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

scout/models/ccv_evaluation.py

@@ -0,0 +1,26 @@
+# -*- coding: utf-8 -*-
+"""
+scout.models.ccv_evaluation
+~~~~~~~~~~~~~~~~~~
+
+Define a document to describe a ClinGen-CGC-VIGG evaluation
+
+Evaluations are stored in its own collection
+
+"""
+
+from datetime import datetime
+
+ccv_evaluation = dict(
+    variant_specific=str,  # md5 document id
+    variant_id=str,  # md5 variant id
+    institute_id=str,  # Institute _id, required
+    case_id=str,  # case_id, required
+    classification=str,  # What did the evaluation end up in?
+    # All evaluations will have an author
+    user_id=str,  # user email, required
+    user_name=str,  # user name
+    criteria=list,  # List of dictionaries with criterias
+    # timestamps
+    created_at=datetime,
+)

scout/models/variant/variant.py

@@ -94,6 +94,7 @@ variant = dict(
     manual_rank=int,  # choices=[0, 1, 2, 3, 4, 5]
     dismiss_variant=list,
     acmg_classification=str,  # choices=ACMG_TERMS
+    ccv_classification=str,  # choices=CCV_TERMS
 )
 
 compound = dict(

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

@@ -40,6 +40,11 @@
         <li class="nav-item">
           <a class="nav-link link-secondary" style="text-decoration: none !important;" href="#acmg_variants">ACMG-classified variants</a>
         </li>
+        {% if cancer %}
+        <li class="nav-item">
+          <a class="nav-link link-secondary" style="text-decoration: none !important;" href="#ccv_variants">ClinGen-CGC-VICC-classified variants</a>
+        </li>
+        {% endif %}
         <li class="nav-item">
           <a class="nav-link link-secondary" style="text-decoration: none !important;" href="#manual_ranked_variants">Manual ranked</a>
         </li>
@@ -64,6 +69,7 @@
    {{ causatives_panel()}}
    {{ pinned_panel() }}
    {{ classified_panel() }}
+   {% if cancer %}{{ ccv_classified_panel() }}{% endif %}
    {{ tagged_panel() }}
    {{ commented_panel() }}
    {{ dismissed_panel() }}
@@ -392,6 +398,33 @@
 </div>
 {% endmacro %}
 
+{% macro ccv_classified_panel() %}
+<div class="card border-warning mb-3" style="border-width: 5px; display: block;">
+  <div class="card-header bg-warning text-dark" style="border-top-left-radius: 0; border-top-right-radius: 0;">
+    <a id="ccv_variants"><strong>Other ClinGen-CGC-VICC-classified Variants</strong></a>
+  </div>
+  <div class="card-body">
+    {% set duplicated_variants = [] %}
+    {% if variants.ccv_classified_detailed %}
+      {% for variant in variants.ccv_classified_detailed|sort(attribute='variant_rank') %}
+        {% if variant['_id'] not in printed_vars %}
+          {% do printed_vars.append(variant['_id']) %}
+          {{ variant_content(variant, loop.index) }}
+          <br>
+        {% else %}
+          {% do duplicated_variants.append(variant['_id']) %}
+        {% endif %}
+      {% endfor %}
+    {% else %}
+      No ClinGen-CGC-VICC-classified variants available for this case
+    {% endif %}
+    {% if variants.ccv_classified_detailed and duplicated_variants|length == variants.ccv_classified_detailed|length %}
+      All ClinGen-CGC-VICC-classified variants are already described in the previous views
+    {% endif %}
+  </div>
+</div>
+{% endmacro %}
+
 {% macro tagged_panel() %}
 <div class="card border-warning mb-3" style="border-width: 5px; display: block;">
   <div class="card-header bg-warning text-dark" style="border-top-left-radius: 0; border-top-right-radius: 0;">
@@ -635,6 +668,9 @@
               <th>Inheritance models</th>
             {% endif %}
             <th>ACMG classification</th>
+            {% if cancer %}
+            <th>ClinGen-CGC-VICC classification</th>
+            {% endif %}
           </tr>
         </thead>
         <tbody>
@@ -683,6 +719,15 @@
                 -
               {% endif %}
             </td>
+            {% if cancer %}
+            <td>
+              {% if variant.ccv_classification %}
+                <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['code']}}">{{variant.ccv_classification['code'] }}</span>
+              {% else %}
+                -
+              {% endif %}
+            </td>
+            {% endif %}
           </tr>
         </tbody>
       </table>

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

@@ -372,7 +372,7 @@
           <select class="form-control form-control-sm" name="collaborator">
             <option selected disabled value="">Select institute</option>
             {% for collab_id, collab_name in collaborators %}
-              <option value="{{ collab_id }}">{{ collab_name }}</option>
+              <option value="{{ collab_id }}">{{ collab_name }} ({{ collab_id }})</option>
             {% endfor %}
           </select>
           <span class="input-group-btn">
@@ -389,7 +389,7 @@
         <select class="form-control form-control-sm" name="collaborator">
           <option>Institute</option>
           {% for collab_id, collab_name in case.o_collaborators %}
-            <option value="{{ collab_id }}">{{ collab_name }}</option>
+            <option value="{{ collab_id }}">{{ collab_name }} ({{ collab_id }})</option>
           {% endfor %}
         </select>
         <div class="input-group-btn">

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

@@ -25,9 +25,7 @@
               <a href="{{ url_for('overview.cases', institute_id=institute._id) }}">
                 {{ institute.display_name }}
               </a>
-              {% if current_user.is_admin %}
                 <span class="text-muted">({{ institute._id }})</span>
-              {% endif %}
                 <span class="badge bg-secondary rounded-pill float-end">{{ case_count }} cases </span>
             </li>
           {% endfor %}

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

@@ -29,7 +29,7 @@
 <div class="container-float">
   <div class="row" id="body-row"> <!--sidebar and main container are on the same row-->
     <div class="col-12">
-        {{ variant_list_content(institute, causatives, acmg_map, callers, inherit_palette) }}
+        {{ variant_list_content(institute, causatives, acmg_map, ccv_map, callers, inherit_palette) }}
     </div>
   </div> <!-- end of div id body-row -->
 </div>

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

@@ -446,7 +446,7 @@
 {% endmacro %}
 
 
-{% macro variant_list_content(institute, variants, acmg_map, callers, inherit_palette) %}
+{% macro variant_list_content(institute, variants, acmg_map, ccv_map, callers, inherit_palette) %}
 <div class="card mt-3">
   <div class="card-body overflow-auto">
     <table id="variants_table" class="table display table-sm">
@@ -469,6 +469,7 @@
           <th data-bs-toggle='tooltip' data-bs-container='body' title="ref/alt-GQ">Zygosity</th>
           <th>Inheritance</th>
           <th>ACMG</th>
+          <th>ClinGen-CGC-VICC</th>
           <th>Case</th>
           <th>Analysis type</th>
           <th>Validated status</th>
@@ -608,6 +609,16 @@
                 {% endif %}
               </a>
             </td>
+            <td><!-- Clingen-CGC-VIGG -->
+              <a href="#" data-bs-toggle="tooltip" title="Clingen-CGC-VIGG classification assigned by Scout users"
+                style="text-decoration: none; color: #000;">
+                {% if 'ccv_classification' in variant %}
+                <span class="badge bg-{{ccv_map[variant.ccv_classification].color}}">{{ccv_map[variant.ccv_classification].short}}</span>
+                {% else %}
+                -
+                {% endif %}
+              </a>
+            </td>
             <td><!-- Case -->
               <a href="{{ url_for('cases.case',
                                         institute_id=institute._id,

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

@@ -58,7 +58,7 @@
         {{validated_chart()}}
       </div>
       <div class="row">
-        <div class="col-12">{{ variant_list_content(institute, verified, acmg_map, callers, inherit_palette) }}</div>
+        <div class="col-12">{{ variant_list_content(institute, verified, acmg_map, ccv_map, callers, inherit_palette) }}</div>
       </div>
     </div>
   </div>

scout/server/blueprints/institutes/views.py

@@ -10,6 +10,8 @@ from scout.constants import (
     ACMG_COMPLETE_MAP,
     ACMG_MAP,
     CALLERS,
+    CCV_COMPLETE_MAP,
+    CCV_MAP,
     INHERITANCE_PALETTE,
     VERBS_ICONS_MAP,
     VERBS_MAP,
@@ -72,6 +74,7 @@ def verified(institute_id):
     return dict(
         acmg_map={key: ACMG_COMPLETE_MAP[value] for key, value in ACMG_MAP.items()},
         callers=CALLERS,
+        ccv_map={key: CCV_COMPLETE_MAP[value] for key, value in CCV_MAP.items()},
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         verified=verified_vars,
@@ -87,6 +90,7 @@ def causatives(institute_id):
         acmg_map={key: ACMG_COMPLETE_MAP[value] for key, value in ACMG_MAP.items()},
         callers=CALLERS,
         causatives=controllers.causatives(institute_obj, request),
+        ccv_map={key: CCV_COMPLETE_MAP[value] for key, value in CCV_MAP.items()},
         institute=institute_obj,
         inherit_palette=INHERITANCE_PALETTE,
     )

scout/server/blueprints/panels/controllers.py

@@ -160,7 +160,6 @@ def update_panel(store, panel_name, csv_lines, option):
     Returns:
         panel_obj(dict)
     """
-    new_genes = []
     panel_obj = store.gene_panel(panel_name)
     if panel_obj is None:
         return None
@@ -202,11 +201,11 @@ def update_panel(store, panel_name, csv_lines, option):
             )
 
         info_data = {
-            "disease_associated_transcripts": new_gene["transcripts"],
-            "reduced_penetrance": new_gene["reduced_penetrance"],
-            "mosaicism": new_gene["mosaicism"],
-            "inheritance_models": new_gene["inheritance_models"],
-            "database_entry_version": new_gene["database_entry_version"],
+            "disease_associated_transcripts": new_gene.get("transcripts", []),
+            "reduced_penetrance": new_gene.get("reduced_penetrance", ""),
+            "mosaicism": new_gene.get("mosaicism", ""),
+            "inheritance_models": new_gene.get("inheritance_models", []),
+            "database_entry_version": new_gene.get("database_entry_version", ""),
         }
         if (
             option == "replace"

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

@@ -223,15 +223,15 @@
           <span data-bs-toggle="tooltip" data-bs-placement="right" data-bs-html="true" title="
             <div class='text-left'>
               <strong>Transcripts</strong>:
-              {{ gene.info.disease_associated_transcripts|join(',') }} <br>
+              {{ gene.info.disease_associated_transcripts|join(',') if gene.info.disease_associated_transcripts }} <br>
               <strong>Reduced penetrance</strong>:
-              {{ 'yes' if gene.info.reduced_penetrance else 'no' }} <br>
+              {{ gene.info.reduced_penetrance if gene.info.reduced_penetrance }} <br>
               <strong>Mosaicism</strong>:
-              {{ 'yes' if gene.info.mosaicism else 'no' }} <br>
+              {{ gene.info.mosaicism if gene.info.mosaicism }} <br>
               <strong>Inheritance models</strong>:
-              {{ gene.info.inheritance_models|join(',') }} <br>
+              {{ gene.info.inheritance_models|join(',') if gene.info.inheritance_models }} <br>
               <strong>Entry version</strong>:
-              {{ gene.info.database_entry_version }} <br>
+              {{ gene.info.database_entry_version if gene.info.database_entry_version }} <br>
             </div>
           ">
             {{ gene.symbol }}

scout/server/blueprints/variant/controllers.py

@@ -16,6 +16,10 @@ from scout.constants import (
     CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
     CANCER_TIER_OPTIONS,
     CASE_TAGS,
+    CCV_COMPLETE_MAP,
+    CCV_CRITERIA,
+    CCV_MAP,
+    CCV_OPTIONS,
     DISMISS_VARIANT_OPTIONS,
     IGV_TRACKS,
     INHERITANCE_PALETTE,
@@ -41,6 +45,7 @@ from scout.server.utils import (
 from .utils import (
     add_gene_info,
     associate_variant_genes_with_case_panels,
+    ccv_evaluation,
     clinsig_human,
     default_panels,
     end_position,
@@ -194,9 +199,11 @@ def variant(
             'cancer_tier_options': CANCER_TIER_OPTIONS,
             'dismiss_variant_options': DISMISS_VARIANT_OPTIONS,
             'ACMG_OPTIONS': ACMG_OPTIONS,
+            'CCV_OPTIONS': CCV_OPTIONS,
             'igv_tracks': IGV_TRACKS,
             'gens_info': <dict>,
             'evaluations': <list(evaluations)>,
+            'ccv_evaluations': <list(evaluations)>,
             'rank_score_results': <list(rank_score_results)>,
         }
 
@@ -340,6 +347,17 @@ def variant(
         evaluation(store, evaluation_obj)
         evaluations.append(evaluation_obj)
 
+    # Prepare classification information for visualisation
+    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]
+
+    ccv_evaluations = []
+    for evaluation_obj in store.get_ccv_evaluations(variant_obj):
+        ccv_evaluation(store, evaluation_obj)
+        ccv_evaluations.append(evaluation_obj)
+
     case_clinvars = store.case_to_clinVars(case_obj.get("display_name"))
 
     if variant_id in case_clinvars:
@@ -379,12 +397,14 @@ def variant(
         "dismiss_variant_options": dismiss_options,
         "mosaic_variant_options": MOSAICISM_OPTIONS,
         "ACMG_OPTIONS": ACMG_OPTIONS,
+        "CCV_OPTIONS": CCV_OPTIONS,
         "case_tag_options": CASE_TAGS,
         "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),
         "gens_info": gens.connection_settings(genome_build),
         "evaluations": evaluations,
+        "ccv_evaluations": ccv_evaluations,
         "rank_score_results": variant_rank_scores(store, case_obj, variant_obj),
     }
 
@@ -442,7 +462,7 @@ def get_loqusdb_obs_cases(
     obs_cases = []
     user_institutes_ids = set([inst["_id"] for inst in user_institutes(store, current_user)])
     for i, case_id in enumerate(obs_families):
-        if len(obs_cases) == 10:
+        if len(obs_cases) == 50:
             break
         if case_id == variant_obj["case_id"]:
             continue
@@ -708,3 +728,130 @@ def variant_acmg_post(
         criteria=criteria,
     )
     return classification
+
+
+def variant_ccv(store: MongoAdapter, institute_id: str, case_name: str, variant_id: str):
+    """Collect data relevant for rendering ClinGen-CCV-VIGG classification form.
+
+    Args:
+        store(scout.adapter.MongoAdapter)
+        institute_id(str): institute_obj['_id']
+        case_name(str): case_obj['display_name']
+        variant_id(str): variant_obj['document_id']
+
+    Returns:
+        data(dict): Things for the template
+    """
+    variant_obj = store.variant(variant_id)
+
+    if not variant_obj:
+        return abort(404)
+
+    institute_obj, case_obj = variant_institute_and_case(
+        store, variant_obj, institute_id, case_name
+    )
+
+    return dict(
+        institute=institute_obj,
+        case=case_obj,
+        variant=variant_obj,
+        CRITERIA=CCV_CRITERIA,
+        CCV_OPTIONS=CCV_OPTIONS,
+    )
+
+
+def check_reset_variant_ccv_classification(
+    store: MongoAdapter, evaluation_obj: dict, link: str
+) -> bool:
+    """Check if this was the last ClinGen-CGC-VIGG evaluation left on the variant.
+    If there is still a classification we want to remove the classification.
+
+    Args:
+            stores(cout.adapter.MongoAdapter)
+            evaluation_obj(dict): ClinGen-CGC-VIGG evaluation object
+            link(str): link for event
+
+    Returns: reset(bool) - True if classification reset was attempted
+
+    """
+
+    if list(store.get_ccv_evaluations_case_specific(evaluation_obj["variant_specific"])):
+        return False
+
+    variant_obj = store.variant(document_id=evaluation_obj["variant_specific"])
+
+    if not variant_obj:
+        return abort(404)
+
+    ccv_classification = variant_obj.get("ccv_classification")
+
+    if not isinstance(ccv_classification, int):
+        return False
+
+    institute_obj, case_obj = variant_institute_and_case(
+        store,
+        variant_obj,
+        evaluation_obj["institute"]["_id"],
+        evaluation_obj["case"]["display_name"],
+    )
+    user_obj = store.user(current_user.email)
+
+    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,
+    )
+    return True
+
+
+def variant_ccv_post(
+    store: MongoAdapter,
+    institute_id: str,
+    case_name: str,
+    variant_id: str,
+    user_email: str,
+    criteria: list,
+) -> dict:
+    """Calculate an ClinGen-CGC-VICC classification based on a list of criteria.
+
+    Args:
+        store(scout.adapter.MongoAdapter)
+        institute_id(str): institute_obj['_id']
+        case_name(str): case_obj['display_name']
+        variant_id(str): variant_obj['document_id']
+        user_mail(str)
+        criteria()
+
+    Returns:
+        data(dict): Things for the template
+
+    """
+    variant_obj = store.variant(variant_id)
+
+    if not variant_obj:
+        return abort(404)
+
+    institute_obj, case_obj = variant_institute_and_case(
+        store, variant_obj, institute_id, case_name
+    )
+
+    user_obj = store.user(user_email)
+    variant_link = url_for(
+        "variant.variant",
+        institute_id=institute_id,
+        case_name=case_name,
+        variant_id=variant_id,
+    )
+    classification = store.submit_ccv_evaluation(
+        institute_obj=institute_obj,
+        case_obj=case_obj,
+        variant_obj=variant_obj,
+        user_obj=user_obj,
+        link=variant_link,
+        criteria=criteria,
+    )
+    return classification

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 %}