wip - fix unit tests

cBioPortal · Jan 3, 2025 · 96e2bd8 · 96e2bd8
1 parent 82cc2b6
commit 96e2bd8
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Showing 2 changed files with 47 additions and 53 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/FederatedDataSourceService.java b/src/main/java/org/cbioportal/service/impl/FederatedDataSourceService.java
@@ -2,6 +2,7 @@
 
 import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalDataBin;
+import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.persistence.fedapi.FederatedDataSource;
 import org.cbioportal.persistence.fedapi.FederatedDataSourceImpl;
@@ -26,6 +27,9 @@
 @Service
 @ConditionalOnProperty(name = "fedapi.mode", havingValue = "DATASOURCE")
 public class FederatedDataSourceService implements FederatedService {
+
+    @Value("fedapi.datasource.display-name")
+    private String displayName;
 
     @Value("#{'${fedapi.datasource.visible-studies}'.split(',')}")
     private List<String> visibleStudies;
@@ -47,7 +51,24 @@ public class FederatedDataSourceService implements FederatedService {
 
     @Override
     public List<ClinicalAttribute> fetchClinicalAttributes() {
-        return clinicalAttributeService.fetchClinicalAttributes(this.visibleStudies, "SUMMARY");
+        var result = clinicalAttributeService.fetchClinicalAttributes(visibleStudies, "SUMMARY");
+        return addDataSourceToClinicalAttributes(result);
+    }
+
+    private List<ClinicalAttribute> addDataSourceToClinicalAttributes(List<ClinicalAttribute> result) {
+        for (String studyId : visibleStudies) {
+            var dataSourceAttr = new ClinicalAttribute();
+            dataSourceAttr.setAttrId("DATA_SOURCE");
+            dataSourceAttr.setPatientAttribute(false);
+            dataSourceAttr.setPriority("1");
+            dataSourceAttr.setCancerStudyIdentifier(studyId);
+            dataSourceAttr.setDatatype("STRING");
+            dataSourceAttr.setDescription("Name of the federated data source this sample originated from.");
+            dataSourceAttr.setDisplayName("Data Source");
+
+            result.add(dataSourceAttr);
+        }
+        return result;
     }
 
     @Override
@@ -58,6 +79,23 @@ public List<ClinicalDataCountItem> fetchClinicalDataCounts(
         filter.getStudyViewFilter().setStudyIds(visibleStudies);
         return cachedClinicalDataCounts(filter);
     }
+
+    private List<ClinicalDataCountItem> addDataSourceToClinicalDataCounts(
+        List<ClinicalDataCountItem> result,
+        int sampleCount
+    ) {
+        var dataSourceCount = new ClinicalDataCount();
+        dataSourceCount.setAttributeId("DATA_SOURCE");
+        dataSourceCount.setValue(displayName);
+        dataSourceCount.setCount(sampleCount);
+
+        var dataSourceCountItem = new ClinicalDataCountItem();
+        dataSourceCountItem.setAttributeId("DATA_SOURCE");
+        dataSourceCountItem.setCounts(List.of(dataSourceCount));
+
+        result.add(dataSourceCountItem);
+        return result;
+    }
 
     public List<ClinicalDataCountItem> cachedClinicalDataCounts(ClinicalDataCountFilter interceptedClinicalDataCountFilter) {
         List<ClinicalDataFilter> attributes = interceptedClinicalDataCountFilter.getAttributes();
@@ -77,6 +115,7 @@ public List<ClinicalDataCountItem> cachedClinicalDataCounts(ClinicalDataCountFil
         List<ClinicalDataCountItem> result = clinicalDataService.fetchClinicalDataCounts(
             studyIds, sampleIds, attributes.stream().map(a -> a.getAttributeId()).collect(Collectors.toList()));
 
+        result = addDataSourceToClinicalDataCounts(result, sampleIds.size());
         return result;
     }
 
@@ -97,14 +136,4 @@ public List<ClinicalDataBin> cachedFetchClinicalDataBinCounts(ClinicalDataBinCou
             false
         );
     }
-
-    private List<String> filterStudyIds(List<String> requestedStudyIds) {
-        var result = new ArrayList<String>();
-        for (String studyId : requestedStudyIds) {
-            if (visibleStudies.contains(studyId)) {
-                result.add(studyId);
-            }
-        }
-        return requestedStudyIds;
-    }
 }
diff --git a/src/test/java/org/cbioportal/service/impl/FederatedDataSourceServiceTest.java b/src/test/java/org/cbioportal/service/impl/FederatedDataSourceServiceTest.java
@@ -128,41 +128,6 @@ public void setup() {
         // This is necessary for initializing Mockito mocks pre-JUnit 4.5
         // See: https://stackoverflow.com/a/15494996/4077294
         MockitoAnnotations.initMocks(this);
-
-//        List<Sample> samples = mockSamples();
-//
-//        // Methods used by fetchClinicalDataCounts
-//
-//        // When cross-checking list of attributes requested
-//        when(
-//            clinicalAttributeRepository.getClinicalAttributesByStudyIdsAndAttributeIds(
-//                /* studyIds */ any(),
-//                /* attributeIds */ any()
-//            )
-//        ).thenReturn(mockClinicalAttributes());
-
-//        // When applying the study view filter to get a list of samples
-//        when(
-//            sampleRepository.fetchSamples(
-//                /* studyIds */ any(),
-//                /* sampleIds */ any(),
-//                /* projection */ any()
-//            )
-//        ).thenReturn(samples);
-//
-//        // When tallying the counts
-//        when(
-//            clinicalDataRepository.fetchClinicalDataCounts(
-//                /* studyIds */ any(),
-//                /* sampleIds */ any(),
-//                /* attributeIds */ any(),
-//                /* clinicalDataType */ any(),
-//                /* projection */ any()
-//            )
-//        ).thenReturn(...);
-//
-//        // Methods used by fetchClinicalDataBinCounts
-
     }
 
     private List<ClinicalAttribute> mockPatientAttributes() {
@@ -443,7 +408,7 @@ public void fetchClinicalAttributes() {
                 /* studyIds */ eq(VISIBLE_STUDIES),
                 /* projection */ eq("SUMMARY")
             )
-        ).thenReturn(attribs);
+        ).thenReturn(new ArrayList<>(attribs)); // create a copy so the original does not get modified
 
         var result = federatedDataSourceService.fetchClinicalAttributes();
 
@@ -468,7 +433,7 @@ public void fetchClinicalDataCounts() {
                 /* studyIds */ any(),
                 /* attributeIds */ any()
             )
-        ).thenReturn(attribs);
+        ).thenReturn(new ArrayList<>(attribs));
 
         // When applying the study view filter to get a list of samples
         when(
@@ -480,7 +445,7 @@ public void fetchClinicalDataCounts() {
                 /* sortBy */ isNull(),
                 /* direction */ isNull()
             )
-        ).thenReturn(samples);
+        ).thenReturn(new ArrayList<>(samples));
 
         // When tallying the counts
         when(
@@ -499,7 +464,7 @@ public void fetchClinicalDataCounts() {
                 /* studyIds */ any(),
                 /* sampleIds */ any()
             )
-        ).thenReturn(patients);
+        ).thenReturn(new ArrayList<>(patients));
 
         var result = federatedDataSourceService.fetchClinicalDataCounts(filter);
 
@@ -532,7 +497,7 @@ public void fetchClinicalDataBinCounts() {
                 /* studyIds */ any(),
                 /* attributeIds */ any()
             )
-        ).thenReturn(attribs);
+        ).thenReturn(new ArrayList<>(attribs));
 
         // When applying the study view filter to get a list of samples
         when(
@@ -544,7 +509,7 @@ public void fetchClinicalDataBinCounts() {
                 /* sortBy */ isNull(),
                 /* direction */ isNull()
             )
-        ).thenReturn(samples);
+        ).thenReturn(new ArrayList<>(samples));
 
         // When fetching clinical data for the samples pre-binning
         when(
@@ -563,7 +528,7 @@ public void fetchClinicalDataBinCounts() {
                 /* studyIds */ any(),
                 /* sampleIds */ any()
             )
-        ).thenReturn(patients);
+        ).thenReturn(new ArrayList<>(patients));
 
         var result = federatedDataSourceService.fetchClinicalDataBinCounts(filter);