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

scout/server/blueprints/institutes/controllers.py

@@ -3,7 +3,7 @@ import datetime
 import logging
 from typing import Dict, List, Optional, Tuple
 
-from flask import Response, current_app, flash, url_for
+from flask import Response, current_app, flash, request, url_for
 from flask_login import current_user
 from pymongo import ASCENDING, DESCENDING
 from pymongo.cursor import Cursor
@@ -11,10 +11,13 @@ from werkzeug.datastructures import Headers, MultiDict
 
 from scout.adapter.mongo.base import MongoAdapter
 from scout.constants import (
+    CANCER_PHENOTYPE_MAP,
     CASE_STATUSES,
     DATE_DAY_FORMATTER,
     ID_PROJECTION,
     PHENOTYPE_GROUPS,
+    PHENOTYPE_MAP,
+    SEX_MAP,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
 from scout.server.blueprints.variant.utils import predictions, update_representative_gene
@@ -422,97 +425,129 @@ def _sort_cases(data, request, all_cases):
     return all_cases
 
 
-def cases(store, request, institute_id):
-    """Preprocess case objects.
+def export_case_samples(institute_id, filtered_cases) -> Response:
+    """Export to CSV file a list of samples from selected cases."""
+    EXPORT_HEADER = [
+        "Sample ID",
+        "Sample Name",
+        "Analysis",
+        "Affected status",
+        "Sex",
+        "Sex confirmed",
+        "Parenthood confirmed",
+        "Predicted ancestry",
+        "Tissue",
+        "Case Name",
+        "Case ID",
+        "Analysis date",
+        "Case Status",
+        "Case phenotypes",
+        "Research",
+        "Track",
+        "Default panels",
+        "Genome build",
+        "SNV/SV rank models",
+    ]
+    export_lines = []
+    export_lines.append("\t".join(EXPORT_HEADER))  # Use tab-separated values
+    for case in filtered_cases:
+        for individual in case.get("individuals", []):
+            export_line = [
+                individual["individual_id"],
+                individual["display_name"],
+                individual.get("analysis_type").upper(),
+                (
+                    CANCER_PHENOTYPE_MAP[individual.get("phenotype", 0)]
+                    if case.get("track") == "cancer"
+                    else PHENOTYPE_MAP[individual.get("phenotype", 0)]
+                ),
+                SEX_MAP[individual.get("sex", 0)],
+                individual.get("confirmed_sex") or "-",
+                individual.get("confirmed_parent") or "-",
+                individual.get("predicted_ancestry") or "-",
+                individual.get("tissue_type") or "-",
+                case["display_name"],
+                case["_id"],
+                case["analysis_date"].strftime("%Y-%m-%d %H:%M:%S"),
+                case["status"],
+                ", ".join(hpo["phenotype_id"] for hpo in case.get("phenotype_terms", [])),
+                case.get("is_research"),
+                case.get("track"),
+                ", ".join(
+                    panel["panel_name"] for panel in case.get("panels") if panel.get("is_default")
+                ),
+                case.get("genome_build"),
+                f"{case.get('rank_model_version', '-')}/{case.get('sv_rank_model_version', '-')}",
+            ]
+            export_lines.append("\t".join(str(item) for item in export_line))
 
-    Add all the necessary information to display the 'cases' view
+    file_content = "\n".join(export_lines)
 
-    Args:
-        store(adapter.MongoAdapter)
-        request(flask.request) request sent by browser to the api_institutes endpoint
-        institute_id(str): An _id of an institute
+    return Response(
+        file_content,
+        mimetype="text/plain",
+        headers={
+            "Content-Disposition": f"attachment;filename={institute_id}_cases_{datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')}.txt"
+        },
+    )
 
-    Returns:
-        data(dict): includes the cases, how many there are and the limit.
-    """
+
+def cases(store: MongoAdapter, request: request, institute_id: str) -> dict:
+    """Preprocess case objects for the 'cases' view."""
     data = {}
+
+    # Initialize data (institute info, filters, and case counts)
     institute_obj = institute_and_case(store, institute_id)
     data["institute"] = institute_obj
-
-    name_query = request.form
-    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
-
     data["form"] = CaseFilterForm(request.form)
+    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
+    data["nr_cases"] = sum(data["status_ncases"].values())
+
+    # Fetch Sanger unevaluated and validated cases
+    sanger_ordered_not_validated = get_sanger_unevaluated(store, institute_id, current_user.email)
+    data["sanger_unevaluated"], data["sanger_validated_by_others"] = sanger_ordered_not_validated
 
+    # Projection for fetching cases
     ALL_CASES_PROJECTION = {
         "analysis_date": 1,
         "assignees": 1,
         "beacon": 1,
         "case_id": 1,
         "display_name": 1,
+        "genome_build": 1,
         "individuals": 1,
         "is_rerun": 1,
         "is_research": 1,
         "mme_submission": 1,
         "owner": 1,
         "panels": 1,
+        "phenotype_terms": 1,
+        "rank_model_version": 1,
         "status": 1,
+        "sv_rank_model_version": 1,
         "track": 1,
         "vcf_files": 1,
     }
 
-    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
-    data["nr_cases"] = sum(data["status_ncases"].values())
-
-    sanger_ordered_not_validated: Tuple[Dict[str, list]] = get_sanger_unevaluated(
-        store, institute_id, current_user.email
-    )
-    data["sanger_unevaluated"]: Dict[str, list] = sanger_ordered_not_validated[0]
-    data["sanger_validated_by_others"]: Dict[str, list] = sanger_ordered_not_validated[1]
-
-    # local function to add info to case obj
-    def populate_case_obj(case_obj):
-        analysis_types = set(ind["analysis_type"] for ind in case_obj["individuals"])
-        if len(analysis_types) > 1:
-            LOG.debug("Set analysis types to {'mixed'}")
-            analysis_types = set(["mixed"])
-
-        case_obj["analysis_types"] = list(analysis_types)
-        case_obj["assignees"] = [
-            store.user(user_email) for user_email in case_obj.get("assignees", [])
-        ]
-        # Check if case was re-runned
-        last_analysis_date = case_obj.get("analysis_date", datetime.datetime.now())
-        all_analyses_dates = set()
-        for analysis in case_obj.get("analyses", [{"date": last_analysis_date}]):
-            all_analyses_dates.add(analysis.get("date", last_analysis_date))
-
-        case_obj["is_rerun"] = len(all_analyses_dates) > 1 or last_analysis_date > max(
-            all_analyses_dates
-        )
-
-        case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
-        case_obj["display_track"] = TRACKS[case_obj.get("track", "rare")]
-        return case_obj
-
+    # Group cases by status
     case_groups = {status: [] for status in CASE_STATUSES}
+    nr_cases_showall_statuses = 0
+    status_show_all_cases = institute_obj.get("show_all_cases_status") or ["prioritized"]
 
-    nr_cases_showall_statuses = (
-        0  # Nr of cases for the case statuses where all cases should be shown
-    )
-    # In institute settings, retrieve all case status categories for which all cases should be displayed
-    status_show_all_cases: List[str] = institute_obj.get("show_all_cases_status") or ["prioritized"]
+    # Process cases for statuses that require all cases to be shown
     for status in status_show_all_cases:
         cases_in_status = store.cases_by_status(
             institute_id=institute_id, status=status, projection=ALL_CASES_PROJECTION
         )
         cases_in_status = _sort_cases(data, request, cases_in_status)
         for case_obj in cases_in_status:
-            populate_case_obj(case_obj)
-            nr_cases_showall_statuses += 1
+            populate_case_obj(case_obj, store)
             case_groups[status].append(case_obj)
+            nr_cases_showall_statuses += 1
 
-    # Retrieve cases for the remaining status categories
+    # Fetch additional cases based on filters
+    name_query = request.form
+    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
     all_cases = store.cases(
         collaborator=institute_id,
         name_query=name_query,
@@ -525,17 +560,20 @@ def cases(store, request, institute_id):
     )
     all_cases = _sort_cases(data, request, all_cases)
 
+    if request.form.get("export"):
+        return export_case_samples(institute_id, all_cases)
+
+    # Process additional cases for the remaining statuses
     nr_cases = 0
     for case_obj in all_cases:
-        case_status = case_obj["status"]
-        if case_status in status_show_all_cases:
-            continue
-        if nr_cases == limit:
-            break
-        populate_case_obj(case_obj)
-        case_groups[case_status].append(case_obj)
-        nr_cases += 1
-
+        if case_obj["status"] not in status_show_all_cases:
+            if nr_cases == limit:
+                break
+            populate_case_obj(case_obj, store)
+            case_groups[case_obj["status"]].append(case_obj)
+            nr_cases += 1
+
+    # Compile the final data
     data["cases"] = [(status, case_groups[status]) for status in CASE_STATUSES]
     data["found_cases"] = nr_cases + nr_cases_showall_statuses
     data["limit"] = limit
@@ -543,8 +581,32 @@ def cases(store, request, institute_id):
     return data
 
 
+def populate_case_obj(case_obj: dict, store: MongoAdapter):
+    """Helper function to populate additional case information."""
+    analysis_types = set(ind["analysis_type"] for ind in case_obj["individuals"])
+    if len(analysis_types) > 1:
+        analysis_types = set(["mixed"])
+    case_obj["analysis_types"] = list(analysis_types)
+
+    case_obj["assignees"] = [store.user(user_email) for user_email in case_obj.get("assignees", [])]
+
+    last_analysis_date = case_obj.get("analysis_date", datetime.datetime.now())
+    all_analyses_dates = {
+        analysis.get("date", last_analysis_date)
+        for analysis in case_obj.get("analyses", [{"date": last_analysis_date}])
+    }
+    case_obj["is_rerun"] = len(all_analyses_dates) > 1 or last_analysis_date > max(
+        all_analyses_dates
+    )
+
+    case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
+    case_obj["display_track"] = TRACKS.get(case_obj.get("track", "rare"))
+
+
 def _get_unevaluated_variants_for_case(
-    case_obj: dict, var_ids_list: List[str], sanger_validated_by_user_by_case: Dict[str, List[str]]
+    case_obj: dict,
+    var_ids_list: List[str],
+    sanger_validated_by_user_by_case: Dict[str, List[str]],
 ) -> Tuple[Dict[str, list]]:
     """Returns the variants with Sanger ordered by a user that need validation or are validated by another user."""
 

scout/server/blueprints/institutes/forms.py

@@ -73,7 +73,8 @@ class InstituteForm(FlaskForm):
     pheno_abbrev = StringField("Abbreviation", validators=[validators.Optional()])
 
     gene_panels = NonValidatingSelectMultipleField(
-        "Gene panels available for variants filtering", validators=[validators.Optional()]
+        "Gene panels available for variants filtering",
+        validators=[validators.Optional()],
     )
 
     gene_panels_matching = NonValidatingSelectMultipleField(
@@ -144,7 +145,8 @@ class GeneVariantFiltersForm(FlaskForm):
     variant_type = SelectMultipleField(choices=[("clinical", "clinical"), ("research", "research")])
     category = SelectMultipleField(choices=CATEGORY_CHOICES)
     hgnc_symbols = TagListField(
-        "HGNC Symbols (comma-separated, case sensitive)", validators=[validators.InputRequired()]
+        "HGNC Symbols (comma-separated, case sensitive)",
+        validators=[validators.InputRequired()],
     )
     rank_score = IntegerField(default=15)
     phenotype_terms = TagListField("HPO terms (comma-separated)")
@@ -181,3 +183,4 @@ class CaseFilterForm(FlaskForm):
     has_rna = BooleanField("Has RNA-seq data")
     validation_ordered = BooleanField("Validation pending")
     search = SubmitField(label="Search")
+    export = SubmitField(label="Filter and export")

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

@@ -249,6 +249,12 @@
     advSearchBlock.hide();
   }
 
+  function StopSpinner() {
+    // Avoid page spinner being stuck on file download
+    $(window).unbind('beforeunload');
+    return true;
+  }
+
   advBlockCheckbox.on('click', function() {
     if($(this).is(':checked')) {
       advSearchBlock.show();

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

@@ -9,7 +9,7 @@
   {% endif %}
 {% endfor %}
 
-<form action="{{ form_action }}" method="POST" accept-charset="utf-8">
+<form action="{{ form_action }}" method="POST" accept-charset="utf-8" onsubmit="return StopSpinner()">
     {{ form.hidden_tag() }}
 
     <div class="row">
@@ -19,7 +19,7 @@
             {{ form.search_institute(class="form-control") }}
         </div>
       {% endif %}
-        <div class="col-md-3 mb-3">
+        <div class="col-md-2 mb-3">
             {{ form.case.label(class="form-label") }}
             {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
         </div>
@@ -27,9 +27,10 @@
             {{ form.search_limit.label(class="form-label") }}
             {{ form.search_limit(class="form-control") }}
         </div>
-        <div class="btn-sm mb-2 col-md-2 mx-auto">
-          {{ form.search(class="btn btn-lg btn-primary mt-4") }}
-          <a href="{{ reset_action }}" class="btn btn-lg btn-secondary mt-4 text-white">Reset search</a>
+        <div class="btn-sm mb-2 col-md-3 mx-auto">
+          {{ form.search(class="btn btn-primary mt-4") }}
+          {{ form.export(class="btn btn-primary mt-4") }}
+          <a href="{{ reset_action }}" class="btn btn-secondary mt-4 text-white">Reset search</a>
         </div>
         <div class="col-md-2 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
           {{ form.advanced_search(class="form-check-input") }}
@@ -446,7 +447,7 @@
 {% 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 +470,7 @@
           <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 +610,16 @@
                 {% 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