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More small bugfixes #502

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merged 2 commits into from
Nov 4, 2023
Merged

More small bugfixes #502

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5684275
fix bugs
katy-sadowski Nov 4, 2023
16990b4
test for cdm_source warning
katy-sadowski Nov 4, 2023
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2 changes: 1 addition & 1 deletion R/writeJsonResultsTo.R
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ writeJsonResultsToTable <- function(connectionDetails,

ParallelLogger::logInfo(sprintf("Writing results to table %s", tableName))

if ("unitConceptId" %in% colnames(df)) {
if ("conceptId" %in% colnames(df)) {
ddl <- SqlRender::loadRenderTranslateSql(
sqlFilename = "result_table_ddl_concept.sql",
packageName = "DataQualityDashboard",
Expand Down
6 changes: 3 additions & 3 deletions inst/sql/sql_server/field_fk_class.sql
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Expand Up @@ -4,7 +4,7 @@ FK_CLASS
Drug era standard concepts, ingredients only

Parameters used in this template:
cdmDatabaseSchema = @cdmDatabaseSchema
schema = @schema
vocabDatabaseSchema = @vocabDatabaseSchema
cdmTableName = @cdmTableName
cdmFieldName = @cdmFieldName
Expand Down Expand Up @@ -32,7 +32,7 @@ FROM (
SELECT
'@cdmTableName.@cdmFieldName' AS violating_field,
cdmTable.*
FROM @cdmDatabaseSchema.@cdmTableName cdmTable
FROM @schema.@cdmTableName cdmTable
LEFT JOIN @vocabDatabaseSchema.concept co
ON cdmTable.@cdmFieldName = co.concept_id
{@cohort & '@runForCohort' == 'Yes'}?{
Expand All @@ -48,7 +48,7 @@ FROM (
(
SELECT
COUNT_BIG(*) AS num_rows
FROM @cdmDatabaseSchema.@cdmTableName cdmTable
FROM @schema.@cdmTableName cdmTable
{@cohort & '@runForCohort' == 'Yes'}?{
JOIN @cohortDatabaseSchema.@cohortTableName c
ON cdmTable.person_id = c.subject_id
Expand Down
6 changes: 3 additions & 3 deletions inst/sql/sql_server/field_fk_domain.sql
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Expand Up @@ -5,7 +5,7 @@ FIELD_FK_DOMAIN
all standard concept ids are part of specified domain

Parameters used in this template:
cdmDatabaseSchema = @cdmDatabaseSchema
schema = @schema
vocabDatabaseSchema = @vocabDatabaseSchema
cdmTableName = @cdmTableName
cdmFieldName = @cdmFieldName
Expand All @@ -32,7 +32,7 @@ FROM (
SELECT
'@cdmTableName.@cdmFieldName' AS violating_field,
cdmTable.*
FROM @cdmDatabaseSchema.@cdmTableName cdmTable
FROM @schema.@cdmTableName cdmTable
LEFT JOIN @vocabDatabaseSchema.concept co
ON cdmTable.@cdmFieldName = co.concept_id
{@cohort & '@runForCohort' == 'Yes'}?{
Expand All @@ -48,7 +48,7 @@ FROM (
(
SELECT
COUNT_BIG(*) AS num_rows
FROM @cdmDatabaseSchema.@cdmTableName cdmTable
FROM @schema.@cdmTableName cdmTable
{@cohort & '@runForCohort' == 'Yes'}?{
JOIN @cohortDatabaseSchema.@cohortTableName c
ON cdmTable.PERSON_ID = c.SUBJECT_ID
Expand Down
10 changes: 5 additions & 5 deletions inst/sql/sql_server/field_plausible_temporal_after.sql
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Expand Up @@ -4,7 +4,7 @@ PLAUSIBLE_TEMPORAL_AFTER
get number of records and the proportion to total number of eligible records with datetimes that do not occur on or after their corresponding datetimes

Parameters used in this template:
cdmDatabaseSchema = @cdmDatabaseSchema
schema = @schema
cdmTableName = @cdmTableName
cdmFieldName = @cdmFieldName
plausibleTemporalAfterTableName = @plausibleTemporalAfterTableName
Expand Down Expand Up @@ -33,9 +33,9 @@ FROM
SELECT
'@cdmTableName.@cdmFieldName' AS violating_field,
cdmTable.*
FROM @cdmDatabaseSchema.@cdmTableName cdmTable
{@cdmDatabaseSchema.@cdmTableName != @cdmDatabaseSchema.@plausibleTemporalAfterTableName}?{
JOIN @cdmDatabaseSchema.@plausibleTemporalAfterTableName plausibleTable ON cdmTable.person_id = plausibleTable.person_id}
FROM @schema.@cdmTableName cdmTable
{@schema.@cdmTableName != @schema.@plausibleTemporalAfterTableName}?{
JOIN @schema.@plausibleTemporalAfterTableName plausibleTable ON cdmTable.person_id = plausibleTable.person_id}
{@cohort & '@runForCohort' == 'Yes'}?{
JOIN @cohortDatabaseSchema.@cohortTableName c ON cdmTable.person_id = c.subject_id
AND c.cohort_definition_id = @cohortDefinitionId
Expand All @@ -55,7 +55,7 @@ FROM
(
SELECT
COUNT_BIG(*) AS num_rows
FROM @cdmDatabaseSchema.@cdmTableName cdmTable
FROM @schema.@cdmTableName cdmTable
{@cohort & '@runForCohort' == 'Yes'}?{
JOIN @cohortDatabaseSchema.@cohortTableName c ON cdmTable.person_id = c.subject_id
AND c.cohort_definition_id = @cohortDefinitionId
Expand Down
27 changes: 27 additions & 0 deletions tests/testthat/test-executeDqChecks.R
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Expand Up @@ -328,3 +328,30 @@ test_that("Incremental insert SQL is valid.", {

DatabaseConnector::renderTranslateExecuteSql(connection, "DROP TABLE @database_schema.dqd_results;", database_schema = resultsDatabaseSchemaEunomia)
})

test_that("Multiple cdm_source rows triggers warning.", {
outputFolder <- tempfile("dqd_")
on.exit(unlink(outputFolder, recursive = TRUE))

connectionDetailsEunomiaCS <- Eunomia::getEunomiaConnectionDetails()
connection <- DatabaseConnector::connect(connectionDetailsEunomiaCS)
on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
DatabaseConnector::renderTranslateExecuteSql(connection, "INSERT INTO @database_schema.cdm_source VALUES ('foo',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);", database_schema = cdmDatabaseSchemaEunomia)

w <- capture_warnings(
results <- executeDqChecks(
connectionDetails = connectionDetailsEunomiaCS,
cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
cdmSourceName = "Eunomia",
checkNames = "measurePersonCompleteness",
outputFolder = outputFolder,
writeToTable = F
))

expect_match(w, "Missing check names", all = FALSE)
expect_match(w, "The cdm_source table has", all = FALSE)

expect_true(nrow(results$CheckResults) > 1)
})

2 changes: 1 addition & 1 deletion tests/testthat/test-writeDBResultsTo.R
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Expand Up @@ -6,7 +6,7 @@ test_that("Write DB results to json", {
connectionDetailsEunomia <- Eunomia::getEunomiaConnectionDetails()
cdmDatabaseSchemaEunomia <- "main"
resultsDatabaseSchemaEunomia <- "main"
writeTableName <- "dqdashboard_results"
writeTableName <- "dqd_db_results"

expect_warning(
results <- DataQualityDashboard::executeDqChecks(
Expand Down
6 changes: 3 additions & 3 deletions tests/testthat/test-writeJsonResultsTo.R
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Expand Up @@ -29,11 +29,11 @@ test_that("Write JSON results", {
connectionDetails = connectionDetailsEunomia,
resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
jsonFilePath = jsonPath,
writeTableName = "dqd_results"
writeTableName = "dqd_json_results"
)
connection <- DatabaseConnector::connect(connectionDetailsEunomia)
on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
tableNames <- DatabaseConnector::getTableNames(connection = connection, databaseSchema = resultsDatabaseSchemaEunomia)
expect_true("dqd_results" %in% tolower(tableNames))
DatabaseConnector::renderTranslateExecuteSql(connection, "DROP TABLE @database_schema.dqd_results;", database_schema = resultsDatabaseSchemaEunomia)
expect_true("dqd_json_results" %in% tolower(tableNames))
DatabaseConnector::renderTranslateExecuteSql(connection, "DROP TABLE @database_schema.dqd_json_results;", database_schema = resultsDatabaseSchemaEunomia)
})