test(pharmcat): update unit tests for new FDA content

PharmGKB · Mar 14, 2024 · 420de6d · 420de6d
1 parent e9a6547
commit 420de6d
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Showing 12 changed files with 671 additions and 83 deletions.
diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java b/src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java
@@ -77,6 +77,12 @@ public Set<GuidelinePackage> getGuidelinesFromSource(DataSource dataSource) {
         .collect(Collectors.toSet());
   }
 
+  public Set<GuidelinePackage> getGuidelinesFromSource(PrescribingGuidanceSource source) {
+    return f_guidelineMap.values().stream()
+        .filter(g -> g.isDataSourceType(source))
+        .collect(Collectors.toSet());
+  }
+
   public Set<String> getChemicalsUsedInSource(DataSource source) {
     return f_guidelineMap.values().stream()
         .map(GuidelinePackage::getGuideline)

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/model/pgkb/GuidelinePackage.java b/src/main/java/org/pharmgkb/pharmcat/reporter/model/pgkb/GuidelinePackage.java
@@ -25,6 +25,9 @@ public class GuidelinePackage implements Comparable<GuidelinePackage> {
   @Expose
   @SerializedName("citations")
   private List<Publication> citations = new ArrayList<>();
+  @Expose
+  @SerializedName("url")
+  private String url;
 
 
   /**
@@ -52,6 +55,10 @@ public List<Publication> getCitations() {
     return citations;
   }
 
+  public String getUrl() {
+    return this.url;
+  }
+
 
   public Set<String> getGenes() {
     return guideline.getRelatedGenes().stream()
@@ -73,19 +80,7 @@ public boolean isDataSourceType(PrescribingGuidanceSource type) {
   @Override
   public String toString() {
     if (guideline != null) {
-      String chemicals = recommendations.stream()
-          .flatMap((r) -> r.getRelatedChemicals().stream())
-          .map(AccessionObject::getName)
-          .distinct()
-          .sorted()
-          .collect(Collectors.joining("_"));
-      return String.format(
-          "%s_%s_%s_and_%s.json",
-          guideline.getSource(),
-          guideline.getObjCls(),
-          chemicals,
-          guideline.getRelatedGenes().stream().map(AccessionObject::getSymbol).collect(Collectors.joining("_"))
-      ).replaceAll("[\\s\\/]", "_");
+      return guideline.getName();
     }
     else {
       return super.toString();

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/AnnotationReport.java b/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/AnnotationReport.java
@@ -16,6 +16,7 @@
 import org.pharmgkb.pharmcat.UnexpectedStateException;
 import org.pharmgkb.pharmcat.reporter.TextConstants;
 import org.pharmgkb.pharmcat.reporter.model.MessageAnnotation;
+import org.pharmgkb.pharmcat.reporter.model.pgkb.OntologyTerm;
 import org.pharmgkb.pharmcat.reporter.model.pgkb.RecommendationAnnotation;
 
 
@@ -86,7 +87,7 @@ public AnnotationReport(RecommendationAnnotation recommendation, String localId)
       m_implications.addAll(recommendation.getImplications());
     }
     m_drugRecommendation = recommendation.getText().getHtmlStripped();
-    m_classification = recommendation.getClassification() != null ? recommendation.getClassification().getTerm() : null;
+    m_classification = normalizeClassification(recommendation.getClassification());
 
     m_population = recommendation.getPopulation();
 
@@ -221,6 +222,13 @@ public void checkDiplotypes() {
     }
   }
 
+  private static String normalizeClassification(OntologyTerm term) {
+    if (term != null && !TextConstants.isUnspecified(term.getTerm())) {
+      return term.getTerm();
+    }
+    return TextConstants.UNSPECIFIED;
+  }
+
 
   @Override
   public int compareTo(@NonNull AnnotationReport o) {

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/DrugReport.java b/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/DrugReport.java
@@ -73,7 +73,7 @@ public DrugReport(String name, List<GuidelinePackage> guidelinePackages, ReportC
     // DPWG drug can have multiple guideline reports
     for (GuidelinePackage guidelinePackage : guidelinePackages) {
       m_source = PrescribingGuidanceSource.typeFor(guidelinePackage.getGuideline());
-      m_urls.add(guidelinePackage.getGuideline().getUrl());
+      m_urls.add(guidelinePackage.getUrl());
       if (guidelinePackage.getCitations() != null) {
         m_citations.addAll(guidelinePackage.getCitations());
       }

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/GuidelineReport.java b/src/main/java/org/pharmgkb/pharmcat/reporter/model/result/GuidelineReport.java
@@ -56,7 +56,7 @@ public GuidelineReport(GuidelinePackage guidelinePackage, ReportContext reportCo
     m_name = guidelinePackage.getGuideline().getName();
     m_source = PrescribingGuidanceSource.typeFor(guidelinePackage.getGuideline());
     m_version = reportContext.getCpicVersion();
-    m_url = guidelinePackage.getGuideline().getUrl();
+    m_url = guidelinePackage.getUrl();
     initializeGenes(guidelinePackage.getGenes(), reportContext);
     matchAnnotations(guidelinePackage, drugName);
   }

diff --git a/src/main/resources/org/pharmgkb/pharmcat/reporter/prescribing_guidance.json b/src/main/resources/org/pharmgkb/pharmcat/reporter/prescribing_guidance.json
diff --git a/src/main/resources/org/pharmgkb/pharmcat/reporter/report.hbs b/src/main/resources/org/pharmgkb/pharmcat/reporter/report.hbs
@@ -233,12 +233,7 @@
                     <tr class="top-aligned {{{rxAnnotationClass source drug}}}">
                       <td>
                         <p>
-                          <b>{{source}}</b>
-                          {{#unless notCalled}}
-                            <sup class="sources">
-                              {{{listSources urls}}}
-                            </sup>
-                          {{/unless}}
+                          <b><a href="{{url}}" target="_blank">{{source}}</a></b>
                         </p>
                         <p>Population:<br />{{capitalizeNA population}}</p>
                         {{{annotationTags this}}}

diff --git a/src/test/java/org/pharmgkb/pharmcat/DpydTest.java b/src/test/java/org/pharmgkb/pharmcat/DpydTest.java
@@ -92,12 +92,11 @@ public static void dpydHasReports(PipelineWrapper testWrapper, RecPresence hasCp
     assertNotNull(dpwgDpydGeneReport);
     assertEquals(1, dpwgDpydGeneReport.getRecommendationDiplotypes().size());
 
-    int numAnnotations = 0;
-
     if (hasCpicReport == RecPresence.YES) {
       testWrapper.testAnyMatchFromSource("fluorouracil", PrescribingGuidanceSource.CPIC_GUIDELINE);
       testWrapper.testAnyMatchFromSource("capecitabine", PrescribingGuidanceSource.CPIC_GUIDELINE);
-      numAnnotations += 1;
+      testWrapper.testMatchedAnnotations("fluorouracil", PrescribingGuidanceSource.CPIC_GUIDELINE, 1);
+      testWrapper.testMatchedAnnotations("capecitabine", PrescribingGuidanceSource.CPIC_GUIDELINE, 1);
 
     } else {
       testWrapper.testNoMatchFromSource("fluorouracil", PrescribingGuidanceSource.CPIC_GUIDELINE);
@@ -107,17 +106,13 @@ public static void dpydHasReports(PipelineWrapper testWrapper, RecPresence hasCp
     if (hasDpwgReport == RecPresence.YES) {
       testWrapper.testAnyMatchFromSource("fluorouracil", PrescribingGuidanceSource.DPWG_GUIDELINE);
       testWrapper.testAnyMatchFromSource("capecitabine", PrescribingGuidanceSource.DPWG_GUIDELINE);
-      numAnnotations += 1;
+      testWrapper.testMatchedAnnotations("fluorouracil", PrescribingGuidanceSource.DPWG_GUIDELINE, 1);
+      testWrapper.testMatchedAnnotations("capecitabine", PrescribingGuidanceSource.DPWG_GUIDELINE, 1);
 
     } else {
       testWrapper.testNoMatchFromSource("fluorouracil", PrescribingGuidanceSource.DPWG_GUIDELINE);
       testWrapper.testNoMatchFromSource("capecitabine", PrescribingGuidanceSource.DPWG_GUIDELINE);
     }
-
-    if (numAnnotations > 0) {
-      testWrapper.testMatchedAnnotations("fluorouracil", numAnnotations);
-      testWrapper.testMatchedAnnotations("capecitabine", numAnnotations);
-    }
   }
 
 
@@ -264,7 +259,7 @@ static void dpydHtmlChecks(Document document, @Nullable List<String> expectedCal
               .map(c -> "DPYD:" + c)
               .toList();
 
-      Elements cpicCapecitabineDips = capecitabineSection.select(".cpic-capecitabine .rx-dip");
+      Elements cpicCapecitabineDips = capecitabineSection.select(".cpic-guideline-capecitabine .rx-dip");
       if (hasCpicAnnotation == RecPresence.YES) {
         assertEquals(expectedRxCalls,
             cpicCapecitabineDips.stream()
@@ -273,21 +268,21 @@ static void dpydHtmlChecks(Document document, @Nullable List<String> expectedCal
 
       } else {
         assertEquals(0, cpicCapecitabineDips.size());
-        Elements unmatchedDips = capecitabineSection.select(".cpic-capecitabine .rx-unmatched-dip");
+        Elements unmatchedDips = capecitabineSection.select(".cpic-guideline-capecitabine .rx-unmatched-dip");
         assertEquals(expectedRxCalls, unmatchedDips.stream()
             .map(e -> cleanupRxDip(e, List.of("DPYD")))
             .toList());
       }
 
-      Elements dpwgCapecitabineDips = capecitabineSection.select(".dpwg-capecitabine .rx-dip");
+      Elements dpwgCapecitabineDips = capecitabineSection.select(".dpwg-guideline-capecitabine .rx-dip");
       if (hasDpwgAnnotation == RecPresence.YES) {
         assertEquals(expectedRxCalls,
             dpwgCapecitabineDips.stream()
                 .map(e -> cleanupRxDip(e, List.of("DPYD")))
                 .toList());
       } else {
         assertEquals(0, dpwgCapecitabineDips.size());
-        Elements unmatchedDips = capecitabineSection.select(".dpwg-capecitabine .rx-unmatched-dip");
+        Elements unmatchedDips = capecitabineSection.select(".dpwg-guideline-capecitabine .rx-unmatched-dip");
         assertEquals(expectedRxCalls, unmatchedDips.stream()
             .map(e -> cleanupRxDip(e, List.of("DPYD")))
             .toList());