From 06444bc14d3e34a06071275f0b5d371a5fb86975 Mon Sep 17 00:00:00 2001
From: iimpulse <Michael.Gargano@jax.org>
Date: Mon, 6 Jan 2025 12:41:28 -0700
Subject: [PATCH] fixing tests for result writers and reports

---
 .../exomiser/core/filters/FilterReport.java          |  4 ++++
 .../exomiser/core/writers/HtmlResultsWriter.java     |  1 +
 .../src/main/resources/templates/results.html        | 12 ++++++++----
 .../exomiser/core/filters/FilterReportTest.java      |  3 ++-
 4 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/filters/FilterReport.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/filters/FilterReport.java
index cd4b2ee38..7e457c02a 100644
--- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/filters/FilterReport.java
+++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/filters/FilterReport.java
@@ -73,6 +73,10 @@ 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;
     }
diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java
index 9a3fecbd3..465b75069 100644
--- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java
+++ b/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
diff --git a/exomiser-core/src/main/resources/templates/results.html b/exomiser-core/src/main/resources/templates/results.html
index 4552a016c..ba8cc3041 100644
--- a/exomiser-core/src/main/resources/templates/results.html
+++ b/exomiser-core/src/main/resources/templates/results.html
@@ -341,7 +341,7 @@ <h2 class="title text-center text-uppercase m-4">
         <div class="tab-pane fade" id="filtering" role="tabpanel">
             <div class="">
                 <div class="vstack gap-3">
-                    <div class="report-wrapper p-2" th:each="report : ${filterReports}">
+                    <div class="report-wrapper p-2" th:if="${filterReports.size() > 0}" th:each="report : ${filterReports}">
                             <div class="report-title-wrapper">
                                 <h5 class="report-title" th:text="${report.filterType.shortName}">Frequency</h5>
                                 <p class="report-description" th:each="message : ${report.messages}"
@@ -351,8 +351,9 @@ <h5 class="report-title" th:text="${report.filterType.shortName}">Frequency</h5>
                                 </p>
                             </div>
                             <div class="report-numbers">
-                                <div class="report-percentloss" th:classappend="${#numbers.formatDecimal(report.getPercentageFilteredFromReport(filterReports.get(0).getTotalEvaluationCount()), 1, 0)} > 0 ? 'report-text-violetred' : ''"
-                                     th:text="${#numbers.formatDecimal(report.getPercentageFilteredFromReport(filterReports.get(0).getTotalEvaluationCount()), 1, 0)} + '%'"></div>
+                                <div class="report-percentloss" th:if="${report != null}"
+                                     th:classappend="${report != null ? (#numbers.formatDecimal(report.getPercentageFilteredFromReport(filterReportEvalCount), 1, 0) > 0 ? 'report-text-violetred' : '') : '' } == 'report-text-violetred' ? 'report-text-violetred' : ''"
+                                     th:text="${#numbers.formatDecimal(report.getPercentageFilteredFromReport(filterReportEvalCount), 1, 0)} + '%'"></div>
                                 <div class="text-sm pass-fail text-end">
                                     <span class="text-muted" th:text="${#numbers.formatDecimal(report.passed, 0, 'COMMA', 0, 'POINT')} + ' Passed'"></span><br>
                                     <span class="text-muted" th:text="${#numbers.formatDecimal(report.failed, 0, 'COMMA', 0, 'POINT')}  + ' Failed'"></span>
@@ -360,7 +361,7 @@ <h5 class="report-title" th:text="${report.filterType.shortName}">Frequency</h5>
                             </div>
 
                     </div>
-                    <p class="summary-report text-lg-end p-2"><strong th:text="${filterReports.get(filterReports.size() - 1).passed}"></strong> Variants Passed All Filters</p>
+                    <p class="summary-report text-lg-end p-2" th:if="${filterReports.size() > 0}"><strong th:text="${filterReports.get(filterReports.size() - 1).passed}"></strong> Variants Passed All Filters</p>
                 </div>
             </div>
         </div>
@@ -392,6 +393,9 @@ <h6 class="m-0" th:text="${gene.getGeneIdentifier().getGeneSymbol()}">
                         <div class="col">
                             <span>Variant Score <b th:text="${#numbers.formatDecimal(gene.getVariantScore(), 1, 3)}">1.00</b></span>
                         </div>
+                        <div class="col">
+                            <span th:if="${gene.getTopGeneScore().getAcmgAssignments().size() > 0}" th:text="${gene.getTopGeneScore().getAcmgAssignments().get(0)}"></span>
+                        </div>
                     </div>
                 </div>
 
diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/filters/FilterReportTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/filters/FilterReportTest.java
index c5cb0ef34..e55654fc3 100644
--- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/filters/FilterReportTest.java
+++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/filters/FilterReportTest.java
@@ -147,7 +147,8 @@ public void testToString() {
 
     @Test
     public void testPercentageFailed(){
-        assertThat(instance.getPercentageFilteredFromBeginning(345), equalTo(((345 - 12) / 345) * 100));
+        double expected = ((double)(345 - 12) / 345) * 100;
+        assertThat(instance.getPercentageFilteredFromBeginning(345), equalTo(expected));
     }
 
 }