Merge pull request #64 from ao508/sample-type-f

Default F sample type abbreviation
mskcc · May 5, 2023 · 09d6606 · 09d6606
2 parents 7b53064 + 6e7988d
commit 09d6606
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Showing 4 changed files with 27 additions and 13 deletions.
diff --git a/src/main/java/org/mskcc/smile/service/CmoLabelGeneratorService.java b/src/main/java/org/mskcc/smile/service/CmoLabelGeneratorService.java
@@ -19,4 +19,6 @@ Status generateSampleStatus(String requestId, IgoSampleManifest sampleManifest,
     Status generateSampleStatus(SampleMetadata sampleMetadata,
             List<SampleMetadata> existingSamples) throws JsonProcessingException;
     Boolean igoSampleRequiresLabelUpdate(String newCmoLabel, String existingCmoLabel);
+    String resolveSampleTypeAbbreviation(String specimenTypeValue, String sampleOriginValue,
+            String cmoSampleClassValue);
 }
diff --git a/src/main/java/org/mskcc/smile/service/impl/CmoLabelGeneratorServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/CmoLabelGeneratorServiceImpl.java
@@ -172,11 +172,6 @@ public String generateCmoSampleLabel(String requestId, IgoSampleManifest sampleM
 
         // resolve sample type abbreviation
         String sampleTypeAbbreviation = resolveSampleTypeAbbreviation(sampleManifest);
-        if (sampleTypeAbbreviation == null) {
-            LOG.error("Could not resolve sample type abbreviation from specimen type,"
-                    + " sample origin, or sample class: " + sampleManifest.toString());
-            return null;
-        }
 
         // resolve the sample counter value to use for the cmo label
         Integer sampleCounter =  resolveSampleIncrementValue(sampleManifest.getIgoId(), existingSamples);
@@ -253,7 +248,9 @@ public Status generateSampleStatus(String requestId, IgoSampleManifest sampleMan
         Status sampleStatus = new Status();
         Map<String, String> validationReport = new HashMap<>();
 
-        if (resolveSampleTypeAbbreviation(sampleManifest) == null) {
+        String sampleTypeAbbreviation = resolveSampleTypeAbbreviation(sampleManifest);
+        if (sampleTypeAbbreviation == null
+                || sampleTypeAbbreviation.equals("F")) {
             validationReport.put("sample type abbreviation",
                     "could not resolve based on specimenType, sampleOrigin, or sampleClass");
         }
@@ -276,8 +273,10 @@ public Status generateSampleStatus(SampleMetadata sampleMetadata,
         Status sampleStatus = new Status();
         Map<String, String> validationReport = new HashMap<>();
 
-        if (resolveSampleTypeAbbreviation(sampleMetadata.getSampleClass(),
-                sampleMetadata.getSampleOrigin(), sampleMetadata.getSampleType()) == null) {
+        String sampleTypeAbbreviation = resolveSampleTypeAbbreviation(sampleMetadata.getSampleClass(),
+                sampleMetadata.getSampleOrigin(), sampleMetadata.getSampleType());
+        if (sampleTypeAbbreviation == null
+                || sampleTypeAbbreviation.equals("F")) {
             validationReport.put("sample type abbreviation",
                     "could not resolve based on specimenType, sampleOrigin, or sampleClass");
         }
@@ -361,7 +360,8 @@ private String resolveNucleicAcidAbbreviation(IgoSampleManifest sampleManifest)
         return resolveNucleicAcidAbbreviation(sampleTypeString, recipe, naToExtract);
     }
 
-    private String resolveSampleTypeAbbreviation(String specimenTypeValue, String sampleOriginValue,
+    @Override
+    public String resolveSampleTypeAbbreviation(String specimenTypeValue, String sampleOriginValue,
             String cmoSampleClassValue) {
         try {
             SpecimenType specimenType = SpecimenType.fromValue(specimenTypeValue);
@@ -389,7 +389,13 @@ private String resolveSampleTypeAbbreviation(String specimenTypeValue, String sa
 
         // if abbreviation is still not resolved then try to resolve from sample class
         CmoSampleClass sampleClass = CmoSampleClass.fromValue(cmoSampleClassValue);
-        return SAMPLE_CLASS_ABBREV_MAP.get(sampleClass);
+        String sampleTypeAbbreviation = SAMPLE_CLASS_ABBREV_MAP.get(sampleClass);
+        if (sampleTypeAbbreviation == null) {
+            LOG.warn("Could not resolve sample type abbreviation from specimen type,"
+                    + " sample origin, or sample class - using default 'F' ");
+            return "F";
+        }
+        return sampleTypeAbbreviation;
     }
 
     /**

diff --git a/src/main/java/org/mskcc/smile/service/impl/LabelGenMessageHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/LabelGenMessageHandlingServiceImpl.java
@@ -28,7 +28,6 @@
 import org.mskcc.smile.model.igo.IgoSampleManifest;
 import org.mskcc.smile.service.CmoLabelGeneratorService;
 import org.mskcc.smile.service.MessageHandlingService;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;

diff --git a/src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java b/src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java
@@ -182,7 +182,7 @@ public void testCmoLabelGenForExistingSampleWithPatientCorrection()
         // if the cmo label before the update is C-MP789JR-X001-d
         Assert.assertEquals("C-newPatient-X001-d02", newCmoLabel);
 
-        
+
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
         Assert.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
@@ -226,7 +226,7 @@ public void testCmoLabelGenForSampleWithOtherSpecimenType()
         // should return null string
         String newCmoLabel = cmoLabelGeneratorService.generateCmoSampleLabel(
                 updatedSample, existingSamples);
-        Assert.assertNull(newCmoLabel);
+        Assert.assertEquals("C-MP789JR-F001-d01", newCmoLabel);
 
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
@@ -270,6 +270,13 @@ public void testCmoCelllineLabelGenerationUpdates() {
                 sampleUpdatedNaExtractLabel, sampleExpectedLabel));
     }
 
+    @Test
+    public void testDefaultSampleTypeAbbreviation() {
+        String sampleTypeAbbrev = cmoLabelGeneratorService.resolveSampleTypeAbbreviation("RapidAutopsy",
+                "Cerebrospinal Fluid", "Other");
+        Assert.assertTrue(sampleTypeAbbrev.equals("F"));
+    }
+
     private IgoSampleManifest getSampleMetadata(String igoId, String cmoPatientId,
             SpecimenType specimenType, NucleicAcid naToExtract, String investigatorSampleId) {
         IgoSampleManifest sample = new IgoSampleManifest();