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|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| Package: DataQualityDashboard | ||
| Type: Package | ||
| Title: Execute and View Data Quality Checks on OMOP CDM Database | ||
| Version: 2.6.0 | ||
| Date: 2024-02-21 | ||
| Version: 2.6.1 | ||
| Date: 2024-07-12 | ||
| Authors@R: c( | ||
| person("Katy", "Sadowski", email = "[email protected]", role = c("aut", "cre")), | ||
| person("Clair", "Blacketer", role = c("aut")), | ||
|
|
@@ -44,7 +44,5 @@ Suggests: | |
| ggplot2, | ||
| Eunomia, | ||
| R.utils | ||
| Remotes: | ||
| ohdsi/Eunomia | ||
| RoxygenNote: 7.2.2 | ||
| RoxygenNote: 7.3.1 | ||
| Encoding: UTF-8 | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,195 @@ | ||
| # Copyright 2024 Observational Health Data Sciences and Informatics | ||
| # | ||
| # This file is part of DataQualityDashboard | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
|
|
||
| #' Determines if all checks are present expected to calculate the 'Not Applicable' status | ||
| #' | ||
| #' @param checkResults A dataframe containing the results of the data quality checks | ||
| #' | ||
| #' @keywords internal | ||
| .hasNAchecks <- function(checkResults) { | ||
| checkNames <- unique(checkResults$checkName) | ||
| return(.containsNAchecks(checkNames)) | ||
| } | ||
|
|
||
| #' Determines if all checks required for 'Not Applicable' status are in the checkNames | ||
| #' | ||
| #' @param checkNames A character vector of check names | ||
| #' | ||
| #' @keywords internal | ||
| .containsNAchecks <- function(checkNames) { | ||
| naCheckNames <- c("cdmTable", "cdmField", "measureValueCompleteness") | ||
| missingNAChecks <- !(naCheckNames %in% checkNames) | ||
| if (any(missingNAChecks)) { | ||
| return(FALSE) | ||
| } | ||
| return(TRUE) | ||
| } | ||
|
|
||
| #' Applies the 'Not Applicable' status to a single check | ||
| #' | ||
| #' @param x Results from a single check | ||
| #' | ||
| #' @keywords internal | ||
| .applyNotApplicable <- function(x) { | ||
| # Errors precede all other statuses | ||
| if (x$isError == 1) { | ||
| return(0) | ||
| } | ||
|
|
||
| # No NA status for cdmTable and cdmField if missing | ||
| if (x$checkName == "cdmTable" || x$checkName == "cdmField") { | ||
| return(0) | ||
| } | ||
|
|
||
| if (any(x$tableIsMissing, x$fieldIsMissing, x$tableIsEmpty, na.rm = TRUE)) { | ||
| return(1) | ||
| } | ||
|
|
||
| # No NA status for measureValueCompleteness if empty | ||
| if (x$checkName == "measureValueCompleteness") { | ||
| return(0) | ||
| } | ||
|
|
||
| if (any(x$fieldIsEmpty, x$conceptIsMissing, x$conceptAndUnitAreMissing, na.rm = TRUE)) { | ||
| return(1) | ||
| } | ||
|
|
||
| return(0) | ||
| } | ||
|
|
||
| #' Determines if check should be notApplicable and the notApplicableReason | ||
| #' | ||
| #' @param checkResults A dataframe containing the results of the data quality checks | ||
| #' | ||
| #' @keywords internal | ||
| .calculateNotApplicableStatus <- function(checkResults) { | ||
| # Look up missing tables and add variable tableIsMissing to checkResults | ||
| missingTables <- checkResults %>% | ||
| dplyr::filter( | ||
| .data$checkName == "cdmTable" | ||
| ) %>% | ||
| dplyr::mutate( | ||
| .data$cdmTableName, | ||
| tableIsMissing = .data$failed == 1, | ||
| .keep = "none" | ||
| ) | ||
|
|
||
| # Look up missing fields and add variable fieldIsMissing to checkResults | ||
| missingFields <- checkResults %>% | ||
| dplyr::filter( | ||
| .data$checkName == "cdmField" | ||
| ) %>% | ||
| dplyr::mutate( | ||
| .data$cdmTableName, | ||
| .data$cdmFieldName, | ||
| fieldIsMissing = .data$failed == 1, | ||
| .keep = "none" | ||
| ) | ||
|
|
||
| # Look up empty tables and add variable tableIsEmpty to checkResults | ||
| emptyTables <- checkResults %>% | ||
| dplyr::filter( | ||
| .data$checkName == "measureValueCompleteness" | ||
| ) %>% | ||
| dplyr::mutate( | ||
| .data$cdmTableName, | ||
| tableIsEmpty = .data$numDenominatorRows == 0, | ||
| .keep = "none" | ||
| ) %>% | ||
| dplyr::distinct() | ||
|
|
||
| # Look up empty fields and add variable fieldIsEmpty to checkResults | ||
| emptyFields <- checkResults %>% | ||
| dplyr::filter( | ||
| .data$checkName == "measureValueCompleteness" | ||
| ) %>% | ||
| dplyr::mutate( | ||
| .data$cdmTableName, | ||
| .data$cdmFieldName, | ||
| fieldIsEmpty = .data$numDenominatorRows == .data$numViolatedRows, | ||
| .keep = "none" | ||
| ) | ||
|
|
||
| # Assign notApplicable status | ||
| checkResults <- checkResults %>% | ||
| dplyr::left_join( | ||
| missingTables, | ||
| by = "cdmTableName" | ||
| ) %>% | ||
| dplyr::left_join( | ||
| missingFields, | ||
| by = c("cdmTableName", "cdmFieldName") | ||
| ) %>% | ||
| dplyr::left_join( | ||
| emptyTables, | ||
| by = "cdmTableName" | ||
| ) %>% | ||
| dplyr::left_join( | ||
| emptyFields, | ||
| by = c("cdmTableName", "cdmFieldName") | ||
| ) %>% | ||
| dplyr::mutate( | ||
| conceptIsMissing = .data$checkLevel == "CONCEPT" & is.na(.data$unitConceptId) & .data$numDenominatorRows == 0, | ||
| conceptAndUnitAreMissing = .data$checkLevel == "CONCEPT" & !is.na(.data$unitConceptId) & .data$numDenominatorRows == 0, | ||
| fieldIsMissing = dplyr::coalesce(.data$fieldIsMissing, !is.na(.data$cdmFieldName)), | ||
| fieldIsEmpty = dplyr::coalesce(.data$fieldIsEmpty, !is.na(.data$cdmFieldName)), | ||
| ) | ||
|
|
||
| checkResults$notApplicable <- NA | ||
| checkResults$notApplicableReason <- NA | ||
|
|
||
| conditionOccurrenceIsMissing <- missingTables %>% | ||
| dplyr::filter(.data$cdmTableName == "CONDITION_OCCURRENCE") %>% | ||
| dplyr::pull(.data$tableIsMissing) | ||
| conditionOccurrenceIsEmpty <- emptyTables %>% | ||
| dplyr::filter(.data$cdmTableName == "CONDITION_OCCURRENCE") %>% | ||
| dplyr::pull(.data$tableIsEmpty) | ||
| for (i in seq_len(nrow(checkResults))) { | ||
| # Special rule for measureConditionEraCompleteness, which should be notApplicable if CONDITION_OCCURRENCE is empty | ||
| if (checkResults[i, "checkName"] == "measureConditionEraCompleteness") { | ||
| if (conditionOccurrenceIsMissing || conditionOccurrenceIsEmpty) { | ||
| checkResults$notApplicable[i] <- 1 | ||
| checkResults$notApplicableReason[i] <- "Table CONDITION_OCCURRENCE is empty." | ||
| } else { | ||
| checkResults$notApplicable[i] <- 0 | ||
| } | ||
| } else { | ||
| checkResults$notApplicable[i] <- .applyNotApplicable(checkResults[i, ]) | ||
| } | ||
| } | ||
|
|
||
| checkResults <- checkResults %>% | ||
| dplyr::mutate( | ||
| notApplicableReason = ifelse( | ||
| .data$notApplicable == 1, | ||
| dplyr::case_when( | ||
| !is.na(.data$notApplicableReason) ~ .data$notApplicableReason, | ||
| .data$tableIsMissing ~ sprintf("Table %s does not exist.", .data$cdmTableName), | ||
| .data$fieldIsMissing ~ sprintf("Field %s.%s does not exist.", .data$cdmTableName, .data$cdmFieldName), | ||
| .data$tableIsEmpty ~ sprintf("Table %s is empty.", .data$cdmTableName), | ||
| .data$fieldIsEmpty ~ sprintf("Field %s.%s is not populated.", .data$cdmTableName, .data$cdmFieldName), | ||
| .data$conceptIsMissing ~ sprintf("%s=%s is missing from the %s table.", .data$cdmFieldName, .data$conceptId, .data$cdmTableName), | ||
| .data$conceptAndUnitAreMissing ~ sprintf("Combination of %s=%s, unitConceptId=%s and VALUE_AS_NUMBER IS NOT NULL is missing from the %s table.", .data$cdmFieldName, .data$conceptId, .data$unitConceptId, .data$cdmTableName) # nolint | ||
| ), | ||
| NA | ||
| ), | ||
| failed = ifelse(.data$notApplicable == 1, 0, .data$failed), | ||
| passed = ifelse(.data$failed == 0 & .data$isError == 0 & .data$notApplicable == 0, 1, 0) | ||
| ) %>% | ||
| dplyr::select(-c("tableIsMissing", "fieldIsMissing", "tableIsEmpty", "fieldIsEmpty", "conceptIsMissing", "conceptAndUnitAreMissing")) | ||
|
|
||
| return(checkResults) | ||
| } |
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