scout-browser 4.94.1__py3-none-any.whl → 4.96.0__py3-none-any.whl

scout/server/blueprints/cases/controllers.py

@@ -13,6 +13,7 @@ from flask_login import current_user
 from requests.auth import HTTPBasicAuth
 from xlsxwriter import Workbook
 
+from scout import __version__
 from scout.adapter import MongoAdapter
 from scout.constants import (
     CANCER_PHENOTYPE_MAP,
@@ -63,6 +64,7 @@ from scout.server.utils import (
     institute_and_case,
 )
 from scout.utils.acmg import get_acmg_temperature
+from scout.utils.ccv import get_ccv_temperature
 
 LOG = logging.getLogger(__name__)
 
@@ -613,19 +615,43 @@ def check_outdated_gene_panel(panel_obj, latest_panel):
 
 
 def add_bayesian_acmg_classification(variant_obj: dict):
-    """Append info to display the ACMG VUS Bayesian score / temperature."""
+    """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:
-        variant_obj["bayesian_acmg"] = get_acmg_temperature(
-            set(
-                [
-                    criterium.get("term")
-                    for criterium in variant_acmg_classifications[0].get("criteria", [])
-                ]
-            )
-        )
+        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):
@@ -642,6 +668,7 @@ def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dic
             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)
             )
@@ -683,6 +710,7 @@ def _append_evaluated_variant_by_type(
         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)
@@ -730,6 +758,7 @@ def case_report_content(store: MongoAdapter, institute_obj: dict, case_obj: dict
     data["manual_rank_options"] = MANUAL_RANK_OPTIONS
     data["genetic_models"] = dict(GENETIC_MODELS)
     data["report_created_at"] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M")
+    data["current_scout_version"] = __version__
 
     case_report_variants(store, case_obj, institute_obj, data)
 

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

@@ -63,7 +63,7 @@
 </nav>
 
 <div id="container" class="container">
-  <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong><br><br>
+  <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong> using <strong>Scout v.{{current_scout_version}}</strong><br><br>
    {{ phenotype_panel() }}
    {{ gene_panels_panel()}}
    {{ causatives_panel()}}
@@ -101,8 +101,11 @@
           <td>
 	          <table class="table table-sm">
 	            <tr>
-	              <td>Case created: <strong>{{case.created_at.strftime('%Y-%m-%d')}}</strong></td>
+                <td>Case created: <strong>{{case.created_at.strftime('%Y-%m-%d')}}</strong></td>
 	              <td>Last updated: <strong>{{case.updated_at.strftime('%Y-%m-%d') if case.updated_at else "n.a." }}</strong></td>
+                {% if case.scout_load_version %}
+                  <td> Loaded with <strong>Scout v.{{case.scout_load_version}}</strong></td>
+                {% endif %}
 	            </tr>
 	          </table>
 	          <br>
@@ -715,7 +718,7 @@
             {% 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 %}
@@ -730,21 +733,50 @@
             {% 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>
         </tbody>
       </table>
+      <table id="severity-table" class="table table-sm" style="background-color: transparent">
+        <thead>
+          <tr>
+            <th>SIFT</th>
+            <th>REVEL score</th>
+            <th>REVEL rank score</th>
+            <th>Polyphen</th>
+            <th>SPIDEX</th>
+            <th>SpliceAI DS max</th>
+        </thead>
+        <tbody>
+          <tr>
+            <td>{{ variant.sift_predictions|join(', ') or '-'}}</td>
+            <td>{{ variant.revel or '-' }}</td>
+            <td>{{ variant.revel_score or '-' }}</td>
+            <td>{{ variant.polyphen_predictions|join(', ') or '-' }}</td>
+            <td>{{ variant.spidex|spidex_human if variant.spidex else none|spidex_human }}</td>
+            <td>{{ variant.spliceai_scores|join(', ') or '-' }}</td>
+          </tr>
+        </tbody>
+      </table>
       <table id="panel-table" class="table table-sm" style="background-color: transparent">
         <thead>
           <tr>
             <th>Affected gene(s)</th>
             <th>Description</th>
             <th>Region annotation</th>
+            <th>Consequence</th>
             <th>Transcript - HGVS - Protein</th>
             <th>Diagnoses [inheritance]</th>
           </tr>
@@ -760,6 +792,7 @@
                 </td>
                 <td>{{gene.description|title}}</td>
                 <td>{{gene.region_annotation}}</td>
+                <td>{{gene.functional_annotation.replace("_"," ")|truncate(20, True)}}</td>
                 <td>
                   {{ variant_transcripts(gene) }}
                 </td>

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

@@ -15,6 +15,7 @@
           {{ reports(institute,case, report_types) }}
           {{ default_gene_panel(institute, case) }}
           {{ analysis_date(case) }}
+          {{ software_version(case) }}
           {{ genome_build(case, case_groups, has_rna_tracks) }}
           {{ rank_model(case) }}
           <li class="list-group-item bg-dark sidebar-separator menu-collapsed"></li>
@@ -190,6 +191,17 @@
 {% endif %}
 {% endmacro %}
 
+{% macro software_version(case) %}
+{% if case.scout_load_version%}
+  <div href="#" class="bg-dark list-group-item text-white" data-bs-toggle="tooltip" title="Scout version used for loading the case" data-bs-placement="right">
+    <div class="d-flex w-100 justify-content-start align-items-center">
+      <span class="fa fa-gear fa-fw me-3"></span>
+      <span class="menu-collapsed">v.{{ case.scout_load_version }}</span>
+    </div>
+  </div>
+{% endif %}
+{% endmacro %}
+
 {% macro genome_build(case, case_groups, has_rna_tracks) %}
 <div href="#" class="bg-dark list-group-item text-white">
   <div class="d-flex w-100 justify-content-start align-items-center">

scout/server/blueprints/clinvar/controllers.py

@@ -363,6 +363,7 @@ def update_clinvar_submission_status(request_obj, institute_id, submission_id):
             f"Removed {deleted_objects} objects and {deleted_submissions} submission from database",
             "info",
         )
+
     if update_status == "submit":
         submitter_key = request_obj.form.get("apiKey")
         send_api_submission(institute_id, submission_id, submitter_key)

scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html

@@ -58,13 +58,6 @@
           <nav aria-label="breadcrumb">
             <ol class="breadcrumb align-items-center">
               <li class="breadcrumb-item">
-                <!-- Download the Variant data CSV file -->
-                <a href="{{ url_for('clinvar.clinvar_download_csv', submission=subm_obj._id, csv_type='variant_data', clinvar_id=subm_obj.clinvar_subm_id or 'None') }}" class="btn btn-primary btn-xs text-white" target="_blank" rel="noopener">
-                  Download variants csv file
-                </a>
-                <a href=" {{ url_for('clinvar.clinvar_download_csv', submission=subm_obj._id, csv_type='case_data', clinvar_id=subm_obj.clinvar_subm_id or 'None') }}" class="btn btn-primary btn-xs text-white" target="_blank" rel="noopener">
-                  Download casedata csv file
-                </a>
                 <a id="download_clinvar_json" href="{{ url_for('clinvar.clinvar_download_json', submission=subm_obj._id, clinvar_id=subm_obj.clinvar_subm_id or 'None') }}" class="btn btn-primary btn-xs text-white" target="_blank" rel="noopener">
                   Download submission json file
                 </a>
@@ -77,8 +70,7 @@
               {% if subm_obj.status != 'submitted' %}
                 <li class="breadcrumb-item"><button type="submit" name="update_submission" value="submitted" class="btn btn-success btn-xs">Mark as submitted</button></li>
               {% endif %}
-
-                <li class="breadcrumb-item"><button type="submit" name="update_submission" value="delete" class="btn btn-danger btn-xs">Delete submission</button></li>
+                <li class="breadcrumb-item"><button type="submit" name="update_submission" value="delete" class="btn btn-danger btn-xs">Delete submission from Scout</button></li>
             </ol>
           </nav>
           </form>
@@ -101,9 +93,13 @@
               {% endif %}
               {% if subm_obj.status == 'submitted' %} <!--Submission status query -->
                  <form id="statusApi_{{subm_obj._id}}" action="{{ url_for('clinvar.clinvar_submission_status', submission_id=subm_obj.clinvar_subm_id) }}" method="POST">
-                   {{ status_modal(subm_obj._id) }}
+                   {{ action_modal("status", subm_obj._id) }}
                    <td style="width: 20%"><button type="button" class="btn btn-sm btn-secondary form-control" name="status_enquiry" value="api_status" data-bs-toggle="modal" data-bs-target="#statusModal_{{subm_obj._id}}">Submission status enquiry</button></td>
                  </form>
+                <form id="deleteApi_{{subm_obj._id}}" action="{{ url_for('clinvar.clinvar_submission_delete', submission_id=subm_obj.clinvar_subm_id) }}" method="POST">
+                   {{ action_modal("remove", subm_obj._id) }}
+                   <td style="width: 20%"><button type="button" class="btn btn-sm btn-danger form-control" name="_enquiry" value="api_status" data-bs-toggle="modal" data-bs-target="#removeModal_{{subm_obj._id}}">Delete submission from ClinVar</button></td>
+                 </form>
               {% endif %}
             </tr>
           </table>
@@ -246,12 +242,12 @@
 </div>
 {% endmacro %}
 
-{% macro status_modal(subm_id) %}
-<div class="modal fade" id="statusModal_{{subm_id}}" tabindex="-1">
+{% macro action_modal(action_type, subm_id) %}
+<div class="modal fade" id="{{action_type}}Modal_{{subm_id}}" tabindex="-1">
   <div class="modal-dialog">
     <div class="modal-content">
       <div class="modal-header">
-        <h5 class="modal-title">Submission status</h5>
+        <h5 class="modal-title">Submission {{action_type}}</h5>
         <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
       </div>
       <div class="modal-body">
@@ -260,7 +256,7 @@
       </div>
       <div class="modal-footer">
         <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
-        <button type="submit" name="show_status" value="status" class="btn btn-primary">Submission status enquiry</button>
+        <button type="submit" name="{{action_type}}" value="{{action_type}}" class="btn btn-primary">Submission {{action_type}} enquiry</button>
       </div>
     </div>
   </div>

scout/server/blueprints/clinvar/views.py

@@ -1,8 +1,7 @@
-import csv
 import logging
 from json import dumps
 from tempfile import NamedTemporaryFile
-from typing import List
+from typing import List, Tuple
 
 from flask import Blueprint, flash, redirect, render_template, request, send_file, url_for
 from flask_login import current_user
@@ -29,10 +28,25 @@ def clinvar_submission_status(submission_id):
     """Sends a request to ClinVar to retrieve and display the status of a submission."""
 
     # flash a message with current submission status for a ClinVar submission
-    clinvar_api.show_submission_status(
-        submission_id=submission_id, api_key=request.form.get("apiKey")
+    flash(
+        f'Response from ClinVar: {clinvar_api.json_submission_status( submission_id=submission_id, api_key=request.form.get("apiKey"))}',
+        "primary",
     )
+    return redirect(request.referrer)
+
+
+@clinvar_bp.route("/clinvar/delete-enquiry/<submission_id>", methods=["POST"])
+def clinvar_submission_delete(submission_id):
+    """Sends a request to ClinVar to delete a successfully processed submission."""
 
+    # Retrieve the actual submission status:
+    delete_res: Tuple[int, dict] = clinvar_api.delete_clinvar_submission(
+        submission_id=submission_id, api_key=request.form.get("apiKey")
+    )
+    flash(
+        f"ClinVar response: { str(delete_res[1]) }",
+        "success" if delete_res[0] == 201 else "warning",
+    )
     return redirect(request.referrer)
 
 
@@ -104,33 +118,6 @@ def clinvar_update_submission(institute_id, submission):
     return redirect(request.referrer)
 
 
-@clinvar_bp.route("/<submission>/download/csv/<csv_type>/<clinvar_id>", methods=["GET"])
-def clinvar_download_csv(submission, csv_type, clinvar_id):
-    """Download a csv (Variant file or CaseData file) for a clinVar submission"""
-
-    clinvar_file_data = controllers.clinvar_submission_file(submission, csv_type, clinvar_id)
-
-    if clinvar_file_data is None:
-        return redirect(request.referrer)
-
-    # Write temp CSV file and serve it in response
-    tmp_csv = NamedTemporaryFile(
-        mode="a+", prefix=clinvar_file_data[0].split(".")[0], suffix=".csv"
-    )
-    writes = csv.writer(tmp_csv, delimiter=",", quoting=csv.QUOTE_ALL)
-    writes.writerow(clinvar_file_data[1])  # Write header
-    writes.writerows(clinvar_file_data[2])  # Write lines
-    tmp_csv.flush()
-    tmp_csv.seek(0)
-
-    return send_file(
-        tmp_csv.name,
-        download_name=clinvar_file_data[0],
-        mimetype="text/csv",
-        as_attachment=True,
-    )
-
-
 @clinvar_bp.route("/<submission>/download/json/<clinvar_id>", methods=["GET"])
 def clinvar_download_json(submission, clinvar_id):
     """Download a json for a clinVar submission"""

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/cancer-variant.html

@@ -235,10 +235,10 @@
           <span class="text-muted">exon </span><strong>{{ primary_gene.exon }}</strong>
         {% endif %}
         {% if primary_transcript and primary_transcript.coding_sequence_name %}
-              {{ primary_transcript.coding_sequence_name | url_decode }}
+              {{ primary_transcript.coding_sequence_name | url_decode | truncate(50, True) }}
         {% endif %}
         {% if primary_transcript and primary_transcript.protein_sequence_name %}
-          <strong>{{ primary_transcript.protein_sequence_name | url_decode }}</strong>
+          <strong>{{ primary_transcript.protein_sequence_name | url_decode | truncate(50, True) }}</strong>
         {% endif %}
         {% if primary_gene and primary_gene.region_annotation %}
           <div>(<span class="font-weight-bold">{{ primary_gene.functional_annotation|truncate(20, True) }}</span> in <span class="font-weight-bold">{{ primary_gene.region_annotation }} region</span>)</div>

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/variant_details.html

@@ -375,7 +375,7 @@
         </li>
         <li class="list-group-item">
           SPIDEX
-          <span class="float-end">{{ variant.spidex_human }}</span>
+          <span class="float-end">{{ variant.spidex|spidex_human if variant.spidex else none|spidex_human }}</span>
         </li>
         <li class="list-group-item">
           <a href="{{ variant.spliceai_link }}" target="_blank" rel="noopener">SpliceAI</a> <a href="https://github.com/Illumina/SpliceAI" target="_blank" rel="noopener">DS max</a>

scout/server/blueprints/variant/views.py

@@ -27,12 +27,19 @@ from scout.server.blueprints.variant.controllers import (
     check_reset_variant_classification,
 )
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
-from scout.server.blueprints.variant.controllers import observations, str_variant_reviewer
+from scout.server.blueprints.variant.controllers import (
+    observations,
+    str_variant_reviewer,
+)
 from scout.server.blueprints.variant.controllers import variant as variant_controller
 from scout.server.blueprints.variant.controllers import variant_acmg as acmg_controller
-from scout.server.blueprints.variant.controllers import variant_acmg_post
+from scout.server.blueprints.variant.controllers import (
+    variant_acmg_post,
+)
 from scout.server.blueprints.variant.controllers import variant_ccv as ccv_controller
-from scout.server.blueprints.variant.controllers import variant_ccv_post
+from scout.server.blueprints.variant.controllers import (
+    variant_ccv_post,
+)
 from scout.server.blueprints.variant.verification_controllers import (
     MissingVerificationRecipientError,
     variant_verification,
@@ -374,7 +381,6 @@ 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 +398,7 @@ 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,

scout/server/blueprints/variants/forms.py

@@ -16,7 +16,7 @@ from wtforms import (
     SubmitField,
     validators,
 )
-from wtforms.widgets import TextInput
+from wtforms.widgets import NumberInput, TextInput
 
 from scout.constants import (
     CALLERS,
@@ -132,8 +132,22 @@ class VariantFiltersForm(FlaskForm):
     )
 
     chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
-    start = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    start = 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 = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 
@@ -264,8 +278,22 @@ class OutlierFiltersForm(FlaskForm):
     )
 
     chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
-    start = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    start = IntegerField(
+        "Start position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=1, message="Start position must be 0 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+    end = IntegerField(
+        "End position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=1, message="End position must be 0 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 

scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -83,17 +83,18 @@
             </td>
             <td>{{ gene_cell(variant) }}</td>
             <td>
+
               <a target="_blank" href="{{ url_for('variant.cancer_variant', institute_id=institute._id, case_name=case.display_name,
                                   variant_id=variant._id, cancer='yes') }}">
                 {% if variant.first_rep_gene.hgvs_identifier %}
-                  <div>{{ variant.first_rep_gene.hgvs_identifier }}</div>
-                  <div>{{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode }}</div>
+                  <div>{{ variant.first_rep_gene.hgvs_identifier|truncate(30, True) }}</div>
+                  <div>{{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode|truncate(30, True) }}</div>
                 {% else %}
-                  <div>{{ variant.reference }}→
+                  <div>{{ variant.reference|truncate(30, True) }}→
                     {% if variant.alternative | length > 5 %}
                       {{ variant.alternative[0] }}...{{ variant.alternative[-1] }}
                     {% else %}
-                      {{ variant.alternative }}
+                      {{ variant.alternative|truncate(30, True) }}
                     {% endif %}
                   </div>
                 {% endif %}