Run All of Us DataQualityDashboard on OMOP tables

[vasanthi014]

GitHub: https://github.com/OHDSI/DataQualityDashboard

[vasanthi014]

@shossain-mizzou This a R script and it can also run against snowflake database. Their requirement is to have CDM_SOURCE table populated, I am looking into CDM_SOURCE table ETL. Meanwhile you can fork the repo and have it setup in a SWB to run with snowflake.

[vasanthi014]

our OMOP.CDM.CDM.CDM_SOURCE table should be good to use.

[shossain-mizzou]

[Level: TABLE] [Check: cdmTable] [CDM Table: DOMAIN] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.DOMAIN' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_DOMAIN_NA.txt 2023-12-13 11:13:33 [Level: TABLE] [Check: cdmTable] [CDM Table: DOMAIN] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.DOMAIN' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_DOMAIN_NA.txt [Level: TABLE] [Check: cdmTable] [CDM Table: RELATIONSHIP] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.RELATIONSHIP' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_RELATIONSHIP_NA.txt 2023-12-13 11:13:33 [Level: TABLE] [Check: cdmTable] [CDM Table: RELATIONSHIP] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.RELATIONSHIP' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_RELATIONSHIP_NA.txt [Level: TABLE] [Check: cdmTable] [CDM Table: CONCEPT_SYNONYM] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.CONCEPT_SYNONYM' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_CONCEPT_SYNONYM_NA.txt 2023-12-13 11:13:33 [Level: TABLE] [Check: cdmTable] [CDM Table: CONCEPT_SYNONYM] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.CONCEPT_SYNONYM' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_CONCEPT_SYNONYM_NA.txt [Level: TABLE] [Check: cdmTable] [CDM Table: SOURCE_TO_CONCEPT_MAP] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.SOURCE_TO_CONCEPT_MAP' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_SOURCE_TO_CONCEPT_MAP_NA.txt 2023-12-13 11:13:33 [Level: TABLE] [Check: cdmTable] [CDM Table: SOURCE_TO_CONCEPT_MAP] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.SOURCE_TO_CONCEPT_MAP' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_SOURCE_TO_CONCEPT_MAP_NA.txt [Level: TABLE] [Check: cdmTable] [CDM Table: DRUG_STRENGTH] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.DRUG_STRENGTH' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_DRUG_STRENGTH_NA.txt 2023-12-13 11:13:33 [Level: TABLE] [Check: cdmTable] [CDM Table: DRUG_STRENGTH] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.CDM.DRUG_STRENGTH' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_DRUG_STRENGTH_NA.txt [Level: TABLE] [Check: cdmTable] [CDM Table: COHORT_DEFINITION] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.RESULTS.COHORT_DEFINITION' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_COHORT_DEFINITION_NA.txt 2023-12-13 11:13:34 [Level: TABLE] [Check: cdmTable] [CDM Table: COHORT_DEFINITION] [CDM Field: NA] Error executing SQL: net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error: Object 'OMOP_CDM.RESULTS.COHORT_DEFINITION' does not exist or not authorized. An error report has been created at output/errors/TABLE_cdmTable_COHORT_DEFINITION_NA.txt

[shossain-mizzou]

results.json

[shossain-mizzou]

@vasanthi014, report can be previewed from the url: https://atlas-dev.nextgenbmi.umsystem.edu/atlas/dashboard/

I have included DataQualityDashboard with the atlas.

[shossain-mizzou]

[vasanthi014]

This is great to look at the data level issues. Good Job @shossain-mizzou