scout-browser 4.80__py3-none-any.whl → 4.82.1__py3-none-any.whl

scout/server/blueprints/institutes/templates/overview/cases.html

@@ -153,7 +153,7 @@
         {% if case.vcf_files.vcf_snv %}
           <a href="{{ url_for('variants.variants', institute_id=case.owner, case_name=case.display_name, variant_type='research') }}">Research SNV and INDELs</a>
         {% elif case.vcf_files.vcf_cancer %}
-          <a href="{{ url_for('variants.cancer_variants', institute_id=case.owner, case_name=case.display_name, variant_type='research') }}">Clinical Somatic Variants</a>
+          <a href="{{ url_for('variants.cancer_variants', institute_id=case.owner, case_name=case.display_name, variant_type='research') }}">Research Somatic Variants</a>
         {% endif %}
       {% else %}
         {% if case.vcf_files.vcf_snv %}
@@ -192,6 +192,54 @@
   </tr>
 {% endmacro %}
 
+{% macro sanger_to_be_validated(unevaluated, validated_by_others) %}
+ <div class="row container alert alert-info alert-dismissible" role="alert">
+  <div class="col-1">
+   <button type="button" class="close" data-bs-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+  </div>
+  <div class="col">
+    You have <strong>{{ unevaluated|length }}</strong> cases with Sanger validations to evaluate.
+    {% if validated_by_others == true %}
+      These variants have been validated by another user, but you ordered the Sanger sequencing. Adding your validation will silence this message.
+    {% endif %}
+    <!-- Button trigger modal -->
+    <button type="button" class="btn btn-primary btn-sm" data-bs-toggle="modal" data-bs-target="#evaluateModal_validated{% if validated_by_others %}_by_others{% endif %}">
+      evaluate
+    </button>
+  </div>
+
+  <!-- Modal -->
+  <div class="modal fade" id="evaluateModal_validated{% if validated_by_others %}_by_others{% endif %}" tabindex="-1" role="dialog" aria-labelledby="sangerModalLabel" aria-hidden="true">
+    <div class="modal-dialog" role="document">
+      <div class="modal-content">
+        <div class="modal-header">
+          <h5 class="modal-title" id="sangerModalLabel">Sanger validations to evaluate:</h5>
+        </div>
+        <div class="modal-body">
+          <ul>
+            {% for uneval_obj in unevaluated %}
+              {% for case, var_list in uneval_obj.items() %}
+              <li>
+                Case <strong><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case) }}" target="_blank">{{case}}</a></strong> ---> <strong>{{var_list|length}}</strong> variants:
+                <ul>
+                  {% for var in var_list %}
+                    <li><a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=case, variant_id=var) }}" target="_blank">{{var}}</a></li>
+                  {% endfor %}
+                </ul>
+              </li>
+              {% endfor %}
+            {% endfor %}
+          </ul>
+        </div>
+        <div class="modal-footer">
+          <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
+        </div>
+      </div>
+    </div>
+  </div>
+</div>
+{% endmacro %}
+
 {% block content_main %}
 <div class="container-float">
   <div class="row" id="body-row"> <!--sidebar and main container are on the same row-->
@@ -208,49 +256,13 @@
       </div>
 
       {% if sanger_unevaluated %}
-        <div class="container alert alert-info alert-dismissible" role="alert">
-          <button type="button" class="close" data-bs-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-          {% if sanger_unevaluated|length > 1%}
-          You have <strong>{{ sanger_unevaluated|length }}</strong> cases with Sanger validations to evaluate!
-          {% else %}
-          You have <strong>1</strong> case with Sanger validations to evaluate!&nbsp;
-          {% endif %}
-          <!-- Button trigger modal -->
-          <button type="button" class="btn btn-primary btn-sm" data-bs-toggle="modal" data-bs-target="#evaluateModal">
-            evaluate
-          </button>
+        {{ sanger_to_be_validated(sanger_unevaluated, false) }}
+      {% endif %}
 
-          <!-- Modal -->
-          <div class="modal fade" id="evaluateModal" tabindex="-1" role="dialog" aria-labelledby="sangerModalLabel" aria-hidden="true">
-            <div class="modal-dialog" role="document">
-              <div class="modal-content">
-                <div class="modal-header">
-                  <h5 class="modal-title" id="sangerModalLabel">Sanger validations to evaluate:</h5>
-                </div>
-                <div class="modal-body">
-                  <ul>
-                    {% for uneval_obj in sanger_unevaluated %}
-                    {% for case, var_list in uneval_obj.items() %}
-                    <li>
-                      Case <strong><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case) }}" target="_blank">{{case}}</a></strong> ---> <strong>{{var_list|length}}</strong> variants:
-                      <ul>
-                        {% for var in var_list %}
-                          <li><a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=case, variant_id=var) }}" target="_blank">{{var}}</a></li>
-                        {% endfor %}
-                      </ul>
-                    </li>
-                    {% endfor %}
-                    {% endfor %}
-                  </ul>
-                </div>
-                <div class="modal-footer">
-                  <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
+      {% if sanger_validated_by_others %}
+        {{ sanger_to_be_validated(sanger_validated_by_others, true) }}
       {% endif %}
+
       <div>
         {% set ordered_statuses = ['prioritized', 'inactive', 'active', 'archived', 'solved', 'ignored'] -%}
         {% for status in ordered_statuses %}

scout/server/blueprints/managed_variants/templates/managed_variants/managed_variants.html

@@ -184,7 +184,7 @@
       <div class="col-sm-7 text-center">
         <input type="file" name="csv_file" class="custom-file-input" required onchange="this.nextElementSibling.innerText = this.files[0].name">
         <label class="custom-file-label" for="csv_file">Choose file</label><br>
-        <p class="help-block">How do I format my <a href="https://clinical-genomics.github.io/scout/user-guide/variants/#Managed-variants-upload-file-format" rel="noopener" target="_blank">managed variants file</a>?</p>
+        <p class="help-block">How do I format my <a href="https://clinical-genomics.github.io/scout/user-guide/variants/#managed-variants-upload-file-format" rel="noopener" target="_blank">managed variants file</a>?</p>
       </div>
       <div class="col-sm-2 text-center">
         <button type="submit" class="btn btn-secondary">Upload</button>

scout/server/blueprints/managed_variants/views.py

@@ -1,7 +1,6 @@
-import datetime
 import logging
 
-from flask import Blueprint, flash, redirect, request, url_for
+from flask import Blueprint, flash, redirect, request
 from flask_login import current_user
 
 from scout.server.extensions import store
@@ -29,12 +28,12 @@ def upload_managed_variants():
 
     csv_file = request.files["csv_file"]
     content = csv_file.stream.read()
-    lines = None
     try:
         if b"\n" in content:
             lines = content.decode("utf-8-sig", "ignore").split("\n")
         else:
             lines = content.decode("windows-1252").split("\r")
+
     except Exception as err:
         flash(
             "Something went wrong while parsing the panel CSV file! ({})".format(err),
@@ -42,7 +41,6 @@ def upload_managed_variants():
         )
         return redirect(request.referrer)
 
-    LOG.debug("Loading lines %s", lines)
     result = controllers.upload_managed_variants(store, lines, institutes, current_user._id)
     flash(
         "In total {} new variants out of {} in file added".format(result[0], result[1]),

scout/server/blueprints/panels/templates/panels/panel.html

@@ -1,3 +1,4 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
 {% extends "layout.html" %}
 
 {% block title %}
@@ -103,18 +104,18 @@
           </span>
         </li>
       {% endif %}
-      {% if case and case.chanjo2_coverage %}
+      {% if case and case.chanjo2_coverage and panel.genes %}
         <li class="list-group-item">
           <label for="coverage_report">Coverage report (chanjo2)</label>
-          <a class="float-end"  href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id, case_name=case.display_name, panel_name=panel.name_and_version, panel_id=panel._id, report_type='report') }}" target="_blank" rel="noopener">
-            {{ case.display_name }}
-          </a>
+          <span class="float-end">
+          {{ chanjo2_report_form(panel.institute, case, panel.name_and_version, 'report', panel.genes|map(attribute='hgnc_id')|join(','), case.display_name) }} <!--chanjo2 report-->
+          </span>
         </li>
         <li class="list-group-item">
           <label for="coverage_report">Coverage overview (chanjo2)</label>
-          <a class="float-end"  href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id, case_name=case.display_name, panel_name=panel.name_and_version, panel_id=panel._id, report_type='overview') }}" target="_blank" rel="noopener">
-            {{ case.display_name }}
-          </a>
+          <span class="float-end">
+          {{ chanjo2_report_form(panel.institute, case, panel.name_and_version, 'overview', panel.genes|map(attribute='hgnc_id')|join(','), case.display_name) }} <!--chanjo2 genes overview -->
+          </span>
         </li>
       {% endif %}
       <li class="list-group-item">

scout/server/blueprints/panels/templates/panels/panel_pdf_case_hits.html

@@ -6,7 +6,7 @@
   <h4>Scout - Institute {{institute.display_name}} - case {{case.display_name}} - {{panel.name_and_version}}: panel extent report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong><br><br>
   {{ hits_panel() }}
   <br>[END OF REPORT]<br><br>
-  <a href="https://clinical-genomics.github.io/scout" target="_blank" rel="noopener">clinical-genomics.github.io/scout</a>
+  <a style="text-decoration:none;" href="https://clinical-genomics.github.io/scout" target="_blank" rel="noopener">clinical-genomics.github.io/scout</a>
 </div>
 {% endblock %}
 
@@ -21,7 +21,7 @@
       Gene panel: <strong>{{panel.name_and_version}}</strong><br>
       Last updated: <strong>{{ panel.date.strftime('%Y-%m-%d') }}</strong>
       {% if case.outdated_panels and panel.panel_name in case.outdated_panels %}
-              <a><span class="badge rounded-pill badge-sm bg-warning" data-bs-toggle="popover" data-bs-placement="left" data-bs-html="true" data-bs-content="Panel version used in the analysis ({{panel.version}}) is outdated. Latest panel version is used in variants filtering.<br /><strong>Genes present in case panel and not in latest version</strong>: {{case.outdated_panels[panel.panel_name]['extra_genes']|join(', ') or '-'}}.<br /><strong>Genes present only in latest version</strong>: {{case.outdated_panels[panel.panel_name]['missing_genes']|join(', ') or '-'}}.">!</span></a>
+              <a><span class="badge rounded-pill py-1 bg-warning" data-bs-toggle="popover" data-bs-placement="left" data-bs-html="true" data-bs-content="Panel version used in the analysis ({{panel.version}}) is outdated. Latest panel version is used in variants filtering.<br /><strong>Genes present in case panel and not in latest version</strong>: {{case.outdated_panels[panel.panel_name]['extra_genes']|join(', ') or '-'}}.<br /><strong>Genes present only in latest version</strong>: {{case.outdated_panels[panel.panel_name]['missing_genes']|join(', ') or '-'}}.">!</span></a>
       {% endif %}<br>
       Panel ID: {{ panel.panel_name }}<br>
       Description: {{ panel.description }}<br>

scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html

@@ -6,14 +6,14 @@
   <h4>Scout - Gene panel report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong><br><br>
   {{ genes_panel() }}
   [END OF REPORT]<br><br>
-  <a href="https://clinical-genomics.github.io/scout" target="_blank">clinical-genomics.github.io/scout</a>
+  <a style="text-decoration:none;" href="https://clinical-genomics.github.io/scout" target="_blank">clinical-genomics.github.io/scout</a>
 </div>
 {% endblock %}
 
 {% macro genes_panel() %}
 <div class="card border-dark mb-3">
   <div class="card-header">
-    Panel: <a href="{{ url_for('panels.panel', panel_id=panel._id) }}">{{panel.name_and_version}}</a>
+    Panel: <a style="text-decoration:none;" href="{{ url_for('panels.panel', panel_id=panel._id) }}">{{panel.name_and_version}}</a>
   </div>
   <div class="card-body">
     <table class="table table-sm">
@@ -58,7 +58,7 @@
         <tr>
           <td>{{loop.index}}</td>
           <td>
-            <a href="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id={{gene.hgnc_id}}" target="_blank">{{gene.hgnc_id}}</a>
+            <a style="text-decoration:none;" href="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id={{gene.hgnc_id}}" target="_blank">{{gene.hgnc_id}}</a>
           </td>
           <td>{{ gene.symbol }}</td>
           <td>{{ gene.disease_associated_transcripts|join(', ') }}</td>

scout/server/blueprints/panels/views.py

@@ -3,18 +3,9 @@ import datetime
 import json
 import logging
 
-from flask import (
-    Blueprint,
-    Response,
-    escape,
-    flash,
-    redirect,
-    render_template,
-    request,
-    send_file,
-    url_for,
-)
+from flask import Blueprint, Response, flash, redirect, render_template, request, send_file, url_for
 from flask_login import current_user
+from markupsafe import escape
 
 from scout.constants import DATE_DAY_FORMATTER
 from scout.export.panel import export_gene_panels

scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html

@@ -21,7 +21,7 @@
   <div class="row mt-3">
     <div class="col-md-12">
       <div class="card">
-        <div class="card-header">HPO terms</div>
+        <div class="card-header">Number of HPO terms present in the database:{{phenotypes|length}}</div>
         <div class="card-body">
           {% if phenotypes|length == 0 %}
             The search didn't return any phenotype term
@@ -54,7 +54,8 @@
   <script type="text/javascript">
     $(document).ready(function() {
       $('#phenotypes_table').DataTable( {
-          paging: false,
+          paging: true,
+          pageLength: 50,
           dom: 'fBrtip',
           buttons: [
             {

scout/server/blueprints/variant/controllers.py

@@ -3,8 +3,9 @@ import os
 from typing import Dict, List, Optional
 
 import requests
-from flask import Markup, abort, current_app, flash, url_for
+from flask import abort, current_app, flash, url_for
 from flask_login import current_user
+from markupsafe import Markup
 
 from scout.adapter import MongoAdapter
 from scout.constants import (
@@ -238,7 +239,7 @@ def variant(
     # The hierarchical call order is relevant: cases are used to populate variants
     update_variant_case_panels(case_obj, variant_obj)
 
-    associate_variant_genes_with_case_panels(store, variant_obj)
+    associate_variant_genes_with_case_panels(case_obj, variant_obj)
 
     # Provide basic info on alignment files availability for this case
     case_has_alignments(case_obj)

scout/server/blueprints/variant/templates/variant/components.html

@@ -241,7 +241,7 @@
   <div class="card panel-default">
     <div class="panel-heading">Compounds (top 20)</div>
     <div class="card-body">
-      {{ compounds_table(institute, case, variant.compounds[:20]) }}
+      {{ compounds_table(institute, case, variant.compounds[:20], is_popover=false) }}
     </div>
   </div>
 {% endmacro %}

scout/server/blueprints/variant/templates/variant/utils.html

@@ -131,7 +131,9 @@
               <th>Variant</th>
               <th>Gene</th>
 	            <th>Type</th>
-              <th>Combined score</th>
+              <th>Combined score
+                <span data-bs-toggle='tooltip' data-bs-title='Combined score is the sum of variants´s score and overlapping variant´s score'>?</span>
+              </th>
               <th>Rank score</th>
               <th>Length</th>
               <th>Region</th>

scout/server/blueprints/variant/templates/variant/variant.html

@@ -5,7 +5,7 @@
 {% 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 %}
+{% from "variant/variant_details.html" import conservations, frequencies, gtcall_panel, mappability, observations_panel, old_observations, severity_list, str_db_card %}
 {% from "variant/components.html" import alignments, clinsig_table, compounds_panel, external_links, external_scripts, external_stylesheets, matching_variants, panel_classify, variant_scripts %}
 {% from "variant/sanger.html" import modal_cancel_sanger, modal_sanger, sanger_button %}
 {% from "variant/rank_score_results.html" import rankscore_panel %}
@@ -90,11 +90,15 @@
         {{ panel_summary() }}
       </div>
       <div class="col-lg-4">
-        {{ frequencies(variant) }}
-        {% if config['LOQUSDB_SETTINGS'] %}
-          {{ observations_panel(variant, observations, case) }}
+        {% if str %}
+          {{ str_db_card(variant) }}
+        {% else %}
+          {{ frequencies(variant) }}
+          {% if config['LOQUSDB_SETTINGS'] %}
+            {{ observations_panel(variant, observations, case) }}
+          {% endif %}
+          {{  old_observations(variant) }}
         {% endif %}
-        {{  old_observations(variant) }}
       </div>
     </div>
     <div class="row">
@@ -227,8 +231,8 @@
           <tr>
             <td>
               Position:
-	      <strong>{{ variant.chromosome }}:<span class="text-muted">{{ variant.position }}</span></strong>
-             <button type="button" class="fa fa-copy btn-xs js-tooltip js-copy" style="background-color: Transparent;outline:none; border: none;" data-bs-toggle="tooltip" data-bs-placement="bottom" data-copy="{{ variant.chromosome }}:{{ variant.position }}" title="Copy to clipboard">
+	            <strong>{{ variant.chromosome }}:<span class="text-muted">{{ variant.position }}</span></strong>
+              <button type="button" class="fa fa-copy btn-xs js-tooltip js-copy" style="background-color: Transparent;outline:none; border: none;" data-bs-toggle="tooltip" data-bs-placement="bottom" data-copy="{{ variant.chromosome }}:{{ variant.position }}" title="Copy to clipboard">
               </button>
             </td>
             <td {% if not mei %}colspan="3"{% endif %}>
@@ -282,13 +286,12 @@
               </strong></span>
             </td>
           </tr>
-
         </tbody>
       </table>
       <table class="table table-bordered table-fixed table-sm">
         <tbody class="border-top">
           <tr>
-            <td>
+            <td {% if str %}colspan="2"{% endif %}>
               Matches OMIM inhert.
               {% if variant.is_matching_inheritance %}
                 <span class="badge bg-success float-end">Yes</span>
@@ -296,12 +299,14 @@
                 <div class="badge bg-warning float-end">No</div>
               {% endif %}
             </td>
-            <td>
-              Frequency
-              <div class="badge bg-{% if variant.frequency == 'common' %}danger{% elif variant.frequency == 'uncommon' %}warning{% else %}success{% endif %} float-end">
-                {{ variant.frequency }}
-              </div>
-            </td>
+            {% if not str %}
+              <td>
+                Frequency
+                <div class="badge bg-{% if variant.frequency == 'common' %}danger{% elif variant.frequency == 'uncommon' %}warning{% else %}success{% endif %} float-end">
+                  {{ variant.frequency }}
+                </div>
+              </td>
+            {% endif %}
           </tr>
         </tbody>
       </table>

scout/server/blueprints/variant/templates/variant/variant_details.html

@@ -105,37 +105,89 @@
   </div>
 {% endmacro %}
 
-{% macro frequencies(variant) %}
+{% macro str_db_card(variant) %}
   <div class="card panel-default">
-    <div class="panel-heading">Frequencies</div>
+    <div class="panel-heading">STR locus details</div>
     <div class="card-body">
-      <table class="table">
+      <table class="table" aria-label="STR locus details">
         <thead class="thead table-light">
-          <tr>
-            <th scope="col">Source</th>
-            <th scope="col">Frequency</th>
-          </tr>
-        </thead>
-        <tbody>
-          {% for freq_name, value, link in variant.frequencies %}
-          <tr>
-            <td>
-              {% if link %}
-                <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
-              {% else %}
-                {{ freq_name }}
+            <tr>
+              <th scope="col">Source</th>
+              <th scope="col">Value</th>
+            </tr>
+          </thead>
+          <tbody>
+            <tr><td>Normal max</td><td>{{ variant.str_normal_max }}</td></tr>
+            <tr><td>Pathologic min</td><td>{{ variant.str_pathologic_min }}</td><tr>
+            {% if variant.str_status == 'full_mutation' %}
+              <tr class="bg-danger">
+            {% elif variant.str_status == 'pre_mutation' %}
+              <tr class="bg-warning">
+            {% else %}
+              <tr>
+	          {% endif %}
+              <td>Motif copies</td><td>{{ variant.str_mc }} <span class="badge bg-secondary text-white">{{ variant.str_status }}</span></td>
+            </tr>
+            <tr><td colspan=2>&nbsp;</td></tr>
+            {% if variant.str_swegen_mean %}
+              <tr><td>SweGen Z-score</td><td>
+                {% if variant.str_mc %}
+                  {{ ((variant.str_mc - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
+                {% endif %}
+              </td></tr>
+              <tr><td>SweGen mean</td><td>{{variant.str_swegen_mean|round(2)}}</td></tr>
+              <tr><td>SweGen std</td><td>{{variant.str_swegen_std|round(2)}}</td></tr>
+              <tr><td colspan=2>&nbsp;</td></tr>
+            {% endif %}
+            {% for gene in variant.genes %}
+              {% if gene.stripy_link %}
+                <tr><td>
+                  <a href="{{ gene.str_gnomad_link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">gnomAD</a>
+                </td><td>{{ gene.hgnc_symbol }}</td></tr>
               {% endif %}
-            </td>
-            <td>
-              {% if value %}
-                <span class="badge bg-secondary">{{ value|human_decimal }}</span>
-              {% else %}
-                -
+              {% if gene.stripy_link %}
+                <tr><td>
+                  <a href="{{ gene.stripy_link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">STRipy</a>
+                </td><td>{{ gene.hgnc_symbol }}</td></tr>
               {% endif %}
-            </td>
-          </tr>
-          {% endfor %}
-        </tbody>
+            {% endfor %}
+          </tbody>
+        </table>
+    </div>
+  </div>
+{% endmacro %}
+
+{% macro frequencies(variant) %}
+  <div class="card panel-default">
+    <div class="panel-heading">Frequencies</div>
+    <div class="card-body">
+      <table class="table">
+          <thead class="thead table-light">
+            <tr>
+              <th scope="col">Source</th>
+              <th scope="col">Frequency</th>
+            </tr>
+          </thead>
+          <tbody>
+            {% for freq_name, value, link in variant.frequencies %}
+              <tr>
+                <td>
+                  {% if link %}
+                    <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
+                  {% else %}
+                    {{ freq_name }}
+                  {% endif %}
+                </td>
+                <td>
+                  {% if value %}
+                    <span class="badge bg-secondary">{{ value|human_decimal }}</span>
+                  {% else %}
+                    -
+                  {% endif %}
+                </td>
+              </tr>
+            {% endfor %}
+          </tbody>
       </table>
     </div>
   </div>

scout/server/blueprints/variant/utils.py

@@ -175,15 +175,13 @@ def update_variant_case_panels(case_obj: dict, variant_obj: dict):
     The case_obj should be up-to-date first. Call update_case_panels() as needed in context:
     to save some resources we do not call it here for each variant.
     """
-
+    variant_obj["case_panels"] = []
     variant_panel_names = variant_obj.get("panels") or []
-    case_panel_objs = [
-        panel
-        for panel in (case_obj.get("panels") or [])
-        if panel["panel_name"] in variant_panel_names
-    ]
-
-    variant_obj["case_panels"] = case_panel_objs
+    for latest_panel in case_obj.get("latest_panels") or []:
+        if latest_panel["panel_name"] not in variant_panel_names:
+            continue
+        if not set(latest_panel["hgnc_ids"]).isdisjoint(variant_obj["hgnc_ids"]):
+            variant_obj["case_panels"].append(latest_panel)
 
 
 def get_extra_info(gene_panels: list) -> Dict[int, dict]:
@@ -660,17 +658,15 @@ def callers(variant_obj):
     return list(calls)
 
 
-def associate_variant_genes_with_case_panels(store: MongoAdapter, variant_obj: Dict) -> None:
+def associate_variant_genes_with_case_panels(case_obj: Dict, variant_obj: Dict) -> None:
     """Add associated gene panels to each gene in variant object"""
 
     genes = variant_obj.get("genes", [])
-    gene_panels = variant_obj.get("case_panels", [])
 
     for gene in genes:
         hgnc_id = gene["hgnc_id"]
         matching_panels = []
-        for panel in gene_panels:
-            genes_on_panel = store.panel_to_genes(panel_id=panel["panel_id"], gene_format="hgnc_id")
-            if hgnc_id in genes_on_panel:
+        for panel in case_obj.get("latest_panels", []):
+            if hgnc_id in panel["hgnc_ids"]:
                 matching_panels.append(panel["panel_name"])
         gene["associated_gene_panels"] = matching_panels

scout/server/blueprints/variants/controllers.py

@@ -51,6 +51,8 @@ from scout.server.utils import (
 from .forms import FILTERSFORMCLASS, CancerSvFiltersForm, FusionFiltersForm, SvFiltersForm
 from .utils import update_case_panels
 
+NUM = re.compile(r"\d+")
+
 LOG = logging.getLogger(__name__)
 
 
@@ -938,6 +940,10 @@ def parse_variant(
     if not "end_chrom" in variant_obj:
         variant_obj["end_chrom"] = variant_obj["chromosome"]
 
+    # common motif count for STR variants
+
+    variant_obj["str_mc"] = get_str_mc(variant_obj)
+
     # variant level links shown on variants page
     variant_obj["cosmic_links"] = cosmic_links(variant_obj)
     variant_obj["str_source_link"] = str_source_link(variant_obj)
@@ -959,6 +965,31 @@ def parse_variant(
     return variant_obj
 
 
+def get_str_mc(variant_obj: dict) -> Optional[int]:
+    """Return variant Short Tandem Repeat motif count, either as given by its ALT MC value
+    from the variant FORMAT field, or as a number given in the ALT on the form
+    '<STR123>'.
+    """
+
+    alt_mc = None
+    if variant_obj["alternative"] == ".":
+        return alt_mc
+
+    for sample in variant_obj["samples"]:
+        if sample["genotype_call"] in ["./.", ".|", "0/0", "0|0"]:
+            continue
+        alt_mc = sample.get("alt_mc")
+    if alt_mc:
+        return alt_mc
+
+    alt_num = NUM.match(variant_obj["alternative"])
+    if alt_num:
+        alt_mc = int(alt_num)
+        return alt_mc
+
+    return None
+
+
 def download_str_variants(case_obj, variant_objs):
     """Download filtered STR variants for a case to a CSV file
 
@@ -995,9 +1026,7 @@ def download_str_variants(case_obj, variant_objs):
         variant_line.append(
             variant.get("str_display_ru", variant.get("str_ru", ""))
         )  # Reference repeat unit
-        variant_line.append(
-            variant.get("alternative", "").replace("STR", "").replace("<", "").replace(">", "")
-        )  # Estimated size
+        variant_line.append(get_str_mc(variant) or ".")  # Estimated size
         variant_line.append(str(variant.get("str_ref", "")))  # Reference size
         variant_line.append(str(variant.get("str_status", "")))  # Status
         gt_cell = ""