Create function for exporting dqdashboard_results table to a json file

R/writeDBResultsTo.R

@@ -20,9 +20,9 @@
 #' @param connectionDetails         A connectionDetails object for connecting to the CDM database
 #' @param resultsDatabaseSchema     The fully qualified database name of the results schema
 #' @param cdmDatabaseSchema         The fully qualified database name of the CDM schema
-#' @param writeTableName            Name of table in the database to write results to
-#' @param outputFolder              The output folder
-#' @param outputFile                The output filename
+#' @param writeTableName            Name of DQD results table in the database to read from
+#' @param outputFolder              The folder to output the json results file to
+#' @param outputFile                The output filename of the json results file
 #'
 #' @export
 #'
@@ -36,43 +36,27 @@ writeDBResultsToJson <- function(connection,
                                     outputFile) {
     startTime <- Sys.time()
 
-    sql <- SqlRender::render(
+    metadata <- DatabaseConnector::renderTranslateQuerySql(
+          connection,
           sql = "select * from @cdmDatabaseSchema.cdm_source;",
-          cdmDatabaseSchema = cdmDatabaseSchema
+          cdmDatabaseSchema = cdmDatabaseSchema,
+          targetDialect = connectionDetails$dbms,
+          snakeCaseToCamelCase = TRUE
         )
 
-    sql <- SqlRender::translate(
-         sql = sql,
-         targetDialect = connectionDetails$dbms
-        )
-
-    metadata <- DatabaseConnector::querySql(
-         connection = connection,
-         sql = sql,
-         snakeCaseToCamelCase = TRUE
-        )
-
-    sql <- SqlRender::render(
+    checkResults <- DatabaseConnector::renderTranslateQuerySql(
+          connection,
           sql = "select * from @resultsDatabaseSchema.@writeTableName;",
           resultsDatabaseSchema = resultsDatabaseSchema,
-          writeTableName = writeTableName
-        )
-
-    sql <- SqlRender::translate(
-          sql = sql,
-          targetDialect = connectionDetails$dbms
-         )
-
-    checkResults <- DatabaseConnector::querySql(
-         connection,
-         sql,
-         snakeCaseToCamelCase = TRUE
+          writeTableName = writeTableName,
+          targetDialect = connectionDetails$dbms,
+          snakeCaseToCamelCase = TRUE
         )
 
     # Quick patch for missing value issues related to SQL Only Implementation
     checkResults["error"][checkResults["error"] == ''] <- NA
     checkResults["warning"][checkResults["warning"] == ''] <- NA
-    checkResults["executionTime"][checkResults["executionTime"] == ''] <- '0.1 secs'
+    checkResults["executionTime"][checkResults["executionTime"] == ''] <- '0 secs'
     checkResults["queryText"][checkResults["queryText"] == ''] <- '[Generated via SQL Only]'
 
     overview <- .summarizeResults(
@@ -89,7 +73,7 @@ writeDBResultsToJson <- function(connection,
     allResults <- list(
         startTimestamp = Sys.time(),
         endTimestamp = Sys.time(),
-        executionTime = sprintf("%.0f %s", delta, attr(delta, "units")),
+        executionTime = '0 secs',
         CheckResults = checkResults,
         Metadata = metadata,
         Overview = overview

tests/testthat/test-writeDBResultsTo.R

@@ -6,22 +6,21 @@ test_that("Write DB results to json", {
   connectionDetailsEunomia <- Eunomia::getEunomiaConnectionDetails()
   cdmDatabaseSchemaEunomia <- "main"
   resultsDatabaseSchemaEunomia <- "main"
+  writeTableName <- "dqdashboard_results"
 
   results <- DataQualityDashboard::executeDqChecks(
-      connectionDetails = connectionDetailsEunomia,
-      cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
-      resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
-      cdmSourceName = "Eunomia",
-      checkNames = "measurePersonCompleteness",
-      outputFolder = outputFolder,
-      writeToTable = TRUE,
-      writeTableName = "dqdashboard_results"
+    connectionDetails = connectionDetailsEunomia,
+    cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
+    resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+    cdmSourceName = "Eunomia",
+    checkNames = "measurePersonCompleteness",
+    outputFolder = outputFolder,
+    writeToTable = TRUE,
+    writeTableName = writeTableName
   )
 
 
   connection <- DatabaseConnector::connect(connectionDetailsEunomia)
-  tableNames <- DatabaseConnector::getTableNames(connection = connection, databaseSchema = resultsDatabaseSchemaEunomia)
-  expect_true("dqdashboard_results" %in% tolower(tableNames))
 
   testExportFile <- "dq-result-test.json"
 
@@ -30,13 +29,26 @@ test_that("Write DB results to json", {
     connectionDetailsEunomia,
     resultsDatabaseSchemaEunomia,
     cdmDatabaseSchemaEunomia,
-    "dqdashboard_results",
+    writeTableName,
     outputFolder,
     testExportFile
-    )
+  )
 
   on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
+
+  # Check that file was exported properly
   expect_true(file.exists(file.path(outputFolder,testExportFile)))
 
+  # Check that export length matches length of db table
+  results <- jsonlite::fromJSON(file.path(outputFolder,testExportFile))
+  table_rows <- DatabaseConnector::renderTranslateQuerySql(
+    connection,
+    sql = "select count(*) from @resultsDatabaseSchema.@writeTableName;",
+    resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+    writeTableName = writeTableName,
+    targetDialect = connectionDetailsEunomia$dbms,
+    snakeCaseToCamelCase = TRUE
+  )
+  expect_true(length(results$CheckResults) == table_rows)
 
 })

vignettes/SqlOnly.rmd

@@ -171,49 +171,18 @@ for (dqdSqlFile in dqdSqlFiles) {
   )
 }
 
-# Get results
-checkResults <- DatabaseConnector::querySql(
-  c,
-  SqlRender::render(
-    "SELECT * FROM @resultsDatabaseSchema.@writeTableName",
-    resultsDatabaseSchema = resultsDatabaseSchema,
-    writeTableName = writeTableName
-  ),
-  snakeCaseToCamelCase = TRUE
-)
-DatabaseConnector::disconnect(c)
-
-# convert check ID column name to correct format
-colnames(checkResults)[colnames(checkResults) == "checkid"] ="checkId"
-
-# Get overview of DQD results
-library(DataQualityDashboard)
-overview <- DataQualityDashboard:::.summarizeResults(checkResults = checkResults)
-
-# Create results object, adding fake metadata
-result <- list(
-  startTimestamp = Sys.time(),
-  endTimestamp = Sys.time(),
-  executionTime = "",
-  Metadata = data.frame(
-    cdmSourceName = cdmSourceName,
-    cdmSourceAbbreviation = cdmSourceName,
-    cdmHolder = "",
-    sourceDescription = "",
-    sourceDocumentationReference = "",
-    cdmEtlReference = "",
-    sourceReleaseDate = "",
-    cdmReleaseDate = "",
-    cdmVersion = cdmVersion,
-    cdmVersionConceptId = 0,
-    vocabularyVersion = "",
-    dqdVersion = as.character(packageVersion("DataQualityDashboard"))
-  ),
-  Overview = overview,
-  CheckResults = checkResults
-)
+# Extract results table to JSON file for viewing or secondary use
+
+DataQualityDashboard::writeDBResultsToJson(
+    c,
+    connectionDetails,
+    resultsDatabaseSchema,
+    cdmDatabaseSchema,
+    writeTableName,
+    jsonOutputFolder,
+    jsonOutputFile
+  )
 
-DataQualityDashboard:::.writeResultsToJson(result, jsonOutputFolder, jsonOutputFile)
 
 jsonFilePath <- R.utils::getAbsolutePath(file.path(jsonOutputFolder, jsonOutputFile))
 DataQualityDashboard::viewDqDashboard(jsonFilePath)