fix: update RetrieveCohortOverlapStats method name

Author: pieterlukasse

controllers/cohortdata.go

@@ -241,7 +241,7 @@ func populateConceptValue(row []string, cohortItem models.PersonConceptAndValue,
 	return row
 }
 
-func (u CohortDataController) RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(c *gin.Context) {
+func (u CohortDataController) RetrieveCohortOverlapStats(c *gin.Context) {
 	errors := make([]error, 4)
 	var sourceId, caseCohortId, controlCohortId int
 	var conceptIds []int64
@@ -264,7 +264,7 @@ func (u CohortDataController) RetrieveCohortOverlapStatsWithoutFilteringOnConcep
 		c.Abort()
 		return
 	}
-	overlapStats, err := u.cohortDataModel.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(sourceId, caseCohortId,
+	overlapStats, err := u.cohortDataModel.RetrieveCohortOverlapStats(sourceId, caseCohortId,
 		controlCohortId, conceptIds, cohortPairs)
 	if err != nil {
 		c.JSON(http.StatusInternalServerError, gin.H{"message": "Error retrieving stats", "error": err.Error()})

models/cohortdata.go

@@ -9,7 +9,7 @@ import (
 
 type CohortDataI interface {
 	RetrieveDataBySourceIdAndCohortIdAndConceptIdsOrderedByPersonId(sourceId int, cohortDefinitionId int, conceptIds []int64) ([]*PersonConceptAndValue, error)
-	RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(sourceId int, caseCohortId int, controlCohortId int, otherFilterConceptIds []int64, filterCohortPairs []utils.CustomDichotomousVariableDef) (CohortOverlapStats, error)
+	RetrieveCohortOverlapStats(sourceId int, caseCohortId int, controlCohortId int, otherFilterConceptIds []int64, filterCohortPairs []utils.CustomDichotomousVariableDef) (CohortOverlapStats, error)
 	RetrieveDataByOriginalCohortAndNewCohort(sourceId int, originalCohortDefinitionId int, cohortDefinitionId int) ([]*PersonIdAndCohort, error)
 	RetrieveHistogramDataBySourceIdAndCohortIdAndConceptIdsAndCohortPairs(sourceId int, cohortDefinitionId int, histogramConceptId int64, filterConceptIds []int64, filterCohortPairs []utils.CustomDichotomousVariableDef) ([]*PersonConceptAndValue, error)
 }
@@ -110,21 +110,20 @@ func (h CohortData) RetrieveHistogramDataBySourceIdAndCohortIdAndConceptIdsAndCo
 }
 
 // Basically the same as the method above, but without the extra filtering on filterConceptId and filterConceptValue:
-func (h CohortData) RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(sourceId int, caseCohortId int, controlCohortId int,
-	otherFilterConceptIds []int64, filterCohortPairs []utils.CustomDichotomousVariableDef) (CohortOverlapStats, error) {
+func (h CohortData) RetrieveCohortOverlapStats(sourceId int, caseCohortId int, controlCohortId int,
+	filterConceptIds []int64, filterCohortPairs []utils.CustomDichotomousVariableDef) (CohortOverlapStats, error) {
 
 	var dataSourceModel = new(Source)
 	omopDataSource := dataSourceModel.GetDataSource(sourceId, Omop)
 	resultsDataSource := dataSourceModel.GetDataSource(sourceId, Results)
 
-	// count persons that are in the intersection of both case and control cohorts, filtering on filterConceptValue:
 	var cohortOverlapStats CohortOverlapStats
 	query := QueryFilterByCohortPairsHelper(filterCohortPairs, resultsDataSource, caseCohortId, "case_cohort_unionedAndIntersectedWithFilters").
 		Select("count(distinct(case_cohort_unionedAndIntersectedWithFilters.subject_id)) as case_control_overlap").
 		Joins("INNER JOIN " + resultsDataSource.Schema + ".cohort as control_cohort ON control_cohort.subject_id = case_cohort_unionedAndIntersectedWithFilters.subject_id") // this one allows for the intersection between case and control and the assessment of the overlap
 
-	if len(otherFilterConceptIds) > 0 {
-		query = QueryFilterByConceptIdsHelper2(query, sourceId, otherFilterConceptIds, omopDataSource, resultsDataSource.Schema, "control_cohort.subject_id")
+	if len(filterConceptIds) > 0 {
+		query = QueryFilterByConceptIdsHelper2(query, sourceId, filterConceptIds, omopDataSource, resultsDataSource.Schema, "control_cohort.subject_id")
 	}
 	query = query.Where("control_cohort.cohort_definition_id = ?", controlCohortId)
 	query, cancel := utils.AddTimeoutToQuery(query)

server/router.go

@@ -48,7 +48,7 @@ func NewRouter() *gin.Engine {
 		// cohort stats and checks:
 		cohortData := controllers.NewCohortDataController(*new(models.CohortData), middlewares.NewTeamProjectAuthz(*new(models.CohortDefinition), &http.Client{}))
 		// :casecohortid/:controlcohortid are just labels here and have no special meaning. Could also just be :cohortAId/:cohortBId here:
-		authorized.POST("/cohort-stats/check-overlap/by-source-id/:sourceid/by-cohort-definition-ids/:casecohortid/:controlcohortid", cohortData.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue)
+		authorized.POST("/cohort-stats/check-overlap/by-source-id/:sourceid/by-cohort-definition-ids/:casecohortid/:controlcohortid", cohortData.RetrieveCohortOverlapStats)
 
 		// full data endpoints:
 		authorized.POST("/cohort-data/by-source-id/:sourceid/by-cohort-definition-id/:cohortid", cohortData.RetrieveDataBySourceIdAndCohortIdAndVariables)

tests/controllers_tests/controllers_test.go

@@ -76,7 +76,7 @@ func (h dummyCohortDataModel) RetrieveHistogramDataBySourceIdAndCohortIdAndConce
 	return cohortData, nil
 }
 
-func (h dummyCohortDataModel) RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(sourceId int, caseCohortId int, controlCohortId int,
+func (h dummyCohortDataModel) RetrieveCohortOverlapStats(sourceId int, caseCohortId int, controlCohortId int,
 	otherFilterConceptIds []int64, filterCohortPairs []utils.CustomDichotomousVariableDef) (models.CohortOverlapStats, error) {
 	var zeroOverlap models.CohortOverlapStats
 	return zeroOverlap, nil
@@ -335,7 +335,7 @@ func TestRetrieveDataBySourceIdAndCohortIdAndVariablesCorrectParams(t *testing.T
 	}
 }
 
-func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T) {
+func TestRetrieveCohortOverlapStats(t *testing.T) {
 	setUp(t)
 	requestContext := new(gin.Context)
 	requestContext.Params = append(requestContext.Params, gin.Param{Key: "sourceid", Value: strconv.Itoa(tests.GetTestSourceId())})
@@ -346,7 +346,7 @@ func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T)
 	requestBody := "{\"variables\":[{\"variable_type\": \"concept\", \"concept_id\": 2000000324},{\"variable_type\": \"concept\", \"concept_id\": 2000006885}]}"
 	requestContext.Request.Body = io.NopCloser(strings.NewReader(requestBody))
 
-	cohortDataController.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(requestContext)
+	cohortDataController.RetrieveCohortOverlapStats(requestContext)
 	// Params above are correct, so request should NOT abort:
 	if requestContext.IsAborted() {
 		t.Errorf("Did not expect this request to abort")
@@ -358,7 +358,7 @@ func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T)
 
 	// the same request should fail if the teamProject authorization fails:
 	requestContext.Request.Body = io.NopCloser(strings.NewReader(requestBody))
-	cohortDataControllerWithFailingTeamProjectAuthz.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(requestContext)
+	cohortDataControllerWithFailingTeamProjectAuthz.RetrieveCohortOverlapStats(requestContext)
 	result = requestContext.Writer.(*tests.CustomResponseWriter)
 	// expect error:
 	if !strings.Contains(result.CustomResponseWriterOut, "access denied") {
@@ -369,13 +369,13 @@ func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T)
 	}
 }
 
-func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValueBadRequest(t *testing.T) {
+func TestRetrieveCohortOverlapStatsBadRequest(t *testing.T) {
 	setUp(t)
 	requestContext := new(gin.Context)
 	requestContext.Params = append(requestContext.Params, gin.Param{Key: "sourceid", Value: strconv.Itoa(tests.GetTestSourceId())})
 	requestContext.Writer = new(tests.CustomResponseWriter)
 
-	cohortDataController.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(requestContext)
+	cohortDataController.RetrieveCohortOverlapStats(requestContext)
 	// Params above are incorrect, so request should abort:
 	if !requestContext.IsAborted() {
 		t.Errorf("Expected this request to abort")

tests/models_tests/models_test.go

@@ -850,14 +850,14 @@ func TestErrorForRetrieveDataBySourceIdAndCohortIdAndConceptIdsOrderedByPersonId
 	tests.FixSomething(models.Results, "cohort", "cohort_definition_id")
 }
 
-func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T) {
+func TestRetrieveCohortOverlapStats(t *testing.T) {
 	// Tests if we get the expected overlap
 	setUp(t)
 	caseCohortId := secondLargestCohort.Id
 	controlCohortId := secondLargestCohort.Id // to ensure we get some overlap, just repeat the same here...
 	otherFilterConceptIds := []int64{}
 	filterCohortPairs := []utils.CustomDichotomousVariableDef{}
-	stats, _ := cohortDataModel.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(testSourceId, caseCohortId, controlCohortId,
+	stats, _ := cohortDataModel.RetrieveCohortOverlapStats(testSourceId, caseCohortId, controlCohortId,
 		otherFilterConceptIds, filterCohortPairs)
 	// basic test:
 	if stats.CaseControlOverlap != int64(secondLargestCohort.CohortSize) {
@@ -874,7 +874,7 @@ func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T)
 			ProvidedName:        "test"},
 	}
 	// then we expect overlap of 5 for extendedCopyOfSecondLargestCohort and largestCohort:
-	stats, _ = cohortDataModel.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(testSourceId, caseCohortId, controlCohortId,
+	stats, _ = cohortDataModel.RetrieveCohortOverlapStats(testSourceId, caseCohortId, controlCohortId,
 		otherFilterConceptIds, filterCohortPairs)
 	if stats.CaseControlOverlap != 5 {
 		t.Errorf("Expected nr persons to be %d, found %d", 5, stats.CaseControlOverlap)
@@ -887,7 +887,7 @@ func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T)
 	otherFilterConceptIds = []int64{histogramConceptId} // extra filter, to cover this part of the code...
 	// then we expect overlap of 5 for extendedCopyOfSecondLargestCohort and largestCohort (the filter on histogramConceptId should not matter
 	// since all in largestCohort have an observation for this concept id):
-	stats2, _ := cohortDataModel.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(testSourceId, caseCohortId, controlCohortId,
+	stats2, _ := cohortDataModel.RetrieveCohortOverlapStats(testSourceId, caseCohortId, controlCohortId,
 		otherFilterConceptIds, filterCohortPairs)
 	if stats2.CaseControlOverlap != stats.CaseControlOverlap {
 		t.Errorf("Expected nr persons to be %d, found %d", stats.CaseControlOverlap, stats2.CaseControlOverlap)
@@ -898,7 +898,7 @@ func TestRetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(t *testing.T)
 	otherFilterConceptIds = []int64{histogramConceptId, dummyContinuousConceptId}
 	// all other arguments are the same as test above, and we expect overlap of 0, showing the otherFilterConceptIds
 	// had the expected effect:
-	stats3, _ := cohortDataModel.RetrieveCohortOverlapStatsWithoutFilteringOnConceptValue(testSourceId, caseCohortId, controlCohortId,
+	stats3, _ := cohortDataModel.RetrieveCohortOverlapStats(testSourceId, caseCohortId, controlCohortId,
 		otherFilterConceptIds, filterCohortPairs)
 	if stats3.CaseControlOverlap != 0 {
 		t.Errorf("Expected nr persons to be 0, found %d", stats3.CaseControlOverlap)