scout-browser 4.93.1__py3-none-any.whl → 4.95.0__py3-none-any.whl

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

@@ -668,6 +668,7 @@
               <th>Inheritance models</th>
             {% endif %}
             <th>ACMG classification</th>
+            <th>Bayesian classification</th>
             {% if cancer %}
             <th>ClinGen-CGC-VICC classification</th>
             {% endif %}
@@ -714,18 +715,32 @@
             {% 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['code']}}">{{variant.ccv_classification['code'] }}</span>
+                <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>

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/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") }}

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/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" data-bs-toggle="tooltip" title="Richards et al 2015"><a href="https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf"  rel="noopener noreferrer" target="_blank" style="color: inherit;  text-decoration: inherit;">ACMG classification</a></label>
   <form action="{{ url_for('variant.variant_update', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
     <div class="d-flex justify-content-between">
       {% for option in ACMG_OPTIONS %}
@@ -168,7 +171,7 @@
           <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 %} 
+          {% 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 %}
@@ -191,6 +194,25 @@
   </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, 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>
@@ -203,6 +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>

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">

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

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

scout/server/blueprints/variant/views.py

@@ -374,7 +374,6 @@ def variant_update(institute_id, case_name, variant_id):
 @templated("variant/acmg.html")
 def evaluation(evaluation_id):
     """Show, edit or delete an ACMG evaluation."""
-
     evaluation_obj = store.get_evaluation(evaluation_id)
     if evaluation_obj is None:
         flash("Evaluation was not found in database", "warning")
@@ -392,7 +391,7 @@ def evaluation(evaluation_id):
         if check_reset_variant_classification(store, evaluation_obj, link):
             flash("Cleared ACMG classification.", "info")
 
-        return redirect(link)
+        return redirect(request.referrer)
 
     return dict(
         evaluation=evaluation_obj,