Generate stats is hard coded to be false

Expected behavior: we need to be able to generate sql with statistics

Actual behavior: Hydra hard codes generate stats to FALSE

Hydra/java/org/ohdsi/hydra/actionHandlers/JsonToSql.java

Line 36 in c623d62

options.generateStats = false;

Impact - the generated SQL has

FROM #final_cohort CO
;

{0 != 0}?{
-- Find the event that is the 'best match' per person.
-- the 'best match' is defined as the event that satisfies the most inclusion rules.
-- ties are solved by choosing the event that matches the earliest inclusion rule, and then earliest.

select q.person_id, q.event_id

Maybe we could replace the use of java with R to generate the sql?

genOp <- CirceR::createGenerateOptions(cohortIdFieldName = "cohort_definition_id",
cohortId = fileName,
cdmSchema = "@cdm_database_schema",
targetTable = "@target_cohort_table",
resultSchema = "@results_database_schema",
vocabularySchema = "@vocabulary_database_schema",
generateStats = TRUE)
sql <- CirceR::buildCohortQuery(expression = cohortExpression, options = genOp)
SqlRender::writeSql(sql = sql, targetFile = file.path(outputFolder, 'inst', 'sql', 'sql_server', paste0(fileName, '.sql')))

We can't replace the Java with R, because Hydra is also used in WebAPI to hydrate packages where R is not available.

We can add an argument allowing one to set generate statistics to TRUE, that would default to the current behavior for backwards compatibility.

Now in the develop branch. I added an example usage here: OHDSI/SkeletonCohortDiagnosticsStudy@ab282ed

I haven't tested it. Leaving that to @gowthamrao .

Thank you @schuemie . That makes sense, because WebApi cannot use R.

Would it be possible to add an option called 'useRtoGenerateSql = FALSE', and if TRUE - it could use the installed version of CirceR for

sql <- CirceR::buildCohortQuery(expression = cohortExpression, options = genOp)

IF TRUE, it would overwrite the SQL output of Java. WebApi wont be impacted because Java would render the SQL by default

Reason: it would allow R users to select CirceR version

This seems to be a very special use case, so I don't want to add a lot of complexity to Hydra (that would also need to have its own testing apparatus) just for that.

If a user would want to use a specific CirceR version instead they can always do that after Hydra is finished, and simply overwrite the SQL files.

Yes - that makes sense. Agree. thanks

I haven't tested it. Leaving that to @gowthamrao .

btw - tested the new code after changes,
works perfectly