Merge pull request #271 from OHDSI/LOINC-new-concept_classes-and-rela…

…tionships LOINC new concept_classes and relationships
OHDSI · Dec 6, 2019 · 1566a2f · 1566a2f
2 parents 8a1002c + 622c322
commit 1566a2f
Showing 1 changed file with 185 additions and 0 deletions.
diff --git a/working/manual_changes/2019/manual_changes_06-Dec-2019.sql b/working/manual_changes/2019/manual_changes_06-Dec-2019.sql
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+--new relationships for LOINC
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pRelationship_name constant varchar(100):='Has system';
+    pRelationship_id constant varchar(100):='Has system';
+    pIs_hierarchical constant int:=0;
+    pDefines_ancestry constant int:=0;
+    pReverse_relationship_id constant varchar(100):='System of';
+    pRelationship_name_rev constant varchar(100):='System of';
+    pIs_hierarchical_rev constant int:=0;
+    pDefines_ancestry_rev constant int:=0;
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    ALTER TABLE relationship DROP CONSTRAINT FPK_RELATIONSHIP_REVERSE;
+
+    --direct
+    SELECT nextval('v5_concept') INTO z;
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pRelationship_name, 'Metadata', 'Relationship', 'Relationship', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO relationship (relationship_id, relationship_name, is_hierarchical, defines_ancestry, reverse_relationship_id, relationship_concept_id)
+      VALUES (pRelationship_id, pRelationship_name, pIs_hierarchical, pDefines_ancestry, pReverse_relationship_id, z);
+
+    --reverse
+    SELECT nextval('v5_concept') INTO z;
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pRelationship_name_rev, 'Metadata', 'Relationship', 'Relationship', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO relationship (relationship_id, relationship_name, is_hierarchical, defines_ancestry, reverse_relationship_id, relationship_concept_id)
+      VALUES (pReverse_relationship_id, pRelationship_name_rev, pIs_hierarchical_rev, pDefines_ancestry_rev, pRelationship_id, z);
+
+    ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
+    DROP SEQUENCE v5_concept;
+END $$;
+
+--new classes for LOINC
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pConcept_class_id constant varchar(100):='LOINC System';
+    pConcept_class_name constant varchar(100):= 'LOINC System';
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    SELECT nextval('v5_concept') INTO z;
+
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pConcept_class_name, 'Metadata', 'Concept Class', 'Concept Class', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO concept_class (concept_class_id, concept_class_name, concept_class_concept_id)
+      VALUES (pConcept_class_id, pConcept_class_name, z);
+
+    DROP SEQUENCE v5_concept;
+END $$;
+
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pConcept_class_id constant varchar(100):='LOINC Component';
+    pConcept_class_name constant varchar(100):= 'LOINC Component';
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    SELECT nextval('v5_concept') INTO z;
+
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pConcept_class_name, 'Metadata', 'Concept Class', 'Concept Class', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO concept_class (concept_class_id, concept_class_name, concept_class_concept_id)
+      VALUES (pConcept_class_id, pConcept_class_name, z);
+
+    DROP SEQUENCE v5_concept;
+END $$;
+
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pConcept_class_id constant varchar(100):='LOINC Scale';
+    pConcept_class_name constant varchar(100):= 'LOINC Scale';
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    SELECT nextval('v5_concept') INTO z;
+
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pConcept_class_name, 'Metadata', 'Concept Class', 'Concept Class', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO concept_class (concept_class_id, concept_class_name, concept_class_concept_id)
+      VALUES (pConcept_class_id, pConcept_class_name, z);
+
+    DROP SEQUENCE v5_concept;
+END $$;
+
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pConcept_class_id constant varchar(100):='LOINC Time';
+    pConcept_class_name constant varchar(100):= 'LOINC Time';
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    SELECT nextval('v5_concept') INTO z;
+
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pConcept_class_name, 'Metadata', 'Concept Class', 'Concept Class', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO concept_class (concept_class_id, concept_class_name, concept_class_concept_id)
+      VALUES (pConcept_class_id, pConcept_class_name, z);
+
+    DROP SEQUENCE v5_concept;
+END $$;
+
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pConcept_class_id constant varchar(100):='LOINC Method';
+    pConcept_class_name constant varchar(100):= 'LOINC Method';
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    SELECT nextval('v5_concept') INTO z;
+
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pConcept_class_name, 'Metadata', 'Concept Class', 'Concept Class', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO concept_class (concept_class_id, concept_class_name, concept_class_concept_id)
+      VALUES (pConcept_class_id, pConcept_class_name, z);
+
+    DROP SEQUENCE v5_concept;
+END $$;
+
+DO $$
+DECLARE
+    z    int;
+    ex   int;
+    pConcept_class_id constant varchar(100):='LOINC Property';
+    pConcept_class_name constant varchar(100):= 'LOINC Property';
+BEGIN
+    DROP SEQUENCE IF EXISTS v5_concept;
+
+    SELECT MAX (concept_id) + 1 INTO ex FROM concept
+      --WHERE concept_id>=200 and concept_id<1000; --only for VIP concepts
+    WHERE concept_id >= 31967 AND concept_id < 72245;
+
+    EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+    SELECT nextval('v5_concept') INTO z;
+
+    INSERT INTO concept (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, pConcept_class_name, 'Metadata', 'Concept Class', 'Concept Class', null, 'OMOP generated', TO_DATE ('19700101', 'YYYYMMDD'), TO_DATE ('20991231', 'YYYYMMDD'), null);
+    INSERT INTO concept_class (concept_class_id, concept_class_name, concept_class_concept_id)
+      VALUES (pConcept_class_id, pConcept_class_name, z);
+
+    DROP SEQUENCE v5_concept;
+END $$;