fix(reporter): improve text for uncallable genes

PharmGKB · Aug 1, 2023 · 7e794b3 · 7e794b3
1 parent e7e7e55
commit 7e794b3
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Showing 6 changed files with 32 additions and 16 deletions.
diff --git a/src/main/java/org/pharmgkb/pharmcat/util/VcfHelper.java b/src/main/java/org/pharmgkb/pharmcat/util/VcfHelper.java
@@ -296,11 +296,13 @@ public static void printVcfHeaders(PrintWriter writer, String source, @Nullable
       if (assemblies.size() > 1) {
         throw new IllegalStateException("Multiple assemblies found: " + assemblies);
       }
-      String assembly = assemblies.iterator().next();
-      SortedSet<String> sortedChr = new TreeSet<>(new ChrNameComparator());
-      sortedChr.addAll(contigs.keySet());
-      for (String chr : sortedChr) {
-        writer.println("##contig=<ID=" + chr + ",assembly=" + assembly + ",species=\"Homo sapiens\">");
+      if (!assemblies.isEmpty()) {
+        String assembly = assemblies.iterator().next();
+        SortedSet<String> sortedChr = new TreeSet<>(new ChrNameComparator());
+        sortedChr.addAll(contigs.keySet());
+        for (String chr : sortedChr) {
+          writer.println("##contig=<ID=" + chr + ",assembly=" + assembly + ",species=\"Homo sapiens\">");
+        }
       }
     }
 

diff --git a/src/main/resources/org/pharmgkb/pharmcat/reporter/report.hbs b/src/main/resources/org/pharmgkb/pharmcat/reporter/report.hbs
@@ -50,14 +50,19 @@
     <h2>Section I: Genotype Summary</h2>
 
     {{#unless (thereAre summaries)}}
-      <p>
-        No genotypes called.
-      </p>
       {{#if (thereAre uncallableGenes)}}
+        <p>
+          No genotypes called.
+        </p>
         {{> uncallableGenesNote }}
       {{/if}}
+      {{#unless (thereAre uncallableGenes)}}
+        <p>
+          No data provided.
+        </p>
+      {{/unless}}
       <p>
-        See <a href="#section-iii">Section III</a> for details.  For a full list of disclaimers and limitations see <a href="#disclaimer">Section IV</a>.
+        For a full list of disclaimers and limitations see <a href="#disclaimer">Section IV</a>.
       </p>
     {{/unless}}
     {{#if (thereAre summaries) }}
@@ -150,11 +155,8 @@
       </table>
 
       {{#if (thereAre uncallableGenes)}}
-        <div class="alert alert-secondary">
+        <div class="alert alert-warning">
           {{> uncallableGenesNote }}
-          <p class="mb-1">
-            See <a href="#section-iii">Section III</a> for details.
-          </p>
         </div>
       {{/if}}
 

diff --git a/src/main/resources/org/pharmgkb/pharmcat/reporter/uncallableGenesNote.hbs b/src/main/resources/org/pharmgkb/pharmcat/reporter/uncallableGenesNote.hbs
@@ -1,6 +1,7 @@
 <p>
   The following {{pluralize "gene" uncallableGenes}} could not be called because there were
-  genetic variations that do not match the allele definition:
+  genetic variations that do not match the allele definition. There could still be actionable variants in these genes.
+  See <a href="#section-iii">Section III</a> for details.
 </p>
 <ul class="mb-2">
   {{#each uncallableGenes}}

diff --git a/src/test/java/org/pharmgkb/pharmcat/PipelineTest.java b/src/test/java/org/pharmgkb/pharmcat/PipelineTest.java
@@ -325,6 +325,13 @@ void testAll(TestInfo testInfo) throws Exception {
   }
 
 
+  @Test
+  void testNoData(TestInfo testInfo) throws Exception {
+    PipelineWrapper testWrapper = new PipelineWrapper(testInfo, false);
+    testWrapper.execute(null, true);
+  }
+
+
   @Test
   void testUndocumentedVariation(TestInfo testInfo) throws Exception {
     PipelineWrapper testWrapper = new PipelineWrapper(testInfo, false);

diff --git a/src/test/java/org/pharmgkb/pharmcat/PipelineWrapper.java b/src/test/java/org/pharmgkb/pharmcat/PipelineWrapper.java
@@ -89,10 +89,14 @@ TestVcfBuilder getVcfBuilder() {
   }
 
   @Nullable Path execute(Path outsideCallPath) throws Exception {
+    return execute(outsideCallPath, false);
+  }
+
+  @Nullable Path execute(Path outsideCallPath, boolean allowNoData) throws Exception {
     Path vcfFile = null;
     VcfFile vcfFileObj = null;
     boolean runMatcher = false;
-    if (m_vcfBuilder.hasData()) {
+    if (m_vcfBuilder.hasData() || allowNoData) {
       runMatcher = true;
       vcfFile = m_vcfBuilder.generate();
       vcfFileObj = new VcfFile(vcfFile, false);

diff --git a/src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherTest.java b/src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherTest.java
@@ -350,7 +350,7 @@ void testCombinationPhased() throws Exception {
   }
 
   @Test
-  void testCombinationUphased() throws Exception {
+  void testCombinationUnphased() throws Exception {
     Path definitionFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcher-combination.json");
     Path vcfFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcher-combinationUnphased.vcf");