From 5e81fcfbacda4ae8c36f09d9869cd58453b5149e Mon Sep 17 00:00:00 2001 From: Victor Rocheleau Date: Fri, 22 Dec 2023 19:08:41 +0000 Subject: [PATCH] patch: validate phenopacket version string to be 2.0 only --- .../tests/example_multiple_phenopackets.json | 14 +- .../chord/tests/example_phenopacket_2_v2.json | 2 +- .../chord/tests/example_phenopacket_v2.json | 2 +- .../tests/example_phenopackets.json | 6 +- .../phenopackets/schemas.py | 2 +- .../phenopackets/tests/examples/covid.json | 2 +- examples/1000g_phenopackets_1_of_3.json | 1670 ++++++++--------- 7 files changed, 849 insertions(+), 849 deletions(-) diff --git a/chord_metadata_service/chord/tests/example_multiple_phenopackets.json b/chord_metadata_service/chord/tests/example_multiple_phenopackets.json index 826d3c355..81fcf41b9 100644 --- a/chord_metadata_service/chord/tests/example_multiple_phenopackets.json +++ b/chord_metadata_service/chord/tests/example_multiple_phenopackets.json @@ -53,7 +53,7 @@ "iri_prefix": "https://ncit.nci.nih.gov" } ], - "phenopacket_schema_version": "2.0.0" + "phenopacket_schema_version": "2.0" } }, { @@ -84,7 +84,7 @@ "meta_data": { "created_by": "Admin", "submitted_by": "Admin", - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "resources": [ { "id": "NCBITaxon:2018-07-27", @@ -141,7 +141,7 @@ "meta_data": { "created_by": "Admin", "submitted_by": "Admin", - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "resources": [ { "id": "NCBITaxon:2018-07-27", @@ -194,7 +194,7 @@ "meta_data": { "created_by": "Admin", "submitted_by": "Admin", - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "resources": [ { "id": "NCBITaxon:2018-07-27", @@ -253,7 +253,7 @@ "meta_data": { "created_by": "Admin", "submitted_by": "Admin", - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "resources": [ { "id": "NCBITaxon:2018-07-27", @@ -303,7 +303,7 @@ "meta_data": { "created_by": "Admin", "submitted_by": "Admin", - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "resources": [ { "id": "NCBITaxon:2018-07-27", @@ -351,7 +351,7 @@ "meta_data": { "created_by": "Admin", "submitted_by": "Admin", - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "resources": [ { "id": "NCBITaxon:2018-07-27", diff --git a/chord_metadata_service/chord/tests/example_phenopacket_2_v2.json b/chord_metadata_service/chord/tests/example_phenopacket_2_v2.json index be381d5eb..b2ca983b3 100644 --- a/chord_metadata_service/chord/tests/example_phenopacket_2_v2.json +++ b/chord_metadata_service/chord/tests/example_phenopacket_2_v2.json @@ -227,7 +227,7 @@ "iri_prefix": "http://purl.obolibrary.org/obo/NCIT_" } ], - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "external_references": [ { "id": "PMID:29221636", diff --git a/chord_metadata_service/chord/tests/example_phenopacket_v2.json b/chord_metadata_service/chord/tests/example_phenopacket_v2.json index 290d17498..891cd8515 100644 --- a/chord_metadata_service/chord/tests/example_phenopacket_v2.json +++ b/chord_metadata_service/chord/tests/example_phenopacket_v2.json @@ -501,7 +501,7 @@ "iri_prefix": "http://purl.obolibrary.org/obo/NCIT_" } ], - "phenopacket_schema_version": "2.0.0", + "phenopacket_schema_version": "2.0", "external_references": [ { "id": "PMID:29221636", diff --git a/chord_metadata_service/experiments/tests/example_phenopackets.json b/chord_metadata_service/experiments/tests/example_phenopackets.json index afdb3887c..e1f68a169 100644 --- a/chord_metadata_service/experiments/tests/example_phenopackets.json +++ b/chord_metadata_service/experiments/tests/example_phenopackets.json @@ -48,7 +48,7 @@ "iri_prefix": "https://ncit.nci.nih.gov" } ], - "phenopacket_schema_version": "2.0.0" + "phenopacket_schema_version": "2.0" }, "biosamples": [ { @@ -217,7 +217,7 @@ "iri_prefix": "https://ncit.nci.nih.gov" } ], - "phenopacket_schema_version": "2.0.0" + "phenopacket_schema_version": "2.0" }, "biosamples": [ { @@ -360,7 +360,7 @@ "iri_prefix": "https://ncit.nci.nih.gov" } ], - "phenopacket_schema_version": "2.0.0" + "phenopacket_schema_version": "2.0" }, "biosamples": [ { diff --git a/chord_metadata_service/phenopackets/schemas.py b/chord_metadata_service/phenopackets/schemas.py index 4200b857b..51be759b9 100644 --- a/chord_metadata_service/phenopackets/schemas.py +++ b/chord_metadata_service/phenopackets/schemas.py @@ -100,7 +100,7 @@ "submitted_by": base_type(SCHEMA_TYPES.STRING), "resources": array_of(RESOURCE_SCHEMA), "updates": array_of(PHENOPACKET_UPDATE_SCHEMA), - "phenopacket_schema_version": enum_of(["2.0", "2.0.0"]), + "phenopacket_schema_version": enum_of(["2.0"]), "external_references": array_of(PHENOPACKET_EXTERNAL_REFERENCE_SCHEMA), "extra_properties": EXTRA_PROPERTIES_SCHEMA }, diff --git a/chord_metadata_service/phenopackets/tests/examples/covid.json b/chord_metadata_service/phenopackets/tests/examples/covid.json index a21b3b614..92ebdccbc 100644 --- a/chord_metadata_service/phenopackets/tests/examples/covid.json +++ b/chord_metadata_service/phenopackets/tests/examples/covid.json @@ -357,7 +357,7 @@ "namespacePrefix": "UCUM", "iriPrefix": "https://units-of-measurement.org/" }], - "phenopacketSchemaVersion": "2.0.0", + "phenopacketSchemaVersion": "2.0", "externalReferences": [{ "id": "DOI:10.1016/j.jaccas.2020.04.001", "reference": "PMID:32292915", diff --git a/examples/1000g_phenopackets_1_of_3.json b/examples/1000g_phenopackets_1_of_3.json index 75395a401..98c955dd9 100644 --- a/examples/1000g_phenopackets_1_of_3.json +++ b/examples/1000g_phenopackets_1_of_3.json @@ -75,7 +75,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9fae782f-29d2-4a6e-900b-d735e8259aff" }, @@ -141,7 +141,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "0185b7e3-2101-4253-ae3b-f3730c8251a5" }, @@ -207,7 +207,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "67487b50-3a05-40a1-bfbb-12d05217a85f" }, @@ -273,7 +273,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "6b3d7e4b-d6ea-4e38-a176-5e418f5f1655" }, @@ -339,7 +339,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "70221771-ffde-41d1-97bf-6fccf4061c24" }, @@ -405,7 +405,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "ce2b260f-7f11-4365-8f0d-386c5fceeea6" }, @@ -471,7 +471,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "ff01c89f-d346-42e9-84fd-ee136fea7af6" }, @@ -537,7 +537,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "15fe00ef-7d84-4437-8916-76f21039d747" }, @@ -603,7 +603,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "b4062703-0f6e-4557-b2f6-b655e5dc290d" }, @@ -669,7 +669,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "5e506613-78f0-4741-b03a-58238604fc4d" }, @@ -735,7 +735,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "512ec8ee-ff50-4b11-a5e5-c058a1115666" }, @@ -801,7 +801,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "87284f47-5ee3-4902-bf84-8e4f21b3504c" }, @@ -867,7 +867,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "fad846b2-d813-4492-9566-a8833457512e" }, @@ -933,7 +933,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "0a3fc976-d428-46ea-8f70-0ae582e6645f" }, @@ -999,7 +999,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "bc496ded-3a44-449e-8238-6a2138267145" }, @@ -1065,7 +1065,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "3ac438c1-80a6-46ac-a2b6-71bcfb8fbdab" }, @@ -1131,7 +1131,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "c9a2091b-5094-49d7-b3b8-c76ee5eaa82b" }, @@ -1197,7 +1197,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "0eb6e29a-13e4-4f92-94e2-a33fab5024b6" }, @@ -1263,7 +1263,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "2f2e2bc1-32e4-46df-9427-603551849cb8" }, @@ -1329,7 +1329,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9da4d76e-7e63-4c65-84e9-08d65fd4843d" }, @@ -1395,7 +1395,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "ccaf488c-e7ed-4bcb-8c6f-fabf52870220" }, @@ -1461,7 +1461,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "227f19c6-55dc-433f-ae21-a4a4e911de86" }, @@ -1527,7 +1527,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9bff673c-cdec-4bd9-a83d-eaf9f529998b" }, @@ -1593,7 +1593,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "d2efadfd-08e2-4807-954f-24ed7588a0ce" }, @@ -1659,7 +1659,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "6904f940-cd7f-43b9-98a6-e23d426d73fe" }, @@ -1725,7 +1725,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "6a97442f-22c3-4246-9196-c8db3f97b81b" }, @@ -1791,7 +1791,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "0bad306d-a72c-4495-a564-528e3844e2b5" }, @@ -1857,7 +1857,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "8d18b40f-b36c-4cea-b0b2-db17e8c35c0a" }, @@ -1923,7 +1923,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "09227f22-94e4-46fd-bdac-42676f4d5205" }, @@ -1989,7 +1989,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "1bd2987b-791b-4e1c-8491-1ce13a692b8b" }, @@ -2055,7 +2055,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "b7ad69bf-708f-4ac6-bc9f-bcc1eca58993" }, @@ -2121,7 +2121,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "cbb6c1a7-9417-4f7e-b408-ac956546635c" }, @@ -2187,7 +2187,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9a78373d-12a2-4f9a-bdb4-0e5a387a9743" }, @@ -2253,7 +2253,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "1fb0bcc9-0f51-4b72-97c9-0d4a0d554a75" }, @@ -2319,7 +2319,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9136dfa0-28c4-4497-aed4-f4d9db565a37" }, @@ -2385,7 +2385,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9fd3ac29-cf23-42fb-a91d-316bf4b9e437" }, @@ -2451,7 +2451,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "0d9ccf99-1726-480c-aa0e-562aa62d2206" }, @@ -2517,7 +2517,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "00b6721e-7de0-459a-89f5-8ca74ba04e5b" }, @@ -2583,7 +2583,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9497b8e6-d90f-46b8-ba0e-fb5284fbd2f6" }, @@ -2649,7 +2649,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "e451f085-1b51-4474-b036-2be927aa78d3" }, @@ -2715,7 +2715,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "137e549f-5f56-4d95-8dfb-feb1380a44b4" }, @@ -2781,7 +2781,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "de45db61-7160-4778-84d9-ecf26c42ee81" }, @@ -2847,7 +2847,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "1adefaf4-419c-40ac-b800-4b91bf250e43" }, @@ -2913,7 +2913,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "6cac5d14-c372-44ff-96d4-40f62939bb92" }, @@ -2979,7 +2979,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "cfb3663f-e6e6-40f2-8940-4770cd6b1e71" }, @@ -3045,7 +3045,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "9fce27a7-d6c9-4ea8-9b19-4027523e6214" }, @@ -3111,7 +3111,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "c967fc03-bdea-47d3-b1d8-e80c43cb76d1" }, @@ -3177,7 +3177,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "17bfa124-115f-42c1-8604-fd595b9c089f" }, @@ -3243,7 +3243,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "cce4d52c-7be7-4ee2-b89a-3917fc5b0463" }, @@ -3309,7 +3309,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "6373b517-d867-439b-982b-2cffd4506c24" }, @@ -3375,7 +3375,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "83194bf2-4395-4372-a6ee-8791bdcbe827" }, @@ -3441,7 +3441,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "229674b6-4c62-42c4-b146-5f814b84663e" }, @@ -3507,7 +3507,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "5e30acc0-3d0c-4b80-a82a-3ae85bc180aa" }, @@ -3573,7 +3573,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - "phenopacketSchemaVersion": "2.0.0" + "phenopacketSchemaVersion": "2.0" }, "id": "c12f3eb1-a0cf-4979-8fa2-7b72fcca69b3" }, @@ -3639,7 +3639,7 @@ "iriPrefix": "https://ncit.nci.nih.gov" } ], - 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