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Custom check in seprate package. #401

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Custom check in seprate package. #401

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13 changes: 8 additions & 5 deletions R/executeDqChecks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
#' @param tableCheckThresholdLoc The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
#' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
#' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.
#'
#' @return If sqlOnly = FALSE, a list object of results
#'
Expand Down Expand Up @@ -77,7 +78,8 @@ executeDqChecks <- function(connectionDetails,
cdmVersion = "5.3",
tableCheckThresholdLoc = "default",
fieldCheckThresholdLoc = "default",
conceptCheckThresholdLoc = "default") {
conceptCheckThresholdLoc = "default",
systemFileNamespace = "DataQualityDashboard") {
# Check input -------------------------------------------------------------------------------------------------------------------
if (!("connectionDetails" %in% class(connectionDetails))){
stop("connectionDetails must be an object of class 'connectionDetails'.")
Expand Down Expand Up @@ -165,24 +167,25 @@ executeDqChecks <- function(connectionDetails,
file = system.file(
"csv",
sprintf("OMOP_CDMv%s_Check_Descriptions.csv", cdmVersion),
package = "DataQualityDashboard"
package = systemFileNamespace
),
stringsAsFactors = FALSE
)

tableChecks <- .readThresholdFile(
checkThresholdLoc = tableCheckThresholdLoc,
defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion)
defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion),
systemFileNamespace
)

fieldChecks <- .readThresholdFile(
checkThresholdLoc = fieldCheckThresholdLoc,
defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion)
defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion, systemFileNamespace)
)

conceptChecks <- .readThresholdFile(
checkThresholdLoc = conceptCheckThresholdLoc,
defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion)
defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion, systemFileNamespace)
)

# ensure we use only checks that are intended to be run -----------------------------------------
Expand Down
12 changes: 6 additions & 6 deletions R/listChecks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -25,16 +25,16 @@
#' @param tableCheckThresholdLoc The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
#' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
#' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
#'
#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.
#'
#' @export
listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default",conceptCheckThresholdLoc = "default") {
listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default",conceptCheckThresholdLoc = "default", systemFileNamespace = "DataQualityDashboard") {
dqChecks <- {}
dqChecks$checkDescriptions <-
read.csv(system.file(
"csv",
sprintf("OMOP_CDMv%s_Check_Descriptions.csv", cdmVersion),
package = "DataQualityDashboard"
package = systemFileNamespace
),
stringsAsFactors = FALSE)

Expand All @@ -45,7 +45,7 @@ listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default",
system.file(
"csv",
sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion),
package = "DataQualityDashboard"
package = systemFileNamespace
),
stringsAsFactors = FALSE,
na.strings = c(" ", "")
Expand All @@ -64,7 +64,7 @@ listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default",
system.file(
"csv",
sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion),
package = "DataQualityDashboard"
package = systemFileNamespace
),
stringsAsFactors = FALSE,
na.strings = c(" ", "")
Expand All @@ -83,7 +83,7 @@ listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default",
system.file(
"csv",
sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion),
package = "DataQualityDashboard"
package = systemFileNamespace
),
stringsAsFactors = FALSE,
na.strings = c(" ", "")
Expand Down
12 changes: 7 additions & 5 deletions R/reEvaluateThresholds.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,8 @@
#' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
#' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
#' @param cdmVersion The CDM version to target for the data source. By default, 5.3 is used.
#'
#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.
#'
#' @export

reEvaluateThresholds <- function(jsonFilePath,
Expand All @@ -36,7 +37,8 @@ reEvaluateThresholds <- function(jsonFilePath,
tableCheckThresholdLoc = "default",
fieldCheckThresholdLoc = "default",
conceptCheckThresholdLoc = "default",
cdmVersion = '5.3') {
cdmVersion = '5.3',
systemFileNamespace = "DataQualityDashboard") {
# Read in results to data frame --------------------------------------
dqdResults <- jsonlite::read_json(path = jsonFilePath)

Expand All @@ -47,10 +49,10 @@ reEvaluateThresholds <- function(jsonFilePath,
df <- do.call(plyr::rbind.fill, df)

# Read in new thresholds ----------------------------------------------
tableChecks <- .readThresholdFile(tableCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion))
fieldChecks <- .readThresholdFile(fieldCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion))
tableChecks <- .readThresholdFile(tableCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion), systemFileNamespace)
fieldChecks <- .readThresholdFile(fieldCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion), systemFileNamespace)
fieldChecks$cdmFieldName <- toupper(fieldChecks$cdmFieldName) # Uppercase in results, lowercase in threshold files
conceptChecks <- .readThresholdFile(conceptCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion))
conceptChecks <- .readThresholdFile(conceptCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion), systemFileNamespace)
conceptChecks$cdmFieldName <- toupper(conceptChecks$cdmFieldName)

newCheckResults <- .evaluateThresholds(df, tableChecks, fieldChecks, conceptChecks)
Expand Down
4 changes: 2 additions & 2 deletions R/readThresholdFile.R
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
.readThresholdFile <- function(checkThresholdLoc, defaultLoc) {
.readThresholdFile <- function(checkThresholdLoc, defaultLoc, systemFileNamespace = "DataQualityDashboard") {
if (checkThresholdLoc == "default") {
result <- read.csv(
file = system.file(
"csv",
defaultLoc,
package = "DataQualityDashboard"
package = systemFileNamespace
),
stringsAsFactors = FALSE,
na.strings = c(" ","")
Expand Down
4 changes: 3 additions & 1 deletion R/runCheck.R
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Original file line number Diff line number Diff line change
Expand Up @@ -50,9 +50,11 @@
setNames(check[c], c)
})

packageName <- if(!is.null(checkDescription$packageName)) checkDescription$packageName else "DataQualityDashboard"

params <- c(list(dbms = connectionDetails$dbms),
list(sqlFilename = checkDescription$sqlFile),
list(packageName = "DataQualityDashboard"),
list(packageName = packageName),
list(warnOnMissingParameters = FALSE),
list(cdmDatabaseSchema = cdmDatabaseSchema),
list(cohortDatabaseSchema = cohortDatabaseSchema),
Expand Down
14 changes: 8 additions & 6 deletions extras/execution.R
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,8 @@
#' @param tableCheckThresholdLoc The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
#' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
#' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
#'
#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.
#'
#' @return If sqlOnly = FALSE, a list object of results
#'
#' @importFrom magrittr %>%
Expand Down Expand Up @@ -192,7 +193,8 @@ executeDqChecks <- function(connectionDetails,
cdmVersion = "5.3.1",
tableCheckThresholdLoc = "default",
fieldCheckThresholdLoc = "default",
conceptCheckThresholdLoc = "default") {
conceptCheckThresholdLoc = "default",
systemFileNamespace = "DataQualityDashboard") {
# Check input -------------------------------------------------------------------------------------------------------------------
if (!("connectionDetails" %in% class(connectionDetails))){
stop("connectionDetails must be an object of class 'connectionDetails'.")
Expand Down Expand Up @@ -277,25 +279,25 @@ executeDqChecks <- function(connectionDetails,
startTime <- Sys.time()

checkDescriptionsDf <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Check_Descriptions.csv", cdmVersion),
package = "DataQualityDashboard"),
package = systemFileNamespace),
stringsAsFactors = FALSE)


if (tableCheckThresholdLoc == "default"){
tableChecks <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion),
package = "DataQualityDashboard"),
package = systemFileNamespace),
stringsAsFactors = FALSE, na.strings = c(" ",""))} else {tableChecks <- read.csv(tableCheckThresholdLoc,
stringsAsFactors = FALSE, na.strings = c(" ",""))}

if (fieldCheckThresholdLoc == "default"){
fieldChecks <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion),
package = "DataQualityDashboard"),
package = systemFileNamespace),
stringsAsFactors = FALSE, na.strings = c(" ",""))} else {fieldChecks <- read.csv(fieldCheckThresholdLoc,
stringsAsFactors = FALSE, na.strings = c(" ",""))}

if (conceptCheckThresholdLoc == "default"){
conceptChecks <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion),
package = "DataQualityDashboard"),
package = systemFileNamespace),
stringsAsFactors = FALSE, na.strings = c(" ",""))} else {conceptChecks <- read.csv(conceptCheckThresholdLoc,
stringsAsFactors = FALSE, na.strings = c(" ",""))}

Expand Down
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