Development

DESCRIPTION

@@ -34,7 +34,8 @@ Imports:
     R6,
     ResultModelManager,
     yaml,
-    stringr
+    stringr,
+    ParallelLogger
 Remotes:
     javier-gracia-tabuenca-tuni/DatabaseConnector@bigquery-DBI-2
 Suggests: 

NAMESPACE

@@ -12,16 +12,19 @@ export(createPlotFromResults)
 export(createReport)
 export(createStratifiedCodeCountsTable)
 export(create_api)
+export(fct_setUpLogger)
 export(getCDMSource)
 export(getCodeCounts)
 export(getCodeCounts_memoise)
 export(getConceptsWithCodeCounts)
 export(getConceptsWithCodeCounts_memoise)
+export(getLogs)
 export(helper_FinnGen_getDatabaseFile)
 export(helper_FinnGen_getDatabaseFileCounts)
 export(helper_createSqliteDatabaseFromDatabase)
 export(pruneLevelsFromResults)
 export(runApiServer)
+export(sendFeedback)
 importFrom(DatabaseConnector,connect)
 importFrom(DatabaseConnector,createConnectionDetails)
 importFrom(DatabaseConnector,createDbiConnectionDetails)

R/fct_logs.R

@@ -0,0 +1,59 @@
+
+#' Set Up Logger
+#'
+#' Sets up a logger with console and file appenders for logging.
+#'
+#' @param sToken The session token to be added to log entries
+#'
+#' @return A logger object.
+#'
+#' @export
+fct_setUpLogger  <- function(sToken=""){
+
+  timestamp  <- timestamp <- as.character(as.numeric(format(Sys.time(), "%d%m%Y%H%M%OS2"))*100)
+  folderWithLog <- file.path(tempdir(),  paste0("logs", timestamp))
+  dir.create(folderWithLog, showWarnings = FALSE)
+  fileName <- file.path(folderWithLog, "log.txt")
+  options(parallelLoggerTempFile = fileName)
+
+  logger <- ParallelLogger::createLogger(
+    threshold = "TRACE",
+    appenders = list(
+      # to console for tracking
+      .createConsoleAppenderForSandboxLogging(sToken=sToken),
+      # to file for showing in app
+      ParallelLogger::createFileAppender(
+        fileName = fileName,
+        layout = ParallelLogger::layoutTimestamp
+      )
+    )
+  )
+  ParallelLogger::clearLoggers()
+  #addDefaultFileLogger(file.path(folderWithLog, "log2.txt"))
+  ParallelLogger::registerLogger(logger)
+
+}
+
+
+#' Create Console Appender for Sandbox Logging
+#'
+#' Creates a console appender for sandbox logging with a specified layout.
+#'
+#' @param layout A layout function for the logger. Defaults to ParallelLogger::layoutParallel.
+#' @param sToken The session token to be added to log entries
+#'
+#' @return An appender object for logging.
+#'
+.createConsoleAppenderForSandboxLogging <- function(layout = ParallelLogger::layoutParallel,sToken) {
+  appendFunction <- function(this, level, message, echoToConsole) {
+    # Avoid note in check:
+    # Should add session id (session$token) to help group logs by session in central log database.
+    # paste0("[sandbox-co2-log] session:", session$token, message)
+    missing(this)
+    message <- paste0("[sandbox-co2-log] --session:",sToken,"-- ",message)
+    writeLines(message, con = stderr())
+  }
+  appender <- list(appendFunction = appendFunction, layout = layout)
+  class(appender) <- "Appender"
+  return(appender)
+}

R/getCDMSource.R

@@ -18,7 +18,7 @@
 #'
 getCDMSource <- function(
     CDMdbHandler) {
-    message("getCDMSource")
+    ParallelLogger::logInfo("getCDMSource: Getting CDM source information")
     #
     # VALIDATE
     #

R/getCodeCounts.R

@@ -36,7 +36,7 @@ getCodeCounts <- function(
     CDMdbHandler,
     conceptId,
     codeCountsTable = "code_counts") {
-    message("getCodeCounts: ", conceptId)
+    ParallelLogger::logInfo("getCodeCounts: Getting code counts for conceptId: ", conceptId)
     #
     # VALIDATE
     #

R/getConceptsWithCodeCounts.R

@@ -37,6 +37,8 @@ getConceptsWithCodeCounts <- function(
     vocabularyDatabaseSchema <- CDMdbHandler$vocabularyDatabaseSchema
     resultsDatabaseSchema <- CDMdbHandler$resultsDatabaseSchema
 
+    ParallelLogger::logInfo("getConceptsWithCodeCounts: Getting concepts with code counts")
+
     #
     # FUNCTION
     #

R/getLogs.R

@@ -0,0 +1,17 @@
+
+#' Get logs from ParallelLogger temp file
+#'
+#' @description
+#' Retrieves log messages from the ParallelLogger temporary log file.
+#' This may help track internal API events, errors, and debug information.
+#'
+#' @return A character vector with each log line as a string.
+#'
+#' @export
+getLogs <- function() {
+    ParallelLogger::logInfo("getLogs: Getting logs")
+    #
+    fileName <- getOption("parallelLoggerTempFile")
+    logs <- readLines(fileName)
+    return(logs)
+}

R/runApiServer.R

@@ -40,8 +40,11 @@ runApiServer <- function(
     # VALIDATE
     #
 
+    fct_setUpLogger()
+    ParallelLogger::logInfo("Starting ROMOPAPI API server")
+
     if (is.null(cohortTableHandlerConfig)) {
-        message("No path to database config provided. Using the test counts only database.")
+        ParallelLogger::logInfo("No path to database config provided. Using the test counts only database.")
         # if not provided, use the test counts only database
         test_databasesConfig <- HadesExtras_readAndParseYaml(
             pathToYalmFile = system.file("testdata", "config", "onlyCounts_databasesConfig.yml", package = "ROMOPAPI"),
@@ -58,6 +61,7 @@ runApiServer <- function(
     }
 
     if (buildCountsTable == TRUE) {
+        ParallelLogger::logInfo("Building code counts tables")
         createCodeCountsTables(CDMdbHandler, codeCountsTable = "code_counts")
     }
 

R/sendFeedback.R

@@ -0,0 +1,21 @@
+
+
+
+#' Send feedback to the API server
+#'
+#' @param feedback A character string containing the feedback to send.
+#'
+#' @return NULL
+#'
+#' @export
+sendFeedback <- function(feedback) {
+
+  #
+  # VALIDATE
+  #
+  feedback |> checkmate::assertCharacter()
+  #
+  # FUNCTION
+  #
+  ParallelLogger::logInfo("FEEDBACK: ", feedback)
+}

inst/plumber/plumber.R

@@ -110,3 +110,19 @@ function(res) {
   # Read and return the file content
   readChar(file_path, file.info(file_path)$size)
 }
+
+#* Get the logs
+#* @get /getLogs
+function() {
+  logs <- getLogs()
+  return(logs)
+}
+
+#* Send feedback to the API server
+#* @post /sendFeedback
+function(res, feedback = "") {
+  feedback <- as.character(feedback)
+  sendFeedback(feedback)
+  res$status <- 200
+  return(list(message = "Feedback sent"))
+}

inst/testdata/config/atlasDev_databasesConfig.yml

@@ -13,8 +13,8 @@ BQ5k:
           bigint: integer64
       tempEmulationSchema: atlas-development-270609.sandbox
     cdm:
-        cdmDatabaseSchema: atlas-development-270609.finngen_omop_r13_v3
-        vocabularyDatabaseSchema: atlas-development-270609.finngen_omop_r13_v3
+        cdmDatabaseSchema: atlas-development-270609.finngen_omop_r13_v3_5k
+        vocabularyDatabaseSchema: atlas-development-270609.finngen_omop_r13_v3_5k
         resultsDatabaseSchema: atlas-development-270609.sandbox
     cohortTable:
         cohortDatabaseSchema: atlas-development-270609.sandbox

inst/testdata/data/createTestingData.R

@@ -8,7 +8,8 @@ conceptIds <- c(
     317009, # Snomed: Asthma
     45596282, # ICD10: Asthma
     21601855, # ATC level 4: C10AA (Statins)
-    2010001615 # test endpoint
+    #2010001615, # test endpoint
+    320136 # Big graph, parent of Asthma snomed concept (Disorders of the respiratory system)
 )
 
 CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")
@@ -45,3 +46,4 @@ dplyr::tbl(connection, "stratified_code_counts") |>
     dplyr::count() |>
     dplyr::pull(n) |>
     expect_gt(0)
+

tests/testmanual/manualtest-runApiServer.R

@@ -0,0 +1,10 @@
+
+
+databaseConfig <- yaml::read_yaml("inst/testdata/config/onlyCounts_databasesConfig.yml")
+
+ROMOPAPI::runApiServer(
+  cohortTableHandlerConfig = databaseConfig$cohortTableHandler,
+  buildCountsTable = FALSE
+)
+
+# http://127.0.0.1:8585/__docs__/