Enhancement/html report

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/filters/FilterReport.java

@@ -69,6 +69,22 @@ public int getFailed() {
         return failed;
     }
 
+    public double getPercentageFilteredFromBeginning(double originalSize) {
+        return ((originalSize - (double) passed) / originalSize) * 100;
+    }
+
+    public double getPercentageFilteredFromReports(double originalSize) {
+        return (failed / originalSize) * 100;
+    }
+
+    public double getPercentageFilteredFromReport(double originalSize) {
+        return (failed / originalSize) * 100;
+    }
+
+    public int getTotalEvaluationCount() {
+        return passed + failed;
+    }
+
     @Override
     public int hashCode() {
         int hash = 5;

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/filters/FilterType.java

@@ -29,7 +29,7 @@
  */
 public enum FilterType {
 
-    FAILED_VARIANT_FILTER("filter", "Failed previous VCF filters"),
+    FAILED_VARIANT_FILTER("filter", "VCF Quality Filter"),
     QUALITY_FILTER("quality", "Quality"),
     INTERVAL_FILTER("interval", "Interval"),
     ENTREZ_GENE_ID_FILTER("gene-id", "Gene id"),

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhivePriorityResult.java

@@ -32,8 +32,10 @@
 import org.monarchinitiative.exomiser.core.prioritisers.model.GeneModelPhenotypeMatch;
 
 import javax.annotation.Nullable;
+import java.lang.reflect.Array;
 import java.util.*;
 import java.util.function.Function;
+import java.util.stream.Collectors;
 
 import static java.util.stream.Collectors.toMap;
 
@@ -289,51 +291,51 @@ public String getHTMLCode() {
         StringBuilder stringBuilder = new StringBuilder();
 
         for (GeneModelPhenotypeMatch geneModelPhenotypeMatch : phenotypeEvidence.values()) {
+            stringBuilder.append("<div class=\"pheno-match-card card col-sm-5\">");
             switch (geneModelPhenotypeMatch.getOrganism()) {
                 case HUMAN:
                     GeneDiseaseModel geneDiseaseModel = (GeneDiseaseModel) geneModelPhenotypeMatch.getModel();
                     String diseaseLink = makeDiseaseLink(geneDiseaseModel.getDiseaseId(), geneDiseaseModel.getDiseaseTerm());
-                    stringBuilder.append(String.format("<dl><dt>Phenotypic similarity %.3f to %s associated with %s.</dt>", geneModelPhenotypeMatch
-                            .getScore(), diseaseLink, geneModelPhenotypeMatch.getHumanGeneSymbol()));
+                    stringBuilder.append(String.format("<h5 class=\"card-header\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Phenotype Score\">%.3f</span>%s <a href=\"https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=%s\" target=\"_blank\" class=\"text-decoration-none\">%s</a></h5>", geneModelPhenotypeMatch
+                            .getScore(), diseaseLink, geneModelPhenotypeMatch.getHumanGeneSymbol(), geneModelPhenotypeMatch.getHumanGeneSymbol()));
                     break;
                 case MOUSE:
-                    stringBuilder.append(String.format("<dl><dt>Phenotypic similarity %.3f to mouse mutant involving <a href=\"http://www.informatics.jax.org/searchtool/Search.do?query=%s\">%s</a>.</dt>", geneModelPhenotypeMatch
+                    stringBuilder.append(String.format("<h5 class=\"card-header\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Phenotype Score\">%.3f</span><span>Mouse Mutant</span> <a class=\"text-decoration-none\" target=\"_blank\" href=\"https://www.informatics.jax.org/searchtool/Search.do?query=%s\">%s</a></h5>", geneModelPhenotypeMatch
                             .getScore(), geneModelPhenotypeMatch.getHumanGeneSymbol(), geneModelPhenotypeMatch.getHumanGeneSymbol()));
                     break;
                 case FISH:
-                    stringBuilder.append(String.format("<dl><dt>Phenotypic similarity %.3f to zebrafish mutant involving <a href=\"http://zfin.org/action/quicksearch/query?query=%s\">%s</a>.</dt>", geneModelPhenotypeMatch
+                    stringBuilder.append(String.format("<h5 class=\"card-header\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Phenotype Score\">%.3f</span><span>Zebrafish Mutant</span> <a class=\"text-decoration-none\" target=\"_blank\" href=\"https://zfin.org/action/quicksearch/query?query=%s\">%s</a></h5>", geneModelPhenotypeMatch
                             .getScore(), geneModelPhenotypeMatch.getHumanGeneSymbol(), geneModelPhenotypeMatch.getHumanGeneSymbol()));
                     break;
             }
             Map<PhenotypeTerm, PhenotypeMatch> bestMatchesForModel = getPhenotypeTermPhenotypeMatchMap(geneModelPhenotypeMatch);
             makeBestPhenotypeMatchHtml(stringBuilder, bestMatchesForModel);
-            stringBuilder.append("</dl>");
+            stringBuilder.append("</div>");
         }
 
         for (GeneModelPhenotypeMatch geneModelPhenotypeMatch : ppiEvidence) {
             String stringDbLink = "http://version10.string-db.org/newstring_cgi/show_network_section.pl?identifiers=" + geneSymbol + "%0D" + geneModelPhenotypeMatch
                     .getHumanGeneSymbol() + "&required_score=700&network_flavor=evidence&species=9606&limit=20";
-
+            stringBuilder.append("<div class=\"pheno-match-card card col-sm-5\">");
             switch (geneModelPhenotypeMatch.getOrganism()) {
                 case HUMAN:
                     GeneDiseaseModel geneDiseaseModel = (GeneDiseaseModel) geneModelPhenotypeMatch.getModel();
                     String diseaseLink = makeDiseaseLink(geneDiseaseModel.getDiseaseId(), geneDiseaseModel.getDiseaseTerm());
-                    stringBuilder.append(String.format("<dl><dt>Proximity score %.3f in <a href=\"%s\">interactome to %s</a> and phenotypic similarity %.3f to %s associated with %s.</dt>", ppiScore, stringDbLink, geneModelPhenotypeMatch
-                            .getHumanGeneSymbol(), geneModelPhenotypeMatch.getScore(), diseaseLink, geneModelPhenotypeMatch
+                    stringBuilder.append(String.format("<h5 class=\"card-header\"><div class=\"d-flex ai-c\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Phenotype Score\">%.3f</span>&nbsp;&nbsp;%s</div> via <div class=\"d-flex ai-c\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Proximity Score\">%.3f</span>&nbsp;&nbsp;<a class=\"text-decoration-none\" target=\"_blank\" href=\"%s\">Interactome Proximity</a></div> to <a href=\"https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=%s\" target=\"_blank\" class=\"text-decoration-none\">%s</a></h5>", geneModelPhenotypeMatch.getScore(), diseaseLink, ppiScore, stringDbLink, geneModelPhenotypeMatch
+                            .getHumanGeneSymbol(), geneModelPhenotypeMatch
                             .getHumanGeneSymbol()));
                     break;
                 case MOUSE:
-                    stringBuilder.append(String.format("<dl><dt>Proximity score %.3f in <a href=\"%s\">interactome to %s</a> and phenotypic similarity %.3f to mouse mutant of %s.</dt>", ppiScore, stringDbLink, geneModelPhenotypeMatch
-                            .getHumanGeneSymbol(), geneModelPhenotypeMatch.getScore(), geneModelPhenotypeMatch.getHumanGeneSymbol()));
+                    stringBuilder.append(String.format("<h5 class=\"card-header\"><div class=\"d-flex ai-c\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Phenotype Score\">%.3f</span><span>&nbsp;&nbsp;Mouse Mutant</span></div> via <div class=\"d-flex ai-c\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Proximity Score\">%.3f</span>&nbsp;&nbsp;<a class=\"text-decoration-none\" target=\"_blank\" href=\"%s\">Interactome Proximity</a></div> to <a href=\"https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=%s\" target=\"_blank\" class=\"text-decoration-none\">%s</a></h5>", geneModelPhenotypeMatch.getScore(), ppiScore, stringDbLink,  geneModelPhenotypeMatch.getHumanGeneSymbol(), geneModelPhenotypeMatch.getHumanGeneSymbol()));
                     break;
                 case FISH:
-                    stringBuilder.append(String.format("<dl><dt>Proximity score %.3f in <a href=\"%s\">interactome to %s</a> and phenotypic similarity %.3f to fish mutant of %s.</dt>", ppiScore, stringDbLink, geneModelPhenotypeMatch
-                            .getHumanGeneSymbol(), geneModelPhenotypeMatch.getScore(), geneModelPhenotypeMatch.getHumanGeneSymbol()));
+                    stringBuilder.append(String.format("<h5 class=\"card-header\"><div class=\"d-flex ai-c\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Phenotype Score\">%.3f</span>&nbsp;&nbsp;<span>Zebrafish</span></div> via <div class=\"d-flex ai-c\"><span class=\"badge bg-secondary\" data-bs-toggle=\"tooltip\" data-bs-placement=\"top\" title=\"Proximity Score\">%.3f</span>&nbsp;&nbsp;<a class=\"text-decoration-none\" target=\"_blank\" href=\"%s\">Interactome Proximity</a></div> to <a href=\"https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=%s\" target=\"_blank\" class=\"text-decoration-none\">%s</a></h5>", geneModelPhenotypeMatch.getScore(), ppiScore, stringDbLink, geneModelPhenotypeMatch.getHumanGeneSymbol(), geneModelPhenotypeMatch
+                            .getHumanGeneSymbol()));
                     break;
             }
             Map<PhenotypeTerm, PhenotypeMatch> bestModelPhenotypeMatches = getPhenotypeTermPhenotypeMatchMap(geneModelPhenotypeMatch);
             makeBestPhenotypeMatchHtml(stringBuilder, bestModelPhenotypeMatches);
-            stringBuilder.append("</dl>");
+            stringBuilder.append("</div>");
         }
         String html = stringBuilder.toString();
         if (html.isEmpty()) {
@@ -353,26 +355,52 @@ private void makeBestPhenotypeMatchText(StringBuilder stringBuilder, Map<Phenoty
     }
 
     private void makeBestPhenotypeMatchHtml(StringBuilder stringBuilder, Map<PhenotypeTerm, PhenotypeMatch> bestModelPhenotypeMatches) {
-        stringBuilder.append("<dt>Best Phenotype Matches:</dt>");
+        Collection<PhenotypeMatch> matches = new ArrayList<>();
+        int unmatched = 0;
+        stringBuilder.append("<div class=\"card-body\">");
+        stringBuilder.append("<div class=\"d-flex px-2\"><div class=\"flex-grow-1 fw-bold\">Sample</div><div class=\"fw-bold\">Reference</div></div>");
         for (PhenotypeTerm queryTerm : queryPhenotypeTerms) {
             if (bestModelPhenotypeMatches.containsKey(queryTerm)) {
                 PhenotypeMatch match = bestModelPhenotypeMatches.get(queryTerm);
-                PhenotypeTerm matchTerm = match.getMatchPhenotype();
-                stringBuilder.append(String.format("<dd>%s, %s - %s, %s</dd>", queryTerm.getId(), queryTerm.getLabel(), matchTerm.getId(), matchTerm.getLabel()));
+                matches.add(match);
             } else {
-                stringBuilder.append(String.format("<dd>%s, %s -</dd>", queryTerm.getId(), queryTerm.getLabel()));
+                unmatched++;
             }
         }
+
+        matches = matches.stream()
+                .sorted((a, b) -> {
+                    boolean aMatches = a.getMatchPhenotypeId().equals(a.getQueryPhenotypeId());
+                    boolean bMatches = b.getMatchPhenotypeId().equals(b.getQueryPhenotypeId());
+                    int compare = Boolean.compare(bMatches, aMatches);
+                    if (compare == 0) {
+                        return Double.compare(b.getSimJ(), a.getSimJ());
+                    }
+                    return compare;
+                })
+                .collect(Collectors.toList());
+
+        for (PhenotypeMatch match: matches){
+            stringBuilder.append(String.format(
+                    "<div class=\"matched-set\"><div class=\"match\"><div class=\"match-left text-sm\"><div class=\"match-id\">%s</div><div class=\"match-name px-2\">%s</div></div>" +
+                    "<div class=\"align-self-center\"><span class=\"badge bg-success\">%.3f</span></div>" +
+                    "<div class=\"match-right text-sm\"><div class=\"match-id\">%s</div><div class=\"match-name px-2\">%s</div></div></div></div>", match.getQueryPhenotypeId(), match.getQueryPhenotype().getLabel(), match.getSimJ(), match.getMatchPhenotype().getId(), match.getMatchPhenotype().getLabel()));
+        }
+
+        stringBuilder.append("</div>");
+        if (unmatched > 0) {
+            stringBuilder.append(String.format("<div class=\"card-footer text-muted text-end\">%s of %s phenotypes unmatched.</div>", unmatched, queryPhenotypeTerms.size()));
+        }
     }
 
     private String makeDiseaseLink(String diseaseId, String diseaseTerm) {
         String[] databaseNameAndIdentifier = diseaseId.split(":");
         String databaseName = databaseNameAndIdentifier[0];
         String id = databaseNameAndIdentifier[1];
         if (databaseName.equals("OMIM")) {
-            return "<a href=\"http://www.omim.org/entry/" + id + "\">" + diseaseTerm + "</a>";
+            return "<a class=\"text-decoration-none\" href=\"http://www.omim.org/entry/" + id + "\" target=\"_blank\">" + diseaseTerm + "</a>";
         } else {
-            return "<a href=\"http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=" + id + "\">" + diseaseTerm + "</a>";
+            return "<a class=\"text-decoration-none\" href=\"http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=" + id + "\" target=\"_blank\">" + diseaseTerm + "</a>";
         }
     }
 

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java

@@ -115,6 +115,7 @@ private Context buildContext(AnalysisResults analysisResults, OutputSettings out
         //write out the analysis reports section
         List<FilterReport> analysisStepReports = ResultsWriterUtils.makeFilterReports(analysis, analysisResults);
         context.setVariable("filterReports", analysisStepReports);
+        context.setVariable("filterReportEvalCount", !analysisStepReports.isEmpty() ? analysisStepReports.get(0).getTotalEvaluationCount() : 0.00);
         //write out the variant type counters
         List<String> sampleNames = analysisResults.getSampleNames();
         List<VariantEffectCount> variantTypeCounters = ResultsWriterUtils.makeVariantEffectCounters(sampleNames, analysisResults

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/filters/FilterReportTest.java

@@ -145,4 +145,10 @@ public void testToString() {
         assertThat(instance.toString(), equalTo(expResult));
     }
 
+    @Test
+    public void testPercentageFailed(){
+        double expected = ((double)(345 - 12) / 345) * 100;
+        assertThat(instance.getPercentageFilteredFromBeginning(345), equalTo(expected));
+    }
+
 }