fix(reporter): change "n/a" phenotype for unknown activity score dipl…

…otypes to "Indeterminate"
PharmGKB · Feb 20, 2025 · 665eef4 · 665eef4
1 parent dae7a76
commit 665eef4
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/Diplotype.java b/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/Diplotype.java
@@ -592,6 +592,7 @@ else if (isUnknownAlleles()) {
           // diplotype -> phenotype
           diplotype.ifPresentOrElse(
               (d) -> m_phenotypes.add(d.getPhenotype()),
+              // TODO(whaleyr): should this be lookupPhenotypeByActivityScore instead?
               () -> m_phenotypes.add(lookupPhenotypesByDiplotype(gp, lookupMap)));
         }
       }
@@ -653,7 +654,11 @@ private String lookupPhenotypesByDiplotype(GenePhenotype gp, Map<String, Integer
       throw new IllegalStateException("More than one phenotype matched for " + this + ": " +
           String.join("; ", keys));
     } else if (keys.isEmpty()) {
-      return TextConstants.NA;
+      if (isActivityScoreType()) {
+        return TextConstants.INDETERMINATE;
+      } else {
+        return TextConstants.NA;
+      }
     } else {
       return keys.iterator().next();
     }
@@ -684,7 +689,7 @@ private SortedSet<String> lookupPhenotypeByActivityScore(GenePhenotype gp, Strin
         .map(DiplotypeRecord::getGeneResult)
         .collect(Collectors.toCollection(TreeSet::new));
     if (rez.isEmpty()) {
-      rez.add(TextConstants.NA);
+      rez.add(TextConstants.INDETERMINATE);
     }
     return rez;
   }

diff --git a/src/test/java/org/pharmgkb/pharmcat/Cyp2d6Test.java b/src/test/java/org/pharmgkb/pharmcat/Cyp2d6Test.java
@@ -119,7 +119,7 @@ void testCyp2d6AlleleWithNoFunction(TestInfo testInfo) throws Exception {
 
     testWrapper.testPrintCalls(DataSource.CPIC, "CYP2D6", "*1/*XXX");
     testWrapper.testPrintCalls(DataSource.DPWG, "CYP2D6", "*1/*XXX");
-    testWrapper.testSourcePhenotype(DataSource.CPIC, "CYP2D6", "n/a");
+    testWrapper.testSourcePhenotype(DataSource.CPIC, "CYP2D6", TextConstants.INDETERMINATE);
 
     // this nonsense allele will still match to "Indeterminate" phenotypes in guidelines for CYP2D6
     testWrapper.testMatchedAnnotations("atomoxetine", PrescribingGuidanceSource.CPIC_GUIDELINE, 2);
@@ -132,7 +132,7 @@ void testCyp2d6AlleleWithNoFunction(TestInfo testInfo) throws Exception {
         .flatMap((g) -> g.getGenotypes().stream())
         .flatMap((g) -> g.getDiplotypes().stream())
         .filter((d) -> d.getGene().equals("CYP2D6"))
-        .allMatch((d) -> d.getPhenotypes().contains(TextConstants.NA)));
+        .allMatch((d) -> d.getPhenotypes().contains(TextConstants.INDETERMINATE)));
 
     GeneReport geneReport = testWrapper.getContext().getGeneReport(DataSource.CPIC, "CYP2D6");
     assertNotNull(geneReport);

diff --git a/src/test/java/org/pharmgkb/pharmcat/PipelineTest.java b/src/test/java/org/pharmgkb/pharmcat/PipelineTest.java
@@ -592,6 +592,7 @@ void testUndocumentedVariationsWithTreatAsReferenceAndCombo(TestInfo testInfo) t
     testWrapper.testRecommendedDiplotypes(DataSource.CPIC, "TPMT", expectedCallsToRecommendedDiplotypes(tpmtExpectedCalls));
     testWrapper.testSourceDiplotypes(DataSource.CPIC, "RYR1", ryr1ExpectedCalls);
     testWrapper.testRecommendedDiplotypes(DataSource.CPIC, "RYR1", expectedCallsToRecommendedDiplotypes(ryr1ExpectedCalls));
+    testWrapper.testRecommendedPhenotype(DataSource.CPIC, "TPMT", TextConstants.NA);
 
     Document document = readHtmlReport(vcfFile);
     assertNull(document.getElementById("gs-undocVarAsRef-TPMT"));

diff --git a/src/test/java/org/pharmgkb/pharmcat/reporter/caller/LowestFunctionGeneCallerTest.java b/src/test/java/org/pharmgkb/pharmcat/reporter/caller/LowestFunctionGeneCallerTest.java
@@ -48,7 +48,7 @@ void infer_outsideCall_noMatch() {
     assertNotNull(dip.getAllele2());
     assertEquals("*5", dip.getAllele2().getName());
     assertEquals(1, dip.getPhenotypes().size());
-    Assertions.assertEquals(TextConstants.NA, dip.getPhenotypes().get(0));
+    Assertions.assertEquals(TextConstants.INDETERMINATE, dip.getPhenotypes().get(0));
   }