Update skeleton for upcoming PLP v5.4.0

[lhjohn]

No description provided.

[lhjohn]

EDIT: Below seems to be resolved with the latest SqlRender and DatabaseConnector.

I am still seeing the following error, where executing the SQL fails.

Extracting data for cohort 5920 to ./ResultsIqviaGERv1944/targetId_5920_L1
Connecting using Redshift driver
|====================================================================================| 100%
Executing SQL took 4.08 secs
Constructing features on server
|====================================================================================| 100%
Executing SQL took 10.9 secs
Fetching data from server
Error in `.createErrorReport()`:
! Error executing SQL:

The error report is empty.

DBMS:
redshift

Error:

This is the traceback.

15: cat(paste(c("\r  |", rep.int(char, nb), rep.int(" ", nw * (width - 
        nb)), sprintf("| %3d%%", pc)), collapse = ""), file = file)
14: pb$up(value)
13: setTxtProgressBar(pb, i/length(sqlStatements))
12: DatabaseConnector::executeSql(connection, sql) at CohortConstruction.R#233
11: runCohortSql(sql = sql, startTime = startTime, incremental = incremental, 
        cohortId = cohortDefinitionSet$cohortId[i], checksum = cohortDefinitionSet$checksum[i], 
        recordKeepingFile = recordKeepingFile) at CohortConstruction.R#259
10: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr = {
       startTime <- lubridate::now()
       generationInfo <- runCohortSql(sql = sql, startTime = startTime, 
           incremental = incremental, cohortId = cohortDefinitionSet$cohortId[i], 
           checksum = cohortDefinitionSet$checksum[i], recordKeepingFile = recordKeepingFile)
   }, error = function(e) {
       endTime <- lubridate::now()
       ParallelLogger::logError("An error occurred while generating cohortName = ", 
           cohortName, ". Error: ", e)
       if (stopIfError) {
           stop()
       }
       return(list(generationStatus = "FAILED", startTime = startTime, 
           endTime = endTime))
   }) at CohortConstruction.R#257
6: FUN(X[[i]], ...)
5: lapply(x, fun, ...)
4: ParallelLogger::clusterApply(cluster, cohortDefinitionSet$cohortId, 
       generateCohort, cohortDefinitionSet = cohortDefinitionSet, 
       connection = connection, connectionDetails = connectionDetails, 
       cdmDatabaseSchema = cdmDatabaseSchema, tempEmulationSchema = tempEmulationSchema, 
       cohortDatabaseSchema = cohortDatabaseSchema, cohortTableNames = cohortTableNames, 
       stopIfError = stopOnError, incremental = incremental, recordKeepingFile = recordKeepingFile, 
       stopOnError = stopOnError, progressBar = TRUE) at CohortConstruction.R#131
3: CohortGenerator::generateCohortSet(connection = connection, cohortDatabaseSchema = databaseDetails$cohortDatabaseSchema, 
       cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = databaseDetails$cohortTable), 
       cdmDatabaseSchema = databaseDetails$cdmDatabaseSchema, tempEmulationSchema = databaseDetails$tempEmulationSchema, 
       cohortDefinitionSet = cohortDefinitionSet) at CreateAllCohorts.R#36
2: createCohorts(databaseDetails = databaseDetails, outputFolder = outputFolder) at Main.R#116
1: EmcDementiaPredictionBase::execute(databaseDetails = databaseDetails, 
       outputFolder = paste0(outputFolder, cdmDatabaseName[i]), 
       createProtocol = createProtocol, createCohorts = createCohorts, 
       runAnalyses = runAnalyses, createValidationPackage = createValidationPackage, 
       analysesToValidate = analysesToValidate, packageResults = packageResults, 
       minCellCount = minCellCount, logSettings = logSettings, sampleSize = sampleSize)

[lhjohn]

This actually worked now with the latest SqlRender and DatabaseConnector, and the exception above is not thrown anymore.