diff --git a/src/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java b/src/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java index ed0054e5..bf3ba2d8 100644 --- a/src/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java +++ b/src/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java @@ -25,6 +25,12 @@ import org.ohdsi.utilities.files.Row; import org.ohdsi.utilities.files.WriteCSVFileWithHeader; +/** + * This class is used as a stand-alone to fetch the structure of the CDM from the server and format it for insertion into Rabbit-In-A-Hat. + * It is not intended to be used by non-developers. + * @author MSCHUEMI + * + */ public class FetchCDMModelFromServer { public static void main(String[] args) { @@ -32,9 +38,14 @@ public static void main(String[] args) { connection.use("cdm5"); WriteCSVFileWithHeader out = new WriteCSVFileWithHeader("c:/temp/CDMV5Model.csv"); - String query = "SELECT table_name,COLUMN_NAME,IS_NULLABLE,DATA_TYPE FROM INFORMATION_SCHEMA.COLUMNS WHERE TABLE_SCHEMA = 'cdm5';"; - for (Row row : connection.query(query)) - out.write(row); + String query = "SELECT table_name,column_name,is_nullable,data_type FROM INFORMATION_SCHEMA.COLUMNS WHERE TABLE_SCHEMA = 'cdm5';"; + for (Row row : connection.query(query)){ + row.upperCaseFieldNames(); + Row newRow = new Row(); + for (String field : row.getFieldNames()) + newRow.add(field, row.get(field).toUpperCase()); + out.write(newRow); + } out.close(); } diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat.java b/src/org/ohdsi/rabbitInAHat/RabbitInAHat.java index fbd949fe..e8a10ebd 100644 --- a/src/org/ohdsi/rabbitInAHat/RabbitInAHat.java +++ b/src/org/ohdsi/rabbitInAHat/RabbitInAHat.java @@ -180,14 +180,14 @@ private JMenuBar createMenuBar() { generateDocItem.setActionCommand("Generate ETL document"); fileMenu.add(generateDocItem); - JMenu editMenu = new JMenu("Edit"); - menuBar.add(editMenu); +// JMenu editMenu = new JMenu("Edit"); +// menuBar.add(editMenu); - JMenu viewMenu = new JMenu("View"); - menuBar.add(viewMenu); +// JMenu viewMenu = new JMenu("View"); +// menuBar.add(viewMenu); - JMenu helpMenu = new JMenu("Help"); - menuBar.add(helpMenu); +// JMenu helpMenu = new JMenu("Help"); +// menuBar.add(helpMenu); return menuBar; } diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV4Model.csv b/src/org/ohdsi/rabbitInAHat/dataModel/CDMV4Model.csv index caf9c290..a30a9058 100644 --- a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV4Model.csv +++ b/src/org/ohdsi/rabbitInAHat/dataModel/CDMV4Model.csv @@ -1,4 +1,4 @@ -TABLE_NAME,COLUMN_NAME,IS_NULLABLE,COLUMN_TYPE +TABLE_NAME,COLUMN_NAME,IS_NULLABLE,DATA_TYPE location,LOCATION_ID,NO,int(11) location,ADDRESS_1,YES,varchar(50) location,ADDRESS_2,YES,varchar(50) diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMv5Model.csv b/src/org/ohdsi/rabbitInAHat/dataModel/CDMv5Model.csv index 09db6781..24a947c9 100644 --- a/src/org/ohdsi/rabbitInAHat/dataModel/CDMv5Model.csv +++ b/src/org/ohdsi/rabbitInAHat/dataModel/CDMv5Model.csv @@ -1,22 +1,20 @@ -TABLE_NAME,COLUMN_NAME,IS_NULLABLE,COLUMN_TYPE -CDM_SOURCE,CDM_SOURCE_NAME,NO,CHARACTER VARYING -CDM_SOURCE,CDM_SOURCE_ABBREVIATION,YES,CHARACTER VARYING -CDM_SOURCE,CDM_HOLDER,YES,CHARACTER VARYING -CDM_SOURCE,SOURCE_DESCRIPTION,YES,TEXT -CDM_SOURCE,SOURCE_DOCUMENTATION_REFERENCE,YES,CHARACTER VARYING -CDM_SOURCE,CDM_ETL_REFERENCE,YES,CHARACTER VARYING -CDM_SOURCE,SOURCE_RELEASE_DATE,YES,DATE -CDM_SOURCE,CDM_RELEASE_DATE,YES,DATE -CDM_SOURCE,CDM_VERSION,YES,CHARACTER VARYING -CDM_SOURCE,VOCABULARY_VERSION,YES,CHARACTER VARYING +TABLE_NAME,COLUMN_NAME,IS_NULLABLE,DATA_TYPE +LOCATION,LOCATION_ID,NO,INTEGER +LOCATION,ADDRESS_1,YES,CHARACTER VARYING +LOCATION,ADDRESS_2,YES,CHARACTER VARYING +LOCATION,CITY,YES,CHARACTER VARYING +LOCATION,STATE,YES,CHARACTER VARYING +LOCATION,ZIP,YES,CHARACTER VARYING +LOCATION,COUNTY,YES,CHARACTER VARYING +LOCATION,LOCATION_SOURCE_VALUE,YES,CHARACTER VARYING PERSON,PERSON_ID,NO,INTEGER PERSON,GENDER_CONCEPT_ID,NO,INTEGER PERSON,YEAR_OF_BIRTH,NO,INTEGER PERSON,MONTH_OF_BIRTH,YES,INTEGER PERSON,DAY_OF_BIRTH,YES,INTEGER PERSON,TIME_OF_BIRTH,YES,CHARACTER VARYING -PERSON,RACE_CONCEPT_ID,YES,INTEGER -PERSON,ETHNICITY_CONCEPT_ID,YES,INTEGER +PERSON,RACE_CONCEPT_ID,NO,INTEGER +PERSON,ETHNICITY_CONCEPT_ID,NO,INTEGER PERSON,LOCATION_ID,YES,INTEGER PERSON,PROVIDER_ID,YES,INTEGER PERSON,CARE_SITE_ID,YES,INTEGER @@ -32,27 +30,12 @@ OBSERVATION_PERIOD,PERSON_ID,NO,INTEGER OBSERVATION_PERIOD,OBSERVATION_PERIOD_START_DATE,NO,DATE OBSERVATION_PERIOD,OBSERVATION_PERIOD_END_DATE,NO,DATE OBSERVATION_PERIOD,PERIOD_TYPE_CONCEPT_ID,NO,INTEGER -SPECIMEN,SPECIMEN_ID,NO,INTEGER -SPECIMEN,PERSON_ID,NO,INTEGER -SPECIMEN,SPECIMEN_CONCEPT_ID,NO,INTEGER -SPECIMEN,SPECIMEN_TYPE_CONCEPT_ID,NO,INTEGER -SPECIMEN,SPECIMEN_DATE,NO,DATE -SPECIMEN,SPECIMEN_TIME,YES,CHARACTER VARYING -SPECIMEN,QUANTITY,YES,DOUBLE PRECISION -SPECIMEN,UNIT_CONCEPT_ID,YES,INTEGER -SPECIMEN,ANATOMIC_SITE_CONCEPT_ID,YES,INTEGER -SPECIMEN,DISEASE_STATUS_CONCEPT_ID,YES,INTEGER -SPECIMEN,SPECIMEN_SOURCE_ID,YES,CHARACTER VARYING -SPECIMEN,SPECIMEN_SOURCE_VALUE,YES,CHARACTER VARYING -SPECIMEN,UNIT_SOURCE_VALUE,YES,CHARACTER VARYING -SPECIMEN,ANATOMIC_SITE_SOURCE_VALUE,YES,CHARACTER VARYING -SPECIMEN,DISEASE_STATUS_SOURCE_VALUE,YES,CHARACTER VARYING -DEATH,PERSON_ID,NO,INTEGER -DEATH,DEATH_DATE,NO,DATE -DEATH,DEATH_TYPE_CONCEPT_ID,NO,INTEGER -DEATH,CAUSE_CONCEPT_ID,YES,INTEGER -DEATH,CAUSE_SOURCE_VALUE,YES,CHARACTER VARYING -DEATH,CAUSE_SOURCE_CONCEPT_ID,YES,INTEGER +CARE_SITE,CARE_SITE_ID,NO,INTEGER +CARE_SITE,CARE_SITE_NAME,YES,CHARACTER VARYING +CARE_SITE,PLACE_OF_SERVICE_CONCEPT_ID,YES,INTEGER +CARE_SITE,LOCATION_ID,YES,INTEGER +CARE_SITE,CARE_SITE_SOURCE_VALUE,YES,CHARACTER VARYING +CARE_SITE,PLACE_OF_SERVICE_SOURCE_VALUE,YES,CHARACTER VARYING VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,NO,INTEGER VISIT_OCCURRENCE,PERSON_ID,NO,INTEGER VISIT_OCCURRENCE,VISIT_CONCEPT_ID,NO,INTEGER @@ -65,18 +48,36 @@ VISIT_OCCURRENCE,PROVIDER_ID,YES,INTEGER VISIT_OCCURRENCE,CARE_SITE_ID,YES,INTEGER VISIT_OCCURRENCE,VISIT_SOURCE_VALUE,YES,CHARACTER VARYING VISIT_OCCURRENCE,VISIT_SOURCE_CONCEPT_ID,YES,INTEGER -PROCEDURE_OCCURRENCE,PROCEDURE_OCCURRENCE_ID,NO,INTEGER -PROCEDURE_OCCURRENCE,PERSON_ID,NO,INTEGER -PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,NO,INTEGER -PROCEDURE_OCCURRENCE,PROCEDURE_DATE,NO,DATE -PROCEDURE_OCCURRENCE,PROCEDURE_TYPE_CONCEPT_ID,NO,INTEGER -PROCEDURE_OCCURRENCE,QUALIFIER_CONCEPT_ID,YES,INTEGER -PROCEDURE_OCCURRENCE,QUANTITY,YES,INTEGER -PROCEDURE_OCCURRENCE,PROVIDER_ID,YES,INTEGER -PROCEDURE_OCCURRENCE,VISIT_OCCURRENCE_ID,YES,INTEGER -PROCEDURE_OCCURRENCE,PROCEDURE_SOURCE_VALUE,YES,CHARACTER VARYING -PROCEDURE_OCCURRENCE,PROCEDURE_SOURCE_CONCEPT_ID,YES,INTEGER -PROCEDURE_OCCURRENCE,QUALIFIER_SOURCE_VALUE,YES,CHARACTER VARYING +PROVIDER,PROVIDER_ID,NO,INTEGER +PROVIDER,PROVIDER_NAME,YES,CHARACTER VARYING +PROVIDER,NPI,YES,CHARACTER VARYING +PROVIDER,DEA,YES,CHARACTER VARYING +PROVIDER,SPECIALTY_CONCEPT_ID,YES,INTEGER +PROVIDER,CARE_SITE_ID,YES,INTEGER +PROVIDER,YEAR_OF_BIRTH,YES,INTEGER +PROVIDER,GENDER_CONCEPT_ID,YES,INTEGER +PROVIDER,PROVIDER_SOURCE_VALUE,YES,CHARACTER VARYING +PROVIDER,SPECIALTY_SOURCE_VALUE,YES,CHARACTER VARYING +PROVIDER,SPECIALTY_SOURCE_CONCEPT_ID,YES,INTEGER +PROVIDER,GENDER_SOURCE_VALUE,YES,CHARACTER VARYING +PROVIDER,GENDER_SOURCE_CONCEPT_ID,YES,INTEGER +CONDITION_OCCURRENCE,CONDITION_OCCURRENCE_ID,NO,INTEGER +CONDITION_OCCURRENCE,PERSON_ID,NO,INTEGER +CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,NO,INTEGER +CONDITION_OCCURRENCE,CONDITION_START_DATE,NO,DATE +CONDITION_OCCURRENCE,CONDITION_END_DATE,YES,DATE +CONDITION_OCCURRENCE,CONDITION_TYPE_CONCEPT_ID,NO,INTEGER +CONDITION_OCCURRENCE,STOP_REASON,YES,CHARACTER VARYING +CONDITION_OCCURRENCE,PROVIDER_ID,YES,INTEGER +CONDITION_OCCURRENCE,VISIT_OCCURRENCE_ID,YES,INTEGER +CONDITION_OCCURRENCE,CONDITION_SOURCE_VALUE,YES,CHARACTER VARYING +CONDITION_OCCURRENCE,CONDITION_SOURCE_CONCEPT_ID,YES,INTEGER +DEATH,PERSON_ID,NO,INTEGER +DEATH,DEATH_DATE,NO,DATE +DEATH,DEATH_TYPE_CONCEPT_ID,NO,INTEGER +DEATH,CAUSE_CONCEPT_ID,YES,INTEGER +DEATH,CAUSE_SOURCE_VALUE,YES,CHARACTER VARYING +DEATH,CAUSE_SOURCE_CONCEPT_ID,YES,INTEGER DRUG_EXPOSURE,DRUG_EXPOSURE_ID,NO,INTEGER DRUG_EXPOSURE,PERSON_ID,NO,INTEGER DRUG_EXPOSURE,DRUG_CONCEPT_ID,NO,INTEGER @@ -85,11 +86,11 @@ DRUG_EXPOSURE,DRUG_EXPOSURE_END_DATE,YES,DATE DRUG_EXPOSURE,DRUG_TYPE_CONCEPT_ID,NO,INTEGER DRUG_EXPOSURE,STOP_REASON,YES,CHARACTER VARYING DRUG_EXPOSURE,REFILLS,YES,INTEGER -DRUG_EXPOSURE,QUANTITY,YES,INTEGER +DRUG_EXPOSURE,QUANTITY,YES,NUMERIC DRUG_EXPOSURE,DAYS_SUPPLY,YES,INTEGER -DRUG_EXPOSURE,SIG,YES,CHARACTER VARYING +DRUG_EXPOSURE,SIG,YES,TEXT DRUG_EXPOSURE,ROUTE_CONCEPT_ID,YES,INTEGER -DRUG_EXPOSURE,EFFECTIVE_DRUG_DOSE,YES,DOUBLE PRECISION +DRUG_EXPOSURE,EFFECTIVE_DRUG_DOSE,YES,NUMERIC DRUG_EXPOSURE,DOSE_UNIT_CONCEPT_ID,YES,INTEGER DRUG_EXPOSURE,LOT_NUMBER,YES,CHARACTER VARYING DRUG_EXPOSURE,PROVIDER_ID,YES,INTEGER @@ -110,51 +111,43 @@ DEVICE_EXPOSURE,PROVIDER_ID,YES,INTEGER DEVICE_EXPOSURE,VISIT_OCCURRENCE_ID,YES,INTEGER DEVICE_EXPOSURE,DEVICE_SOURCE_VALUE,YES,CHARACTER VARYING DEVICE_EXPOSURE,DEVICE_SOURCE_CONCEPT_ID,YES,INTEGER -CONDITION_OCCURRENCE,CONDITION_OCCURRENCE_ID,NO,INTEGER -CONDITION_OCCURRENCE,PERSON_ID,NO,INTEGER -CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,NO,INTEGER -CONDITION_OCCURRENCE,CONDITION_START_DATE,NO,DATE -CONDITION_OCCURRENCE,CONDITION_END_DATE,YES,DATE -CONDITION_OCCURRENCE,CONDITION_TYPE_CONCEPT_ID,NO,INTEGER -CONDITION_OCCURRENCE,STOP_REASON,YES,CHARACTER VARYING -CONDITION_OCCURRENCE,PROVIDER_ID,YES,INTEGER -CONDITION_OCCURRENCE,VISIT_OCCURRENCE_ID,YES,INTEGER -CONDITION_OCCURRENCE,CONDITION_SOURCE_VALUE,YES,CHARACTER VARYING -CONDITION_OCCURRENCE,CONDITION_SOURCE_CONCEPT_ID,YES,INTEGER +PROCEDURE_OCCURRENCE,PROCEDURE_OCCURRENCE_ID,NO,INTEGER +PROCEDURE_OCCURRENCE,PERSON_ID,NO,INTEGER +PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,NO,INTEGER +PROCEDURE_OCCURRENCE,PROCEDURE_DATE,NO,DATE +PROCEDURE_OCCURRENCE,PROCEDURE_TYPE_CONCEPT_ID,NO,INTEGER +PROCEDURE_OCCURRENCE,MODIFIER_CONCEPT_ID,YES,INTEGER +PROCEDURE_OCCURRENCE,QUANTITY,YES,INTEGER +PROCEDURE_OCCURRENCE,PROVIDER_ID,YES,INTEGER +PROCEDURE_OCCURRENCE,VISIT_OCCURRENCE_ID,YES,INTEGER +PROCEDURE_OCCURRENCE,PROCEDURE_SOURCE_VALUE,YES,CHARACTER VARYING +PROCEDURE_OCCURRENCE,PROCEDURE_SOURCE_CONCEPT_ID,YES,INTEGER +PROCEDURE_OCCURRENCE,QUALIFIER_SOURCE_VALUE,YES,CHARACTER VARYING MEASUREMENT,MEASUREMENT_ID,NO,INTEGER MEASUREMENT,PERSON_ID,NO,INTEGER MEASUREMENT,MEASUREMENT_CONCEPT_ID,NO,INTEGER MEASUREMENT,MEASUREMENT_DATE,NO,DATE MEASUREMENT,MEASUREMENT_TIME,YES,CHARACTER VARYING MEASUREMENT,MEASUREMENT_TYPE_CONCEPT_ID,NO,INTEGER -MEASUREMENT,OPERATOR_CONCEPT_ID,NO,INTEGER -MEASUREMENT,VALUE_AS_NUMBER,YES,DOUBLE PRECISION +MEASUREMENT,OPERATOR_CONCEPT_ID,YES,INTEGER +MEASUREMENT,VALUE_AS_NUMBER,YES,NUMERIC MEASUREMENT,VALUE_AS_CONCEPT_ID,YES,INTEGER MEASUREMENT,UNIT_CONCEPT_ID,YES,INTEGER -MEASUREMENT,RANGE_LOW,YES,DOUBLE PRECISION -MEASUREMENT,RANGE_HIGH,YES,DOUBLE PRECISION +MEASUREMENT,RANGE_LOW,YES,NUMERIC +MEASUREMENT,RANGE_HIGH,YES,NUMERIC MEASUREMENT,PROVIDER_ID,YES,INTEGER MEASUREMENT,VISIT_OCCURRENCE_ID,YES,INTEGER MEASUREMENT,MEASUREMENT_SOURCE_VALUE,YES,CHARACTER VARYING MEASUREMENT,MEASUREMENT_SOURCE_CONCEPT_ID,YES,INTEGER MEASUREMENT,UNIT_SOURCE_VALUE,YES,CHARACTER VARYING MEASUREMENT,VALUE_SOURCE_VALUE,YES,CHARACTER VARYING -NOTE,NOTE_ID,NO,INTEGER -NOTE,PERSON_ID,NO,INTEGER -NOTE,NOTE_DATE,NO,DATE -NOTE,NOTE_TIME,YES,CHARACTER VARYING -NOTE,NOTE_CONCEPT_ID,NO,INTEGER -NOTE,FREE_TEXT,NO,TEXT -NOTE,PROVIDER_ID,YES,INTEGER -NOTE,VISIT_OCCURRENCE_ID,YES,INTEGER -NOTE,NOTE_SOURCE_VALUE,YES,CHARACTER VARYING OBSERVATION,OBSERVATION_ID,NO,INTEGER OBSERVATION,PERSON_ID,NO,INTEGER OBSERVATION,OBSERVATION_CONCEPT_ID,NO,INTEGER OBSERVATION,OBSERVATION_DATE,NO,DATE OBSERVATION,OBSERVATION_TIME,YES,CHARACTER VARYING OBSERVATION,OBSERVATION_TYPE_CONCEPT_ID,NO,INTEGER -OBSERVATION,VALUE_AS_NUMBER,YES,DOUBLE PRECISION +OBSERVATION,VALUE_AS_NUMBER,YES,NUMERIC OBSERVATION,VALUE_AS_STRING,YES,CHARACTER VARYING OBSERVATION,VALUE_AS_CONCEPT_ID,YES,INTEGER OBSERVATION,QUALIFIER_CONCEPT_ID,YES,INTEGER @@ -165,87 +158,90 @@ OBSERVATION,OBSERVATION_SOURCE_VALUE,YES,CHARACTER VARYING OBSERVATION,OBSERVATION_SOURCE_CONCEPT_ID,YES,INTEGER OBSERVATION,UNIT_SOURCE_VALUE,YES,CHARACTER VARYING OBSERVATION,QUALIFIER_SOURCE_VALUE,YES,CHARACTER VARYING +NOTE,NOTE_ID,NO,INTEGER +NOTE,PERSON_ID,NO,INTEGER +NOTE,NOTE_DATE,NO,DATE +NOTE,NOTE_TIME,YES,CHARACTER VARYING +NOTE,NOTE_TYPE_CONCEPT_ID,NO,INTEGER +NOTE,NOTE_TEXT,NO,TEXT +NOTE,PROVIDER_ID,YES,INTEGER +NOTE,VISIT_OCCURRENCE_ID,YES,INTEGER +NOTE,NOTE_SOURCE_VALUE,YES,CHARACTER VARYING +SPECIMEN,SPECIMEN_ID,NO,INTEGER +SPECIMEN,PERSON_ID,NO,INTEGER +SPECIMEN,SPECIMEN_CONCEPT_ID,NO,INTEGER +SPECIMEN,SPECIMEN_TYPE_CONCEPT_ID,NO,INTEGER +SPECIMEN,SPECIMEN_DATE,NO,DATE +SPECIMEN,SPECIMEN_TIME,YES,CHARACTER VARYING +SPECIMEN,QUANTITY,YES,NUMERIC +SPECIMEN,UNIT_CONCEPT_ID,YES,INTEGER +SPECIMEN,ANATOMIC_SITE_CONCEPT_ID,YES,INTEGER +SPECIMEN,DISEASE_STATUS_CONCEPT_ID,YES,INTEGER +SPECIMEN,SPECIMEN_SOURCE_ID,YES,CHARACTER VARYING +SPECIMEN,SPECIMEN_SOURCE_VALUE,YES,CHARACTER VARYING +SPECIMEN,UNIT_SOURCE_VALUE,YES,CHARACTER VARYING +SPECIMEN,ANATOMIC_SITE_SOURCE_VALUE,YES,CHARACTER VARYING +SPECIMEN,DISEASE_STATUS_SOURCE_VALUE,YES,CHARACTER VARYING FACT_RELATIONSHIP,DOMAIN_CONCEPT_ID_1,NO,INTEGER FACT_RELATIONSHIP,FACT_ID_1,NO,INTEGER FACT_RELATIONSHIP,DOMAIN_CONCEPT_ID_2,NO,INTEGER FACT_RELATIONSHIP,FACT_ID_2,NO,INTEGER FACT_RELATIONSHIP,RELATIONSHIP_CONCEPT_ID,NO,INTEGER -LOCATION,LOCATION_ID,NO,INTEGER -LOCATION,ADDRESS_1,YES,CHARACTER VARYING -LOCATION,ADDRESS_2,YES,CHARACTER VARYING -LOCATION,CITY,YES,CHARACTER VARYING -LOCATION,STATE,YES,CHARACTER VARYING -LOCATION,ZIP,YES,CHARACTER VARYING -LOCATION,COUNTY,YES,CHARACTER VARYING -LOCATION,LOCATION_SOURCE_VALUE,YES,CHARACTER VARYING -CARE_SITE,CARE_SITE_ID,NO,INTEGER -CARE_SITE,PLACE_OF_SERVICE_CONCEPT_ID,YES,INTEGER -CARE_SITE,LOCATION_ID,YES,INTEGER -CARE_SITE,CARE_SITE_SOURCE_VALUE,YES,CHARACTER VARYING -CARE_SITE,PLACE_OF_SERVICE_SOURCE_VALUE,YES,CHARACTER VARYING -PROVIDER,PROVIDER_ID,NO,INTEGER -PROVIDER,NPI,YES,CHARACTER VARYING -PROVIDER,DEA,YES,CHARACTER VARYING -PROVIDER,SPECIALTY_CONCEPT_ID,YES,INTEGER -PROVIDER,CARE_SITE_ID,YES,INTEGER -PROVIDER,YEAR_OF_BIRTH,YES,INTEGER -PROVIDER,GENDER_CONCEPT_ID,YES,INTEGER -PROVIDER,PROVIDER_SOURCE_VALUE,YES,CHARACTER VARYING -PROVIDER,SPECIALTY_SOURCE_VALUE,YES,CHARACTER VARYING -PROVIDER,GENDER_SOURCE_VALUE,YES,CHARACTER VARYING -PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_ID,NO,INTEGER -PAYER_PLAN_PERIOD,PERSON_ID,NO,INTEGER -PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_START_DATE,NO,DATE -PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_END_DATE,NO,DATE -PAYER_PLAN_PERIOD,PAYER_SOURCE_VALUE,YES,CHARACTER VARYING -PAYER_PLAN_PERIOD,PLAN_SOURCE_VALUE,YES,CHARACTER VARYING -PAYER_PLAN_PERIOD,FAMILY_SOURCE_VALUE,YES,CHARACTER VARYING -VISIT_COST,VISIT_COST_ID,NO,INTEGER -VISIT_COST,VISIT_OCCURRENCE_ID,NO,INTEGER -VISIT_COST,CURRENCY_CONCEPT_ID,YES,INTEGER -VISIT_COST,PAID_COPAY,YES,DOUBLE PRECISION -VISIT_COST,PAID_COINSURANCE,YES,DOUBLE PRECISION -VISIT_COST,PAID_TOWARD_DEDUCTIBLE,YES,DOUBLE PRECISION -VISIT_COST,PAID_BY_PAYER,YES,DOUBLE PRECISION -VISIT_COST,PAID_BY_COORDINATION_BENEFITS,YES,DOUBLE PRECISION -VISIT_COST,TOTAL_OUT_OF_POCKET,YES,DOUBLE PRECISION -VISIT_COST,TOTAL_PAID,YES,DOUBLE PRECISION -VISIT_COST,PAYER_PLAN_PERIOD_ID,YES,INTEGER PROCEDURE_COST,PROCEDURE_COST_ID,NO,INTEGER PROCEDURE_COST,PROCEDURE_OCCURRENCE_ID,NO,INTEGER PROCEDURE_COST,CURRENCY_CONCEPT_ID,YES,INTEGER -PROCEDURE_COST,PAID_COPAY,YES,DOUBLE PRECISION -PROCEDURE_COST,PAID_COINSURANCE,YES,DOUBLE PRECISION -PROCEDURE_COST,PAID_TOWARD_DEDUCTIBLE,YES,DOUBLE PRECISION -PROCEDURE_COST,PAID_BY_PAYER,YES,DOUBLE PRECISION -PROCEDURE_COST,PAID_BY_COORDINATION_BENEFITS,YES,DOUBLE PRECISION -PROCEDURE_COST,TOTAL_OUT_OF_POCKET,YES,DOUBLE PRECISION -PROCEDURE_COST,TOTAL_PAID,YES,DOUBLE PRECISION +PROCEDURE_COST,PAID_COPAY,YES,NUMERIC +PROCEDURE_COST,PAID_COINSURANCE,YES,NUMERIC +PROCEDURE_COST,PAID_TOWARD_DEDUCTIBLE,YES,NUMERIC +PROCEDURE_COST,PAID_BY_PAYER,YES,NUMERIC +PROCEDURE_COST,PAID_BY_COORDINATION_BENEFITS,YES,NUMERIC +PROCEDURE_COST,TOTAL_OUT_OF_POCKET,YES,NUMERIC +PROCEDURE_COST,TOTAL_PAID,YES,NUMERIC +PROCEDURE_COST,REVENUE_CODE_CONCEPT_ID,YES,INTEGER PROCEDURE_COST,PAYER_PLAN_PERIOD_ID,YES,INTEGER +PROCEDURE_COST,REVENUE_CODE_SOURCE_VALUE,YES,CHARACTER VARYING +VISIT_COST,VISIT_COST_ID,NO,INTEGER +VISIT_COST,VISIT_OCCURRENCE_ID,NO,INTEGER +VISIT_COST,CURRENCY_CONCEPT_ID,YES,INTEGER +VISIT_COST,PAID_COPAY,YES,NUMERIC +VISIT_COST,PAID_COINSURANCE,YES,NUMERIC +VISIT_COST,PAID_TOWARD_DEDUCTIBLE,YES,NUMERIC +VISIT_COST,PAID_BY_PAYER,YES,NUMERIC +VISIT_COST,PAID_BY_COORDINATION_BENEFITS,YES,NUMERIC +VISIT_COST,TOTAL_OUT_OF_POCKET,YES,NUMERIC +VISIT_COST,TOTAL_PAID,YES,NUMERIC +VISIT_COST,PAYER_PLAN_PERIOD_ID,YES,INTEGER DRUG_COST,DRUG_COST_ID,NO,INTEGER DRUG_COST,DRUG_EXPOSURE_ID,NO,INTEGER DRUG_COST,CURRENCY_CONCEPT_ID,YES,INTEGER -DRUG_COST,PAID_COPAY,YES,DOUBLE PRECISION -DRUG_COST,PAID_COINSURANCE,YES,DOUBLE PRECISION -DRUG_COST,PAID_TOWARD_DEDUCTIBLE,YES,DOUBLE PRECISION -DRUG_COST,PAID_BY_PAYER,YES,DOUBLE PRECISION -DRUG_COST,PAID_BY_COORDINATION_BENEFITS,YES,DOUBLE PRECISION -DRUG_COST,TOTAL_OUT_OF_POCKET,YES,DOUBLE PRECISION -DRUG_COST,TOTAL_PAID,YES,DOUBLE PRECISION -DRUG_COST,INGREDIENT_COST,YES,DOUBLE PRECISION -DRUG_COST,DISPENSING_FEE,YES,DOUBLE PRECISION -DRUG_COST,AVERAGE_WHOLESALE_PRICE,YES,DOUBLE PRECISION +DRUG_COST,PAID_COPAY,YES,NUMERIC +DRUG_COST,PAID_COINSURANCE,YES,NUMERIC +DRUG_COST,PAID_TOWARD_DEDUCTIBLE,YES,NUMERIC +DRUG_COST,PAID_BY_PAYER,YES,NUMERIC +DRUG_COST,PAID_BY_COORDINATION_BENEFITS,YES,NUMERIC +DRUG_COST,TOTAL_OUT_OF_POCKET,YES,NUMERIC +DRUG_COST,TOTAL_PAID,YES,NUMERIC +DRUG_COST,INGREDIENT_COST,YES,NUMERIC +DRUG_COST,DISPENSING_FEE,YES,NUMERIC +DRUG_COST,AVERAGE_WHOLESALE_PRICE,YES,NUMERIC DRUG_COST,PAYER_PLAN_PERIOD_ID,YES,INTEGER +PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_ID,NO,INTEGER +PAYER_PLAN_PERIOD,PERSON_ID,NO,INTEGER +PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_START_DATE,NO,DATE +PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_END_DATE,NO,DATE +PAYER_PLAN_PERIOD,PAYER_SOURCE_VALUE,YES,CHARACTER VARYING +PAYER_PLAN_PERIOD,PLAN_SOURCE_VALUE,YES,CHARACTER VARYING +PAYER_PLAN_PERIOD,FAMILY_SOURCE_VALUE,YES,CHARACTER VARYING DEVICE_COST,DEVICE_COST_ID,NO,INTEGER DEVICE_COST,DEVICE_EXPOSURE_ID,NO,INTEGER DEVICE_COST,CURRENCY_CONCEPT_ID,YES,INTEGER -DEVICE_COST,PAID_COPAY,YES,DOUBLE PRECISION -DEVICE_COST,PAID_COINSURANCE,YES,DOUBLE PRECISION -DEVICE_COST,PAID_TOWARD_DEDUCTIBLE,YES,DOUBLE PRECISION -DEVICE_COST,PAID_BY_PAYER,YES,DOUBLE PRECISION -DEVICE_COST,PAID_BY_COORDINATION_BENEFITS,YES,DOUBLE PRECISION -DEVICE_COST,TOTAL_OUT_OF_POCKET,YES,DOUBLE PRECISION -DEVICE_COST,TOTAL_PAID,YES,DOUBLE PRECISION +DEVICE_COST,PAID_COPAY,YES,NUMERIC +DEVICE_COST,PAID_COINSURANCE,YES,NUMERIC +DEVICE_COST,PAID_TOWARD_DEDUCTIBLE,YES,NUMERIC +DEVICE_COST,PAID_BY_PAYER,YES,NUMERIC +DEVICE_COST,PAID_BY_COORDINATION_BENEFITS,YES,NUMERIC +DEVICE_COST,TOTAL_OUT_OF_POCKET,YES,NUMERIC +DEVICE_COST,TOTAL_PAID,YES,NUMERIC DEVICE_COST,PAYER_PLAN_PERIOD_ID,YES,INTEGER DRUG_ERA,DRUG_ERA_ID,NO,INTEGER DRUG_ERA,PERSON_ID,NO,INTEGER @@ -258,7 +254,7 @@ DOSE_ERA,DOSE_ERA_ID,NO,INTEGER DOSE_ERA,PERSON_ID,NO,INTEGER DOSE_ERA,DRUG_CONCEPT_ID,NO,INTEGER DOSE_ERA,UNIT_CONCEPT_ID,NO,INTEGER -DOSE_ERA,DOSE_VALUE,NO,DOUBLE PRECISION +DOSE_ERA,DOSE_VALUE,NO,NUMERIC DOSE_ERA,DOSE_ERA_START_DATE,NO,DATE DOSE_ERA,DOSE_ERA_END_DATE,NO,DATE CONDITION_ERA,CONDITION_ERA_ID,NO,INTEGER @@ -267,15 +263,36 @@ CONDITION_ERA,CONDITION_CONCEPT_ID,NO,INTEGER CONDITION_ERA,CONDITION_ERA_START_DATE,NO,DATE CONDITION_ERA,CONDITION_ERA_END_DATE,NO,DATE CONDITION_ERA,CONDITION_OCCURRENCE_COUNT,YES,INTEGER -COHORT,COHORT_ID,NO,INTEGER +CDM_SOURCE,CDM_SOURCE_NAME,NO,CHARACTER VARYING +CDM_SOURCE,CDM_SOURCE_ABBREVIATION,YES,CHARACTER VARYING +CDM_SOURCE,CDM_HOLDER,YES,CHARACTER VARYING +CDM_SOURCE,SOURCE_DESCRIPTION,YES,TEXT +CDM_SOURCE,SOURCE_DOCUMENTATION_REFERENCE,YES,CHARACTER VARYING +CDM_SOURCE,CDM_ETL_REFERENCE,YES,CHARACTER VARYING +CDM_SOURCE,SOURCE_RELEASE_DATE,YES,DATE +CDM_SOURCE,CDM_RELEASE_DATE,YES,DATE +CDM_SOURCE,CDM_VERSION,YES,CHARACTER VARYING +CDM_SOURCE,VOCABULARY_VERSION,YES,CHARACTER VARYING COHORT,COHORT_DEFINITION_ID,NO,INTEGER -COHORT,COHORT_START_DATE,NO,DATE -COHORT,COHORT_END_DATE,YES,DATE COHORT,SUBJECT_ID,NO,INTEGER -COHORT,STOP_REASON,YES,CHARACTER VARYING +COHORT,COHORT_START_DATE,NO,DATE +COHORT,COHORT_END_DATE,NO,DATE COHORT_DEFINITION,COHORT_DEFINITION_ID,NO,INTEGER COHORT_DEFINITION,COHORT_DEFINITION_NAME,NO,CHARACTER VARYING COHORT_DEFINITION,COHORT_DEFINITION_DESCRIPTION,YES,TEXT COHORT_DEFINITION,DEFINITION_TYPE_CONCEPT_ID,NO,INTEGER COHORT_DEFINITION,COHORT_DEFINITION_SYNTAX,YES,TEXT -COHORT_DEFINITION,EXECUTION_DATE,YES,DATE \ No newline at end of file +COHORT_DEFINITION,SUBJECT_CONCEPT_ID,NO,INTEGER +COHORT_DEFINITION,COHORT_INITIATION_DATE,YES,DATE +COHORT_ATTRIBUTE,COHORT_DEFINITION_ID,NO,INTEGER +COHORT_ATTRIBUTE,COHORT_START_DATE,NO,DATE +COHORT_ATTRIBUTE,COHORT_END_DATE,NO,DATE +COHORT_ATTRIBUTE,SUBJECT_ID,NO,INTEGER +COHORT_ATTRIBUTE,ATTRIBUTE_DEFINITION_ID,NO,INTEGER +COHORT_ATTRIBUTE,VALUE_AS_NUMBER,YES,NUMERIC +COHORT_ATTRIBUTE,VALUE_AS_CONCEPT_ID,YES,INTEGER +ATTRIBUTE_DEFINITION,ATTRIBUTE_DEFINITION_ID,NO,INTEGER +ATTRIBUTE_DEFINITION,ATTRIBUTE_NAME,NO,CHARACTER VARYING +ATTRIBUTE_DEFINITION,ATTRIBUTE_DESCRIPTION,YES,TEXT +ATTRIBUTE_DEFINITION,ATTRIBUTE_TYPE_CONCEPT_ID,NO,INTEGER +ATTRIBUTE_DEFINITION,ATTRIBUTE_SYNTAX,YES,TEXT \ No newline at end of file diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/Database.java b/src/org/ohdsi/rabbitInAHat/dataModel/Database.java index 5bbf0b59..0e771dd7 100644 --- a/src/org/ohdsi/rabbitInAHat/dataModel/Database.java +++ b/src/org/ohdsi/rabbitInAHat/dataModel/Database.java @@ -48,8 +48,8 @@ public void setTables(List tables) { public static Database generateCDMModel() { Database database = new Database(); Map nameToTable = new HashMap(); - //for (Row row : new ReadCSVFileWithHeader(Database.class.getResourceAsStream("CDMv5Model.csv"))) { - for (Row row : new ReadCSVFileWithHeader(Database.class.getResourceAsStream("CDMV4Model.csv"))) { + for (Row row : new ReadCSVFileWithHeader(Database.class.getResourceAsStream("CDMv5Model.csv"))) { + //for (Row row : new ReadCSVFileWithHeader(Database.class.getResourceAsStream("CDMV4Model.csv"))) { Table table = nameToTable.get(row.get("TABLE_NAME").toLowerCase()); if (table == null) { table = new Table(); @@ -59,7 +59,7 @@ public static Database generateCDMModel() { } Field field = new Field(row.get("COLUMN_NAME").toLowerCase(), table); field.setNullable(row.get("IS_NULLABLE").equals("YES")); - field.setType(row.get("COLUMN_TYPE")); + field.setType(row.get("DATA_TYPE")); table.getFields().add(field); } // database.defaultOrdering = new ArrayList
(database.tables);