Merge pull request #577 from ob325/develop

added parameter for checkSeverity, updated docs & vignette

R/executeDqChecks.R

@@ -35,6 +35,7 @@
 #' @param writeToCsv                Boolean to indicate if the check results will be written to a csv file. Default is FALSE
 #' @param csvFile                   (OPTIONAL) CSV file to write results
 #' @param checkLevels               Choose which DQ check levels to execute. Default is all 3 (TABLE, FIELD, CONCEPT)
+#' @param checkSeverity             Choose which DQ check severity levels to execute. Default is all 3 (fatal, convention, characterization) 
 #' @param checkNames                (OPTIONAL) Choose which check names to execute. Names can be found in inst/csv/OMOP_CDM_v[cdmVersion]_Check_Descriptions.csv. Note that "cdmTable", "cdmField" and "measureValueCompleteness" are always executed.
 #' @param cohortDefinitionId        The cohort definition id for the cohort you wish to run the DQD on. The package assumes a standard OHDSI cohort table
 #'                                  with the fields cohort_definition_id and subject_id.
@@ -77,6 +78,7 @@ executeDqChecks <- function(connectionDetails,
                             csvFile = "",
                             checkLevels = c("TABLE", "FIELD", "CONCEPT"),
                             checkNames = c(),
+                            checkSeverity = c("fatal", "convention", "characterization"),
                             cohortDefinitionId = c(),
                             cohortDatabaseSchema = resultsDatabaseSchema,
                             cohortTableName = "cohort",
@@ -110,7 +112,14 @@ executeDqChecks <- function(connectionDetails,
          You passed in ', paste(checkLevels, collapse = ", "))
   }
 
-  stopifnot(is.null(checkNames) | is.character(checkNames), is.null(tablesToExclude) | is.character(tablesToExclude))
+  if (!all(checkSeverity %in% c("fatal", "convention", "characterization"))) {
+    stop('checkSeverity argument must be a subset of c("fatal", "convention", "characterization").
+         You passed in ', paste(checkSeverity, collapse = ", "))
+  }
+
+  stopifnot(is.null(checkNames) | is.character(checkNames), 
+            is.character(checkSeverity),
+            is.null(tablesToExclude) | is.character(tablesToExclude))
   stopifnot(is.character(cdmVersion))
 
   # Warning if check names for determining NA is missing
@@ -241,6 +250,7 @@ executeDqChecks <- function(connectionDetails,
   })]
 
   checkDescriptionsDf <- checkDescriptionsDf[checkDescriptionsDf$checkLevel %in% checkLevels &
+    checkDescriptionsDf$severity %in% checkSeverity &                                               
     checkDescriptionsDf$evaluationFilter != "" &
     checkDescriptionsDf$sqlFile != "" &
     checkDescriptionsDf$checkName %in% checksToInclude, ]

tests/testthat/test-executeDqChecks.R

@@ -375,3 +375,24 @@ test_that("Execute checks on Synthea/Eunomia to test new variable executionTimeS
   )
   expect_true(is.numeric(results$executionTimeSeconds))
 })
+
+
+test_that("checkNames are filtered by checkSeverity", {
+  outputFolder <- tempfile("dqd_")
+  on.exit(unlink(outputFolder, recursive = TRUE))
+
+  results <- executeDqChecks(
+    connectionDetails = connectionDetailsEunomia,
+    cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
+    resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+    cdmSourceName = "Eunomia",
+    checkSeverity = "fatal",
+    outputFolder = outputFolder,
+    writeToTable = F
+  )
+
+  expectedCheckNames <- c("cdmTable", "cdmField", "isRequired", "cdmDatatype", 
+                          "isPrimaryKey", "isForeignKey") 
+  expect_true(all(results$CheckResults$checkName %in% expectedCheckNames)) 
+})
+

vignettes/DataQualityDashboard.rmd

@@ -101,6 +101,9 @@ checkLevels <- c("TABLE", "FIELD", "CONCEPT")
 # which DQ checks to run? ------------------------------------
 checkNames <- c() # Names can be found in inst/csv/OMOP_CDM_v5.3_Check_Descriptions.csv
 
+# which DQ severity levels to run? ----------------------------
+checkSeverity <- c("fatal", "convention", "characterization") 
+
 # want to EXCLUDE a pre-specified list of checks? run the following code:
 #
 # checksToExclude <- c() # Names of check types to exclude from your DQD run
@@ -129,6 +132,7 @@ DataQualityDashboard::executeDqChecks(connectionDetails = connectionDetails,
                               writeToCsv = writeToCsv,
                               csvFile = csvFile,
                               checkLevels = checkLevels,
+			      checkSeverity = checkSeverity,
                               tablesToExclude = tablesToExclude,
                               checkNames = checkNames)