add association bkg trait column to curation

EBISPOT · Jul 2, 2021 · 1d0190b · 1d0190b
1 parent 866bdf5
commit 1d0190b
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Showing 3 changed files with 29 additions and 2 deletions.
diff --git a/...ci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java b/...ci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java
@@ -41,6 +41,8 @@ public class SnpAssociationTableView {
 
     private String efoTraits;
 
+    private String backgroundEfoTraits;
+
     private Float orPerCopyNum;
 
     private Float orPerCopyRecip;
@@ -93,6 +95,7 @@ public SnpAssociationTableView(Long associationId,
                                    String betaUnit,
                                    String description,
                                    String efoTraits,
+                                   String backgroundEfoTraits,
                                    String lastMappingDate,
                                    String lastMappingPerformedBy,
                                    String multiSnpHaplotype,
@@ -120,6 +123,7 @@ public SnpAssociationTableView(Long associationId,
         this.betaUnit = betaUnit;
         this.description = description;
         this.efoTraits = efoTraits;
+        this.backgroundEfoTraits = backgroundEfoTraits;
         this.lastMappingDate = lastMappingDate;
         this.lastMappingPerformedBy = lastMappingPerformedBy;
         this.multiSnpHaplotype = multiSnpHaplotype;
@@ -213,6 +217,14 @@ public void setEfoTraits(String efoTraits) {
         this.efoTraits = efoTraits;
     }
 
+    public String getBackgroundEfoTraits() {
+        return backgroundEfoTraits;
+    }
+
+    public void setBackgroundEfoTraits(String backgroundEfoTraits) {
+        this.backgroundEfoTraits = backgroundEfoTraits;
+    }
+
     public String getLastMappingDate() {
         return lastMappingDate;
     }
@@ -376,4 +388,4 @@ public AssociationExtension getAssociationExtension() {
     public void setAssociationExtension(AssociationExtension associationExtension) {
         this.associationExtension = associationExtension;
     }
-}
+}
diff --git a/...on/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java b/...on/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java
@@ -223,6 +223,13 @@ public SnpAssociationTableView createSnpAssociationTableView(Association associa
         associationEfoTraits = String.join(", ", efoTraits);
         snpAssociationTableView.setEfoTraits(associationEfoTraits);
 
+        Collection<String> backgroundEfoTraits = new ArrayList<>();
+        for (EfoTrait efoTrait: association.getBkgEfoTraits()) {
+            backgroundEfoTraits.add(efoTrait.getTrait());
+        }
+        String associationBackgroundEfoTraits = String.join(",", backgroundEfoTraits);
+        snpAssociationTableView.setBackgroundEfoTraits(associationBackgroundEfoTraits);
+
         // Set OR values
         snpAssociationTableView.setOrPerCopyNum(association.getOrPerCopyNum());
         snpAssociationTableView.setOrPerCopyRecip(association.getOrPerCopyRecip());

diff --git a/goci-interfaces/goci-curation/src/main/resources/templates/study_association.html b/goci-interfaces/goci-curation/src/main/resources/templates/study_association.html
@@ -182,6 +182,7 @@
                     <th style="font-size: small">p-Value (mantissa x 10 exponent)</th>
                     <th style="font-size: small">p-Value Description</th>
                     <th style="font-size: small">EFO trait</th>
+                    <th style="font-size: small">Background EFO trait</th>
                     <th style="font-size: small">OR</th>
                     <th style="font-size: small">OR reciprocal</th>
                     <th style="font-size: small">Beta</th>
@@ -485,6 +486,13 @@
                                        th:text="'Warning: EFO trait not assigned'"></span>
                                 </td>
 
+                                <td>
+                                    <p th:text="${snpAssociationTableView.backgroundEfoTraits} ?: ''"></p>
+                                    <span style="font-style: italic; color:red; font-size: small"
+                                          th:if="*{#strings.isEmpty(snpAssociationTableView.backgroundEfoTraits)}"
+                                          th:text="'Warning: EFO trait not assigned'"></span>
+                                </td>
+
                                 <td th:text="${snpAssociationTableView.orPerCopyNum} ?: ''"></td>
                                 <td>
                                     <p th:text="${snpAssociationTableView.orPerCopyRecip} ?: ''"></p>
@@ -616,4 +624,4 @@
 </script>
 
 </body>
-</html>
+</html>