scout-browser 4.92__py3-none-any.whl → 4.94__py3-none-any.whl

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

@@ -74,7 +74,7 @@
     {{ matching_variants(managed_variant, causatives, variant.matching_ranked, variant.matching_tiered) }}
     <div class="row">
       <div class="col-sm-3">
-        {{ 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-sm-4">{{ panel_summary() }}</div>
       <div class="col-sm-3">

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

@@ -0,0 +1,183 @@
+{% extends "layout.html" %}
+
+{% block title %}
+  {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} - Classify
+{% endblock %}
+
+{% block top_nav %}
+  {{ super() }}
+  <li class="nav-item">
+    <a class="nav-link text-nowrap" href="{{ url_for('cases.index') }}">Institutes</a>
+  </li>
+  <li class="nav-item">
+    <a class="nav-link text-nowrap" href="{{ url_for('overview.cases', institute_id=institute._id) }}">
+      {{ institute.display_name }}
+    </a>
+  </li>
+  <li class="nav-item">
+    <a class="nav-link text-nowrap" href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name) }}">
+      {{ case.display_name }}
+    </a>
+  </li>
+  <li class="nav-item active d-flex align-items-center">
+    <span class="navbar-text">{{ variant.display_name }}</span>
+  </li>
+{% endblock %}
+
+{% block content_main %}
+  <div class="container mt-3 mb-5">
+    <form action="{{ url_for('variant.variant_ccv', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
+      <div class="card panel-default mt-3">
+        <div class="card-body">
+          {% if evaluation %}
+             <h4>
+              {{ evaluation.ccv_classification.label }}
+              <span class="badge bg-info">{{ evaluation.ccv_classification.short|safe }}</span>
+            </h4>
+            By {{ evaluation.user_name }} on {{ evaluation.created_at.date() }}
+            {% if edit %}
+              <br><br>
+              <button class="btn btn-primary form-control" data-bs-toggle="tooltip" title="Editing this classification will result in a new classification">Reclassify</button>
+            {% endif %}
+          {% elif not evaluation %}
+            <button class="btn btn-primary form-control">Submit</button>
+          {% endif %}
+          <div id="conflicts_div" class="bg-warning"></div>
+        </div>
+      </div>
+
+      <div class="d-flex flex-row justify-content-between mt-3">
+        {% for category, criteria_group in CRITERIA.items() %}
+          <div class="flex-column {{ 'me-3' if not loop.last }}">
+            <h4>Evidence of {{ category }}</h4>
+            {% for evidence, criteria in criteria_group.items() %}
+              <ul class="list-group mt-3">
+                <li class="list-group-item">{{ evidence }}</li>
+                {% for criterion_code, criterion in criteria.items() %}
+                  {% if evaluation and evaluation.ccv_criteria.get(criterion_code).comment %}
+                    {% set comment = evaluation.ccv_criteria.get(criterion_code).comment %}
+                  {% endif %}
+                  {% if evaluation and evaluation.ccv_criteria.get(criterion_code).links %}
+                    {% set link = evaluation.ccv_criteria.get(criterion_code).links[0] %}
+                  {% endif %}
+                  {% if evaluation and evaluation.ccv_criteria.get(criterion_code).modifier %}
+                    {% set modifier = evaluation.ccv_criteria.get(criterion_code).modifier %}
+                  {% endif %}
+                  <div class="list-group-item">
+                    <div class="d-flex justify-content-between">
+                      <div data-bs-toggle="tooltip" data-bs-placement="top" title="{{ criterion.description|safe }}">
+                        <span class="badge bg-info me-1">{{ criterion_code }}</span>
+                        {{ criterion.short|safe}}
+                      </div>
+                      <div class="form-check form-switch">
+                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.ccv_criteria }} {{ 'disabled' if evaluation and edit is false }}>
+                        <label class="form-check-label" for="checkbox-{{ criterion_code }}"></label>
+                      </div>
+                    </div>
+                    <div id="comment-{{ criterion_code }}" class="{{ 'collapse' if not (comment or link or modifier) }} mt-2">
+                      {% if criterion.documentation %}<div class="row"><span class="me-1 fw-light text-wrap">{{ criterion.documentation | safe }}</span></div>{% endif %}
+                      <div class="row">
+                        <select {{ 'disabled' if evaluation and edit is false}} id="modifier-{{ criterion_code }}" name="modifier-{{ criterion_code }}" class="form-control form-select">
+                          <option value="" {% if not modifier %}selected{% endif %}>Strength modifier...</option>
+                          {% for level in "Strong", "Moderate", "Supporting" %}
+                            {% if(level != evidence) %}
+                              <option id="{{ criterion_code }}-{{ level }}" value="{{ level }}" {% if modifier == level %}selected{% endif %}>{{ level }}</option>
+                            {% endif %}
+                          {% endfor %}
+                        </select>
+                      </div>
+                      <div class="row">
+                        <textarea {{ 'disabled' if evaluation and edit is false }} class="form-control"
+                          name="comment-{{ criterion_code }}" rows="3" placeholder="Comment (optional)">{{ comment }}</textarea>
+                      </div>
+                      <input type="url" {{ 'disabled' if evaluation and edit is false }} class="form-control" name="link-{{ criterion_code }}"
+                        placeholder="{{ link or 'Supporting link (optional)' }}" value="">
+                    </div>
+                  </div>
+                {% endfor %}
+                </li>
+              </ul>
+            {% endfor %}
+          </div>
+        {% endfor %}
+      </div>
+    <!-- classification preview in the footer-->
+      <div class="mt-3 fixed-bottom bg-light border">
+        <div class="row">
+          <div class="col-3" style="font-size:1.5em">
+            <a href="https://doi.org/10.1016/j.gim.2022.01.001" data-bs-toggle="tooltip" title="Suggested classification based on Horak et al 2022." rel="noopener noreferrer" target="_blank"><span id="temperature_span" class="badge"></span></a>
+          </div>
+          <div class="col-6 text-center">
+          {% for option in CCV_OPTIONS %}
+            <a id="ccv-{{ option.code }}" href="https://doi.org/10.1016/j.gim.2022.01.001" class="btn ccv-preview" data-bs-toggle="tooltip" title="Suggested classification based on Horak et al 2022." rel="noopener noreferrer" target="_blank">{{ option.label }}</a>
+          {% endfor %}
+          </div>
+        </div>
+      </div>
+    </form>
+  </div>
+{% endblock %}
+
+{% block scripts %}
+  {{ super() }}
+
+  <script>
+
+    window.onload=function() {
+        update_classification();
+    }
+
+    $(function () {
+      $('[data-bs-toggle="tooltip"]').tooltip();
+
+      $('.form-switch').change(function(event) {
+        var el = $('#comment-' + event.target.value);
+        if (event.target.checked) {
+          el.collapse('show');
+        } else {
+          el.collapse('hide');
+        }
+        update_classification()
+      });
+
+      $('.form-select').change(function(event) {
+            update_classification()
+      });
+    });
+
+
+    function update_classification() {
+      var criteria = $(':checked').map(function(idx, elem) {
+        const modifiers = ["Strong", "Moderate", "Supporting"];
+        for (possible_modifier of modifiers) {
+          var modifier_option;
+          if(elem.value !== null && elem.value !== '') {
+            modifier_option = document.getElementById(elem.value + '-' + possible_modifier)
+          }
+          if(modifier_option) {
+            if (modifier_option.selected) {
+              return 'criterion=' + elem.value + '_' + possible_modifier
+            }
+          }
+        }
+        return 'criterion=' + elem.value
+      });
+
+
+      $.getJSON('/api/v1/ccv?' + criteria.toArray().join('&'), function(data) {
+        // reset the selection
+        $('.ccv-preview').removeClass('btn-primary');
+        // add new selection
+        $('#ccv-' + data.classification).addClass('btn-primary');
+
+        var temperature_span = document.getElementById("temperature_span");
+        temperature_span.innerHTML = 'Score ' + data.points + ' <span class="fa ' + data.temperature_icon + '"></span> ' + data.temperature + ' (' + data.point_classification + ')'
+        temperature_span.className = 'badge bg-' + data.temperature_class
+
+        // Update any classification conflicts
+        var conflicts_div = document.getElementById("conflicts_div");
+        conflicts_div.innerHTML = data.conflicts.join("<br>");
+      });
+    }
+  </script>
+{% endblock %}

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/tx_overview.html

@@ -76,15 +76,15 @@
               </td> <!-- end of ID col-->
 
               <td> <!-- HGVS Description col -->
-                {% set hgvs_c = (tx.coding_sequence_name or '')|truncate(20, True) %}
+                {% set hgvs_c = (tx.coding_sequence_name or '')|truncate(30, True) %}
                 {% if variant.chromosome in ["MT","M"] %}
                   {% set mt_notation = "m." ~ variant.position ~ variant.reference ~ ">" ~ variant.alternative %}
-                  {{ mt_notation|truncate(20,True) }} <span class="text-muted">({{ hgvs_c }})</span>
+                  {{ mt_notation|truncate(30,True) }} <span class="text-muted">({{ hgvs_c }})</span>
                 {% else %}
                   {{ hgvs_c }}
                 {% endif %}
                 <span class="text-muted float-end">
-                  {{ (tx.protein_sequence_name or '')|url_decode }}
+                  {{ (tx.protein_sequence_name or '')|url_decode|truncate(30, True) }}
                 </span>
               </td> <!-- end of HGVS Description col -->
 

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(