Update unit tests for GENIE treatment fix

cBioPortal · Jan 27, 2023 · 86e7402 · 86e7402
1 parent 9e01993
commit 86e7402
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Showing 2 changed files with 21 additions and 4 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
@@ -76,22 +76,38 @@ public void getTreatmentAgentsByPatientId() {
     }
 
     @Test
-    public void getSamplesByPatientId() {
+    public void getSamplesByPatientIdWhenNoMatchingSamples() {
         ClinicalEventSample clinicalEventSample = new ClinicalEventSample();
         clinicalEventSample.setPatientId("TCGA-A1-A0SD");
         clinicalEventSample.setSampleId("TCGA-A1-A0SD-01");
         clinicalEventSample.setStudyId("study_tcga_pub");
         clinicalEventSample.setTimeTaken(211);
 
         HashMap<String, List<ClinicalEventSample>> expected = new HashMap<>();
-        expected.put("TCGA-A1-A0SD", Collections.singletonList(clinicalEventSample));
-
 
         Map<String, List<ClinicalEventSample>> actual = treatmentRepository.getSamplesByPatientId(
             Collections.singletonList("TCGA-A1-A0SD-01"),
             Collections.singletonList("study_tcga_pub")
         );
+
+        Assert.assertEquals(actual, expected);
+    }
 
+    @Test
+    public void getSamplesByPatientId() {
+        ClinicalEventSample clinicalEventSample = new ClinicalEventSample();
+        clinicalEventSample.setPatientId("TCGA-A1-A0SB");
+        clinicalEventSample.setSampleId("TCGA-A1-A0SB-01");
+        clinicalEventSample.setStudyId("study_tcga_pub");
+        clinicalEventSample.setTimeTaken(211);
+
+        HashMap<String, List<ClinicalEventSample>> expected = new HashMap<>();
+        expected.put("TCGA-A1-A0SB", Collections.singletonList(clinicalEventSample));
+
+        Map<String, List<ClinicalEventSample>> actual = treatmentRepository.getSamplesByPatientId(
+            Collections.singletonList("TCGA-A1-A0SB-01"),
+            Collections.singletonList("study_tcga_pub")
+        );
 
         Assert.assertEquals(actual, expected);
     }
@@ -140,7 +156,7 @@ public void getTreatmentCount() {
 
     @Test
     public void getSampleCount() {
-        Integer expected = 4;
+        Integer expected = 2;
         Integer actual = treatmentRepository.getSampleCount(Collections.singletonList("study_tcga_pub"));
 
         Assert.assertEquals(actual, expected);

diff --git a/persistence/persistence-mybatis/src/test/resources/testSql.sql b/persistence/persistence-mybatis/src/test/resources/testSql.sql
@@ -452,6 +452,7 @@ INSERT INTO clinical_event (CLINICAL_EVENT_ID,PATIENT_ID,START_DATE,STOP_DATE,EV
 INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (1,'STATUS','radiographic_progression');
 INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (1,'SAMPLE_ID','TCGA-A1-A0SB-01');
 INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (2,'SURGERY','OA II Initial');
+INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (2,'SAMPLE_ID','TCGA-A1-A0SB-01');
 INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (3,'EVENT_TYPE_DETAILED','AA III Recurrence1');
 INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (3,'AGENT','Madeupanib');
 INSERT INTO clinical_event_data (CLINICAL_EVENT_ID,KEY,VALUE) VALUES (3,'AGENT_TARGET','Directly to forehead, Elbow');