38 tool createlogger with ohdsi parallellogger

DESCRIPTION

@@ -28,7 +28,8 @@ Imports:
     glue,
     stringr,
     zip,
-    here
+    here,
+    fs
 Config/roxygen2/version: 8.0.0
 Suggests: 
     testthat (>= 3.0.0)

NAMESPACE

@@ -4,9 +4,13 @@ export(arrangeCdmNames)
 export(assertCdmNames)
 export(createResultsDir)
 export(getPkgZips)
+export(setLoggers)
 export(unZipStudyFiles)
 export(zipStudyFiles)
-importFrom(ParallelLogger,logInfo)
+importFrom(ParallelLogger,createFileAppender)
+importFrom(ParallelLogger,createLogger)
+importFrom(ParallelLogger,layoutParallel)
+importFrom(ParallelLogger,registerLogger)
 importFrom(checkmate,assertCharacter)
 importFrom(checkmate,assertDirectoryExists)
 importFrom(checkmate,assertFileExists)
@@ -16,6 +20,7 @@ importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
 importFrom(cli,cli_alert_warning)
+importFrom(fs,path_ext_set)
 importFrom(glue,glue)
 importFrom(glue,glue_collapse)
 importFrom(here,here)

R/createResultsDir.R

@@ -17,42 +17,65 @@
 #'   \item \code{resultsDirName}: The name of the results subdirectory.
 #' }
 #'
-#' @importFrom ParallelLogger logInfo
+#' @importFrom cli cli_alert_info
 #' @importFrom checkmate assertDirectoryExists
 #' @importFrom glue glue
 #'
 #' @export
+#'
+#' @examples
+#' outputDir <- file.path(
+#'    tempdir(),
+#'    "examples"
+#' )
+#' directories <- createResultsDir(
+#'    outputDir,
+#'    dbname = "OMOP"
+#'    )
+#' unlink(outputDir, recursive = TRUE)
 createResultsDir <- function(
     outputDir = NULL,
     dbname
     ) {
   # Set folder location for results ----
-  ParallelLogger::logInfo("Setting location for results")
+  cli::cli_alert_info(
+    "Creating locations to save results"
+    )
   if (is.null(outputDir)) {
     outputDir <- getwd()
-    checkmate::assertDirectoryExists(outputDir)
+    checkmate::assertDirectoryExists(
+      outputDir
+      )
   } else {
     if (!dir.exists(outputDir)) {
-      dir.create(outputDir)
-      checkmate::assertDirectoryExists(outputDir)
+      dir.create(
+        outputDir
+        )
+      checkmate::assertDirectoryExists(
+        outputDir
+        )
     } else {
-      outputDir <- normalizePath(outputDir)
-      checkmate::assertDirectoryExists(outputDir)
+      outputDir <- normalizePath(
+        outputDir
+        )
+      checkmate::assertDirectoryExists(
+        outputDir
+        )
     }
   }
-
-  resultsDirName <- glue::glue("results_{dbname}")
-
+  resultsDirName <- glue::glue(
+    "results_{dbname}"
+    )
   resultsDir <- file.path(
     outputDir,
     resultsDirName
   )
-
   if (!dir.exists(resultsDir)) {
     dir.create(resultsDir)
   }
-
-  checkmate::assertDirectoryExists(resultsDir)
+  checkmate::assertDirectoryExists(
+    resultsDir
+    )
   return(
     list(
       outputDir = outputDir,

R/getPkgZips.R

@@ -13,15 +13,14 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' pkg_status_list <- getPkgZips()
-#'
 #' # Format supp in this way:
 #' devtools <- list(Package = "devtools", Version = "2.5.1")
 #' duckdb <- list(Package = "duckdb", Version = "1.5.2")
 #' supp <- list(Packages = list(devtools = devtools, duckdb = duckdb))
-#'
 #' pkg_status_list <- getPkgZips(supplement = supp)
-#'
+#' }
 #' @details
 #' If the package version is not found under any of the R minor releases, the package will be downloaded from the specified `backupRrel` regardless of package version specified in renv.lock
 #' @importFrom renv lockfile_read

R/setLoggers.R

@@ -0,0 +1,115 @@
+#' `setLoggers()` as text files in the results directory
+#'
+#' @description
+#' Sets `ohdsi/ParallelLogger` log and error report for a study. Logger
+#' registered as 'OMOP_STUDY_LOGGER' and error report as 'OMOP_STUDY_ERROR_REPORT'.
+#' Please note: avoid using inside a tryCatch() or similar because events
+#' will not be 'obsorbed' and not recorded by ParallelLogger.
+#'
+#' @param resultsDir A valid folder where to save the results of a study.
+#'    This function will work best with the folder structure formed by
+#'    `createsResultsDir()`
+#' @param logFileName A file name in character. Default 'log'
+#' @param errorFileName A file name in character. Default 'error'
+#' @param eventLevel TRACE is the default, captures all the output from
+#'    the console
+#' @param errorLevel ERROR is the default, captures errors and fatal events
+#'
+#' @returns Invisible
+#'
+#' @importFrom checkmate assertDirectoryExists
+#' @importFrom checkmate assertCharacter
+#' @importFrom fs path_ext_set
+#' @importFrom ParallelLogger registerLogger createLogger createFileAppender layoutParallel
+#' @importFrom cli cli_alert_info
+#' @importFrom glue glue
+#'
+#' @export
+#'
+#' @examples
+#' outputDir <- file.path(
+#'    tempdir(),
+#'    "examples"
+#' )
+#' directories <- createResultsDir(
+#'    outputDir,
+#'    dbname = "OMOP"
+#'    )
+#' setLoggers(
+#'   resultsDir = directories$resultsDir
+#'   )
+#' ParallelLogger::clearLoggers()
+#' unlink(outputDir, recursive = TRUE)
+setLoggers <- function(
+    resultsDir,
+    logFileName = "log",
+    errorFileName = "error",
+    eventLevel = "TRACE",
+    errorLevel = "ERROR"
+) {
+
+  checkmate::assertDirectoryExists(resultsDir)
+  checkmate::assertCharacter(logFileName)
+  checkmate::assertCharacter(errorFileName)
+
+  stopifnot(
+    'eventLevel should be one of:
+    "TRACE", "DEBUG", "INFO", "WARN",
+    "ERROR", "FATAL"' = eventLevel %in% c(
+      "TRACE", "DEBUG", "INFO", "WARN", "ERROR", "FATAL"
+    )
+  )
+
+  # Logger ----
+  logFileLocation <- file.path(
+    resultsDir,
+    fs::path_ext_set(
+      logFileName,
+      ".txt"
+    )
+  )
+  ParallelLogger::registerLogger(
+    logger <- ParallelLogger::createLogger(
+      name =  "OMOP_STUDY_LOGGER",
+      threshold = eventLevel,
+      appenders = list(
+        ParallelLogger::createFileAppender(
+          layout = ParallelLogger::layoutParallel,
+          fileName = logFileLocation
+        )
+      )
+    )
+  )
+  ParallelLogger::logInfo(
+    glue::glue(
+      "Logger file will be created at: {resultsDir}"
+    )
+  )
+  checkmate::assertFileExists(logFileLocation)
+
+  # Error ---------------
+  errorFileLocation <- file.path(
+    resultsDir,
+    fs::path_ext_set(
+      errorFileName,
+      ".txt"
+    )
+  )
+
+  ParallelLogger::registerLogger(
+    ParallelLogger::createLogger(
+      name = "OMOP_STUDY_ERROR_REPORT",
+      threshold = errorLevel,
+      appenders = list(
+        ParallelLogger::createFileAppender(
+          layout = ParallelLogger::layoutErrorReport,
+          fileName = errorFileLocation,
+          overwrite = TRUE,
+          expirationTime = 60
+        )
+      )
+    )
+  )
+
+ return(invisible())
+}

R/unzipStudyFiles.R

@@ -15,6 +15,23 @@
 #' @importFrom glue glue
 #'
 #' @export
+#'
+#' @examples
+#'  \dontrun{
+#' path <- testthat::test_path(
+#'    "data",
+#'    "results_execution"
+#' )
+#' outputDir <- file.path(
+#'   tempdir(),
+#'   "examples"
+#' )
+#' unZipStudyFiles(
+#'   path = path,
+#'   outputDir = outputDir
+#' )
+#' unlink(outputDir, recursive = TRUE)
+#' }
 unZipStudyFiles <- function(
     path,
     pattern,

R/zipStudyFiles.R

@@ -12,6 +12,22 @@
 #' @importFrom glue glue
 #'
 #' @export
+#' @examples
+#' outputDir <- file.path(
+#'    tempdir(),
+#'    "examples"
+#'    )
+#' dbname <- "IPCI"
+#' directories <- createResultsDir(
+#'   outputDir,
+#'   dbname = dbname
+#' )
+#' zipStudyFiles(
+#'   resultsDirName = directories$resultsDir,
+#'   outputDir = directories$outputDir,
+#'   dbname = dbname
+#' )
+#' unlink(outputDir, recursive = TRUE)
 zipStudyFiles <- function(
     resultsDirName,
     outputDir,