Merge branch 'main' into version_4.79.1

Clinical-Genomics · Mar 13, 2024 · ad2401b · ad2401b
2 parents 630f90a + ece9e06
commit ad2401b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 ## [4.79.1]
 ### Fixed
 - Exporting variants without rank score causing page to crash
+- Display custom annotations also on cancer variant page
 
 ## [4.79]
 ### Added

diff --git a/scout/server/blueprints/variant/templates/variant/cancer-variant.html b/scout/server/blueprints/variant/templates/variant/cancer-variant.html
@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "utils.html" import comments_panel, activity_panel %}
-{% from "variant/utils.html" import overlapping_panel, genes_panel, transcripts_panel, proteins_panel, pin_button, causative_button, modal_causative %}
+{% from "variant/utils.html" import overlapping_panel, genes_panel, transcripts_panel, proteins_panel, pin_button, causative_button, modal_causative, custom_annotations %}
 {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %}
 {% from "variant/variant_details.html" import frequencies, gtcall_panel, observations_panel, old_observations, mappability_list, severity_list %}
 {% from "variant/buttons.html" import database_buttons, variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button, splice_junctions_button %}
@@ -279,7 +279,17 @@ <h6 class="card-header">Variant callers</h6>
     <!--IGV URLS-->
     <div class="ms-4">Alignment</div>
       {{ alignments(institute, case, variant, current_user, config, igv_tracks, rna_tracks) }}
-  </div>
+    </div>
+
+    <!-- Display eventual custom annotations-->
+    {% if variant.custom %}
+      <ul class="list-group list-group-flush" style="margin-bottom: 1rem">
+        <li class="list-group-item">
+          {{ custom_annotations(variant) }}
+        </li>
+      </ul>
+    {% endif %}
+
 {% endmacro %}
 
 

diff --git a/scout/server/blueprints/variant/templates/variant/sv-variant.html b/scout/server/blueprints/variant/templates/variant/sv-variant.html
@@ -2,7 +2,7 @@
 {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %}
 {% from "variant/variant_details.html" import old_observations %}
 {% from "variant/components.html" import external_scripts, external_stylesheets, matching_variants, variant_scripts %}
-{% from "variant/utils.html" import causative_button, genes_panel, igv_track_selection, modal_causative, overlapping_panel, sv_alignments, pin_button, transcripts_panel %}
+{% from "variant/utils.html" import causative_button, genes_panel, igv_track_selection, modal_causative, overlapping_panel, sv_alignments, pin_button, transcripts_panel, custom_annotations %}
 {% from "variant/rank_score_results.html" import rankscore_panel %}
 {% from "variant/gene_disease_relations.html" import orpha_omim_phenotypes %}
 {% from "variant/variant_details.html" import frequencies, gtcall_panel, observations_panel %}
@@ -277,16 +277,16 @@
             {{ splice_junctions_button(institute._id, case.display_name, variant._id) }}
           </li>
         {% endif %}
+      </ul>
+
       {% if variant.custom %}
-        {% for pair in variant.custom %}
-        <li class="list-group-item">
-          <div class="row d-flex justify-content-between">
-            <div>{{pair[0]}}</div><div class="float-end">{{pair[1]}}</div>
-          </div>
-        </li>
-        {% endfor %}
+         <!-- Display eventual custom annotations-->
+        <ul class="list-group list-group-flush" style="margin-bottom: 1rem">
+          <li class="list-group-item">
+            {{ custom_annotations(variant) }}
+          </li>
+        </ul>
       {% endif %}
-      </ul>
     </div> <!-- end of card body -->
   </div> <!-- end of card -->
 

diff --git a/scout/server/blueprints/variant/templates/variant/utils.html b/scout/server/blueprints/variant/templates/variant/utils.html
@@ -418,3 +418,26 @@ <h6>Phenotype terms (HPO):</h6>
   </button>
   {% endif %}
 {% endmacro %}
+
+
+{% macro custom_annotations(variant) %}
+<table class="table table-bordered table-sm">
+  <caption></caption>
+	<thead class="thead table-light">
+	  <th>Custom annotation</th>
+	  <th>Value</th>
+	</thead>
+	<tbody>
+	  {% for pair in variant.custom %}
+	  <tr>
+	    <td>
+	      {{ pair[0] }}
+	    </td>
+	    <td>
+	      {{ pair[1] }}
+	    </td>
+	  </tr>
+	  {% endfor %}
+	</tbody>
+</table>
+{% endmacro %}
diff --git a/scout/server/blueprints/variant/templates/variant/variant.html b/scout/server/blueprints/variant/templates/variant/variant.html
@@ -2,7 +2,7 @@
 {% from "variant/buttons.html" import database_buttons %}
 {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %}
 {% from "variants/utils.html" import compounds_table %}
-{% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel %}
+{% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel, custom_annotations %}
 {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %}
 {% from "variant/gene_disease_relations.html" import autozygosity_panel, genemodels_panel, inheritance_panel, orpha_omim_phenotypes %}
 {% from "variant/variant_details.html" import frequencies, gtcall_panel, old_observations, observations_panel, severity_list, conservations, mappability %}
@@ -398,25 +398,14 @@ <h6 class="font-weight-bold">{{ image.title }}</h6>
         {{ database_buttons(variant) }}
       {% endif %}
       {{ alignments(institute, case, variant, current_user, config, igv_tracks, has_rna_tracks) }}
+
+     <!-- Display eventual custom annotations-->
       {% if variant.custom %}
-      <table class="table table-bordered table-sm">
-	<thead class="thead table-light">
-	  <th>Custom annotation</th>
-	  <th>Value</th>
-	</thead>
-	<tbody>
-	  {% for pair in variant.custom %}
-	  <tr>
-	    <td>
-	      {{ pair[0] }}
-	    </td>
-	    <td>
-	      {{ pair[1] }}
-	    </td>
-	  </tr>
-	  {% endfor %}
-	</tbody>
-      </table>
+      <ul class="list-group list-group-flush" style="margin-bottom: 1rem">
+        <li class="list-group-item">
+          {{ custom_annotations(variant) }}
+        </li>
+      </ul>
       {% endif %}
 
     </div> <!-- end of card body -->