scout-browser 4.79.1__py3-none-any.whl → 4.81__py3-none-any.whl

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

@@ -44,7 +44,9 @@
           </div>
           <div class="col-md-8">
             {{ synopsis_panel() }}
+            <div class="panel-default">
             {{ comments_panel(institute, case, current_user, comments) }}
+            </div>
           </div>
         </div> <!-- end of div class row -->
 

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

@@ -83,8 +83,18 @@
       </div>
     </div>
 
-    <!-- If connected to a chanjo instance, display coverage report -->
-    {% if config.SQLALCHEMY_DATABASE_URI and case.track != "cancer" %}
+    <!-- If connected to a chanjo or chanjo2 instance, display coverage report -->
+    {% if case.chanjo2_coverage %}
+      <div href="#" class="bg-dark list-group-item text-white">
+        <div class="d-flex flex-row flex-fill bd-highlight">
+          <span class="menu-collapsed">Coverage (chanjo2)</span>
+          <a href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id, case_name=case.display_name, panel_name=case.panel_names|join(', '), report_type='report') }}" target="_blank" rel="noopener">
+            <span class="fa fa-link"></span>
+          </a>
+        </div>
+      </div>
+    {% endif %}
+    {% if case.chanjo_coverage %}
       <div href="#" class="bg-dark list-group-item text-white">
         <div class="d-flex flex-row flex-fill bd-highlight">
           <span class="menu-collapsed">Coverage</span>

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

@@ -7,6 +7,7 @@
         <thead class="table-light thead">
           <tr style="cursor: pointer; white-space: nowrap">
             <th>Panel <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by gene panel name"></i></th>
+            <th >Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by default panel"></i></th>
             <th>Version <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by panel version"></i></th>
             <th>Genes <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by number of genes"></i></th>
           </tr>
@@ -21,8 +22,10 @@
                     <span class="badge bg-danger">Removed</span>
                   {% endif %}
                 </a>
+              </td>
+              <td >
                 {% if panel.is_default %}
-                  <span class="badge bg-dark float-end">Default</span>
+                  <span class="badge bg-dark">Default</span>
                 {% endif %}
               </td>
               <td>{{ panel.version }} <small class="text">({{ panel.updated_at.date() }})</small></td>
@@ -91,21 +94,6 @@
         {% endif %}
         )
         {% if case.dynamic_gene_list_edited %} <span class="text-danger ml-3"> (edited) </span> {% endif %}
-        {% if case.track != 'cancer' and config.SQLALCHEMY_DATABASE_URI and case.dynamic_gene_list|length > 0 %}
-          <span class="pull-right">
-            <a href="#" onclick="document.getElementById('hpo-report-form').submit();">Coverage report</a>
-            <form id="hpo-report-form" action="{{ url_for('report.report', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name="HPO panel", level=institute.coverage_cutoff) }}" method="POST" target="_blank">
-              <input type="hidden" name="gene_ids" value="{{ case.dynamic_gene_list|map(attribute='hgnc_id')|join(',') }}">
-            </form>
-          </span>
-          <span class="pull-right">&nbsp;&nbsp;&nbsp;</span>
-          <span class="pull-right">
-            <a href="#" onclick="document.getElementById('hpo-overview-form').submit();">Coverage overview</a>
-            <form id="hpo-overview-form" action="{{ url_for('report.genes', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name="HPO panel", level=institute.coverage_cutoff) }}" method="POST" target="_blank">
-              <input type="hidden" name="gene_ids" value="{{ case.dynamic_gene_list|map(attribute='hgnc_id')|join(',') }}">
-            </form>
-          </span>
-        {% endif %}
       </h6>
     </div>
 
@@ -142,8 +130,8 @@
         </div>
       </div>
 
-      <div class="row mt-2"> <!-- Show variants in dynamic gene list -->
-        <div class="row">
+      <div>
+        <div class="row"> <!-- Show variants in dynamic gene list -->
           <form action="{{ url_for('cases.update_clinical_filter_hpo', institute_id=institute._id, case_name=case.display_name)+'#hpo_clinical_filter' }}" method="POST">
             <div class="form-check form-switch">
               <input type="checkbox" class="form-check-input" id="hpo_clinical_filter" onChange="this.form.submit()" name="hpo_clinical_filter"{% if case.hpo_clinical_filter %}checked{% endif %}>
@@ -207,11 +195,46 @@
            {% endif %}
           </div>
         </div>
-      </div> <!-- End of Show variants in dynamic gene list -->
+        {% if case.chanjo_coverage or case.chanjo2_coverage and case.dynamic_gene_list|length > 0 %}
+        <div class="row mt-1">
+          <div class="btn-group btn-group-sm">
+            {% if case.chanjo_coverage %}
+              <a class="btn btn-secondary btn-sm text-white" href="#section" onClick="document.getElementById('hpo-report-form').submit();" >Coverage report</a>
+              <form id="hpo-report-form" action="{{ url_for('report.report', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name='HPO panel', level=institute.coverage_cutoff) }}" method="POST" target="_blank">
+                <input type="hidden" name="gene_ids" value="{{ case.dynamic_gene_list|map(attribute='hgnc_id')|join(',') }}">
+              </form>
+
+              <a class="btn btn-secondary btn-sm text-white" href="#section" onClick="document.getElementById('hpo-overview-form').submit();" >Coverage overview</a>
+              <form id="hpo-overview-form" action="{{ url_for('report.genes', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name='HPO panel', level=institute.coverage_cutoff) }}" method="POST" target="_blank">
+                <input type="hidden" name="gene_ids" value="{{ case.dynamic_gene_list|map(attribute='hgnc_id')|join(',') }}">
+              </form>
+            {% endif %}
+
+            {% if case.chanjo2_coverage %}
+              <a class="btn btn-secondary btn-sm text-white"
+                href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id,
+                                 case_name=case.display_name, panel_name='HPO Panel', report_type='report') }}" target="_blank" rel="noopener">
+                  Coverage report (Chanjo2)
+              </a>
+
+              <a class="btn btn-secondary btn-sm text-white"
+                href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id,
+                                 case_name=case.display_name, panel_name='HPO Panel', report_type='overview') }}" target="_blank" rel="noopener">
+                  Coverage overview (Chanjo2)
+              </a>
+            {% endif %}
+
+          </div>
+        </div>
+        {% endif %} <!-- End of if case.chanjo_coverage or case.chanjo2_coverage -->
+
+        <div class="row mt-1">
+          <div class="btn-group btn-group-sm"> <!-- Download genes in HPO gene panel -->
+            <a class="btn btn-sm btn-primary text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="clinical") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Clinical HPO gene panel</a>
+            <a class="btn btn-sm btn-primary text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="research") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Research HPO gene panel</a>
+          </div>
+        </div>
 
-      <div class="btn-group d-flex justify-content-center mt-2"> <!-- Download genes in HPO gene panel -->
-        <a class="btn btn-sm btn-primary mt-1 text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="clinical") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Clinical HPO gene panel</a>
-        <a class="btn btn-sm btn-primary mt-1 text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="research") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Research HPO gene panel</a>
       </div>
 
     {% endif %}

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

@@ -1,4 +1,5 @@
 {% from "variants/indicators.html" import clinical_assessments_badge, research_assessments_badge %}
+{% from "clinvar/clinvar_howto.html" import clinvar_howto_modal %}
 
 {% macro matchmaker_modal(institute, case, suspects, mme_nodes ) %}
 <div class="modal fade" id="matchmaker_modal" tabindex="-1" role="dialog" aria-hidden="true">
@@ -379,20 +380,21 @@
         {% endif %}
       </div>
     </div>
-    <div style="max-height:300px; overflow-y: scroll;">
+    <div class="mb-3" style="max-height:300px; overflow-y: scroll;">
       <ul class="list-group">
         {% for variant in causatives %}
           <li class="list-group-item list-group-item-action">
             {% if variant._id %}
               {% do already_displayed_variant_ids.append( variant._id ) %}
               <div class="row">
-                <div class="col-10">
+                <div class="col">
+                   <i class="far fa-check-circle"></i>
                   {{ pretty_link_variant(variant, case) }}
                   {{ variant_validation_badge(variant) }}
                   {{ clinical_assessments_badge(variant) }}
                   {{ tumor_allele_freq(variant) }}
                 </div>
-                <div class="col-2">
+                <div class="col-auto" style="width:fit-content;">
                   {{ remove_form(url_for('cases.mark_causative',
                                          institute_id=institute._id,
                                          case_name=case.display_name,
@@ -415,7 +417,7 @@
             {% if variant._id %}
               {% do already_displayed_variant_ids.append(variant._id) %}
               <div class="row">
-                <div class="col-10">
+                <div class="col">
                   <i class="far fa-check-circle"></i>
                   {% if variant.category == "snv" %}
                     <a href="{{ url_for('variant.variant',
@@ -433,7 +435,7 @@
   		             {% endif %}
                    </a>
                 </div>
-                <div class="col-2">
+                <div class="col-2" style="width:fit-content;">
                   {{ remove_form(url_for('cases.mark_causative',
                                          institute_id=institute._id,
                                          case_name=case.display_name,
@@ -444,6 +446,7 @@
               </div>
               <div class="row">
                 <div class="col-4">
+                  <i class="far fa-check-circle" style="color:transparent; background-color:transparent"></i>
                   Diagnoses
                 </div>
                 <div class="col-8">
@@ -464,6 +467,7 @@
               </div>
               <div class="row">
                 <div class="col-4">
+                   <i class="far fa-check-circle" style="color:transparent; background-color:transparent"></i>
                   HPO terms
                 </div>
                 <div class="col-8">
@@ -531,18 +535,18 @@
 {% endmacro %}
 
 {% macro suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) %}
+   {{ clinvar_howto_modal() }}
   <div class="card mt-3">
-    <div class="d-flex align-items-center" data-bs-toggle='tooltip' title="Displays all variants that has been pinned for this case">
-      <h6><span class="fa fa-map-pin ms-3 mt-2"></span>&nbsp;Pinned variants ({{suspects|length}})
-      </h6>
+    <div class="d-flex align-items-center" data-bs-toggle='tooltip' title="Displays all variants that have been pinned or included in a ClinVar submission for this case">
+      <h6><span class="fa fa-map-pin ms-3 mt-2"></span>&nbsp;Variants pinned ({{suspects|length}}) or included in a ClinVar submission({{ case.clinvar_variants.items()|length }}) <a data-bs-target="#howto" href="#" data-bs-toggle="modal">?</a></h6>
+    </div>
+    <div class="mb-3" style="max-height:300px; overflow-y: scroll;">
+    <ul class="list-group">
       {% if not suspects|length %}
         <span class="text-muted ms-3 mt-2">
           <h6>No pinned variants</h6>
         </span>
       {% endif %}
-    </div>
-    <div style="max-height:300px; overflow-y: scroll;">
-    <ul class="list-group">
       {% for variant in suspects %}
         <li class="list-group-item">
           {% if variant._id %}
@@ -560,7 +564,7 @@
                   </div>
                 </div>
               </div>
-              <div class="col-5">
+              <div class="col-auto">
               <form action="{{ url_for('cases.mark_validation',
                                          institute_id=variant.institute,
                                          case_name=case.display_name,
@@ -573,7 +577,8 @@
                   </select>
                 </form>
               </div>
-            <div class="col-2">
+              <div class="col">{{ clinvar_var_status(variant, case, institute) }}</div>
+            <div class="col-auto" style="width: fit-content;">
               {{ remove_form(url_for('cases.pin_variant',
                                      institute_id=institute._id,
                                      case_name=case.display_name,
@@ -587,10 +592,43 @@
         </li>
       {% endfor %}
     </ul>
-    </div>
+    {{ clinvar_vars_summary(suspects, case, institute) }}
+      </div>
   </div>
 {% endmacro %}
 
+{% macro clinvar_var_status(variant, case, institute) %}
+    {% if variant._id and variant.category != 'str' %}
+        <form id="clinvar_submit" class="d-flex justify-content-center" action="{{ url_for('clinvar.clinvar_add_variant', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
+            {% if case.clinvar_variants and variant._id in case.clinvar_variants.keys() %}
+                (included in ClinVar submission)
+            {% else %}
+                <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
+            {% endif %}
+        </form>
+    {% endif %}
+{% endmacro %}
+
+{% macro clinvar_vars_summary(suspects, case, institute) %}
+    {% if case.clinvar_variants %}
+        {% if case.clinvar_variants_not_in_suspects | length >0 %}
+            <div class="d-flex align-content-center flex-wrap">
+                <div class="col-auto d-flex align-items-center wrap">
+                    <h6 class="m-2">&nbsp;Variants present in a ClinVar submission, no longer pinned:</h6>
+                </div>
+                {% for entry in case.clinvar_variants_not_in_suspects %}
+                    <div class="m-2">{{ pretty_link_variant(entry, case) }}</div>
+                {% endfor %}
+            </div>
+        {% endif %}
+            <div class="card-footer d-flex justify-content-center pb-0" style="background-color:inherit;">
+                <a href="{{url_for('clinvar.clinvar_submissions', institute_id=institute._id)}}"
+                    class="btn btn-secondary btn-sm text-white mx-3" target="_blank" rel="noopener noreferrer">View ClinVar
+                    submissions <i class="fas fa-arrow-circle-right"></i></a>
+            </div>
+    {% endif %}
+{% endmacro %}
+
 {% macro matching_causatives(other_causatives, institute, case, default=False) %}
     <div data-bs-toggle='tooltip' class="panel-heading" title="If there are any variants in this case
       that have been marked as causative in another case for this insitute. {% if default %}Variants in default panels for the case only.{% endif %}">

scout/server/blueprints/cases/views.py

@@ -313,6 +313,28 @@ def pdf_case_report(institute_id, case_name):
     )
 
 
+@cases_bp.route("/<institute_id>/<case_name>/chanjo2_report/<report_type>", methods=["GET"])
+def chanjo2_coverage_report(institute_id: str, case_name: str, report_type: str):
+    """Return the HTML coverage report or coverage overview created by chanjo2."""
+
+    REPORT_TYPES = ["report", "overview"]
+    if report_type not in REPORT_TYPES:
+        flash(f"Wrong value for report_type parameter. Accepted values: {REPORT_TYPES}", "warning")
+        return redirect(request.referrer)
+
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+    report_html_content: str = controllers.chanjo2_coverage_report_contents(
+        institute_obj=institute_obj,
+        case_obj=case_obj,
+        panel_name=request.args.get("panel_name"),
+        panel_id=request.args.get("panel_id"),
+        report_type=report_type,
+    )
+    if report_html_content is None:
+        return redirect(request.referrer)
+    return report_html_content
+
+
 @cases_bp.route("/<institute_id>/<case_name>/mt_report", methods=["GET"])
 def mt_report(institute_id, case_name):
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)

scout/server/blueprints/clinvar/controllers.py

@@ -245,6 +245,8 @@ def _set_conditions(clinvar_var: dict, form: ImmutableMultiDict):
     clinvar_var["condition_id_value"] = ";".join(
         [f"{condition_prefix}{condition_id}" for condition_id in form.getlist("conditions")]
     )
+    if bool(form.get("multiple_condition_explanation")):
+        clinvar_var["explanation_for_multiple_conditions"] = form["multiple_condition_explanation"]
 
 
 def parse_variant_form_fields(form):

scout/server/blueprints/clinvar/form.py

@@ -26,6 +26,7 @@ from scout.constants import (
     COLLECTION_METHOD,
     CONDITION_PREFIX,
     GERMLINE_CLASSIF_TERMS,
+    MULTIPLE_CONDITION_EXPLANATION,
 )
 
 LOG = logging.getLogger(__name__)
@@ -65,6 +66,10 @@ class ClinVarVariantForm(FlaskForm):
         "Condition ID type", choices=[(key, key) for key, value in CONDITION_PREFIX.items()]
     )
     conditions = SelectMultipleField("Condition ID value, without prefix")
+    multiple_condition_explanation = SelectField(
+        "Explanation for multiple conditions",
+        choices=[(item, item) for item in MULTIPLE_CONDITION_EXPLANATION],
+    )
 
     # Extra fields:
     assertion_method = StringField("Assertion method", default=ASSERTION_METHOD)

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

@@ -232,7 +232,7 @@
 
               <fieldset data-step="6">
                 <legend>Associated Conditions</legend>
-                <h3 class="fs-subtitle">The condition for which the variant is interpreted. Examples available at <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#condition" target="_blank" rel="noopener">ClinVar</a>"</h3>
+                <h3 class="fs-subtitle">The condition for which the variant is interpreted. Examples available at <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#condition" target="_blank" rel="noopener">ClinVar</a></h3>
 
                 <div class="row">
                   <div class="col-6" id="clinvar_condition_container">
@@ -249,7 +249,7 @@
                       {% endfor %}
                     </select>
                     <br><br>
-                    {{variant_data.var_form.conditions.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required field. Include data from ONE DATABASE TYPE ONLY (i.e. only OMIM terms, only HPO terms etc)"><strong>*?</strong></span>
+                    {{variant_data.var_form.conditions.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required field. Include data from ONE DATABASE TYPE ONLY (i.e. only OMIM terms, only HPO terms etc). If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s).  i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records."><strong>*?</strong></span>
                     <select class="select2" id="condition_tags" name="conditions" multiple="true" style="width:100%;">
                       {% if variant_data.var_form.omim_terms.choices %}
                         {% for term, _ in variant_data.var_form.omim_terms.choices %}
@@ -265,6 +265,18 @@
                         {% endfor %}
                       {% endif %}
                     </select>
+
+                    <div class="mt-3">
+                      {{variant_data.var_form.multiple_condition_explanation.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required if you provide more than one condition ID."><strong>?</strong></span>
+                      <select name="multiple_condition_explanation" id="multiple_condition_explanation" class="form-control, btn-secondary">
+                        <option selected value>-</option>
+                        {% for choice, _ in variant_data.var_form.multiple_condition_explanation.choices %}
+                          <option value="{{choice}}">{{choice}}</option>
+                        {% endfor %}
+                      </select>
+                    </div>
+
+
                   </div>
                   <div class="col-6">
                     {{ variant_data.var_form.omim_terms.label(class="fw-bold, text-dark" )}}<br>
@@ -360,7 +372,22 @@ var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
 
 // Validates fields for conditions associated to a variant
 function validateConditions(){
-  return $("#condition_tags option:selected").length > 0;
+  if ($("#condition_tags option:selected").length == 0) {
+    alert("Please provide at least one condition ID");
+    return false;
+  }
+
+  if ($("#condition_tags option:selected").length > 1 && $("#multiple_condition_explanation option:selected").text() === "-") {
+    alert("When multiple condition IDs are provided then an option for 'Explanation for multiple conditions' must be provided");
+    return false;
+  }
+
+  if ($("#condition_tags option:selected").length == 1 && $("#multiple_condition_explanation option:selected").text() !== "-") {
+    alert("Please deselect the selected option in 'Explanation for multiple conditions' since only one condition ID was provided.");
+    return false;
+  }
+
+  return true
 }
 
 var current_fs, next_fs, previous_fs; //fieldsets
@@ -383,12 +410,10 @@ $(".next").click(function(){
   // check to see if the validator for the specific step we are on passed or not.
   if(validationPassed == false){
     // do not proceed
-    alert("Please fill in required field");
     animating = false;
     return;
   }
 
-
 	next_fs = $(this).parent().next();
 
 	//activate next step on progressbar using the index of next_fs

scout/server/blueprints/diagnoses/templates/diagnoses/diagnoses.html

@@ -83,7 +83,7 @@
   <table id="super_secret_table_template" style="position: absolute; width: 1px; height: 1px; margin: -1px; border: 0; padding: 0; white-space: nowrap; clip-path: inset(100%); clip: rect(0 0 0 0); overflow: hidden;">
   <tr id="diagnosis-row">
     <td><a id="external-link" href="http://omim.org/entry/" target="_blank" rel=noopener ></a></td>
-    <td><a id="internal-link" href="{{ url_for('diagnoses.diagnosis',disease_id='')}}"><span class="fa fa-link"></span></a></td>
+    <td><a id="internal-link" href="{{ url_for('diagnoses.diagnosis',disease_id='')}}" target="_blank"><span class="fa fa-link"></span></a></td>
     <td><span id="description" class="text-body"></span></td>
     <td id="inheritance-container"><!-- inheritance-->
       <span id="inheritance" class="badge bg-info m-1"></span>

scout/server/blueprints/institutes/static/select2_darktheme.css

@@ -0,0 +1,62 @@
+/* Dark Theme compatibility for select2 multiselects*/
+@media (prefers-color-scheme: dark) {
+
+    .select2-dropdown,
+    .select2-selection {
+        color: #b1b1b1 !important;
+        background-color: #222 !important;
+        border: 1px solid #515151 !important;
+    }
+
+    .select2-results__option {
+        display: flex;
+        gap: 0.5rem;
+        color: #b1b1b1 !important;
+        background-color: #222 !important;
+    }
+
+    .select2-results__option:hover,
+    .select2-results__option[aria-selected=true]:hover {
+        color: #dfe0e1 !important;
+        background-color: #343a40 !important;
+    }
+
+    .select2-selection__choice:has(> span:hover) {
+        opacity: 0.5;
+    }
+
+    /* Filters adjusts color of svg used as remove-button for selected options */
+    .select2-selection__choice__remove:first-child {
+        background-color: transparent !important;
+        filter: brightness(70) saturate(0%);
+    }
+
+    .select2-selection__choice__remove:hover {
+        filter: invert(1)
+    }
+
+    .select2-results__option[aria-selected=true],
+    .select2-result__option,
+    .select2-selection__choice,
+    .select2-selection__choice__remove {
+        color: #fafafa !important;
+        background-color: #626262 !important;
+        border-color: #626262 !important;
+    }
+
+    /* This is a check mark displayed for the selected options */
+    .select2-results__option[aria-selected=true]::after {
+        content: '';
+        display: block;
+        width: 0.5em;
+        height: 1em;
+        border-style: solid;
+        border-width: 0 0.26em 0.26em 0;
+        -webkit-transform-style: preserve-3d;
+        transform-style: preserve-3d;
+        -webkit-transform: rotate(45deg);
+        -ms-transform: rotate(45deg);
+        -o-transform: rotate(45deg);
+        transform: rotate(45deg);
+    }
+}

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

@@ -11,6 +11,7 @@
   <link href="https://cdn.jsdelivr.net/npm/select2@4.0.13/dist/css/select2.min.css" rel="stylesheet" integrity="sha512-nMNlpuaDPrqlEls3IX/Q56H36qvBASwb3ipuo3MxeWbsQB1881ox0cRv7UPTgBlriqoynt35KjEwgGUeUXIPnw==" crossorigin="anonymous" referrerpolicy="no-referrer"/>
   <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.14.0-beta3/css/bootstrap-select.min.css" integrity="sha512-g2SduJKxa4Lbn3GW+Q7rNz+pKP9AWMR++Ta8fgwsZRCUsawjPvF/BxSMkGS61VsR9yinGoEgrHPGPn2mrj8+4w==" crossorigin="anonymous" referrerpolicy="no-referrer" />
   <link href="https://cdn.jsdelivr.net/npm/select2-bootstrap-5-theme@1.2.0/dist/select2-bootstrap-5-theme.min.css" rel="stylesheet" />
+  <link rel="stylesheet" href="{{ url_for('overview.static', filename='select2_darktheme.css') }}"/>
 {% endblock %}
 
 {% block top_nav %}
@@ -124,5 +125,4 @@
         });
     });
   </script>
-
 {% endblock %}

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

@@ -81,7 +81,7 @@
           <label for="mainainer">Maintainers</label>
           <span class="float-end" id="maintainer"> {{ panel.maintainer_names|join(", ") }}</span>
       </li>
-      {% if config.SQLALCHEMY_DATABASE_URI and case %}
+      {% if case and case.chanjo_coverage %}
         <li class="list-group-item">
           <label for="coverage_report">Coverage report</label>
           <a class="float-end" id="coverage_report" href="#" onclick="document.getElementById('report-form').submit();">
@@ -103,6 +103,20 @@
           </span>
         </li>
       {% endif %}
+      {% if case and case.chanjo2_coverage %}
+        <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>
+        </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>
+        </li>
+      {% endif %}
       <li class="list-group-item">
         <div class="d-flex justify-content-between">
           <a href="{{ url_for('panels.panel_export_pdf', panel_id=panel._id) }}" class="btn btn-secondary btn-sm" download>Export to PDF</a>

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

@@ -21,6 +21,8 @@ from scout.export.panel import export_gene_panels
 from scout.server.blueprints.cases.controllers import check_outdated_gene_panel
 from scout.server.extensions import store
 from scout.server.utils import (
+    case_has_chanjo2_coverage,
+    case_has_chanjo_coverage,
     html_to_pdf_file,
     institute_and_case,
     jsonconverter,
@@ -140,7 +142,6 @@ def panel(panel_id):
         raw_hgnc_id = request.form["hgnc_id"]
         if "|" in raw_hgnc_id:
             raw_hgnc_id = raw_hgnc_id.split(" | ", 1)[0]
-        hgnc_id = 0
         try:
             hgnc_id = int(raw_hgnc_id)
         except ValueError:
@@ -168,6 +169,9 @@ def panel(panel_id):
     if request.args.get("case_id"):
         case_obj = store.case(request.args["case_id"])
 
+        case_has_chanjo_coverage(case_obj)
+        case_has_chanjo2_coverage(case_obj)
+
         case_obj["outdated_panels"] = {}
         panel_name = panel_obj["panel_name"]
         latest_panel = store.gene_panel(panel_name)

scout/server/blueprints/variant/controllers.py

@@ -505,8 +505,11 @@ def observations(store: MongoAdapter, loqusdb: LoqusDB, variant_obj: dict) -> Di
             if obs_data[loqus_id].get("total"):
                 obs_data[loqus_id]["observations"] = 0
             continue
-
-        # collect cases where observations occurred
+        # Check if the current case is represented in the loqusdb instance
+        obs_data[loqus_id]["case_match"] = variant_obj["case_id"] in obs_data[loqus_id].get(
+            "families", []
+        )
+        # collect other cases where observations occurred
         obs_data[loqus_id]["cases"] = get_loqusdb_obs_cases(
             store, variant_obj, category, obs_data[loqus_id].get("families", [])
         )