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

scout/server/blueprints/cases/controllers.py

@@ -62,6 +62,8 @@ from scout.server.utils import (
     case_has_rna_tracks,
     institute_and_case,
 )
+from scout.utils.acmg import get_acmg_temperature
+from scout.utils.ccv import get_ccv_temperature
 
 LOG = logging.getLogger(__name__)
 
@@ -611,6 +613,46 @@ def check_outdated_gene_panel(panel_obj, latest_panel):
     return extra_genes, missing_genes
 
 
+def add_bayesian_acmg_classification(variant_obj: dict):
+    """Append info to display the ACMG VUS Bayesian score / temperature.
+    Criteria have a term and a modifier field on the db document
+    that are joined together in a string to conform to a regular
+    ACMG term format. A set of such terms are passed on for evaluation
+    to the same function as the ACMG classification form uses.
+    """
+    variant_acmg_classifications = list(
+        store.get_evaluations_case_specific(document_id=variant_obj["_id"])
+    )
+    if variant_acmg_classifications:
+        terms = set()
+        for criterium in variant_acmg_classifications[0].get("criteria", []):
+            term = criterium.get("term")
+            if criterium.get("modifier"):
+                term += f"_{criterium.get('modifier')}"
+            terms.add(term)
+        variant_obj["bayesian_acmg"] = get_acmg_temperature(terms)
+
+
+def add_bayesian_ccv_classification(variant_obj: dict):
+    """Append info to display the CCV VUS Bayesian score / temperature.
+    Criteria have a term and a modifier field on the db document
+    that are joined together in a string to conform to a regular
+    CCV term format. A set of such terms are passed on for evaluation
+    to the same function as the CCV classification form uses.
+    """
+    variant_ccv_classifications = list(
+        store.get_ccv_evaluations_case_specific(document_id=variant_obj["_id"])
+    )
+    if variant_ccv_classifications:
+        terms = set()
+        for criterium in variant_ccv_classifications[0].get("ccv_criteria", []):
+            term = criterium.get("term")
+            if criterium.get("modifier"):
+                term += f"_{criterium.get('modifier')}"
+            terms.add(term)
+        variant_obj["bayesian_ccv"] = get_ccv_temperature(terms)
+
+
 def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dict, data: dict):
     """Gather evaluated variants info to include in case report."""
 
@@ -624,6 +666,8 @@ def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dic
                 continue
             if case_key == "partial_causatives":
                 var_obj["phenotypes"] = case_obj["partial_causatives"][var_id]
+            add_bayesian_acmg_classification(var_obj)
+            add_bayesian_ccv_classification(var_obj)
             evaluated_variants_by_type[eval_category].append(
                 _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
             )
@@ -663,6 +707,10 @@ def _append_evaluated_variant_by_type(
     """
     for eval_category, variant_key in CASE_REPORT_VARIANT_TYPES.items():
         if variant_key in var_obj and var_obj[variant_key] is not None:
+
+            add_bayesian_acmg_classification(var_obj)
+            add_bayesian_ccv_classification(var_obj)
+
             evaluated_variants_by_type[eval_category].append(
                 _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
             )

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 +668,10 @@
               <th>Inheritance models</th>
             {% endif %}
             <th>ACMG classification</th>
+            <th>Bayesian classification</th>
+            {% if cancer %}
+            <th>ClinGen-CGC-VICC classification</th>
+            {% endif %}
           </tr>
         </thead>
         <tbody>
@@ -678,11 +715,34 @@
             {% endif %}
             <td>
               {% if variant.acmg_classification %}
-                <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['code'] }}</span>
+                <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['label']}}">{{variant.acmg_classification['label'] }}</span>
               {% else %}
                 -
               {% endif %}
+            <td>
+              {% if variant.bayesian_acmg %}
+                <span class="badge rounded-pill bg-{{variant.bayesian_acmg.temperature_class}}">Score {{variant.bayesian_acmg.points|string}} <span class='fa {{variant.bayesian_acmg.temperature_icon}}'></span> {{variant.bayesian_acmg.temperature}} ({{variant.bayesian_acmg.point_classification}})</span>
+              {% else %}
+                -
+              {% endif %}
+            </td>
             </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['label']}}">{{variant.ccv_classification['label'] }}</span>
+              {% else %}
+                -
+              {% endif %}
+              {% if variant.bayesian_ccv %}
+                 <span class="badge rounded-pill bg-{{variant.bayesian_ccv.temperature_class}}">Score {{variant.bayesian_ccv.points|string}} <span class='fa {{variant.bayesian_ccv.temperature_icon}}'></span>
+                 {% if variant.bayesian_ccv.point_classification == "VUS" %}
+                 {{variant.bayesian_ccv.temperature}}
+                {% endif %}
+                </span>
+              {% 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/cases/views.py

@@ -7,6 +7,7 @@ import shutil
 from ast import literal_eval
 from io import BytesIO
 from operator import itemgetter
+from tempfile import NamedTemporaryFile, mkdtemp
 from typing import Generator, Optional, Union
 
 from cairosvg import svg2png
@@ -286,7 +287,9 @@ def pdf_case_report(institute_id, case_name):
     # Workaround to be able to print the case pedigree to pdf
     if case_obj.get("madeline_info") and case_obj.get("madeline_info") != "":
         try:
-            write_to = os.path.join(cases_bp.static_folder, "madeline.png")
+            write_to = NamedTemporaryFile(
+                mode="a+", prefix=case_obj.get("_id"), suffix="madeline.png"
+            )
             svg2png(
                 bytestring=case_obj["madeline_info"],
                 write_to=write_to,
@@ -322,11 +325,8 @@ def mt_report(institute_id, case_name):
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
 
     # create a temp folder to write excel files into
-    temp_excel_dir = os.path.join(
-        cases_bp.static_folder, "_".join([case_obj["display_name"], "mt_reports"])
-    )
-    os.makedirs(temp_excel_dir, exist_ok=True)
 
+    temp_excel_dir = mkdtemp(suffix="_".join([case_obj["display_name"], "mt_reports"]))
     if controllers.mt_excel_files(store, case_obj, temp_excel_dir):
         data = zip_dir_to_obj(temp_excel_dir)
 

scout/server/blueprints/clinvar/controllers.py

@@ -399,11 +399,10 @@ def json_api_submission(submission_id):
         afile.flush()
         afile.seek(0)
 
-    with NamedTemporaryFile(
-        mode="a+", prefix="Variant", suffix=".csv"
-    ) as variant_file, NamedTemporaryFile(
-        mode="a+", prefix="CaseData", suffix=".csv"
-    ) as casedata_file:
+    with (
+        NamedTemporaryFile(mode="a+", prefix="Variant", suffix=".csv") as variant_file,
+        NamedTemporaryFile(mode="a+", prefix="CaseData", suffix=".csv") as casedata_file,
+    ):
         # Write temp Variant CSV file
         _, variants_header, variants_lines = clinvar_submission_file(
             submission_id, "variant_data", "SUB000"

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>