scout-browser 4.99.0__py3-none-any.whl → 4.100.1__py3-none-any.whl

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

@@ -10,12 +10,25 @@
   <li class="nav-item">
     <a class="nav-link" href="{{ url_for('cases.index') }}">Institutes</a>
   </li>
-  <li class="nav-item">
-    <a class="nav-link" href="{{ url_for('panels.panels') }}">Gene Panels</a>
-  </li>
-  <li class="nav-item active d-flex align-items-center">
-    <span class="navbar-text">{{ panel.display_name }} {{ panel.version }}</span>
-  </li>
+  {% if case %}
+    <li class="nav-item">
+      <a class="nav-link" href="{{ url_for('overview.cases', institute_id=institute._id) }}">
+        {{ institute.display_name }}
+      </a>
+    </li>
+    <li class="nav-item d-flex align-items-center">
+      <a class="nav-link" href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name) }}">
+        {{ case.display_name }}
+      </a>
+    </li>
+  {% else %}
+    <li class="nav-item">
+      <a class="nav-link" href="{{ url_for('panels.panels') }}">Gene Panels</a>
+    </li>
+  {% endif %}
+    <li class="nav-item active d-flex align-items-center">
+      <span class="navbar-text">{{ panel.display_name }} {{ panel.version }}</span>
+    </li>
 {% endblock %}
 
 {% block content_main %}

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

@@ -56,7 +56,14 @@
       $('#phenotypes_table').DataTable( {
           paging: true,
           pageLength: 50,
-          dom: 'fBrtip',
+          layout: {
+            topStart: 'buttons',
+            topEnd: {
+                search: {
+                    placeholder: 'Filter...'
+                }
+            }
+          },
           buttons: [
             {
               extend: 'excelHtml5',

scout/server/blueprints/variant/controllers.py

@@ -367,11 +367,13 @@ def variant(
     if variant_id in case_clinvars:
         variant_obj["clinvar_clinsig"] = case_clinvars.get(variant_id)["clinsig"]
 
-    overlapping_vars = []
+    overlapping_variants, overlapping_outliers = [], []
     if get_overlapping:
-        for var in store.hgnc_overlapping(variant_obj):
+        overlapping_variants, overlapping_outliers = map(list, store.hgnc_overlapping(variant_obj))
+
+        for var in overlapping_variants:
             var.update(predictions(var.get("genes", [])))
-            overlapping_vars.append(var)
+
     variant_obj["end_chrom"] = variant_obj.get("end_chrom", variant_obj["chromosome"])
 
     dismiss_options = DISMISS_VARIANT_OPTIONS
@@ -395,7 +397,8 @@ def variant(
         "causatives": other_causatives,
         "managed_variant": managed_variant,
         "events": events,
-        "overlapping_vars": overlapping_vars,
+        "overlapping_vars": overlapping_variants,
+        "overlapping_outliers": overlapping_outliers,
         "manual_rank_options": MANUAL_RANK_OPTIONS,
         "cancer_tier_options": CANCER_TIER_OPTIONS,
         "dismiss_variant_options": dismiss_options,
@@ -406,9 +409,6 @@ def variant(
         "inherit_palette": INHERITANCE_PALETTE,
         "igv_tracks": get_igv_tracks("38" if variant_obj["is_mitochondrial"] else genome_build),
         "has_rna_tracks": case_has_rna_tracks(case_obj),
-        "gene_has_full_coverage": get_gene_has_full_coverage(
-            institute_obj, case_obj, variant_obj, genome_build
-        ),
         "gens_info": gens.connection_settings(genome_build),
         "evaluations": evaluations,
         "ccv_evaluations": ccv_evaluations,
@@ -416,16 +416,19 @@ def variant(
     }
 
 
-def get_gene_has_full_coverage(
-    institute_obj, case_obj, variant_obj, genome_build
-) -> Dict[int, bool]:
+def get_gene_has_full_coverage(institute_obj, case_obj, variant_obj) -> Dict[int, bool]:
     """
     Query chanjo2, if configured and d4 files are available for this case,
     for coverage completeness on the genes touching this variant.
     """
+    case_has_chanjo2_coverage(case_obj)
     if not case_obj.get("chanjo2_coverage"):
         return {}
 
+    genome_build = str(case_obj.get("genome_build", "37"))
+    if genome_build not in ["37", "38"]:
+        genome_build = "37"
+
     gene_has_full_coverage: dict = {
         hgnc_id: chanjo2.get_gene_complete_coverage(
             hgnc_id=hgnc_id,
@@ -653,6 +656,12 @@ def variant_acmg(store: MongoAdapter, institute_id: str, case_name: str, variant
         store, variant_obj, institute_id, case_name
     )
 
+    genome_build = str(case_obj.get("genome_build", "37"))
+    if genome_build not in ["37", "38"]:
+        genome_build = "37"
+
+    add_gene_info(store, variant_obj, genome_build=genome_build)
+
     return dict(
         institute=institute_obj,
         case=case_obj,

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

@@ -105,6 +105,15 @@
           </div>
         {% endfor %}
       </div>
+    <!-- external links -->
+    <div class="card panel-default mt-3">
+      <div class="card-body">
+        Search ClinGen Criteria Specifications (CSPEC):
+        {% for gene in variant.genes %}
+          <a href="{{ gene.cspec_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}</a>
+        {% endfor %}
+      </div>
+    </div>
     <!-- classification preview in the footer-->
       <div class="mt-3 fixed-bottom bg-light border">
         <div class="row">

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

@@ -104,7 +104,7 @@
     </div>
 
     <div class="row">
-      <div class="col-12">{{ overlapping_panel(variant, overlapping_vars, case, institute) }}</div>
+      <div class="col-12">{{ overlapping_panel(variant, overlapping_vars, overlapping_outliers, case, institute) }}</div>
       {% if rank_score_results %}
         <div class="col-12">{{ rankscore_panel(rank_score_results) }}</div>
       {% endif %}

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

@@ -132,27 +132,31 @@
         </div>
       {% endif %}
       {% for gene in variant.genes %}
-        <div class="d-flex flex-wrap ms-1">
+        <div class="ms-1">
         {% if gene.alamut_link %}
           <a href="{{ gene.alamut_link }}" class="btn btn-sm btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate">Alamut {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} c.</a>
         {% endif %}
         </div>
       {% endfor %}
-      {{ gene_coverage(institute, variant, case, config) }}
     </li>
     <li class="list-group-item">
       <div>
         {{ igv_track_selection(igv_tracks, current_user) }}
       </div>
     </li>
+    {% if (case.chanjo_coverage and config.chanjo_report) or case.chanjo2_coverage %}
+      <li class="list-group-item d-flex justify-content-between">
+        {{ gene_coverage(institute, variant, case, config) }}
+      </li>
+    {% endif %}
   </ul>
 {% endmacro %}
 
 {% macro gene_coverage(institute, variant, case, config) %}
   {% if case.chanjo_coverage and config.chanjo_report %}
-    <div class="d-flex flex-wrap ms-1">
+    <div class="d-flex flex-wrap ms-1" data-bs-toggle="tooltip" title="Chanjo coverage reports">
       {% for gene in variant.genes %}
-        <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}" data-bs-toggle="tooltip" title="Chanjo coverage report">
+        <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}">
           Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
         </a>
       {% endfor %}
@@ -160,14 +164,12 @@
   {% endif %}
   {% if case.chanjo2_coverage %}
     <div class="d-flex flex-wrap ms-1" data-bs-toggle="tooltip" title="Chanjo2 coverage reports">
-      {% for gene in variant.genes %}
-        {{ chanjo2_report_form(institute, case, gene.hgnc_symbol, 'overview', gene.hgnc_id, "Gene coverage " + (gene.common.hgnc_symbol if gene.common else gene.hgnc_id), "btn btn-sm btn-secondary text-white") }} <!--chanjo2 genes overview -->
-        {% if gene.common.hgnc_id in gene_has_full_coverage and gene.common.hgnc_id[gene.common.hgnc_id] %}
-          <span class="bg-success fa-solid fa-circle-check" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Chanjo2 coverage is at 100% completeness."></span>
-        {% else %}
-          <span class="bg-warning fa-solid fa-triangle-exclamation" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Note that Chanjo2 coverage is below 100% completeness."></span>
-        {% endif %}
-      {% endfor %}
+        {% for gene in variant.genes %}
+          <div class="btn-group" style="display:flex">
+            {{ chanjo2_report_form(institute, case, gene.hgnc_symbol if gene.hgnc_symbol else gene.hgnc_id, 'overview', gene.hgnc_id, "Gene coverage " ~ (gene.hgnc_symbol if gene.hgnc_symbol else gene.hgnc_id), "btn btn-sm btn-secondary text-white") }} <!--chanjo2 genes overview -->
+          <span class="btn complete-coverage-indicator align-items-center btn-info text-white btn-sm" style="display:flex" id="coverage-indicator-{{gene.hgnc_id}}-button" data-bs-toggle="tooltip" data-bs-placement="bottom" data-loading-text="Checking completeness..." title="Checking completeness..."><span style="display:flex" id="coverage-indicator-{{gene.hgnc_id}}-icon" class='align-self-center blink_me fa-solid fa-circle-question'></span><span style="display:flex" id="coverage-indicator-{{gene.hgnc_id}}-text" class='align-self-center'>Checking</span></span>
+          </div>
+        {% endfor %}
     </div>
   {% endif %}
 {% endmacro %}
@@ -338,8 +340,8 @@
       <div class="card-body mt-1 ms-3 mb-1" style="padding: 0;">
         Matching manually ranked variants:&nbsp;
         {% for manual_rank, manual_rank_info in matching_manual_ranked.items() %}
-          <a style="padding: 0;" class="btn btn-{{manual_rank_info.label_class}} btn-small" data-bs-toggle="collapse" href="#collapse_mr{{manual_rank}}" role="button" aria-expanded="false" aria-controls="collapseExample">
-            {{manual_rank_info.label}} ({{manual_rank_info.links|length}}x)
+          <a style="padding: 0;" class="btn btn-{{manual_rank_info.label_class}} btn-small" data-bs-toggle="collapse" href="#collapse_mr{{manual_rank}}" role="button" aria-expanded="false" aria-controls="#collapse_mr{{manual_rank}}">
+            <span class="collapse-button-icon me-1"></span>{{manual_rank_info.label}} ({{manual_rank_info.links|length}}x)
           </a>
           <div class="collapse" id="collapse_mr{{manual_rank}}">
             <div>
@@ -360,8 +362,8 @@
       <div class="card-body mt-1 ms-3 mb-1" style="padding: 0;">
         Matching tiered:&nbsp;
         {% for tier, tiered_info in matching_tiered.items() %}
-          <a style="padding: 0;" class="btn btn-{{tiered_info.label}} btn-xs" data-bs-toggle="collapse" href="#collapse_{{tier}}" aria-expanded="false" aria-controls="collapseExample">
-            {{tier}} ({{tiered_info.links|length}}x)
+          <a style="padding: 0;" class="btn btn-{{tiered_info.label_class}} btn-xs" data-bs-toggle="collapse" href="#collapse_{{tier}}" aria-expanded="false" aria-controls="collapse_{{tier}}">
+            <span class="collapse-button-icon me-1"></span>{{tier}} ({{tiered_info.links|length}}x)
           </a>
           <div class="collapse" id="collapse_{{tier}}">
             <div>
@@ -431,6 +433,7 @@
             <a href="{{ gene.oncokb_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">OncoKB</a>
             <a href="{{ gene.civic_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">CIViC</a>
             <a href="{{ gene.ckb_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">CKB</a>
+            <a href="{{ gene.cancer_hotspots_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">Cancer Hotspots</a>
           {% endif %}
           {% if str %}
             <a href="{{ gene.stripy_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">STRipy</a>

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

@@ -74,7 +74,7 @@
        {% if variant.category == "cancer_sv" %}
         {{matching_variants(managed_variant, causatives, variant.matching_tiered) }}
        {% else %}
-        {{matching_variants(managed_variant, causatives) }}
+        {{matching_variants(managed_variant, causatives, variant.matching_ranked) }}
        {% endif %}
       </div>
    </div>
@@ -122,7 +122,7 @@
   </div>
 
   <div class="row">
-    <div class="col-12">{{ overlapping_panel(variant, overlapping_vars, case, institute) }}</div>
+    <div class="col-12">{{ overlapping_panel(variant, overlapping_vars, overlapping_outliers, case, institute) }}</div>
   </div>
 
   <div class="mt-3 row">

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

@@ -116,7 +116,7 @@
 </div>
 {% endmacro %}
 
-{% macro overlapping_panel(variant, overlapping_vars, case, institute) %}
+{% macro overlapping_panel(variant, overlapping_vars, overlapping_outliers, case, institute) %}
   <div class="card panel-default">
     {% if variant.category != "snv" %}
       <div class="panel-heading">Gene overlapping variants</div>
@@ -141,27 +141,39 @@
             </tr>
           </thead>
           <tbody>
-          {% for overlapping_variant in overlapping_vars %}
+          {% for overlapping_variant in overlapping_vars + overlapping_outliers %}
             <tr>
               <td>
                 {% if overlapping_variant.category in ("sv", "cancer_sv") %}
                   <a href="{{url_for('variant.sv_variant', institute_id=institute._id,
                                    case_name=case.display_name, variant_id=overlapping_variant._id)}}" target="_blank">
-                    {{ overlapping_variant.display_name|truncate(20, True) }}
+                    {{ overlapping_variant.display_name|truncate(50, True) }}
                   </a>
-                {% else %}
+                {% elif overlapping_variant.category == "outlier" %}
+                  {{ overlapping_variant.display_name|truncate(50, True) }}
+                {% else  %}
                   <a href="{{url_for('variant.variant', institute_id=institute._id,
                                  case_name=case.display_name, variant_id=overlapping_variant._id)}}" target="_blank">
-                    {{ overlapping_variant.display_name|truncate(20, True) }}
+                    {{ overlapping_variant.display_name|truncate(50, True) }}
                   </a>
                 {% endif %}
               </td>
               <td>{{ overlapping_variant.hgnc_symbols|join(', ')|truncate(40, True) }}</td>
               <td>{{ overlapping_variant.sub_category|upper }}</td>
-	            <td class="text-end">{{ variant.rank_score + overlapping_variant.rank_score }}</td>
-              <td class="text-end">{{ overlapping_variant.rank_score }}</td>
+              {% if overlapping_variant.rank_score %}
+	              <td class="text-end">{{ variant.rank_score + overlapping_variant.rank_score }}</td>
+                <td class="text-end">{{ overlapping_variant.rank_score }}</td>
+              {% else %}
+                <td class="text-end">-</td><td class="text-end">-</td>
+              {% endif %}
+
               <td class="text-end">{{ overlapping_variant.length }}</td>
-              <td>{{ overlapping_variant.region_annotations|join(', ')|truncate(40, True) }}</td>
+              <td>
+                {{ overlapping_variant.region_annotations|join(', ')|truncate(40, True) }}
+                {% if overlapping_variant.sub_category == "splicing" %}
+                  {{ overlapping_variant.potential_impact }} - fs {{ overlapping_variant.causes_frameshift }}
+                {% endif %}
+              </td>
               <td>{{ overlapping_variant.functional_annotations|join(', ')|truncate(40, True) }}</td>
             </tr>
           {% else %}

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

@@ -152,7 +152,7 @@
     {% endif %}
     {{ rankscore_panel(rank_score_results) }}
     <div class="row">
-      <div class="col-12">{{ overlapping_panel(variant, overlapping_vars, case, institute) }}</div>
+      <div class="col-12">{{ overlapping_panel(variant, overlapping_vars, overlapping_outliers, case, institute) }}</div>
     </div>
     <div class="mt-3 row">
       <div class="col-12">
@@ -432,5 +432,46 @@
     set_scrolly_table('proteins_panel_table')
     set_scrolly_table('transcripts_panel_table')
 
+    function update_gene_has_full_coverage() {
+      $.getJSON('{{ url_for("variant.gene_has_full_coverage", institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}', function (data) {
+        if($.isEmptyObject(data.gene_has_full_coverage)) {
+            const complete_coverage_indicator_elements = document.getElementsByClassName("complete-coverage-indicator");
+            for(let complete_coverage_indicator of complete_coverage_indicator_elements) {
+              complete_coverage_indicator.style.display = "none"
+            }
+        }
+        for (const [hgnc_id, has_complete_coverage] of Object.entries(data.gene_has_full_coverage)) {
+          // reset the temp color for the outer span and icon of the inner span
+          console.log()
+          var coverage_indicator_button = document.getElementById('coverage-indicator-'+hgnc_id+'-button');
+          var coverage_indicator_icon = document.getElementById('coverage-indicator-'+hgnc_id+'-icon');
+          var coverage_indicator_text = document.getElementById('coverage-indicator-'+hgnc_id+'-text');
+
+          // this is the outer, button span
+          coverage_indicator_button.classList.remove('btn-info');
+          // this is the inner, icon span
+          coverage_indicator_icon.classList.remove('blink_me','fa-circle-question');
+
+          if (has_complete_coverage) {
+            coverage_indicator_button.classList.add('btn-success');
+            coverage_indicator_button.setAttribute('data-bs-original-title', "Chanjo2 coverage is at 100% completeness.");
+            coverage_indicator_icon.classList.add('fa-circle-check');
+            coverage_indicator_text.textContent = "Complete"
+          } else {
+            coverage_indicator_button.classList.add('btn-warning');
+            coverage_indicator_button.setAttribute('data-bs-original-title', "Note that Chanjo2 coverage is below 100% completeness.");
+            coverage_indicator_icon.classList.add('fa-triangle-exclamation');
+            coverage_indicator_text.textContent = "Incomplete"
+          }
+        }
+      }).fail(function() {
+          const complete_coverage_indicator_elements = document.getElementsByClassName("complete-coverage-indicator");
+          for(let complete_coverage_indicator of complete_coverage_indicator_elements) {
+            complete_coverage_indicator.style.display = "none"
+          }
+      });
+    };
+
+    $( window ).on( "load", function() { update_gene_has_full_coverage(); })
   </script>
 {% endblock %}

scout/server/blueprints/variant/views.py

@@ -28,6 +28,7 @@ from scout.server.blueprints.variant.controllers import (
 )
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
 from scout.server.blueprints.variant.controllers import (
+    get_gene_has_full_coverage,
     observations,
     str_variant_reviewer,
 )
@@ -423,6 +424,17 @@ def acmg():
     return jsonify({"classification": classification, "conflicts": acmg_conflicts, **acmg_bayesian})
 
 
+@variant_bp.route("/api/v1/gene_has_full_coverage/<institute_id>/<case_name>/<variant_id>/")
+def gene_has_full_coverage(institute_id, case_name, variant_id):
+    """Check if gene has full coverage using chanjo2 endpoint"""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+    variant_obj = store.variant(variant_id)
+
+    return jsonify(
+        {"gene_has_full_coverage": get_gene_has_full_coverage(institute_obj, case_obj, variant_obj)}
+    )
+
+
 @variant_bp.route("/ccv_evaluations/<evaluation_id>", methods=["GET", "POST"])
 @templated("variant/ccv.html")
 def ccv_evaluation(evaluation_id):

scout/server/blueprints/variants/controllers.py

@@ -49,7 +49,12 @@ from scout.server.utils import (
     user_institutes,
 )
 
-from .forms import FILTERSFORMCLASS, CancerSvFiltersForm, FusionFiltersForm, SvFiltersForm
+from .forms import (
+    FILTERSFORMCLASS,
+    CancerSvFiltersForm,
+    FusionFiltersForm,
+    SvFiltersForm,
+)
 from .utils import update_case_panels
 
 NUM = re.compile(r"\d+")
@@ -111,6 +116,13 @@ def populate_institute_soft_filters(form, institute_obj):
         form.institute_soft_filters.data = ",".join(institute_obj["soft_filters"])
 
 
+def set_overlapping_variants(variant_obj: dict):
+    """Define DNA or WTS variants that are overlapping with a gene of a variant."""
+    overlapping_variants, overlapping_outliers = store.hgnc_overlapping(variant_obj)
+    variant_obj["overlapping"] = list(overlapping_variants) or None
+    variant_obj["overlapping_outliers"] = list(overlapping_outliers) or None
+
+
 def variants(
     store,
     institute_obj,
@@ -137,8 +149,7 @@ def variants(
 
     variants = []
     for variant_obj in variant_res:
-        overlapping_svs = list(store.hgnc_overlapping(variant_obj))
-        variant_obj["overlapping"] = overlapping_svs or None
+        set_overlapping_variants(variant_obj)
 
         evaluations = []
         is_research = variant_obj["variant_type"] == "research"
@@ -233,8 +244,7 @@ def sv_variants(store, institute_obj, case_obj, variants_query, variant_count, p
     case_dismissed_vars = store.case_dismissed_variants(institute_obj, case_obj)
 
     for variant_obj in variants_query.skip(skip_count).limit(per_page):
-        overlapping_svs = list(store.hgnc_overlapping(variant_obj))
-        variant_obj["overlapping"] = overlapping_svs or None
+        set_overlapping_variants(variant_obj)
 
         # show previous classifications for research variants
         clinical_var_obj = variant_obj
@@ -282,8 +292,7 @@ def mei_variants(
     case_dismissed_vars = store.case_dismissed_variants(institute_obj, case_obj)
 
     for variant_obj in variants_query.skip(skip_count).limit(per_page):
-        overlapping = list(store.hgnc_overlapping(variant_obj))
-        variant_obj["overlapping"] = overlapping or None
+        set_overlapping_variants(variant_obj)
 
         # show previous classifications for research variants
         clinical_var_obj = variant_obj
@@ -1454,8 +1463,7 @@ def cancer_variants(store, institute_id, case_name, variants_query, variant_coun
         variant_obj["second_rep_gene"] = secondary_gene
         variant_obj["clinical_assessments"] = get_manual_assessments(variant_obj)
 
-        overlapping = list(store.hgnc_overlapping(variant_obj))
-        variant_obj["overlapping"] = overlapping or None
+        set_overlapping_variants(variant_obj)
 
         evaluations = []
         # Get previous ClinGen-CGC-VIGG evaluations of the variant from other cases

scout/server/blueprints/variants/forms.py

@@ -28,6 +28,7 @@ from scout.constants import (
     CLINSIG_MAP,
     FEATURE_TYPES,
     GENETIC_MODELS,
+    ONC_CLNSIG,
     OUTLIER_TYPES,
     SO_TERMS,
     SPIDEX_LEVELS,
@@ -38,6 +39,7 @@ from scout.constants import (
 LOG = logging.getLogger(__name__)
 
 CLINSIG_OPTIONS = list(CLINSIG_MAP.items())
+ONC_CLNSIG_OPTIONS = [(term.lower().replace(" ", "_"), term) for term in ONC_CLNSIG]
 FUNC_ANNOTATIONS = [(term, term.replace("_", " ")) for term in SO_TERMS]
 REGION_ANNOTATIONS = [(term, term.replace("_", " ")) for term in FEATURE_TYPES]
 SV_TYPE_CHOICES = [(term, term.replace("_", " ").upper()) for term in SV_TYPES]
@@ -112,8 +114,9 @@ class VariantFiltersForm(FlaskForm):
     compound_rank_score = IntegerField("Compound rank score")
     compound_follow_filter = BooleanField("Compounds follow filter")
     cadd_inclusive = BooleanField("CADD inclusive")
-    clinsig = NonValidatingSelectMultipleField("ClinVar CLINSIG", choices=CLINSIG_OPTIONS)
+    clinsig = NonValidatingSelectMultipleField("ClinVar significance", choices=CLINSIG_OPTIONS)
     clinsig_exclude = BooleanField("Exclude")
+    clinvar_tag = BooleanField("ClinVar hits only")
     prioritise_clinvar = BooleanField("Prioritise ClinVar")
 
     gnomad_frequency = BetterDecimalField("gnomadAF", validators=[validators.Optional()])
@@ -183,7 +186,6 @@ class FiltersForm(VariantFiltersForm):
     spidex_human = SelectMultipleField("SPIDEX", choices=SPIDEX_CHOICES)
 
     clinical_filter = SubmitField(label="Clinical filter")
-    clinvar_tag = BooleanField("ClinVar hits only")
 
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE
@@ -196,8 +198,11 @@ class CancerFiltersForm(VariantFiltersForm):
     alt_count = IntegerField("Min alt count", validators=[validators.Optional()])
     control_frequency = BetterDecimalField("Normal alt AF <", validators=[validators.Optional()])
     tumor_frequency = BetterDecimalField("Tumor alt AF >", validators=[validators.Optional()])
-    clinvar_tag = BooleanField("ClinVar hits only")
     cosmic_tag = BooleanField("Cosmic hits")
+    clinsig_onc = NonValidatingSelectMultipleField(
+        "ClinVar oncogenicity", choices=ONC_CLNSIG_OPTIONS
+    )
+    clinsig_onc_exclude = BooleanField("Exclude")
     mvl_tag = BooleanField("Managed Variants hits")
     local_obs_cancer_somatic_old = IntegerField(
         "Local somatic obs. (archive)", validators=[validators.Optional()]

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

@@ -440,10 +440,16 @@
     data-bs-html="true" data-bs-trigger="hover click"
     {% if variant.category == "SNV" %}
       data-bs-content="<div>Gene overlapping non-SNVs</div>
-      {{ overlapping_tooltip_table(institute, case, variant.overlapping[:20]) }}">Gene overlapping</a>
+      {{ overlapping_tooltip_table(institute, case, variant.overlapping[:20]) }}">Gene overlapping (DNA)</a>
     {% else %}
       data-bs-content="<div>Gene overlapping variants</div>
-      {{ overlapping_tooltip_table(institute, case, variant.overlapping[:40]) }}">Gene overlapping</a>
+      {{ overlapping_tooltip_table(institute, case, variant.overlapping[:40]) }}">Gene overlapping (DNA)</a>
     {% endif %}
   {% endif %}
+
+  {% if variant.overlapping_outliers %}
+    <a href="#" class="badge bg-success text-white" data-bs-toggle="popover" data-bs-placement="left"
+    data-bs-html="true" data-bs-trigger="hover click" data-bs-content="<div>Gene overlapping WTS outliers</div>
+      {{ overlapping_tooltip_table(institute, case, variant.overlapping_outliers[:40]) }}">Gene overlapping (WTS)</a>
+  {% endif %}
 {% endmacro %}

scout/server/blueprints/variants/templates/variants/indicators.html

@@ -41,25 +41,23 @@
 
 {% macro other_tiered_variants(variant) %}
   {% if variant.matching_tiered %}
-    <span class="popovers badge bg-dark" data-bs-toggle="popover" data-bs-html="true" title=""
-        data-bs-content="
+    <span class="badge bg-dark" data-bs-toggle="popover" data-bs-html="true" data-bs-trigger="hover click"
+          data-bs-title="Previously <b>T</b>iered as"
+          data-bs-content="
           {% for tier, tiered_info in variant.matching_tiered.items() %}
-            <span class='badge bg-{{tiered_info.label}}'>{{tier}} ({{tiered_info.links|length}}x)</span>
-          {% endfor %}
-        "
-       data-original-title="Previously tiered as">T</span>
+            <span class='badge bg-{{tiered_info.label_class}}'>{{tier}} ({{tiered_info.links|length}}x)</span>
+          {% endfor %}">T</span>
   {% endif %} <!-- end of if variant.matching_tiered -->
 {% endmacro %}
 
 {% macro matching_manual_rank(variant) %}
   {% if variant.matching_ranked %}
-    <span class="popovers badge bg-dark" data-bs-toggle="popover" data-bs-html="true"
-        data-bs-content="
+    <span class="badge bg-dark" data-bs-toggle="popover" data-bs-html="true" data-bs-trigger="hover click"
+        data-bs-title="Previously <b>M</b>anually ranked as"
+          data-bs-content="
           {% for manual_rank, manual_rank_info in variant.matching_ranked.items() %}
-            <div>{{manual_rank_info.label}} - {{manual_rank_info.description}} ({{manual_rank_info.links|length}}x)</div>
-          {% endfor %}
-        "
-       data-original-title="Previously ranked as">M</span>
+            <div><span class='badge bg-{{ manual_rank_info.label_class }}'>{{manual_rank_info.label}}</span> - {{manual_rank_info.description}} ({{manual_rank_info.links|length}}x)</div>
+          {% endfor %}">M</span>
   {% endif %}
 {% endmacro %}
 
@@ -120,7 +118,7 @@
 {% macro group_assessments_badge(variant) %}
   {% if variant.group_assessments %}
     {% for assessment in (variant.group_assessments or []) %}
-      <span class="badge bg-{{ assessment.display_class }}" data-bs-html="true" data-bs-toggle="tooltip" data-bs-placement="right"
+      <span class="badge bg-{{ assessment.display_class }}<b>" data-bs-html="true" data-bs-toggle="tooltip" data-bs-placement="right"
         title="Cohort {{ assessment.title }}">
         {{ assessment.label }}</span>
     {% endfor %}