scout-browser 4.90__py3-none-any.whl → 4.91__py3-none-any.whl

scout/server/blueprints/cases/templates/cases/case_sma.html

@@ -30,61 +30,68 @@
   <div class="card col-md-12">
     <h4 class="mt-3">Case: {{case.display_name}}</h4>
     <div class="card-body">
-
       <div class="row">
-            <div class="col-xs-12 col-md-12">{{ smn_individuals_table(case, institute, tissue_types) }}</div>
-        </div> <!-- end of div class row -->
-        <div class="row">
-          <div class="col-md-4">
-            {% if case.madeline_info and case.individuals|length > 1 %}
-              {{ pedigree_panel() }}
-            {% else %}
-              <p>No pedigree picture available.</p>
-            {% endif %}
-          </div>
-          <div class="col-md-8">
-            {{ synopsis_panel() }}
-            <div class="panel-default">
-            {{ comments_panel(institute, case, current_user, comments) }}
-            </div>
+        <div class="col-xs-12 col-md-12">{{ smn_individuals_table(case, institute, tissue_types) }}</div>
+      </div> <!-- end of div class row -->
+      <div class="row">
+        <div class="col-md-4">
+          {% if case.madeline_info and case.individuals|length > 1 %}
+            {{ pedigree_panel() }}
+          {% else %}
+            <p>No pedigree picture available.</p>
+          {% endif %}
+        </div>
+        <div class="col-md-8">
+          {{ synopsis_panel() }}
+          <div class="panel-default">
+          {{ comments_panel(institute, case, current_user, comments) }}
           </div>
-        </div> <!-- end of div class row -->
+        </div>
+      </div> <!-- end of div class row -->
 
-        <span class="d-flex">
-          {% if case.vcf_files.vcf_snv %}
-          <span class="me-3">
-            <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
-              <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
-              <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-              <span><button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes SMN1 and SMN2">SNVs</button></span>
-            </form>
-          </span>
-          {% endif %}
-          {% if case.vcf_files.vcf_sv %}
+      <span class="d-flex">
+        {% if case.vcf_files.vcf_snv %}
+        <span class="me-3">
+          <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
+            <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
+            <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+            <span><button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes SMN1 and SMN2">SNVs</button></span>
+          </form>
+        </span>
+        {% endif %}
+        {% if case.vcf_files.vcf_sv %}
           <span class="me-3">
             <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
               <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
               <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-              <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button></span>
+              <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button>
             </form>
           </span>
-          {% endif %}
-          {% if case.bam_files %}
-            <span class="me-3"><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn1']['chrom'], start=region['smn1']['start'], stop=region['smn1']['end'] )}}" target="_blank">IGV viewer SMN1</a></span>
-            <span class="me-3"><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn2']['chrom'], start=region['smn2']['start'], stop=region['smn2']['end'] )}}" target="_blank">IGV viewer SMN2</a></span>
-          {% else %}
-            <span class="me-3 text-muted">BAM file(s) missing</span>
-          {% endif %}
-        </div>
+        {% endif %}
 
-        <div class="row">
-          <div class="col-sm-12">{{activity_panel(events)}}</div>
-        </div>
+        <span class="me-3"
+          {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
+          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn1']['chrom'], start=region['smn1']['start'], stop=region['smn1']['end'] )}}" target="_blank"
+            class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
+            IGV DNA SMN1
+          </a>
+        </span>
+        <span class="me-3"
+          {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
+          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn2']['chrom'], start=region['smn2']['start'], stop=region['smn2']['end'] )}}" target="_blank"
+            class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
+            IGV DNA SMN2
+          </a>
+        </span>
+      </span>
 
-        {{ modal_synopsis() }}
+      <div class="row">
+        <div class="col-sm-12">{{activity_panel(events)}}</div>
+      </div>
+
+      {{ modal_synopsis() }}
     </div> <!-- end of card body -->
   </div> <!-- end of card div-->
-</div>
 </div> <!-- end of div class col -->
 {% endmacro %}
 

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -197,22 +197,37 @@
       <span class="menu-collapsed">Genome build {{ case.genome_build }}</span>
   </div>
 </div>
-<div href="#" class="bg-dark list-group-item d-inline-block text-white">
-  {% if case.bam_files %}
+  <div href="#" class="bg-dark list-group-item d-inline-block text-white"
+    {% if not case.bam_files %} data-bs-toggle="tooltip" title="Alignment file(s) missing" {% endif %}>
     <form action="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name']) }}" target="_blank" rel="noopener">
-      <button role="submit" class="btn btn-xs form-control btn-secondary">I<span class="menu-collapsed">GV viewer</span></button>
+      <button type="submit" class="btn btn-xs form-control btn-secondary"
+        {% if not case.bam_files %}
+          disabled="disabled"><span class="fa fa-times-circle fa-fw me-1"></span>
+        {% else %}><span class="fa fa-magnifying-glass fa-fw me-1"></span>
+        {% endif %}
+        <span class="menu-collapsed">IGV g</span>D<span class="menu-collapsed">NA</span>
+      </button>
     </form>
-  {% else %}
-    <span class="fa fa-times-circle fa-fw me-3"></span><span class="text-muted menu-collapsed">Alignment missing</span>
-  {% endif %}
-</div>
-{% if has_rna_tracks %}
-  <div href="#" class="bg-dark list-group-item d-inline-block text-white">
-    <form action="{{url_for('alignviewers.sashimi_igv', institute_id=case['owner'], case_name=case['display_name']) }}" target="_blank" rel="noopener">
-      <button role="submit" data-bs-toggle="tooltip" data-bs-placement="top" title="Available in build GRCh{{ case.rna_genome_build or '38' }}" class="btn btn-xs form-control btn-secondary">R<span class="menu-collapsed">NA splicing</span></button>
+  </div>
+  <div href="#" class="bg-dark list-group-item d-inline-block text-white"
+    {% if not case.mt_bams %} data-bs-toggle="tooltip" title="Alignment file(s) missing" {% endif %}>
+    <form action="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom='M', start=1, stop=16569) }}" target="_blank" rel="noopener">
+      <button type="submit" class="btn btn-xs form-control btn-secondary"
+        {% if not case.mt_bams %}
+          disabled="disabled"><span class="fa fa-times-circle fa-fw me-1"></span>
+        {% else %}
+          ><span class="fa fa-magnifying-glass fa-fw me-1"></span>
+        {% endif %}
+      <span class="menu-collapsed">IGV </span>m<span class="menu-collapsed">tDNA</span></button>
     </form>
   </div>
-{% endif %}
+  {% if has_rna_tracks %}
+    <div href="#" class="bg-dark list-group-item d-inline-block text-white">
+      <form action="{{url_for('alignviewers.sashimi_igv', institute_id=case['owner'], case_name=case['display_name']) }}" target="_blank" rel="noopener">
+        <button type="submit" class="btn btn-xs form-control btn-secondary" data-bs-toggle="tooltip" data-bs-placement="top" title="Available in build GRCh{{ case.rna_genome_build or '38' }}"><span class="fa fa-magnifying-glass fa-fw me-1"></span><span class="menu-collapsed">IGV </span>R<span class="menu-collapsed">NA</span></button>
+      </form>
+    </div>
+  {% endif %}
 {% endmacro %}
 
 {% macro rank_model(case) %}

scout/server/blueprints/cases/views.py

@@ -25,6 +25,8 @@ from flask import (
     url_for,
 )
 from flask_login import current_user
+from pymongo.errors import OperationFailure
+from werkzeug.datastructures import ImmutableMultiDict
 
 from scout.constants import DATE_DAY_FORMATTER
 from scout.server.blueprints.variants.controllers import activate_case
@@ -619,7 +621,13 @@ def caselist(institute_id):
     if query is None:
         return abort(500)
 
-    matching_cases = store.cases(owner=institute_id, name_query="case:" + query)
+    name_query = ImmutableMultiDict(
+        {
+            "case": query,
+        }
+    )
+
+    matching_cases = store.cases(owner=institute_id, name_query=name_query)
     display_names = []
     if institute_id:  # called from case page, where institute_id is provided
         display_names = sorted([case["display_name"] for case in matching_cases])
@@ -643,13 +651,16 @@ def hpoterms():
     query = request.args.get("query")
     if query is None:
         return abort(500)
-    terms = sorted(store.hpo_terms(query=query), key=itemgetter("hpo_number"))
-    json_terms = [
-        {"name": "{} | {}".format(term["_id"], term["description"]), "id": term["_id"]}
-        for term in terms[:7]
-    ]
+    try:
+        terms = sorted(store.hpo_terms(query=query), key=itemgetter("hpo_number"))
+        json_terms = [
+            {"name": "{} | {}".format(term["_id"], term["description"]), "id": term["_id"]}
+            for term in terms[:7]
+        ]
 
-    return jsonify(json_terms)
+        return jsonify(json_terms)
+    except OperationFailure as of:
+        return jsonify({"error": of._message})
 
 
 @cases_bp.route("/api/v1/disease-terms")

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

@@ -101,8 +101,8 @@
               {% endif %}
               {% if subm_obj.status == 'submitted' %} <!--Submission status query -->
                  <form id="statusApi_{{subm_obj._id}}" action="{{ url_for('clinvar.clinvar_submission_status', submission_id=subm_obj.clinvar_subm_id) }}" method="POST">
-                   {{ status_modal() }}
-                   <td style="width: 20%"><button type="button" class="btn btn-sm btn-secondary form-control" name="status_enquiry" value="api_status" data-bs-toggle="modal" data-bs-target="#statusModal">Submission status enquiry</button></td>
+                   {{ status_modal(subm_obj._id) }}
+                   <td style="width: 20%"><button type="button" class="btn btn-sm btn-secondary form-control" name="status_enquiry" value="api_status" data-bs-toggle="modal" data-bs-target="#statusModal_{{subm_obj._id}}">Submission status enquiry</button></td>
                  </form>
               {% endif %}
             </tr>
@@ -156,7 +156,7 @@
                   <td><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id]) }}" target="_blank" rel="noopener">{{subm_obj.cases[subm_variant.case_id]}}</a></td>
                   <td>{{subm_variant.ref_seq or '-'}}</td>
                   <td>{{subm_variant.gene_symbol or '-'}}</td>
-                  <td>{{subm_variant.hgvs|truncate(25,true,'..') or '-'}}</td>
+                  <td>{{subm_variant.hgvs|truncate(100,true,'..') or '-'}}</td>
                   <td>{{subm_variant.clinsig}}</td>
                   <td>{{subm_variant.added_by or "N/A"}}</td>
                   <form id="delete_variant_{{subm_variant._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='variant_data') }}" method="POST">
@@ -170,7 +170,7 @@
                           <ul class="list-group">
                           {% for key, value in variant_header_fields.items() %}
                             {% if subm_variant[key]%}
-                              <li class="list-group-item">{{ value }}: <strong>{{ subm_variant[key]|replace(subm_variant[key][75:], '..') if subm_variant[key]|length > 75 else subm_variant[key]}}</strong></li>
+                              <li class="list-group-item">{{ value }}: <strong>{{ subm_variant[key]}}</strong></li>
                               {% endif %}
                           {% endfor %}
                           </ul>
@@ -214,7 +214,7 @@
                     </form>
                     <td><button id="{{case._id}}" type="button" class="btn btn-primary btn-xs cd_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
                     <td><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=subm_obj.cases[case.case_id]) }}" target="_blank" rel="noopener">{{subm_obj.cases[case.case_id]}}</a></td>
-                    <td>{{var_key_name[case.linking_id]|truncate(25,true,'..')}}</td>
+                    <td>{{var_key_name[case.linking_id]|truncate(100,true,'..')}}</td>
                     <td>{{case.allele_origin}}</td>
                     <form id="delete_casedata_{{case._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='case_data') }}" method="POST">
                       <td><button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
@@ -246,8 +246,8 @@
 </div>
 {% endmacro %}
 
-{% macro status_modal() %}
-<div class="modal fade" id="statusModal" tabindex="-1">
+{% macro status_modal(subm_id) %}
+<div class="modal fade" id="statusModal_{{subm_id}}" tabindex="-1">
   <div class="modal-dialog">
     <div class="modal-content">
       <div class="modal-header">

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

@@ -390,10 +390,10 @@ function validateConditions(){
     return false;
   }
 
-  // Make sure that provided conditions are numbers, except when condition type is MeSH
+  // Make sure that provided conditions are numbers, except when condition type is MeSH or MedGen
   var selectedConditionsValues = $('#condition_tags').val();
   for (let i = 0; i < selectedConditionsValues.length; i++) {
-    if (isNaN(selectedConditionsValues[i]) && $('#condition_type').val() != 'MeSH'){
+    if (isNaN(selectedConditionsValues[i]) && !['Mesh', 'MedGen'].includes($('#condition_type').val())){
       alert(`Condition ID "${selectedConditionsValues[i]}" has an invalid format.`);
       return false;
     }