Updates to resolved sample type abbreviation values (#96)

Sample type abbreviations R, M, and P now resolve to T Adjacent Tissue now resolves to sample type abbreviation 'A' Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Jan 29, 2025 · 8355378 · 8355378
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -39,9 +39,6 @@ Please follow these checks if any changes were made to any classes in the web, s
 ### II. Message handlers checklist:
 - [ ] Changes introduced affect the workflow of incoming messages.
 - [ ] Messages are following the expected workflow when published to the topic(s) changed or introduced in this pull request.
-- [ ] Unit tests were added or updated to ensure messages are handled as expected.
-
-If no unit tests were updated or added, then please explain why: [insert details here]
 
 Please describe how the workflow and messaging was tested/simulated:
 

diff --git a/src/main/java/org/mskcc/smile/service/impl/CmoLabelGeneratorServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/CmoLabelGeneratorServiceImpl.java
@@ -96,12 +96,12 @@ private static Map<SampleOrigin, String> initSampleOriginAbbrevMap() {
     private static Map<CmoSampleClass, String> initCmoSampleClassAbbrevMap() {
         Map<CmoSampleClass, String> map = new HashMap<>();
         map.put(CmoSampleClass.UNKNOWN_TUMOR, "T");
-        map.put(CmoSampleClass.LOCAL_RECURRENCE, "R");
-        map.put(CmoSampleClass.PRIMARY, "P");
-        map.put(CmoSampleClass.RECURRENCE, "R");
-        map.put(CmoSampleClass.METASTASIS, "M");
+        map.put(CmoSampleClass.LOCAL_RECURRENCE, "T");
+        map.put(CmoSampleClass.PRIMARY, "T");
+        map.put(CmoSampleClass.RECURRENCE, "T");
+        map.put(CmoSampleClass.METASTASIS, "T");
         map.put(CmoSampleClass.NORMAL, "N");
-        map.put(CmoSampleClass.ADJACENT_NORMAL, "N");
+        map.put(CmoSampleClass.ADJACENT_NORMAL, "A");
         map.put(CmoSampleClass.ADJACENT_TISSUE, "T");
         return map;
     }

diff --git a/src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java b/src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java
@@ -80,7 +80,7 @@ public void testCmoLabelGenForSampleUpdate() throws Exception {
         // generate cmoLabel for sample with updates
         String newCmoLabel = cmoLabelGeneratorService.generateCmoSampleLabel(
                 updatedSample, existingSamples, DEFAULT_SAMPLES_BY_ALT_ID);
-        Assertions.assertEquals("C-MP789JR-P003-d01", newCmoLabel);
+        Assertions.assertEquals("C-MP789JR-T003-d01", newCmoLabel);
 
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
@@ -286,7 +286,7 @@ public void testNewSampleExistingAltIdDnaNucAcid() throws Exception {
         // if no samples exist by the same alt id then the new sample should receive tumor counter #3
         String cmoLabelNoAltIds = cmoLabelGeneratorService.generateCmoSampleLabel(newSample1,
                 existingSamples, DEFAULT_SAMPLES_BY_ALT_ID);
-        Assertions.assertEquals("C-MP789JR-P003-d01", cmoLabelNoAltIds);
+        Assertions.assertEquals("C-MP789JR-T003-d01", cmoLabelNoAltIds);
 
         // set up samples by alt id as same as existing samples
         List<SampleMetadata> samplesByAltId =
@@ -296,7 +296,7 @@ public void testNewSampleExistingAltIdDnaNucAcid() throws Exception {
         // and dna counter
         String cmoLabelWithAltIds = cmoLabelGeneratorService.generateCmoSampleLabel(newSample1,
                 existingSamples, samplesByAltId);
-        Assertions.assertEquals("C-MP789JR-P001-d02", cmoLabelWithAltIds);
+        Assertions.assertEquals("C-MP789JR-T001-d02", cmoLabelWithAltIds);
         newSample1.setCmoSampleName(cmoLabelWithAltIds);
         samplesByAltId.add(newSample1);
 
@@ -308,7 +308,7 @@ public void testNewSampleExistingAltIdDnaNucAcid() throws Exception {
         newSample2.setSampleClass("Non-PDX");
         String cmoLabelWithAltIds2 = cmoLabelGeneratorService.generateCmoSampleLabel(newSample2,
                 existingSamples, samplesByAltId);
-        Assertions.assertEquals("C-MP789JR-P001-d03", cmoLabelWithAltIds2);
+        Assertions.assertEquals("C-MP789JR-T001-d03", cmoLabelWithAltIds2);
         newSample2.setCmoSampleName(cmoLabelWithAltIds2);
         samplesByAltId.add(newSample2);
     }