scout-browser 4.92__py3-none-any.whl → 4.95.0__py3-none-any.whl

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/managed_variants/forms.py

@@ -10,6 +10,7 @@ from wtforms import (
     SubmitField,
     validators,
 )
+from wtforms.widgets import NumberInput
 
 from scout.constants import CHROMOSOMES, SV_TYPES
 
@@ -24,8 +25,22 @@ CATEGORY_CHOICES = [
 
 
 class ManagedVariantForm(FlaskForm):
-    position = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    position = IntegerField(
+        "Start position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="Start position must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+    end = IntegerField(
+        "End position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="End position must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
     cytoband_start = SelectField("Cytoband start", choices=[])
     cytoband_end = SelectField("Cytoband end", choices=[])
     description = StringField(label="Description")

scout/server/blueprints/managed_variants/templates/managed_variants/managed_variants.html

@@ -212,8 +212,8 @@
     <tbody>
       <tr>
       <td>{{ add_form.chromosome(class_="form-control") }}</td>
-      <td><input type="number" name="position" id="position" class="form-control" required></td>
-      <td><input type="number" name="end" id="end" class="form-control"></td>
+      <td><input type="number" name="position" id="position" class="form-control" required min="1"></td>
+      <td><input type="number" name="end" id="end" class="form-control" min="1"></td>
       <td><input type="text" name="reference" id="reference" class="form-control" required></td>
       <td><input type="text" name="alternative" id="alternative" class="form-control" required></td>
       <td>{{ add_form.category(class_="form-control", onchange="populateSubTypeSelect('add_variant')") }}</td>

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 %}

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

@@ -38,9 +38,13 @@
   <li class="list-group-item {{ 'list-group-item-info' if current_variant }}">
     <div class="d-flex">
       <span>
-        <a href="{{ url_for('variant.evaluation', evaluation_id=data._id) }}">
+        {% if variant.category in ["snv", "cancer_snv"] %}
+          <a href="{{ url_for('variant.evaluation', evaluation_id=data._id) }}">
+            {{ data.classification.label }}
+          </a>
+        {% else %}
           {{ data.classification.label }}
-        </a>
+        {% endif %}
         <span class="badge bg-info">{{ data.classification.short }}</span>
       </span>
       <span>
@@ -133,7 +137,6 @@
 {% endmacro %}
 
 {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
-  <label class="mt-3">ACMG classification</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 +148,75 @@
   </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 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_sv(variant, institute, case, ACMG_OPTIONS, evaluations) %}
+  <div class="mt-3">
+    ACMG (INDEL) <a href="https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf"  rel="noopener noreferrer" target="_blank" style="text-decoration: inherit;" data-bs-toggle="tooltip" title="Richards et al 2015">classification</a>
+  </div>
+  <div>
+    {{ acmg_form(institute, case, variant, ACMG_OPTIONS, variant.acmg_classification.code if variant.acmg_classification) }}
+  </div>
+  <div class="mt-3">
+    ACMG SV classification <a href="https://pubmed.ncbi.nlm.nih.gov/31690835/" target="_blank" rel="noopener noreferrer" referrerpolicy="no-referrer">guidelines</a> & <a href="https://cnvcalc.clinicalgenome.org/cnvcalc/" target="_blank" rel="noopener noreferrer" referrerpolicy="no-referrer">guide</a>.
+  </div>
+  {% if evaluations %} <!-- scrollable previous ACMG evaluations div-->
+    <div class="list-group mt-3" style="max-height:200px;overflow-y: scroll;">
+      {% for evaluation in evaluations %}
+        {{ acmg_classification_item(variant, evaluation) }}
+      {% endfor %}
+    </div>
+  {% endif %}
+{% endmacro %}
 
-{% macro panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) %}
+{% 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) }}
@@ -158,6 +225,7 @@
       {% if case.track != "cancer" %}
         {{ mosaic_variant_button(variant, institute, case, mosaic_variant_options) }}
       {% endif %}
+      ACMG <a href="https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf"  rel="noopener noreferrer" target="_blank" style="text-decoration: inherit;" data-bs-toggle="tooltip" title="Richards et al 2015">classification</a>
       {{ acmg_form(institute, case, variant, ACMG_OPTIONS, variant.acmg_classification.code if variant.acmg_classification) }}
       <div class="mt-3">
         <a href="{{ url_for('variant.variant_acmg', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" class="btn btn-outline-secondary form-control">Classify</a>
@@ -169,6 +237,19 @@
           {% 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/sv-variant.html

@@ -1,7 +1,7 @@
 {% extends "layout.html" %}
 {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %}
 {% from "variant/variant_details.html" import old_observations %}
-{% from "variant/components.html" import external_scripts, external_stylesheets, matching_variants, variant_scripts %}
+{% from "variant/components.html" import external_scripts, external_stylesheets, matching_variants, panel_classify_sv, variant_scripts %}
 {% from "variant/utils.html" import causative_button, genes_panel, igv_track_selection, modal_causative, overlapping_panel, sv_alignments, pin_button, transcripts_panel, custom_annotations, gene_panels %}
 {% from "variant/rank_score_results.html" import rankscore_panel %}
 {% from "variant/gene_disease_relations.html" import orpha_omim_phenotypes %}
@@ -196,7 +196,7 @@
             {{ variant_tag_button(variant, institute, case, manual_rank_options) }}
           </div>
           <div>
-            ACMG classification <a href="https://pubmed.ncbi.nlm.nih.gov/31690835/" target="_blank" rel="noopener noreferrer" referrerpolicy="no-referrer">guidelines</a> & <a href="https://cnvcalc.clinicalgenome.org/cnvcalc/" target="_blank" rel="noopener noreferrer" referrerpolicy="no-referrer">guide</a>.
+            {{ panel_classify_sv(variant, institute, case, ACMG_OPTIONS, evaluations) }}
           </div>
         </div>
         <div class="list-group mt-3">