Merge pull request #502 from katy-sadowski/katy__schema_param

More small bugfixes
OHDSI · Nov 4, 2023 · b3a1f5e · b3a1f5e
2 parents eb295b0 + 16990b4
commit b3a1f5e
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Showing 7 changed files with 43 additions and 16 deletions.
diff --git a/R/writeJsonResultsTo.R b/R/writeJsonResultsTo.R
@@ -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",

diff --git a/inst/sql/sql_server/field_fk_class.sql b/inst/sql/sql_server/field_fk_class.sql
@@ -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
@@ -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'}?{
@@ -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

diff --git a/inst/sql/sql_server/field_fk_domain.sql b/inst/sql/sql_server/field_fk_domain.sql
@@ -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
@@ -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'}?{
@@ -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

diff --git a/inst/sql/sql_server/field_plausible_temporal_after.sql b/inst/sql/sql_server/field_plausible_temporal_after.sql
@@ -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
@@ -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
@@ -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 

diff --git a/tests/testthat/test-executeDqChecks.R b/tests/testthat/test-executeDqChecks.R
@@ -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)
+})
+
diff --git a/tests/testthat/test-writeDBResultsTo.R b/tests/testthat/test-writeDBResultsTo.R
@@ -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(

diff --git a/tests/testthat/test-writeJsonResultsTo.R b/tests/testthat/test-writeJsonResultsTo.R
@@ -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)
 })