Permit label generator when existing sample label DNE (#135)

* Permit label generator when existing sample label DNE

Permits the label generator to run when a sample with existing data does not
already have a label assigned to it even if there aren't any changes to the
label metadata itself.

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

* PR template update

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

---------

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

Author: ao508

.github/PULL_REQUEST_TEMPLATE.md

@@ -44,10 +44,10 @@ Please describe how the workflow and messaging was tested/simulated:
 
 **Describe your testing environment:**
 
-- NATS [local, local docker, dev server, production]
-- Neo4j [local, local docker, dev server, production]
-- SMILE Server [local, local docker, dev server, production]
-- Message publishing simulation [nats cli, docker nats cli, smile publisher tool, other (describe below)]
+- NATS: [local, local docker, dev server, production]
+- Neo4j: [local, local docker, dev server, production]
+- SMILE Server: [local, local docker, dev server, production]
+- Message publishing simulation: [nats cli, docker nats cli, smile publisher tool, other (describe below)]
 
 Other: [insert details on how messages were published or simulated for testing]
 

src/main/java/org/mskcc/smile/service/impl/CmoLabelGeneratorServiceImpl.java

@@ -125,8 +125,11 @@ public Boolean sampleHasLabelSpecificUpdates(CmoLabelParts sample,
         for (CmoLabelParts existingSample : existingPatientSamples) {
             if (existingSample.getPrimaryId().equals(sample.getPrimaryId())) {
                 try {
-                    return !jsonComparator.isConsistent(mapper.writeValueAsString(sample),
+                    // if there are data differences or the existing sample does not have a label then
+                    // return true to permit label generation
+                    Boolean isConsistentData = jsonComparator.isConsistent(mapper.writeValueAsString(sample),
                             mapper.writeValueAsString(existingSample));
+                    return (!isConsistentData || StringUtils.isBlank(existingSample.getCmoSampleName()));
                 } catch (JsonProcessingException ex) {
                     LOG.error("Encountered JSON processing error while comparing sample "
                             + "label parts to existing sample label parts.", ex);

src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java

@@ -734,11 +734,18 @@ public void testHasApplicableMetadataUpdatesToIsCmoSampleStatus() throws Excepti
         // labels should be ignored during comparison
         Assertions.assertTrue(
                 cmoLabelGeneratorService.sampleHasLabelSpecificUpdates(sm1Updated, Arrays.asList(sm1)));
-        // assert false if isCmoSample is also false (i.e., no change at all in label parts data)
-        CmoLabelParts sm1UpdatedFalse = initSmileSampleLabelParts("12345_C_7", "", "C-BRCD03", "ABF-89D",
+        // assert true if no change at all metadata but existing sample does not already have a label
+        CmoLabelParts sm1NoUpdatesNoLabel = initSmileSampleLabelParts("12345_C_7", "", "C-BRCD03", "ABF-89D",
                 "Normal", "cfDNA", NucleicAcid.DNA, "Plasma", "cfDNA", "12345_C", "Normal", Boolean.FALSE);
-        Assertions.assertFalse(
-                cmoLabelGeneratorService.sampleHasLabelSpecificUpdates(sm1UpdatedFalse, Arrays.asList(sm1)));
+        Assertions.assertTrue(cmoLabelGeneratorService.sampleHasLabelSpecificUpdates(sm1NoUpdatesNoLabel,
+                Arrays.asList(sm1)));
+
+        // assert false if no change at all in metadata and existing sample already has a label
+        sm1.setCmoSampleName("C-BRCD03-L001-d01");
+        CmoLabelParts sm1NoUpdatesWLabel = initSmileSampleLabelParts("12345_C_7", "", "C-BRCD03", "ABF-89D",
+                "Normal", "cfDNA", NucleicAcid.DNA, "Plasma", "cfDNA", "12345_C", "Normal", Boolean.FALSE);
+        Assertions.assertFalse(cmoLabelGeneratorService.sampleHasLabelSpecificUpdates(sm1NoUpdatesWLabel,
+                Arrays.asList(sm1)));
     }
 
     private CmoLabelParts getSampleWithPrimaryIdAndLabel(String primaryId, String cmoSampleName)