Ignore F-to-F sample type label updates (#127)

Ignore updates to labels if the sample type abbreviation for the new and existing label
are both F. These are not meaningful changes.

An exception is made if there are changes to the CMO patient ID prefix.

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

Author: ao508

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

@@ -120,6 +120,8 @@ private static Map<CmoSampleClass, String> initCmoSampleClassAbbrevMap() {
      *  1. cmo patient id prefix
      *  2. sample type abbreviation
      *  3. nucleic acid abbreviation
+     * Note: if an existing label and the updated label both have sample type abbreviation 'F'
+     *  then keep the existing label since update is not meaningful to begin with
      * @param newCmoLabel
      * @param existingCmoLabel
      * @return Boolean
@@ -155,28 +157,36 @@ public Boolean igoSampleRequiresLabelUpdate(String newCmoLabel, String existingC
                     + "from database. Sample will be published to IGO_SAMPLE_UPDATE topic.");
             return Boolean.TRUE;
         }
+
         // compare sample type abbreviation
-        if (!compareMatcherGroups(matcherNewLabel, matcherExistingLabel, CMO_SAMPLE_TYPE_ABBREV_GROUP)) {
-            String newSampleType = parseSampleTypeAbbrevFromCmoLabel(newCmoLabel);
-            String existingSampleType = parseSampleTypeAbbrevFromCmoLabel(existingCmoLabel);
+        Boolean isMatchingSampleTypeAbbrev = compareMatcherGroups(matcherNewLabel,
+                matcherExistingLabel, CMO_SAMPLE_TYPE_ABBREV_GROUP);
+        String newSampleType = parseSampleTypeAbbrevFromCmoLabel(newCmoLabel);
+        String existingSampleType = parseSampleTypeAbbrevFromCmoLabel(existingCmoLabel);
+        if (!isMatchingSampleTypeAbbrev) {
             if (!isSameKindOfSampleTypeAbbreviation(newSampleType, existingSampleType)) {
                 LOG.info("Sample Type abbreviation differs between incoming IGO sample and matching IGO "
                         + "sample from database. Sample will be published to IGO_SAMPLE_UPDATE topic.");
                 return Boolean.TRUE;
             }
+        } else if (isMatchingSampleTypeAbbrev && existingSampleType.equals("F")) {
+            return Boolean.FALSE;
         }
+
         // compare sample counter (may change if alt id numbering corrections are being made)
         if (!compareMatcherGroups(matcherNewLabel, matcherExistingLabel, CMO_SAMPLE_COUNTER_GROUP)) {
             LOG.info("Sample Type counter differs between incoming IGO sample and matching IGO sample "
                     + "from database. Sample will be published to IGO_SAMPLE_UPDATE topic.");
             return Boolean.TRUE;
         }
+
         // compare nucleic acid abbreviation
         if (!compareMatcherGroups(matcherNewLabel, matcherExistingLabel, CMO_SAMPLE_NUCACID_ABBREV_GROUP)) {
             LOG.info("Nucleic Acid abbreviation differs between incoming IGO sample and matching IGO sample "
                     + "from database. Sample will be published to IGO_SAMPLE_UPDATE topic.");
             return Boolean.TRUE;
         }
+
         // compare nucleic acid counter (may change if alt id numbering corrections are being made)
         if (!compareNucleicAcidCounterGroups(matcherNewLabel, matcherExistingLabel)) {
             LOG.info("Nucleic Acid counter differs between incoming IGO sample and matching IGO sample "

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

@@ -500,6 +500,30 @@ public void testLabelRequiresUpdate() throws Exception {
         Assertions.assertTrue(requiresUpdate);
     }
 
+    @Test
+    public void testSampleTypeFLabelRequiresUpdateChecks() throws Exception {
+        // existing label for comparison
+        String existingLabel = "C-MPJKLE-F002-d01";
+
+        // does not require an update
+        String newLabel1 = "C-MPJKLE-F001-d01";
+        Boolean requiresUpdate1 = cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(newLabel1,
+                existingLabel);
+        Assertions.assertFalse(requiresUpdate1);
+
+        // requires an update because sample type T is a meaningful change
+        String newLabel2 = "C-MPJKLE-T001-d01";
+        Boolean requiresUpdate2 = cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(newLabel2,
+                existingLabel);
+        Assertions.assertTrue(requiresUpdate2);
+
+        // requires an update because cmo patient id change is meaningful even though sample types are both F
+        String newLabel3 = "C-ABCDEF-F001-d01";
+        Boolean requiresUpdate3 = cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(newLabel3,
+                existingLabel);
+        Assertions.assertTrue(requiresUpdate3);
+    }
+
     @Test
     public void testUpdateToSampleType() throws Exception {
         SampleMetadata sample1ExistingData = initSampleMetadata("SAMPLE_A_1", "C-BRC0DE-F001-d01",