Use rlang::inform instead of PL logInfo

R/CohortConstruction.R

@@ -249,7 +249,7 @@ generateCohort <- function(cohortId = NULL,
       connection <- DatabaseConnector::connect(connectionDetails)
       on.exit(DatabaseConnector::disconnect(connection))
     }
-    ParallelLogger::logInfo(i, "/", nrow(cohortDefinitionSet), "- Generating cohort: ", cohortName, " (id = ", cohortId, ")")
+    rlang::inform(paste0(i, "/", nrow(cohortDefinitionSet), "- Generating cohort: ", cohortName, " (id = ", cohortId, ")"))
     sql <- cohortDefinitionSet$sql[i]
 
     if (!isSubset) {

R/CohortCount.R

@@ -67,7 +67,7 @@ getCohortCounts <- function(connectionDetails = NULL,
   if (tolower(cohortTable) %in% tablesInServer) {
     counts <- DatabaseConnector::querySql(connection, sql, snakeCaseToCamelCase = TRUE)
     delta <- Sys.time() - start
-    ParallelLogger::logInfo(paste("Counting cohorts took", signif(delta, 3), attr(delta, "units")))
+    rlang::inform(paste("Counting cohorts took", signif(delta, 3), attr(delta, "units")))
     if (!is.null(cohortDefinitionSet)) {
       # If the user has NOT specified a list of cohortIds
       # to use to filter the cohortDefinitionSet, then

R/CohortDefinitionSet.R

@@ -244,7 +244,7 @@ getCohortDefinitionSet <- function(settingsFileName = "Cohorts.csv",
       path <- system.file(fileName, package = packageName)
     }
     if (verbose) {
-      ParallelLogger::logInfo(paste0(" -- Loading ", basename(fileName), " from ", path))
+      rlang::inform(paste0(" -- Loading ", basename(fileName), " from ", path))
     }
     if (!file.exists(path)) {
       if (grepl(".json$", tolower(basename(fileName))) && warnOnMissingJson) {
@@ -259,7 +259,7 @@ getCohortDefinitionSet <- function(settingsFileName = "Cohorts.csv",
   }
 
   # Read the settings file which holds the cohortDefinitionSet
-  ParallelLogger::logInfo("Loading cohortDefinitionSet")
+  rlang::inform("Loading cohortDefinitionSet")
   settings <- readCsv(file = getPath(fileName = settingsFileName), warnOnCaseMismatch = FALSE)
 
   assert_settings_columns(names(settings), getPath(fileName = settingsFileName))
@@ -313,12 +313,12 @@ getCohortDefinitionSet <- function(settingsFileName = "Cohorts.csv",
   # Loading cohort subset definitions with their associated targets
   if (loadSubsets & nrow(subsetsToLoad) > 0) {
     if (dir.exists(subsetJsonFolder)) {
-      ParallelLogger::logInfo("Loading Cohort Subset Definitions")
+      rlang::inform("Loading Cohort Subset Definitions")
 
       ## Loading subsets that apply to the saved definition sets
       for (i in unique(subsetsToLoad$subsetDefinitionId)) {
         subsetFile <- file.path(subsetJsonFolder, paste0(i, ".json"))
-        ParallelLogger::logInfo("Loading Cohort Subset Defintion ", subsetFile)
+        rlang::inform(paste0("Loading Cohort Subset Defintion ", subsetFile))
         subsetDef <- CohortSubsetDefinition$new(ParallelLogger::loadSettingsFromJson(subsetFile))
         # Find target cohorts for this subset definition
         subsetTargetIds <- unique(subsetsToLoad[subsetsToLoad$subsetDefinitionId == i, ]$subsetParent)
@@ -397,7 +397,7 @@ saveCohortDefinitionSet <- function(cohortDefinitionSet,
 
   # Export the cohortDefinitionSet to the settings folder
   if (verbose) {
-    ParallelLogger::logInfo("Exporting cohortDefinitionSet to ", settingsFileName)
+    rlang::inform(paste0("Exporting cohortDefinitionSet to ", settingsFileName))
   }
   # Write the settings file and ensure that the "sql" and "json" columns are
   # not included
@@ -425,7 +425,7 @@ saveCohortDefinitionSet <- function(cohortDefinitionSet,
     }
 
     if (verbose) {
-      ParallelLogger::logInfo("Exporting (", i, "/", nrow(cohortDefinitionSet), "): ", cohortName)
+      rlang::inform(paste0("Exporting (", i, "/", nrow(cohortDefinitionSet), "): ", cohortName))
     }
 
     if (!is.na(json) && nchar(json) > 0) {
@@ -441,7 +441,7 @@ saveCohortDefinitionSet <- function(cohortDefinitionSet,
     }
   }
 
-  ParallelLogger::logInfo("Cohort definition saved")
+  rlang::inform("Cohort definition saved")
 }
 
 .getSettingsFileRequiredColumns <- function() {

R/CohortSample.R

@@ -262,7 +262,7 @@ sampleCohortDefinitionSet <- function(cohortDefinitionSet,
       )
 
       if (nrow(sampleTable) == 0) {
-        ParallelLogger::logInfo("No entires found for ", targetCohortId, " was it generated?")
+        rlang::inform(paste0("No entires found for ", targetCohortId, " was it generated?"))
         return(sampledCohortDefinition)
       }
       # Called only for side effects

R/CohortStats.R

@@ -71,7 +71,7 @@ insertInclusionRuleNames <- function(connectionDetails = NULL,
 
   # Insert the inclusion rules
   if (nrow(inclusionRules) > 0) {
-    ParallelLogger::logInfo("Inserting inclusion rule names")
+    rlang::inform("Inserting inclusion rule names")
     DatabaseConnector::insertTable(
       connection = connection,
       databaseSchema = cohortDatabaseSchema,
@@ -107,7 +107,7 @@ getStatsTable <- function(connectionDetails,
     databaseId <- NULL
   }
 
-  ParallelLogger::logInfo("- Fetching data from ", table)
+  rlang::inform("- Fetching data from ", table)
   sql <- "SELECT {@database_id != ''}?{CAST('@database_id' as VARCHAR(255)) as database_id,} t.* FROM @cohort_database_schema.@table t"
   data <- DatabaseConnector::renderTranslateQuerySql(
     sql = sql,

R/CohortTables.R

@@ -98,13 +98,13 @@ createCohortTables <- function(connectionDetails = NULL,
     for (i in 1:length(cohortTableNames)) {
       if (toupper(cohortTableNames[i]) %in% toupper(tables)) {
         createTableFlagList[i] <- FALSE
-        ParallelLogger::logInfo("Table \"", cohortTableNames[i], "\" already exists and in incremental mode, so not recreating it.")
+        rlang::inform(paste0("Table \"", cohortTableNames[i], "\" already exists and in incremental mode, so not recreating it."))
       }
     }
   }
 
   if (any(unlist(createTableFlagList, use.names = FALSE))) {
-    ParallelLogger::logInfo("Creating cohort tables")
+    rlang::inform("Creating cohort tables")
     createSampleTable <- ifelse(
       test = is.null(createTableFlagList$cohortSampleTable),
       yes = FALSE,
@@ -137,7 +137,7 @@ createCohortTables <- function(connectionDetails = NULL,
     DatabaseConnector::executeSql(connection, sql, progressBar = FALSE, reportOverallTime = FALSE)
 
     logCreateTableMessage <- function(schema, tableName) {
-      ParallelLogger::logInfo("- Created table ", schema, ".", tableName)
+      rlang::inform(paste0("- Created table ", schema, ".", tableName))
     }
     for (i in 1:length(createTableFlagList)) {
       if (createTableFlagList[[i]]) {
@@ -146,7 +146,7 @@ createCohortTables <- function(connectionDetails = NULL,
     }
 
     delta <- Sys.time() - start
-    ParallelLogger::logInfo("Creating cohort tables took ", round(delta, 2), attr(delta, "units"))
+    rlang::inform(paste0("Creating cohort tables took ", round(delta, 2), attr(delta, "units")))
   }
 }
 
@@ -173,7 +173,7 @@ dropCohortStatsTables <- function(connectionDetails = NULL,
 
   # Export the stats
   dropTable <- function(table) {
-    ParallelLogger::logInfo("- Dropping ", table)
+    rlang::inform(paste0("- Dropping ", table))
     sql <- "TRUNCATE TABLE @cohort_database_schema.@table;
             DROP TABLE @cohort_database_schema.@table;"
     DatabaseConnector::renderTranslateExecuteSql(

R/Export.R

@@ -73,7 +73,7 @@ exportCohortStatsTables <- function(connectionDetails,
   exportStats <- function(data,
                           fileName) {
     fullFileName <- file.path(cohortStatisticsFolder, fileName)
-    ParallelLogger::logInfo("- Saving data to - ", fullFileName)
+    rlang::inform(paste0("- Saving data to - ", fullFileName))
     if (incremental) {
       if (snakeCaseToCamelCase) {
         cohortDefinitionIds <- unique(data$cohortDefinitionId)

R/Incremental.R

@@ -70,7 +70,7 @@ isTaskRequired <- function(..., checksum, recordKeepingFile, verbose = TRUE) {
       if (verbose) {
         key <- list(...)
         key <- paste(sprintf("%s = '%s'", names(key), key), collapse = ", ")
-        ParallelLogger::logInfo("Skipping ", key, " because it is unchanged from earlier run")
+        rlang::inform(paste0("Skipping ", key, " because it is unchanged from earlier run"))
       }
       return(FALSE)
     } else {
@@ -115,7 +115,7 @@ getRequiredTasks <- function(..., checksum, recordKeepingFile) {
     tasks$checksum <- NULL
     if (length(idx) > 0) {
       text <- paste(sprintf("%s = %s", names(tasks), tasks[idx, ]), collapse = ", ")
-      ParallelLogger::logInfo("Skipping ", text, " because it is unchanged from earlier run")
+      rlang::inform(paste0("Skipping ", text, " because it is unchanged from earlier run"))
       tasks <- tasks[-idx, ]
     }
   }

R/NegativeControlCohorts.R

@@ -163,7 +163,7 @@ generateNegativeControlOutcomeCohorts <- function(connectionDetails = NULL,
     stop(paste0("Table: ", cohortTable, " not found in schema: ", cohortDatabaseSchema, ". Please use `createCohortTable` to ensure the cohort table is created before generating cohorts."))
   }
 
-  ParallelLogger::logInfo("Generating negative control outcome cohorts")
+  rlang::inform("Generating negative control outcome cohorts")
 
   # Send the negative control outcome cohort set to the server for use
   # in processing. This temp table will hold the mapping between

tests/testthat/test-CohortDefinitionSet.R

@@ -179,7 +179,7 @@ test_that("Call saveCohortDefinitionSet with missing json", {
     ))
   }
 
-  expect_output(
+  expect_message(
     saveCohortDefinitionSet(
       cohortDefinitionSet = cohortsToCreate,
       settingsFileName = file.path(tempdir(), "settings"),