Merge branch 'main' into subject_id_search

CHANGELOG.md

@@ -10,6 +10,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Options for selectively updating OMICS variants (fraser, outrider) on a case
 - Log users' activity to file by specifying `USERS_ACTIVITY_LOG_PATH` parameter in app config
 - `Mean MT coverage`, `Mean chrom 14 coverage` and `Estimated mtDNA copy number` on MT coverage file from chanjo2 if available
+- In ClinVar multistep form, preselect ACMG criteria according to the variant's ACMG classification, if available
 - Subject id search from caseS page (supporting multiple sample types e.g.) - adding indexes to speed up caseS queries
 ### Changed
 - Documentation for OMICS variants and updating a case

scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html

@@ -209,14 +209,20 @@ <h3 class="fs-subtitle">The mode of inheritance specific to the variant-disease
                 <legend class="text-dark">Germline Classification</legend>
                 <h3 class="fs-subtitle">Represents a variant-level classification for a disease, rather than an interpretation of the clinical significance of a variant for a specific patient.</h3>
 
+                {% set scout_classif = variant_data.var_obj.classification|replace("_"," ") if variant_data.var_obj.classification else "n.a." %}
+
                 <div class="row">
                   <div class="col-4">
                     <span class="text-dark">Classification in Scout:</span><br>
-                    <span class="badge bg-secondary">{{variant_data.var_obj.classification|replace("_"," ")|upper if variant_data.var_obj.classification else "n.a."}}</span>
+                    <span class="badge bg-secondary">{{ scout_classif|upper }}</span>
                   </div>
                   <div class="col-8">
                     {{variant_data.var_form.clinsig.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required field"><strong>*</strong></span>
-                    {{variant_data.var_form.clinsig(class="form-control, btn-secondary")}}
+                    <select name="clinsig" class="form-control, btn-secondary">
+                      {% for classif, classif_value in variant_data.var_form.clinsig.choices %}
+                        <option value="{{classif_value}}" {% if classif==scout_classif|capitalize %} selected {% endif %}>{{classif}}</option>
+                      {% endfor %}
+                    </select>
                   </div>
                 </div>
                 <br><br><br>