Merge pull request #501 from katy-sadowski/katy__warnings

Small fixes
OHDSI · Nov 4, 2023 · eb295b0 · eb295b0
2 parents ef06bfc + 460ffb1
commit eb295b0
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Showing 6 changed files with 30 additions and 29 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -31,4 +31,4 @@ importFrom(tools,file_path_sans_ext)
 importFrom(utils,install.packages)
 importFrom(utils,menu)
 importFrom(utils,packageVersion)
-importFrom(utils,write.table)
+importFrom(utils,write.table)
diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R
@@ -93,6 +93,10 @@ executeDqChecks <- function(connectionDetails,
   if (!str_detect(cdmVersion, regex(acceptedCdmRegex))) {
     stop("cdmVersion must contain a version of the form '5.X' where X is an integer between 2 and 4 inclusive.")
   }
+
+  if (sqlOnlyIncrementalInsert == TRUE && sqlOnly == FALSE) {
+    stop("Set `sqlOnly` to TRUE in order to use `sqlOnlyIncrementalInsert` mode.")
+  }
 
   stopifnot(is.character(cdmDatabaseSchema), is.character(resultsDatabaseSchema), is.numeric(numThreads))
   stopifnot(is.character(cdmSourceName), is.logical(sqlOnly), is.character(outputFolder), is.logical(verboseMode))
@@ -134,6 +138,10 @@ executeDqChecks <- function(connectionDetails,
     if (nrow(metadata) < 1) {
       stop("Please populate the cdm_source table before executing data quality checks.")
     }
+    if (nrow(metadata) > 1) {
+      metadata <- metadata[1,]
+      warning("The cdm_source table has more than 1 row. A single row from this table has been selected to populate DQD metadata.")
+    }
     metadata$dqdVersion <- as.character(packageVersion("DataQualityDashboard"))
     DatabaseConnector::disconnect(connection)
   } else {

diff --git a/R/runCheck.R b/R/runCheck.R
@@ -124,7 +124,7 @@
 
     dfs <- do.call(rbind, dfs)
 
-    if (sqlOnlyIncrementalInsert) {
+    if (sqlOnly && sqlOnlyIncrementalInsert) {
       sqlToUnion <- dfs$query
       if (length(sqlToUnion) > 0) {
         .writeSqlOnlyQueries(sqlToUnion, sqlOnlyUnionCount, resultsDatabaseSchema, writeTableName, connectionDetails$dbms, outputFolder, checkDescription)

diff --git a/R/writeDBResultsTo.R b/R/writeDBResultsTo.R
@@ -17,7 +17,6 @@
 #' Write DQD results database table to json
 #'
 #' @param connection                A connection object
-#' @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 DQD results table in the database to read from
@@ -28,7 +27,6 @@
 #'
 
 writeDBResultsToJson <- function(connection,
-                                    connectionDetails,
                                     resultsDatabaseSchema,
                                     cdmDatabaseSchema,
                                     writeTableName,
@@ -37,18 +35,16 @@ writeDBResultsToJson <- function(connection,
     metadata <- DatabaseConnector::renderTranslateQuerySql(
           connection,
           sql = "select * from @cdmDatabaseSchema.cdm_source;",
-          cdmDatabaseSchema = cdmDatabaseSchema,
-          targetDialect = connectionDetails$dbms,
-          snakeCaseToCamelCase = TRUE
+          snakeCaseToCamelCase = TRUE,
+          cdmDatabaseSchema = cdmDatabaseSchema
         )
 
     checkResults <- DatabaseConnector::renderTranslateQuerySql(
           connection,
           sql = "select * from @resultsDatabaseSchema.@writeTableName;",
+          snakeCaseToCamelCase = TRUE,
           resultsDatabaseSchema = resultsDatabaseSchema,
-          writeTableName = writeTableName,
-          targetDialect = connectionDetails$dbms,
-          snakeCaseToCamelCase = TRUE
+          writeTableName = writeTableName
         )
 
     # Quick patch for missing value issues related to SQL Only Implementation

diff --git a/man/writeDBResultsToJson.Rd b/man/writeDBResultsToJson.Rd
diff --git a/tests/testthat/test-writeDBResultsTo.R b/tests/testthat/test-writeDBResultsTo.R
@@ -8,25 +8,26 @@ test_that("Write DB results to json", {
   resultsDatabaseSchemaEunomia <- "main"
   writeTableName <- "dqdashboard_results"
 
-  results <- DataQualityDashboard::executeDqChecks(
-    connectionDetails = connectionDetailsEunomia,
-    cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
-    resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
-    cdmSourceName = "Eunomia",
-    checkNames = "measurePersonCompleteness",
-    outputFolder = outputFolder,
-    writeToTable = TRUE,
-    writeTableName = writeTableName
+  expect_warning(
+    results <- DataQualityDashboard::executeDqChecks(
+      connectionDetails = connectionDetailsEunomia,
+      cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
+      resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+      cdmSourceName = "Eunomia",
+      checkNames = "measurePersonCompleteness",
+      outputFolder = outputFolder,
+      writeToTable = TRUE,
+      writeTableName = writeTableName
+    ),
+    regexp = "^Missing check names.*"
   )
 
-
   connection <- DatabaseConnector::connect(connectionDetailsEunomia)
 
   testExportFile <- "dq-result-test.json"
 
   DataQualityDashboard::writeDBResultsToJson(
     connection,
-    connectionDetailsEunomia,
     resultsDatabaseSchemaEunomia,
     cdmDatabaseSchemaEunomia,
     writeTableName,
@@ -46,7 +47,6 @@ test_that("Write DB results to json", {
     sql = "select count(*) from @resultsDatabaseSchema.@writeTableName;",
     resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
     writeTableName = writeTableName,
-    targetDialect = connectionDetailsEunomia$dbms,
     snakeCaseToCamelCase = TRUE
   )
   expect_true(length(results$CheckResults) == table_rows)