145 lines
14 KiB
Bash
145 lines
14 KiB
Bash
#!/bin/bash
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#
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#CLINICAL
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#
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echo "\n\n--\n--CLINICAL\n--\n" > "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- VISIT_OCCURENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.visit_occurence.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONDITION_OCCURENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.condition_occurence.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DEATH" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEATH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.death.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DEVICE_EXPOSURE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEVICE_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.device_exposure.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DRUG_EXPOSURE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DRUG_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.drug_exposure.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- FACT_RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/FACT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.FACT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- MEASUREMENT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/MEASUREMENT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.MEASUREMENT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- NOTE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.NOTE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- VISIT_DETAIL" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_DETAIL.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.VISIT_DETAIL.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- SPECIMEN" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/SPECIMEN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.SPECIMEN.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- PROCEDURE_OCCURRENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PROCEDURE_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- PERSON" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PERSON.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PERSON.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- OBSERVATION_PERIOD" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.OBSERVATION_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- OBSERVATION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.OBSERVATION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- NOTE_NLP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.NOTE_NLP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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#
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#ECONOMIC
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#
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echo "\n\n--\n--ECONOMIC\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- COST" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COST.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- PAYER_PLAN_PERIOD" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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#
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#METADATA
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#
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echo "\n\n--\n--METADATA\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CDM_SOURCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CDM_SOURCE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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#
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#DERIVED
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#
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echo "\n\n--\n--DERIVED\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- COHORT_ATTRIBUTE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- COHORT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COHORT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONDITION_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONDITION_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DOSE_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DOSE_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DRUG_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DRUG_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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#
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#SYSTEM
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#
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echo "\n\n--\n--SYSTEM\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CARE_SITE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CARE_SITE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- LOCATION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.LOCATION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- PROVIDER" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PROVIDER.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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#
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#SYSTEM
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#
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echo "\n\n--\n--SYSTEM\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- ATTRIBUTE_DEFINITION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- COHORT_DEFINITION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COHORT_DEFINITION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONCEPT_ANCESTOR" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_ANCESTOR.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONCEPT_CLASS" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_CLASS.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONCEPT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONCEPT_RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- CONCEPT_SYNONYM" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_SYNONYM.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DOMAIN" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DOMAIN.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- DRUG_STRENGTH" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DRUG_STRENGTH.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- SOURCE_TO_CONCEPT_MAP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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echo "\n\n-- VOCABULARY" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.VOCABULARY.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
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