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V1.0 module bug fixes #163

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merged 3 commits into from
Sep 5, 2024
Merged

V1.0 module bug fixes #163

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df5e3f4
Bug fixes for C & CI Modules
anthonysena Sep 4, 2024
327195e
Generate stats
anthonysena Sep 5, 2024
b798f62
minCharacterizationMean setting
anthonysena Sep 5, 2024
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12 changes: 8 additions & 4 deletions R/Module-Characterization.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ CharacterizationModule <- R6::R6Class(

jobContext <- private$jobContext
workFolder <- jobContext$moduleExecutionSettings$workSubFolder
resultsFolder <- jobContext$moduleExecutionSettings$resultsSubFolder

Characterization::runCharacterizationAnalyses(
connectionDetails = connectionDetails,
Expand All @@ -32,13 +33,13 @@ CharacterizationModule <- R6::R6Class(
outcomeDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
outcomeTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable,
cdmDatabaseSchema = jobContext$moduleExecutionSettings$cdmDatabaseSchema,
characterizationSettings = jobContext$settings,
characterizationSettings = jobContext$settings$analysis,
databaseId = jobContext$moduleExecutionSettings$cdmDatabaseMetaData$databaseId,
outputDirectory = jobContext$moduleExecutionSettings$resultsSubFolder,
outputDirectory = resultsFolder,
executionPath = workFolder,
csvFilePrefix = self$tablePrefix,
minCellCount = jobContext$moduleExecutionSettings$minCellCount,
minCharacterizationMean = jobContext$moduleExecutionSettings$minCharacterizationMean,
minCharacterizationMean = jobContext$settings$minCharacterizationMean,
incremental = jobContext$moduleExecutionSettings$incremental,
threads = as.double(ifelse(Sys.getenv('CharacterizationThreads') == "", 1,Sys.getenv('CharacterizationThreads') ))
)
Expand Down Expand Up @@ -241,7 +242,10 @@ CharacterizationModule <- R6::R6Class(
)

specifications <- super$createModuleSpecifications(
moduleSpecifications = analysis
moduleSpecifications = list(
analysis = analysis,
minCharacterizationMean = minCharacterizationMean
)
)
return(specifications)
}
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4 changes: 3 additions & 1 deletion R/Module-CohortGenerator.R
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Expand Up @@ -28,7 +28,9 @@ CohortGeneratorModule <- R6::R6Class(
super$execute(connectionDetails, analysisSpecifications, executionSettings)

jobContext <- private$jobContext
cohortDefinitionSet <- super$.createCohortDefinitionSetFromJobContext()
cohortDefinitionSet <- super$.createCohortDefinitionSetFromJobContext(
generateStats = jobContext$settings$generateStats
)
negativeControlOutcomeSettings <- private$.createNegativeControlOutcomeSettingsFromJobContext()
resultsFolder <- jobContext$moduleExecutionSettings$resultsSubFolder
if (!dir.exists(resultsFolder)) {
Expand Down
2 changes: 1 addition & 1 deletion R/Module-CohortIncidence.R
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Expand Up @@ -40,7 +40,7 @@ CohortIncidenceModule <- R6::R6Class(
buildOptions <- CohortIncidence::buildOptions(
cohortTable = paste0(private$jobContext$moduleExecutionSettings$workDatabaseSchema, ".", private$jobContext$moduleExecutionSettings$cohortTableNames$cohortTable),
cdmDatabaseSchema = private$jobContext$moduleExecutionSettings$cdmDatabaseSchema,
sourceName = as.character(jobContext$moduleExecutionSettings$cdmDatabaseMetaData$databaseId),
sourceName = as.character(private$jobContext$moduleExecutionSettings$cdmDatabaseMetaData$databaseId),
refId = refId
)

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