scout-browser 4.96.0__py3-none-any.whl → 4.98.0__py3-none-any.whl

scout/server/blueprints/cases/controllers.py

@@ -1088,11 +1088,12 @@ def update_default_panels(store, current_user, institute_id, case_name, panel_id
     store.update_default_panels(institute_obj, case_obj, user_obj, link, panel_objs)
 
 
-def update_clinical_filter_hpo(store, current_user, institute_id, case_name, hpo_clinical_filter):
+def update_clinical_filter_hpo(store, current_user, institute_obj, case_obj, hpo_clinical_filter):
     """Update HPO clinical filter use for a case."""
-    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     user_obj = store.user(current_user.email)
-    link = url_for("cases.case", institute_id=institute_id, case_name=case_name)
+    link = url_for(
+        "cases.case", institute_id=institute_obj["_id"], case_name=case_obj["display_name"]
+    )
     store.update_clinical_filter_hpo(institute_obj, case_obj, user_obj, link, hpo_clinical_filter)
 
 
@@ -1493,3 +1494,22 @@ def add_link_for_disease(case_obj: dict):
         for diagnosis in case_diagnoses:
             #: Add link
             diagnosis.update({"disease_link": disease_link(disease_id=diagnosis["disease_id"])})
+
+
+def remove_dynamic_genes(store: dict, case_obj: dict, institute_obj: dict, request_form: dict):
+    """Remove one or more genes from the dynamic gene list. If there are no more
+    genes on the list, also stop using the HPO panel for clinical filter."""
+    case_dynamic_genes = [dyn_gene["hgnc_id"] for dyn_gene in case_obj.get("dynamic_gene_list")]
+    genes_to_remove = [int(gene_id) for gene_id in request_form.getlist("dynamicGene")]
+    hgnc_ids = list(set(case_dynamic_genes) - set(genes_to_remove))
+    store.update_dynamic_gene_list(
+        case_obj,
+        hgnc_ids=hgnc_ids,
+        delete_only=True,
+    )
+    if not hgnc_ids:
+        hpo_clinical_filter = False
+        case_obj["hpo_clinical_filter"] = hpo_clinical_filter
+        update_clinical_filter_hpo(
+            store, current_user, institute_obj, case_obj, hpo_clinical_filter
+        )

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

@@ -295,6 +295,9 @@
         {% if case.vcf_files.vcf_fusion_research %}
           <a class="btn btn-dark btn-sm text-white" href="{{ url_for('variants.fusion_variants', institute_id=institute._id, case_name=case.display_name, variant_type='research') }}">Research fusion variants</a>
         {% endif %}
+        {% if case.omics_files and (case.omics_files.fraser_research or case.omics_files.outrider_research) %}
+          <a class="btn btn-dark btn-sm text-white" href="{{ url_for('omics_variants.outliers', institute_id=institute._id, case_name=case.display_name, variant_type='research') }}">Research WTS variants</a>
+        {% endif %}
       </div>
     </div>
   </div>

scout/server/blueprints/cases/templates/cases/chanjo2_form.html

@@ -1,4 +1,4 @@
-{% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text) %}
+{% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text, link_class = "link-primary") %}
 
   {% set form_name = "chanjo2_"+panel_name+"_"+report_type %}
   {% set form_action = config.CHANJO2_URL+"/"+report_type %}
@@ -40,7 +40,7 @@
     {% if panel_name == "HPO Panel" %}
       <button type="submit" class="btn btn-secondary btn-sm text-white"> Coverage {{report_type}} (Chanjo2) </button>
     {% else %}
-      <a class="link-primary" onclick="this.closest('form').submit();return false;">{{link_text}}</a>
+      <a class="{{ link_class }}" onclick="this.closest('form').submit();return false;">{{link_text}}</a>
     {% endif %}
   </form>
 

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

@@ -79,8 +79,7 @@
           <span class="mr-3" data-bs-toggle="tooltip" data-bs-placement="bottom" title="{{ case.dynamic_panel_phenotypes|join(', ') }}">
               {{ case.dynamic_panel_phenotypes|length }} phenotypes
           </span>
-        {% endif %}
-        )
+        {% endif %})
         {% if case.dynamic_gene_list_edited %} <span class="text-danger ml-3"> (edited) </span> {% endif %}
       </h6>
     </div>
@@ -119,6 +118,7 @@
       </div>
 
       <div>
+        {% if case.track == 'rare' %}
         <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">
@@ -128,6 +128,7 @@
             </div>
           </form>
         </div>
+        {% endif %}
         <div class="row mt-3">
           <div class="btn-group btn-group-sm">
           {% if case.track == 'cancer' %}
@@ -180,7 +181,12 @@
                Clinical HPO MEIs
              </a>
             {% endif %}
-           {% endif %}
+            {% if case.has_outliers %}
+              <a class="btn btn-secondary btn-sm text-white" href="{{ url_for('omics_variants.outliers',
+                institute_id=institute._id, case_name=case.display_name, variant_type='clinical',
+                gene_panels=['hpo']) }}" target="_blank" rel="noopener">Clinical HPO WTS</a>
+            {% endif %}
+          {% endif %}
           </div>
         </div>
         {% if case.chanjo_coverage or case.chanjo2_coverage and case.dynamic_gene_list|length > 0 %}

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

@@ -17,7 +17,9 @@
              title="Measure of the tumor mutational burden">TMB</th>
             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
              title="Measure of microsatellite instability">MSI</th>
-            <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
+             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
+             title="Homologous Recombination Deficiency">HRD</th>
+             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
              title="Measure of tumor purity">Tumor Purity</th>
             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
              title="Downloadable CytoSure file">CGH</th>
@@ -41,6 +43,7 @@
               <td>{{ ind.analysis_type|upper }}</td>
               <td>{{ ind.tmb or 'N/A' }}</td>
               <td>{{ ind.msi or 'N/A' }}</td>
+              <td>{{ ind.hrd or 'N/A' }}</td>
               {% if ind.phenotype_human == "tumor" %}
                 <td>
                   <div class="d-flex align-items-center">

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

@@ -291,29 +291,33 @@
 
 {% macro pretty_variant(variant) %}
 
-  {% if variant.category in "str" %}
-        {{ variant.str_repid }} {{ variant.alternative | replace("<", " ") | replace(">", "")}}
-
-  {% elif variant.category in ("snv", "cancer") %}
-    {% set display_genes = [] %}
-    {% for gene in variant.genes %}
-      {% if gene.hgvs_identifier and gene.hgnc_symbol  %}
-        {{ "" if display_genes.append(gene.hgnc_symbol + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
-      {% elif gene.hgnc_symbol %}
-        {{ "" if display_genes.append(gene.hgnc_symbol) }}
-      {% elif gene.hgvs_identifier and gene.hgnc_id %}
-        {{ "" if display_genes.append( gene.hgnc_id|string + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
+  {% if variant.category %}
+    {% if variant.category in "str" %}
+      {{ variant.str_repid }} {{ variant.alternative | replace("<", " ") | replace(">", "")}}
+
+    {% elif variant.category in ("snv", "cancer") %}
+      {% set display_genes = [] %}
+      {% for gene in variant.genes %}
+        {% if gene.hgvs_identifier and gene.hgnc_symbol  %}
+          {{ "" if display_genes.append(gene.hgnc_symbol + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
+        {% elif gene.hgnc_symbol %}
+          {{ "" if display_genes.append(gene.hgnc_symbol) }}
+        {% elif gene.hgvs_identifier and gene.hgnc_id %}
+          {{ "" if display_genes.append( gene.hgnc_id|string + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
+        {% endif %}
+      {% endfor %}
+
+      {% if not display_genes %}
+          {{ "" if display_genes.append( variant.simple_id|truncate(40,True) ) }}
       {% endif %}
-    {% endfor %}
 
-    {% if not display_genes %}
-        {{ "" if display_genes.append( variant.simple_id|truncate(40,True) ) }}
-    {% endif %}
+      {{ display_genes|join(", ") }}
 
-    {{ display_genes|join(", ") }}
-  {% else %} <!-- structural variants -->
-    {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
+    {% else %} <!-- structural variants -->
+      {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
+    {% endif %}
   {% endif %}
+
 {% endmacro %}
 
 {% macro pretty_link_variant(variant, case) %}

scout/server/blueprints/cases/views.py

@@ -486,6 +486,7 @@ def phenotypes_actions(institute_id, case_name):
     hpo_ids = request.form.getlist("hpo_id")
     user_obj = store.user(current_user.email)
 
+    ### match action for 3.10
     if action == "PHENOMIZER":
         diseases = controllers.phenomizer_diseases(hpo_ids, case_obj)
         if diseases:
@@ -511,14 +512,8 @@ def phenotypes_actions(institute_id, case_name):
             )
         store.update_dynamic_gene_list(case_obj, hgnc_ids=list(hgnc_ids), add_only=True)
 
-    if action == "REMOVEGENES":  # Remove one or more genes from the dynamic gene list
-        case_dynamic_genes = [dyn_gene["hgnc_id"] for dyn_gene in case_obj.get("dynamic_gene_list")]
-        genes_to_remove = [int(gene_id) for gene_id in request.form.getlist("dynamicGene")]
-        store.update_dynamic_gene_list(
-            case_obj,
-            hgnc_ids=list(set(case_dynamic_genes) - set(genes_to_remove)),
-            delete_only=True,
-        )
+    if action == "REMOVEGENES":
+        controllers.remove_dynamic_genes(store, case_obj, institute_obj, request.form)
 
     if action == "GENES":
         hgnc_symbols = parse_raw_gene_symbols(request.form.getlist("genes"))
@@ -928,9 +923,10 @@ def default_panels(institute_id, case_name):
 @cases_bp.route("/<institute_id>/<case_name>/update-clinical-filter-hpo", methods=["POST"])
 def update_clinical_filter_hpo(institute_id, case_name):
     """Update default panels for a case."""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     hpo_clinical_filter = request.form.get("hpo_clinical_filter")
     controllers.update_clinical_filter_hpo(
-        store, current_user, institute_id, case_name, hpo_clinical_filter
+        store, current_user, institute_obj, case_obj, hpo_clinical_filter
     )
     return redirect(request.referrer)
 

scout/server/blueprints/clinvar/controllers.py

@@ -2,7 +2,7 @@ import csv
 import logging
 from datetime import datetime
 from tempfile import NamedTemporaryFile
-from typing import List, Optional
+from typing import List, Optional, Tuple
 
 from flask import flash
 from flask_login import current_user
@@ -17,6 +17,7 @@ from scout.constants.clinvar import (
 )
 from scout.constants.variant_tags import MANUAL_RANK_OPTIONS
 from scout.models.clinvar import clinvar_variant
+from scout.server.blueprints.variant.utils import add_gene_info
 from scout.server.extensions import clinvar_api, store
 from scout.utils.hgvs import validate_hgvs
 from scout.utils.scout_requests import fetch_refseq_version
@@ -26,18 +27,15 @@ from .form import CaseDataForm, SNVariantForm, SVariantForm
 LOG = logging.getLogger(__name__)
 
 
-def _get_var_tx_hgvs(case_obj, variant_obj):
-    """Retrieve all transcripts / hgvs for a given variant
-    Args:
-        case_obj(scout.models.Case)
-        variant_obj(scout.models.Variant)
-    Returns:
-        list of tuples. example: [("NM_002340.6:c.1840C>T", "NM_002340.6:c.1840C>T (validated)" ), ("NM_001145436.2:c.1840C>T", "NM_001145436.2:c.1840C>T"), .. ]
-    """
+def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]:
+    """Retrieve all transcripts / hgvs for a given variant."""
+
     build = str(case_obj.get("genome_build", "37"))
     tx_hgvs_list = [("", "Do not specify")]
+    add_gene_info(store, variant_obj, genome_build=build)
     for gene in variant_obj.get("genes", []):
         for tx in gene.get("transcripts", []):
+            mane_select = tx.get("mane_select_transcript")
             if all([tx.get("refseq_id"), tx.get("coding_sequence_name")]):
                 for refseq in tx.get("refseq_identifiers"):
                     refseq_version = fetch_refseq_version(refseq)  # adds version to a refseq ID
@@ -48,10 +46,12 @@ def _get_var_tx_hgvs(case_obj, variant_obj):
 
                     label = hgvs_simple
                     if validated:
-                        label += " (validated)"
+                        label += "_validated_"
 
-                    tx_hgvs_list.append((hgvs_simple, label))
+                    if mane_select and mane_select == refseq_version:
+                        label += "_mane-select_"
 
+                    tx_hgvs_list.append((hgvs_simple, label))
     return tx_hgvs_list
 
 

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

@@ -110,26 +110,34 @@
                     <table style="width:100%; table-layout: auto; border-collapse: collapse;">
                       <caption></caption>
                       <tr><th></th></tr>
-                    {% set ns = namespace(label='', validated=false) %}
                     {% for item_row in variant_data.var_form.tx_hgvs | batch(3) %}
                       <tr>
                       {% for item in item_row %}
-                        <td style="width: 3%; text-align: right; vertical-align: baseline;">{{item}}</td>
+                        {% set ns = namespace(label='', validated=false, mane_select=false) %}
 
-                        {% if "(validated)" in item.label.text %}
+                        {% if "_validated_" in item.label.text %}
                           {% set ns.validated = true %}
-                        {% else %}
-                          {% set ns.validated = false %}
                         {% endif %}
-                        {% set ns.label = item.label.text | replace(" (validated)", "") %}
+                        {% if "_mane-select_" in item.label.text %}
+                          {% set ns.mane_select = true %}
+                        {% endif %}
+                        {% set ns.label = item.label.text | replace("_validated_", "") | replace("_mane-select_", "")  %}
+
+                        <td style="width: 3%; text-align: right; vertical-align: baseline;">
+                          <input type="radio" name="tx_hgvs" value="{{ ns.label }}"
+                            {% if ns.mane_select %}checked{% endif %}>
+                        </td>
 
                         <td style="width: 30%; text-align: left; ">
                           <p class="text-dark"
-                          {% if ns.label|length > 25 %}
+                          {% if ns.label|length > 50 %}
                            data-bs-toggle="tooltip" title="{{ns.label}}">{{ ns.label|truncate(25,true,'..') }}
                           {% else %}
                             >{{ ns.label }}
                           {% endif %}
+                          {% if ns.mane_select %}
+                            <span class='badge bg-dark'>MANE SELECT</span>
+                          {% endif %}
                           {% if ns.validated %}
                             <em class="fa fa-check text-success" aria-hidden="true" data-bs-toggle="tooltip" title="Verified by VariantValidator"></em>
                           {% endif %}

scout/server/blueprints/institutes/controllers.py

@@ -20,7 +20,10 @@ from scout.constants import (
     SEX_MAP,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
-from scout.server.blueprints.variant.utils import predictions, update_representative_gene
+from scout.server.blueprints.variant.utils import (
+    predictions,
+    update_representative_gene,
+)
 from scout.server.extensions import beacon, store
 from scout.server.utils import institute_and_case, user_institutes
 
@@ -328,6 +331,21 @@ def get_clinvar_submitters(form: MultiDict) -> Optional[List[str]]:
     return clinvar_submitters
 
 
+def get_soft_filters(form: MultiDict) -> Optional[list]:
+    """
+    Return a list with custom soft filters or None.
+    This is not available on the form for unprivileged users, only admin.
+    """
+    if current_user.is_admin is False:
+        return None
+
+    soft_filters = []
+    for filter in form.getlist("soft_filters"):
+        soft_filters.append(filter)
+
+    return soft_filters
+
+
 def get_loqusdb_ids(form: MultiDict) -> Optional[List[str]]:
     """
     Return loqusdb ids from the form multiselect.
@@ -390,6 +408,7 @@ def update_institute_settings(store: MongoAdapter, institute_obj: Dict, form: Mu
         check_show_all_vars=form.get("check_show_all_vars"),
         clinvar_key=form.get("clinvar_key"),
         clinvar_submitters=get_clinvar_submitters(form),
+        soft_filters=get_soft_filters(form),
     )
     return updated_institute
 

scout/server/blueprints/institutes/forms.py

@@ -95,7 +95,11 @@ class InstituteForm(FlaskForm):
 
     alamut_institution = StringField("Alamut Institution ID", validators=[validators.Optional()])
 
-    check_show_all_vars = BooleanField("Preselect 'Show also variants only present in unaffected'")
+    check_show_all_vars = BooleanField("Preselect 'Include variants only present in unaffected'")
+
+    soft_filters = NonValidatingSelectMultipleField(
+        "Default soft filters", validators=[validators.Optional()]
+    )
 
     clinvar_key = StringField("API key", widget=PasswordInput(hide_value=False))
 

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

@@ -34,8 +34,21 @@
   <div class="row" id="body-row"> <!--sidebar and main container are on the same row-->
     {{ institute_actionbar(institute) }} <!-- This is the sidebar -->
     <div class="col">
+
       <div class="card">
-        <div class="card-header"><b>Filters created for institute on variants pages</b></div>
+        <div class="card-header"><b>Soft filters created by an admin on the institute's settings page</b></div>
+        <div class="card-body">
+          {% for filter_tag in institute.soft_filters %}
+            <span class="badge bg-secondary">{{filter_tag}}</span>
+          {% else%}
+            No soft filters available
+          {% endfor %}
+
+        </div>
+      </div>
+
+      <div class="card mt-3">
+        <div class="card-header"><b>Custom filters created for institute on variants pages</b></div>
         <div class="card-body">
           <ul class="list-group">
            <li class="list-group-item list-group-item-heading">

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

@@ -104,6 +104,13 @@
       placeholder: "Add Sanger email",
     });
 
+    $('#soft_filters').select2({
+      tags: true,
+      theme: 'bootstrap-5',
+      tokenSeparators: [','],
+      placeholder: "germline_risk",
+    });
+
     $('#clinvar_tags').select2({
       tags: true,
       theme: 'bootstrap-5',

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

@@ -285,7 +285,7 @@
             </div>
             <!-- End of cohorts settings -->
 
-            <!-- Variants and panels searching -->
+             <!-- Variants and panels searching -->
             <div class="row mt-5 d-flex align-items-center">
             <fieldset>
               <legend>Variants and gene panels searching</legend>
@@ -349,6 +349,25 @@
               </div>
               <!-- End of loqusdb settings -->
 
+              <!-- Custom soft filters for variants -->
+              <div class="row mt-5 d-flex align-items-center">
+                <fieldset>
+                  <legend>Variants custom soft filters</legend>
+                  <div class="row">
+                    <div class="col-sm-6 col-lg-4">
+                      {{form.soft_filters.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Values to filter variant documents with by default. For example germline_risk or in_normal.")}}
+                      <select class="select2" id="soft_filters" name="soft_filters" multiple="true" style="width:100%;">
+                        {% if institute.soft_filters %}
+                          {% for filter in institute.soft_filters %}
+                            <option value="{{filter}}" selected>{{filter}}</option>
+                          {% endfor %}
+                        {% endif %}
+                      </select>
+                    </div>
+                  </div>
+              </div>
+              <!-- End of custom soft filters for variants -->
+
               <!-- Alamut settings -->
               <div class="row mt-5 d-flex align-items-center">
                 <fieldset><legend>Alamut Plus<a class="ms-2 text-decoration-none" href="https://extranet.interactive-biosoftware.com/alamut-visual-plus_API.html" target="_blank" rel="noopener">*</a></legend>

scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html

@@ -59,7 +59,7 @@
               <tr>
                 <th style="width:14%" title="HGNC symbols">Gene</th>
                 <th style="width:7%" title="Sub-category">Type</th>
-                <th style="width:7%" title="Value - delta Psi or l2fc ">Value</th>
+                <th style="width:7%" title="Value - delta Psi or l2fc">Value</th>
                 <th title="Functional annotation">Func. annotation</th>
                 <th style="width:7%" title="P-value">P-value</th>
                 <th style="width:10%" title="Individual">Ind</th>
@@ -246,6 +246,13 @@
   <div class="col-6">
     {{ stash_filter_buttons(form, institute, case) }}
   </div>
+
+  <div class="col-2 offset-2">
+      <div class="btn-group">
+        {{ form.sort_by(class="form-select btn btn-primary", style="width: auto;") }}
+        {{ form.sort_order(class="form-select btn btn-primary", style="width: auto;") }}
+      </div>
+    </div>
 </div>
 {% endmacro %}
 
@@ -266,7 +273,7 @@
     <div class="col-4 d-flex justify-content-center">
       Filter returns {{result_size}} / {{ total_variants }} variants.
     </div>
-    <div class="col-4 d-flex flex-column justify-content-end">
+    <div class="col-4 d-flex justify-content-end">
       <div class="d-flex justify-content-end">Showing {%if more_variants %}page {{page}}{%else%}last page{% endif %} with {{nvars}} variants.</div>
     </div>
   </div>

scout/server/blueprints/omics_variants/views.py

@@ -11,6 +11,9 @@ from scout.server.blueprints.variants.controllers import (
     get_variants_page,
     populate_chrom_choices,
     populate_filters_form,
+    populate_persistent_filters_choices,
+    set_hpo_clinical_filter,
+    update_form_hgnc_symbols,
 )
 from scout.server.blueprints.variants.forms import OutlierFiltersForm
 from scout.server.extensions import store
@@ -43,8 +46,7 @@ def outliers(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    set_hpo_clinical_filter(case_obj, request.form)
 
     # update status of case if visited for the first time
     activate_case(store, institute_obj, case_obj, current_user)
@@ -63,12 +65,6 @@ def outliers(institute_id, case_name):
             store, institute_obj, case_obj, user_obj, category, request.form
         )
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # populate available panel choices
     form.gene_panels.choices = gene_panel_choices(store, institute_obj, case_obj)
 
@@ -78,7 +74,7 @@ def outliers(institute_id, case_name):
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
-    # controllers.update_form_hgnc_symbols(store, case_obj, form)
+    update_form_hgnc_symbols(store, case_obj, form)
     variants_query = store.omics_variants(
         case_obj["_id"], query=form.data, category=category, build=genome_build
     )
@@ -96,7 +92,9 @@ def outliers(institute_id, case_name):
         case=case_obj,
         cytobands=cytobands,
         expand_search=get_expand_search(request.form),
-        filters=available_filters,
+        filters=populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,

scout/server/blueprints/variant/controllers.py

@@ -32,10 +32,12 @@ from scout.server.blueprints.variant.utils import (
     update_variant_case_panels,
 )
 from scout.server.blueprints.variants.utils import update_case_panels
-from scout.server.extensions import LoqusDB, config_igv_tracks, gens
+from scout.server.extensions import LoqusDB, chanjo2, config_igv_tracks, gens
 from scout.server.links import disease_link, get_variant_links
 from scout.server.utils import (
     case_has_alignments,
+    case_has_chanjo2_coverage,
+    case_has_chanjo_coverage,
     case_has_mt_alignments,
     case_has_rna_tracks,
     user_institutes,
@@ -257,6 +259,8 @@ def variant(
     # Provide basic info on alignment files availability for this case
     case_has_alignments(case_obj)
     case_has_mt_alignments(case_obj)
+    case_has_chanjo_coverage(case_obj)
+    case_has_chanjo2_coverage(case_obj)
 
     # Collect all the events for the variant
     events = list(store.events(institute_obj, case=case_obj, variant_id=variant_id))
@@ -402,6 +406,9 @@ 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,
@@ -409,6 +416,28 @@ def variant(
     }
 
 
+def get_gene_has_full_coverage(
+    institute_obj, case_obj, variant_obj, genome_build
+) -> Dict[int, bool]:
+    """
+    Query chanjo2, if configured and d4 files are available for this case,
+    for coverage completeness on the genes touching this variant.
+    """
+    if not case_obj.get("chanjo2_coverage"):
+        return {}
+
+    gene_has_full_coverage: dict = {
+        hgnc_id: chanjo2.get_gene_complete_coverage(
+            hgnc_id=hgnc_id,
+            threshold=institute_obj.get("coverage_cutoff") or 15,
+            individuals=case_obj.get("individuals"),
+            build=genome_build,
+        )
+        for hgnc_id in [gene.get("hgnc_id") for gene in variant_obj.get("genes")]
+    }
+    return gene_has_full_coverage
+
+
 def variant_rank_scores(store: MongoAdapter, case_obj: dict, variant_obj: dict) -> list:
     """Retrive rank score values and ranges for the variant
 

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

@@ -223,9 +223,25 @@
       {% if tmp_gene_info %}
         {% set primary_transcript = tmp_gene_info[1] %}
         {% set nr_genes = variant.genes | length %}
-        <a target="_blank" href="{{ url_for('genes.gene', hgnc_id=primary_gene.hgnc_id) }}" data-bs-toggle="tooltip" title="Preferred gene for variant {% if nr_genes > 1 %} out of {{ nr_genes }} {% endif %}- shows conceptually highest impact change. See Severity card and Transcripts table below for more details."><h5 class="card-title">
-          {{ primary_gene.hgnc_symbol }}; {{ primary_gene.description }} {% if nr_genes > 1 %} <span class="badge bg-info">+ {{ nr_genes-1 }} genes</span>{% endif %}
-        </h5></a>
+        <table class="table table-bordered table-fixed table-sm">
+          <thead class="thead table-light border-top">
+            <tr class="active">
+              <th>Gene</th>
+              <th>Description</th>
+              <th data-bs-toggle="tooltip" title="Gene tolerance to a single copy of a truncating mutation (pLI) | Loss-of-function observed/expected upper bound fraction (LOEUF)">pLI score|LOEUF</th>
+            </tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>
+                <a target="_blank" href="{{ url_for('genes.gene', hgnc_id=primary_gene.hgnc_id) }}" data-bs-toggle="tooltip" title="Preferred gene for variant {% if nr_genes > 1 %} out of {{ nr_genes }} {% endif %}- shows conceptually highest impact change. See Severity card and Transcripts table below for more details.">{{ primary_gene.hgnc_symbol }}</a>
+                {% if nr_genes > 1 %} <span class="badge bg-info">+ {{ nr_genes-1 }} genes</span>{% endif %}
+              </td>
+              <td>{{primary_gene.description}}</td>
+              <td>{{primary_gene.pli_score|round(2) if primary_gene.pli_score else "n.a."}} | {{primary_gene.loeuf|round(2) if primary_gene.loeuf else "n.a."}}</td>
+            </tr>
+          </tbody>
+        </table>
       {% endif %}
       <ul class="list-group list-group-flush" style="margin-bottom: 1rem">
         {% if primary_transcript %}