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OHDSI / DataQualityDashboard

A tool to help improve data quality standards in observational data science.
https://ohdsi.github.io/DataQualityDashboard
Apache License 2.0
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Missing standardConceptFieldName in the v5.4 quality checks #571

Closed SantanM closed 4 weeks ago

SantanM commented 1 month ago

In the checks defined in inst/csv/OMOP_CDMv5.4_Field_Level.csv for v5.4, the values of standardConceptFieldName for the fields ADMITTED_FROM_SOURCE_VALUE & DISCHARGED_TO_SOURCE_VALUE in tables VISIT_OCCURRENCE & VISIT_DETAIL are missing. Therefore, when executing DQD sourceValueCompleteness checks fail for these fields in the corresponding tables.

Error logs is as follows - 

2024-10-15 13:38:26 [Main thread]   ERROR   DataQualityDashboard    3   [Level: FIELD] [Check: sourceValueCompleteness] [CDM Table: VISIT_DETAIL] [CDM Field: ADMITTED_FROM_SOURCE_VALUE] Error executing SQL: org.postgresql.util.PSQLException: ERROR: column cdmtable.na does not exist   Position: 559 An error report has been created at  ../output/errors/FIELD_sourceValueCompleteness_VISIT_DETAIL_ADMITTED_FROM_SOURCE_VALUE.txt
2024-10-15 13:38:26 [Main thread]   ERROR   DataQualityDashboard    3   [Level: FIELD] [Check: sourceValueCompleteness] [CDM Table: VISIT_DETAIL] [CDM Field: DISCHARGED_TO_SOURCE_VALUE] Error executing SQL: org.postgresql.util.PSQLException: ERROR: column cdmtable.na does not exist   Position: 559 An error report has been created at  ../output/errors/FIELD_sourceValueCompleteness_VISIT_DETAIL_DISCHARGED_TO_SOURCE_VALUE.txt
2024-10-15 13:38:26 [Main thread]   ERROR   DataQualityDashboard    3   [Level: FIELD] [Check: sourceValueCompleteness] [CDM Table: VISIT_OCCURRENCE] [CDM Field: ADMITTED_FROM_SOURCE_VALUE] Error executing SQL: org.postgresql.util.PSQLException: ERROR: column cdmtable.na does not exist   Position: 567 An error report has been created at  ../output/errors/FIELD_sourceValueCompleteness_VISIT_OCCURRENCE_ADMITTED_FROM_SOURCE_VALUE.txt
2024-10-15 13:38:26 [Main thread]   ERROR   DataQualityDashboard    3   [Level: FIELD] [Check: sourceValueCompleteness] [CDM Table: VISIT_OCCURRENCE] [CDM Field: DISCHARGED_TO_SOURCE_VALUE] Error executing SQL: org.postgresql.util.PSQLException: ERROR: column cdmtable.na does not exist   Position: 567 An error report has been created at  ../output/errors/FIELD_sourceValueCompleteness_VISIT_OCCURRENCE_DISCHARGED_TO_SOURCE_VALUE.txt

I could create a PR to add these values when the issue is acknowledged.

katy-sadowski commented 4 weeks ago

This is a known issue - we'll fix it in the next release! https://github.com/OHDSI/DataQualityDashboard/issues/560