Add more tests and comments

cBioPortal · Jul 12, 2023 · dc487c2 · dc487c2
1 parent fcac80a
commit dc487c2
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Showing 2 changed files with 20 additions and 13 deletions.
diff --git a/...atis/src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java b/...atis/src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java
@@ -135,16 +135,19 @@ public void getShallowSamplesByPatientId() {
 
     @Test
     public void hasTreatmentData() {
-        Boolean actual = treatmentRepository.hasTreatmentData(Collections.singletonList("study_tcga_pub"), ClinicalEventKeyCode.Agent);
-
-        Assert.assertEquals(actual, true);
+
+        Assert.assertEquals(true, treatmentRepository.hasTreatmentData(Collections.singletonList("study_tcga_pub"), ClinicalEventKeyCode.Agent));
+
+        Assert.assertEquals(false, treatmentRepository.hasTreatmentData(Collections.singletonList("acc_tcga"), ClinicalEventKeyCode.Agent));
+
     }
 
     @Test
-    public void getSampleCount() {
-        Boolean actual = treatmentRepository.hasSampleTimelineData(Collections.singletonList("study_tcga_pub"));
-
-        Assert.assertEquals(actual, true);
+    public void hasSampleTimelineData() {
+
+        Assert.assertEquals(true, treatmentRepository.hasSampleTimelineData(Collections.singletonList("study_tcga_pub")));
+
+        Assert.assertEquals(false, treatmentRepository.hasSampleTimelineData(Collections.singletonList("acc_tcga")));
     }
 
 }
diff --git a/service/src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java b/service/src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java
@@ -12,8 +12,6 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static java.util.stream.Collectors.*;
-
 @Service
 public class TreatmentServiceImpl implements TreatmentService {
     @Autowired
@@ -163,20 +161,26 @@ public List<PatientTreatmentRow> getAllPatientTreatmentRows(
 
         Map<String, List<Treatment>> treatmentSet = treatmentRepository.getTreatments(sampleIds, studyIds, key)
             .stream()
-            .collect(groupingBy(Treatment::getTreatment));
+            .collect(Collectors.groupingBy(Treatment::getTreatment));
 
+        /*
+            This logic transforms treatmentSet to list of PatientTreatmentRow. transformation steps:
+            - key in treatmentSet is going to be treatment
+            - get all unique patient ids -> this is going to give count
+            - get all clinicalEventSamples using above unique patient ids
+         */
         return treatmentSet.entrySet()
             .stream()
             .map(entry -> {
                 String treatment = entry.getKey();
-                Set<String> patientIds = entry.getValue().stream().map(Treatment::getPatientId).collect(toSet());
+                Set<String> patientIds = entry.getValue().stream().map(Treatment::getPatientId).collect(Collectors.toSet());
                 Set<ClinicalEventSample> clinicalEventSamples = patientIds
                     .stream()
                     .flatMap(patientId -> samplesByPatient.getOrDefault(patientId, new ArrayList<>()).stream())
-                    .collect(toSet());
+                    .collect(Collectors.toSet());
                 return new PatientTreatmentRow(treatment, patientIds.size(), clinicalEventSamples);
             })
-            .collect(toList());
+            .collect(Collectors.toList());
     }
 
     @Override