scout-browser 4.92__py3-none-any.whl → 4.93.1__py3-none-any.whl

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

@@ -133,7 +133,7 @@
 {% endmacro %}
 
 {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
-  <label class="mt-3">ACMG classification</label>
+  <label class="mt-3" data-bs-toggle="tooltip" title="Richards et al 2015"><a href="https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf"  rel="noopener noreferrer" target="_blank" style="color: inherit;  text-decoration: inherit;">ACMG classification</a></label>
   <form action="{{ url_for('variant.variant_update', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
     <div class="d-flex justify-content-between">
       {% for option in ACMG_OPTIONS %}
@@ -145,11 +145,56 @@
   </form>
 {% endmacro %}
 
+{% macro ccv_classification_item(variant, data) %}
+  {% set current_variant = (data.variant_specific == variant._id) %}
+  <li class="list-group-item {{ 'list-group-item-info' if current_variant }}">
+    <div class="d-flex">
+      <span>
+        <a href="{{ url_for('variant.ccv_evaluation', evaluation_id=data._id) }}">
+          {{ data.ccv_classification.label }}
+        </a>
+        <span class="badge bg-info">{{ data.ccv_classification.short }}</span>
+      </span>
+      <span>
+        {% if not current_variant %}
+          <small>{{ data.case.display_name }}</small>
+        {% endif %}
+      </span>
+    </div>
+    <span>
+      <small class="text-muted">
+      {{ data.user_name }} on {{ data.created_at.date() }}
+      {% if current_variant %}
+          <form action="{{ url_for('variant.ccv_evaluation', evaluation_id=data._id) }}" method="POST" style="display: inline-block;">
+            <button class="btn btn-xs btn-link" >Delete</button>
+          </form>
+          {% if data.ccv_criteria %} 
+            <a class="btn btn-xs btn-link" href="{{ url_for('variant.ccv_evaluation', evaluation_id=data._id, edit=True) }}" data-bs-toggle="tooltip" title="Editing this classification will result in a new classification">Edit</a>
+          {% endif %}
+      {% endif %}
+      </small>
+    </span>
+  </li>
+{% endmacro %}
 
-{% macro panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) %}
+
+{% macro ccv_form(institute, case, variant, CCV_OPTIONS, selected=None) %}
+  <label class="mt-3" data-bs-toggle="tooltip" title="Horak et al 2022"><a href="https://doi.org/10.1016/j.gim.2022.01.001" rel="noopener noreferrer" target="_blank" style="color: inherit;  text-decoration: inherit;">ClinGen-CGC-VICC Oncogenicity classification</a></label>
+  <form action="{{ url_for('variant.variant_update', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
+    <div class="d-flex justify-content-between">
+      {% for option in CCV_OPTIONS %}
+      <button class="btn btn-{{ option.color if (option.code == selected or not selected) else 'outline-secondary' }} form-control {{ 'me-1' if not loop.last }}" name="ccv_classification" value="{{ option.code }}" title="{{ option.label }}">
+          {{ option.short }}
+        </button>
+      {% endfor %}
+    </div>
+  </form>
+{% endmacro %}
+
+{% macro panel_classify(variant, institute, case, ACMG_OPTIONS, CCV_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations, ccv_evaluations) %}
   <div class="card panel-default">
     <div class="panel-heading">Classify</div>
-    <div class="card-body">
+    <div class="card-body" style="margin-top: -30px">
       {{ variant_tag_button(variant, institute, case, manual_rank_options) }}
       {% if case.track == "cancer" %}
        {{ variant_tier_button(variant, institute, case, cancer_tier_options) }}
@@ -169,6 +214,19 @@
           {% endfor %}
         </div>
       {% endif %}
+      {% if case.track == "cancer" %}
+      {{ ccv_form(institute, case, variant, CCV_OPTIONS, variant.ccv_classification.code if variant.ccv_classification) }}
+      <div class="mt-3">
+        <a href="{{ url_for('variant.variant_ccv', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" class="btn btn-outline-secondary form-control">Classify</a>
+      </div>
+      {% if ccv_evaluations %} <!-- scrollable previous ClinGen-CGC-VICC evaluations div-->
+        <div class="list-group mt-3" style="max-height:200px;overflow-y: scroll;">
+          {% for ccv_evaluation in ccv_evaluations %}
+            {{ ccv_classification_item(variant, ccv_evaluation) }}
+          {% endfor %}
+        </div>
+      {% endif %}
+     {% endif %}
     </div>
   </div>
 {% endmacro %}

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

@@ -84,7 +84,7 @@
 
     <div class="row">
       <div class="col-lg-3 col-md-6">
-        {{ panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) }}
+        {{ panel_classify(variant, institute, case, ACMG_OPTIONS, CCV_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations, ccv_evaluations) }}
       </div>
       <div class="col-lg-5 col-md-6">
         {{ panel_summary() }}

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

@@ -200,6 +200,20 @@
   </div>
 {% endmacro %}
 
+{% macro observation_badge(observed_case) %}
+
+  {% if observed_case.variant and observed_case.variant.category == "snv"%}
+  <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=observed_case.case.owner, case_name=observed_case.case.display_name, variant_id=observed_case.variant._id) }}">{{ observed_case.case.display_name }}</a>
+  {% elif observed_case.variant and observed_case.variant.category == "sv"%}
+  <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=observed_case.case.owner, case_name=observed_case.case.display_name, variant_id=observed_case.variant._id) }}">{{ observed_case.case.display_name }}</a>
+  {% else %}
+  <span data-bs-toggle="tooltip" title="Missing link, this might be caused by variants not loaded after a rerun or inexact SV matching.">
+    <span class="ml-3 badge rounded-pill bg-light text-dark">{{ observed_case.case.display_name }}</span>
+  </span>
+  {% endif %}
+
+{% endmacro %}
+
 {% macro observations_panel(variant, observations, case) %}
   <div class="card panel-default">
     <div class="panel-heading d-flex justify-content-between">
@@ -240,19 +254,23 @@
                      </span>
                   {% endif %}
                   {% endif %}
-                  {% for data in obs.cases %}
-                     {% if data.variant and data.variant.category == "snv"%}
-                       <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
-                     {% elif data.variant and data.variant.category == "sv"%}
-                       <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
-                     {% else %}
-                       <span data-bs-toggle="tooltip" title="Missing link, this might be caused by variants not loaded after a rerun or inexact SV matching.">
-                         <span class="ml-3 badge rounded-pill bg-light text-dark">{{ data.case.display_name }}</span>
-                       </span>
-                     {% endif %}
+                  {% for observed_case in obs.cases %}
+                    {% if loop.index <= 10 %}
+                      {{ observation_badge(observed_case) }}
+                    {% endif %}
                   {% endfor %}
+
                   {% if obs.cases|length > 10 %}
-                     + more
+                    <span class="collapse" id="additionalCases_{{ loqusid }}">
+                      {% for observed_case in obs.cases %}
+                        {% if loop.index > 10 %}
+                          {{ observation_badge(observed_case) }}
+                        {% endif %}
+                      {% endfor %}
+                    </span>
+                    <button class="btn btn-link p-0 toggle-button" type="button" data-bs-toggle="collapse" href="#additionalCases_{{ loqusid }}">
+                      <span class="toggle-text">Show more/less</span>
+                    </button>
                   {% endif %}
                 </td>
               </tr>

scout/server/blueprints/variant/utils.py

@@ -2,7 +2,14 @@ import logging
 from typing import Dict, List, Optional, Tuple
 
 from scout.adapter import MongoAdapter
-from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS, VARIANT_FILTERS
+from scout.constants import (
+    ACMG_COMPLETE_MAP,
+    CALLERS,
+    CCV_COMPLETE_MAP,
+    CLINSIG_MAP,
+    SO_TERMS,
+    VARIANT_FILTERS,
+)
 from scout.server.links import add_gene_links, add_tx_links
 
 LOG = logging.getLogger(__name__)
@@ -472,6 +479,19 @@ def evaluation(store, evaluation_obj):
     return evaluation_obj
 
 
+def ccv_evaluation(store, evaluation_obj):
+    """Fetch and fill-in evaluation object."""
+    evaluation_obj["institute"] = store.institute(evaluation_obj["institute_id"])
+    evaluation_obj["case"] = store.case(evaluation_obj["case_id"])
+    evaluation_obj["variant"] = store.variant(evaluation_obj["variant_specific"])
+    evaluation_obj["ccv_criteria"] = {
+        criterion["term"]: criterion for criterion in evaluation_obj["ccv_criteria"]
+    }
+    evaluation_obj["ccv_classification"] = CCV_COMPLETE_MAP.get(
+        evaluation_obj["ccv_classification"]
+    )
+
+
 def transcript_str(transcript_obj, gene_name=None):
     """Generate amino acid change as a string.
 

scout/server/blueprints/variant/views.py

@@ -13,13 +13,26 @@ from flask import (
 from flask_login import current_user
 from markupsafe import Markup
 
-from scout.constants import ACMG_CRITERIA, ACMG_MAP, ACMG_OPTIONS
-from scout.server.blueprints.variant.controllers import check_reset_variant_classification
+from scout.constants import (
+    ACMG_CRITERIA,
+    ACMG_MAP,
+    ACMG_OPTIONS,
+    CCV_CRITERIA,
+    CCV_MAP,
+    CCV_OPTIONS,
+)
+from scout.server.blueprints.variant.controllers import ccv_evaluation as ccv_evaluation_controller
+from scout.server.blueprints.variant.controllers import (
+    check_reset_variant_ccv_classification,
+    check_reset_variant_classification,
+)
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
 from scout.server.blueprints.variant.controllers import observations, str_variant_reviewer
 from scout.server.blueprints.variant.controllers import variant as variant_controller
 from scout.server.blueprints.variant.controllers import variant_acmg as acmg_controller
 from scout.server.blueprints.variant.controllers import variant_acmg_post
+from scout.server.blueprints.variant.controllers import variant_ccv as ccv_controller
+from scout.server.blueprints.variant.controllers import variant_ccv_post
 from scout.server.blueprints.variant.verification_controllers import (
     MissingVerificationRecipientError,
     variant_verification,
@@ -27,6 +40,7 @@ from scout.server.blueprints.variant.verification_controllers import (
 from scout.server.extensions import loqusdb, store
 from scout.server.utils import institute_and_case, public_endpoint, templated
 from scout.utils.acmg import get_acmg, get_acmg_conflicts, get_acmg_temperature
+from scout.utils.ccv import get_ccv, get_ccv_conflicts, get_ccv_temperature
 from scout.utils.ensembl_rest_clients import EnsemblRestApiClient
 
 LOG = logging.getLogger(__name__)
@@ -205,9 +219,40 @@ def variant_acmg(institute_id, case_name, variant_id):
     )
 
 
+@variant_bp.route("/<institute_id>/<case_name>/<variant_id>/ccv", methods=["GET", "POST"])
+@templated("variant/ccv.html")
+def variant_ccv(institute_id, case_name, variant_id):
+    """ClinGen-CCG-VICC classification form."""
+    if request.method == "GET":
+        data = ccv_controller(store, institute_id, case_name, variant_id)
+        return data
+
+    criteria = []
+    criteria_terms = request.form.getlist("criteria")
+    for term in criteria_terms:
+        criteria.append(
+            dict(
+                term=term,
+                comment=request.form.get("comment-{}".format(term)),
+                links=[request.form.get("link-{}".format(term))],
+            )
+        )
+    ccv = variant_ccv_post(store, institute_id, case_name, variant_id, current_user.email, criteria)
+    flash("classified as: {}".format(ccv), "info")
+    return redirect(
+        url_for(
+            ".variant",
+            institute_id=institute_id,
+            case_name=case_name,
+            variant_id=variant_id,
+        )
+    )
+
+
 @variant_bp.route("/<institute_id>/<case_name>/<variant_id>/update", methods=["POST"])
 def variant_update(institute_id, case_name, variant_id):
-    """Update user-defined information about a variant: manual rank & ACMG."""
+    """Update user-defined information about a variant: manual rank, cancer tier,
+    CLinGen-CGC-VICC classification, dismissal & mosaic tags."""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     variant_obj = store.variant(variant_id)
     user_obj = store.user(current_user.email)
@@ -250,6 +295,7 @@ def variant_update(institute_id, case_name, variant_id):
             flash("Variant tag was updated", "info")
         else:
             flash("Variant tag was reset", "info")
+
     elif request.form.get("acmg_classification"):
         new_acmg = request.form["acmg_classification"]
         acmg_classification = variant_obj.get("acmg_classification")
@@ -268,6 +314,24 @@ def variant_update(institute_id, case_name, variant_id):
         )
         flash("updated ACMG classification: {}".format(new_acmg), "info")
 
+    elif request.form.get("ccv_classification"):
+        new_ccv = request.form["ccv_classification"]
+        ccv_classification = variant_obj.get("ccv_classification")
+        # If there already is a classification and the same one is sent again this means that
+        # We want to remove the classification
+        if isinstance(ccv_classification, int) and (new_ccv == CCV_MAP[ccv_classification]):
+            new_ccv = None
+
+        store.submit_ccv_evaluation(
+            variant_obj=variant_obj,
+            user_obj=user_obj,
+            institute_obj=institute_obj,
+            case_obj=case_obj,
+            link=link,
+            classification=new_ccv,
+        )
+        flash("updated ClinGen-CGC-VIGG classification: {}".format(new_ccv), "info")
+
     new_dismiss = request.form.getlist("dismiss_variant")
     if new_dismiss:
         store.update_dismiss_variant(
@@ -353,6 +417,53 @@ def acmg():
     return jsonify({"classification": classification, "conflicts": acmg_conflicts, **acmg_bayesian})
 
 
+@variant_bp.route("/ccv_evaluations/<evaluation_id>", methods=["GET", "POST"])
+@templated("variant/ccv.html")
+def ccv_evaluation(evaluation_id):
+    """Show, edit or delete an ClinGen-CGC-VIGG evaluation."""
+
+    evaluation_obj = store.get_ccv_evaluation(evaluation_id)
+    if evaluation_obj is None:
+        flash("Evaluation was not found in database", "warning")
+        return redirect(request.referrer)
+    ccv_evaluation_controller(store, evaluation_obj)
+    if request.method == "POST":
+        link = url_for(
+            ".variant",
+            institute_id=evaluation_obj["institute"]["_id"],
+            case_name=evaluation_obj["case"]["display_name"],
+            variant_id=evaluation_obj["variant_specific"],
+        )
+        store.delete_ccv_evaluation(evaluation_obj)
+
+        if check_reset_variant_ccv_classification(store, evaluation_obj, link):
+            flash("Cleared ClinGen-CGC-VIGG classification.", "info")
+
+        return redirect(link)
+
+    return dict(
+        evaluation=evaluation_obj,
+        edit=bool(request.args.get("edit")),
+        institute=evaluation_obj["institute"],
+        case=evaluation_obj["case"],
+        variant=evaluation_obj["variant"],
+        CRITERIA=CCV_CRITERIA,
+        CCV_OPTIONS=CCV_OPTIONS,
+    )
+
+
+@variant_bp.route("/api/v1/ccv")
+@public_endpoint
+def ccv():
+    """Calculate an ClinGen-CVC-VIGG classification from submitted criteria."""
+    criteria = request.args.getlist("criterion")
+    classification = get_ccv(criteria)
+
+    ccv_bayesian = get_ccv_temperature(criteria)
+    ccv_conflicts = get_ccv_conflicts(criteria)
+    return jsonify({"classification": classification, "conflicts": ccv_conflicts, **ccv_bayesian})
+
+
 @variant_bp.route(
     "/<institute_id>/<case_name>/<variant_id>/<order>",
     methods=["POST"],

scout/server/blueprints/variants/controllers.py

@@ -17,6 +17,8 @@ from scout.constants import (
     CANCER_EXPORT_HEADER,
     CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
     CANCER_TIER_OPTIONS,
+    CCV_COMPLETE_MAP,
+    CCV_MAP,
     CHROMOSOMES,
     CHROMOSOMES_38,
     CLINSIG_MAP,
@@ -362,6 +364,7 @@ def get_manual_assessments(variant_obj):
     ## display manual input of interest: classified, commented, tagged, mosaicism or dismissed.
     assessment_keywords = [
         "acmg_classification",
+        "ccv_classification",
         "manual_rank",
         "cancer_tier",
         "dismiss_variant",
@@ -402,6 +405,16 @@ def get_manual_assessments(variant_obj):
                 assessment["label"] = classification["short"]
                 assessment["display_class"] = classification["color"]
 
+            if assessment_type == "ccv_classification":
+                ccv_classification = variant_obj[assessment_type]
+                if isinstance(ccv_classification, int):
+                    ccv_code = CCV_MAP[ccv_classification]
+                    ccv_classification = CCV_COMPLETE_MAP[ccv_code]
+
+                assessment["title"] = "ClinGen-CGC-VIGG: {}".format(ccv_classification["label"])
+                assessment["label"] = ccv_classification["short"]
+                assessment["display_class"] = ccv_classification["color"]
+
             if assessment_type == "dismiss_variant":
                 dismiss_variant_options = {
                     **DISMISS_VARIANT_OPTIONS,
@@ -918,6 +931,11 @@ def parse_variant(
         acmg_code = ACMG_MAP[variant_obj["acmg_classification"]]
         variant_obj["acmg_classification"] = ACMG_COMPLETE_MAP[acmg_code]
 
+    ccv_classification = variant_obj.get("ccv_classification")
+    if isinstance(ccv_classification, int):
+        ccv_code = CCV_MAP[variant_obj["ccv_classification"]]
+        variant_obj["ccv_classification"] = CCV_COMPLETE_MAP[ccv_code]
+
     # convert length for SV variants
     variant_length = variant_obj.get("length")
     variant_obj["length"] = {100000000000: "inf", -1: "n.d."}.get(variant_length, variant_length)
@@ -1409,6 +1427,19 @@ def cancer_variants(store, institute_id, case_name, variants_query, variant_coun
                     secondary_gene = gene
         variant_obj["second_rep_gene"] = secondary_gene
         variant_obj["clinical_assessments"] = get_manual_assessments(variant_obj)
+
+        evaluations = []
+        # Get previous ClinGen-CGC-VIGG evaluations of the variant from other cases
+        for evaluation_obj in store.get_ccv_evaluations(variant_obj):
+            if evaluation_obj["case_id"] == case_obj["_id"]:
+                continue
+
+            ccv_classification = evaluation_obj["ccv_classification"]
+
+            evaluation_obj["ccv_classification"] = CCV_COMPLETE_MAP.get(ccv_classification)
+            evaluations.append(evaluation_obj)
+        variant_obj["ccv_evaluations"] = evaluations
+
         variants_list.append(variant_obj)
 
     data = dict(

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

@@ -2,7 +2,7 @@
 
 {% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
 {% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
-{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
+{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, ccv_evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
 
 {% block title %}
   {{ variant_type|capitalize }} somatic variants
@@ -109,6 +109,7 @@
               {{ comments_badge(case, institute, variant) }}
               {{ causative_badge(variant, case) }}
               {{ other_tiered_variants(variant) }}
+              {{ ccv_evaluations_badge(variant) }}
             </td>
             <td>{{ rank_cell(variant) }}</td>
             <td>{{ cadd_cell(variant) }}</td>

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

@@ -161,94 +161,84 @@
 
 {% macro gene_cell(variant, inherit_palette) %}
   <div class="align-items-center">
-    {% if variant.category == "cancer" or variant.category == "sv_cancer" %}
-      <a data-bs-toggle="tooltip" data-bs-html="true" title="
+
+    {% macro gene_tooltip(gene) %}
+      <div>
         <div>
+          <strong>{{ gene.hgnc_symbol }}</strong>: {{ gene.description }}
+        </div>
+        {% if gene.inheritance %}
           <div>
-            <strong>{{ variant.first_rep_gene.hgnc_symbol }}</strong>: {{ variant.first_rep_gene.description }}
+            <strong>Models</strong>: {{ gene.inheritance|join(',') }}
           </div>
-          {% if variant.first_rep_gene.inheritance %}
-            <div>
-              <strong>Models</strong>: {{ variant.first_rep_gene.inheritance|join(',') }}
-            </div>
-          {% endif %}
-        {% if variant.first_rep_gene.phenotypes %}
+        {% endif %}
+        {% if gene.phenotypes %}
           <div><strong>OMIM disease</strong>
-          {% for disease in variant.first_rep_gene.phenotypes %}
-            <div>
-                {{ disease.description }}
-            </div>
+          {% for disease in gene.phenotypes %}
+            <div>{{ disease.description }}</div>
           {% endfor %}
           </div>
         {% endif %}
-        </div>"
-        {% if variant.first_rep_gene %}
-          href="{{ url_for('genes.gene', hgnc_id=variant.first_rep_gene.hgnc_id) }}"
-        {% endif %}>
-        {{ variant.first_rep_gene.hgnc_symbol or variant.first_rep_gene.hgnc_id }}
-        {% if variant.secondary_gene %}
-          <span class="text-muted">
-            ({{ variant.second_rep_gene.hgnc_symbol or variant.second_rep_gene.hgnc_id }})
-          </span>
-        {% endif %}
+      </div>
+    {% endmacro %}
+
+    {% macro gene_link(gene) %}
+      <a
+        data-bs-toggle="tooltip"
+        data-bs-html="true"
+        title="{{ gene_tooltip(gene) }}"
+        href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}"
+      >
+        {{ gene.hgnc_symbol or gene.hgnc_id }}
       </a>
+    {% endmacro %}
+
+    {% macro panel_badge(variant, gene_id=0) %}
+
+      {% set matching_panels = [] %}
+      {% for panel in variant.case_panels|rejectattr('removed')|list %}
+        {% if gene_id in panel.hgnc_ids %}
+           {% set _ = matching_panels.append(panel) %}
+        {% endif %}
+      {% endfor %}
 
-      {% set panel_count = variant.case_panels|rejectattr('removed')|list|length %}
-      {% if panel_count > 0%}
-          <a
-            class="badge bg-secondary text-white"
-            data-bs-toggle="popover"
-            data-bs-html="true"
-            data-bs-trigger="hover click"
-            title="Overlapping gene panels"
-            data-bs-content="{% for panel in variant.case_panels|sort(attribute='panel_name',case_sensitive=False)|rejectattr('removed') %}
-              {{ panel.panel_name|safe }}<br>
-              {% endfor %}"
-            >{{panel_count}}
-          </a>
+      {% set panel_count = matching_panels|length %}
+      <a
+        class="badge bg-secondary text-white"
+        data-bs-toggle="popover"
+        data-bs-html="true"
+        data-bs-trigger="hover click"
+        title="Overlapping gene panels"
+        data-bs-content="{% for panel in matching_panels %}
+          {{ panel.panel_name|safe }}<br>
+        {% endfor %}"
+      >{{ panel_count }}</a>
+    {% endmacro %}
+
+    {% if variant.category in ["cancer", "sv_cancer"] %}
+      {% if variant.first_rep_gene %}
+        {{ gene_link(variant.first_rep_gene) }}
+      {% endif %}
+      {% if variant.secondary_gene %}
+        <span class="text-muted">
+          ({{ variant.second_rep_gene.hgnc_symbol or variant.second_rep_gene.hgnc_id }})
+        </span>
+      {% endif %}
+      {% if variant.first_rep_gene or variant.second_rep_gene %}
+        {{ panel_badge(variant, variant.first_rep_gene.hgnc_id or variant.second_rep_gene.hgnc_id) }}
       {% endif %}
     {% else %}
-      {% set panel_count = variant.case_panels|rejectattr('removed')|list|count %}
       {% for gene in variant.genes %}
         <div>
-        <a data-bs-toggle="tooltip" data-bs-html="true" title="
-        <div>
-          <div>
-            <strong>{{ gene.hgnc_symbol }}</strong>: {{ gene.description }}
-          </div>
-          {% if gene.inheritance %}
-            <div>
-              <strong>Models</strong>: {{ gene.inheritance|join(',') }}
-            </div>
-          {% endif %}
-          {% if gene.phenotypes %}
-            <div><strong>OMIM disease</strong>
-            {% for disease in gene.phenotypes %}
-              <div>
-                  {{ disease.description }}
-              </div>
-            {% endfor %}
-            </div>
-          {% endif %}
-        </div>"
-          href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">{{ gene.hgnc_symbol or gene.hgnc_id }}
-        {% for model in gene.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}</a>
-        {% if panel_count > 0 %}
-          <a
-            class="badge bg-secondary text-white"
-            data-bs-toggle="popover"
-            data-bs-html="true"
-            data-bs-trigger="hover click"
-            data-bs-content="{% for panel in variant.case_panels|sort(attribute='panel_name',case_sensitive=False)|rejectattr('removed') %}
-              {{ panel.panel_name|safe }}<br>
-              {% endfor %}"
-            title="Overlapping gene panels">{{panel_count}}
-          </a>
-        {% endif %}
-      </div>
+          {{ gene_link(gene) }}
+          {% for model in gene.inheritance %}
+            {{ inheritance_badge(model, inherit_palette) }}
+          {% endfor %}
+          {{ panel_badge(variant, gene.hgnc_id) }}
+        </div>
       {% endfor %}
-
     {% endif %}
+
   </div>
 {% endmacro %}
 

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

@@ -74,6 +74,17 @@
   {% endif %}
 {% endmacro %}
 
+{% macro ccv_evaluations_badge(variant) %}
+  {% if variant.ccv_evaluations %}
+    {% for evaluation in (variant.ccv_evaluations or []) %}
+      <span class="badge bg-secondary" style="margin-left:1px" data-bs-toggle="tooltip" data-bs-placement="right"
+        title="Previously classified as {{ evaluation.ccv_classification.label }}">
+        {{ evaluation.ccv_classification.short }}
+      </span>
+    {% endfor %}
+  {% endif %}
+{% endmacro %}
+
 {% macro dismissals_badge(variant) %}
   {% if variant.dismissals %}
       <span class="badge bg-secondary" style="margin-left:1px" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top"

scout/server/static/custom_images.js

@@ -1,3 +1,11 @@
+const imgMaxWidth = window.innerWidth*0.7;
+const imgMaxHeight = window.innerHeight*0.7;
+
+function calculateAspectRatioFit(srcWidth, srcHeight, maxWidth, maxHeight) {
+    let ratio = Math.min(maxWidth / srcWidth, maxHeight / srcHeight);
+    return [srcWidth*ratio, srcHeight*ratio];
+}
+
 /**
  * This function fetches an image from disk and displays it in a specified div
  * @param {string} imageUrl - The URL of the image to fetch
@@ -9,15 +17,24 @@
 		 .then(blob => {
 				 const img = document.createElement("img");
 				 img.src = URL.createObjectURL(blob);
+				 if (width > imgMaxWidth || height > imgMaxHeight) {
+				 		const resized_pixels = calculateAspectRatioFit(width, height, imgMaxWidth, imgMaxHeight);
+				 		width = resized_pixels[0];
+				 		height = resized_pixels[1];
+				 }
 				 if (width) {
 				 	img.style.width = width+'px';
 				 }
 				 if (height) {
 				 	img.style.height = height+'px';
 				 }
-				 // Display the image in the specified div
+				 // Add the image to a link and add the link to the div
+				 const link = document.createElement('a');
+				 link.appendChild(img);
+				 link.href = img.src;
+				 link.setAttribute('target', "_blank");
 				 const div = document.getElementById(divId);
-				 div.appendChild(img);
+				 div.appendChild(link);
 		})
 		.catch(error => console.error(error));
 }