Refactor Strategus module approach

R/Module-PatientLevelPrediction.R

@@ -41,7 +41,7 @@ PatientLevelPredictionModule <- R6::R6Class(
       )
 
       jobContext$settings <- private$.setCovariateSchemaTable(
-        modelDesignList = jobContext$settings,
+        modelDesignList = jobContext$settings$modelDesignList,
         cohortDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
         cohortTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable
       )
@@ -97,8 +97,6 @@ PatientLevelPredictionModule <- R6::R6Class(
     #' @param resultsExecutionSettings The results execution settings
     uploadResults = function(resultsConnectionDetails, analysisSpecifications, resultsExecutionSettings) {
       super$uploadResults(resultsConnectionDetails, analysisSpecifications, resultsExecutionSettings)
-      conn <- DatabaseConnector::connect(resultsConnectionDetails)
-      on.exit(DatabaseConnector::disconnect(conn))
 
       databaseSchemaSettings <- PatientLevelPrediction::createDatabaseSchemaSettings(
         resultSchema = resultsExecutionSettings$resultsDatabaseSchema,
@@ -109,7 +107,7 @@ PatientLevelPredictionModule <- R6::R6Class(
       resultsFolder <- private$jobContext$moduleExecutionSettings$resultsSubFolder
       PatientLevelPrediction::insertCsvToDatabase(
         csvFolder = resultsFolder,
-        conn = conn,
+        connectionDetails = resultsConnectionDetails,
         databaseSchemaSettings = databaseSchemaSettings,
         modelSaveLocation = file.path(resultsFolder, "dbmodels"),
         csvTableAppend = ""

extras/R6ClassFun.R

@@ -222,7 +222,6 @@ for (exposureOfInterestId in exposureOfInterestIds) {
   }
 }
 
-# Analysis settings ------------------------------------------------------------
 getDbSccsDataArgs <- SelfControlledCaseSeries::createGetDbSccsDataArgs(
   studyStartDate = "",
   studyEndDate = "",
@@ -297,7 +296,6 @@ sccsAnalysis1 <- SelfControlledCaseSeries::createSccsAnalysis(
 
 sccsAnalysisList <- list(sccsAnalysis1)
 
-# SCCS module specs ------------------------------------------------------------
 sccsModuleSpecifications <- sccsModuleSettingsCreator$createModuleSpecifications(
   sccsAnalysisList = sccsAnalysisList,
   exposuresOutcomeList = exposuresOutcomeList,
@@ -357,13 +355,14 @@ plpModuleSpecifications <- plpModuleSettingsCreator$createModuleSpecifications(
 analysisSpecifications <- createEmptyAnalysisSpecificiations() |>
   addSharedResources(cohortSharedResourcesSpecifications) |>
   addSharedResources(ncoCohortSharedResourceSpecifications) |>
+  # WORKING
   addModuleSpecifications(cgModuleSettings) |>
   addModuleSpecifications(cdModuleSpecifications) |>
   addModuleSpecifications(cmModuleSpecifications) |>
-  addModuleSpecifications(sccsModuleSpecifications)
-  # NOT WORKING
+  addModuleSpecifications(sccsModuleSpecifications) |>
+  addModuleSpecifications(plpModuleSpecifications)
+# NOT WORKING
   #addModuleSpecifications(cModuleSpecifications) |>
-  #addModuleSpecifications(plpModuleSpecifications)
   # MOSTLY WORKING
   #addModuleSpecifications(ciModuleSettings) |>
 
@@ -391,7 +390,6 @@ connectionDetails <- Eunomia::getEunomiaConnectionDetails(
   overwrite = TRUE
 )
 #debugonce(Strategus::execute)
-#debugonce(CohortDiagnostics:::computeCohortCounts)
 Strategus::execute(
   analysisSpecifications = analysisSpecifications,
   executionSettings = executionSettings,