new reference package

OHDSI · Jan 22, 2020 · 1c928f2 · 1c928f2
1 parent f81ac7e
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diff --git a/working/packages/reference_pack/AddNewConcept.sql b/working/packages/reference_pack/AddNewConcept.sql
@@ -0,0 +1,92 @@
+/*
+Adds new concept
+
+Usage:
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewConcept(
+    pConcept_name     =>'test concept name',
+    pDomain_id        =>'Drug',
+    pVocabulary_id    =>'SNOMED',
+    pConcept_class_id =>'Ingredient',
+    pStandard_concept =>'S',
+    pConcept_code     =>'123_test2'
+);
+END $_$;
+
+OR (if you want to get the concept_id):
+
+SELECT vocabulary_pack.AddNewConcept(
+    pConcept_name     =>'test concept name',
+    pDomain_id        =>'Drug',
+    pVocabulary_id    =>'SNOMED',
+    pConcept_class_id =>'Ingredient',
+    pStandard_concept =>'S',
+    pConcept_code     =>'123_test3'
+);
+*/
+
+CREATE OR REPLACE FUNCTION vocabulary_pack.AddNewConcept (
+  pConcept_name concept.concept_name%TYPE,
+  pDomain_id concept.domain_id%TYPE,
+  pVocabulary_id concept.vocabulary_id%TYPE,
+  pConcept_class_id concept.concept_class_id%TYPE,
+  pStandard_concept concept.standard_concept%TYPE,
+  pConcept_code concept.concept_code%TYPE,
+  pValid_start_date concept.valid_start_date%TYPE = TO_DATE ('19700101', 'YYYYMMDD'),
+  pValid_end_date concept.valid_end_date%TYPE = TO_DATE ('20991231', 'YYYYMMDD'),
+  pInvalid_reason concept.invalid_reason%TYPE = NULL
+)
+RETURNS int4 AS
+$BODY$
+DECLARE
+  z  INT;
+  ex INT;
+BEGIN
+  IF COALESCE(pStandard_concept,'S') NOT IN ('S','C') THEN RAISE EXCEPTION 'Incorrect value for pStandard_concept: %', pStandard_concept; END IF;
+  IF pStandard_concept='S' AND pInvalid_reason IS NOT NULL THEN RAISE EXCEPTION 'pStandard_concept cannot be S (pInvalid_reason is not null)'; END IF;
+
+  pConcept_name:=REGEXP_REPLACE(pConcept_name, '[[:cntrl:]]+', ' ', 'g');
+  pConcept_name:=REGEXP_REPLACE(pConcept_name, ' {2,}', ' ', 'g');
+  pConcept_name:=TRIM(pConcept_name);
+  pConcept_name:=REPLACE(pConcept_name, '–', '-');
+
+  pConcept_code:=REGEXP_REPLACE(pConcept_code, '[[:cntrl:]]+', ' ', 'g');
+  pConcept_code:=REGEXP_REPLACE(pConcept_code, ' {2,}', ' ', 'g');
+  pConcept_code:=TRIM(pConcept_code);
+  pConcept_code:=REPLACE(pConcept_code, '–', '-');  
+
+  DROP SEQUENCE IF EXISTS v5_concept;
+
+  SELECT MAX (concept_id) + 1 INTO ex FROM concept
+  WHERE concept_id >= 31967 AND concept_id < 72245;
+
+  EXECUTE 'CREATE SEQUENCE v5_concept INCREMENT BY 1 START WITH ' || ex || ' CACHE 20';
+
+  --insert the concept
+  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_name, pDomain_id, pVocabulary_id, pConcept_class_id, pStandard_concept, pConcept_code, pValid_start_date, pValid_end_date, pInvalid_reason);
+
+  --insert the mapping
+  IF pStandard_concept='S' THEN
+    INSERT INTO concept_relationship (concept_id_1, concept_id_2, relationship_id, valid_start_date, valid_end_date, invalid_reason)
+      VALUES (z, z, 'Maps to', pValid_start_date, TO_DATE('20991231', 'YYYYMMDD'), NULL),
+             (z, z, 'Mapped from', pValid_start_date, TO_DATE('20991231', 'YYYYMMDD'), NULL);
+  END IF;
+
+  --insert the synonym (=pConcept_name)
+  INSERT INTO concept_synonym (concept_id, concept_synonym_name, language_concept_id)
+    VALUES (z, pConcept_name, 4180186 /*English*/);
+
+  DROP SEQUENCE v5_concept;
+
+  RETURN z;
+END;
+$BODY$
+LANGUAGE 'plpgsql'
+VOLATILE
+CALLED ON NULL INPUT
+SECURITY INVOKER
+COST 100
+SET client_min_messages = error;
diff --git a/working/packages/reference_pack/AddNewRelationship.sql b/working/packages/reference_pack/AddNewRelationship.sql
@@ -0,0 +1,73 @@
+/*
+Adds new relationship
+
+Usage:
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewRelationship(
+    pRelationship_name       =>'Has system',
+    pRelationship_id         =>'Has system',
+    pIs_hierarchical         =>0,
+    pDefines_ancestry        =>0,
+    pReverse_relationship_id =>'System of',
+    pRelationship_name_rev   =>'System of',
+    pIs_hierarchical_rev     =>0,
+    pDefines_ancestry_rev    =>0
+);
+END $_$;
+*/
+
+CREATE OR REPLACE FUNCTION vocabulary_pack.AddNewRelationship (
+  pRelationship_name relationship.relationship_name%TYPE,
+  pRelationship_id relationship.relationship_id%TYPE,
+  pIs_hierarchical int,
+  pDefines_ancestry int,
+  pReverse_relationship_id relationship.reverse_relationship_id%TYPE,
+  pRelationship_name_rev relationship.relationship_name%TYPE,
+  pIs_hierarchical_rev int,
+  pDefines_ancestry_rev int
+)
+RETURNS void AS
+$BODY$
+DECLARE
+  z  INT;
+  ex INT;
+BEGIN
+  IF COALESCE(pIs_hierarchical,-1) NOT IN (0,1) THEN RAISE EXCEPTION 'Incorrect value for pIs_hierarchical: %', pIs_hierarchical; END IF;
+  IF COALESCE(pDefines_ancestry,-1) NOT IN (0,1) THEN RAISE EXCEPTION 'Incorrect value for pDefines_ancestry: %', pDefines_ancestry; END IF;
+  IF COALESCE(pIs_hierarchical_rev,-1) NOT IN (0,1) THEN RAISE EXCEPTION 'Incorrect value for pIs_hierarchical_rev: %', pIs_hierarchical_rev; END IF;
+  IF COALESCE(pDefines_ancestry_rev,-1) NOT IN (0,1) THEN RAISE EXCEPTION 'Incorrect value for pDefines_ancestry_rev: %', pDefines_ancestry_rev; END IF;
+  IF pDefines_ancestry=1 AND pDefines_ancestry_rev=1 THEN RAISE EXCEPTION 'pDefines_ancestry and pDefines_ancestry_rev are both equal to 1'; END IF;
+
+  DROP SEQUENCE IF EXISTS v5_concept;
+
+  SELECT MAX (concept_id) + 1 INTO ex FROM concept
+  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;
+$BODY$
+LANGUAGE 'plpgsql'
+VOLATILE
+CALLED ON NULL INPUT
+SECURITY INVOKER
+COST 100
+SET client_min_messages = error;
diff --git a/working/packages/reference_pack/AddNewSynonym.sql b/working/packages/reference_pack/AddNewSynonym.sql
@@ -0,0 +1,58 @@
+/*
+Adds new synonym
+
+Usage:
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewSynonym(
+    pConcept_id          =>123,
+    pSynonym_name        =>'test synonym',
+    pLanguage_concept_id =>4180186
+);
+END $_$;
+
+OR you can combine with the AddNewConcept:
+
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewSynonym(
+    pConcept_id          =>vocabulary_pack.AddNewConcept(
+                            pConcept_name     =>'test concept name 5',
+                            pDomain_id        =>'Drug',
+                            pVocabulary_id    =>'SNOMED',
+                            pConcept_class_id =>'Ingredient',
+                            pStandard_concept =>'S',
+                            pConcept_code     =>'123_test5'
+                        ),
+    pSynonym_name        =>'test synonym 5',
+    pLanguage_concept_id =>4180186
+);
+END $_$;
+*/
+
+CREATE OR REPLACE FUNCTION vocabulary_pack.AddNewSynonym (
+  pConcept_id concept_synonym.concept_id%TYPE,
+  pSynonym_name concept_synonym.concept_synonym_name%TYPE,
+  pLanguage_concept_id concept_synonym.language_concept_id%TYPE = 4180186 /*English*/
+)
+RETURNS void AS
+$BODY$
+DECLARE
+  z  INT;
+  ex INT;
+BEGIN
+  pSynonym_name:=REGEXP_REPLACE(pSynonym_name, '[[:cntrl:]]+', ' ', 'g');
+  pSynonym_name:=REGEXP_REPLACE(pSynonym_name, ' {2,}', ' ', 'g');
+  pSynonym_name:=TRIM(pSynonym_name);
+  pSynonym_name:=REPLACE(pSynonym_name, '–', '-');
+
+  INSERT INTO concept_synonym (concept_id, concept_synonym_name, language_concept_id)
+    VALUES (pConcept_id, pSynonym_name, pLanguage_concept_id);
+END;
+$BODY$
+LANGUAGE 'plpgsql'
+VOLATILE
+CALLED ON NULL INPUT
+SECURITY INVOKER
+COST 100
+SET client_min_messages = error;
diff --git a/...ages/vocabulary_pack/AddNewVocabulary.sql → ...kages/reference_pack/AddNewVocabulary.sql b/...ages/vocabulary_pack/AddNewVocabulary.sql → ...kages/reference_pack/AddNewVocabulary.sql