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Merge pull request #144 from GMOD/1.4-1.3.3.013-add-type_id-linkers
V1.3.3.013 Add type_id and rank to all contact and project linker tables
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chado/migrations/V1.3.3.013__add_type_id_to_contact_and_project_linkers.sql
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| /* https://github.com/GMOD/Chado/issues/140 */ | ||
| /* Upgrade unique constraints with nullable columns if PostgreSQL version > 15 */ | ||
| CREATE OR REPLACE PROCEDURE addUniqueLinkerConstraint(table_name varchar, constraint_name varchar, columns varchar[]) | ||
| LANGUAGE plpgsql | ||
| AS $$ | ||
| DECLARE | ||
| newer_than_15 boolean; | ||
| BEGIN | ||
| -- Determine the version of PostgreSQL | ||
| SELECT CASE WHEN current_setting('server_version_num')::INT > 150000 THEN true ELSE false END AS supported INTO newer_than_15; | ||
|
|
||
| -- IF the version is newer then we can use the new UNIQUE NULLS NOT DISTINCT | ||
| -- which does not treat 2 records that are the same but include NULL as distict. | ||
| IF newer_than_15 THEN | ||
| EXECUTE format('ALTER TABLE %s ADD CONSTRAINT %s UNIQUE NULLS NOT DISTINCT (%s)', table_name, constraint_name, array_to_string(columns, ',')); | ||
| -- IF the version is <15 then we use the original UNIQUE style constraint | ||
| ELSE | ||
| EXECUTE format('ALTER TABLE %s ADD CONSTRAINT %s UNIQUE (%s)', table_name, constraint_name, array_to_string(columns, ',')); | ||
| END IF; | ||
| END | ||
| $$; | ||
| /* Contact Linkers */ | ||
| /* -- Feature */ | ||
| ALTER TABLE feature_contact ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN feature_contact.type_id IS 'Indicates the type of linkage such as the role of the contact. For example, a type_id referencing the term Curator (NCIT:C69141) indicates that the linked contact curated a particular gene model.'; | ||
| ALTER TABLE feature_contact ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN feature_contact.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique feature - contact combination.'; | ||
| ALTER TABLE feature_contact ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE feature_contact DROP CONSTRAINT feature_contact_c1; | ||
| CALL addUniqueLinkerConstraint('feature_contact', 'feature_contact_c1', ARRAY['feature_id', 'contact_id', 'type_id']); | ||
| /* -- Featuremap */ | ||
| ALTER TABLE featuremap_contact ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN featuremap_contact.type_id IS 'Indicates the type of linkage such as the role of the contact. For example, a type_id referencing the term Curator (NCIT:C69141) indicates that the linked contact curated this genetic map.'; | ||
| ALTER TABLE featuremap_contact ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN featuremap_contact.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique featuremap - contact combination.'; | ||
| ALTER TABLE featuremap_contact ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE featuremap_contact DROP CONSTRAINT featuremap_contact_c1; | ||
| CALL addUniqueLinkerConstraint('featuremap_contact', 'featuremap_contact_c1', ARRAY['featuremap_id', 'contact_id', 'type_id']); | ||
| /* -- Library */ | ||
| ALTER TABLE library_contact ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN library_contact.type_id IS 'Indicates the type of linkage such as the role of the contact. For example, a type_id referencing the term Distributor (NCIT:C48289) indicates that the linked contact organization distributes this library.'; | ||
| ALTER TABLE library_contact ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN library_contact.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique library - contact combination.'; | ||
| ALTER TABLE library_contact ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE library_contact DROP CONSTRAINT library_contact_c1; | ||
| CALL addUniqueLinkerConstraint('library_contact', 'library_contact_c1', ARRAY['library_id', 'contact_id', 'type_id']); | ||
| /* -- ND Experiment */ | ||
| ALTER TABLE nd_experiment_contact ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN nd_experiment_contact.type_id IS 'Indicates the type of linkage such as the role of the contact. For example, a type_id referencing the term Data Collector (AGRO:00000379) indicates that the data in this natural diversity experiment was collected by the linked contact.'; | ||
| ALTER TABLE nd_experiment_contact ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN nd_experiment_contact.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique ND Experiment - contact combination.'; | ||
| ALTER TABLE nd_experiment_contact ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| CALL addUniqueLinkerConstraint('nd_experiment_contact', 'nd_experiment_contact_c1', ARRAY['nd_experiment_id', 'contact_id', 'type_id']); | ||
| /* -- Project */ | ||
| ALTER TABLE project_contact ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN project_contact.type_id IS 'Indicates the type of linkage such as the role of the contact. For example, a type_id referencing the term Funder (EFO:0001736) indicates that the linked contact organization funded the research described in this project.'; | ||
| ALTER TABLE project_contact ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN project_contact.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique project - contact combination.'; | ||
| ALTER TABLE project_contact ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE project_contact DROP CONSTRAINT project_contact_c1; | ||
| CALL addUniqueLinkerConstraint('project_contact', 'project_contact_c1', ARRAY['project_id', 'contact_id', 'type_id']); | ||
| /* -- Pubauthor */ | ||
| ALTER TABLE pubauthor_contact ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN pubauthor_contact.type_id IS 'Indicates the type of linkage such as the role of the contact. For example, a type_id referencing the term Exact (NCIT:C86021) indicates that the linked contact represents the same person as the author of the publication.'; | ||
| ALTER TABLE pubauthor_contact ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN pubauthor_contact.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique publication author - contact combination.'; | ||
| ALTER TABLE pubauthor_contact ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE pubauthor_contact DROP CONSTRAINT pubauthor_contact_c1; | ||
| CALL addUniqueLinkerConstraint('pubauthor_contact', 'pubauthor_contact_c1', ARRAY['pubauthor_id', 'contact_id', 'type_id']); | ||
| /* Project Linkers */ | ||
| /* -- Features */ | ||
| ALTER TABLE project_feature ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN project_feature.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Reference Object (NCIT:C48294) indicates that the linked project references this feature in the course of their research.'; | ||
| ALTER TABLE project_feature ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN project_feature.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique feature - project combination.'; | ||
| ALTER TABLE project_feature ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE project_feature DROP CONSTRAINT project_feature_c1; | ||
| CALL addUniqueLinkerConstraint('project_feature', 'project_feature_c1', ARRAY['feature_id', 'project_id', 'type_id']); | ||
| /* -- Publications */ | ||
| ALTER TABLE project_pub ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN project_pub.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Reference Object (NCIT:C48294) indicates that the linked project references this publication in the course of their research.'; | ||
| ALTER TABLE project_pub ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN project_pub.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique publication - project combination.'; | ||
| ALTER TABLE project_pub ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE project_pub DROP CONSTRAINT project_pub_c1; | ||
| CALL addUniqueLinkerConstraint('project_pub', 'project_pub_c1', ARRAY['pub_id', 'project_id', 'type_id']); | ||
| /* -- ND Experiments */ | ||
| ALTER TABLE nd_experiment_project ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN nd_experiment_project.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Output (REPRODUCEME:Output) indicates that the linked project carried out this experiment in the course of their research.'; | ||
| ALTER TABLE nd_experiment_project ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN nd_experiment_project.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique nd experiment - project combination.'; | ||
| ALTER TABLE nd_experiment_project ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE nd_experiment_project DROP CONSTRAINT nd_experiment_project_c1; | ||
| CALL addUniqueLinkerConstraint('nd_experiment_project', 'nd_experiment_project_c1', ARRAY['nd_experiment_id', 'project_id', 'type_id']); | ||
| /* -- Analysis */ | ||
| /* Already has a rank */ | ||
| COMMENT ON COLUMN project_analysis.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique analysis - project combination.'; | ||
| ALTER TABLE project_analysis ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN project_analysis.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Output (REPRODUCEME:Output) indicates that the linked project carried out this analysis in the course of their research.'; | ||
| ALTER TABLE project_analysis ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE project_analysis DROP CONSTRAINT project_analysis_c1; | ||
| CALL addUniqueLinkerConstraint('project_analysis', 'project_analysis_c1', ARRAY['analysis_id', 'project_id', 'type_id']); | ||
| /* -- Stock */ | ||
| ALTER TABLE project_stock ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN project_stock.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Output (REPRODUCEME:Output) indicates that the linked project produced this genetic stock (e.g. bred a new cultivar, extracted a DNA sample) in the course of their research.'; | ||
| ALTER TABLE project_stock ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN project_stock.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique stock - project combination.'; | ||
| ALTER TABLE project_stock ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE project_stock DROP CONSTRAINT project_stock_c1; | ||
| CALL addUniqueLinkerConstraint('project_stock', 'project_stock_c1', ARRAY['stock_id', 'project_id', 'type_id']); | ||
| /* -- Assay */ | ||
| ALTER TABLE assay_project ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN assay_project.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Output (REPRODUCEME:Output) indicates that the linked project carried out this assay in the course of their research.'; | ||
| ALTER TABLE assay_project ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN assay_project.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique assay - project combination.'; | ||
| ALTER TABLE assay_project ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE assay_project DROP CONSTRAINT assay_project_c1; | ||
| CALL addUniqueLinkerConstraint('assay_project', 'assay_project_c1', ARRAY['assay_id', 'project_id', 'type_id']); | ||
| /* -- Dbxref */ | ||
| ALTER TABLE project_dbxref ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN project_dbxref.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term doi (REPRODUCEME:doi) indicates that the linked dbxref is a persistent identifier for this project.'; | ||
| ALTER TABLE project_dbxref ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN project_dbxref.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique dbxref - project combination.'; | ||
| ALTER TABLE project_dbxref ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE project_dbxref DROP CONSTRAINT project_dbxref_c1; | ||
| CALL addUniqueLinkerConstraint('project_dbxref', 'project_dbxref_c1', ARRAY['dbxref_id', 'project_id', 'type_id']); | ||
| /* -- biomaterial_project */ | ||
| ALTER TABLE biomaterial_project ADD COLUMN type_id bigint; | ||
| COMMENT ON COLUMN biomaterial_project.type_id IS 'Indicates the type of linkage such as the way the project uses this item. For example, a type_id referencing the term Output (REPRODUCEME:Output) indicates that the linked project collected this genetic stock (e.g. collected a field sample, extracted a DNA sample) in the course of their research.'; | ||
| ALTER TABLE biomaterial_project ADD COLUMN rank int DEFAULT 0; | ||
| COMMENT ON COLUMN biomaterial_project.rank IS 'Indicates the ordering of contacts with the same type_id. Currently this is not part of the unique key; therefore, there should only be one rank per unique biomaterial - project combination.'; | ||
| ALTER TABLE biomaterial_project ADD FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL; | ||
| ALTER TABLE biomaterial_project DROP CONSTRAINT biomaterial_project_c1; | ||
| CALL addUniqueLinkerConstraint('biomaterial_project', 'biomaterial_project_c1', ARRAY['biomaterial_id', 'project_id', 'type_id']); |