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ohdsi-studies / Covid19SubjectsAesiIncidenceRate

Extending on our previous work by Li et al. in understanding the incidence rates of adverse events of special interest (AESI) for COVID-19, this work will look at the rates of these AESIs in patients who had COVDI-19 disease.
https://ohdsi-studies.github.io/Covid19SubjectsAesiIncidenceRate/Protocol.html
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com.microsoft.sqlserver.jdbc.SQLServerException: The connection is closed. #24

Closed ericaVoss closed 2 years ago

ericaVoss commented 2 years ago

There looks to be an issue with a connection closing, however I'm wondering if there is some issue running the package. Like why is a concept set expression missing?

errorReportSql.txt Covid19SubjectsAesiIncidenceRate_ErrorReportR.txt Covid19SubjectsAesiIncidenceRate_log.txt

ericaVoss commented 2 years ago

Okay, a few questions:

  1. Does the Vocabulary have the indexes applied?
  2. Where is the Vocabulary in relation to the CDM?

Once I have a better understanding of the situation I might have you test just running the query that is dying: https://github.com/OHDSI/CohortDiagnostics/blob/master/inst/sql/sql_server/CreateConceptCountTable.sql#L20-L96 (this tool helps you convert OHDSI SQL to something you can run on the DB directly https://data.ohdsi.org/SqlDeveloper/)

ericaVoss commented 2 years ago

While the Vocab exists in a different schema, it is on the same box. So even though we need to go through indexes to talk to the Vocab (because the program assumes vocab and the CDM are together) - I don't think this is impacting generating results.

I did notice that the indexes set up in the current environment are not the ones suggested. The current recommendation is to apply those indexes: CDM 5.3 Indexes

ericaVoss commented 2 years ago

The team ultimately worked on indexing in the environment