally by the repository to identify an association between a sample and a subject. - sample_source_db_id: + ir_sample_source_id: type: integer description: > Identifier used internally by the repository to identify an From 6113a6043e33a56f002b084dc1d4f695eadfa0e5 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 13 Oct 2017 16:15:49 +1300 Subject: [PATCH 09/46] Initial version of an AIRR compliant rearrangement file (MiAIRR). --- MiAIRR_rearrangement.yaml | 73 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 MiAIRR_rearrangement.yaml diff --git a/MiAIRR_rearrangement.yaml b/MiAIRR_rearrangement.yaml new file mode 100644 index 0000000..eeb9289 --- /dev/null +++ b/MiAIRR_rearrangement.yaml @@ -0,0 +1,73 @@ +# +# Schema definitions for AIRR minimal standards objects +# + +# The MiAIRR rearrangements + +Rearrangements: + discriminator: MiAIRR + type: object + properties: + germline_database: + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + type: string + description: | + C region with allele (AIRR) + junction_nt: + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) + + + type: object + properties: + study_id: + type: string + study_title: + type: string + study_description: + type: string + inclusion_exclusion_criteria: + type: string + grants: + type: string + lab_name: + type: string + collected_by: + type: string + submitted_by: + type: string + lab_address: + type: string + pub_ids: + type: string \ No newline at end of file From a4b3cab9d044b4045058f368e3f0bb75fb18b06f Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 13 Oct 2017 16:21:05 +1300 Subject: [PATCH 10/46] Got rid of stray text at the end of the file... Opps... --- MiAIRR_rearrangement.yaml | 25 +------------------------ 1 file changed, 1 insertion(+), 24 deletions(-) diff --git a/MiAIRR_rearrangement.yaml b/MiAIRR_rearrangement.yaml index eeb9289..3bf934c 100644 --- a/MiAIRR_rearrangement.yaml +++ b/MiAIRR_rearrangement.yaml @@ -47,27 +47,4 @@ Rearrangements: type: integer description: | Number of times the sequence has been duplicated in a file (AIRR) - - - type: object - properties: - study_id: - type: string - study_title: - type: string - study_description: - type: string - inclusion_exclusion_criteria: - type: string - grants: - type: string - lab_name: - type: string - collected_by: - type: string - submitted_by: - type: string - lab_address: - type: string - pub_ids: - type: string \ No newline at end of file + \ No newline at end of file From 2cbf5c9256c14e0dbf531a95f2a89ad793d4cc1f Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 13 Oct 2017 16:31:09 +1300 Subject: [PATCH 11/46] Used the external definition of the MiAIRR rearrangements. Defined locally for now, but eventually should use the file from the AIRR git repo. Also cleaned up a bunch of old repo model stuff that is no longer required because of external references... --- iReceptor_Data_Service_API_V2.json | 273 +--------------------------- iReceptor_Data_Service_API_V2.yaml | 277 +---------------------------- 2 files changed, 4 insertions(+), 546 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index c6411f1..9cae71c 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -34,7 +34,7 @@ "items": { "allOf": [ { - "$ref": "#/definitions/airr_sequence_annotation_model" + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/Rearrangements" }, { "$ref": "#/definitions/ireceptor_sequence_annotation_model" @@ -152,67 +152,10 @@ }, "ir_sample_source_id": { "type": "integer", - "description": "Identifier used internally by the repository to identify an association between a sample and a sample source.\n" + "description": "Identifier used internally by the repository to identify an association between a sample and a sample source. \n" } } }, - "airr_sequence_annotation_model": { - "type": "object", - "properties": { - "germline_database": { - "type": "string", - "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" - }, - "cell_index": { - "type": "integer", - "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" - }, - "v_allele": { - "type": "string", - "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" - }, - "d_allele": { - "type": "string", - "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" - }, - "j_allele": { - "type": "string", - "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" - }, - "c_allele": { - "type": "string", - "description": "C region with allele (AIRR) \n" - }, - "junction_nt": { - "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" - }, - "junction_aa": { - "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" - }, - "duplicate_count": { - "type": "integer", - "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" - } - } - }, - "extended_sequence_model": { - "allOf": [ - { - "$ref": "#/definitions/airr_sequence_annotation_model" - }, - { - "type": "object", - "properties": { - "an_extended_model_element": { - "type": "string", - "description": "This does not seem to extend the model, it replaces it!" - } - } - } - ] - }, "ireceptor_sequence_annotation_model": { "type": "object", "properties": { @@ -668,218 +611,6 @@ "description": "e.g. VQuest\n" } } - }, - "summary_model": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sequence_count": { - "type": "integer", - "description": "The number of sequences that match the filter for this sample.\n" - }, - "study_id": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "study_title": { - "type": "string", - "description": "Publication or Protocol Title (e.g. My Study) (AIRR)\n" - }, - "study_type": { - "type": "string", - "description": "Type of project/study (e.g. Cancer) (AIRR)\n" - }, - "inclusion_exclusion_criteria": { - "type": "string", - "description": "Study inclusion/exclusion criteria (AIRR)\n" - }, - "grants": { - "type": "string", - "description": "Grant funding agency (AIRR)\n" - }, - "lab_name": { - "type": "string", - "description": "Lab name (AIRR) \n" - }, - "collected_by": { - "type": "string", - "description": "Contact information (data collection) (AIRR)\n" - }, - "submitted_by": { - "type": "string", - "description": "Contact information (data deposition) (AIRR)\n" - }, - "lab_address": { - "type": "string", - "description": "Lab address (AIRR)\n" - }, - "pubs_ids": { - "type": "string", - "description": "Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR)\n" - }, - "subject_id": { - "type": "string", - "description": "UID assigned by submitter (e.g. SUB856413) (AIRR)\n" - }, - "organism": { - "type": "string", - "description": "Organism-based (human, mouse) or synthetic (AIRR)\n" - }, - "sex": { - "type": "string", - "description": "Sex (e.g. M/F) (AIRR)\n" - }, - "age": { - "type": "string", - "description": "Age - Time duration and unit (e.g. 200 days) (AIRR)\n" - }, - "age_event": { - "type": "string", - "description": "Age event (e.g. Enrollment) (AIRR)\n" - }, - "ancestry_population": { - "type": "string", - "description": "Ancestry population (AIRR)\n" - }, - "ethnicity": { - "type": "string", - "description": "Ethnicity (e.g. Tamil) (AIRR)\n" - }, - "race": { - "type": "string", - "description": "Race (e.g. South Indian) (AIRR)\n" - }, - "species_name": { - "type": "string", - "description": "Species name (e.g. Homo Sapiens) (AIRR)\n" - }, - "strain_name": { - "type": "string", - "description": "Strain name (e.g. C57BL/6J) (AIRR)\n" - }, - "linked_subjects": { - "type": "string", - "description": "Relation to other subjects (SubjectID e.g. SUB1355648) (AIRR)\n" - }, - "link_type": { - "type": "string", - "description": "Relation type (.e.g sister, father, daughter) (AIRR)\n" - }, - "sample_id": { - "type": "string", - "description": "Biological sample ID - UID assigned by submitter (AIRR)\n" - }, - "sample_type": { - "type": "string", - "description": "Sample type (e.g. Tissue, body fluid) (AIRR)\n" - }, - "tissue": { - "type": "string", - "description": "Anatomic site (e.g. spleen) (AIRR)\n" - }, - "disease_state_sample": { - "type": "string", - "description": "Disease state of sample (e.g. tumor vs margin) (AIRR)\n" - }, - "collection_date": { - "type": "string", - "description": "Sample collection time (e.g. 10 days) (AIRR)\n" - }, - "collection_time_event": { - "type": "string", - "description": "Collection time event (T0) (e.g. vaccination, recruitment, etc) (AIRR)\n" - }, - "source_commercial": { - "type": "string", - "description": "Commercial source of sample (e.g. XYZ Pharma) (AIRR)\n" - }, - "cell_subset": { - "type": "string", - "description": "Cell subset (Controlled vocabulary) (AIRR)\n" - }, - "cell_phenotype": { - "type": "string", - "description": "Cell subset phenotype (lab specific description) (AIRR)\n" - }, - "study_group_description": { - "type": "string", - "description": "Study group description (e.g. Case vs. Control) (AIRR)\n" - }, - "library_source": { - "type": "string", - "description": "Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) (AIRR)\n" - }, - "subject_age": { - "type": "integer", - "description": "e.g. 1\n" - }, - "marker_1": { - "type": "string", - "description": "e.g. CR19\n" - }, - "marker_2": { - "type": "string", - "description": "e.g. CR20\n" - }, - "marker_3": { - "type": "string", - "description": "e.g. CR21\n" - }, - "marker_4": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_5": { - "type": "string", - "description": "e.g. null\n" - }, - "marker_6": { - "type": "string", - "description": "e.g. null\n" - }, - "subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a subject.\n" - }, - "project_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a project.\n" - }, - "project_parent_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a parent/child relationship between this project and its parent project.\n" - }, - "lab_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a lab.\n" - }, - "case_control_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" - }, - "sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a sample.\n" - }, - "dna_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a DNA type.\n" - }, - "project_sample_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association a project with a sample.\n" - }, - "sample_subject_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association between a sample and a subject.\n" - }, - "sample_source_db_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association between a sample and a sample source.\n" - } - } - } } }, "schemes": [ diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index fc0e60a..c2c9e46 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -30,7 +30,7 @@ definitions: type: array items: allOf: - - $ref: '#/definitions/airr_sequence_annotation_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/Rearrangements' - $ref: '#/definitions/ireceptor_sequence_annotation_model' # The AIRR Minimal Standards model for metadata above the sequence annotation level. airr_summary_model: @@ -138,57 +138,7 @@ definitions: type: integer description: > Identifier used internally by the repository to identify an - association between a sample and a sample source. - airr_sequence_annotation_model: - type: object - properties: - germline_database: - type: string - description: > - Source of germline V(D)J segments, with version number or - date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) - cell_index: - type: integer - description: | - Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - type: string - description: | - V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - type: string - description: | - D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - type: string - description: | - J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - type: string - description: | - C region with allele (AIRR) - junction_nt: - type: string - description: > - JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) - junction_aa: - type: string - description: > - JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) - duplicate_count: - type: integer - description: | - Number of times the sequence has been duplicated in a file (AIRR) - extended_sequence_model: - allOf: - - $ref: '#/definitions/airr_sequence_annotation_model' - - type: object - properties: - an_extended_model_element: - type: string - description: This does not seem to extend the model, it replaces it! + association between a sample and a sample source. ireceptor_sequence_annotation_model: type: object properties: @@ -646,229 +596,6 @@ definitions: type: string description: | e.g. VQuest - summary_model: - type: array - items: - type: object - properties: - sequence_count: - type: integer - description: > - The number of sequences that match the filter for this - sample. - study_id: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - study_title: - type: string - description: | - Publication or Protocol Title (e.g. My Study) (AIRR) - study_type: - type: string - description: | - Type of project/study (e.g. Cancer) (AIRR) - inclusion_exclusion_criteria: - type: string - description: | - Study inclusion/exclusion criteria (AIRR) - grants: - type: string - description: | - Grant funding agency (AIRR) - lab_name: - type: string - description: | - Lab name (AIRR) - collected_by: - type: string - description: | - Contact information (data collection) (AIRR) - submitted_by: - type: string - description: | - Contact information (data deposition) (AIRR) - lab_address: - type: string - description: | - Lab address (AIRR) - pubs_ids: - type: string - description: | - Alphanumeric UID assigned by NCBI (e.g. PRJNA349) (AIRR) - subject_id: - type: string - description: "UID assigned by submitter (e.g.\_SUB856413) (AIRR)\n" - organism: - type: string - description: | - Organism-based (human, mouse) or synthetic (AIRR) - sex: - type: string - description: | - Sex (e.g. M/F) (AIRR) - age: - type: string - description: | - Age - Time duration and unit (e.g. 200 days) (AIRR) - age_event: - type: string - description: | - Age event (e.g. Enrollment) (AIRR) - ancestry_population: - type: string - description: | - Ancestry population (AIRR) - ethnicity: - type: string - description: | - Ethnicity (e.g. Tamil) (AIRR) - race: - type: string - description: | - Race (e.g. South Indian) (AIRR) - species_name: - type: string - description: | - Species name (e.g. Homo Sapiens) (AIRR) - strain_name: - type: string - description: | - Strain name (e.g. C57BL/6J) (AIRR) - linked_subjects: - type: string - description: > - Relation to other subjects (SubjectID e.g. SUB1355648) - (AIRR) - link_type: - type: string - description: | - Relation type (.e.g sister, father, daughter) (AIRR) - sample_id: - type: string - description: | - Biological sample ID - UID assigned by submitter (AIRR) - sample_type: - type: string - description: | - Sample type (e.g. Tissue, body fluid) (AIRR) - tissue: - type: string - description: | - Anatomic site (e.g. spleen) (AIRR) - disease_state_sample: - type: string - description: | - Disease state of sample (e.g. tumor vs margin) (AIRR) - collection_date: - type: string - description: | - Sample collection time (e.g. 10 days) (AIRR) - collection_time_event: - type: string - description: > - Collection time event (T0) (e.g. vaccination, recruitment, - etc) (AIRR) - source_commercial: - type: string - description: | - Commercial source of sample (e.g. XYZ Pharma) (AIRR) - cell_subset: - type: string - description: | - Cell subset (Controlled vocabulary) (AIRR) - cell_phenotype: - type: string - description: | - Cell subset phenotype (lab specific description) (AIRR) - study_group_description: - type: string - description: | - Study group description (e.g. Case vs. Control) (AIRR) - library_source: - type: string - description: > - Target substrate (Controlled vocabulary e.g. cDNA/gDNA/RNA) - (AIRR) - subject_age: - type: integer - description: | - e.g. 1 - marker_1: - type: string - description: | - e.g. CR19 - marker_2: - type: string - description: | - e.g. CR20 - marker_3: - type: string - description: | - e.g. CR21 - marker_4: - type: string - description: | - e.g. null - marker_5: - type: string - description: | - e.g. null - marker_6: - type: string - description: | - e.g. null - subject_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - subject. - project_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - project. - project_parent_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - parent/child - relationship between this project and its parent project. - lab_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - lab. - case_control_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - element in the case_control table. - sample_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - sample. - dna_db_id: - type: integer - description: > - Identifier used internally by the repository to identify a - DNA type. - project_sample_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association a project with a sample. - sample_subject_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association between a sample and a subject. - sample_source_db_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association between a sample and a sample source. schemes: - https produces: From d6b1dbd46d9ae517c6658c1f227eb9c33d9f7be7 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Mon, 16 Oct 2017 12:52:14 +1300 Subject: [PATCH 12/46] Consistency fixes so they V1 API elements are all in the V2 API with IR_ prefixes. --- iReceptor_Data_Service_API_V2.json | 12 ++++++++---- iReceptor_Data_Service_API_V2.yaml | 14 +++++++++----- 2 files changed, 17 insertions(+), 9 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 9cae71c..66aab22 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -88,7 +88,7 @@ }, "ir_sra_run_id": { "type": "string", - "description": "" + "description": "e.g. SRR4102110\n" }, "ir_marker_1": { "type": "string", @@ -114,9 +114,9 @@ "type": "string", "description": "e.g. null\n" }, - "ir_subject_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a subject.\n" + "ir_project_sample_note": { + "type": "string", + "description": "A note about the sample.\n" }, "ir_project_id": { "type": "integer", @@ -130,6 +130,10 @@ "type": "integer", "description": "Identifier used internally by the repository to identify a lab.\n" }, + "ir_disease_state_id": { + "type": "integer", + "description": "Identifier used internally by the repository to identify a an element in the disease state table.\n" + }, "ir_case_control_id": { "type": "integer", "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index c2c9e46..f525c48 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -63,7 +63,7 @@ definitions: ir_sra_run_id: type: string description: | - + e.g. SRR4102110 ir_marker_1: type: string description: | @@ -88,11 +88,10 @@ definitions: type: string description: | e.g. null - ir_subject_id: - type: integer + ir_project_sample_note: + type: string description: > - Identifier used internally by the repository to identify a - subject. + A note about the sample. ir_project_id: type: integer description: > @@ -109,6 +108,11 @@ definitions: description: > Identifier used internally by the repository to identify a lab. + ir_disease_state_id: + type: integer + description: > + Identifier used internally by the repository to identify a + an element in the disease state table. ir_case_control_id: type: integer description: > From 888f5b8c060d06a3745e82eabbf70c7f4e941806 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 12:20:50 +1300 Subject: [PATCH 13/46] Added object definitions for the Formats rearrangements... --- Formats_rearrangement.yaml | 132 +++++++++++++++++++++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 Formats_rearrangement.yaml diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml new file mode 100644 index 0000000..70ea9c8 --- /dev/null +++ b/Formats_rearrangement.yaml @@ -0,0 +1,132 @@ +# +# Schema definitions for AIRR Formats rearrangement objects +# + +# The Formats rearrangements +# Note: This is an extension of the MiAIRR rearrangements, and assumes that +# the MiAIRR has defined the MiAIRR rearrangement objects. + +Formats_Rearrangements: + discriminator: AIRRFormats + type: object + required: + - sequence_id + - sequence + - sample_id + - constant + - functional + - rev_comp + - v_score + - d_score + - j_score + - v_cigar + - d_cigar + - j_cigar + properties: + sequence_id: + type: string + description: Read/sequence identifier + sequence: + type: string + description: Nucleotide sequence (e.g., the "read" sequence; revcomp'd if + necessary) + sample_id: + type: string + description: The biological sample this read derives from (e.g., from BioSample + database) + constant: + type: string + description: Constant region gene (e.g., IGHG4, IGHA2, IGHE, TRBC) + functional: + type: boolean + description: VDJ sequence is predicted to be functional + rev_comp: + type: boolean + description: Sequence is reverse complemented + v_score: + type: float + description: V alignment score + d_score: + type: float + description: D alignment score + j_score: + type: float + description: J alignment score + v_cigar: + type: string + description: V alignment CIGAR string + d_cigar: + type: string + description: D alignment CIGAR string + j_cigar: + type: string + description: J alignment CIGAR string + v_evalue: + type: float + description: V alignment E-value (when applicable) + d_evalue: + type: float + description: D alignment E-value (when applicable) + j_evalue: + type: float + description: J alignment E-value (when applicable) + v_identity: + type: float + description: V alignment identity + d_identity: + type: float + description: D alignment identity + j_identity: + type: float + description: J alignment identity + vdj_score: + type: float + description: Score for aligners that consider the full sequence as a whole + vdj_evalue: + type: float + description: E-value for aligners that consider the full sequence as a whole + vdj_identity: + type: float + description: Identity for aligners that consider the full sequence as a whole + fwr1_start: + type: integer + description: FWR1 start coordinate in sequence (transferred from germline) + cdr1_start: + type: integer + description: CDR1 start coord in sequence (transferred from germline) + fwr2_start: + type: integer + description: FWR2 start coord in sequence (transferred from germline) + cdr2_start: + type: integer + description: CDR2 start coord in sequence (transferred from germline) + fwr3_start: + type: integer + description: FWR3 start coord in sequence (transferred from germline) + cdr3_start: + type: integer + description: CDR3 start coord in sequence (transferred from germline) + v_end: + type: integer + description: End coordinate of the V segment (generally inside the CDR3) + d_start: + type: integer + description: Start coordinate of the D segment + d_end: + type: integer + description: End coordinate of the D segment + j_start: + type: integer + description: Start coordinate of the J segment (generally inside the CDR3) + cdr3_end: + type: integer + description: CDR3 end coord in sequence (transferred from germline) + fwr4_end: + type: integer + description: FWR4 end coord in sequence (transferred from germline) + duplicate_count: + type: integer + description: Number of duplicate reads for this sequence + clone: + type: string + description: Clone assignment for this sequence From 51043fbb1c048d05d3f56a24d4544a4601694646 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 12:23:10 +1300 Subject: [PATCH 14/46] Renamed object to MiAIRR_Rearrangements to differentiate it from Formats_Rearrangements. --- MiAIRR_rearrangement.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/MiAIRR_rearrangement.yaml b/MiAIRR_rearrangement.yaml index 3bf934c..c24fa6b 100644 --- a/MiAIRR_rearrangement.yaml +++ b/MiAIRR_rearrangement.yaml @@ -1,10 +1,10 @@ # -# Schema definitions for AIRR minimal standards objects +# Schema definitions for AIRR minimal standards rearrangement objects # # The MiAIRR rearrangements -Rearrangements: +MiAIRR_Rearrangements: discriminator: MiAIRR type: object properties: From 026e1ce666c457e653b7b89b7effe946f23ce42e Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 12:50:35 +1300 Subject: [PATCH 15/46] Used the external definition Formats_rearrangements.yaml to define the Formats part of the sequences API response. --- iReceptor_Data_Service_API_V2.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index f525c48..cdbf52a 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -26,11 +26,17 @@ definitions: - $ref: '#/definitions/ireceptor_sequence_count_model' - $ref: '#/definitions/airr_summary_model' - $ref: '#/definitions/ireceptor_summary_model' + # A definition of the sequence response for an iReceptor API call. This + # response is used wherever sequence data is provided by an API call. + # It is a composite of the sequence fields defined by the MiAIRR standard, + # the sequence fields defined by the AIRR Formats working group, and any + # ancillary fields defined by iReceptor. ireceptor_sequence_response: type: array items: allOf: - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/Rearrangements' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements' - $ref: '#/definitions/ireceptor_sequence_annotation_model' # The AIRR Minimal Standards model for metadata above the sequence annotation level. airr_summary_model: From ce78e58e87e30e888a9da69a00e91afc6d830ced Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 12:50:35 +1300 Subject: [PATCH 16/46] Used the external definition Formats_rearrangements.yaml to define the Formats part of the sequences API response. --- iReceptor_Data_Service_API_V2.json | 5 ++++- iReceptor_Data_Service_API_V2.yaml | 8 +++++++- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 66aab22..7d28d0a 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -34,7 +34,10 @@ "items": { "allOf": [ { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/Rearrangements" + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" + }, + { + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements" }, { "$ref": "#/definitions/ireceptor_sequence_annotation_model" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index f525c48..cdbf52a 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -26,11 +26,17 @@ definitions: - $ref: '#/definitions/ireceptor_sequence_count_model' - $ref: '#/definitions/airr_summary_model' - $ref: '#/definitions/ireceptor_summary_model' + # A definition of the sequence response for an iReceptor API call. This + # response is used wherever sequence data is provided by an API call. + # It is a composite of the sequence fields defined by the MiAIRR standard, + # the sequence fields defined by the AIRR Formats working group, and any + # ancillary fields defined by iReceptor. ireceptor_sequence_response: type: array items: allOf: - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/Rearrangements' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements' - $ref: '#/definitions/ireceptor_sequence_annotation_model' # The AIRR Minimal Standards model for metadata above the sequence annotation level. airr_summary_model: From c4a663230c9f49c6c6bfbad58f4413c4d75e310f Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 13:01:13 +1300 Subject: [PATCH 17/46] Removed the required fields for now, don't want to limit testing the spec with required fields. --- Formats_rearrangement.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml index 70ea9c8..7da06f8 100644 --- a/Formats_rearrangement.yaml +++ b/Formats_rearrangement.yaml @@ -9,19 +9,19 @@ Formats_Rearrangements: discriminator: AIRRFormats type: object - required: - - sequence_id - - sequence - - sample_id - - constant - - functional - - rev_comp - - v_score - - d_score - - j_score - - v_cigar - - d_cigar - - j_cigar +# required: +# - sequence_id +# - sequence +# - sample_id +# - constant +# - functional +# - rev_comp +# - v_score +# - d_score +# - j_score +# - v_cigar +# - d_cigar +# - j_cigar properties: sequence_id: type: string From 24a913f99eab8fe20dd29f06e410ae7eb00881ee Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 13:06:00 +1300 Subject: [PATCH 18/46] Moved the comment out of the body to remove confusion. --- Formats_rearrangement.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml index 7da06f8..32f38f9 100644 --- a/Formats_rearrangement.yaml +++ b/Formats_rearrangement.yaml @@ -5,10 +5,6 @@ # The Formats rearrangements # Note: This is an extension of the MiAIRR rearrangements, and assumes that # the MiAIRR has defined the MiAIRR rearrangement objects. - -Formats_Rearrangements: - discriminator: AIRRFormats - type: object # required: # - sequence_id # - sequence @@ -22,6 +18,10 @@ Formats_Rearrangements: # - v_cigar # - d_cigar # - j_cigar + +Formats_Rearrangements: + discriminator: AIRRFormats + type: object properties: sequence_id: type: string From 3450a7109bb9f2d29c6c66a6f7adfb956022bf4c Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 13:35:15 +1300 Subject: [PATCH 19/46] Cleaned up the formats fields so they map to their Master branch specs/rearrangements.yaml --- Formats_rearrangement.yaml | 84 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 80 insertions(+), 4 deletions(-) diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml index 32f38f9..ddea8d6 100644 --- a/Formats_rearrangement.yaml +++ b/Formats_rearrangement.yaml @@ -12,12 +12,16 @@ # - constant # - functional # - rev_comp +# - c_call # - v_score # - d_score # - j_score +# - c_score # - v_cigar # - d_cigar # - j_cigar +# - c_cigar + Formats_Rearrangements: discriminator: AIRRFormats @@ -43,6 +47,9 @@ Formats_Rearrangements: rev_comp: type: boolean description: Sequence is reverse complemented + c_call: + type: string + description: C gene assignment v_score: type: float description: V alignment score @@ -52,6 +59,9 @@ Formats_Rearrangements: j_score: type: float description: J alignment score + c_score: + type: float + description: C alignment score v_cigar: type: string description: V alignment CIGAR string @@ -61,6 +71,9 @@ Formats_Rearrangements: j_cigar: type: string description: J alignment CIGAR string + c_cigar: + type: string + description: C alignment CIGAR string v_evalue: type: float description: V alignment E-value (when applicable) @@ -88,45 +101,108 @@ Formats_Rearrangements: vdj_identity: type: float description: Identity for aligners that consider the full sequence as a whole + v_start: + type: integer + description: Position of first V nucleotide in 'sequence' field + v_germ_start: + type: integer + description: Position of 'v_start' field in IMGT numbered germline V(D)J sequence fwr1_start: type: integer description: FWR1 start coordinate in sequence (transferred from germline) + fwr1_end: + type: integer + description: FWR1 end coordinate in sequence (transferred from germline) cdr1_start: type: integer description: CDR1 start coord in sequence (transferred from germline) + cdr1_end: + type: integer + description: CDR1 end coord in sequence (transferred from germline) fwr2_start: type: integer description: FWR2 start coord in sequence (transferred from germline) + fwr2_end: + type: integer + description: FWR2 end coord in sequence (transferred from germline) cdr2_start: type: integer description: CDR2 start coord in sequence (transferred from germline) + cdr2_end: + type: integer + description: CDR2 end coord in sequence (transferred from germline) fwr3_start: type: integer description: FWR3 start coord in sequence (transferred from germline) + fwr3_end: + type: integer + description: FWR3 end coord in sequence (transferred from germline) cdr3_start: type: integer description: CDR3 start coord in sequence (transferred from germline) + cdr3_end: + type: integer + description: CDR3 end coord in sequence (transferred from germline) + fwr4_start: + type: integer + description: FWR3 start coord in sequence (transferred from germline) + fwr4_end: + type: integer + description: FWR4 end coord in sequence (transferred from germline) v_end: type: integer description: End coordinate of the V segment (generally inside the CDR3) d_start: type: integer description: Start coordinate of the D segment + d_germ_start: + type: integer + description: Position of 'd_start' field in IMGT numbered germline V(D)J sequence d_end: type: integer description: End coordinate of the D segment j_start: type: integer description: Start coordinate of the J segment (generally inside the CDR3) - cdr3_end: + j_germ_start: type: integer - description: CDR3 end coord in sequence (transferred from germline) - fwr4_end: + description: Position of 'j_start' field in IMGT numbered germline V(D)J sequence + j_end: type: integer - description: FWR4 end coord in sequence (transferred from germline) + description: End coordinate of the J segment + junction_length: + type: integer + description: Number of junction nucleotides in sequence_vdj + np1_length: + type: integer + description: Number of of nucleotides between sample V and D sequences + np2_length: + type: integer + description: Number of of nucleotides between sample D and J sequences + n1_length: + type: integer + description: Nucleotides 5' of the D-segment + n2_length: + type: integer + description: Nucleotides 3' of the D-segment + p3v_length: + type: integer + description: Palindromic nucleotides 3' of the V-segment + p5d_length: + type: integer + description: Palindromic nucleotides 5' of the D-segment + p3d_length: + type: integer + description: Palindromic nucleotides 3' of the D-segment + p5j_length: + type: integer + description: Palindromic nucleotides 5' of the J-segment duplicate_count: type: integer description: Number of duplicate reads for this sequence + consensus_count: + type: integer + description: Number of reads contributing to the consensus for this sequence clone: type: string description: Clone assignment for this sequence From 49a9bd08ab6e4f843bd177c737db42651f16c616 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 13:53:38 +1300 Subject: [PATCH 20/46] Darn, missed one parameter... Fixed... --- Formats_rearrangement.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml index ddea8d6..009b5fb 100644 --- a/Formats_rearrangement.yaml +++ b/Formats_rearrangement.yaml @@ -101,6 +101,9 @@ Formats_Rearrangements: vdj_identity: type: float description: Identity for aligners that consider the full sequence as a whole + vdj_cigar: + type: string + description: VDJ alignment CIGAR string v_start: type: integer description: Position of first V nucleotide in 'sequence' field From a8ab125012cf5b1f2a4ae4ee7a10a5f4c524dea6 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 14:45:46 +1300 Subject: [PATCH 21/46] Added external files to define the iReceptor specific models. All models are now in external files, making the spec relatively clean from the model/response perspective. --- iReceptor_Data_Service_API_V2.yaml | 556 +---------------------------- ireceptor_sequence.yaml | 460 ++++++++++++++++++++++++ ireceptor_summary.yaml | 93 +++++ 3 files changed, 557 insertions(+), 552 deletions(-) create mode 100644 ireceptor_sequence.yaml create mode 100644 ireceptor_summary.yaml diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index cdbf52a..808d0b8 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -18,14 +18,15 @@ basePath: /v2 definitions: # A definition of the summary response for an iReceptor API call. This # response is used wherever summary data at the sample level is provided - # by an API call. + # by an API call. It is composed of the sequence count, the relevant AIRR + # model elements, and the revelant iReceptor model elements. ireceptor_summary_response: type: array items: allOf: - $ref: '#/definitions/ireceptor_sequence_count_model' - $ref: '#/definitions/airr_summary_model' - - $ref: '#/definitions/ireceptor_summary_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequences.yaml#/ireceptor_summary_model' # A definition of the sequence response for an iReceptor API call. This # response is used wherever sequence data is provided by an API call. # It is a composite of the sequence fields defined by the MiAIRR standard, @@ -37,7 +38,7 @@ definitions: allOf: - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements' - - $ref: '#/definitions/ireceptor_sequence_annotation_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequences.yaml#/ireceptor_sequence_annotation_model' # The AIRR Minimal Standards model for metadata above the sequence annotation level. airr_summary_model: allOf: @@ -57,555 +58,6 @@ definitions: sequence_count: type: integer example: 123456 - # This model defines ancillary information returned by iReceptor - # on top of that provided by the AIRR standard. - ireceptor_summary_model: - type: object - properties: - ir_subject_age: - type: integer - description: | - e.g. 1 - ir_sra_run_id: - type: string - description: | - e.g. SRR4102110 - ir_marker_1: - type: string - description: | - e.g. CR19 - ir_marker_2: - type: string - description: | - e.g. CR20 - ir_marker_3: - type: string - description: | - e.g. CR21 - ir_marker_4: - type: string - description: | - e.g. null - ir_marker_5: - type: string - description: | - e.g. null - ir_marker_6: - type: string - description: | - e.g. null - ir_project_sample_note: - type: string - description: > - A note about the sample. - ir_project_id: - type: integer - description: > - Identifier used internally by the repository to identify a - project. - ir_project_parent_id: - type: integer - description: > - Identifier used internally by the repository to identify a - parent/child - relationship between this project and its parent project. - ir_lab_id: - type: integer - description: > - Identifier used internally by the repository to identify a - lab. - ir_disease_state_id: - type: integer - description: > - Identifier used internally by the repository to identify a - an element in the disease state table. - ir_case_control_id: - type: integer - description: > - Identifier used internally by the repository to identify an - element in the case_control table. - ir_sample_id: - type: integer - description: > - Identifier used internally by the repository to identify a - sample. - ir_dna_id: - type: integer - description: > - Identifier used internally by the repository to identify a - DNA type. - ir_project_sample_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association a project with a sample. - ir_sample_subject_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association between a sample and a subject. - ir_sample_source_id: - type: integer - description: > - Identifier used internally by the repository to identify an - association between a sample and a sample source. - ireceptor_sequence_annotation_model: - type: object - properties: - seq_id: - type: integer - description: | - e.g. 1 - seq_name: - type: string - project_sample_id: - type: integer - description: | - e.g. 6 - id: - type: integer - description: | - e.g. 1 - sequence_id: - type: integer - description: | - e.g. 1 - vgene_string: - type: string - description: | - e.g IGHV4-59*01 or IGHV4-59*07 - vgene_family: - type: string - description: | - e.g. IGHV4 - vgene_gene: - type: string - description: | - e.g. IGHV4-59 - dgene_string: - type: string - description: | - e.g. Homsap IGHD3-10*01 F - dgene_family: - type: string - description: | - e.g. IGHD3 - dgene_gene: - type: string - description: | - e.g. IGHD3-10 - jgene_string: - type: string - description: | - e.g. Homsap IGHJ4*02 F - jgene_family: - type: string - description: | - e.g. IGHJ4 - jgene_gene: - type: string - description: | - e.g. IGHJ4 - functionality: - type: string - description: | - e.g. productive - functionality_comment: - type: string - description: | - e.g. "" - orientation: - type: string - description: | - e.g. + - vgene_score: - type: integer - description: | - e.g. 1127 - vgene_probability: - type: integer - description: | - e.g. 95 - dregion_reading_frame: - type: integer - description: | - e.g. 2 - cdr1_length: - type: integer - description: | - e.g. 8 - cdr2_length: - type: integer - description: | - e.g. 7 - cdr3_length: - type: integer - description: | - e.g. 13 - vdjregion_sequence_nt: - type: string - description: | - vdj region nucleotide sequence - vjregion_sequence_nt: - type: string - description: | - vj region nucleotide sequence - djregion_sequence_nt: - type: string - description: | - dj region nucleotide sequence - vregion_sequence_nt: - type: string - description: | - v region nucleotide sequence - dregion_sequence_nt: - type: string - description: | - d region nucleotide sequence - jregion_sequence_nt: - type: string - description: | - j region nucleotide sequence - fr1region_sequence_nt: - type: string - description: | - fr1 region nucleotide sequence - fr2region_sequence_nt: - type: string - description: | - fr2 region nucleotide sequence - fr3region_sequence_nt: - type: string - description: | - fr3 region nucleotide sequence - fr4region_sequence_nt: - type: string - description: | - fr4 region nucleotide sequence - cdr1region_sequence_nt: - type: string - description: | - cdr1 region nucleotide sequence - cdr2region_sequence_nt: - type: string - description: | - cdr2 region nucleotide sequence - cdr3region_sequence_nt: - type: string - description: | - cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: - type: string - description: | - gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: - type: string - description: | - gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: - type: string - description: | - gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: - type: string - description: | - gapped v region nucleotide sequence - dregion_sequence_nt_gapped: - type: string - description: | - gapped d region nucleotide sequence - jregion_sequence_nt_gapped: - type: string - description: | - gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: - type: string - description: | - gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: - type: string - description: | - gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: - type: string - description: | - gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: - type: string - description: | - gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: - type: string - description: | - gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: - type: string - description: | - gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: - type: string - description: | - gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: - type: string - description: | - gapped junction nucleotide sequence - vdjregion_sequence_aa: - type: string - description: | - vdj region amino acid sequence - vjregion_sequence_aa: - type: string - description: | - vj region amino acid sequence - djregion_sequence_aa: - type: string - description: | - dj region amino acid sequence - vregion_sequence_aa: - type: string - description: | - v region amino acid sequence - dregion_sequence_aa: - type: string - description: | - d region amino acid sequence - jregion_sequence_aa: - type: string - description: | - j region amino acid sequence - fr1region_sequence_aa: - type: string - description: | - fr1 region amino acid sequence - fr2region_sequence_aa: - type: string - description: | - fr2 region amino acid sequence - fr3region_sequence_aa: - type: string - description: | - fr3 region amino acid sequence - fr4region_sequence_aa: - type: string - description: | - fr4 region amino acid sequence - cdr1region_sequence_aa: - type: string - description: | - cdr1 region amino acid sequence - cdr2region_sequence_aa: - type: string - description: | - cdr2 region amino acid sequence - cdr3region_sequence_aa: - type: string - description: | - cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: - type: string - description: | - gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: - type: string - description: | - gapped vj region amino acid sequence - djregion_sequence_aa_gapped: - type: string - description: | - gapped dj region amino acid sequence - vregion_sequence_aa_gapped: - type: string - description: | - gapped v region amino acid sequence - dregion_sequence_aa_gapped: - type: string - description: | - gapped d region amino acid sequence - jregion_sequence_aa_gapped: - type: string - description: | - gapped j region amino acid sequence - fr1region_sequence_aa_gapped: - type: string - description: | - gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: - type: string - description: | - gapped fr2 region amino acid sequence - fr3region_sequence_aa_gapped: - type: string - description: | - gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: - type: string - description: | - gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: - type: string - description: | - gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: - type: string - description: | - gapped cdr2 region amino acid sequence - cdr3region_sequence_aa_gapped: - type: string - description: | - gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: - type: string - description: | - gapped junction amino acid sequence - vdjregion_start: - type: integer - description: | - e.g. 1 - vdjregion_end: - type: integer - description: | - e.g. 321 - vjregion_start: - type: integer - description: | - e.g. 0 - vjregion_end: - type: integer - description: | - e.g. 0 - djregion_start: - type: integer - description: | - e.g. 254 - djregion_end: - type: integer - description: | - e.g. 321 - vregion_start: - type: integer - description: | - e.g. 286 - vregion_end: - type: integer - description: | - e.g. 252 - dregion_start: - type: integer - description: | - e.g. 254 - dregion_end: - type: integer - description: | - e.g. 321 - jregion_start: - type: integer - description: | - e.g. 286 - jregion_end: - type: integer - description: | - e.g. 321 - fr1region_start: - type: integer - description: | - e.g. 1 - fr1region_end: - type: integer - description: | - e.g. 38 - fr2region_start: - type: integer - description: | - e.g. 63 - fr2region_end: - type: integer - description: | - e.g. 113 - fr3region_start: - type: integer - description: | - e.g. 135 - fr3region_end: - type: integer - description: | - e.g. 248 - fr4region_start: - type: integer - description: | - e.g. 288 - fr4region_end: - type: integer - description: | - e.g. 321 - cdr1region_start: - type: integer - description: | - e.g. 39 - cdr1region_end: - type: integer - description: | - e.g. 321 - cdr2region_start: - type: integer - description: | - e.g. 62 - cdr2region_end: - type: integer - description: | - e.g. 134 - cdr3region_start: - type: integer - description: | - e.g. 249 - cdr3region_end: - type: integer - description: | - e.g. 287 - junction_start: - type: integer - description: | - e.g. 246 - junction_end: - type: integer - description: | - e.g. 290 - vregion_mutation_string: - type: string - description: > - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: - type: string - description: | - e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr2region_mutation_string: - type: string - description: | - e.g. - fr3region_mutation_string: - type: string - description: > - e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + - -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr1region_mutation_string: - type: string - description: | - e.g. - cdr2region_mutation_string: - type: string - description: | - e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: - type: string - description: | - e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - annotation_tool: - type: string - description: | - e.g. VQuest schemes: - https produces: diff --git a/ireceptor_sequence.yaml b/ireceptor_sequence.yaml new file mode 100644 index 0000000..1d8fcd2 --- /dev/null +++ b/ireceptor_sequence.yaml @@ -0,0 +1,460 @@ +# This model defines ancillary information returned by iReceptor +# as part of the sequence API. + + ireceptor_sequence_annotation_model: + type: object + properties: + seq_id: + type: integer + description: | + e.g. 1 + seq_name: + type: string + project_sample_id: + type: integer + description: | + e.g. 6 + id: + type: integer + description: | + e.g. 1 + sequence_id: + type: integer + description: | + e.g. 1 + vgene_string: + type: string + description: | + e.g IGHV4-59*01 or IGHV4-59*07 + vgene_family: + type: string + description: | + e.g. IGHV4 + vgene_gene: + type: string + description: | + e.g. IGHV4-59 + dgene_string: + type: string + description: | + e.g. Homsap IGHD3-10*01 F + dgene_family: + type: string + description: | + e.g. IGHD3 + dgene_gene: + type: string + description: | + e.g. IGHD3-10 + jgene_string: + type: string + description: | + e.g. Homsap IGHJ4*02 F + jgene_family: + type: string + description: | + e.g. IGHJ4 + jgene_gene: + type: string + description: | + e.g. IGHJ4 + functionality: + type: string + description: | + e.g. productive + functionality_comment: + type: string + description: | + e.g. "" + orientation: + type: string + description: | + e.g. + + vgene_score: + type: integer + description: | + e.g. 1127 + vgene_probability: + type: integer + description: | + e.g. 95 + dregion_reading_frame: + type: integer + description: | + e.g. 2 + cdr1_length: + type: integer + description: | + e.g. 8 + cdr2_length: + type: integer + description: | + e.g. 7 + cdr3_length: + type: integer + description: | + e.g. 13 + vdjregion_sequence_nt: + type: string + description: | + vdj region nucleotide sequence + vjregion_sequence_nt: + type: string + description: | + vj region nucleotide sequence + djregion_sequence_nt: + type: string + description: | + dj region nucleotide sequence + vregion_sequence_nt: + type: string + description: | + v region nucleotide sequence + dregion_sequence_nt: + type: string + description: | + d region nucleotide sequence + jregion_sequence_nt: + type: string + description: | + j region nucleotide sequence + fr1region_sequence_nt: + type: string + description: | + fr1 region nucleotide sequence + fr2region_sequence_nt: + type: string + description: | + fr2 region nucleotide sequence + fr3region_sequence_nt: + type: string + description: | + fr3 region nucleotide sequence + fr4region_sequence_nt: + type: string + description: | + fr4 region nucleotide sequence + cdr1region_sequence_nt: + type: string + description: | + cdr1 region nucleotide sequence + cdr2region_sequence_nt: + type: string + description: | + cdr2 region nucleotide sequence + cdr3region_sequence_nt: + type: string + description: | + cdr3 region nucleotide sequence + vdjregion_sequence_nt_gapped: + type: string + description: | + gapped vdj region nucleotide sequence + vjregion_sequence_nt_gapped: + type: string + description: | + gapped vj region nucleotide sequence + djregion_sequence_nt_gapped: + type: string + description: | + gapped dj region nucleotide sequence + vregion_sequence_nt_gapped: + type: string + description: | + gapped v region nucleotide sequence + dregion_sequence_nt_gapped: + type: string + description: | + gapped d region nucleotide sequence + jregion_sequence_nt_gapped: + type: string + description: | + gapped j region nucleotide sequence + fr1region_sequence_nt_gapped: + type: string + description: | + gapped fr1 region nucleotide sequence + fr2region_sequence_nt_gapped: + type: string + description: | + gapped fr2 region nucleotide sequence + fr3region_sequence_nt_gapped: + type: string + description: | + gapped fr3 region nucleotide sequence + fr4region_sequence_nt_gapped: + type: string + description: | + gapped fr4 region nucleotide sequence + cdr1region_sequence_nt_gapped: + type: string + description: | + gapped cdr1 region nucleotide sequence + cdr2region_sequence_nt_gapped: + type: string + description: | + gapped cdr2 region nucleotide sequence + cdr3region_sequence_nt_gapped: + type: string + description: | + gapped cdr3 region nucleotide sequence + junction_sequence_nt_gapped: + type: string + description: | + gapped junction nucleotide sequence + vdjregion_sequence_aa: + type: string + description: | + vdj region amino acid sequence + vjregion_sequence_aa: + type: string + description: | + vj region amino acid sequence + djregion_sequence_aa: + type: string + description: | + dj region amino acid sequence + vregion_sequence_aa: + type: string + description: | + v region amino acid sequence + dregion_sequence_aa: + type: string + description: | + d region amino acid sequence + jregion_sequence_aa: + type: string + description: | + j region amino acid sequence + fr1region_sequence_aa: + type: string + description: | + fr1 region amino acid sequence + fr2region_sequence_aa: + type: string + description: | + fr2 region amino acid sequence + fr3region_sequence_aa: + type: string + description: | + fr3 region amino acid sequence + fr4region_sequence_aa: + type: string + description: | + fr4 region amino acid sequence + cdr1region_sequence_aa: + type: string + description: | + cdr1 region amino acid sequence + cdr2region_sequence_aa: + type: string + description: | + cdr2 region amino acid sequence + cdr3region_sequence_aa: + type: string + description: | + cdr3 region amino acid sequence + vdjregion_sequence_aa_gapped: + type: string + description: | + gapped vdj region amino acid sequence + vjregion_sequence_aa_gapped: + type: string + description: | + gapped vj region amino acid sequence + djregion_sequence_aa_gapped: + type: string + description: | + gapped dj region amino acid sequence + vregion_sequence_aa_gapped: + type: string + description: | + gapped v region amino acid sequence + dregion_sequence_aa_gapped: + type: string + description: | + gapped d region amino acid sequence + jregion_sequence_aa_gapped: + type: string + description: | + gapped j region amino acid sequence + fr1region_sequence_aa_gapped: + type: string + description: | + gapped fr1 region amino acid sequence + fr2region_sequence_aa_gapped: + type: string + description: | + gapped fr2 region amino acid sequence + fr3region_sequence_aa_gapped: + type: string + description: | + gapped fr3 region amino acid sequence + fr4region_sequence_aa_gapped: + type: string + description: | + gapped fr4 region amino acid sequence + cdr1region_sequence_aa_gapped: + type: string + description: | + gapped cdr1 region amino acid sequence + cdr2region_sequence_aa_gapped: + type: string + description: | + gapped cdr2 region amino acid sequence + cdr3region_sequence_aa_gapped: + type: string + description: | + gapped cdr3 region amino acid sequence + junction_sequence_aa_gapped: + type: string + description: | + gapped junction amino acid sequence + vdjregion_start: + type: integer + description: | + e.g. 1 + vdjregion_end: + type: integer + description: | + e.g. 321 + vjregion_start: + type: integer + description: | + e.g. 0 + vjregion_end: + type: integer + description: | + e.g. 0 + djregion_start: + type: integer + description: | + e.g. 254 + djregion_end: + type: integer + description: | + e.g. 321 + vregion_start: + type: integer + description: | + e.g. 286 + vregion_end: + type: integer + description: | + e.g. 252 + dregion_start: + type: integer + description: | + e.g. 254 + dregion_end: + type: integer + description: | + e.g. 321 + jregion_start: + type: integer + description: | + e.g. 286 + jregion_end: + type: integer + description: | + e.g. 321 + fr1region_start: + type: integer + description: | + e.g. 1 + fr1region_end: + type: integer + description: | + e.g. 38 + fr2region_start: + type: integer + description: | + e.g. 63 + fr2region_end: + type: integer + description: | + e.g. 113 + fr3region_start: + type: integer + description: | + e.g. 135 + fr3region_end: + type: integer + description: | + e.g. 248 + fr4region_start: + type: integer + description: | + e.g. 288 + fr4region_end: + type: integer + description: | + e.g. 321 + cdr1region_start: + type: integer + description: | + e.g. 39 + cdr1region_end: + type: integer + description: | + e.g. 321 + cdr2region_start: + type: integer + description: | + e.g. 62 + cdr2region_end: + type: integer + description: | + e.g. 134 + cdr3region_start: + type: integer + description: | + e.g. 249 + cdr3region_end: + type: integer + description: | + e.g. 287 + junction_start: + type: integer + description: | + e.g. 246 + junction_end: + type: integer + description: | + e.g. 290 + vregion_mutation_string: + type: string + description: > + e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - + +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - + -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| + fr1region_mutation_string: + type: string + description: | + e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| + fr2region_mutation_string: + type: string + description: | + e.g. + fr3region_mutation_string: + type: string + description: > + e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" + cdr1region_mutation_string: + type: string + description: | + e.g. + cdr2region_mutation_string: + type: string + description: | + e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" + cdr3region_mutation_string: + type: string + description: | + e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t + annotation_tool: + type: string + description: | + e.g. VQuest \ No newline at end of file diff --git a/ireceptor_summary.yaml b/ireceptor_summary.yaml new file mode 100644 index 0000000..a8ade18 --- /dev/null +++ b/ireceptor_summary.yaml @@ -0,0 +1,93 @@ + # This model defines ancillary information returned by iReceptor + # as part of the sample summary API. + + ireceptor_summary_model: + type: object + properties: + ir_subject_age: + type: integer + description: | + e.g. 1 + ir_sra_run_id: + type: string + description: | + e.g. SRR4102110 + ir_marker_1: + type: string + description: | + e.g. CR19 + ir_marker_2: + type: string + description: | + e.g. CR20 + ir_marker_3: + type: string + description: | + e.g. CR21 + ir_marker_4: + type: string + description: | + e.g. null + ir_marker_5: + type: string + description: | + e.g. null + ir_marker_6: + type: string + description: | + e.g. null + ir_project_sample_note: + type: string + description: > + A note about the sample. + ir_project_id: + type: integer + description: > + Identifier used internally by the repository to identify a + project. + ir_project_parent_id: + type: integer + description: > + Identifier used internally by the repository to identify a + parent/child + relationship between this project and its parent project. + ir_lab_id: + type: integer + description: > + Identifier used internally by the repository to identify a + lab. + ir_disease_state_id: + type: integer + description: > + Identifier used internally by the repository to identify a + an element in the disease state table. + ir_case_control_id: + type: integer + description: > + Identifier used internally by the repository to identify an + element in the case_control table. + ir_sample_id: + type: integer + description: > + Identifier used internally by the repository to identify a + sample. + ir_dna_id: + type: integer + description: > + Identifier used internally by the repository to identify a + DNA type. + ir_project_sample_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association a project with a sample. + ir_sample_subject_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association between a sample and a subject. + ir_sample_source_id: + type: integer + description: > + Identifier used internally by the repository to identify an + association between a sample and a sample source. \ No newline at end of file From 655a31f187c838764ba87676c7654199c8a0706f Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Tue, 17 Oct 2017 14:59:49 +1300 Subject: [PATCH 22/46] YAML and JSON files using working external models for all model components (for API responses only). --- iReceptor_Data_Service_API_V2.json | 541 +---------------------------- iReceptor_Data_Service_API_V2.yaml | 4 +- 2 files changed, 4 insertions(+), 541 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 7d28d0a..f40c128 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -24,7 +24,7 @@ "$ref": "#/definitions/airr_summary_model" }, { - "$ref": "#/definitions/ireceptor_summary_model" + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_summary.yaml#/ireceptor_summary_model" } ] } @@ -40,7 +40,7 @@ "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements" }, { - "$ref": "#/definitions/ireceptor_sequence_annotation_model" + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequence.yaml#/ireceptor_sequence_annotation_model" } ] } @@ -81,543 +81,6 @@ "example": 123456 } } - }, - "ireceptor_summary_model": { - "type": "object", - "properties": { - "ir_subject_age": { - "type": "integer", - "description": "e.g. 1\n" - }, - "ir_sra_run_id": { - "type": "string", - "description": "e.g. SRR4102110\n" - }, - "ir_marker_1": { - "type": "string", - "description": "e.g. CR19\n" - }, - "ir_marker_2": { - "type": "string", - "description": "e.g. CR20\n" - }, - "ir_marker_3": { - "type": "string", - "description": "e.g. CR21\n" - }, - "ir_marker_4": { - "type": "string", - "description": "e.g. null\n" - }, - "ir_marker_5": { - "type": "string", - "description": "e.g. null\n" - }, - "ir_marker_6": { - "type": "string", - "description": "e.g. null\n" - }, - "ir_project_sample_note": { - "type": "string", - "description": "A note about the sample.\n" - }, - "ir_project_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a project.\n" - }, - "ir_project_parent_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a parent/child relationship between this project and its parent project.\n" - }, - "ir_lab_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a lab.\n" - }, - "ir_disease_state_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a an element in the disease state table.\n" - }, - "ir_case_control_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an element in the case_control table.\n" - }, - "ir_sample_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a sample.\n" - }, - "ir_dna_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify a DNA type.\n" - }, - "ir_project_sample_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association a project with a sample.\n" - }, - "ir_sample_subject_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association between a sample and a subject.\n" - }, - "ir_sample_source_id": { - "type": "integer", - "description": "Identifier used internally by the repository to identify an association between a sample and a sample source. \n" - } - } - }, - "ireceptor_sequence_annotation_model": { - "type": "object", - "properties": { - "seq_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "seq_name": { - "type": "string" - }, - "project_sample_id": { - "type": "integer", - "description": "e.g. 6\n" - }, - "id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "sequence_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vgene_string": { - "type": "string", - "description": "e.g IGHV4-59*01 or IGHV4-59*07\n" - }, - "vgene_family": { - "type": "string", - "description": "e.g. IGHV4\n" - }, - "vgene_gene": { - "type": "string", - "description": "e.g. IGHV4-59\n" - }, - "dgene_string": { - "type": "string", - "description": "e.g. Homsap IGHD3-10*01 F\n" - }, - "dgene_family": { - "type": "string", - "description": "e.g. IGHD3\n" - }, - "dgene_gene": { - "type": "string", - "description": "e.g. IGHD3-10\n" - }, - "jgene_string": { - "type": "string", - "description": "e.g. Homsap IGHJ4*02 F\n" - }, - "jgene_family": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "jgene_gene": { - "type": "string", - "description": "e.g. IGHJ4\n" - }, - "functionality": { - "type": "string", - "description": "e.g. productive\n" - }, - "functionality_comment": { - "type": "string", - "description": "e.g. \"\"\n" - }, - "orientation": { - "type": "string", - "description": "e.g. +\n" - }, - "vgene_score": { - "type": "integer", - "description": "e.g. 1127\n" - }, - "vgene_probability": { - "type": "integer", - "description": "e.g. 95\n" - }, - "dregion_reading_frame": { - "type": "integer", - "description": "e.g. 2\n" - }, - "cdr1_length": { - "type": "integer", - "description": "e.g. 8\n" - }, - "cdr2_length": { - "type": "integer", - "description": "e.g. 7\n" - }, - "cdr3_length": { - "type": "integer", - "description": "e.g. 13\n" - }, - "vdjregion_sequence_nt": { - "type": "string", - "description": "vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt": { - "type": "string", - "description": "vj region nucleotide sequence\n" - }, - "djregion_sequence_nt": { - "type": "string", - "description": "dj region nucleotide sequence\n" - }, - "vregion_sequence_nt": { - "type": "string", - "description": "v region nucleotide sequence\n" - }, - "dregion_sequence_nt": { - "type": "string", - "description": "d region nucleotide sequence\n" - }, - "jregion_sequence_nt": { - "type": "string", - "description": "j region nucleotide sequence\n" - }, - "fr1region_sequence_nt": { - "type": "string", - "description": "fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt": { - "type": "string", - "description": "fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt": { - "type": "string", - "description": "fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt": { - "type": "string", - "description": "fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt": { - "type": "string", - "description": "cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt": { - "type": "string", - "description": "cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt": { - "type": "string", - "description": "cdr3 region nucleotide sequence\n" - }, - "vdjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vdj region nucleotide sequence\n" - }, - "vjregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped vj region nucleotide sequence\n" - }, - "djregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped dj region nucleotide sequence\n" - }, - "vregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped v region nucleotide sequence\n" - }, - "dregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped d region nucleotide sequence\n" - }, - "jregion_sequence_nt_gapped": { - "type": "string", - "description": "gapped j region nucleotide sequence\n" - }, - "fr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr1 region nucleotide sequence\n" - }, - "fr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr2 region nucleotide sequence\n" - }, - "fr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr3 region nucleotide sequence\n" - }, - "fr4region_sequence_nt_gapped": { - "type": "string", - "description": "gapped fr4 region nucleotide sequence\n" - }, - "cdr1region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr1 region nucleotide sequence\n" - }, - "cdr2region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr2 region nucleotide sequence\n" - }, - "cdr3region_sequence_nt_gapped": { - "type": "string", - "description": "gapped cdr3 region nucleotide sequence\n" - }, - "junction_sequence_nt_gapped": { - "type": "string", - "description": "gapped junction nucleotide sequence\n" - }, - "vdjregion_sequence_aa": { - "type": "string", - "description": "vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa": { - "type": "string", - "description": "vj region amino acid sequence\n" - }, - "djregion_sequence_aa": { - "type": "string", - "description": "dj region amino acid sequence\n" - }, - "vregion_sequence_aa": { - "type": "string", - "description": "v region amino acid sequence\n" - }, - "dregion_sequence_aa": { - "type": "string", - "description": "d region amino acid sequence\n" - }, - "jregion_sequence_aa": { - "type": "string", - "description": "j region amino acid sequence\n" - }, - "fr1region_sequence_aa": { - "type": "string", - "description": "fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa": { - "type": "string", - "description": "fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa": { - "type": "string", - "description": "fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa": { - "type": "string", - "description": "fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa": { - "type": "string", - "description": "cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa": { - "type": "string", - "description": "cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa": { - "type": "string", - "description": "cdr3 region amino acid sequence\n" - }, - "vdjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vdj region amino acid sequence\n" - }, - "vjregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped vj region amino acid sequence\n" - }, - "djregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped dj region amino acid sequence\n" - }, - "vregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped v region amino acid sequence\n" - }, - "dregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped d region amino acid sequence\n" - }, - "jregion_sequence_aa_gapped": { - "type": "string", - "description": "gapped j region amino acid sequence\n" - }, - "fr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr1 region amino acid sequence\n" - }, - "fr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr2 region amino acid sequence\n" - }, - "fr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr3 region amino acid sequence\n" - }, - "fr4region_sequence_aa_gapped": { - "type": "string", - "description": "gapped fr4 region amino acid sequence\n" - }, - "cdr1region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr1 region amino acid sequence\n" - }, - "cdr2region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr2 region amino acid sequence\n" - }, - "cdr3region_sequence_aa_gapped": { - "type": "string", - "description": "gapped cdr3 region amino acid sequence\n" - }, - "junction_sequence_aa_gapped": { - "type": "string", - "description": "gapped junction amino acid sequence\n" - }, - "vdjregion_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "vdjregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vjregion_start": { - "type": "integer", - "description": "e.g. 0\n" - }, - "vjregion_end": { - "type": "integer", - "description": "e.g. 0\n" - }, - "djregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "djregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "vregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "vregion_end": { - "type": "integer", - "description": "e.g. 252\n" - }, - "dregion_start": { - "type": "integer", - "description": "e.g. 254\n" - }, - "dregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "jregion_start": { - "type": "integer", - "description": "e.g. 286\n" - }, - "jregion_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "fr1region_start": { - "type": "integer", - "description": "e.g. 1\n" - }, - "fr1region_end": { - "type": "integer", - "description": "e.g. 38\n" - }, - "fr2region_start": { - "type": "integer", - "description": "e.g. 63\n" - }, - "fr2region_end": { - "type": "integer", - "description": "e.g. 113\n" - }, - "fr3region_start": { - "type": "integer", - "description": "e.g. 135\n" - }, - "fr3region_end": { - "type": "integer", - "description": "e.g. 248\n" - }, - "fr4region_start": { - "type": "integer", - "description": "e.g. 288\n" - }, - "fr4region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr1region_start": { - "type": "integer", - "description": "e.g. 39\n" - }, - "cdr1region_end": { - "type": "integer", - "description": "e.g. 321\n" - }, - "cdr2region_start": { - "type": "integer", - "description": "e.g. 62\n" - }, - "cdr2region_end": { - "type": "integer", - "description": "e.g. 134\n" - }, - "cdr3region_start": { - "type": "integer", - "description": "e.g. 249\n" - }, - "cdr3region_end": { - "type": "integer", - "description": "e.g. 287\n" - }, - "junction_start": { - "type": "integer", - "description": "e.g. 246\n" - }, - "junction_end": { - "type": "integer", - "description": "e.g. 290\n" - }, - "vregion_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\n" - }, - "fr1region_mutation_string": { - "type": "string", - "description": "e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|\n" - }, - "fr2region_mutation_string": { - "type": "string", - "description": "e.g. \n" - }, - "fr3region_mutation_string": { - "type": "string", - "description": "e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|\"\n" - }, - "cdr1region_mutation_string": { - "type": "string", - "description": "e.g.\n" - }, - "cdr2region_mutation_string": { - "type": "string", - "description": "e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|\"\n" - }, - "cdr3region_mutation_string": { - "type": "string", - "description": "e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t\n" - }, - "annotation_tool": { - "type": "string", - "description": "e.g. VQuest\n" - } - } } }, "schemes": [ diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 808d0b8..1bfa3c1 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -26,7 +26,7 @@ definitions: allOf: - $ref: '#/definitions/ireceptor_sequence_count_model' - $ref: '#/definitions/airr_summary_model' - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequences.yaml#/ireceptor_summary_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_summary.yaml#/ireceptor_summary_model' # A definition of the sequence response for an iReceptor API call. This # response is used wherever sequence data is provided by an API call. # It is a composite of the sequence fields defined by the MiAIRR standard, @@ -38,7 +38,7 @@ definitions: allOf: - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements' - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequences.yaml#/ireceptor_sequence_annotation_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequence.yaml#/ireceptor_sequence_annotation_model' # The AIRR Minimal Standards model for metadata above the sequence annotation level. airr_summary_model: allOf: From 57db8a42b6b404820cbf86729957d82e3017f09d Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 18 Oct 2017 14:16:17 +1300 Subject: [PATCH 23/46] Created a parameters section with parameters for rearangements. Updated the API calls to use the defined parameters. --- iReceptor_Data_Service_API_V2.json | 352 ++++++++++++++++++++--------- iReceptor_Data_Service_API_V2.yaml | 315 +++++++++++++++----------- 2 files changed, 430 insertions(+), 237 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index f40c128..365ef5f 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -78,11 +78,156 @@ "properties": { "sequence_count": { "type": "integer", + "description": "Number of sequences found that met the search criteria for this sample", "example": 123456 } } } }, + "parameters": { + "ir_username": { + "name": "ir_username", + "in": "query", + "description": "Username of the individual requesting access to the iReceptor repository node.\n", + "required": true, + "type": "string" + }, + "ir_sample_id_list": { + "name": "ir_sample_id_list", + "in": "query", + "description": "List of unique identifiers (specific to the repository) that identifies the samples to apply the query to.\n", + "required": true, + "type": "array", + "items": { + "type": "integer" + } + }, + "ir_data_format": { + "name": "ir_data_format", + "in": "query", + "description": "'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", + "required": false, + "type": "string" + }, + "study_id": { + "name": "study_id", + "type": "string", + "in": "query" + }, + "study_title": { + "name": "study_title", + "type": "string", + "in": "query" + }, + "study_description": { + "name": "study_description", + "type": "string", + "in": "query" + }, + "inclusion_exclusion_criteria": { + "name": "inclusion_exclusion_criteria", + "type": "string", + "in": "query" + }, + "grants": { + "name": "grants", + "type": "string", + "in": "query" + }, + "lab_name": { + "name": "lab_name", + "type": "string", + "in": "query" + }, + "collected_by": { + "name": "collected_by", + "type": "string", + "in": "query" + }, + "submitted_by": { + "name": "submitted_by", + "type": "string", + "in": "query" + }, + "lab_address": { + "name": "lab_address", + "type": "string", + "in": "query" + }, + "pub_ids": { + "name": "pub_ids", + "type": "string", + "in": "query" + }, + "germline_database": { + "name": "germline_database", + "in": "query", + "type": "string", + "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" + }, + "cell_index": { + "name": "cell_index", + "in": "query", + "type": "integer", + "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" + }, + "v_allele": { + "name": "v_allele", + "in": "query", + "type": "string", + "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" + }, + "d_allele": { + "name": "d_allele", + "in": "query", + "type": "string", + "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" + }, + "j_allele": { + "name": "j_allele", + "in": "query", + "type": "string", + "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" + }, + "c_allele": { + "name": "c_allele", + "in": "query", + "type": "string", + "description": "C region with allele (AIRR) \n" + }, + "junction_nt": { + "name": "junction_nt", + "in": "query", + "type": "string", + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" + }, + "junction_aa": { + "name": "junction_aa", + "in": "query", + "type": "string", + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" + }, + "duplicate_count": { + "name": "duplicate_count", + "in": "query", + "type": "integer", + "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" + }, + "ir_junction_nt_length": { + "name": "ir_junction_nt_length", + "in": "query", + "description": "Length of JUNCTION in nucleotide base pairs (iReceptor)", + "required": false, + "type": "integer" + }, + "ir_junction_aa_length": { + "name": "ir_junction_aa_length", + "in": "query", + "description": "Length of JUNCTION in amino acids (iReceptor)", + "required": false, + "type": "integer" + } + }, "schemes": [ "https" ], @@ -166,11 +311,7 @@ ], "parameters": [ { - "name": "username", - "in": "query", - "description": "Username of the individual requesting access to the iReceptor repository node.\n", - "required": true, - "type": "string" + "$ref": "#/parameters/ir_username" }, { "name": "lab_id", @@ -415,39 +556,37 @@ ], "parameters": [ { - "name": "username", - "in": "query", - "description": "Username of the individual requesting access to the iReceptor repository node.\n", - "required": true, - "type": "string" + "$ref": "#/parameters/ir_username" }, { - "name": "project_sample_id_list", - "in": "query", - "required": true, - "type": "array", - "items": { - "type": "integer" - } + "$ref": "#/parameters/ir_sample_id_list" }, { - "name": "cdr3_length", - "in": "query", - "description": "length of complementarity determining region in nucleotide base pairs", - "required": false, - "type": "integer" + "$ref": "#/parameters/germline_database" }, { - "name": "vgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/v_allele" }, { - "name": "jgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/d_allele" + }, + { + "$ref": "#/parameters/j_allele" + }, + { + "$ref": "#/parameters/c_allele" + }, + { + "$ref": "#/parameters/junction_nt" + }, + { + "$ref": "#/parameters/junction_aa" + }, + { + "$ref": "#/parameters/ir_junction_nt_length" + }, + { + "$ref": "#/parameters/ir_junction_aa_length" } ], "operationId": "getSequenceSummary", @@ -493,46 +632,40 @@ ], "parameters": [ { - "name": "username", - "in": "query", - "description": "Username of the individual requesting access to the iReceptor repository node.\n", - "required": true, - "type": "string" + "$ref": "#/parameters/ir_username" }, { - "name": "project_sample_id_list", - "in": "query", - "required": true, - "type": "array", - "items": { - "type": "integer" - } + "$ref": "#/parameters/ir_sample_id_list" }, { - "name": "cdr3_length", - "in": "query", - "description": "length of complementarity determining region in nucleotide base pairs", - "required": false, - "type": "integer" + "$ref": "#/parameters/ir_data_format" }, { - "name": "vgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/germline_database" }, { - "name": "jgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/v_allele" }, { - "name": "format", - "in": "query", - "description": "'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", - "required": false, - "type": "string" + "$ref": "#/parameters/d_allele" + }, + { + "$ref": "#/parameters/j_allele" + }, + { + "$ref": "#/parameters/c_allele" + }, + { + "$ref": "#/parameters/junction_nt" + }, + { + "$ref": "#/parameters/junction_aa" + }, + { + "$ref": "#/parameters/ir_junction_nt_length" + }, + { + "$ref": "#/parameters/ir_junction_aa_length" } ], "operationId": "getSequenceData", @@ -637,39 +770,37 @@ ], "parameters": [ { - "name": "username", - "in": "query", - "description": "Username of the individual requesting access to the iReceptor repository node.\n", - "required": true, - "type": "string" + "$ref": "#/parameters/ir_username" }, { - "name": "project_sample_id_list", - "in": "query", - "required": true, - "type": "array", - "items": { - "type": "integer" - } + "$ref": "#/parameters/ir_sample_id_list" }, { - "name": "cdr3_length", - "in": "query", - "description": "length of complementarity determining region in nucleotide base pairs", - "required": false, - "type": "integer" + "$ref": "#/parameters/germline_database" }, { - "name": "vgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/v_allele" }, { - "name": "jgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/d_allele" + }, + { + "$ref": "#/parameters/j_allele" + }, + { + "$ref": "#/parameters/c_allele" + }, + { + "$ref": "#/parameters/junction_nt" + }, + { + "$ref": "#/parameters/junction_aa" + }, + { + "$ref": "#/parameters/ir_junction_nt_length" + }, + { + "$ref": "#/parameters/ir_junction_aa_length" } ], "operationId": "getCloneSummary", @@ -715,39 +846,40 @@ ], "parameters": [ { - "name": "username", - "in": "query", - "description": "Username of the individual requesting access to the iReceptor repository node.\n", - "required": true, - "type": "string" + "$ref": "#/parameters/ir_username" }, { - "name": "project_sample_id_list", - "in": "query", - "required": true, - "type": "array", - "items": { - "type": "integer" - } + "$ref": "#/parameters/ir_sample_id_list" }, { - "name": "cdr3_length", - "in": "query", - "description": "length of complementarity determining region in nucleotide base pairs", - "required": false, - "type": "integer" + "$ref": "#/parameters/ir_data_format" }, { - "name": "vgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/germline_database" }, { - "name": "jgene_string", - "in": "query", - "required": false, - "type": "string" + "$ref": "#/parameters/v_allele" + }, + { + "$ref": "#/parameters/d_allele" + }, + { + "$ref": "#/parameters/j_allele" + }, + { + "$ref": "#/parameters/c_allele" + }, + { + "$ref": "#/parameters/junction_nt" + }, + { + "$ref": "#/parameters/junction_aa" + }, + { + "$ref": "#/parameters/ir_junction_nt_length" + }, + { + "$ref": "#/parameters/ir_junction_aa_length" } ], "operationId": "getCloneData", diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 1bfa3c1..de024b6 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -57,7 +57,148 @@ definitions: properties: sequence_count: type: integer + description: Number of sequences found that met the search criteria for this sample example: 123456 +parameters: + ir_username: + name: ir_username + in: query + description: > + Username of the individual requesting access to the iReceptor + repository node. + required: true + type: string + ir_sample_id_list: + name: ir_sample_id_list + in: query + description: > + List of unique identifiers (specific to the repository) that identifies the samples + to apply the query to. + required: true + type: array + items: + type: integer + ir_data_format: + name: ir_data_format + in: query + description: >- + Data format to return the sequence data in, one of:
+ 'csv' - vQuest based CSV (as per /v1)(default)
+ 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
+ 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) + required: false + type: string + study_id: + name: study_id + type: string + in: query + study_title: + name: study_title + type: string + in: query + study_description: + name: study_description + type: string + in: query + inclusion_exclusion_criteria: + name: inclusion_exclusion_criteria + type: string + in: query + grants: + name: grants + type: string + in: query + lab_name: + name: lab_name + type: string + in: query + collected_by: + name: collected_by + type: string + in: query + submitted_by: + name: submitted_by + type: string + in: query + lab_address: + name: lab_address + type: string + in: query + pub_ids: + name: pub_ids + type: string + in: query + germline_database: + name: germline_database + in: query + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + cell_index: + name: cell_index + in: query + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) + v_allele: + name: v_allele + in: query + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) + d_allele: + name: d_allele + in: query + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) + j_allele: + name: j_allele + in: query + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) + c_allele: + name: c_allele + in: query + type: string + description: | + C region with allele (AIRR) + junction_nt: + name: junction_nt + in: query + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region (nucleotide)) (AIRR) + junction_aa: + name: junction_aa + in: query + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region (amino acid)) (AIRR) + duplicate_count: + name: duplicate_count + in: query + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) + ir_junction_nt_length: + name: ir_junction_nt_length + in: query + description: >- + Length of JUNCTION in nucleotide base pairs (iReceptor) + required: false + type: integer + ir_junction_aa_length: + name: ir_junction_aa_length + in: query + description: >- + Length of JUNCTION in amino acids (iReceptor) + required: false + type: integer schemes: - https produces: @@ -123,13 +264,7 @@ paths: tags: - samples parameters: - - name: username - in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true - type: string + - $ref: '#/parameters/ir_username' - name: lab_id in: query description: | @@ -346,34 +481,17 @@ paths: tags: - sequences parameters: - - name: username - in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true - type: string - - name: project_sample_id_list - in: query - required: true - type: array - items: - type: integer - - name: cdr3_length - in: query - description: >- - length of complementarity determining region in nucleotide base - pairs - required: false - type: integer - - name: vgene_string - in: query - required: false - type: string - - name: jgene_string - in: query - required: false - type: string + - $ref: '#/parameters/ir_username' + - $ref: '#/parameters/ir_sample_id_list' + - $ref: '#/parameters/germline_database' + - $ref: '#/parameters/v_allele' + - $ref: '#/parameters/d_allele' + - $ref: '#/parameters/j_allele' + - $ref: '#/parameters/c_allele' + - $ref: '#/parameters/junction_nt' + - $ref: '#/parameters/junction_aa' + - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/ir_junction_aa_length' operationId: getSequenceSummary responses: '200': @@ -416,42 +534,18 @@ paths: tags: - sequences parameters: - - name: username - in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true - type: string - - name: project_sample_id_list - in: query - required: true - type: array - items: - type: integer - - name: cdr3_length - in: query - description: >- - length of complementarity determining region in nucleotide base - pairs - required: false - type: integer - - name: vgene_string - in: query - required: false - type: string - - name: jgene_string - in: query - required: false - type: string - - name: format - in: query - description: >- - 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as - per /v1 with tab delimiters instead of commas); 'airr' - AIRR - Formats rearrangements TSV (as per AIRR formats rearrangements spec) - required: false - type: string + - $ref: '#/parameters/ir_username' + - $ref: '#/parameters/ir_sample_id_list' + - $ref: '#/parameters/ir_data_format' + - $ref: '#/parameters/germline_database' + - $ref: '#/parameters/v_allele' + - $ref: '#/parameters/d_allele' + - $ref: '#/parameters/j_allele' + - $ref: '#/parameters/c_allele' + - $ref: '#/parameters/junction_nt' + - $ref: '#/parameters/junction_aa' + - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/ir_junction_aa_length' operationId: getSequenceData responses: '200': @@ -549,34 +643,17 @@ paths: tags: - clones parameters: - - name: username - in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true - type: string - - name: project_sample_id_list - in: query - required: true - type: array - items: - type: integer - - name: cdr3_length - in: query - description: >- - length of complementarity determining region in nucleotide base - pairs - required: false - type: integer - - name: vgene_string - in: query - required: false - type: string - - name: jgene_string - in: query - required: false - type: string + - $ref: '#/parameters/ir_username' + - $ref: '#/parameters/ir_sample_id_list' + - $ref: '#/parameters/germline_database' + - $ref: '#/parameters/v_allele' + - $ref: '#/parameters/d_allele' + - $ref: '#/parameters/j_allele' + - $ref: '#/parameters/c_allele' + - $ref: '#/parameters/junction_nt' + - $ref: '#/parameters/junction_aa' + - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/ir_junction_aa_length' operationId: getCloneSummary responses: '200': @@ -610,34 +687,18 @@ paths: tags: - clones parameters: - - name: username - in: query - description: > - Username of the individual requesting access to the iReceptor - repository node. - required: true - type: string - - name: project_sample_id_list - in: query - required: true - type: array - items: - type: integer - - name: cdr3_length - in: query - description: >- - length of complementarity determining region in nucleotide base - pairs - required: false - type: integer - - name: vgene_string - in: query - required: false - type: string - - name: jgene_string - in: query - required: false - type: string + - $ref: '#/parameters/ir_username' + - $ref: '#/parameters/ir_sample_id_list' + - $ref: '#/parameters/ir_data_format' + - $ref: '#/parameters/germline_database' + - $ref: '#/parameters/v_allele' + - $ref: '#/parameters/d_allele' + - $ref: '#/parameters/j_allele' + - $ref: '#/parameters/c_allele' + - $ref: '#/parameters/junction_nt' + - $ref: '#/parameters/junction_aa' + - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/ir_junction_aa_length' operationId: getCloneData responses: '200': From af5cfe8e299fa6b239e463611220e7434762c8f4 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 18 Oct 2017 14:27:57 +1300 Subject: [PATCH 24/46] Got rid of ir_ prefixes for now, made parameters not mandatory... --- iReceptor_Data_Service_API_V2.json | 12 ++++++------ iReceptor_Data_Service_API_V2.yaml | 10 +++++----- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 365ef5f..c256d86 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -86,26 +86,26 @@ }, "parameters": { "ir_username": { - "name": "ir_username", + "name": "username", "in": "query", "description": "Username of the individual requesting access to the iReceptor repository node.\n", - "required": true, + "required": false, "type": "string" }, "ir_sample_id_list": { - "name": "ir_sample_id_list", + "name": "project_sample_id_list", "in": "query", "description": "List of unique identifiers (specific to the repository) that identifies the samples to apply the query to.\n", - "required": true, + "required": false, "type": "array", "items": { "type": "integer" } }, "ir_data_format": { - "name": "ir_data_format", + "name": "format", "in": "query", - "description": "'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", + "description": "Data format to return the sequence data in, one of:
'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", "required": false, "type": "string" }, diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index de024b6..2123e73 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -61,25 +61,25 @@ definitions: example: 123456 parameters: ir_username: - name: ir_username + name: username in: query description: > Username of the individual requesting access to the iReceptor repository node. - required: true + required: false type: string ir_sample_id_list: - name: ir_sample_id_list + name: project_sample_id_list in: query description: > List of unique identifiers (specific to the repository) that identifies the samples to apply the query to. - required: true + required: false type: array items: type: integer ir_data_format: - name: ir_data_format + name: format in: query description: >- Data format to return the sequence data in, one of:
From 41157c996d76612659f2b82d4578394fa0bf9a89 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 18 Oct 2017 15:18:53 +1300 Subject: [PATCH 25/46] Added parameters for the /samples entry point, both AIRR compliant names as well as iReceptor extensions (prefixed with ir_). --- iReceptor_Data_Service_API_V2.json | 202 +++++++++++++++------------ iReceptor_Data_Service_API_V2.yaml | 215 +++++++++++++++-------------- 2 files changed, 227 insertions(+), 190 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index c256d86..64fdc22 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -86,24 +86,24 @@ }, "parameters": { "ir_username": { - "name": "username", + "name": "ir_username", "in": "query", - "description": "Username of the individual requesting access to the iReceptor repository node.\n", + "description": "Username of the individual requesting access to the iReceptor repository node. If the iReceptor repository is a public repository, then this parameter is not required. If the repository is not public then the username must be supplied and the repository will determine the access for that user for that repository.\n", "required": false, "type": "string" }, "ir_sample_id_list": { - "name": "project_sample_id_list", + "name": "ir_project_sample_id_list", "in": "query", - "description": "List of unique identifiers (specific to the repository) that identifies the samples to apply the query to.\n", + "description": "List of unique identifiers (specific to the repository) that identify the samples to apply the query to.\n", "required": false, "type": "array", "items": { - "type": "integer" + "type": "string" } }, "ir_data_format": { - "name": "format", + "name": "ir_data_format", "in": "query", "description": "Data format to return the sequence data in, one of:
'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", "required": false, @@ -124,41 +124,102 @@ "type": "string", "in": "query" }, - "inclusion_exclusion_criteria": { - "name": "inclusion_exclusion_criteria", + "lab_name": { + "name": "lab_name", "type": "string", "in": "query" }, - "grants": { - "name": "grants", + "subject_id": { + "name": "subject_id", "type": "string", "in": "query" }, - "lab_name": { - "name": "lab_name", + "organism": { + "name": "organism", + "type": "string", + "in": "query" + }, + "sex": { + "name": "sex", "type": "string", "in": "query" }, - "collected_by": { - "name": "collected_by", + "ethnicity": { + "name": "ethnicity", "type": "string", "in": "query" }, - "submitted_by": { - "name": "submitted_by", + "study_group_description": { + "name": "study_group_description", "type": "string", "in": "query" }, - "lab_address": { - "name": "lab_address", + "sample_id": { + "name": "sample_id", "type": "string", "in": "query" }, - "pub_ids": { - "name": "pub_ids", + "tissue": { + "name": "tissue", "type": "string", "in": "query" }, + "disease_state_sample": { + "name": "disease_state_sample", + "type": "string", + "in": "query" + }, + "cell_subset": { + "name": "cell_subset", + "type": "string", + "in": "query" + }, + "cell_phenotype": { + "name": "cell_phenotype", + "type": "string", + "in": "query" + }, + "library_source": { + "name": "library_source", + "type": "string", + "in": "query" + }, + "platform": { + "name": "platform", + "type": "string", + "in": "query" + }, + "ir_lab_id": { + "name": "ir_lab_id", + "in": "query", + "description": "e.g. 1\n", + "required": false, + "type": "string" + }, + "ir_project_id": { + "name": "ir_project_id", + "in": "query", + "description": "e.g. 1\n", + "required": false, + "type": "array", + "items": { + "type": "string" + } + }, + "ir_subject_age_min": { + "name": "ir_subject_age_min", + "in": "query", + "description": "e.g. 10\n", + "required": false, + "type": "integer" + }, + "ir_subject_age_max": { + "name": "ir_subject_age_max", + "in": "query", + "description": "e.g. 12\n", + "required": false, + "type": "integer" + }, "germline_database": { "name": "germline_database", "in": "query", @@ -311,101 +372,64 @@ ], "parameters": [ { - "$ref": "#/parameters/ir_username" + "$ref": "#/parameters/study_id" }, { - "name": "lab_id", - "in": "query", - "description": "e.g. 1\n", - "required": false, - "type": "integer" + "$ref": "#/parameters/study_title" }, { - "name": "project_id", - "in": "query", - "description": "e.g. 1\n", - "required": false, - "type": "array", - "items": { - "type": "integer" - } + "$ref": "#/parameters/study_description" + }, + { + "$ref": "#/parameters/lab_name" + }, + { + "$ref": "#/parameters/subject_id" + }, + { + "$ref": "#/parameters/organism" + }, + { + "$ref": "#/parameters/sex" + }, + { + "$ref": "#/parameters/ethnicity" + }, + { + "$ref": "#/parameters/study_group_description" }, { - "name": "subject_code", - "in": "query", - "description": "e.g. test\n", - "required": false, - "type": "string" + "$ref": "#/parameters/sample_id" }, { - "name": "subject_gender", - "in": "query", - "description": "e.g. Male or Female\n", - "required": false, - "type": "string" + "$ref": "#/parameters/tissue" }, { - "name": "subject_species", - "in": "query", - "description": "e.g. Human\n", - "required": false, - "type": "string" + "$ref": "#/parameters/disease_state_sample" }, { - "name": "subject_ethnicity", - "in": "query", - "description": "e.g. Caucasian\n", - "required": false, - "type": "string" + "$ref": "#/parameters/cell_subset" }, { - "name": "subject_age_min", - "in": "query", - "description": "e.g. 10\n", - "required": false, - "type": "integer" + "$ref": "#/parameters/cell_phenotype" }, { - "name": "subject_age_max", - "in": "query", - "description": "e.g. 12\n", - "required": false, - "type": "integer" + "$ref": "#/parameters/library_source" }, { - "name": "case_control_name", - "in": "query", - "description": "e.g. Control\n", - "required": false, - "type": "string" + "$ref": "#/parameters/platform" }, { - "name": "sample_name", - "in": "query", - "description": "e.g. test2\n", - "required": false, - "type": "string" + "$ref": "#/parameters/ir_lab_id" }, { - "name": "sample_source_name", - "in": "query", - "description": "e.g. Blood (PBMC)\n", - "required": false, - "type": "string" + "$ref": "#/parameters/ir_project_id" }, { - "name": "ireceptor_cell_subset_name", - "in": "query", - "description": "e.g. NaiveB\n", - "required": false, - "type": "string" + "$ref": "#/parameters/ir_subject_age_min" }, { - "name": "dna_type", - "in": "query", - "description": "e.g. cDNA, gDNA\n", - "required": false, - "type": "string" + "$ref": "#/parameters/ir_subject_age_max" } ], "operationId": "getSamples", diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 2123e73..829ffc5 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -60,26 +60,32 @@ definitions: description: Number of sequences found that met the search criteria for this sample example: 123456 parameters: + # + # Generally useful parameters for all API entry points. + # ir_username: - name: username + name: ir_username in: query description: > Username of the individual requesting access to the iReceptor - repository node. + repository node. If the iReceptor repository is a public repository, + then this parameter is not required. If the repository is not public + then the username must be supplied and the repository will determine + the access for that user for that repository. required: false type: string ir_sample_id_list: - name: project_sample_id_list + name: ir_project_sample_id_list in: query description: > - List of unique identifiers (specific to the repository) that identifies the samples + List of unique identifiers (specific to the repository) that identify the samples to apply the query to. required: false type: array items: - type: integer + type: string ir_data_format: - name: format + name: ir_data_format in: query description: >- Data format to return the sequence data in, one of:
@@ -88,6 +94,11 @@ parameters: 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) required: false type: string + # + # MiAIRR compliant parameters for /samples entry points. + # Note: Currently only those parameters used by iReceptor repositories + # are defined here. + # study_id: name: study_id type: string @@ -100,34 +111,94 @@ parameters: name: study_description type: string in: query - inclusion_exclusion_criteria: - name: inclusion_exclusion_criteria + lab_name: + name: lab_name type: string in: query - grants: - name: grants + subject_id: + name: subject_id type: string in: query - lab_name: - name: lab_name + organism: + name: organism type: string in: query - collected_by: - name: collected_by + sex: + name: sex type: string in: query - submitted_by: - name: submitted_by + ethnicity: + name: ethnicity type: string in: query - lab_address: - name: lab_address + study_group_description: + name: study_group_description type: string in: query - pub_ids: - name: pub_ids + sample_id: + name: sample_id type: string in: query + tissue: + name: tissue + type: string + in: query + disease_state_sample: + name: disease_state_sample + type: string + in: query + cell_subset: + name: cell_subset + type: string + in: query + cell_phenotype: + name: cell_phenotype + type: string + in: query + library_source: + name: library_source + type: string + in: query + platform: + name: platform + type: string + in: query + # + # iReceptor specific parameters for the /samples API entry point. + # + ir_lab_id: + name: ir_lab_id + in: query + description: | + e.g. 1 + required: false + type: string + ir_project_id: + name: ir_project_id + in: query + description: | + e.g. 1 + required: false + type: array + items: + type: string + ir_subject_age_min: + name: ir_subject_age_min + in: query + description: | + e.g. 10 + required: false + type: integer + ir_subject_age_max: + name: ir_subject_age_max + in: query + description: | + e.g. 12 + required: false + type: integer + # + # MiAIRR compliant parameters for rearrangements (/sequences* entry points) + # germline_database: name: germline_database in: query @@ -185,6 +256,9 @@ parameters: type: integer description: | Number of times the sequence has been duplicated in a file (AIRR) + # + # iReceptor specific parameters for rearrangements (/sequences* entry points) + # ir_junction_nt_length: name: ir_junction_nt_length in: query @@ -264,87 +338,26 @@ paths: tags: - samples parameters: - - $ref: '#/parameters/ir_username' - - name: lab_id - in: query - description: | - e.g. 1 - required: false - type: integer - - name: project_id - in: query - description: | - e.g. 1 - required: false - type: array - items: - type: integer - - name: subject_code - in: query - description: | - e.g. test - required: false - type: string - - name: subject_gender - in: query - description: | - e.g. Male or Female - required: false - type: string - - name: subject_species - in: query - description: | - e.g. Human - required: false - type: string - - name: subject_ethnicity - in: query - description: | - e.g. Caucasian - required: false - type: string - - name: subject_age_min - in: query - description: | - e.g. 10 - required: false - type: integer - - name: subject_age_max - in: query - description: | - e.g. 12 - required: false - type: integer - - name: case_control_name - in: query - description: | - e.g. Control - required: false - type: string - - name: sample_name - in: query - description: | - e.g. test2 - required: false - type: string - - name: sample_source_name - in: query - description: | - e.g. Blood (PBMC) - required: false - type: string - - name: ireceptor_cell_subset_name - in: query - description: | - e.g. NaiveB - required: false - type: string - - name: dna_type - in: query - description: | - e.g. cDNA, gDNA - required: false - type: string + - $ref: '#/parameters/study_id' + - $ref: '#/parameters/study_title' + - $ref: '#/parameters/study_description' + - $ref: '#/parameters/lab_name' + - $ref: '#/parameters/subject_id' + - $ref: '#/parameters/organism' + - $ref: '#/parameters/sex' + - $ref: '#/parameters/ethnicity' + - $ref: '#/parameters/study_group_description' + - $ref: '#/parameters/sample_id' + - $ref: '#/parameters/tissue' + - $ref: '#/parameters/disease_state_sample' + - $ref: '#/parameters/cell_subset' + - $ref: '#/parameters/cell_phenotype' + - $ref: '#/parameters/library_source' + - $ref: '#/parameters/platform' + - $ref: '#/parameters/ir_lab_id' + - $ref: '#/parameters/ir_project_id' + - $ref: '#/parameters/ir_subject_age_min' + - $ref: '#/parameters/ir_subject_age_max' operationId: getSamples responses: '200': From 7064d2a1bfb0f4458216563fbbb06565fc61bbf5 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 18 Oct 2017 16:39:51 +1300 Subject: [PATCH 26/46] Implemented parameters for the POST methods of the API using models. Was able to reuse the models from the Responses so repitition is relatively minimal. Still need to move the models to external files, but that can come later when AIRR has its process sorted out. --- iReceptor_Data_Service_API_V2.json | 190 +++++++++++------------------ iReceptor_Data_Service_API_V2.yaml | 172 +++++++++----------------- 2 files changed, 131 insertions(+), 231 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 64fdc22..e506b9e 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -82,6 +82,58 @@ "example": 123456 } } + }, + "ireceptor_samples_parameters_model": { + "type": "object", + "required": [ + "ir_username" + ], + "properties": { + "ir_username": { + "type": "string", + "description": "Username of the individual requesting access to the iReceptor repository node.\n" + }, + "ir_lab_id": { + "type": "integer", + "description": "e.g. 1\n" + }, + "ir_project_id": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "e.g. 1\n" + } + } + }, + "ireceptor_sequences_parameters_model": { + "type": "object", + "required": [ + "ir_username" + ], + "properties": { + "ir_username": { + "type": "string", + "description": "Username of the individual requesting access to the iReceptor repository node.\n" + }, + "ir_project_sample_id_list": { + "type": "array", + "items": { + "type": "integer" + } + }, + "ir_data_format": { + "description": "'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)\n ir_junction_nt_length:" + }, + "ir_junction_nt_length": { + "type": "integer", + "description": "Length of JUNCTION in nucleotide base pairs (iReceptor)" + }, + "ir_junction_aa_length": { + "type": "integer", + "description": "Length of JUNCTION in amino acids (iReceptor)" + } + } } }, "parameters": { @@ -371,6 +423,15 @@ "samples" ], "parameters": [ + { + "$ref": "#/parameters/ir_username" + }, + { + "$ref": "#/parameters/ir_lab_id" + }, + { + "$ref": "#/parameters/ir_project_id" + }, { "$ref": "#/parameters/study_id" }, @@ -419,12 +480,6 @@ { "$ref": "#/parameters/platform" }, - { - "$ref": "#/parameters/ir_lab_id" - }, - { - "$ref": "#/parameters/ir_project_id" - }, { "$ref": "#/parameters/ir_subject_age_min" }, @@ -468,80 +523,14 @@ "in": "body", "required": true, "schema": { - "type": "object", - "required": [ - "username" - ], - "properties": { - "username": { - "type": "string", - "description": "Username of the individual requesting access to the iReceptor repository node.\n" - }, - "lab_id": { - "type": "integer", - "description": "e.g. 1\n" - }, - "project_id": { - "type": "array", - "items": { - "type": "integer" - }, - "description": "e.g. 1\n" - }, - "subject_code": { - "type": "string", - "description": "e.g. test\n" - }, - "subject_gender": { - "type": "string", - "description": "e.g. Male\n" - }, - "subject_ethnicity": { - "type": "string", - "description": "e.g. Caucasian\n" - }, - "subject_species": { - "type": "string", - "description": "e.g. Human\n" - }, - "subject_age_min": { - "type": "integer", - "description": "e.g. 10\n" - }, - "subject_age_max": { - "type": "integer", - "description": "e.g. 12\n" - }, - "case_control_name": { - "type": "string", - "description": "e.g. Control\n" + "allOf": [ + { + "$ref": "#/definitions/airr_summary_model" }, - "sample_name": { - "type": "string", - "description": "e.g. test2\n" - }, - "sample_source_name": { - "type": "array", - "items": { - "type": "string" - }, - "description": "e.g. Blood (PBMC)\n" - }, - "ireceptor_cell_subset_name": { - "type": "array", - "items": { - "type": "string" - }, - "description": "e.g. NaiveB\n" - }, - "dna_type": { - "type": "array", - "items": { - "type": "string" - }, - "description": "e.g. cDNA\n" + { + "$ref": "#/definitions/ireceptor_samples_parameters_model" } - } + ] } } ], @@ -727,35 +716,14 @@ "name": "query", "in": "body", "schema": { - "type": "object", - "required": [ - "username" - ], - "properties": { - "username": { - "type": "string", - "description": "Username of the individual requesting access to the iReceptor repository node.\n" - }, - "project_sample_id_list": { - "type": "array", - "items": { - "type": "integer" - } - }, - "cdr3_length": { - "description": "length of complementarity determining region in nucleotide base pairs\n", - "type": "integer" + "allOf": [ + { + "$ref": "#/definitions/ireceptor_sequences_parameters_model" }, - "vgene_string": { - "type": "string" - }, - "jgene_string": { - "type": "string" - }, - "format": { - "description": "'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)" + { + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" } - } + ] } } ], @@ -912,18 +880,6 @@ "description": "A successful call returns an array of sequence data. Optional \"output\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"output\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format. \n", "schema": { "$ref": "#/definitions/ireceptor_sequence_response" - }, - "examples": { - "application/json": { - "seq_name": "M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0\n", - "v_allele": "IGHV4-59*01 or IGHV4-59*07\n", - "d_allele": "IGHD3-10*01\n", - "j_allele": "IGHJ4*02\n", - "citation": { - "doi": "10.1093/cid/ciw767", - "title": "RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.\n" - } - } } }, "400": { diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 829ffc5..d516c81 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -59,6 +59,55 @@ definitions: type: integer description: Number of sequences found that met the search criteria for this sample example: 123456 + ireceptor_samples_parameters_model: + type: object + required: + - ir_username + properties: + ir_username: + type: string + description: > + Username of the individual requesting access to the iReceptor + repository node. + ir_lab_id: + type: integer + description: | + e.g. 1 + ir_project_id: + type: array + items: + type: integer + description: | + e.g. 1 + ireceptor_sequences_parameters_model: + type: object + required: + - ir_username + properties: + ir_username: + type: string + description: > + Username of the individual requesting access to the iReceptor + repository node. + ir_project_sample_id_list: + type: array + items: + type: integer + ir_data_format: + description: >- + 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based + TSV (as per /v1 with tab delimiters instead of commas); 'airr' + - AIRR Formats rearrangements TSV (as per AIRR formats + rearrangements spec) + ir_junction_nt_length: + ir_junction_nt_length: + type: integer + description: >- + Length of JUNCTION in nucleotide base pairs (iReceptor) + ir_junction_aa_length: + type: integer + description: >- + Length of JUNCTION in amino acids (iReceptor) parameters: # # Generally useful parameters for all API entry points. @@ -338,6 +387,9 @@ paths: tags: - samples parameters: + - $ref: '#/parameters/ir_username' + - $ref: '#/parameters/ir_lab_id' + - $ref: '#/parameters/ir_project_id' - $ref: '#/parameters/study_id' - $ref: '#/parameters/study_title' - $ref: '#/parameters/study_description' @@ -354,8 +406,6 @@ paths: - $ref: '#/parameters/cell_phenotype' - $ref: '#/parameters/library_source' - $ref: '#/parameters/platform' - - $ref: '#/parameters/ir_lab_id' - - $ref: '#/parameters/ir_project_id' - $ref: '#/parameters/ir_subject_age_min' - $ref: '#/parameters/ir_subject_age_max' operationId: getSamples @@ -398,75 +448,9 @@ paths: in: body required: true schema: - type: object - required: - - username - properties: - username: - type: string - description: > - Username of the individual requesting access to the iReceptor - repository node. - lab_id: - type: integer - description: | - e.g. 1 - project_id: - type: array - items: - type: integer - description: | - e.g. 1 - subject_code: - type: string - description: | - e.g. test - subject_gender: - type: string - description: | - e.g. Male - subject_ethnicity: - type: string - description: | - e.g. Caucasian - subject_species: - type: string - description: | - e.g. Human - subject_age_min: - type: integer - description: | - e.g. 10 - subject_age_max: - type: integer - description: | - e.g. 12 - case_control_name: - type: string - description: | - e.g. Control - sample_name: - type: string - description: | - e.g. test2 - sample_source_name: - type: array - items: - type: string - description: | - e.g. Blood (PBMC) - ireceptor_cell_subset_name: - type: array - items: - type: string - description: | - e.g. NaiveB - dna_type: - type: array - items: - type: string - description: | - e.g. cDNA + allOf: + - $ref: '#/definitions/airr_summary_model' + - $ref: '#/definitions/ireceptor_samples_parameters_model' operationId: postSamples responses: '200': @@ -596,34 +580,9 @@ paths: - name: query in: body schema: - type: object - required: - - username - properties: - username: - type: string - description: > - Username of the individual requesting access to the iReceptor - repository node. - project_sample_id_list: - type: array - items: - type: integer - cdr3_length: - description: > - length of complementarity determining region in nucleotide - base pairs - type: integer - vgene_string: - type: string - jgene_string: - type: string - format: - description: >- - 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based - TSV (as per /v1 with tab delimiters instead of commas); 'airr' - - AIRR Formats rearrangements TSV (as per AIRR formats - rearrangements spec) + allOf: + - $ref: '#/definitions/ireceptor_sequences_parameters_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' operationId: postSequenceData responses: '200': @@ -724,21 +683,6 @@ paths: comma-separated format. schema: $ref: '#/definitions/ireceptor_sequence_response' - examples: - application/json: - seq_name: | - M00930:18:000000000-A3782:1:1101:11543:3128_1:N:0 - v_allele: | - IGHV4-59*01 or IGHV4-59*07 - d_allele: | - IGHD3-10*01 - j_allele: | - IGHJ4*02 - citation: - doi: 10.1093/cid/ciw767 - title: > - RNA-Seq Analysis of Gene Expression, Viral Pathogen, and - B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. '400': description: malformed request '401': From dcd8f1c71ddb8ea3c869726f99987f2cf12bd713 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Wed, 18 Oct 2017 16:43:23 +1300 Subject: [PATCH 27/46] Removed some erroneous text in a description field. --- iReceptor_Data_Service_API_V2.json | 2 +- iReceptor_Data_Service_API_V2.yaml | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index e506b9e..4e3181a 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -123,7 +123,7 @@ } }, "ir_data_format": { - "description": "'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)\n ir_junction_nt_length:" + "description": "'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)" }, "ir_junction_nt_length": { "type": "integer", diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index d516c81..c461ca9 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -99,7 +99,6 @@ definitions: TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) - ir_junction_nt_length: ir_junction_nt_length: type: integer description: >- From 7ce5c5f010e545e2629dc459b11607209683315c Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Wed, 18 Oct 2017 01:59:58 -0500 Subject: [PATCH 28/46] use number as type --- Formats_rearrangement.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml index 009b5fb..de4dd99 100644 --- a/Formats_rearrangement.yaml +++ b/Formats_rearrangement.yaml @@ -51,16 +51,16 @@ Formats_Rearrangements: type: string description: C gene assignment v_score: - type: float + type: number description: V alignment score d_score: - type: float + type: number description: D alignment score j_score: - type: float + type: number description: J alignment score c_score: - type: float + type: number description: C alignment score v_cigar: type: string @@ -75,31 +75,31 @@ Formats_Rearrangements: type: string description: C alignment CIGAR string v_evalue: - type: float + type: number description: V alignment E-value (when applicable) d_evalue: - type: float + type: number description: D alignment E-value (when applicable) j_evalue: - type: float + type: number description: J alignment E-value (when applicable) v_identity: - type: float + type: number description: V alignment identity d_identity: - type: float + type: number description: D alignment identity j_identity: - type: float + type: number description: J alignment identity vdj_score: - type: float + type: number description: Score for aligners that consider the full sequence as a whole vdj_evalue: - type: float + type: number description: E-value for aligners that consider the full sequence as a whole vdj_identity: - type: float + type: number description: Identity for aligners that consider the full sequence as a whole vdj_cigar: type: string From 71f8ba5213b38c930314ec3dd61c24c43c83de97 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Thu, 19 Oct 2017 07:22:02 +1300 Subject: [PATCH 29/46] Changed float to number as not supported in swagger and swagger tools... --- Formats_rearrangement.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/Formats_rearrangement.yaml b/Formats_rearrangement.yaml index 009b5fb..de4dd99 100644 --- a/Formats_rearrangement.yaml +++ b/Formats_rearrangement.yaml @@ -51,16 +51,16 @@ Formats_Rearrangements: type: string description: C gene assignment v_score: - type: float + type: number description: V alignment score d_score: - type: float + type: number description: D alignment score j_score: - type: float + type: number description: J alignment score c_score: - type: float + type: number description: C alignment score v_cigar: type: string @@ -75,31 +75,31 @@ Formats_Rearrangements: type: string description: C alignment CIGAR string v_evalue: - type: float + type: number description: V alignment E-value (when applicable) d_evalue: - type: float + type: number description: D alignment E-value (when applicable) j_evalue: - type: float + type: number description: J alignment E-value (when applicable) v_identity: - type: float + type: number description: V alignment identity d_identity: - type: float + type: number description: D alignment identity j_identity: - type: float + type: number description: J alignment identity vdj_score: - type: float + type: number description: Score for aligners that consider the full sequence as a whole vdj_evalue: - type: float + type: number description: E-value for aligners that consider the full sequence as a whole vdj_identity: - type: float + type: number description: Identity for aligners that consider the full sequence as a whole vdj_cigar: type: string From 0fdffb901e8fce5e06ee705e73926f7be4b70778 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 20 Oct 2017 16:14:57 +1300 Subject: [PATCH 30/46] Fixes to API definition to bring up to data with expected December API spec, hopefully with no more changes. As of this update, the API spec and the /v2/samples SQL service API response are in sync --- iReceptor_Data_Service_API_V2.json | 172 +++++++++++++++++++---------- iReceptor_Data_Service_API_V2.yaml | 158 +++++++++++++++++--------- 2 files changed, 218 insertions(+), 112 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 4e3181a..88f7fb7 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -76,14 +76,14 @@ "ireceptor_sequence_count_model": { "type": "object", "properties": { - "sequence_count": { + "ir_sequence_count": { "type": "integer", "description": "Number of sequences found that met the search criteria for this sample", "example": 123456 } } }, - "ireceptor_samples_parameters_model": { + "ireceptor_core_samples_parameters_model": { "type": "object", "required": [ "ir_username" @@ -94,19 +94,45 @@ "description": "Username of the individual requesting access to the iReceptor repository node.\n" }, "ir_lab_id": { - "type": "integer", + "type": "string", "description": "e.g. 1\n" }, "ir_project_id": { "type": "array", "items": { - "type": "integer" + "type": "string" }, "description": "e.g. 1\n" } } }, - "ireceptor_sequences_parameters_model": { + "ireceptor_ancillary_samples_parameters_model": { + "type": "object", + "properties": { + "ir_subject_age_min": { + "type": "integer", + "description": "e.g. 30\n" + }, + "ir_subject_age_max": { + "type": "integer", + "description": "e.g. 50\n" + } + } + }, + "airr_formats_sequences_parameters_model": { + "type": "object", + "properties": { + "junction_length": { + "type": "integer", + "description": "Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues)\n" + }, + "functional": { + "type": "string", + "description": "Filter for sequences that are either functional, non-functional, or both\n" + } + } + }, + "ireceptor_core_sequences_parameters_model": { "type": "object", "required": [ "ir_username" @@ -119,15 +145,20 @@ "ir_project_sample_id_list": { "type": "array", "items": { - "type": "integer" + "type": "string" } }, "ir_data_format": { "description": "'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)" - }, - "ir_junction_nt_length": { - "type": "integer", - "description": "Length of JUNCTION in nucleotide base pairs (iReceptor)" + } + } + }, + "ireceptor_ancillary_sequences_parameters_model": { + "type": "object", + "properties": { + "ir_show_unproductive": { + "type": "string", + "description": "By default, only productive sequences are returned. In order to return unproductive sequences, set this parameter to \"T\"" }, "ir_junction_aa_length": { "type": "integer", @@ -144,23 +175,6 @@ "required": false, "type": "string" }, - "ir_sample_id_list": { - "name": "ir_project_sample_id_list", - "in": "query", - "description": "List of unique identifiers (specific to the repository) that identify the samples to apply the query to.\n", - "required": false, - "type": "array", - "items": { - "type": "string" - } - }, - "ir_data_format": { - "name": "ir_data_format", - "in": "query", - "description": "Data format to return the sequence data in, one of:
'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", - "required": false, - "type": "string" - }, "study_id": { "name": "study_id", "type": "string", @@ -312,13 +326,13 @@ "name": "junction_nt", "in": "query", "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region (nucleotide)) (AIRR)\n" + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region + preserved residues (nucleotide)) (AIRR)\n" }, "junction_aa": { "name": "junction_aa", "in": "query", "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region (amino acid)) (AIRR)\n" + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region + preserved residues (amino acid)) (AIRR)\n" }, "duplicate_count": { "name": "duplicate_count", @@ -326,17 +340,56 @@ "type": "integer", "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" }, + "junction_length": { + "name": "junction_length", + "in": "query", + "type": "integer", + "description": "Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues)\n" + }, + "functional": { + "name": "functional", + "in": "query", + "type": "string", + "description": "Filter for sequences that are either functional, non-functional, or both\n" + }, + "ir_sample_id_list": { + "name": "ir_project_sample_id_list", + "in": "query", + "description": "List of unique identifiers (specific to the repository) that identify the samples to apply the query to.\n", + "required": false, + "type": "array", + "items": { + "type": "string" + } + }, + "ir_data_format": { + "name": "ir_data_format", + "in": "query", + "description": "Data format to return the sequence data in, one of:
'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", + "required": false, + "type": "string" + }, + "ir_show_unproductive": { + "name": "ir_show_unproductive", + "in": "query", + "description": "By default, only productive sequences are returned. In order to return unproductive sequences, set this parameter to \"T\"\n", + "required": false, + "type": "array", + "items": { + "type": "string" + } + }, "ir_junction_nt_length": { "name": "ir_junction_nt_length", "in": "query", - "description": "Length of JUNCTION in nucleotide base pairs (iReceptor)", + "description": "Length of JUNCTION (CDR3 + preserved residues) in nucleotide base pairs (iReceptor)", "required": false, "type": "integer" }, "ir_junction_aa_length": { "name": "ir_junction_aa_length", "in": "query", - "description": "Length of JUNCTION in amino acids (iReceptor)", + "description": "Length of JUNCTION (CDR3 + preserved residues) in amino acids (iReceptor)", "required": false, "type": "integer" } @@ -524,11 +577,14 @@ "required": true, "schema": { "allOf": [ + { + "$ref": "#/definitions/ireceptor_core_samples_parameters_model" + }, { "$ref": "#/definitions/airr_summary_model" }, { - "$ref": "#/definitions/ireceptor_samples_parameters_model" + "$ref": "#/definitions/ireceptor_ancillary_samples_parameters_model" } ] } @@ -574,9 +630,6 @@ { "$ref": "#/parameters/ir_sample_id_list" }, - { - "$ref": "#/parameters/germline_database" - }, { "$ref": "#/parameters/v_allele" }, @@ -587,16 +640,16 @@ "$ref": "#/parameters/j_allele" }, { - "$ref": "#/parameters/c_allele" + "$ref": "#/parameters/junction_aa" }, { - "$ref": "#/parameters/junction_nt" + "$ref": "#/parameters/junction_length" }, { - "$ref": "#/parameters/junction_aa" + "$ref": "#/parameters/functional" }, { - "$ref": "#/parameters/ir_junction_nt_length" + "$ref": "#/parameters/ir_show_unproductive" }, { "$ref": "#/parameters/ir_junction_aa_length" @@ -653,9 +706,6 @@ { "$ref": "#/parameters/ir_data_format" }, - { - "$ref": "#/parameters/germline_database" - }, { "$ref": "#/parameters/v_allele" }, @@ -666,16 +716,16 @@ "$ref": "#/parameters/j_allele" }, { - "$ref": "#/parameters/c_allele" + "$ref": "#/parameters/junction_aa" }, { - "$ref": "#/parameters/junction_nt" + "$ref": "#/parameters/junction_length" }, { - "$ref": "#/parameters/junction_aa" + "$ref": "#/parameters/functional" }, { - "$ref": "#/parameters/ir_junction_nt_length" + "$ref": "#/parameters/ir_show_unproductive" }, { "$ref": "#/parameters/ir_junction_aa_length" @@ -718,10 +768,16 @@ "schema": { "allOf": [ { - "$ref": "#/definitions/ireceptor_sequences_parameters_model" + "$ref": "#/definitions/ireceptor_core_sequences_parameters_model" }, { "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" + }, + { + "$ref": "#/definitions/airr_formats_sequences_parameters_model" + }, + { + "$ref": "#/definitions/ireceptor_ancillary_sequences_parameters_model" } ] } @@ -767,9 +823,6 @@ { "$ref": "#/parameters/ir_sample_id_list" }, - { - "$ref": "#/parameters/germline_database" - }, { "$ref": "#/parameters/v_allele" }, @@ -780,16 +833,16 @@ "$ref": "#/parameters/j_allele" }, { - "$ref": "#/parameters/c_allele" + "$ref": "#/parameters/junction_aa" }, { - "$ref": "#/parameters/junction_nt" + "$ref": "#/parameters/junction_length" }, { - "$ref": "#/parameters/junction_aa" + "$ref": "#/parameters/functional" }, { - "$ref": "#/parameters/ir_junction_nt_length" + "$ref": "#/parameters/ir_show_unproductive" }, { "$ref": "#/parameters/ir_junction_aa_length" @@ -846,9 +899,6 @@ { "$ref": "#/parameters/ir_data_format" }, - { - "$ref": "#/parameters/germline_database" - }, { "$ref": "#/parameters/v_allele" }, @@ -859,16 +909,16 @@ "$ref": "#/parameters/j_allele" }, { - "$ref": "#/parameters/c_allele" + "$ref": "#/parameters/junction_aa" }, { - "$ref": "#/parameters/junction_nt" + "$ref": "#/parameters/junction_length" }, { - "$ref": "#/parameters/junction_aa" + "$ref": "#/parameters/functional" }, { - "$ref": "#/parameters/ir_junction_nt_length" + "$ref": "#/parameters/ir_show_unproductive" }, { "$ref": "#/parameters/ir_junction_aa_length" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index c461ca9..ab86b56 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -55,11 +55,11 @@ definitions: ireceptor_sequence_count_model: type: object properties: - sequence_count: + ir_sequence_count: type: integer description: Number of sequences found that met the search criteria for this sample example: 123456 - ireceptor_samples_parameters_model: + ireceptor_core_samples_parameters_model: type: object required: - ir_username @@ -70,16 +70,44 @@ definitions: Username of the individual requesting access to the iReceptor repository node. ir_lab_id: - type: integer + type: string description: | e.g. 1 ir_project_id: type: array items: - type: integer + type: string description: | e.g. 1 - ireceptor_sequences_parameters_model: + ireceptor_ancillary_samples_parameters_model: + type: object + properties: + ir_subject_age_min: + type: integer + description: | + e.g. 30 + ir_subject_age_max: + type: integer + description: | + e.g. 50 + # + # AIRR Formats compliant extended parameters for rearrangements (/sequences* entry points) + # + airr_formats_sequences_parameters_model: + type: object + properties: + junction_length: + type: integer + description: | + Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues) + functional: + type: string + description: | + Filter for sequences that are either functional, non-functional, or both + # + # iReceptor extensions to the MiAIRR and AIRR Formats parameter models. + # + ireceptor_core_sequences_parameters_model: type: object required: - ir_username @@ -92,17 +120,21 @@ definitions: ir_project_sample_id_list: type: array items: - type: integer + type: string ir_data_format: description: >- 'csv' - vQuest based CSV (as per /v1); 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas); 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) - ir_junction_nt_length: - type: integer + ireceptor_ancillary_sequences_parameters_model: + type: object + properties: + ir_show_unproductive: + type: string description: >- - Length of JUNCTION in nucleotide base pairs (iReceptor) + By default, only productive sequences are returned. In order to return + unproductive sequences, set this parameter to "T" ir_junction_aa_length: type: integer description: >- @@ -122,26 +154,6 @@ parameters: the access for that user for that repository. required: false type: string - ir_sample_id_list: - name: ir_project_sample_id_list - in: query - description: > - List of unique identifiers (specific to the repository) that identify the samples - to apply the query to. - required: false - type: array - items: - type: string - ir_data_format: - name: ir_data_format - in: query - description: >- - Data format to return the sequence data in, one of:
- 'csv' - vQuest based CSV (as per /v1)(default)
- 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
- 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) - required: false - type: string # # MiAIRR compliant parameters for /samples entry points. # Note: Currently only those parameters used by iReceptor repositories @@ -290,14 +302,14 @@ parameters: type: string description: > JUNCTION nucleotide sequence (Sequence of the CDR3 - region (nucleotide)) (AIRR) + region + preserved residues (nucleotide)) (AIRR) junction_aa: name: junction_aa in: query type: string description: > JUNCTION amino acid sequence (Sequence of the CDR3 - region (amino acid)) (AIRR) + region + preserved residues (amino acid)) (AIRR) duplicate_count: name: duplicate_count in: query @@ -305,20 +317,65 @@ parameters: description: | Number of times the sequence has been duplicated in a file (AIRR) # + # AIRR Formats compliant extended parameters for rearrangements (/sequences* entry points) + # + junction_length: + name: junction_length + in: query + type: integer + description: | + Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues) + functional: + name: functional + in: query + type: string + description: | + Filter for sequences that are either functional, non-functional, or both + # # iReceptor specific parameters for rearrangements (/sequences* entry points) # + ir_sample_id_list: + name: ir_project_sample_id_list + in: query + description: > + List of unique identifiers (specific to the repository) that identify the samples + to apply the query to. + required: false + type: array + items: + type: string + ir_data_format: + name: ir_data_format + in: query + description: >- + Data format to return the sequence data in, one of:
+ 'csv' - vQuest based CSV (as per /v1)(default)
+ 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
+ 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) + required: false + type: string + ir_show_unproductive: + name: ir_show_unproductive + in: query + description: > + By default, only productive sequences are returned. In order to return + unproductive sequences, set this parameter to "T" + required: false + type: array + items: + type: string ir_junction_nt_length: name: ir_junction_nt_length in: query description: >- - Length of JUNCTION in nucleotide base pairs (iReceptor) + Length of JUNCTION (CDR3 + preserved residues) in nucleotide base pairs (iReceptor) required: false type: integer ir_junction_aa_length: name: ir_junction_aa_length in: query description: >- - Length of JUNCTION in amino acids (iReceptor) + Length of JUNCTION (CDR3 + preserved residues) in amino acids (iReceptor) required: false type: integer schemes: @@ -448,8 +505,9 @@ paths: required: true schema: allOf: + - $ref: '#/definitions/ireceptor_core_samples_parameters_model' - $ref: '#/definitions/airr_summary_model' - - $ref: '#/definitions/ireceptor_samples_parameters_model' + - $ref: '#/definitions/ireceptor_ancillary_samples_parameters_model' operationId: postSamples responses: '200': @@ -479,14 +537,13 @@ paths: parameters: - $ref: '#/parameters/ir_username' - $ref: '#/parameters/ir_sample_id_list' - - $ref: '#/parameters/germline_database' - $ref: '#/parameters/v_allele' - $ref: '#/parameters/d_allele' - $ref: '#/parameters/j_allele' - - $ref: '#/parameters/c_allele' - - $ref: '#/parameters/junction_nt' - $ref: '#/parameters/junction_aa' - - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/junction_length' + - $ref: '#/parameters/functional' + - $ref: '#/parameters/ir_show_unproductive' - $ref: '#/parameters/ir_junction_aa_length' operationId: getSequenceSummary responses: @@ -533,14 +590,13 @@ paths: - $ref: '#/parameters/ir_username' - $ref: '#/parameters/ir_sample_id_list' - $ref: '#/parameters/ir_data_format' - - $ref: '#/parameters/germline_database' - $ref: '#/parameters/v_allele' - $ref: '#/parameters/d_allele' - $ref: '#/parameters/j_allele' - - $ref: '#/parameters/c_allele' - - $ref: '#/parameters/junction_nt' - $ref: '#/parameters/junction_aa' - - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/junction_length' + - $ref: '#/parameters/functional' + - $ref: '#/parameters/ir_show_unproductive' - $ref: '#/parameters/ir_junction_aa_length' operationId: getSequenceData responses: @@ -580,8 +636,10 @@ paths: in: body schema: allOf: - - $ref: '#/definitions/ireceptor_sequences_parameters_model' + - $ref: '#/definitions/ireceptor_core_sequences_parameters_model' - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' + - $ref: '#/definitions/airr_formats_sequences_parameters_model' + - $ref: '#/definitions/ireceptor_ancillary_sequences_parameters_model' operationId: postSequenceData responses: '200': @@ -616,14 +674,13 @@ paths: parameters: - $ref: '#/parameters/ir_username' - $ref: '#/parameters/ir_sample_id_list' - - $ref: '#/parameters/germline_database' - $ref: '#/parameters/v_allele' - $ref: '#/parameters/d_allele' - $ref: '#/parameters/j_allele' - - $ref: '#/parameters/c_allele' - - $ref: '#/parameters/junction_nt' - $ref: '#/parameters/junction_aa' - - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/junction_length' + - $ref: '#/parameters/functional' + - $ref: '#/parameters/ir_show_unproductive' - $ref: '#/parameters/ir_junction_aa_length' operationId: getCloneSummary responses: @@ -661,14 +718,13 @@ paths: - $ref: '#/parameters/ir_username' - $ref: '#/parameters/ir_sample_id_list' - $ref: '#/parameters/ir_data_format' - - $ref: '#/parameters/germline_database' - $ref: '#/parameters/v_allele' - $ref: '#/parameters/d_allele' - $ref: '#/parameters/j_allele' - - $ref: '#/parameters/c_allele' - - $ref: '#/parameters/junction_nt' - $ref: '#/parameters/junction_aa' - - $ref: '#/parameters/ir_junction_nt_length' + - $ref: '#/parameters/junction_length' + - $ref: '#/parameters/functional' + - $ref: '#/parameters/ir_show_unproductive' - $ref: '#/parameters/ir_junction_aa_length' operationId: getCloneData responses: From 8a396e5281939347271e40167d099139625a0300 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Fri, 20 Oct 2017 06:23:18 -0500 Subject: [PATCH 31/46] add consumes --- iReceptor_Data_Service_API_V2.json | 5 ++++- iReceptor_Data_Service_API_V2.yaml | 2 ++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 4e3181a..6f2909b 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -347,6 +347,9 @@ "produces": [ "application/json" ], + "consumes": [ + "application/x-www-form-urlencoded" + ], "tags": [ { "name": "info", @@ -901,4 +904,4 @@ } } } -} \ No newline at end of file +} diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index c461ca9..87250a3 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -325,6 +325,8 @@ schemes: - https produces: - application/json +consumes: + - application/x-www-form-urlencoded tags: - name: info description: Service information From b735dfa06997adaba3de3ae63749b76c19cea5f5 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Fri, 20 Oct 2017 08:22:59 -0500 Subject: [PATCH 32/46] add json for consumes --- iReceptor_Data_Service_API_V2.json | 3 ++- iReceptor_Data_Service_API_V2.yaml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index f2dafea..b65156d 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -401,7 +401,8 @@ "application/json" ], "consumes": [ - "application/x-www-form-urlencoded" + "application/x-www-form-urlencoded", + "application/json" ], "tags": [ { diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 00b10e0..8b4b242 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -384,6 +384,7 @@ produces: - application/json consumes: - application/x-www-form-urlencoded + - application/json tags: - name: info description: Service information From 5f9d4f7cbd39e3c8f29226c221b8bb45af6aaa78 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Sat, 21 Oct 2017 09:28:21 +1300 Subject: [PATCH 33/46] Changed "preserved residue" to "conserved residue" in describing Junction. --- iReceptor_Data_Service_API_V2.json | 14 +++++++------- iReceptor_Data_Service_API_V2.yaml | 12 ++++++------ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index f2dafea..da94936 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -124,7 +124,7 @@ "properties": { "junction_length": { "type": "integer", - "description": "Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues)\n" + "description": "Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues)\n" }, "functional": { "type": "string", @@ -326,13 +326,13 @@ "name": "junction_nt", "in": "query", "type": "string", - "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region + preserved residues (nucleotide)) (AIRR)\n" + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region + conserved residues (nucleotide)) (AIRR)\n" }, "junction_aa": { "name": "junction_aa", "in": "query", "type": "string", - "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region + preserved residues (amino acid)) (AIRR)\n" + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region + conserved residues (amino acid)) (AIRR)\n" }, "duplicate_count": { "name": "duplicate_count", @@ -344,7 +344,7 @@ "name": "junction_length", "in": "query", "type": "integer", - "description": "Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues)\n" + "description": "Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues)\n" }, "functional": { "name": "functional", @@ -382,14 +382,14 @@ "ir_junction_nt_length": { "name": "ir_junction_nt_length", "in": "query", - "description": "Length of JUNCTION (CDR3 + preserved residues) in nucleotide base pairs (iReceptor)", + "description": "Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor)", "required": false, "type": "integer" }, "ir_junction_aa_length": { "name": "ir_junction_aa_length", "in": "query", - "description": "Length of JUNCTION (CDR3 + preserved residues) in amino acids (iReceptor)", + "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor)", "required": false, "type": "integer" } @@ -954,4 +954,4 @@ } } } -} +} \ No newline at end of file diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 00b10e0..a78e3e3 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -99,7 +99,7 @@ definitions: junction_length: type: integer description: | - Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues) + Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues) functional: type: string description: | @@ -302,14 +302,14 @@ parameters: type: string description: > JUNCTION nucleotide sequence (Sequence of the CDR3 - region + preserved residues (nucleotide)) (AIRR) + region + conserved residues (nucleotide)) (AIRR) junction_aa: name: junction_aa in: query type: string description: > JUNCTION amino acid sequence (Sequence of the CDR3 - region + preserved residues (amino acid)) (AIRR) + region + conserved residues (amino acid)) (AIRR) duplicate_count: name: duplicate_count in: query @@ -324,7 +324,7 @@ parameters: in: query type: integer description: | - Number of junction nucleotides in sequence_vdj (CDR3 + preserved residues) + Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues) functional: name: functional in: query @@ -368,14 +368,14 @@ parameters: name: ir_junction_nt_length in: query description: >- - Length of JUNCTION (CDR3 + preserved residues) in nucleotide base pairs (iReceptor) + Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor) required: false type: integer ir_junction_aa_length: name: ir_junction_aa_length in: query description: >- - Length of JUNCTION (CDR3 + preserved residues) in amino acids (iReceptor) + Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor) required: false type: integer schemes: From b2b738089a3e9ad28c55b8b5bc5096d01295b348 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Wed, 25 Oct 2017 06:21:55 -0500 Subject: [PATCH 34/46] form parameters for /samples --- iReceptor_Data_Service_API_V2.json | 209 +++++++++++++++++++++++++---- iReceptor_Data_Service_API_V2.yaml | 134 ++++++++++++++++-- 2 files changed, 309 insertions(+), 34 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 8cb9bdd..72ad845 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -33,15 +33,9 @@ "type": "array", "items": { "allOf": [ - { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" - }, - { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements" - }, - { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequence.yaml#/ireceptor_sequence_annotation_model" - } + { + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/airr-formats/specs/definitions.yaml#/Rearrangement" + } ] } }, @@ -175,86 +169,173 @@ "required": false, "type": "string" }, + "ir_username_form": { + "name": "ir_username", + "in": "formData", + "description": "Username of the individual requesting access to the iReceptor repository node. If the iReceptor repository is a public repository, then this parameter is not required. If the repository is not public then the username must be supplied and the repository will determine the access for that user for that repository.\n", + "required": true, + "type": "string" + }, "study_id": { "name": "study_id", "type": "string", "in": "query" }, + "study_id_form": { + "name": "study_id", + "type": "string", + "in": "formData" + }, "study_title": { "name": "study_title", "type": "string", "in": "query" }, + "study_title_form": { + "name": "study_title", + "type": "string", + "in": "formData" + }, "study_description": { "name": "study_description", "type": "string", "in": "query" }, + "study_description_form": { + "name": "study_description", + "type": "string", + "in": "formData" + }, "lab_name": { "name": "lab_name", "type": "string", "in": "query" }, + "lab_name_form": { + "name": "lab_name", + "type": "string", + "in": "formData" + }, "subject_id": { "name": "subject_id", "type": "string", "in": "query" }, + "subject_id_form": { + "name": "subject_id", + "type": "string", + "in": "formData" + }, "organism": { "name": "organism", "type": "string", "in": "query" }, + "organism_form": { + "name": "organism", + "type": "string", + "in": "formData" + }, "sex": { "name": "sex", "type": "string", "in": "query" }, + "sex_form": { + "name": "sex", + "type": "string", + "in": "formData" + }, "ethnicity": { "name": "ethnicity", "type": "string", "in": "query" }, + "ethnicity_form": { + "name": "ethnicity", + "type": "string", + "in": "formData" + }, "study_group_description": { "name": "study_group_description", "type": "string", "in": "query" }, + "study_group_description_form": { + "name": "study_group_description", + "type": "string", + "in": "formData" + }, "sample_id": { "name": "sample_id", "type": "string", "in": "query" }, + "sample_id_form": { + "name": "sample_id", + "type": "string", + "in": "formData" + }, "tissue": { "name": "tissue", "type": "string", "in": "query" }, + "tissue_form": { + "name": "tissue", + "type": "string", + "in": "formData" + }, "disease_state_sample": { "name": "disease_state_sample", "type": "string", "in": "query" }, + "disease_state_sample_form": { + "name": "disease_state_sample", + "type": "string", + "in": "formData" + }, "cell_subset": { "name": "cell_subset", "type": "string", "in": "query" }, + "cell_subset_form": { + "name": "cell_subset", + "type": "string", + "in": "formData" + }, "cell_phenotype": { "name": "cell_phenotype", "type": "string", "in": "query" }, + "cell_phenotype_form": { + "name": "cell_phenotype", + "type": "string", + "in": "formData" + }, "library_source": { "name": "library_source", "type": "string", "in": "query" }, + "library_source_form": { + "name": "library_source", + "type": "string", + "in": "formData" + }, "platform": { "name": "platform", "type": "string", "in": "query" }, + "platform_form": { + "name": "platform", + "type": "string", + "in": "formData" + }, "ir_lab_id": { "name": "ir_lab_id", "in": "query", @@ -262,6 +343,13 @@ "required": false, "type": "string" }, + "ir_lab_id_form": { + "name": "ir_lab_id", + "in": "formData", + "description": "e.g. 1\n", + "required": false, + "type": "string" + }, "ir_project_id": { "name": "ir_project_id", "in": "query", @@ -272,6 +360,16 @@ "type": "string" } }, + "ir_project_id_form": { + "name": "ir_project_id", + "in": "formData", + "description": "e.g. 1\n", + "required": false, + "type": "array", + "items": { + "type": "string" + } + }, "ir_subject_age_min": { "name": "ir_subject_age_min", "in": "query", @@ -279,6 +377,13 @@ "required": false, "type": "integer" }, + "ir_subject_age_min_form": { + "name": "ir_subject_age_min", + "in": "formData", + "description": "e.g. 10\n", + "required": false, + "type": "integer" + }, "ir_subject_age_max": { "name": "ir_subject_age_max", "in": "query", @@ -286,6 +391,13 @@ "required": false, "type": "integer" }, + "ir_subject_age_max_form": { + "name": "ir_subject_age_max", + "in": "formData", + "description": "e.g. 12\n", + "required": false, + "type": "integer" + }, "germline_database": { "name": "germline_database", "in": "query", @@ -576,22 +688,67 @@ ], "parameters": [ { - "name": "query", - "in": "body", - "required": true, - "schema": { - "allOf": [ - { - "$ref": "#/definitions/ireceptor_core_samples_parameters_model" - }, - { - "$ref": "#/definitions/airr_summary_model" - }, - { - "$ref": "#/definitions/ireceptor_ancillary_samples_parameters_model" - } - ] - } + "$ref": "#/parameters/ir_username_form" + }, + { + "$ref": "#/parameters/ir_lab_id_form" + }, + { + "$ref": "#/parameters/ir_project_id_form" + }, + { + "$ref": "#/parameters/study_id_form" + }, + { + "$ref": "#/parameters/study_title_form" + }, + { + "$ref": "#/parameters/study_description_form" + }, + { + "$ref": "#/parameters/lab_name_form" + }, + { + "$ref": "#/parameters/subject_id_form" + }, + { + "$ref": "#/parameters/organism_form" + }, + { + "$ref": "#/parameters/sex_form" + }, + { + "$ref": "#/parameters/ethnicity_form" + }, + { + "$ref": "#/parameters/study_group_description_form" + }, + { + "$ref": "#/parameters/sample_id_form" + }, + { + "$ref": "#/parameters/tissue_form" + }, + { + "$ref": "#/parameters/disease_state_sample_form" + }, + { + "$ref": "#/parameters/cell_subset_form" + }, + { + "$ref": "#/parameters/cell_phenotype_form" + }, + { + "$ref": "#/parameters/library_source_form" + }, + { + "$ref": "#/parameters/platform_form" + }, + { + "$ref": "#/parameters/ir_subject_age_min_form" + }, + { + "$ref": "#/parameters/ir_subject_age_max_form" } ], "operationId": "postSamples", @@ -955,4 +1112,4 @@ } } } -} \ No newline at end of file +} diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 0993518..19f239d 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -154,6 +154,17 @@ parameters: the access for that user for that repository. required: false type: string + ir_username_form: + name: ir_username + in: formData + description: > + Username of the individual requesting access to the iReceptor + repository node. If the iReceptor repository is a public repository, + then this parameter is not required. If the repository is not public + then the username must be supplied and the repository will determine + the access for that user for that repository. + required: false + type: string # # MiAIRR compliant parameters for /samples entry points. # Note: Currently only those parameters used by iReceptor repositories @@ -163,66 +174,130 @@ parameters: name: study_id type: string in: query + study_id_form: + name: study_id + type: string + in: formData study_title: name: study_title type: string in: query + study_title_form: + name: study_title + type: string + in: formData study_description: name: study_description type: string in: query + study_description_form: + name: study_description + type: string + in: formData lab_name: name: lab_name type: string in: query + lab_name_form: + name: lab_name + type: string + in: formData subject_id: name: subject_id type: string in: query + subject_id_form: + name: subject_id + type: string + in: formData organism: name: organism type: string in: query + organism_form: + name: organism + type: string + in: formData sex: name: sex type: string in: query + sex_form: + name: sex + type: string + in: formData ethnicity: name: ethnicity type: string in: query + ethnicity_form: + name: ethnicity + type: string + in: formData study_group_description: name: study_group_description type: string in: query + study_group_description_form: + name: study_group_description + type: string + in: formData sample_id: name: sample_id type: string in: query + sample_id_form: + name: sample_id + type: string + in: formData tissue: name: tissue type: string in: query + tissue_form: + name: tissue + type: string + in: formData disease_state_sample: name: disease_state_sample type: string in: query + disease_state_sample_form: + name: disease_state_sample + type: string + in: formData cell_subset: name: cell_subset type: string in: query + cell_subset_form: + name: cell_subset + type: string + in: formData cell_phenotype: name: cell_phenotype type: string in: query + cell_phenotype_form: + name: cell_phenotype + type: string + in: formData library_source: name: library_source type: string in: query + library_source_form: + name: library_source + type: string + in: formData platform: name: platform type: string in: query + platform_form: + name: platform + type: string + in: formData # # iReceptor specific parameters for the /samples API entry point. # @@ -233,6 +308,13 @@ parameters: e.g. 1 required: false type: string + ir_lab_id_form: + name: ir_lab_id + in: formData + description: | + e.g. 1 + required: false + type: string ir_project_id: name: ir_project_id in: query @@ -242,6 +324,15 @@ parameters: type: array items: type: string + ir_project_id_form: + name: ir_project_id + in: formData + description: | + e.g. 1 + required: false + type: array + items: + type: string ir_subject_age_min: name: ir_subject_age_min in: query @@ -249,6 +340,13 @@ parameters: e.g. 10 required: false type: integer + ir_subject_age_min_form: + name: ir_subject_age_min + in: formData + description: | + e.g. 10 + required: false + type: integer ir_subject_age_max: name: ir_subject_age_max in: query @@ -256,6 +354,13 @@ parameters: e.g. 12 required: false type: integer + ir_subject_age_max_form: + name: ir_subject_age_max + in: formData + description: | + e.g. 12 + required: false + type: integer # # MiAIRR compliant parameters for rearrangements (/sequences* entry points) # @@ -503,14 +608,27 @@ paths: tags: - samples parameters: - - name: query - in: body - required: true - schema: - allOf: - - $ref: '#/definitions/ireceptor_core_samples_parameters_model' - - $ref: '#/definitions/airr_summary_model' - - $ref: '#/definitions/ireceptor_ancillary_samples_parameters_model' + - $ref: '#/parameters/ir_username_form' + - $ref: '#/parameters/ir_lab_id_form' + - $ref: '#/parameters/ir_project_id_form' + - $ref: '#/parameters/study_id_form' + - $ref: '#/parameters/study_title_form' + - $ref: '#/parameters/study_description_form' + - $ref: '#/parameters/lab_name_form' + - $ref: '#/parameters/subject_id_form' + - $ref: '#/parameters/organism_form' + - $ref: '#/parameters/sex_form' + - $ref: '#/parameters/ethnicity_form' + - $ref: '#/parameters/study_group_description_form' + - $ref: '#/parameters/sample_id_form' + - $ref: '#/parameters/tissue_form' + - $ref: '#/parameters/disease_state_sample_form' + - $ref: '#/parameters/cell_subset_form' + - $ref: '#/parameters/cell_phenotype_form' + - $ref: '#/parameters/library_source_form' + - $ref: '#/parameters/platform_form' + - $ref: '#/parameters/ir_subject_age_min_form' + - $ref: '#/parameters/ir_subject_age_max_form' operationId: postSamples responses: '200': From 4732a8bf297b2090d0bdd5f8fbc7a17f2c6e857c Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Thu, 26 Oct 2017 14:45:21 +1300 Subject: [PATCH 35/46] Created "formData" parameters for sequences. Added post methods for sequences_* APIs. Changed /clones_* APIs to be post only. --- iReceptor_Data_Service_API_V2.json | 296 ++++++++++++++++++++++++----- iReceptor_Data_Service_API_V2.yaml | 242 +++++++++++++++++++---- 2 files changed, 452 insertions(+), 86 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 72ad845..3c83766 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -33,9 +33,15 @@ "type": "array", "items": { "allOf": [ - { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/airr-formats/specs/definitions.yaml#/Rearrangement" - } + { + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" + }, + { + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements" + }, + { + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequence.yaml#/ireceptor_sequence_annotation_model" + } ] } }, @@ -173,7 +179,7 @@ "name": "ir_username", "in": "formData", "description": "Username of the individual requesting access to the iReceptor repository node. If the iReceptor repository is a public repository, then this parameter is not required. If the repository is not public then the username must be supplied and the repository will determine the access for that user for that repository.\n", - "required": true, + "required": false, "type": "string" }, "study_id": { @@ -404,66 +410,132 @@ "type": "string", "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" }, + "germline_database_form": { + "name": "germline_database", + "in": "formData", + "type": "string", + "description": "Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR)\n" + }, "cell_index": { "name": "cell_index", "in": "query", "type": "integer", "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" }, + "cell_index_form": { + "name": "cell_index", + "in": "formData", + "type": "integer", + "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" + }, "v_allele": { "name": "v_allele", "in": "query", "type": "string", "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" }, + "v_allele_form": { + "name": "v_allele", + "in": "formData", + "type": "string", + "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" + }, "d_allele": { "name": "d_allele", "in": "query", "type": "string", "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" }, + "d_allele_form": { + "name": "d_allele", + "in": "formData", + "type": "string", + "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" + }, "j_allele": { "name": "j_allele", "in": "query", "type": "string", "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" }, + "j_allele_form": { + "name": "j_allele", + "in": "formData", + "type": "string", + "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" + }, "c_allele": { "name": "c_allele", "in": "query", "type": "string", "description": "C region with allele (AIRR) \n" }, + "c_allele_form": { + "name": "c_allele", + "in": "formData", + "type": "string", + "description": "C region with allele (AIRR) \n" + }, "junction_nt": { "name": "junction_nt", "in": "query", "type": "string", "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region + conserved residues (nucleotide)) (AIRR)\n" }, + "junction_nt_form": { + "name": "junction_nt", + "in": "formData", + "type": "string", + "description": "JUNCTION nucleotide sequence (Sequence of the CDR3 region + conserved residues (nucleotide)) (AIRR)\n" + }, "junction_aa": { "name": "junction_aa", "in": "query", "type": "string", "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region + conserved residues (amino acid)) (AIRR)\n" }, + "junction_aa_form": { + "name": "junction_aa", + "in": "formData", + "type": "string", + "description": "JUNCTION amino acid sequence (Sequence of the CDR3 region + conserved residues (amino acid)) (AIRR)\n" + }, "duplicate_count": { "name": "duplicate_count", "in": "query", "type": "integer", "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" }, + "duplicate_count_form": { + "name": "duplicate_count", + "in": "formData", + "type": "integer", + "description": "Number of times the sequence has been duplicated in a file (AIRR)\n" + }, "junction_length": { "name": "junction_length", "in": "query", "type": "integer", "description": "Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues)\n" }, + "junction_length_form": { + "name": "junction_length", + "in": "formData", + "type": "integer", + "description": "Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues)\n" + }, "functional": { "name": "functional", "in": "query", "type": "string", "description": "Filter for sequences that are either functional, non-functional, or both\n" }, + "functional_form": { + "name": "functional", + "in": "formData", + "type": "string", + "description": "Filter for sequences that are either functional, non-functional, or both\n" + }, "ir_sample_id_list": { "name": "ir_project_sample_id_list", "in": "query", @@ -474,6 +546,16 @@ "type": "string" } }, + "ir_sample_id_list_form": { + "name": "ir_project_sample_id_list", + "in": "formData", + "description": "List of unique identifiers (specific to the repository) that identify the samples to apply the query to.\n", + "required": false, + "type": "array", + "items": { + "type": "string" + } + }, "ir_data_format": { "name": "ir_data_format", "in": "query", @@ -481,6 +563,13 @@ "required": false, "type": "string" }, + "ir_data_format_form": { + "name": "ir_data_format", + "in": "formData", + "description": "Data format to return the sequence data in, one of:
'csv' - vQuest based CSV (as per /v1)(default)
'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec)", + "required": false, + "type": "string" + }, "ir_show_unproductive": { "name": "ir_show_unproductive", "in": "query", @@ -491,6 +580,16 @@ "type": "string" } }, + "ir_show_unproductive_form": { + "name": "ir_show_unproductive", + "in": "formData", + "description": "By default, only productive sequences are returned. In order to return unproductive sequences, set this parameter to \"T\"\n", + "required": false, + "type": "array", + "items": { + "type": "string" + } + }, "ir_junction_nt_length": { "name": "ir_junction_nt_length", "in": "query", @@ -498,12 +597,26 @@ "required": false, "type": "integer" }, + "ir_junction_nt_length_form": { + "name": "ir_junction_nt_length", + "in": "formData", + "description": "Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor)", + "required": false, + "type": "integer" + }, "ir_junction_aa_length": { "name": "ir_junction_aa_length", "in": "query", "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor)", "required": false, "type": "integer" + }, + "ir_junction_aa_length_form": { + "name": "ir_junction_aa_length", + "in": "formData", + "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor)", + "required": false, + "type": "integer" } }, "schemes": [ @@ -754,7 +867,7 @@ "operationId": "postSamples", "responses": { "200": { - "description": "A successful call returns the metadata for each sample, including the number of sequences found for that sample.\n", + "description": "A successful call returns an array of sample summary metadata for each sample that meets the search criteria. The metadata returned for each sample includes the number of sequences found for that sample as well as the study/subject/sample data for that sample. The metadata for each sample in the response contains a set of AIRR compliant data as well as repository specific data that is required to query the repository about those types of elements. \n", "schema": { "$ref": "#/definitions/ireceptor_summary_response" } @@ -780,7 +893,7 @@ "/sequences_summary": { "x-swagger-router-controller": "sequences", "get": { - "description": "This service returns a summary of sequences that matches the GET provided filter. \"username\" parameter refers to external_users table.\n", + "description": "This service returns a summary of sequences that matches the GET provided filter. \"ir_username\" parameter refers to user requesting access to the repository.\n", "tags": [ "sequences" ], @@ -848,6 +961,76 @@ "description": "method not allowed" } } + }, + "post": { + "description": "This service returns a summary of sequences that matches the POST provided filter. \"ir_username\" parameter refers to user requesting access to the repository.\n", + "tags": [ + "sequences" + ], + "parameters": [ + { + "$ref": "#/parameters/ir_username_form" + }, + { + "$ref": "#/parameters/ir_sample_id_list_form" + }, + { + "$ref": "#/parameters/v_allele_form" + }, + { + "$ref": "#/parameters/d_allele_form" + }, + { + "$ref": "#/parameters/j_allele_form" + }, + { + "$ref": "#/parameters/junction_aa_form" + }, + { + "$ref": "#/parameters/junction_length_form" + }, + { + "$ref": "#/parameters/functional_form" + }, + { + "$ref": "#/parameters/ir_show_unproductive_form" + }, + { + "$ref": "#/parameters/ir_junction_aa_length_form" + } + ], + "operationId": "postSequenceSummary", + "responses": { + "200": { + "description": "A successful call returns two components, an aggregated summary of the data that satisfies the query and an example subset of the annotated sequence data that meets the query criteria. The aggreated data returns a summary similar to that returned by the /samples API entry point, returning the number of sequences and the study/subject/sample meta-data for each sample. The example subset of sequence data that is returned is a small subset of annotated sequences that met the search criteria. The number of sequences returned is given in the \"num_sequences\" paramter to the query and the format in which the sequences are returned is provided by the \"sequence_format\" parameter to the query.\n", + "schema": { + "type": "object", + "properties": { + "summary": { + "$ref": "#/definitions/ireceptor_summary_response" + }, + "items": { + "$ref": "#/definitions/ireceptor_sequence_response" + } + } + } + }, + "400": { + "description": "malformed request" + }, + "401": { + "description": "authentication error" + }, + "403": { + "description": "authorization error" + }, + "404": { + "description": "data not found" + }, + "405": { + "description": "method not allowed" + } + } } }, "/sequences_data": { @@ -924,24 +1107,37 @@ ], "parameters": [ { - "name": "query", - "in": "body", - "schema": { - "allOf": [ - { - "$ref": "#/definitions/ireceptor_core_sequences_parameters_model" - }, - { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" - }, - { - "$ref": "#/definitions/airr_formats_sequences_parameters_model" - }, - { - "$ref": "#/definitions/ireceptor_ancillary_sequences_parameters_model" - } - ] - } + "$ref": "#/parameters/ir_username_form" + }, + { + "$ref": "#/parameters/ir_sample_id_list_form" + }, + { + "$ref": "#/parameters/ir_data_format_form" + }, + { + "$ref": "#/parameters/v_allele_form" + }, + { + "$ref": "#/parameters/d_allele_form" + }, + { + "$ref": "#/parameters/j_allele_form" + }, + { + "$ref": "#/parameters/junction_aa_form" + }, + { + "$ref": "#/parameters/junction_length_form" + }, + { + "$ref": "#/parameters/functional_form" + }, + { + "$ref": "#/parameters/ir_show_unproductive_form" + }, + { + "$ref": "#/parameters/ir_junction_aa_length_form" } ], "operationId": "postSequenceData", @@ -972,44 +1168,44 @@ }, "/clones_summary": { "x-swagger-router-controller": "clones", - "get": { + "post": { "description": "This service returns a summary of sequence clones that match the GET provided filter. \"username\" parameter refers to external_users table.\n", "tags": [ "clones" ], "parameters": [ { - "$ref": "#/parameters/ir_username" + "$ref": "#/parameters/ir_username_form" }, { - "$ref": "#/parameters/ir_sample_id_list" + "$ref": "#/parameters/ir_sample_id_list_form" }, { - "$ref": "#/parameters/v_allele" + "$ref": "#/parameters/v_allele_form" }, { - "$ref": "#/parameters/d_allele" + "$ref": "#/parameters/d_allele_form" }, { - "$ref": "#/parameters/j_allele" + "$ref": "#/parameters/j_allele_form" }, { - "$ref": "#/parameters/junction_aa" + "$ref": "#/parameters/junction_aa_form" }, { - "$ref": "#/parameters/junction_length" + "$ref": "#/parameters/junction_length_form" }, { - "$ref": "#/parameters/functional" + "$ref": "#/parameters/functional_form" }, { - "$ref": "#/parameters/ir_show_unproductive" + "$ref": "#/parameters/ir_show_unproductive_form" }, { - "$ref": "#/parameters/ir_junction_aa_length" + "$ref": "#/parameters/ir_junction_aa_length_form" } ], - "operationId": "getCloneSummary", + "operationId": "postCloneSummary", "responses": { "200": { "description": "A successful call returns an summary of clone data as an array of 'category' = count pairs in which the 'category' are string tags of parameters of interest from a controlled vocabulary term set.\n", @@ -1045,47 +1241,47 @@ }, "/clones_data": { "x-swagger-router-controller": "clones", - "get": { + "post": { "description": "This service returns a list of clones that matches the GET provided filter. \"username\" parameter refers to external_users table.\n", "tags": [ "clones" ], "parameters": [ { - "$ref": "#/parameters/ir_username" + "$ref": "#/parameters/ir_username_form" }, { - "$ref": "#/parameters/ir_sample_id_list" + "$ref": "#/parameters/ir_sample_id_list_form" }, { - "$ref": "#/parameters/ir_data_format" + "$ref": "#/parameters/ir_data_format_form" }, { - "$ref": "#/parameters/v_allele" + "$ref": "#/parameters/v_allele_form" }, { - "$ref": "#/parameters/d_allele" + "$ref": "#/parameters/d_allele_form" }, { - "$ref": "#/parameters/j_allele" + "$ref": "#/parameters/j_allele_form" }, { - "$ref": "#/parameters/junction_aa" + "$ref": "#/parameters/junction_aa_form" }, { - "$ref": "#/parameters/junction_length" + "$ref": "#/parameters/junction_length_form" }, { - "$ref": "#/parameters/functional" + "$ref": "#/parameters/functional_form" }, { - "$ref": "#/parameters/ir_show_unproductive" + "$ref": "#/parameters/ir_show_unproductive_form" }, { - "$ref": "#/parameters/ir_junction_aa_length" + "$ref": "#/parameters/ir_junction_aa_length_form" } ], - "operationId": "getCloneData", + "operationId": "postCloneData", "responses": { "200": { "description": "A successful call returns an array of sequence data. Optional \"output\" parameter determines the output format. Default is a JSON response, limited to top 50 results. If \"output\" is set to \"csv\", it will return all the matching sequence annotations, in addition to sample information and annotation tool information, in a comma-separated format. \n", @@ -1112,4 +1308,4 @@ } } } -} +} \ No newline at end of file diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 19f239d..0fd3e94 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -371,36 +371,73 @@ parameters: description: > Source of germline V(D)J segments, with version number or date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) + germline_database_form: + name: germline_database + in: formData + type: string + description: > + Source of germline V(D)J segments, with version number or + date accessed (e.g. IMGT/V-QUEST Release 201736-4 (7 September 2017)) (AIRR) cell_index: name: cell_index in: query type: integer description: | Cell Index (UID linking sequences from the same cell) (AIRR) + cell_index_form: + name: cell_index + in: formData + type: integer + description: | + Cell Index (UID linking sequences from the same cell) (AIRR) v_allele: name: v_allele in: query type: string description: | V gene with allele (e.g. IGHV4-59*01) (AIRR) + v_allele_form: + name: v_allele + in: formData + type: string + description: | + V gene with allele (e.g. IGHV4-59*01) (AIRR) d_allele: name: d_allele in: query type: string description: | D gene with allele (e.g. IGHD3-10*01) (AIRR) + d_allele_form: + name: d_allele + in: formData + type: string + description: | + D gene with allele (e.g. IGHD3-10*01) (AIRR) j_allele: name: j_allele in: query type: string description: | J gene with allele (e.g. IGHJ4*02) (AIRR) + j_allele_form: + name: j_allele + in: formData + type: string + description: | + J gene with allele (e.g. IGHJ4*02) (AIRR) c_allele: name: c_allele in: query type: string description: | C region with allele (AIRR) + c_allele_form: + name: c_allele + in: formData + type: string + description: | + C region with allele (AIRR) junction_nt: name: junction_nt in: query @@ -408,6 +445,13 @@ parameters: description: > JUNCTION nucleotide sequence (Sequence of the CDR3 region + conserved residues (nucleotide)) (AIRR) + junction_nt_form: + name: junction_nt + in: formData + type: string + description: > + JUNCTION nucleotide sequence (Sequence of the CDR3 + region + conserved residues (nucleotide)) (AIRR) junction_aa: name: junction_aa in: query @@ -415,12 +459,25 @@ parameters: description: > JUNCTION amino acid sequence (Sequence of the CDR3 region + conserved residues (amino acid)) (AIRR) + junction_aa_form: + name: junction_aa + in: formData + type: string + description: > + JUNCTION amino acid sequence (Sequence of the CDR3 + region + conserved residues (amino acid)) (AIRR) duplicate_count: name: duplicate_count in: query type: integer description: | Number of times the sequence has been duplicated in a file (AIRR) + duplicate_count_form: + name: duplicate_count + in: formData + type: integer + description: | + Number of times the sequence has been duplicated in a file (AIRR) # # AIRR Formats compliant extended parameters for rearrangements (/sequences* entry points) # @@ -430,12 +487,24 @@ parameters: type: integer description: | Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues) + junction_length_form: + name: junction_length + in: formData + type: integer + description: | + Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues) functional: name: functional in: query type: string description: | Filter for sequences that are either functional, non-functional, or both + functional_form: + name: functional + in: formData + type: string + description: | + Filter for sequences that are either functional, non-functional, or both # # iReceptor specific parameters for rearrangements (/sequences* entry points) # @@ -449,6 +518,16 @@ parameters: type: array items: type: string + ir_sample_id_list_form: + name: ir_project_sample_id_list + in: formData + description: > + List of unique identifiers (specific to the repository) that identify the samples + to apply the query to. + required: false + type: array + items: + type: string ir_data_format: name: ir_data_format in: query @@ -459,6 +538,16 @@ parameters: 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) required: false type: string + ir_data_format_form: + name: ir_data_format + in: formData + description: >- + Data format to return the sequence data in, one of:
+ 'csv' - vQuest based CSV (as per /v1)(default)
+ 'tsv' - vQuest based TSV (as per /v1 with tab delimiters instead of commas);
+ 'airr' - AIRR Formats rearrangements TSV (as per AIRR formats rearrangements spec) + required: false + type: string ir_show_unproductive: name: ir_show_unproductive in: query @@ -469,6 +558,16 @@ parameters: type: array items: type: string + ir_show_unproductive_form: + name: ir_show_unproductive + in: formData + description: > + By default, only productive sequences are returned. In order to return + unproductive sequences, set this parameter to "T" + required: false + type: array + items: + type: string ir_junction_nt_length: name: ir_junction_nt_length in: query @@ -476,6 +575,13 @@ parameters: Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor) required: false type: integer + ir_junction_nt_length_form: + name: ir_junction_nt_length + in: formData + description: >- + Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor) + required: false + type: integer ir_junction_aa_length: name: ir_junction_aa_length in: query @@ -483,6 +589,13 @@ parameters: Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor) required: false type: integer + ir_junction_aa_length_form: + name: ir_junction_aa_length + in: formData + description: >- + Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor) + required: false + type: integer schemes: - https produces: @@ -633,8 +746,13 @@ paths: responses: '200': description: > - A successful call returns the metadata for each sample, including - the number of sequences found for that sample. + A successful call returns an array of sample summary metadata for + each sample that meets the search criteria. The metadata returned + for each sample includes the number of sequences found for that sample + as well as the study/subject/sample data for that sample. The metadata + for each sample in the response contains a set of AIRR compliant data + as well as repository specific data that is required to query the + repository about those types of elements. schema: $ref: '#/definitions/ireceptor_summary_response' '400': @@ -652,7 +770,8 @@ paths: get: description: > This service returns a summary of sequences that matches the GET - provided filter. "username" parameter refers to external_users table. + provided filter. "ir_username" parameter refers to user requesting + access to the repository. tags: - sequences parameters: @@ -696,6 +815,54 @@ paths: description: data not found '405': description: method not allowed + post: + description: > + This service returns a summary of sequences that matches the POST + provided filter. "ir_username" parameter refers to user requesting + access to the repository. + tags: + - sequences + parameters: + - $ref: '#/parameters/ir_username_form' + - $ref: '#/parameters/ir_sample_id_list_form' + - $ref: '#/parameters/v_allele_form' + - $ref: '#/parameters/d_allele_form' + - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/junction_aa_form' + - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/functional_form' + - $ref: '#/parameters/ir_show_unproductive_form' + - $ref: '#/parameters/ir_junction_aa_length_form' + operationId: postSequenceSummary + responses: + '200': + description: > + A successful call returns two components, an aggregated summary of the data + that satisfies the query and an example subset of the annotated sequence data + that meets the query criteria. The aggreated data returns a summary similar + to that returned by the /samples API entry point, returning the number of + sequences and the study/subject/sample meta-data for each sample. The example + subset of sequence data that is returned is a small subset of annotated sequences + that met the search criteria. The number of sequences returned is given in the + "num_sequences" paramter to the query and the format in which the sequences are + returned is provided by the "sequence_format" parameter to the query. + schema: + type: object + properties: + summary: + $ref: '#/definitions/ireceptor_summary_response' + items: + $ref: '#/definitions/ireceptor_sequence_response' + '400': + description: malformed request + '401': + description: authentication error + '403': + description: authorization error + '404': + description: data not found + '405': + description: method not allowed /sequences_data: x-swagger-router-controller: sequences get: @@ -753,14 +920,17 @@ paths: tags: - sequences parameters: - - name: query - in: body - schema: - allOf: - - $ref: '#/definitions/ireceptor_core_sequences_parameters_model' - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' - - $ref: '#/definitions/airr_formats_sequences_parameters_model' - - $ref: '#/definitions/ireceptor_ancillary_sequences_parameters_model' + - $ref: '#/parameters/ir_username_form' + - $ref: '#/parameters/ir_sample_id_list_form' + - $ref: '#/parameters/ir_data_format_form' + - $ref: '#/parameters/v_allele_form' + - $ref: '#/parameters/d_allele_form' + - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/junction_aa_form' + - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/functional_form' + - $ref: '#/parameters/ir_show_unproductive_form' + - $ref: '#/parameters/ir_junction_aa_length_form' operationId: postSequenceData responses: '200': @@ -786,24 +956,24 @@ paths: description: method not allowed /clones_summary: x-swagger-router-controller: clones - get: + post: description: > This service returns a summary of sequence clones that match the GET provided filter. "username" parameter refers to external_users table. tags: - clones parameters: - - $ref: '#/parameters/ir_username' - - $ref: '#/parameters/ir_sample_id_list' - - $ref: '#/parameters/v_allele' - - $ref: '#/parameters/d_allele' - - $ref: '#/parameters/j_allele' - - $ref: '#/parameters/junction_aa' - - $ref: '#/parameters/junction_length' - - $ref: '#/parameters/functional' - - $ref: '#/parameters/ir_show_unproductive' - - $ref: '#/parameters/ir_junction_aa_length' - operationId: getCloneSummary + - $ref: '#/parameters/ir_username_form' + - $ref: '#/parameters/ir_sample_id_list_form' + - $ref: '#/parameters/v_allele_form' + - $ref: '#/parameters/d_allele_form' + - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/junction_aa_form' + - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/functional_form' + - $ref: '#/parameters/ir_show_unproductive_form' + - $ref: '#/parameters/ir_junction_aa_length_form' + operationId: postCloneSummary responses: '200': description: > @@ -829,25 +999,25 @@ paths: description: method not allowed /clones_data: x-swagger-router-controller: clones - get: + post: description: > This service returns a list of clones that matches the GET provided filter. "username" parameter refers to external_users table. tags: - clones parameters: - - $ref: '#/parameters/ir_username' - - $ref: '#/parameters/ir_sample_id_list' - - $ref: '#/parameters/ir_data_format' - - $ref: '#/parameters/v_allele' - - $ref: '#/parameters/d_allele' - - $ref: '#/parameters/j_allele' - - $ref: '#/parameters/junction_aa' - - $ref: '#/parameters/junction_length' - - $ref: '#/parameters/functional' - - $ref: '#/parameters/ir_show_unproductive' - - $ref: '#/parameters/ir_junction_aa_length' - operationId: getCloneData + - $ref: '#/parameters/ir_username_form' + - $ref: '#/parameters/ir_sample_id_list_form' + - $ref: '#/parameters/ir_data_format_form' + - $ref: '#/parameters/v_allele_form' + - $ref: '#/parameters/d_allele_form' + - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/junction_aa_form' + - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/functional_form' + - $ref: '#/parameters/ir_show_unproductive_form' + - $ref: '#/parameters/ir_junction_aa_length_form' + operationId: postCloneData responses: '200': description: > From 1319e3e5b7da8b0c53908a57932338e8ca5d5a5e Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Fri, 27 Oct 2017 08:16:04 -0500 Subject: [PATCH 36/46] point to v0.1.0 of airr-standards --- iReceptor_Data_Service_API_V2.json | 23 ++++++++++------------- iReceptor_Data_Service_API_V2.yaml | 19 +++++++++---------- 2 files changed, 19 insertions(+), 23 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 3c83766..2cc4b5e 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -34,10 +34,7 @@ "items": { "allOf": [ { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements" - }, - { - "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Rearrangement" }, { "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequence.yaml#/ireceptor_sequence_annotation_model" @@ -48,28 +45,28 @@ "airr_summary_model": { "allOf": [ { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Study" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Study" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Subject" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Subject" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Diagnosis" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Diagnosis" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Sample" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Sample" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/CellProcessing" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/CellProcessing" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/NucleicAcidProcessing" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/NucleicAcidProcessing" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/RawSequenceData" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/RawSequenceData" }, { - "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/SoftwareProcessing" + "$ref": "https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/SoftwareProcessing" } ] }, @@ -1308,4 +1305,4 @@ } } } -} \ No newline at end of file +} diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 0fd3e94..5b0ac7f 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -36,20 +36,19 @@ definitions: type: array items: allOf: - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/MiAIRR_rearrangement.yaml#/MiAIRR_Rearrangements' - - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/Formats_rearrangement.yaml#/Formats_Rearrangements' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Rearrangement' - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_sequence.yaml#/ireceptor_sequence_annotation_model' # The AIRR Minimal Standards model for metadata above the sequence annotation level. airr_summary_model: allOf: - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Study' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Subject' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Diagnosis' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/Sample' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/CellProcessing' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/NucleicAcidProcessing' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/RawSequenceData' - - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/master/specs/definitions.yaml#/SoftwareProcessing' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Study' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Subject' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Diagnosis' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/Sample' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/CellProcessing' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/NucleicAcidProcessing' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/RawSequenceData' + - $ref: 'https://raw.githubusercontent.com/airr-community/airr-standards/v0.1.0/specs/definitions.yaml#/SoftwareProcessing' # A simple model to represent a sequence count, used to make the # composite responses clean in that they all refer to models. ireceptor_sequence_count_model: From c475908c4c3bd100d6b3734fde6da8ebc43809a1 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Tue, 31 Oct 2017 06:06:45 -0500 Subject: [PATCH 37/46] update fields --- iReceptor_Data_Service_API_V2.yaml | 127 +++++++++++++++++------------ 1 file changed, 76 insertions(+), 51 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 5b0ac7f..8d6cfc4 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -249,13 +249,29 @@ parameters: name: sample_id type: string in: formData + sample_type: + name: sample_type + type: array + items: + type: string + in: query + sample_type_form: + name: sample_type + type: array + items: + type: string + in: formData tissue: name: tissue - type: string + type: array + items: + type: string in: query tissue_form: name: tissue - type: string + type: array + items: + type: string in: formData disease_state_sample: name: disease_state_sample @@ -267,11 +283,15 @@ parameters: in: formData cell_subset: name: cell_subset - type: string + type: array + items: + type: string in: query cell_subset_form: name: cell_subset - type: string + type: array + items: + type: string in: formData cell_phenotype: name: cell_phenotype @@ -281,13 +301,17 @@ parameters: name: cell_phenotype type: string in: formData - library_source: - name: library_source - type: string + template_class: + name: template_class + type: array + items: + type: string in: query - library_source_form: - name: library_source - type: string + template_class_form: + name: template_class + type: array + items: + type: string in: formData platform: name: platform @@ -389,50 +413,50 @@ parameters: type: integer description: | Cell Index (UID linking sequences from the same cell) (AIRR) - v_allele: - name: v_allele + v_call: + name: v_call in: query type: string description: | V gene with allele (e.g. IGHV4-59*01) (AIRR) - v_allele_form: - name: v_allele + v_call_form: + name: v_call in: formData type: string description: | V gene with allele (e.g. IGHV4-59*01) (AIRR) - d_allele: - name: d_allele + d_call: + name: d_call in: query type: string description: | D gene with allele (e.g. IGHD3-10*01) (AIRR) - d_allele_form: - name: d_allele + d_call_form: + name: d_call in: formData type: string description: | D gene with allele (e.g. IGHD3-10*01) (AIRR) - j_allele: - name: j_allele + j_call: + name: j_call in: query type: string description: | J gene with allele (e.g. IGHJ4*02) (AIRR) - j_allele_form: - name: j_allele + j_call_form: + name: j_call in: formData type: string description: | J gene with allele (e.g. IGHJ4*02) (AIRR) - c_allele: - name: c_allele + c_call: + name: c_call in: query type: string description: | C region with allele (AIRR) - c_allele_form: - name: c_allele + c_call_form: + name: c_call in: formData type: string description: | @@ -495,13 +519,13 @@ parameters: functional: name: functional in: query - type: string + type: boolean description: | Filter for sequences that are either functional, non-functional, or both functional_form: name: functional in: formData - type: string + type: boolean description: | Filter for sequences that are either functional, non-functional, or both # @@ -556,7 +580,7 @@ parameters: required: false type: array items: - type: string + type: boolean ir_show_unproductive_form: name: ir_show_unproductive in: formData @@ -566,7 +590,7 @@ parameters: required: false type: array items: - type: string + type: boolean ir_junction_nt_length: name: ir_junction_nt_length in: query @@ -601,7 +625,6 @@ produces: - application/json consumes: - application/x-www-form-urlencoded - - application/json tags: - name: info description: Service information @@ -676,11 +699,12 @@ paths: - $ref: '#/parameters/ethnicity' - $ref: '#/parameters/study_group_description' - $ref: '#/parameters/sample_id' + - $ref: '#/parameters/sample_type' - $ref: '#/parameters/tissue' - $ref: '#/parameters/disease_state_sample' - $ref: '#/parameters/cell_subset' - $ref: '#/parameters/cell_phenotype' - - $ref: '#/parameters/library_source' + - $ref: '#/parameters/template_class' - $ref: '#/parameters/platform' - $ref: '#/parameters/ir_subject_age_min' - $ref: '#/parameters/ir_subject_age_max' @@ -733,11 +757,12 @@ paths: - $ref: '#/parameters/ethnicity_form' - $ref: '#/parameters/study_group_description_form' - $ref: '#/parameters/sample_id_form' + - $ref: '#/parameters/sample_type_form' - $ref: '#/parameters/tissue_form' - $ref: '#/parameters/disease_state_sample_form' - $ref: '#/parameters/cell_subset_form' - $ref: '#/parameters/cell_phenotype_form' - - $ref: '#/parameters/library_source_form' + - $ref: '#/parameters/template_class_form' - $ref: '#/parameters/platform_form' - $ref: '#/parameters/ir_subject_age_min_form' - $ref: '#/parameters/ir_subject_age_max_form' @@ -776,9 +801,9 @@ paths: parameters: - $ref: '#/parameters/ir_username' - $ref: '#/parameters/ir_sample_id_list' - - $ref: '#/parameters/v_allele' - - $ref: '#/parameters/d_allele' - - $ref: '#/parameters/j_allele' + - $ref: '#/parameters/v_call' + - $ref: '#/parameters/d_call' + - $ref: '#/parameters/j_call' - $ref: '#/parameters/junction_aa' - $ref: '#/parameters/junction_length' - $ref: '#/parameters/functional' @@ -824,9 +849,9 @@ paths: parameters: - $ref: '#/parameters/ir_username_form' - $ref: '#/parameters/ir_sample_id_list_form' - - $ref: '#/parameters/v_allele_form' - - $ref: '#/parameters/d_allele_form' - - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/v_call_form' + - $ref: '#/parameters/d_call_form' + - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' - $ref: '#/parameters/functional_form' @@ -877,9 +902,9 @@ paths: - $ref: '#/parameters/ir_username' - $ref: '#/parameters/ir_sample_id_list' - $ref: '#/parameters/ir_data_format' - - $ref: '#/parameters/v_allele' - - $ref: '#/parameters/d_allele' - - $ref: '#/parameters/j_allele' + - $ref: '#/parameters/v_call' + - $ref: '#/parameters/d_call' + - $ref: '#/parameters/j_call' - $ref: '#/parameters/junction_aa' - $ref: '#/parameters/junction_length' - $ref: '#/parameters/functional' @@ -922,9 +947,9 @@ paths: - $ref: '#/parameters/ir_username_form' - $ref: '#/parameters/ir_sample_id_list_form' - $ref: '#/parameters/ir_data_format_form' - - $ref: '#/parameters/v_allele_form' - - $ref: '#/parameters/d_allele_form' - - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/v_call_form' + - $ref: '#/parameters/d_call_form' + - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' - $ref: '#/parameters/functional_form' @@ -964,9 +989,9 @@ paths: parameters: - $ref: '#/parameters/ir_username_form' - $ref: '#/parameters/ir_sample_id_list_form' - - $ref: '#/parameters/v_allele_form' - - $ref: '#/parameters/d_allele_form' - - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/v_call_form' + - $ref: '#/parameters/d_call_form' + - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' - $ref: '#/parameters/functional_form' @@ -1008,9 +1033,9 @@ paths: - $ref: '#/parameters/ir_username_form' - $ref: '#/parameters/ir_sample_id_list_form' - $ref: '#/parameters/ir_data_format_form' - - $ref: '#/parameters/v_allele_form' - - $ref: '#/parameters/d_allele_form' - - $ref: '#/parameters/j_allele_form' + - $ref: '#/parameters/v_call_form' + - $ref: '#/parameters/d_call_form' + - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' - $ref: '#/parameters/functional_form' From d83534a9a4e9b25f3bd8cfff1028604dd9bbc8ed Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Tue, 31 Oct 2017 06:14:51 -0500 Subject: [PATCH 38/46] update fields --- iReceptor_Data_Service_API_V2.json | 143 ++++++++++++++++++----------- 1 file changed, 91 insertions(+), 52 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 2cc4b5e..6d22934 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -279,14 +279,36 @@ "type": "string", "in": "formData" }, + "sample_type": { + "name": "sample_type", + "type": "array", + "items": { + "type": "string" + }, + "in": "query" + }, + "sample_type_form": { + "name": "sample_type", + "type": "array", + "items": { + "type": "string" + }, + "in": "formData" + }, "tissue": { "name": "tissue", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "query" }, "tissue_form": { "name": "tissue", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "formData" }, "disease_state_sample": { @@ -301,12 +323,18 @@ }, "cell_subset": { "name": "cell_subset", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "query" }, "cell_subset_form": { "name": "cell_subset", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "formData" }, "cell_phenotype": { @@ -319,14 +347,20 @@ "type": "string", "in": "formData" }, - "library_source": { - "name": "library_source", - "type": "string", + "template_class": { + "name": "template_class", + "type": "array", + "items": { + "type": "string" + }, "in": "query" }, - "library_source_form": { - "name": "library_source", - "type": "string", + "template_class_form": { + "name": "template_class", + "type": "array", + "items": { + "type": "string" + }, "in": "formData" }, "platform": { @@ -425,50 +459,50 @@ "type": "integer", "description": "Cell Index (UID linking sequences from the same cell) (AIRR)\n" }, - "v_allele": { - "name": "v_allele", + "v_call": { + "name": "v_call", "in": "query", "type": "string", "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" }, - "v_allele_form": { - "name": "v_allele", + "v_call_form": { + "name": "v_call", "in": "formData", "type": "string", "description": "V gene with allele (e.g. IGHV4-59*01) (AIRR)\n" }, - "d_allele": { - "name": "d_allele", + "d_call": { + "name": "d_call", "in": "query", "type": "string", "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" }, - "d_allele_form": { - "name": "d_allele", + "d_call_form": { + "name": "d_call", "in": "formData", "type": "string", "description": "D gene with allele (e.g. IGHD3-10*01) (AIRR)\n" }, - "j_allele": { - "name": "j_allele", + "j_call": { + "name": "j_call", "in": "query", "type": "string", "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" }, - "j_allele_form": { - "name": "j_allele", + "j_call_form": { + "name": "j_call", "in": "formData", "type": "string", "description": "J gene with allele (e.g. IGHJ4*02) (AIRR)\n" }, - "c_allele": { - "name": "c_allele", + "c_call": { + "name": "c_call", "in": "query", "type": "string", "description": "C region with allele (AIRR) \n" }, - "c_allele_form": { - "name": "c_allele", + "c_call_form": { + "name": "c_call", "in": "formData", "type": "string", "description": "C region with allele (AIRR) \n" @@ -524,13 +558,13 @@ "functional": { "name": "functional", "in": "query", - "type": "string", + "type": "boolean", "description": "Filter for sequences that are either functional, non-functional, or both\n" }, "functional_form": { "name": "functional", "in": "formData", - "type": "string", + "type": "boolean", "description": "Filter for sequences that are either functional, non-functional, or both\n" }, "ir_sample_id_list": { @@ -574,7 +608,7 @@ "required": false, "type": "array", "items": { - "type": "string" + "type": "boolean" } }, "ir_show_unproductive_form": { @@ -584,7 +618,7 @@ "required": false, "type": "array", "items": { - "type": "string" + "type": "boolean" } }, "ir_junction_nt_length": { @@ -623,8 +657,7 @@ "application/json" ], "consumes": [ - "application/x-www-form-urlencoded", - "application/json" + "application/x-www-form-urlencoded" ], "tags": [ { @@ -741,6 +774,9 @@ { "$ref": "#/parameters/sample_id" }, + { + "$ref": "#/parameters/sample_type" + }, { "$ref": "#/parameters/tissue" }, @@ -754,7 +790,7 @@ "$ref": "#/parameters/cell_phenotype" }, { - "$ref": "#/parameters/library_source" + "$ref": "#/parameters/template_class" }, { "$ref": "#/parameters/platform" @@ -836,6 +872,9 @@ { "$ref": "#/parameters/sample_id_form" }, + { + "$ref": "#/parameters/sample_type_form" + }, { "$ref": "#/parameters/tissue_form" }, @@ -849,7 +888,7 @@ "$ref": "#/parameters/cell_phenotype_form" }, { - "$ref": "#/parameters/library_source_form" + "$ref": "#/parameters/template_class_form" }, { "$ref": "#/parameters/platform_form" @@ -902,13 +941,13 @@ "$ref": "#/parameters/ir_sample_id_list" }, { - "$ref": "#/parameters/v_allele" + "$ref": "#/parameters/v_call" }, { - "$ref": "#/parameters/d_allele" + "$ref": "#/parameters/d_call" }, { - "$ref": "#/parameters/j_allele" + "$ref": "#/parameters/j_call" }, { "$ref": "#/parameters/junction_aa" @@ -972,13 +1011,13 @@ "$ref": "#/parameters/ir_sample_id_list_form" }, { - "$ref": "#/parameters/v_allele_form" + "$ref": "#/parameters/v_call_form" }, { - "$ref": "#/parameters/d_allele_form" + "$ref": "#/parameters/d_call_form" }, { - "$ref": "#/parameters/j_allele_form" + "$ref": "#/parameters/j_call_form" }, { "$ref": "#/parameters/junction_aa_form" @@ -1048,13 +1087,13 @@ "$ref": "#/parameters/ir_data_format" }, { - "$ref": "#/parameters/v_allele" + "$ref": "#/parameters/v_call" }, { - "$ref": "#/parameters/d_allele" + "$ref": "#/parameters/d_call" }, { - "$ref": "#/parameters/j_allele" + "$ref": "#/parameters/j_call" }, { "$ref": "#/parameters/junction_aa" @@ -1113,13 +1152,13 @@ "$ref": "#/parameters/ir_data_format_form" }, { - "$ref": "#/parameters/v_allele_form" + "$ref": "#/parameters/v_call_form" }, { - "$ref": "#/parameters/d_allele_form" + "$ref": "#/parameters/d_call_form" }, { - "$ref": "#/parameters/j_allele_form" + "$ref": "#/parameters/j_call_form" }, { "$ref": "#/parameters/junction_aa_form" @@ -1178,13 +1217,13 @@ "$ref": "#/parameters/ir_sample_id_list_form" }, { - "$ref": "#/parameters/v_allele_form" + "$ref": "#/parameters/v_call_form" }, { - "$ref": "#/parameters/d_allele_form" + "$ref": "#/parameters/d_call_form" }, { - "$ref": "#/parameters/j_allele_form" + "$ref": "#/parameters/j_call_form" }, { "$ref": "#/parameters/junction_aa_form" @@ -1254,13 +1293,13 @@ "$ref": "#/parameters/ir_data_format_form" }, { - "$ref": "#/parameters/v_allele_form" + "$ref": "#/parameters/v_call_form" }, { - "$ref": "#/parameters/d_allele_form" + "$ref": "#/parameters/d_call_form" }, { - "$ref": "#/parameters/j_allele_form" + "$ref": "#/parameters/j_call_form" }, { "$ref": "#/parameters/junction_aa_form" From a22465dc587a69f18ca106d1598c1e4510f1c4fd Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Tue, 31 Oct 2017 06:45:08 -0500 Subject: [PATCH 39/46] update fields --- iReceptor_Data_Service_API_V2.json | 40 ++++++++++++------------------ iReceptor_Data_Service_API_V2.yaml | 32 +++++++++--------------- 2 files changed, 28 insertions(+), 44 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 6d22934..8e5575f 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -251,22 +251,34 @@ }, "ethnicity": { "name": "ethnicity", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "query" }, "ethnicity_form": { "name": "ethnicity", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "formData" }, "study_group_description": { "name": "study_group_description", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "query" }, "study_group_description_form": { "name": "study_group_description", - "type": "string", + "type": "array", + "items": { + "type": "string" + }, "in": "formData" }, "sample_id": { @@ -373,20 +385,6 @@ "type": "string", "in": "formData" }, - "ir_lab_id": { - "name": "ir_lab_id", - "in": "query", - "description": "e.g. 1\n", - "required": false, - "type": "string" - }, - "ir_lab_id_form": { - "name": "ir_lab_id", - "in": "formData", - "description": "e.g. 1\n", - "required": false, - "type": "string" - }, "ir_project_id": { "name": "ir_project_id", "in": "query", @@ -738,9 +736,6 @@ { "$ref": "#/parameters/ir_username" }, - { - "$ref": "#/parameters/ir_lab_id" - }, { "$ref": "#/parameters/ir_project_id" }, @@ -836,9 +831,6 @@ { "$ref": "#/parameters/ir_username_form" }, - { - "$ref": "#/parameters/ir_lab_id_form" - }, { "$ref": "#/parameters/ir_project_id_form" }, diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 8d6cfc4..3a3b625 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -227,19 +227,27 @@ parameters: in: formData ethnicity: name: ethnicity - type: string + type: array + items: + type: string in: query ethnicity_form: name: ethnicity - type: string + type: array + items: + type: string in: formData study_group_description: name: study_group_description - type: string + type: array + items: + type: string in: query study_group_description_form: name: study_group_description - type: string + type: array + items: + type: string in: formData sample_id: name: sample_id @@ -324,20 +332,6 @@ parameters: # # iReceptor specific parameters for the /samples API entry point. # - ir_lab_id: - name: ir_lab_id - in: query - description: | - e.g. 1 - required: false - type: string - ir_lab_id_form: - name: ir_lab_id - in: formData - description: | - e.g. 1 - required: false - type: string ir_project_id: name: ir_project_id in: query @@ -687,7 +681,6 @@ paths: - samples parameters: - $ref: '#/parameters/ir_username' - - $ref: '#/parameters/ir_lab_id' - $ref: '#/parameters/ir_project_id' - $ref: '#/parameters/study_id' - $ref: '#/parameters/study_title' @@ -745,7 +738,6 @@ paths: - samples parameters: - $ref: '#/parameters/ir_username_form' - - $ref: '#/parameters/ir_lab_id_form' - $ref: '#/parameters/ir_project_id_form' - $ref: '#/parameters/study_id_form' - $ref: '#/parameters/study_title_form' From 131c04b823aa03731a2895fd64119c3baa443058 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Tue, 31 Oct 2017 07:54:50 -0500 Subject: [PATCH 40/46] update fields --- iReceptor_Data_Service_API_V2.json | 12 ++++++------ iReceptor_Data_Service_API_V2.yaml | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 8e5575f..9913077 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -375,13 +375,13 @@ }, "in": "formData" }, - "platform": { - "name": "platform", + "sequencing_platform": { + "name": "sequencing_platform", "type": "string", "in": "query" }, - "platform_form": { - "name": "platform", + "sequencing_platform_form": { + "name": "sequencing_platform", "type": "string", "in": "formData" }, @@ -788,7 +788,7 @@ "$ref": "#/parameters/template_class" }, { - "$ref": "#/parameters/platform" + "$ref": "#/parameters/sequencing_platform" }, { "$ref": "#/parameters/ir_subject_age_min" @@ -883,7 +883,7 @@ "$ref": "#/parameters/template_class_form" }, { - "$ref": "#/parameters/platform_form" + "$ref": "#/parameters/sequencing_platform_form" }, { "$ref": "#/parameters/ir_subject_age_min_form" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 3a3b625..d3563b1 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -321,12 +321,12 @@ parameters: items: type: string in: formData - platform: - name: platform + sequencing_platform: + name: sequencing_platform type: string in: query - platform_form: - name: platform + sequencing_platform_form: + name: sequencing_platform type: string in: formData # @@ -698,7 +698,7 @@ paths: - $ref: '#/parameters/cell_subset' - $ref: '#/parameters/cell_phenotype' - $ref: '#/parameters/template_class' - - $ref: '#/parameters/platform' + - $ref: '#/parameters/sequencing_platform' - $ref: '#/parameters/ir_subject_age_min' - $ref: '#/parameters/ir_subject_age_max' operationId: getSamples @@ -755,7 +755,7 @@ paths: - $ref: '#/parameters/cell_subset_form' - $ref: '#/parameters/cell_phenotype_form' - $ref: '#/parameters/template_class_form' - - $ref: '#/parameters/platform_form' + - $ref: '#/parameters/sequencing_platform_form' - $ref: '#/parameters/ir_subject_age_min_form' - $ref: '#/parameters/ir_subject_age_max_form' operationId: postSamples From f3efa6e0a6159ed3c6e6b265468bbc5fef207524 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 3 Nov 2017 14:08:45 +1300 Subject: [PATCH 41/46] Removed the "sample_type" parameter, as it is not supported in the queries on all nodes. --- iReceptor_Data_Service_API_V2.json | 24 +----------------------- iReceptor_Data_Service_API_V2.yaml | 14 -------------- 2 files changed, 1 insertion(+), 37 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 9913077..69b6a75 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -291,22 +291,6 @@ "type": "string", "in": "formData" }, - "sample_type": { - "name": "sample_type", - "type": "array", - "items": { - "type": "string" - }, - "in": "query" - }, - "sample_type_form": { - "name": "sample_type", - "type": "array", - "items": { - "type": "string" - }, - "in": "formData" - }, "tissue": { "name": "tissue", "type": "array", @@ -769,9 +753,6 @@ { "$ref": "#/parameters/sample_id" }, - { - "$ref": "#/parameters/sample_type" - }, { "$ref": "#/parameters/tissue" }, @@ -864,9 +845,6 @@ { "$ref": "#/parameters/sample_id_form" }, - { - "$ref": "#/parameters/sample_type_form" - }, { "$ref": "#/parameters/tissue_form" }, @@ -1336,4 +1314,4 @@ } } } -} +} \ No newline at end of file diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index d3563b1..396b51d 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -257,18 +257,6 @@ parameters: name: sample_id type: string in: formData - sample_type: - name: sample_type - type: array - items: - type: string - in: query - sample_type_form: - name: sample_type - type: array - items: - type: string - in: formData tissue: name: tissue type: array @@ -692,7 +680,6 @@ paths: - $ref: '#/parameters/ethnicity' - $ref: '#/parameters/study_group_description' - $ref: '#/parameters/sample_id' - - $ref: '#/parameters/sample_type' - $ref: '#/parameters/tissue' - $ref: '#/parameters/disease_state_sample' - $ref: '#/parameters/cell_subset' @@ -749,7 +736,6 @@ paths: - $ref: '#/parameters/ethnicity_form' - $ref: '#/parameters/study_group_description_form' - $ref: '#/parameters/sample_id_form' - - $ref: '#/parameters/sample_type_form' - $ref: '#/parameters/tissue_form' - $ref: '#/parameters/disease_state_sample_form' - $ref: '#/parameters/cell_subset_form' From 822a78e09411844320089f13cd55cba66f71aa01 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Fri, 3 Nov 2017 14:11:34 +1300 Subject: [PATCH 42/46] Prefixed all ireceptor specific sequence annotation fields with ir_ to differentiate them from the AIRR fields (and to be consistent with other API entry points. iReceptor specific fields should all have ir_ in front of them. --- ireceptor_sequence.yaml | 220 ++++++++++++++++++++-------------------- 1 file changed, 110 insertions(+), 110 deletions(-) diff --git a/ireceptor_sequence.yaml b/ireceptor_sequence.yaml index 1d8fcd2..0112f55 100644 --- a/ireceptor_sequence.yaml +++ b/ireceptor_sequence.yaml @@ -4,285 +4,285 @@ ireceptor_sequence_annotation_model: type: object properties: - seq_id: + ir_seq_id: type: integer description: | e.g. 1 - seq_name: + ir_seq_name: type: string - project_sample_id: + ir_project_sample_id: type: integer description: | e.g. 6 - id: + ir_id: type: integer description: | e.g. 1 - sequence_id: + ir_sequence_id: type: integer description: | e.g. 1 - vgene_string: + ir_vgene_string: type: string description: | e.g IGHV4-59*01 or IGHV4-59*07 - vgene_family: + ir_vgene_family: type: string description: | e.g. IGHV4 - vgene_gene: + ir_vgene_gene: type: string description: | e.g. IGHV4-59 - dgene_string: + ir_dgene_string: type: string description: | e.g. Homsap IGHD3-10*01 F - dgene_family: + ir_dgene_family: type: string description: | e.g. IGHD3 - dgene_gene: + ir_dgene_gene: type: string description: | e.g. IGHD3-10 - jgene_string: + ir_jgene_string: type: string description: | e.g. Homsap IGHJ4*02 F - jgene_family: + ir_jgene_family: type: string description: | e.g. IGHJ4 - jgene_gene: + ir_jgene_gene: type: string description: | e.g. IGHJ4 - functionality: + ir_functionality: type: string description: | e.g. productive - functionality_comment: + ir_functionality_comment: type: string description: | e.g. "" - orientation: + ir_orientation: type: string description: | e.g. + - vgene_score: + ir_vgene_score: type: integer description: | e.g. 1127 - vgene_probability: + ir_vgene_probability: type: integer description: | e.g. 95 - dregion_reading_frame: + ir_dregion_reading_frame: type: integer description: | e.g. 2 - cdr1_length: + ir_cdr1_length: type: integer description: | e.g. 8 - cdr2_length: + ir_cdr2_length: type: integer description: | e.g. 7 - cdr3_length: + ir_cdr3_length: type: integer description: | e.g. 13 - vdjregion_sequence_nt: + ir_vdjregion_sequence_nt: type: string description: | vdj region nucleotide sequence - vjregion_sequence_nt: + ir_vjregion_sequence_nt: type: string description: | vj region nucleotide sequence - djregion_sequence_nt: + ir_djregion_sequence_nt: type: string description: | dj region nucleotide sequence - vregion_sequence_nt: + ir_vregion_sequence_nt: type: string description: | v region nucleotide sequence - dregion_sequence_nt: + ir_dregion_sequence_nt: type: string description: | d region nucleotide sequence - jregion_sequence_nt: + ir_jregion_sequence_nt: type: string description: | j region nucleotide sequence - fr1region_sequence_nt: + ir_fr1region_sequence_nt: type: string description: | fr1 region nucleotide sequence - fr2region_sequence_nt: + ir_fr2region_sequence_nt: type: string description: | fr2 region nucleotide sequence - fr3region_sequence_nt: + ir_fr3region_sequence_nt: type: string description: | fr3 region nucleotide sequence - fr4region_sequence_nt: + ir_fr4region_sequence_nt: type: string description: | fr4 region nucleotide sequence - cdr1region_sequence_nt: + ir_cdr1region_sequence_nt: type: string description: | cdr1 region nucleotide sequence - cdr2region_sequence_nt: + ir_cdr2region_sequence_nt: type: string description: | cdr2 region nucleotide sequence - cdr3region_sequence_nt: + ir_cdr3region_sequence_nt: type: string description: | cdr3 region nucleotide sequence - vdjregion_sequence_nt_gapped: + ir_vdjregion_sequence_nt_gapped: type: string description: | gapped vdj region nucleotide sequence - vjregion_sequence_nt_gapped: + ir_vjregion_sequence_nt_gapped: type: string description: | gapped vj region nucleotide sequence - djregion_sequence_nt_gapped: + ir_djregion_sequence_nt_gapped: type: string description: | gapped dj region nucleotide sequence - vregion_sequence_nt_gapped: + ir_vregion_sequence_nt_gapped: type: string description: | gapped v region nucleotide sequence - dregion_sequence_nt_gapped: + ir_dregion_sequence_nt_gapped: type: string description: | gapped d region nucleotide sequence - jregion_sequence_nt_gapped: + ir_jregion_sequence_nt_gapped: type: string description: | gapped j region nucleotide sequence - fr1region_sequence_nt_gapped: + ir_fr1region_sequence_nt_gapped: type: string description: | gapped fr1 region nucleotide sequence - fr2region_sequence_nt_gapped: + ir_fr2region_sequence_nt_gapped: type: string description: | gapped fr2 region nucleotide sequence - fr3region_sequence_nt_gapped: + ir_fr3region_sequence_nt_gapped: type: string description: | gapped fr3 region nucleotide sequence - fr4region_sequence_nt_gapped: + ir_fr4region_sequence_nt_gapped: type: string description: | gapped fr4 region nucleotide sequence - cdr1region_sequence_nt_gapped: + ir_cdr1region_sequence_nt_gapped: type: string description: | gapped cdr1 region nucleotide sequence - cdr2region_sequence_nt_gapped: + ir_cdr2region_sequence_nt_gapped: type: string description: | gapped cdr2 region nucleotide sequence - cdr3region_sequence_nt_gapped: + ir_cdr3region_sequence_nt_gapped: type: string description: | gapped cdr3 region nucleotide sequence - junction_sequence_nt_gapped: + ir_junction_sequence_nt_gapped: type: string description: | gapped junction nucleotide sequence - vdjregion_sequence_aa: + ir_vdjregion_sequence_aa: type: string description: | vdj region amino acid sequence - vjregion_sequence_aa: + ir_vjregion_sequence_aa: type: string description: | vj region amino acid sequence - djregion_sequence_aa: + ir_djregion_sequence_aa: type: string description: | dj region amino acid sequence - vregion_sequence_aa: + ir_vregion_sequence_aa: type: string description: | v region amino acid sequence - dregion_sequence_aa: + ir_dregion_sequence_aa: type: string description: | d region amino acid sequence - jregion_sequence_aa: + ir_jregion_sequence_aa: type: string description: | j region amino acid sequence - fr1region_sequence_aa: + ir_fr1region_sequence_aa: type: string description: | fr1 region amino acid sequence - fr2region_sequence_aa: + ir_fr2region_sequence_aa: type: string description: | fr2 region amino acid sequence - fr3region_sequence_aa: + ir_fr3region_sequence_aa: type: string description: | fr3 region amino acid sequence - fr4region_sequence_aa: + ir_fr4region_sequence_aa: type: string description: | fr4 region amino acid sequence - cdr1region_sequence_aa: + ir_cdr1region_sequence_aa: type: string description: | cdr1 region amino acid sequence - cdr2region_sequence_aa: + ir_cdr2region_sequence_aa: type: string description: | cdr2 region amino acid sequence - cdr3region_sequence_aa: + ir_cdr3region_sequence_aa: type: string description: | cdr3 region amino acid sequence - vdjregion_sequence_aa_gapped: + ir_vdjregion_sequence_aa_gapped: type: string description: | gapped vdj region amino acid sequence - vjregion_sequence_aa_gapped: + ir_vjregion_sequence_aa_gapped: type: string description: | gapped vj region amino acid sequence - djregion_sequence_aa_gapped: + ir_djregion_sequence_aa_gapped: type: string description: | gapped dj region amino acid sequence - vregion_sequence_aa_gapped: + ir_vregion_sequence_aa_gapped: type: string description: | gapped v region amino acid sequence - dregion_sequence_aa_gapped: + ir_dregion_sequence_aa_gapped: type: string description: | gapped d region amino acid sequence - jregion_sequence_aa_gapped: + ir_jregion_sequence_aa_gapped: type: string description: | gapped j region amino acid sequence - fr1region_sequence_aa_gapped: + ir_fr1region_sequence_aa_gapped: type: string description: | gapped fr1 region amino acid sequence - fr2region_sequence_aa_gapped: + ir_fr2region_sequence_aa_gapped: type: string description: | gapped fr2 region amino acid sequence @@ -290,15 +290,15 @@ type: string description: | gapped fr3 region amino acid sequence - fr4region_sequence_aa_gapped: + ir_fr4region_sequence_aa_gapped: type: string description: | gapped fr4 region amino acid sequence - cdr1region_sequence_aa_gapped: + ir_cdr1region_sequence_aa_gapped: type: string description: | gapped cdr1 region amino acid sequence - cdr2region_sequence_aa_gapped: + ir_cdr2region_sequence_aa_gapped: type: string description: | gapped cdr2 region amino acid sequence @@ -306,59 +306,59 @@ type: string description: | gapped cdr3 region amino acid sequence - junction_sequence_aa_gapped: + ir_junction_sequence_aa_gapped: type: string description: | gapped junction amino acid sequence - vdjregion_start: + ir_vdjregion_start: type: integer description: | e.g. 1 - vdjregion_end: + ir_vdjregion_end: type: integer description: | e.g. 321 - vjregion_start: + ir_vjregion_start: type: integer description: | e.g. 0 - vjregion_end: + ir_vjregion_end: type: integer description: | e.g. 0 - djregion_start: + ir_djregion_start: type: integer description: | e.g. 254 - djregion_end: + ir_djregion_end: type: integer description: | e.g. 321 - vregion_start: + ir_vregion_start: type: integer description: | e.g. 286 - vregion_end: + ir_vregion_end: type: integer description: | e.g. 252 - dregion_start: + ir_dregion_start: type: integer description: | e.g. 254 - dregion_end: + ir_dregion_end: type: integer description: | e.g. 321 - jregion_start: + ir_jregion_start: type: integer description: | e.g. 286 - jregion_end: + ir_jregion_end: type: integer description: | e.g. 321 - fr1region_start: + ir_fr1region_start: type: integer description: | e.g. 1 @@ -366,95 +366,95 @@ type: integer description: | e.g. 38 - fr2region_start: + ir_fr2region_start: type: integer description: | e.g. 63 - fr2region_end: + ir_fr2region_end: type: integer description: | e.g. 113 - fr3region_start: + ir_fr3region_start: type: integer description: | e.g. 135 - fr3region_end: + ir_fr3region_end: type: integer description: | e.g. 248 - fr4region_start: + ir_fr4region_start: type: integer description: | e.g. 288 - fr4region_end: + ir_fr4region_end: type: integer description: | e.g. 321 - cdr1region_start: + ir_cdr1region_start: type: integer description: | e.g. 39 - cdr1region_end: + ir_cdr1region_end: type: integer description: | e.g. 321 - cdr2region_start: + ir_cdr2region_start: type: integer description: | e.g. 62 - cdr2region_end: + ir_cdr2region_end: type: integer description: | e.g. 134 - cdr3region_start: + ir_cdr3region_start: type: integer description: | e.g. 249 - cdr3region_end: + ir_cdr3region_end: type: integer description: | e.g. 287 - junction_start: + ir_junction_start: type: integer description: | e.g. 246 - junction_end: + ir_junction_end: type: integer description: | e.g. 290 - vregion_mutation_string: + ir_vregion_mutation_string: type: string description: > e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)|a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c| - fr1region_mutation_string: + ir_fr1region_mutation_string: type: string description: | e.g. a41>c|g42>t|c43>g,P15>A(- - -)|g51>t,E17>D(+ - +)| - fr2region_mutation_string: + ir_fr2region_mutation_string: type: string description: | e.g. - fr3region_mutation_string: + ir_fr3region_mutation_string: type: string description: > e.g. c198>g,N66>K(+ - -)|a220>g,S74>G(+ + -)|a229>t,T77>S(+ - +)|g275>c,S92>T(+ - +)|t279>c|" - cdr1region_mutation_string: + ir_cdr1region_mutation_string: type: string description: | e.g. - cdr2region_mutation_string: + ir_cdr2region_mutation_string: type: string description: | e.g. a166>c,I56>L(+ + +)|t172>a,Y58>N(- - -)|c195>t|" - cdr3region_mutation_string: + ir_cdr3region_mutation_string: type: string description: | e.g. g317>c,R106>T(- - -)|a318>c,R106>T(- - -)|g319>t - annotation_tool: + ir_annotation_tool: type: string description: | e.g. VQuest \ No newline at end of file From 1f8c656d30535fc776b99df3eefc545ddabce337 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Sat, 11 Nov 2017 18:34:04 +1300 Subject: [PATCH 43/46] Updated API to include ir_filtered_sequence_count as a response field. --- iReceptor_Data_Service_API_V2.json | 43 +++++++++++++++++++++++++----- iReceptor_Data_Service_API_V2.yaml | 29 +++++++++++++++----- 2 files changed, 58 insertions(+), 14 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 69b6a75..f4a4d9a 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -13,7 +13,7 @@ "host": "ipa.ireceptor.org", "basePath": "/v2", "definitions": { - "ireceptor_summary_response": { + "ireceptor_sample_summary_response": { "type": "array", "items": { "allOf": [ @@ -29,6 +29,25 @@ ] } }, + "ireceptor_sequence_summary_response": { + "type": "array", + "items": { + "allOf": [ + { + "$ref": "#/definitions/ireceptor_sequence_count_model" + }, + { + "$ref": "#/definitions/ireceptor_filtered_sequence_count_model" + }, + { + "$ref": "#/definitions/airr_summary_model" + }, + { + "$ref": "https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_summary.yaml#/ireceptor_summary_model" + } + ] + } + }, "ireceptor_sequence_response": { "type": "array", "items": { @@ -75,11 +94,21 @@ "properties": { "ir_sequence_count": { "type": "integer", - "description": "Number of sequences found that met the search criteria for this sample", + "description": "Number of sequences found that met the sample search criteria for this sample", "example": 123456 } } }, + "ireceptor_filtered_sequence_count_model": { + "type": "object", + "properties": { + "ir_filtered_sequence_count": { + "type": "integer", + "description": "Number of sequences found that met the sequence search criteria for this sample", + "example": 4321 + } + } + }, "ireceptor_core_samples_parameters_model": { "type": "object", "required": [ @@ -783,7 +812,7 @@ "200": { "description": "A successful call returns an array of sample summary metadata for\neach sample that meets the search criteria. The metadata returned\nfor each sample includes the number of sequences found for that sample\nas well as the study/subject/sample data for that sample. The metadata\nfor each sample in the response contains a set of AIRR compliant data\nas well as repository specific data that is required to query the\nrepository about those types of elements. \n", "schema": { - "$ref": "#/definitions/ireceptor_summary_response" + "$ref": "#/definitions/ireceptor_sample_summary_response" } }, "400": { @@ -875,7 +904,7 @@ "200": { "description": "A successful call returns an array of sample summary metadata for each sample that meets the search criteria. The metadata returned for each sample includes the number of sequences found for that sample as well as the study/subject/sample data for that sample. The metadata for each sample in the response contains a set of AIRR compliant data as well as repository specific data that is required to query the repository about those types of elements. \n", "schema": { - "$ref": "#/definitions/ireceptor_summary_response" + "$ref": "#/definitions/ireceptor_sample_summary_response" } }, "400": { @@ -943,7 +972,7 @@ "type": "object", "properties": { "summary": { - "$ref": "#/definitions/ireceptor_summary_response" + "$ref": "#/definitions/ireceptor_sequence_summary_response" }, "items": { "$ref": "#/definitions/ireceptor_sequence_response" @@ -1013,7 +1042,7 @@ "type": "object", "properties": { "summary": { - "$ref": "#/definitions/ireceptor_summary_response" + "$ref": "#/definitions/ireceptor_sequence_summary_response" }, "items": { "$ref": "#/definitions/ireceptor_sequence_response" @@ -1219,7 +1248,7 @@ "type": "object", "properties": { "summary": { - "$ref": "#/definitions/ireceptor_summary_response" + "$ref": "#/definitions/ireceptor_sequence_summary_response" }, "items": { "$ref": "#/definitions/ireceptor_sequence_response" diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 396b51d..aa216f5 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -20,13 +20,21 @@ definitions: # response is used wherever summary data at the sample level is provided # by an API call. It is composed of the sequence count, the relevant AIRR # model elements, and the revelant iReceptor model elements. - ireceptor_summary_response: + ireceptor_sample_summary_response: type: array items: allOf: - $ref: '#/definitions/ireceptor_sequence_count_model' - $ref: '#/definitions/airr_summary_model' - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_summary.yaml#/ireceptor_summary_model' + ireceptor_sequence_summary_response: + type: array + items: + allOf: + - $ref: '#/definitions/ireceptor_sequence_count_model' + - $ref: '#/definitions/ireceptor_filtered_sequence_count_model' + - $ref: '#/definitions/airr_summary_model' + - $ref: 'https://raw.githubusercontent.com/sfu-ireceptor/api/AIRR-compliance/ireceptor_summary.yaml#/ireceptor_summary_model' # A definition of the sequence response for an iReceptor API call. This # response is used wherever sequence data is provided by an API call. # It is a composite of the sequence fields defined by the MiAIRR standard, @@ -56,8 +64,15 @@ definitions: properties: ir_sequence_count: type: integer - description: Number of sequences found that met the search criteria for this sample + description: Number of sequences found that met the sample search criteria for this sample example: 123456 + ireceptor_filtered_sequence_count_model: + type: object + properties: + ir_filtered_sequence_count: + type: integer + description: Number of sequences found that met the sequence search criteria for this sample + example: 4321 ireceptor_core_samples_parameters_model: type: object required: @@ -700,7 +715,7 @@ paths: as well as repository specific data that is required to query the repository about those types of elements. schema: - $ref: '#/definitions/ireceptor_summary_response' + $ref: '#/definitions/ireceptor_sample_summary_response' '400': description: malformed request '401': @@ -756,7 +771,7 @@ paths: as well as repository specific data that is required to query the repository about those types of elements. schema: - $ref: '#/definitions/ireceptor_summary_response' + $ref: '#/definitions/ireceptor_sample_summary_response' '400': description: malformed request '401': @@ -804,7 +819,7 @@ paths: type: object properties: summary: - $ref: '#/definitions/ireceptor_summary_response' + $ref: '#/definitions/ireceptor_sequence_summary_response' items: $ref: '#/definitions/ireceptor_sequence_response' '400': @@ -852,7 +867,7 @@ paths: type: object properties: summary: - $ref: '#/definitions/ireceptor_summary_response' + $ref: '#/definitions/ireceptor_sequence_summary_response' items: $ref: '#/definitions/ireceptor_sequence_response' '400': @@ -986,7 +1001,7 @@ paths: type: object properties: summary: - $ref: '#/definitions/ireceptor_summary_response' + $ref: '#/definitions/ireceptor_sequence_summary_response' items: $ref: '#/definitions/ireceptor_sequence_response' '400': From 3db24eafd5ef0997dca61898fa8da6c224e1f1d2 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Fri, 17 Nov 2017 04:15:33 -0600 Subject: [PATCH 44/46] set default for functional parameter --- iReceptor_Data_Service_API_V2.json | 4 +++- iReceptor_Data_Service_API_V2.yaml | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index f4a4d9a..5fb3cd8 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -570,12 +570,14 @@ "name": "functional", "in": "query", "type": "boolean", + "default": true, "description": "Filter for sequences that are either functional, non-functional, or both\n" }, "functional_form": { "name": "functional", "in": "formData", "type": "boolean", + "default": true, "description": "Filter for sequences that are either functional, non-functional, or both\n" }, "ir_sample_id_list": { @@ -1343,4 +1345,4 @@ } } } -} \ No newline at end of file +} diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index aa216f5..813fbae 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -517,12 +517,14 @@ parameters: name: functional in: query type: boolean + default: true description: | Filter for sequences that are either functional, non-functional, or both functional_form: name: functional in: formData type: boolean + default: true description: | Filter for sequences that are either functional, non-functional, or both # From eca2606c50771b6ba5e17e833f296d8206ba1168 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Sat, 18 Nov 2017 10:55:54 +1300 Subject: [PATCH 45/46] Changed ir_junction_aa_length to junction_aa_length --- iReceptor_Data_Service_API_V2.json | 74 +++++++++++++++--------------- iReceptor_Data_Service_API_V2.yaml | 49 ++++++++++---------- 2 files changed, 62 insertions(+), 61 deletions(-) diff --git a/iReceptor_Data_Service_API_V2.json b/iReceptor_Data_Service_API_V2.json index 5fb3cd8..7d12a8d 100644 --- a/iReceptor_Data_Service_API_V2.json +++ b/iReceptor_Data_Service_API_V2.json @@ -152,6 +152,10 @@ "type": "integer", "description": "Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues)\n" }, + "junction_aa_length": { + "type": "integer", + "description": "Length of JUNCTION in amino acids" + }, "functional": { "type": "string", "description": "Filter for sequences that are either functional, non-functional, or both\n" @@ -185,10 +189,6 @@ "ir_show_unproductive": { "type": "string", "description": "By default, only productive sequences are returned. In order to return unproductive sequences, set this parameter to \"T\"" - }, - "ir_junction_aa_length": { - "type": "integer", - "description": "Length of JUNCTION in amino acids (iReceptor)" } } } @@ -566,6 +566,20 @@ "type": "integer", "description": "Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues)\n" }, + "junction_aa_length": { + "name": "junction_aa_length", + "in": "query", + "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids", + "required": false, + "type": "integer" + }, + "junction_aa_length_form": { + "name": "junction_aa_length", + "in": "formData", + "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids", + "required": false, + "type": "integer" + }, "functional": { "name": "functional", "in": "query", @@ -647,20 +661,6 @@ "description": "Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor)", "required": false, "type": "integer" - }, - "ir_junction_aa_length": { - "name": "ir_junction_aa_length", - "in": "query", - "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor)", - "required": false, - "type": "integer" - }, - "ir_junction_aa_length_form": { - "name": "ir_junction_aa_length", - "in": "formData", - "description": "Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor)", - "required": false, - "type": "integer" } }, "schemes": [ @@ -957,13 +957,13 @@ "$ref": "#/parameters/junction_length" }, { - "$ref": "#/parameters/functional" + "$ref": "#/parameters/junction_aa_length" }, { - "$ref": "#/parameters/ir_show_unproductive" + "$ref": "#/parameters/functional" }, { - "$ref": "#/parameters/ir_junction_aa_length" + "$ref": "#/parameters/ir_show_unproductive" } ], "operationId": "getSequenceSummary", @@ -1027,13 +1027,13 @@ "$ref": "#/parameters/junction_length_form" }, { - "$ref": "#/parameters/functional_form" + "$ref": "#/parameters/junction_aa_length_form" }, { - "$ref": "#/parameters/ir_show_unproductive_form" + "$ref": "#/parameters/functional_form" }, { - "$ref": "#/parameters/ir_junction_aa_length_form" + "$ref": "#/parameters/ir_show_unproductive_form" } ], "operationId": "postSequenceSummary", @@ -1103,13 +1103,13 @@ "$ref": "#/parameters/junction_length" }, { - "$ref": "#/parameters/functional" + "$ref": "#/parameters/junction_aa_length" }, { - "$ref": "#/parameters/ir_show_unproductive" + "$ref": "#/parameters/functional" }, { - "$ref": "#/parameters/ir_junction_aa_length" + "$ref": "#/parameters/ir_show_unproductive" } ], "operationId": "getSequenceData", @@ -1168,13 +1168,13 @@ "$ref": "#/parameters/junction_length_form" }, { - "$ref": "#/parameters/functional_form" + "$ref": "#/parameters/junction_aa_length_form" }, { - "$ref": "#/parameters/ir_show_unproductive_form" + "$ref": "#/parameters/functional_form" }, { - "$ref": "#/parameters/ir_junction_aa_length_form" + "$ref": "#/parameters/ir_show_unproductive_form" } ], "operationId": "postSequenceData", @@ -1233,13 +1233,13 @@ "$ref": "#/parameters/junction_length_form" }, { - "$ref": "#/parameters/functional_form" + "$ref": "#/parameters/junction_aa_length_form" }, { - "$ref": "#/parameters/ir_show_unproductive_form" + "$ref": "#/parameters/functional_form" }, { - "$ref": "#/parameters/ir_junction_aa_length_form" + "$ref": "#/parameters/ir_show_unproductive_form" } ], "operationId": "postCloneSummary", @@ -1309,13 +1309,13 @@ "$ref": "#/parameters/junction_length_form" }, { - "$ref": "#/parameters/functional_form" + "$ref": "#/parameters/junction_aa_length_form" }, { - "$ref": "#/parameters/ir_show_unproductive_form" + "$ref": "#/parameters/functional_form" }, { - "$ref": "#/parameters/ir_junction_aa_length_form" + "$ref": "#/parameters/ir_show_unproductive_form" } ], "operationId": "postCloneData", @@ -1345,4 +1345,4 @@ } } } -} +} \ No newline at end of file diff --git a/iReceptor_Data_Service_API_V2.yaml b/iReceptor_Data_Service_API_V2.yaml index 813fbae..ccda0d5 100644 --- a/iReceptor_Data_Service_API_V2.yaml +++ b/iReceptor_Data_Service_API_V2.yaml @@ -114,6 +114,10 @@ definitions: type: integer description: | Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues) + junction_aa_length: + type: integer + description: >- + Length of JUNCTION in amino acids functional: type: string description: | @@ -149,10 +153,7 @@ definitions: description: >- By default, only productive sequences are returned. In order to return unproductive sequences, set this parameter to "T" - ir_junction_aa_length: - type: integer - description: >- - Length of JUNCTION in amino acids (iReceptor) + parameters: # # Generally useful parameters for all API entry points. @@ -513,6 +514,20 @@ parameters: type: integer description: | Number of junction nucleotides in sequence_vdj (CDR3 + conserved residues) + junction_aa_length: + name: junction_aa_length + in: query + description: >- + Length of JUNCTION (CDR3 + conserved residues) in amino acids + required: false + type: integer + junction_aa_length_form: + name: junction_aa_length + in: formData + description: >- + Length of JUNCTION (CDR3 + conserved residues) in amino acids + required: false + type: integer functional: name: functional in: query @@ -604,20 +619,6 @@ parameters: Length of JUNCTION (CDR3 + conserved residues) in nucleotide base pairs (iReceptor) required: false type: integer - ir_junction_aa_length: - name: ir_junction_aa_length - in: query - description: >- - Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor) - required: false - type: integer - ir_junction_aa_length_form: - name: ir_junction_aa_length - in: formData - description: >- - Length of JUNCTION (CDR3 + conserved residues) in amino acids (iReceptor) - required: false - type: integer schemes: - https produces: @@ -801,9 +802,9 @@ paths: - $ref: '#/parameters/j_call' - $ref: '#/parameters/junction_aa' - $ref: '#/parameters/junction_length' + - $ref: '#/parameters/junction_aa_length' - $ref: '#/parameters/functional' - $ref: '#/parameters/ir_show_unproductive' - - $ref: '#/parameters/ir_junction_aa_length' operationId: getSequenceSummary responses: '200': @@ -849,9 +850,9 @@ paths: - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/junction_aa_length_form' - $ref: '#/parameters/functional_form' - $ref: '#/parameters/ir_show_unproductive_form' - - $ref: '#/parameters/ir_junction_aa_length_form' operationId: postSequenceSummary responses: '200': @@ -902,9 +903,9 @@ paths: - $ref: '#/parameters/j_call' - $ref: '#/parameters/junction_aa' - $ref: '#/parameters/junction_length' + - $ref: '#/parameters/junction_aa_length' - $ref: '#/parameters/functional' - $ref: '#/parameters/ir_show_unproductive' - - $ref: '#/parameters/ir_junction_aa_length' operationId: getSequenceData responses: '200': @@ -947,9 +948,9 @@ paths: - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/junction_aa_length_form' - $ref: '#/parameters/functional_form' - $ref: '#/parameters/ir_show_unproductive_form' - - $ref: '#/parameters/ir_junction_aa_length_form' operationId: postSequenceData responses: '200': @@ -989,9 +990,9 @@ paths: - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/junction_aa_length_form' - $ref: '#/parameters/functional_form' - $ref: '#/parameters/ir_show_unproductive_form' - - $ref: '#/parameters/ir_junction_aa_length_form' operationId: postCloneSummary responses: '200': @@ -1033,9 +1034,9 @@ paths: - $ref: '#/parameters/j_call_form' - $ref: '#/parameters/junction_aa_form' - $ref: '#/parameters/junction_length_form' + - $ref: '#/parameters/junction_aa_length_form' - $ref: '#/parameters/functional_form' - $ref: '#/parameters/ir_show_unproductive_form' - - $ref: '#/parameters/ir_junction_aa_length_form' operationId: postCloneData responses: '200': From 49112e0dbb471ba5fd3fe06cd902d0734b92c2d1 Mon Sep 17 00:00:00 2001 From: Brian Corrie Date: Sat, 18 Nov 2017 11:35:42 +1300 Subject: [PATCH 46/46] Added junction_aa_length to the repsonse. --- ireceptor_sequence.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/ireceptor_sequence.yaml b/ireceptor_sequence.yaml index 0112f55..8001bda 100644 --- a/ireceptor_sequence.yaml +++ b/ireceptor_sequence.yaml @@ -4,6 +4,10 @@ ireceptor_sequence_annotation_model: type: object properties: + junction_aa_length: + type: integer + description: >- + Length of JUNCTION in amino acids ir_seq_id: type: integer description: |