test(reporter): update unit tests for new RYR1/CACNA1S guideline stru…

…cture
PharmGKB · Dec 23, 2023 · da43730 · da43730
1 parent f5df05a
commit da43730
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Showing 3 changed files with 8 additions and 7 deletions.
diff --git a/src/test/java/org/pharmgkb/pharmcat/PipelineTest.java b/src/test/java/org/pharmgkb/pharmcat/PipelineTest.java
@@ -127,7 +127,7 @@ public static void htmlChecks(Document document, Map<String, List<String>> expec
     }
   }
 
-  private static void htmlCheckGene(Document document, String gene, List<String> expectedCalls) {
+  static void htmlCheckGene(Document document, String gene, List<String> expectedCalls) {
     Preconditions.checkNotNull(expectedCalls);
     if (expectedCalls == NO_DATA) {
       expectedCalls = null;
@@ -151,7 +151,7 @@ private static void htmlCheckGene(Document document, String gene, List<String> e
     } else {
       // check section i
       Elements gsDips = document.select(".gs-" + gene + " .gs-dip");
-      assertEquals(expectedCalls.size(), gsDips.size());
+      assertEquals(expectedCalls.size(), gsDips.size(), "diplotype count mismatched for " + gene);
       assertEquals(expectedCalls,
           gsDips.stream()
               .map(e -> e.child(0).text())
@@ -546,7 +546,6 @@ void testRyr6(TestInfo testInfo) throws Exception {
         .variation("RYR1", "rs137933390", "A", "G")
         .variation("RYR1", "rs145573319", "A", "G")
     ;
-    Path vcfFile = testWrapper.execute(null);
 
     testWrapper.testCalledByMatcher("CACNA1S");
     testWrapper.testNotCalledByMatcher("RYR1");

diff --git a/src/test/java/org/pharmgkb/pharmcat/ToxicGenesTest.java b/src/test/java/org/pharmgkb/pharmcat/ToxicGenesTest.java
@@ -72,7 +72,8 @@ void testUncallable_partial_haplotype(TestInfo testInfo) throws Exception {
   void testCacna1sHomoRef(TestInfo testInfo) throws Exception {
     PipelineWrapper testWrapper = new PipelineWrapper(testInfo, false);
     testWrapper.getVcfBuilder()
-        .reference("CACNA1S");
+        .reference("CACNA1S")
+        .reference("RYR1");
     Path vcfFile = testWrapper.execute(null);
 
     List<String> expectedCalls = List.of(TextConstants.HOMOZYGOUS_REFERENCE);
@@ -88,6 +89,7 @@ void testCacna1sHomoRef(TestInfo testInfo) throws Exception {
     Document document = readHtmlReport(vcfFile);
     htmlChecks(document, new ImmutableMap.Builder<String, List<String>>()
             .put("CACNA1S", expectedCalls)
+            .put("RYR1", expectedCalls)
             .build(),
         "desflurane", RecPresence.YES, RecPresence.NO);
   }
@@ -508,7 +510,7 @@ void testRyr1HomoRefCacna1sRef(TestInfo testInfo) throws Exception {
     testWrapper.testPrintCalls(DataSource.CPIC, "RYR1", expectedCalls);
 
     // each gene has its own annotation so 2 CPIC annotations match, one for each gene
-    testWrapper.testMatchedAnnotations("desflurane", DataSource.CPIC, 2);
+    testWrapper.testMatchedAnnotations("desflurane", DataSource.CPIC, 1);
     testWrapper.testNoMatchFromSource("desflurane", DataSource.DPWG);
 
 

diff --git a/src/test/java/org/pharmgkb/pharmcat/reporter/ReporterTest.java b/src/test/java/org/pharmgkb/pharmcat/reporter/ReporterTest.java
@@ -28,6 +28,7 @@ void testCypc2c9VariantPassthrough() throws Exception {
 
     // test the CYP2C9 data
     GeneReport geneReport = reportContext.getGeneReport(DataSource.CPIC, "CYP2C9");
+    assertNotNull(geneReport);
     assertTrue(geneReport.isReportable());
     assertTrue(geneReport.isCalled());
     assertFalse(geneReport.isOutsideCall());
@@ -51,7 +52,6 @@ void testCypc2c9VariantPassthrough() throws Exception {
     DrugReport desfluraneReport = reportContext.getDrugReports().get(DataSource.CPIC).values().stream()
         .filter(d -> d.getName().equals("desflurane")).findFirst()
         .orElseThrow(() -> new RuntimeException("No desflurane drug report found"));
-    // desflurane has been split in two, one for each gene
-    assertEquals(2, desfluraneReport.getGuidelines().stream().filter(GuidelineReport::isMatched).count());
+    assertEquals(1, desfluraneReport.getGuidelines().stream().filter(GuidelineReport::isMatched).count());
   }
 }