validateSchema - needs to be valid for all of 5.x

[alondhe]

Expected behavior

validateSchema works on 5.3.

Actual behavior

validateSchema function appears to not work with v5.3 due to effective_drug_dose field being deprecated.

Steps to reproduce behavior

Run validateSchema function on 5.3 CDM

[leeevans]

validateSchema() function also appears not to work with v5.3.1 due to CDM DDL replacement of time columns _time with _datetime.

for example validateSchema() is looking for v5.3 CDM column observation.observation_time instead of observation.observation_datetime

See below quoted info at URL: https://github.com/OHDSI/CommonDataModel/issues/61

*[Suggest moving forward with fields called _DATETIME, removing the _TIME fields. The _DATE fields will remain required.]**

"

[ambuj369]

@alondhe @leeevans I am working on OMOP CDM 5.3 and downloaded Achilles master branch using devtools::install_github("OHDSI/ACHILLES")

Now, when I do validate schema with version 5.3 mentioned, it says org.postgresql.util.PSQLException: ERROR: column "qualifier_source_value" does not exist

Checking upon validateSchema.sql, I found that it is referring to procedure_occurrence section in it which is not a part of OMOP CDM 5.3 schema.

My question is , is it a good practice to comment out such steps in validateSchema.sql OR is there is any specific version of Achilles which should be downloaded to prevent such errors.

Thank You.

[alondhe]

Hi @ambuj369 - good catch. That should be modifier_source_value. I'll make a PR to fix this.

[bfurey]

Against the v5.2.2 schema, I get the following error when running validateSchema

Error: Error executing SQL:
org.postgresql.util.PSQLException: ERROR: column "revenue_code_source_value" does not exist
  Hint: Perhaps you meant to reference the column "cost.reveue_code_source_value".
  Position: 6720

[DaveBarman]

The procedure_occurrence issue above is persisting with latest I pulled from git today. Also, I get failure on location due to all caps 'STATE' field name. I see that procedure_datetime is also missing from procedure_occurrence check.

Edit: Appears visit_detail_id is also missing. This is from OMOP CDM 5.3

[fdefalco]

validate schema is being removed from achilles in favor of these validations as part of the DataQualityDashboard checks.