fix(phenotyper): pass through outside calls even if no recommendation…

…s are available Fix-for: #154
PharmGKB · Sep 22, 2023 · 03f7f7c · 03f7f7c
1 parent 0183251
commit 03f7f7c
Show file tree

Hide file tree

Showing 13 changed files with 81 additions and 47 deletions.
diff --git a/docs/examples/pharmcat.example.match.html b/docs/examples/pharmcat.example.match.html
@@ -234,7 +234,7 @@ <h3>VKORC1</h3>
   <hr />
   <footer class="container-fluid">
     <p>
-      <small>Generated on 09/20/23.</small>
+      <small>Generated on 09/22/23.</small>
     </p>
   </footer>
 </div>

diff --git a/docs/examples/pharmcat.example.match.json b/docs/examples/pharmcat.example.match.json
@@ -3,7 +3,7 @@
     "namedAlleleMatcherVersion": "2.0.0",
     "genomeBuild": "GRCh38.p13",
     "inputFilename": "pharmcat.example.vcf",
-    "timestamp": "Sep 20, 2023, 3:53:35 PM",
+    "timestamp": "Sep 22, 2023, 3:03:49 PM",
     "topCandidatesOnly": true,
     "findCombinations": false,
     "callCyp2d": false

diff --git a/docs/examples/pharmcat.example.report.html b/docs/examples/pharmcat.example.report.html
@@ -404,8 +404,8 @@
   </div>
   <div class="metadata">
     <table>
-      <tr><th>Date created</th><td>September 20, 2023</td></tr>
-      <tr><th>PharmCAT Version</th><td>v2.7.1-13-g4406afea</td></tr>
+      <tr><th>Date created</th><td>September 22, 2023</td></tr>
+      <tr><th>PharmCAT Version</th><td>v2.7.1-19-g0d11f2b6</td></tr>
       <tr><th>CPIC Version</th><td></td></tr>
     </table>
   </div>
@@ -1435,18 +1435,18 @@ <h2>Section I: Genotype Summary</h2>
             </td>
           </tr>
 
-          <tr class="top-aligned gs-IFNL3/4">
+          <tr class="top-aligned gs-IFNL3_4">
             <td>
 
                 <div class="drugName">
 
-                    <a href="#peginterferon_alfa_2a">peginterferon alfa-2a</a>
+                    <a href="#peginterferon_alfa-2a">peginterferon alfa-2a</a>
 
                 </div>
 
                 <div class="drugName">
 
-                    <a href="#peginterferon_alfa_2b">peginterferon alfa-2b</a>
+                    <a href="#peginterferon_alfa-2b">peginterferon alfa-2b</a>
 
                 </div>
 
@@ -1459,7 +1459,7 @@ <h2>Section I: Genotype Summary</h2>
             </td>
             <td>
               <span class="noWrap">
-                <a href="#IFNL3/4" class="normalWrap">IFNL3/4</a>
+                <a href="#IFNL3_4" class="normalWrap">IFNL3/4</a>
 
                 <sup><a href="#genotypes-ddagger">&ddagger;</a></sup>
               </span>
@@ -8603,8 +8603,8 @@ <h4 id="other-considerations">Other Considerations</h4>
 
         </section>
 
-        <section class="guideline peginterferon_alfa_2a">
-          <h3 id="peginterferon_alfa_2a">peginterferon alfa-2a</h3>
+        <section class="guideline peginterferon_alfa-2a">
+          <h3 id="peginterferon_alfa-2a">peginterferon alfa-2a</h3>
 
 
 
@@ -8621,7 +8621,7 @@ <h3 id="peginterferon_alfa_2a">peginterferon alfa-2a</h3>
             <tbody>
 
 
-                <tr class="top-aligned cpic-peginterferon_alfa_2a">
+                <tr class="top-aligned cpic-peginterferon_alfa-2a">
                   <td class="top-aligned">
                     <p>
                       <b>CPIC</b>
@@ -8667,8 +8667,8 @@ <h3 id="peginterferon_alfa_2a">peginterferon alfa-2a</h3>
 
         </section>
 
-        <section class="guideline peginterferon_alfa_2b">
-          <h3 id="peginterferon_alfa_2b">peginterferon alfa-2b</h3>
+        <section class="guideline peginterferon_alfa-2b">
+          <h3 id="peginterferon_alfa-2b">peginterferon alfa-2b</h3>
 
 
 
@@ -8685,7 +8685,7 @@ <h3 id="peginterferon_alfa_2b">peginterferon alfa-2b</h3>
             <tbody>
 
 
-                <tr class="top-aligned cpic-peginterferon_alfa_2b">
+                <tr class="top-aligned cpic-peginterferon_alfa-2b">
                   <td class="top-aligned">
                     <p>
                       <b>CPIC</b>
@@ -12492,7 +12492,7 @@ <h2>Section III: Allele Matching Details</h2>
 
           <li><a href="#HLA-B">HLA-B allele match data</a></li>
 
-          <li><a href="#IFNL3/4">IFNL3/4 allele match data</a></li>
+          <li><a href="#IFNL3_4">IFNL3/4 allele match data</a></li>
 
           <li><a href="#MT-RNR1">MT-RNR1 allele match data</a></li>
 
@@ -18028,7 +18028,7 @@ <h4>Other Positions of Interest</h4>
               <tbody>
 
                 <tr>
-                  <td id="94645745">chr10:94645745</td>
+                  <td id="chr10_94645745">chr10:94645745</td>
                   <td id="rs12777823">rs12777823</td>
 
 
@@ -26105,8 +26105,8 @@ <h3 id="HLA-B">HLA-B allele match data</h3>
 
       </section>
 
-      <section class="gene IFNL3/4">
-        <h3 id="IFNL3/4">IFNL3/4 allele match data</h3>
+      <section class="gene IFNL3_4">
+        <h3 id="IFNL3_4">IFNL3/4 allele match data</h3>
 
 
           <table>

diff --git a/docs/examples/pharmcat.example.report.json b/docs/examples/pharmcat.example.report.json
@@ -1,7 +1,7 @@
 {
   "title": "pharmcat.example",
-  "timestamp": "Sep 20, 2023, 3:53:36 PM",
-  "pharmcatVersion": "v2.7.1-13-g4406afea",
+  "timestamp": "Sep 22, 2023, 3:03:50 PM",
+  "pharmcatVersion": "v2.7.1-19-g0d11f2b6",
   "cpicVersion": null,
   "dpwgVersion": "2023-09-07-21-06",
   "genes": {

diff --git a/src/main/java/org/pharmgkb/pharmcat/Env.java b/src/main/java/org/pharmgkb/pharmcat/Env.java
@@ -4,7 +4,6 @@
 import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.SortedSet;
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.pharmgkb.pharmcat.definition.DefinitionReader;
 import org.pharmgkb.pharmcat.phenotype.PhenotypeMap;
@@ -75,19 +74,16 @@ public PgkbGuidelineCollection getDrugs() {
   }
 
 
-  public SortedSet<String> getGenes() {
-    return m_drugs.getGenes();
-  }
-
   public boolean hasGene(DataSource source, String gene) {
     return m_drugs.getGenesUsedInSource(source).contains(gene);
   }
 
   /**
-   * Checks if gene is used in any drug recommendation from any source.
+   * Checks if gene can be called by NamedAlleleMatcher or is used in any drug recommendation from any source.
    */
   public boolean hasGene(String gene) {
-    return getGenes().contains(gene);
+    return m_definitionReader.getGenes().contains(gene) ||
+        m_drugs.getGenesWithRecommendations().contains(gene);
   }
 
   /**

diff --git a/src/main/java/org/pharmgkb/pharmcat/Pipeline.java b/src/main/java/org/pharmgkb/pharmcat/Pipeline.java
@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.io.PrintWriter;
-import java.lang.invoke.MethodHandles;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -25,8 +24,6 @@
 import org.pharmgkb.pharmcat.reporter.format.HtmlFormat;
 import org.pharmgkb.pharmcat.reporter.format.JsonFormat;
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 
 /**
@@ -35,7 +32,6 @@
  * @author Mark Woon
  */
 public class Pipeline implements Callable<PipelineResult> {
-  private static final Logger sf_logger = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
   public enum Mode {
     /**
      * Default mode.  Prints informative messages to console.
@@ -286,16 +282,14 @@ public PipelineResult call() throws IOException {
           for (OutsideCall call : OutsideCallParser.parse(m_phenotyperOutsideCallsFile)) {
             if (!m_env.hasGene(call.getGene())) {
               String msg = "Discarded outside call for " + call.getGene() + " because it is not supported by PharmCAT.";
-              warnings.put(call.getGene(), List.of(msg));
-              sf_logger.warn(msg);
+              output.add(AnsiConsole.styleWarning(msg));
               continue;
             }
             if (!m_env.isActivityScoreGene(call.getGene())) {
               if (call.getDiplotype() == null && call.getPhenotype() == null) {
                 String msg = call.getGene() + " is not an activity score gene but has outside call with only an " +
                     "activity score.  PharmCAT will not be able to provide any recommendations based on this gene.";
-                warnings.put(call.getGene(), List.of(msg));
-                sf_logger.warn(msg);
+                output.add(AnsiConsole.styleWarning(msg));
               }
             }
             outsideCalls.add(call);

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java b/src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java
@@ -85,7 +85,7 @@ public Set<String> getChemicalsUsedInSource(DataSource source) {
         .collect(Collectors.toSet());
   }
 
-  public SortedSet<String> getGenes() {
+  public SortedSet<String> getGenesWithRecommendations() {
     if (m_genes == null) {
       m_genes = f_guidelinePackages.stream()
           .flatMap(p -> p.getRecommendations().stream())

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/handlebars/ReportHelpers.java b/src/main/java/org/pharmgkb/pharmcat/reporter/handlebars/ReportHelpers.java
@@ -575,7 +575,8 @@ public static String externalHref(String href, String text) {
   }
 
   public static String sanitizeCssSelector(String value) {
-    return value.replaceAll("\\W+", "_")
+    return value.replaceAll("[^\\w-]+", "_")
+        .replaceAll("_-_", "-")
         .replaceAll("_+", "_")
         .replaceAll("^_+", "")
         .replaceAll("_+$", "");

diff --git a/src/main/java/org/pharmgkb/pharmcat/util/DataManager.java b/src/main/java/org/pharmgkb/pharmcat/util/DataManager.java
@@ -196,7 +196,7 @@ public static void main(String[] args) {
           definitionReader = DefinitionReader.defaultReader();
         }
 
-        List<String> genesUsedInDrugRecommendations = new ArrayList<>(pgkbGuidelineCollection.getGenes());
+        List<String> genesUsedInDrugRecommendations = new ArrayList<>(pgkbGuidelineCollection.getGenesWithRecommendations());
         genesUsedInDrugRecommendations.removeAll(definitionReader.getGeneAlleleCount().keySet());
         genesUsedInDrugRecommendations.stream()
             .filter(g -> !g.startsWith("HLA"))

diff --git a/src/main/resources/org/pharmgkb/pharmcat/reporter/report.hbs b/src/main/resources/org/pharmgkb/pharmcat/reporter/report.hbs
@@ -89,7 +89,7 @@
         </thead>
         <tbody>
         {{#each summaries}}
-          <tr class="top-aligned gs-{{symbol}}">
+          <tr class="top-aligned gs-{{{sanitizeCssSelector symbol}}}">
             <td>
               {{#each relatedDrugs}}
                 <div class="drugName">
@@ -103,7 +103,7 @@
             </td>
             <td>
               <span class="noWrap">
-                <a href="#{{symbol}}" class="normalWrap">{{symbol}}</a>
+                <a href="#{{{sanitizeCssSelector symbol}}}" class="normalWrap">{{symbol}}</a>
                 {{#if hasMessages}}<sup><a href="#genotypes-dagger">&dagger;</a></sup>{{/if}}
                 {{#if showUnphasedNote}}<sup><a href="#genotypes-ddagger">&ddagger;</a></sup>{{/if}}
               </span>
@@ -142,10 +142,10 @@
                 </p>
               {{/if}}
               {{#if treatUndocumentedVariationsAsReference}}
-                <p class="tdNote" id="gs-undocVarAsRef-{{symbol}}">
+                <p class="tdNote" id="gs-undocVarAsRef-{{{sanitizeCssSelector symbol}}}">
                   There are genetic variations in this gene that do not match what is in the allele definition.
                   <b>These undocumented variations were replaced with reference.</b>
-                  See <a href="#{{symbol}}">Section III</a> for details.
+                  See <a href="#{{{sanitizeCssSelector symbol}}}">Section III</a> for details.
                 </p>
               {{/if}}
             </td>
@@ -359,7 +359,7 @@
     {{#if (thereAre geneReports)}}
       <ol>
         {{#each geneReports}}
-          <li><a href="#{{geneDisplay}}">{{geneDisplay}} allele match data</a></li>
+          <li><a href="#{{{sanitizeCssSelector geneDisplay}}}">{{geneDisplay}} allele match data</a></li>
         {{/each}}
       </ol>
     {{/if}}
@@ -369,8 +369,8 @@
 
 
     {{#each geneReports}}
-      <section class="gene {{geneDisplay}}">
-        <h3 id="{{geneDisplay}}">{{geneDisplay}} allele match data</h3>
+      <section class="gene {{{sanitizeCssSelector geneDisplay}}}">
+        <h3 id="{{{sanitizeCssSelector geneDisplay}}}">{{geneDisplay}} allele match data</h3>
 
         {{#if (amdNoCall)}}
           <div class="alert alert-warning no-data">
@@ -504,7 +504,7 @@
               <tbody>
               {{#each variantOfInterestReports}}
                 <tr>
-                  <td id="{{position}}">{{chr}}:{{position}}</td>
+                  <td id="{{chr}}_{{position}}">{{chr}}:{{position}}</td>
                   <td id="{{dbSnpId}}">{{dbSnpId}}</td>
                   {{#if missing}}
                     <td class="missingVariant"><em>missing</em></td>

diff --git a/src/test/java/org/pharmgkb/pharmcat/PharmCATTest.java b/src/test/java/org/pharmgkb/pharmcat/PharmCATTest.java
@@ -245,6 +245,45 @@ void outsideCallsOnly(TestInfo testInfo) throws Exception {
     }
   }
 
+  @Test
+  void outsideCallsNoRecs(TestInfo testInfo) throws Exception {
+    Path vcfFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/reference.vcf");
+    Path outsideCallFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/PharmCATTest-outsideCallsNoRecs.tsv");
+
+    Path outputDir = TestUtils.getTestOutputDir(testInfo, true);
+    Path matcherOutput = outputDir.resolve("reference.match.json");
+    Path phenotyperOutput = outputDir.resolve("reference.phenotype.json");
+    Path reporterOutput = outputDir.resolve("reference.report.html");
+
+    try {
+      String systemOut = tapSystemOut(() -> PharmCAT.main(new String[] {
+          "-vcf", vcfFile.toString(),
+          "-po", outsideCallFile.toString(),
+          "-o", outputDir.toString(),
+      }));
+      System.out.println(systemOut);
+      assertTrue(systemOut.contains("Done."));
+      assertTrue(Files.exists(matcherOutput));
+      assertTrue(Files.exists(phenotyperOutput));
+      assertTrue(Files.exists(reporterOutput));
+
+      Collection<GeneReport> reports = Phenotyper.read(phenotyperOutput).getGeneReports().get(DataSource.CPIC)
+          .values();
+      Optional<GeneReport> grOpt = reports.stream()
+          .filter(gr -> gr.getGene().equals("IFNL3"))
+          .findFirst();
+      assertTrue(grOpt.isPresent());
+      assertTrue(grOpt.get().isCalled());
+      assertTrue(grOpt.get().isOutsideCall());
+
+      Document document = Jsoup.parse(reporterOutput.toFile());
+      assertEquals(1, document.select(".gene.IFNL3_4 .alert-warning.pcat-outside-call").size());
+
+    } finally {
+      TestUtils.deleteTestFiles(outputDir);
+    }
+  }
+
   /**
    * This test is dependent on CYP2C19 definition.
    * It may fail if CYP2C19 definition changes too much.

diff --git a/src/test/java/org/pharmgkb/pharmcat/reporter/handlebars/ReportHelpersTest.java b/src/test/java/org/pharmgkb/pharmcat/reporter/handlebars/ReportHelpersTest.java
@@ -17,6 +17,8 @@ class ReportHelpersTest {
   void testSanitizeCssSelector() {
     assertEquals("ABC", ReportHelpers.sanitizeCssSelector("__ABC__"));
     assertEquals("ABC", ReportHelpers.sanitizeCssSelector("(ABC)!"));
-    assertEquals("A_B_C", ReportHelpers.sanitizeCssSelector("A B - C"));
+    assertEquals("A_B-C", ReportHelpers.sanitizeCssSelector("A B - C"));
+    assertEquals("MT-RNR1", ReportHelpers.sanitizeCssSelector("MT-RNR1"));
+    assertEquals("IFNL3_4", ReportHelpers.sanitizeCssSelector("IFNL3/4"));
   }
 }
diff --git a/src/test/resources/org/pharmgkb/pharmcat/PharmCATTest-outsideCallsNoRecs.tsv b/src/test/resources/org/pharmgkb/pharmcat/PharmCATTest-outsideCallsNoRecs.tsv
@@ -0,0 +1,2 @@
+IFNL3	rs12979860 variant (T)/rs12979860 variant (T)
+CYP4F2	*1/*3
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		IFNL3 rs12979860 variant (T)/rs12979860 variant (T)
		CYP4F2 1/3