bugfixes in assay length

GC-HBOC · Feb 26, 2024 · d1910f7 · d1910f7
1 parent 26f5702
commit d1910f7
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Showing 4 changed files with 22 additions and 4 deletions.
diff --git a/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py b/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py
@@ -153,6 +153,8 @@ def save_to_db(self, info, variant_id, conn):
                 #submissions = functions.decode_vcf(submission)#.replace('\\', ',').replace('_', ' ').replace(',', ', ').replace('  ', ' ').replace('&', ';').split('|')
                 conn.insert_clinvar_submission(clinvar_variant_annotation_id, submissions[1], submissions[2], submissions[3], submissions[4], submissions[5], submissions[6])
 
+
+
         assay_type_dict = conn.get_assay_type_id_dict()
         conn.delete_assays(variant_id = variant_id,user_id = None) # delete only automatically annotated assays
         # CSpec splicing assays

diff --git a/src/common/db_IO.py b/src/common/db_IO.py
@@ -1246,7 +1246,7 @@ def preprocess_submission_condition(self, submission_condition):
             submission_condition.append("missing")
         elif len(submission_condition) > 2:
             functions.eprint("WARNING: the clinvar submission condition: " + str(submission_condition) + " has more than two entries. Although it should only have 2: id and description. Will be neglecting everything after the first two entries.")
-            submission_condition = submission_condition[0:2]
+            submission_condition = [submission_condition[0], ':'.join(submission_condition[1:])]
         return submission_condition
 
     def get_variant_consequences(self, variant_id):

diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
@@ -92,9 +92,20 @@ <h4>Overview</h4>
 
 <div class="bst bsb">
     <h4>Changelog</h4>
-    <div class="underline">v 1.8.1 (23.02.2024)</div>
+
+    <div class="underline">v 1.8.2 (26.02.2024)</div>
     <div class="btn-pvs">!! The automatic classification algorithm is currently under construction. HerediVar is already prepared for it. Thus, you might encounter disabled buttons or dummy data. It will be enabled in a future update</div>
     <div class="btn-pvs">!! Scores from likelihood ratio tests are currently under construction. A simple reannotation is required to show them on HerediVar once they are ready to be downloaded from HerediCaRe.</div>
+    <div>
+        Bugfixes:
+        <ul>
+            <li>Fixed a bug where the SpliceAI score was not shown correctly when it is "."</li>
+            <li>In rare cases the submission condition in ClinVar submissions is na with a description. This case is now handled properly and does not produce erroneous links.</li>
+            <li>Fixed a bug when the assay comment for splicing assays could not be inserted due to length</li>
+        </ul>
+    </div>
+
+    <div class="underline">v 1.8.1 (23.02.2024)</div>
     <div>
         General changes:
         <ul>
@@ -107,7 +118,6 @@ <h4>Changelog</h4>
             <li>Fixed default strength for supporting criteria in ACMG standard scheme</li>
             <li>Fixed wrapping of PVS1_mod criterium</li>
             <li>Fixed a bug where the SpliceAI scores would not show on longer indels</li>
-            <li>Fixed a bug where the SpliceAI score was not shown correctly when it is "."</li>
         </ul>
     </div>
     <div class="underline">v 1.8 (21.02.2024)</div>

diff --git a/src/frontend_celery/webapp/templates/variant/variant_base.html b/src/frontend_celery/webapp/templates/variant/variant_base.html
@@ -301,9 +301,15 @@ <h4 class="card-subcaption">ClinVar classifications</h4>
                                             <td>{{ submission.review_status }}</td>
                                             <td>
                                                 {% for clinvar_submission_condition in submission.conditions %}
+                                                    {% if clinvar_submission_condition.condition_id == 'na' %}
+                                                    <div>
+                                                        {{clinvar_submission_condition.title}}
+                                                    </div>
+                                                    {% else %}
                                                     <div>
                                                         {{ macros.external_link(clinvar_submission_condition.title, "https://www.ncbi.nlm.nih.gov/medgen/" + clinvar_submission_condition.condition_id) }}
                                                     </div>
+                                                    {% endif %}
                                                 {% endfor %}
                                             </td>
                                             <td>{{ submission.submitter }}</td>
@@ -434,7 +440,7 @@ <h4 class="card-subcaption">Assays</h4>
                                             {% for assay_metadata_title in assay.metadata %}
                                             <div class="d-flex">
                                                 <div class="width_medium">{{assay.metadata[assay_metadata_title].metadata_type.display_title}}</div>
-                                                <div class="width_medium">{{assay.metadata[assay_metadata_title].value}}</div>
+                                                <div class="width_large flex-grow-1">{{assay.metadata[assay_metadata_title].value}}</div>
                                             </div>
                                             {% endfor %}
                                         </td>