fix(reporter): show function in section 3 even when there is a no call

PharmGKB · Jul 26, 2023 · 4e2ea20 · 4e2ea20
1 parent 65a1309
commit 4e2ea20
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/ReportContext.java b/src/main/java/org/pharmgkb/pharmcat/reporter/ReportContext.java
@@ -195,7 +195,7 @@ public Map<DataSource, SortedMap<String, DrugReport>> getDrugReports() {
   /**
    * Gets the set of all {@link GeneReport} objects that are reported in this context
    */
-  public Map<DataSource, SortedMap<String, GeneReport>> getGeneReports() {
+  public SortedMap<DataSource, SortedMap<String, GeneReport>> getGeneReports() {
     return m_geneReports;
   }
 

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/format/HtmlFormat.java b/src/main/java/org/pharmgkb/pharmcat/reporter/format/HtmlFormat.java
@@ -120,7 +120,8 @@ private Map<String,Object> compile(ReportContext reportContext) {
     boolean hasUndocumentedVariationsAsReference = false;
 
     SortedSetMultimap<String, GeneReport> geneReportMap = TreeMultimap.create();
-    for (DataSource source : reportContext.getGeneReports().keySet()) {
+    Map<String, Map<String, String>> functionMap = new HashMap<>();
+    for (DataSource source : new TreeSet<>(reportContext.getGeneReports().keySet())) {
       if (!m_sources.contains(source)) {
         continue;
       }
@@ -129,12 +130,21 @@ private Map<String,Object> compile(ReportContext reportContext) {
         if (geneReport.isIgnored()) {
           continue;
         }
+
         String symbol = geneReport.getGeneDisplay();
         totalGenes.add(symbol);
         if (!m_compact) {
           geneReportMap.put(symbol, geneReport);
         }
 
+        // CPIC gets sorted first, this will pick CPIC over DPWG
+        if (!functionMap.containsKey(symbol)) {
+          GenePhenotype genePhenotype = getEnv().getPhenotype(symbol, source);
+          if (genePhenotype != null) {
+            functionMap.put(symbol, genePhenotype.getHaplotypes());
+          }
+        }
+
         if (geneReport.isNoData()) {
           noDataGenes.add(symbol);
           continue;
@@ -168,7 +178,6 @@ private Map<String,Object> compile(ReportContext reportContext) {
     List<Map<String, Object>> summaries = new ArrayList<>();
     List<GeneReport> geneReports = new ArrayList<>();
     Multimap<String, Map<String, Object>> geneSummariesByDrug = HashMultimap.create();
-    Map<String, Map<String, String>> functionMap = new HashMap<>();
     for (String symbol : genes) {
       if (noDataGenes.contains(symbol)) {
         continue;
@@ -195,16 +204,6 @@ private Map<String,Object> compile(ReportContext reportContext) {
       ((Set<String>)geneSummary.get("relatedDrugs"))
           .forEach(d -> geneSummariesByDrug.put(d, geneSummary));
       geneReports.add(reports.first());
-
-      // CPIC gets sorted first, this will pick CPIC over DPWG
-      for (GeneReport gr : reports) {
-        GenePhenotype genePhenotype = getEnv().getPhenotype(symbol, gr.getPhenotypeSource());
-        if (genePhenotype == null) {
-          continue;
-        }
-        functionMap.put(symbol, genePhenotype.getHaplotypes());
-        break;
-      }
     }
     result.put("genes", genes);
     result.put("noDataGenes", noDataGenes);

diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/handlebars/ReportHelpers.java b/src/main/java/org/pharmgkb/pharmcat/reporter/handlebars/ReportHelpers.java
@@ -14,6 +14,7 @@
 import java.util.stream.Stream;
 import com.google.common.html.HtmlEscapers;
 import org.apache.commons.lang3.StringUtils;
+import org.pharmgkb.pharmcat.phenotype.model.GenePhenotype;
 import org.pharmgkb.pharmcat.reporter.TextConstants;
 import org.pharmgkb.pharmcat.reporter.format.html.Report;
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
@@ -407,7 +408,7 @@ public static String amdAlleleFunction(Map<String, Map<String, String>> function
         return allele + " - " + function;
       }
     }
-    return allele + " - Unassigned function";
+    return allele + " - " + GenePhenotype.UNASSIGNED_FUNCTION;
   }
 
   public static String amdNoDataMessage(Collection<String> compactNoDataGenes) {