moved all code needed for testing the custom gorm type ConceptType in…

…to the test functions previous test code was forcing the RetriveAllBySourceId to query both concept_class_id next to the mapping for modified ConceptType
uc-cdis · May 11, 2022 · 4001cc3 · 4001cc3
1 parent 9092888
commit 4001cc3
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Showing 3 changed files with 75 additions and 23 deletions.
diff --git a/models/concept.go b/models/concept.go
@@ -13,12 +13,11 @@ type ConceptI interface {
 	RetrieveBreakdownStatsBySourceIdAndCohortIdAndConceptIds(sourceId int, cohortDefinitionId int, filterConceptIds []int, breakdownConceptId int) ([]*ConceptBreakdown, error)
 }
 type Concept struct {
-	ConceptId      int         `json:"concept_id"`
-	ConceptName    string      `json:"concept_name"`
-	DomainId       string      `json:"domain_id"`
-	DomainName     string      `json:"domain_name"`
-	ConceptClassId string      `json:"concept_class_id"`
-	ConceptType    ConceptType `json:"concept_type"`
+	ConceptId   int         `json:"concept_id"`
+	ConceptName string      `json:"concept_name"`
+	DomainId    string      `json:"domain_id"`
+	DomainName  string      `json:"domain_name"`
+	ConceptType ConceptType `json:"concept_type"`
 }
 
 type ConceptAndPersonsWithDataStats struct {
@@ -27,23 +26,23 @@ type ConceptAndPersonsWithDataStats struct {
 }
 
 type ConceptStats struct {
-	ConceptId         int     `json:"concept_id"`
-	PrefixedConceptId string  `json:"prefixed_concept_id"`
-	ConceptName       string  `json:"concept_name"`
-	DomainId          string  `json:"domain_id"`
-	DomainName        string  `json:"domain_name"`
-	ConceptType       string  `json:"concept_type"`
-	CohortSize        int     `json:"cohort_size"`
-	NmissingRatio     float32 `json:"n_missing_ratio"`
+	ConceptId         int         `json:"concept_id"`
+	PrefixedConceptId string      `json:"prefixed_concept_id"`
+	ConceptName       string      `json:"concept_name"`
+	DomainId          string      `json:"domain_id"`
+	DomainName        string      `json:"domain_name"`
+	ConceptType       ConceptType `json:"concept_type"`
+	CohortSize        int         `json:"cohort_size"`
+	NmissingRatio     float32     `json:"n_missing_ratio"`
 }
 
 type ConceptSimple struct {
-	ConceptId         int    `json:"concept_id"`
-	PrefixedConceptId string `json:"prefixed_concept_id"`
-	ConceptName       string `json:"concept_name"`
-	DomainId          string `json:"domain_id"`
-	DomainName        string `json:"domain_name"`
-	ConceptType       string `json:"concept_type"`
+	ConceptId         int         `json:"concept_id"`
+	PrefixedConceptId string      `json:"prefixed_concept_id"`
+	ConceptName       string      `json:"concept_name"`
+	DomainId          string      `json:"domain_id"`
+	DomainName        string      `json:"domain_name"`
+	ConceptType       ConceptType `json:"concept_type"`
 }
 
 type ConceptBreakdown struct {
@@ -60,7 +59,7 @@ func (h Concept) RetriveAllBySourceId(sourceId int) ([]*Concept, error) {
 
 	var concepts []*Concept
 	result := omopDataSource.Db.Model(&Concept{}).
-		Select("concept_id, concept_name, domain.domain_id, domain.domain_name, concept_class_id, concept_class_id as concept_type").
+		Select("concept_id, concept_name, domain.domain_id, domain.domain_name, concept_class_id as concept_type").
 		Joins("INNER JOIN " + omopDataSource.Schema + ".domain as domain ON concept.domain_id = domain.domain_id").
 		Order("concept_name").
 		Scan(&concepts)

diff --git a/tests/models_tests/models_test.go b/tests/models_tests/models_test.go
@@ -103,12 +103,34 @@ func TestRetriveAllBySourceId(t *testing.T) {
 	if len(concepts) != 4 {
 		t.Errorf("Found %d", len(concepts))
 	}
-	if concepts[0].ConceptType == "?" {
-		t.Errorf("Expected ConceptType value, Found '?' as value instead'")
+	if strings.Contains(string(concepts[0].ConceptType), "unexpected missing value") {
+		t.Errorf("Expected ConceptType value, Found 'missing value' instead'")
 	}
 	if strings.Contains(string(concepts[0].ConceptType), "_") || len(concepts[0].ConceptType) == 0 {
 		t.Errorf("Expected ConceptType value to be length > 0 and not contain _, but found %s", concepts[0].ConceptType)
 	}
+}
+
+type TestConceptFields struct {
+	ConceptClassId string
+	ConceptType    models.ConceptType
+}
+
+func TestCustomGormDataTypeConceptType(t *testing.T) {
+	setUp(t)
+	var concepts []*TestConceptFields
+	omopDataSource := tests.GetOmopDataSource()
+	// in this test we want to check if the custom ConceptType field is indeed a subset of concept_class_id,
+	// so we query both concept_class_id and "concept_class_id as concept_type" (this last one should result in transformed
+	// values after Scan() is done):
+	omopDataSource.Db.Model(&models.Concept{}).
+		Select("concept_class_id, concept_class_id as concept_type").
+		Scan(&concepts)
+
+	if len(concepts) != 4 {
+		t.Errorf("Found %d", len(concepts))
+	}
+
 	// in the current version we extract the concept type from concept class id (see models/customgormtypes.go). This test
 	// ensures this is the case:
 	for _, concept := range concepts {
@@ -118,6 +140,29 @@ func TestRetriveAllBySourceId(t *testing.T) {
 	}
 }
 
+func TestCustomGormDataTypeConceptTypeWrongMapping(t *testing.T) {
+	setUp(t)
+	var concepts []*TestConceptFields
+	omopDataSource := tests.GetOmopDataSource()
+	// in this test we want to check if the custom ConceptType field contains an error if the mapping
+	// is made from another field that does not contain the expected format.
+	omopDataSource.Db.Model(&models.Concept{}).
+		Select("concept_class_id, concept_name as concept_type").
+		Scan(&concepts)
+
+	if len(concepts) != 4 {
+		t.Errorf("Found %d", len(concepts))
+	}
+
+	// in the current version we extract the concept type from concept class id (see models/customgormtypes.go). This test
+	// ensures this is the case:
+	for _, concept := range concepts {
+		if !strings.Contains(string(concept.ConceptType), "unexpected missing value") {
+			t.Errorf("The ConceptType should contain 'missing value' error in this case")
+		}
+	}
+}
+
 func TestRetrieveStatsBySourceIdAndCohortIdAndConceptIds(t *testing.T) {
 	setUp(t)
 	conceptsStats, _ := conceptModel.RetrieveStatsBySourceIdAndCohortIdAndConceptIds(testSourceId,

diff --git a/tests/testutils.go b/tests/testutils.go
@@ -11,6 +11,7 @@ import (
 
 	"github.com/uc-cdis/cohort-middleware/db"
 	"github.com/uc-cdis/cohort-middleware/models"
+	"github.com/uc-cdis/cohort-middleware/utils"
 )
 
 func GetTestSourceId() int {
@@ -58,6 +59,12 @@ func ExecSQLString(sqlString string, sourceId int) {
 	}
 }
 
+func GetOmopDataSource() *utils.DbAndSchema {
+	var dataSourceModel = new(models.Source)
+	omopDataSource := dataSourceModel.GetDataSource(GetTestSourceId(), models.Omop)
+	return omopDataSource
+}
+
 func GetSchemaNameForType(sourceType models.SourceType) string {
 	sourceModel := new(models.Source)
 	dbSchema, _ := sourceModel.GetSourceSchemaNameBySourceIdAndSourceType(GetTestSourceId(), sourceType)
@@ -84,6 +91,7 @@ func GetIntAttributeValue[T any](item T, attributeName string) int {
 
 // returns an int array with the attribute values of the given attribute
 // for each item in "items" array.
+// TODO - can also simply be done wit something like: db.Model(&users).Pluck("age", &ages), where var ages []int64
 func MapIntAttr[T any](items []T, attributeName string) []int {
 	result := make([]int, len(items))
 	for i := range items {