From 1d0190bc985f92952b2fcdf2698fe24b06b670aa Mon Sep 17 00:00:00 2001
From: ala <ala@ebi.ac.uk>
Date: Fri, 2 Jul 2021 12:34:15 +0100
Subject: [PATCH] add association bkg trait column to curation

---
 .../curation/model/SnpAssociationTableView.java    | 14 +++++++++++++-
 .../service/SnpAssociationTableViewService.java    |  7 +++++++
 .../resources/templates/study_association.html     | 10 +++++++++-
 3 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java b/goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java
index f9b4297adf..4ca9dcd978 100644
--- a/goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java
+++ b/goci-interfaces/goci-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;
     }
-}
\ No newline at end of file
+}
diff --git a/goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java b/goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java
index 9229781ffe..224cf804b6 100644
--- a/goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java
+++ b/goci-interfaces/goci-curation/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
index 4c2f684d5a..83b4c038d2 100644
--- 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>
\ No newline at end of file
+</html>