scout-browser 4.95.0__py3-none-any.whl → 4.96.0__py3-none-any.whl

scout/adapter/mongo/case.py

@@ -982,7 +982,6 @@ class CaseHandler(object):
                         variant_type=variant_type,
                         category=category,
                     )
-                # add variants
                 self.load_variants(
                     case_obj=case_obj,
                     variant_type=variant_type,
@@ -994,33 +993,34 @@ class CaseHandler(object):
                     ),
                 )
 
-        except (IntegrityError, ValueError, ConfigError, KeyError) as error:
-            LOG.warning(error)
-
-        self._load_omics_variants(case_obj, build=genome_build, update=update)
-
-        if existing_case:
-            self.update_case_data_sharing(old_case=existing_case, new_case=case_obj)
-            case_obj["rerun_requested"] = False
-            if case_obj["status"] in ["active", "archived"]:
-                case_obj["status"] = "inactive"
-
-            case_obj["variants_stats"] = self.case_variants_count(
-                case_id=case_obj["_id"],
-                institute_id=institute_obj["_id"],
-                force_update_case=True,
-            )
+                self._load_omics_variants(case_obj, build=genome_build, update=update)
 
-            self.update_case_cli(case_obj, institute_obj)
-            # update Sanger status for the new inserted variants
-            self.update_case_sanger_variants(institute_obj, case_obj, old_sanger_variants)
+        except (IntegrityError, ValueError, ConfigError, KeyError) as error:
+            LOG.exception(error)
+            raise error
+        else:
+            if not existing_case:
+                LOG.info("Loading case %s into database", case_obj["display_name"])
+                self.add_case(case_obj, institute_obj)
+        finally:
+            if existing_case:
+                self.update_case_data_sharing(old_case=existing_case, new_case=case_obj)
+                case_obj["rerun_requested"] = False
+                if case_obj["status"] in ["active", "archived"]:
+                    case_obj["status"] = "inactive"
+
+                case_obj["variants_stats"] = self.case_variants_count(
+                    case_id=case_obj["_id"],
+                    institute_id=institute_obj["_id"],
+                    force_update_case=True,
+                )
 
-            if keep_actions and old_evaluated_variants:
-                self.update_variant_actions(institute_obj, case_obj, old_evaluated_variants)
+                self.update_case_cli(case_obj, institute_obj)
+                # update Sanger status for the new inserted variants
+                self.update_case_sanger_variants(institute_obj, case_obj, old_sanger_variants)
 
-        else:
-            LOG.info("Loading case %s into database", case_obj["display_name"])
-            self.add_case(case_obj, institute_obj)
+                if keep_actions and old_evaluated_variants:
+                    self.update_variant_actions(institute_obj, case_obj, old_evaluated_variants)
 
         return case_obj
 
@@ -1146,6 +1146,7 @@ class CaseHandler(object):
                 "RNAfusion_report": case_obj.get("RNAfusion_report"),
                 "RNAfusion_report_research": case_obj.get("RNAfusion_report_research"),
                 "rna_delivery_report": case_obj.get("rna_delivery_report"),
+                "scout_load_version": case_obj.get("scout_load_version"),
                 "smn_tsv": case_obj.get("smn_tsv"),
                 "status": case_obj.get("status"),
                 "sv_rank_model_version": case_obj.get("sv_rank_model_version"),

scout/build/case.py

@@ -1,6 +1,7 @@
 import logging
 from datetime import datetime
 from typing import Dict
+from scout import __version__
 
 from scout.constants import CUSTOM_CASE_REPORTS, PHENOTYPE_GROUPS
 from scout.exceptions import ConfigError, IntegrityError
@@ -154,6 +155,7 @@ def build_case(case_data, adapter):
     now = datetime.now()
     case_obj["created_at"] = now
     case_obj["updated_at"] = now
+    case_obj["scout_load_version"] = __version__
 
     if case_data.get("suspects"):
         case_obj["suspects"] = case_data["suspects"]
@@ -162,7 +164,7 @@ def build_case(case_data, adapter):
 
     case_obj["synopsis"] = case_data.get("synopsis", "")
 
-    case_obj["status"] = "inactive"
+    case_obj["status"] = case_data.get("status") or "inactive"
     case_obj["is_research"] = False
     case_obj["research_requested"] = False
     case_obj["rerun_requested"] = False

scout/constants/acmg.py

@@ -309,48 +309,55 @@ ACMG_CRITERIA["benign impact"] = OrderedDict(
 
 ACMG_POTENTIAL_CONFLICTS = [
     (
-        "PVS1",
-        "PM4",
+        {"PVS1", "PM4"},
         "Use of PVS1 and PM4 together risks double-counting evidence (Tayoun et al 2019).",
     ),
     (
-        "PVS1",
-        "PM1",
+        {"PVS1", "PM1"},
         "Use of PVS1 and PM1 together is not recommended (Durkie et al 2024).",
     ),
     (
-        "PVS1",
-        "PP2",
+        {"PVS1", "PP2"},
         "Use of PVS1 and PP2 together is not recommended (Durkie et al 2024).",
     ),
     (
-        "PVS1",
-        "PS3",
+        {"PVS1", "PS3"},
         "Note that for RNA PS3 should only be taken with PVS1 for well established functional assays, not splicing alone (Walker 2023).",
     ),
     (
-        "PS1",
-        "PM4",
+        {"PS1", "PM4"},
         "Use of PS1 and PM4 together is not recommended (Durkie et al 2024).",
     ),
     (
-        "PS1",
-        "PM5",
+        {"PS1", "PM5"},
         "Use of PS1 and PM5 together conflicts with original definition (Richards et al 2015).",
     ),
     (
-        "PS1",
-        "PP3",
+        {"PS1", "PP3"},
         "Use of PS1 and PP3 together risks double-counting evidence (Tayoun et al 2019).",
     ),
     (
-        "PS2",
-        "PM6",
+        {"PS2", "PM6"},
         "Use of PS2 and PM6 together conflicts with original definition (Richards et al 2015).",
     ),
     (
-        "PM1",
-        "PP2",
+        {"PM1", "PP2"},
         "Avoid double-counting evidence for constraints in both PM1 and PP2 (Durkie et al 2024).",
     ),
+    (
+        {"PP1", "PP4"},
+        "When applying phenotype specificity and segregation data together, a point-system is available from ClinGen SVI (Biesecker et al 2024).",
+    ),
+    (
+        {"BS4", "PP4"},
+        "When applying phenotype specificity and segregation data together, a point-system is available from ClinGen SVI (Biesecker et al 2024).",
+    ),
+    (
+        {"PS2", "PP4"},
+        "Consider using PS2 without the PP4 criterion, based on the SVI Recommendation for de novo Criteria (PS2 & PM6).",
+    ),
+    (
+        {"PM6", "PP4"},
+        "Consider using PM6 without the PP4 criterion, based on the SVI Recommendation for de novo Criteria (PS2 & PM6).",
+    ),
 ]

scout/demo/cancer.load_config.yaml

@@ -44,9 +44,7 @@ delivery_report: scout/demo/delivery_report.html
 cnv_report: scout/demo/cancer_cnv_report.pdf
 coverage_qc_report: scout/demo/cancer_coverage_qc_report.html
 
-
-# meta data
-rank_model_version: '1.1'
+# metadata
 rank_score_threshold: -100
 analysis_date: 2018-10-12 14:00:46
 human_genome_build: '37'

scout/demo/rnafusion.load_config.yaml

@@ -22,3 +22,4 @@ RNAfusion_inspector_research: scout/demo/rnafusion_inspector_example.html
 analysis_date: 2022-11-02 14:00:46
 human_genome_build: '38'
 track: cancer
+status: 'prioritized'

scout/models/case/case_loading_models.py

@@ -8,6 +8,8 @@ from os.path import abspath, dirname, exists, isabs
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
+from scout.constants import CASE_STATUSES
+
 try:
     from typing import Literal
 except ImportError:
@@ -436,6 +438,7 @@ class CaseLoader(BaseModel):
     smn_tsv: Optional[str] = None
     sv_rank_model_version: Optional[str] = None
     synopsis: Optional[Union[List[str], str]] = None
+    status: Optional[Literal[tuple(CASE_STATUSES)]] = None
     track: Literal["rare", "cancer"] = "rare"
     vcf_files: Optional[VcfFiles]
 

scout/parse/case.py

@@ -34,6 +34,7 @@ def parse_case_data(**kwargs):
         RNAfusion_report: Path to the RNA fusion report
         RNAfusion_report_research: Path to the research RNA fusion report
         smn_tsv(str): Path to an SMN tsv file
+        status(str): Optional case status ("prioritized", "inactive", "ignored", "active", "solved", "archived")
         vcf_cancer(str): Path to a vcf file
         vcf_cancer_sv(str): Path to a vcf file
         vcf_fusion(str): Path to a vcf file

scout/server/app.py

@@ -13,6 +13,7 @@ from flask_login import current_user
 from markdown import markdown as python_markdown
 from markupsafe import Markup
 
+from scout.constants import SPIDEX_HUMAN
 from scout.log import init_log
 
 from . import extensions
@@ -199,6 +200,17 @@ def register_filters(app):
             return "{:,}".format(int(value)).replace(",", " ")
         return value
 
+    @app.template_filter()
+    def spidex_human(spidex):
+        """Translate SPIDEX annotation to human readable string."""
+        if spidex is None:
+            return "not_reported"
+        if abs(spidex) < SPIDEX_HUMAN["low"]["pos"][1]:
+            return "low"
+        if abs(spidex) < SPIDEX_HUMAN["medium"]["pos"][1]:
+            return "medium"
+        return "high"
+
     @app.template_filter()
     def human_decimal(number, ndigits=4):
         """Return a standard representation of a decimal number.

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,
@@ -757,6 +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>
@@ -746,12 +749,34 @@
           </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>
@@ -767,6 +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/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/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,

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 %}

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

@@ -3,7 +3,7 @@
 {% from "variant/buttons.html" import reviewer_button%}
 {% from "variant/gene_disease_relations.html" import inheritance_badge %}
 {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general %}
-{% from "variants/utils.html" import cell_rank, dismiss_variants_block, filter_form_footer, update_stash_filter_button_status, pagination_footer, pagination_hidden_div, str_filters, filter_script_main %}
+{% from "variants/utils.html" import callers_cell, cell_rank, dismiss_variants_block, filter_form_footer, update_stash_filter_button_status, pagination_footer, pagination_hidden_div, str_filters, filter_script_main %}
 
 
 {% block title %}
@@ -60,13 +60,14 @@
       <thead class="thead table-light">
         <tr>
           <th style="width:8%" title="Index">Index</th>
-          <th title="Repeat ID">Repeat locus</th>
-          <th title="Repeat unit">Reference repeat unit</th>
-          <th title="ALT">Estimated size</th>
-          <th title="ReferenceSize">Reference size</th>
-          <th title="Status">Status</th>
+          <th title="Repeat locus ID">Repeat locus</th>
+          <th style="width:8%" title="Reference repeat unit">Ref RU</th>
+          <th style="width:6%" title="ALT">Est size</th>
+          <th style="width:6%" title="ReferenceSize">Ref size</th>
+          <th style="width:8%" title="Caller and call filter status">Qual</th>
+          <th style="width:8%" title="Status">Status</th>
           <th title="GT">Genotype</th>
-          <th title="Chromosome" style="width:6%">Chr.</th>
+          <th style="width:6%" title="Chromosome" style="width:6%">Chr.</th>
           <th title="Position" style="width:20%">Position</th>
         </tr>
       </thead>
@@ -95,11 +96,14 @@
 	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru or variant.reference }}</td>
             <td class="text-end"><b><span data-bs-toggle="tooltip" title="{{ variant.alternative }}">{{ variant.str_mc }}</span></b></td>
             <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
+            <td>{{ callers_cell(variant) }}</td>
             <td>{{ str_status(variant) }}</td>
             <td>{% for sample in variant.samples %}
                   {% if sample.genotype_call != "./." %}
-                    <div class="float-start">{{ sample.display_name }}</div>
-                    <div class="float-end">{{ sample.genotype_call }}</div><br>
+                    <div class="row">
+                      <div class="col-8">{{ sample.display_name }}</div>
+                      <div class="col-4 text-end">{{ sample.genotype_call }}</div>
+                    </div>
                   {% endif %}
                 {% endfor %}
             </td>

scout/server/extensions/clinvar_extension.py

@@ -1,5 +1,7 @@
 import json
 import logging
+from io import StringIO
+from typing import Optional, Tuple
 
 import requests
 from flask import flash
@@ -17,6 +19,7 @@ class ClinVarApi:
 
     def init_app(self, app):
         self.convert_service = "/".join([PRECLINVAR_URL, "csv_2_json"])
+        self.delete_service = "/".join([PRECLINVAR_URL, "delete"])
         self.submit_service_url = app.config.get("CLINVAR_API_URL") or CLINVAR_API_URL_DEFAULT
 
     def set_header(self, api_key) -> dict:
@@ -77,10 +80,61 @@ class ClinVarApi:
         except Exception as ex:
             return self.submit_service_url, None, ex
 
-    def show_submission_status(self, submission_id: str, api_key=None):
+    def json_submission_status(self, submission_id: str, api_key=None) -> dict:
         """Retrieve the status of a ClinVar submission using the https://submit.ncbi.nlm.nih.gov/api/v1/submissions/SUBnnnnnn/actions/ endpoint."""
 
         header: dict = self.set_header(api_key)
         actions_url = f"{self.submit_service_url}{submission_id}/actions/"
         actions_resp: requests.models.Response = requests.get(actions_url, headers=header)
-        flash(f"Response from ClinVar: {actions_resp.json()}", "primary")
+        return actions_resp.json()
+
+    def get_clinvar_scv_accession(self, url: str) -> Optional[str]:
+        """Downloads a submission summary from the given URL into a temporary file and parses this file to retrieve a SCV accession, if available."""
+        # Send a GET request to download the file
+        response = requests.get(url)
+        response.raise_for_status()  # Raise an error if the request failed
+
+        # Use an in-memory file-like object to hold the JSON content
+        with StringIO(response.text) as memory_file:
+
+            json_data = json.load(memory_file)
+
+            submission_data: dict = json_data["submissions"][0]
+            processing_status: str = submission_data["processingStatus"]
+            if processing_status != "Success":
+                flash(
+                    f"Could not delete provided submission because its processing status is '{processing_status}'.",
+                    "warning",
+                )
+                return
+            return submission_data["identifiers"]["clinvarAccession"]
+
+    def delete_clinvar_submission(self, submission_id: str, api_key=None) -> Tuple[int, dict]:
+        """Remove a successfully processed submission from ClinVar."""
+
+        try:
+            submission_status_doc: dict = self.json_submission_status(
+                submission_id=submission_id, api_key=api_key
+            )
+
+            subm_response: dict = submission_status_doc["actions"][0]["responses"][0]
+            submission_status = subm_response["status"]
+
+            if submission_status != "processed":
+                return (
+                    500,
+                    f"Clinvar submission status should be 'processed' and in order to attempt data deletion. Submission status is '{submission_status}'.",
+                )
+
+            # retrieve ClinVar SCV accession (SCVxxxxxxxx) from file url returned by subm_response
+            subm_summary_url: str = subm_response["files"][0]["url"]
+            scv_accession: Optional(str) = self.get_clinvar_scv_accession(url=subm_summary_url)
+
+            # Remove ClinVar submission using preClinVar's 'delete' endpoint
+            resp = requests.post(
+                self.delete_service, data={"api_key": api_key, "clinvar_accession": scv_accession}
+            )
+            return resp.status_code, resp.json()
+
+        except Exception as ex:
+            return 500, str(ex)

scout/server/links.py

@@ -3,7 +3,6 @@ from urllib.parse import quote
 
 from flask import current_app
 
-from scout.constants import SPIDEX_HUMAN
 from scout.utils.convert import amino_acid_residue_change_3_to_1
 
 SHALLOW_REFERENCE_STR_LOCI = ["ARX", "HOXA13"]
@@ -486,7 +485,6 @@ def get_variant_links(institute_obj: dict, variant_obj: dict, build: int = None)
         ensembl_link=ensembl_link(variant_obj, build),
         mitomap_link=mitomap_link(variant_obj),
         hmtvar_link=hmtvar_link(variant_obj),
-        spidex_human=spidex_human(variant_obj),
         spliceai_link=spliceai_link(variant_obj, build),
         str_source_link=str_source_link(variant_obj),
         snp_links=snp_links(variant_obj),
@@ -908,18 +906,6 @@ def hmtvar_link(variant_obj):
     return url_template.format(id=variant_obj.get("hmtvar_variant_id"))
 
 
-def spidex_human(variant_obj):
-    """Translate SPIDEX annotation to human readable string."""
-    if variant_obj.get("spidex") is None:
-        return "not_reported"
-    if abs(variant_obj["spidex"]) < SPIDEX_HUMAN["low"]["pos"][1]:
-        return "low"
-    if abs(variant_obj["spidex"]) < SPIDEX_HUMAN["medium"]["pos"][1]:
-        return "medium"
-
-    return "high"
-
-
 def external_primer_order_link(variant_obj, build=None):
     """Compose link for primers orders based on the configuration paramaters EXTERNAL_PRIMER_ORDER_LINK_(37|38)"""
     build = build or 37

scout/utils/acmg.py

@@ -1,6 +1,6 @@
 # coding=UTF-8
 
-from typing import Optional
+from typing import List, Optional
 
 from scout.constants import ACMG_COMPLETE_MAP
 from scout.constants.acmg import ACMG_POTENTIAL_CONFLICTS
@@ -362,12 +362,12 @@ def get_acmg_temperature(acmg_terms: set) -> Optional[dict]:
     }
 
 
-def get_acmg_conflicts(acmg_terms: set) -> list:
-    """Check potential conflict paris, return list of reference strings."""
+def get_acmg_conflicts(acmg_terms: List[str]) -> List[str]:
+    """Check for potential conflicting terms, return a list of references as strings."""
 
     conflicts = []
-    for t1, t2, reference in ACMG_POTENTIAL_CONFLICTS:
-        if t1 in acmg_terms and t2 in acmg_terms:
+    for conflict_set, reference in ACMG_POTENTIAL_CONFLICTS:
+        if conflict_set.issubset(set(acmg_terms)):
             conflicts.append(reference)
 
     return conflicts

{scout_browser-4.95.0.dist-info → scout_browser-4.96.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.95.0
+Version: 4.96.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md

{scout_browser-4.95.0.dist-info → scout_browser-4.96.0.dist-info}/RECORD

@@ -4,7 +4,7 @@ scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
 scout/adapter/mongo/acmg.py,sha256=v2Zuw-6APVmcnBnNXa18WJEu2vj5GUhZNiKMkruJsBI,4170
 scout/adapter/mongo/base.py,sha256=iIa2AjGNztKHcZzolY0T6r7Oh0guj6R1putztp4OTNY,4427
-scout/adapter/mongo/case.py,sha256=aHHCOeB1wjEX98HKBpDFWC0zZ149Orn93XkW0m7Wj7A,65148
+scout/adapter/mongo/case.py,sha256=TS2erNplLCulGoF7zRMr_3eW1MyJd3VL2mOW7XsOZJM,65342
 scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
 scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
 scout/adapter/mongo/ccv.py,sha256=VIz-Yqzm-1UVPDKvZkBllO4BOKXzvKCXcQUjTtZCHTI,4165
@@ -31,7 +31,7 @@ scout/adapter/mongo/variant_events.py,sha256=yNnMM58P1LbYFw73rWzti6l2zWa_G93ozUT
 scout/adapter/mongo/variant_loader.py,sha256=C05StRMFVChopcolPYXFIbh_S-FhYHu4NvBCpiBLOeE,28327
 scout/build/__init__.py,sha256=GUWEaXTpwsJil_KtrXBQJpZIwCQFSgo8NlK49R9IkA8,521
 scout/build/acmg.py,sha256=M21MrrP_dtEyOuu6t-jBDdaqYcHPMLcwJlt9fHG2ycE,1523
-scout/build/case.py,sha256=7Hry6ja0KvVhNQ1ecXy3HuaR7dY2x9O8f8FpYt4P6jo,11404
+scout/build/case.py,sha256=LtYx6zQcCoGCss48qf7uluzTlXVH0Pl-WhqYzkbIcZ8,11510
 scout/build/ccv.py,sha256=cfAWSQ5cSBWURkL9_fPm1Y5aRcTIDOE9ieSWaYLufB4,1660
 scout/build/disease.py,sha256=Zew9AF_z1NbbKcO3uJZ2wgni501SkfnYRgnaCZ4m8FY,2020
 scout/build/hpo.py,sha256=LJBCTq-x09D0CSKcUHB8a6ynuUrVh_7Ia0ooA1BxMys,1207
@@ -126,7 +126,7 @@ scout/commands/view/panels.py,sha256=a0fQcP9-SDPuRYV7aEgIGUCYaMN6V47h6finpcdoomU
 scout/commands/view/transcripts.py,sha256=59WyNNp7zHPJIz9QgzrkoeKaSXTtuLli0VuL8IidEmY,1277
 scout/commands/view/users.py,sha256=MKlmhDYRM7Yf-Trmi1ijEuqsDIUn326bdFADyDs7XYg,832
 scout/constants/__init__.py,sha256=ke7uVYgqn6dqByEQdfLQ1H061yOvaNyt8E-WP84Dgr8,5854
-scout/constants/acmg.py,sha256=hYPzoLUqpuTjGXfIN80Nb1njriesH9oAELu1scp-ByU,18083
+scout/constants/acmg.py,sha256=N9X2sJLbK6g6tDPhW0gYQifImzaowb4F6jfTYUBr-Z0,18717
 scout/constants/case_tags.py,sha256=O-BwEzU36MSpN7qqd-aSvoi4-VDRY8rM5hQ7Jg7DMgs,9447
 scout/constants/ccv.py,sha256=YP82qWCrjv3JB8d2LkUdBlBZolk0uF3nhNmkNgmebiI,9734
 scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
@@ -187,7 +187,7 @@ scout/demo/ADM1059A2.test.cgh,sha256=29YOnGgPB3wxWwxVwf_mCLrhZ4Cf5hqVxw_DUggBe7Y
 scout/demo/ADM1059A3.d4,sha256=Da7zycL1LjrzhX1171G1sJTedyOLUyYMc_e5EAhI4eQ,961059
 scout/demo/ADM1059A3.test.cgh,sha256=29YOnGgPB3wxWwxVwf_mCLrhZ4Cf5hqVxw_DUggBe7Y,29
 scout/demo/__init__.py,sha256=ggXVz3_6ZUAzIZtuaK8kz3C6BuxSfaQ56PAzinJcYoI,2061
-scout/demo/cancer.load_config.yaml,sha256=1wz9eTRI54lu4TERQ3WJbbkEhrdLHhm1X_IMktXZX2M,1401
+scout/demo/cancer.load_config.yaml,sha256=T4v2xvUA5vv3kZ8HT_7uQFq20xG1qq4YguVcTdqyKzE,1373
 scout/demo/cancer_cnv_report.pdf,sha256=_2_nj7Hc9SdE_mwDBqoquOFTLzZq5URnslADRMFjOm4,1910043
 scout/demo/cancer_coverage_qc_report.html,sha256=BlE_d6i68fK6VPv1wCyEmJy3qGSU67-in5Y1BGustU8,6914
 scout/demo/cancer_test.ped,sha256=NN_IGuCTulYXQ18u1eFcvj_AwTnlSpu9eHurQZfkoys,36
@@ -211,7 +211,7 @@ scout/demo/panelapp_panels_reduced.json,sha256=dwvRRwfIIFq6H4ze0wyOIllN-LSreK5jh
 scout/demo/reduced_mt.bam,sha256=DlC0lBAQrqbNrRSJ27MrOVmF5_bjRINmHwMn45a0-_c,492247
 scout/demo/reduced_mt.bam.bai,sha256=S8k17QiK9jkLHM3usZP-Rsc5xGe5kvHfbMbB3-KKIRM,808
 scout/demo/reference_info.yaml,sha256=-9kgT14q-IY3xzz9iPSoV22hR7u89xOq4FJMEOqb3-0,7526
-scout/demo/rnafusion.load_config.yaml,sha256=7a8Tox78q4RiioeTXivioheexrmPL4W9G3SCwNUlo_0,540
+scout/demo/rnafusion.load_config.yaml,sha256=nbx-uEnEY4wA0ro8mJI4cRHk--h3Tbtj0sJD7BYO6Jk,562
 scout/demo/rnafusion_inspector_example.html,sha256=rDxfsZR4vYyhxD_gzA9pKPpposOcHe0tqq7UpzP6Dbo,1547345
 scout/demo/rnafusion_report_example.html,sha256=Ktd1UuW41pNYI7qT84cyYconJJQJxx7AkkAD3767tsc,1755020
 scout/demo/scout_example_tumor_only.SV.CNV.sorted.vcf.gz,sha256=lABVdx4zlpUuP2uL92ZYsHIiQNZNl35bGXlUECyiLGE,3443
@@ -398,13 +398,13 @@ scout/models/phenotype_term.py,sha256=jY7dbfPzgE14M1gWqifm5YKkwMlrtfFa_WBHMT1_og
 scout/models/user.py,sha256=oercrjpf9fLomqAcN0Fv1BL_XPjOrS_vchURo0RP7es,1134
 scout/models/case/__init__.py,sha256=Sqczn7Wm9KYZtPGAHCvwX_6j9vlaK-0myJtSDlS-448,121
 scout/models/case/case.py,sha256=Wu2D6IZKkFXLeF7emcBr7n1HQ7Mj9rO-cN-8T9rhkSU,5282
-scout/models/case/case_loading_models.py,sha256=GNeXZFrJ_1ISSxqO2VpKXazCLksLsPbTNL67csIIwQQ,21568
+scout/models/case/case_loading_models.py,sha256=Fs1jxbaHBsxC3l3_ECHFczukWFWQwPhigXW4035rZS8,21670
 scout/models/variant/__init__.py,sha256=H-IZ2hSTSVS28S8FZzA8j2Cyu1PHQFXyMWJFtCucPAk,40
 scout/models/variant/gene.py,sha256=98CG_JcAklGGFIrUulf1_olQalV65kXQO-gOf7VQZ0A,1095
 scout/models/variant/transcript.py,sha256=rfflEbTs7Bn4HDENqrxtGopQ_0HKnrVLLyBcrj4NpwM,1720
 scout/models/variant/variant.py,sha256=SppFVdCYrlZiMBce38YrAykYZZ-0el3DzrArJHtC1yU,4473
 scout/parse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-scout/parse/case.py,sha256=-sGKWYWcskMagrDpEoeCIAJacwCR2feC8SwWvT0FJVw,11577
+scout/parse/case.py,sha256=P7ya8LaV5G_R-5AOwPU5mMbGdc1sG7Ojt16JXTgrpKo,11690
 scout/parse/cytoband.py,sha256=7flY3b_wegupHHBLRcs4KyM1ns-uzuTfVHm4CycnupE,1055
 scout/parse/disease_terms.py,sha256=-JIm4GWEvqg9nmWehK18mlIQ-N5nZhT2u5pbfDRXoxE,7437
 scout/parse/ensembl.py,sha256=nnqOVtLgWh9wbtHnzGIidnNIvRoOp2bTct5OuAFSSB0,10618
@@ -444,10 +444,10 @@ scout/resources/cytoBand_hg19.txt.gz,sha256=pheUD5b9NlVuvwwnbKwDc2FG80Yg70gvPxVX
 scout/resources/cytoBand_hg38.txt.gz,sha256=sqSVmvPlktQ-0hTiTapJM-5UgyV6xDoYZuTF0kPuETs,6105
 scout/resources/custom_igv_tracks/mane.bb,sha256=flEexDxHmbX7IwwrMM0P5DWOxcSCjmHxGNlyg_WqElQ,3519360
 scout/server/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
-scout/server/app.py,sha256=70YdN9eWL1ySEYkuAHKOk_WA4Fm5dcIwtIZEcEf-xA0,10836
+scout/server/app.py,sha256=S29_mBkNFWr7JDHB0I3JEyzdNwn7Qw28mKV7X5VMoN0,11254
 scout/server/auto.py,sha256=8B6GwfOaUChkTLuLgYQDFMWlxGuHkEegF1argH2G2Ik,401
 scout/server/config.py,sha256=BFx6ix8D3KM90FqmaHLxv_feudO2kN2CkX1UWBGTjXE,5923
-scout/server/links.py,sha256=f2h_zUFt4Tm_383ZmdIGsA6mUVQbpQmJ199ZTzUWemE,28115
+scout/server/links.py,sha256=rJTHO4G40uLiWCtPr2n0Q0pBMtSOhjjh7F41jBoufM4,27656
 scout/server/utils.py,sha256=d1fGdSwo-XjNHVjHd-uT3mGmUJ8yYB6weT7VgHo9nxM,12592
 scout/server/blueprints/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 scout/server/blueprints/alignviewers/__init__.py,sha256=XMVed2ekVUAvroqENDHSr2pwM8otqau8ZA-rbH1T2U8,59
@@ -460,7 +460,7 @@ scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=x2
 scout/server/blueprints/api/__init__.py,sha256=HR6HjS7ot1K_8Lt5eQdNT154z_FCdHGSigy8r2LpNCI,26
 scout/server/blueprints/api/views.py,sha256=pbl78wfhrm1T8JmiJDYF3BbTbfFrlF-hQRbuv2GWI0s,3729
 scout/server/blueprints/cases/__init__.py,sha256=_c17kPFITFYcIVphF4V9bf0PZBer8bU3rtVWQnljKDU,52
-scout/server/blueprints/cases/controllers.py,sha256=UzzFpDfS66f2ZL7cwDdpDFFRR_OtJzds9kc7Wx0U0wc,55747
+scout/server/blueprints/cases/controllers.py,sha256=08QudunYV7deJ2YYTa3Y4TxJ6zLaE8OxXdWHpJWAAPA,55825
 scout/server/blueprints/cases/views.py,sha256=MQDOnLuywAQkVBgYaZAbaj9f6tps18bpo4nDFm77S4s,43165
 scout/server/blueprints/cases/static/case_images.js,sha256=pb_gG7DNQc-1lADqSII8YvjBwmHyeQWYVtuu2jyrTlU,14997
 scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAjaRWhjL-bK5bsQnLpH54HZak,541
@@ -468,11 +468,11 @@ scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkk
 scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
 scout/server/blueprints/cases/templates/cases/case.html,sha256=9Fcn-OFA1yIHchD0PjDs7-Y8I7Qqr8o6cavN0eOi5rI,37183
 scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
-scout/server/blueprints/cases/templates/cases/case_report.html,sha256=-ATAfUnT4a6dmdUSFuGjGPK7r6_XgOXPJtC-Lu8hOgs,66304
+scout/server/blueprints/cases/templates/cases/case_report.html,sha256=lum4fIh6ur_bdnMeYLFGXht0LaF2t-T1StAk8F0cZ5o,67481
 scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=99rmRyDXFXjooB52TI5_ebJKv1ZAJbVXEw4deHfSVMA,7285
 scout/server/blueprints/cases/templates/cases/case_tabular_view.html,sha256=ko-LDUKmIoTazMZ2nFWvPEZsgObU07RwqIkDYFjokoY,4317
 scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=5Wmk7DM8LI3MynqzxeTzAr_EoEBwVVo31djcI5ZlTdo,2164
-scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=H45WZK2qVY47wgttdASjRooRKFs2wQXAnH18u80hRfg,30895
+scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=Zk-ezZ_Ae7gtDw2pDCvyXk-iFoPcD5y3h1THLPKPgk8,31404
 scout/server/blueprints/cases/templates/cases/diseases.html,sha256=ETTQI0Nrl_v86NoX9mFZcvWD-qM1IJoqPmHPWn__Grw,1677
 scout/server/blueprints/cases/templates/cases/gene_panel.html,sha256=lkC_Piqaq-paYr4GUCwQaR8EgGOUXDMoW5sPLDW7yzg,11628
 scout/server/blueprints/cases/templates/cases/index.html,sha256=y91d7yI64Fbz7wS8CSsi3vcCo6rFmS0mnstUipnVHUQ,1136
@@ -482,12 +482,12 @@ scout/server/blueprints/cases/templates/cases/matchmaker.html,sha256=kPYnmcZJ1gm
 scout/server/blueprints/cases/templates/cases/phenotype.html,sha256=7vz5XPUExD6vc-wdijLKnPzaOFm9mQxOZ_ITAL3y7U8,16420
 scout/server/blueprints/cases/templates/cases/utils.html,sha256=gHcxf3DOGcJJZMfjKY4NgvU_tjta5OnyWrKZy9pfGyY,35981
 scout/server/blueprints/clinvar/__init__.py,sha256=BV3aH2AbiA2WWrUEMbGd0H9MefFd2eTsRE9ShywbzpI,30
-scout/server/blueprints/clinvar/controllers.py,sha256=lCrVlokjnSURvsYkm6sTMxrZOL1Xj3VQAWbYr1o_mEY,24251
+scout/server/blueprints/clinvar/controllers.py,sha256=usIiPsk-Ku_mUq975LRpxgibnD6wtupmveVE_RcERkk,24252
 scout/server/blueprints/clinvar/form.py,sha256=2h42YJzaOtsdEglxqt7F1i2ncjSU_IHNt-m4QOJytK4,5148
-scout/server/blueprints/clinvar/views.py,sha256=hPyTJA7Qy6QOL-ENSG1N0atnQXuYCb-iiO8fuNDjJns,6036
+scout/server/blueprints/clinvar/views.py,sha256=nXZMPjldV_wuvj9k5_hsfkVGCvFlhT8fssS-tMlVXYk,5710
 scout/server/blueprints/clinvar/static/form_style.css,sha256=Tro2w0Su9st2ZRpt8PjF7qXYet-0n6Eyol4oh94JafU,4073
 scout/server/blueprints/clinvar/templates/clinvar/clinvar_howto.html,sha256=phFsRl6Hv94sy4GueBN0MXYbQsW6qmR1NoH-3Iwt2zs,4852
-scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html,sha256=NqR66lFN-Svm0IC0FZTts1oPK8S80t69SRSgT-727LA,18185
+scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html,sha256=zJJehPFmxwL6tTChYQBvtOKn3Q2v6RD8pBLiJF6jHaQ,18095
 scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html,sha256=zfU_dPLtjiX8NE7IGTfABt9q46Li8rWFXyyMSvc_U-E,32017
 scout/server/blueprints/dashboard/__init__.py,sha256=9YTjGeFexyEbl4P-gs7j8VEjyhnVwHZFfz57eTtod1M,69
 scout/server/blueprints/dashboard/controllers.py,sha256=x6EWKROskF4iyZ5_hAgL7CWp1X3CXHp-7v0JVsDHKZU,9612
@@ -607,10 +607,10 @@ scout/server/blueprints/variant/__init__.py,sha256=SlD8-Aoj9Jq9aVTJjtFfsu-0sUVfk
 scout/server/blueprints/variant/controllers.py,sha256=dnx5YFVF62V2kAspfGpw0Mr0qUH1VoU1EBTP1hvIlZM,29691
 scout/server/blueprints/variant/utils.py,sha256=BMezzz9Y9ZoGMaLKRbQopJUkWWUo1M9Xi-pw82Vdm4k,25079
 scout/server/blueprints/variant/verification_controllers.py,sha256=eKzP222e7xuFOaQaI9MLOrD9RWtI8uGB1cJYbcXLzF0,10972
-scout/server/blueprints/variant/views.py,sha256=lP6K0BD0d4TDxOMFiQ-UUxF4UkoALzX-nxo_aSY7muI,18969
+scout/server/blueprints/variant/views.py,sha256=82gYXNREV17l8XTWCaptrv5lDfJOG4kiqAaX5IN62Do,19000
 scout/server/blueprints/variant/templates/variant/acmg.html,sha256=Fk4vL1Pu4G3wZsfiUO2jBlFLFoRgFAeqChlIyas5Bb4,8758
 scout/server/blueprints/variant/templates/variant/buttons.html,sha256=4vlnvJKhr28qqzevlecAIvumvOgLZhGyPYQm68AnKzU,7608
-scout/server/blueprints/variant/templates/variant/cancer-variant.html,sha256=ZUnZYURdlLfiJ1Ryok5oRVa96bvBErhIgym2VlWlryQ,14001
+scout/server/blueprints/variant/templates/variant/cancer-variant.html,sha256=vBtPp_jvMeRlwQ71TjGNdG8eCFU27ylFExza5_kJiqg,14043
 scout/server/blueprints/variant/templates/variant/ccv.html,sha256=X33qKY1EvzoLldko1hK5tgE__xxNU54vq6fRzFew6Vc,8671
 scout/server/blueprints/variant/templates/variant/components.html,sha256=dmKxuSrJgvKRtRAzXMN9W2-uZwsLwzde0W4CHqnBb-Q,26185
 scout/server/blueprints/variant/templates/variant/gene_disease_relations.html,sha256=1U77akxqbb4AS2GSyvFwGD6D7rP68L3KXKLUmP73664,7256
@@ -621,7 +621,7 @@ scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=4FBomOY
 scout/server/blueprints/variant/templates/variant/tx_overview.html,sha256=EXLBDh_SgNVEO7MPMjlmfO6MDhtDcj0JyvZdRgxbwSM,6756
 scout/server/blueprints/variant/templates/variant/utils.html,sha256=lF-w3400plEn0gVpHG-9k7N9L_p1U-PFGitcT_YlZw8,25414
 scout/server/blueprints/variant/templates/variant/variant.html,sha256=JA0jI1ITvKamJY88U6-uBXYrHRZa3H2oyBUROtX9TKw,17874
-scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=KAdrLo8UTxO1Nr5ggfdn663E7xMq1rK0A2PrKXCJGjM,21049
+scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=FeuANKP5gL9SWwYnC-4-dXyZOgy0Nq6FXAjED3nuqjI,21097
 scout/server/blueprints/variants/__init__.py,sha256=W1KCz9kEbVlNO0o3NvLitYLQoP_3JSJ5KSjhpcjlUBQ,55
 scout/server/blueprints/variants/controllers.py,sha256=ILJt2Jl9ShkePgZI1Grff-_gcxlZFzQ8zoQ86iZPxOI,74205
 scout/server/blueprints/variants/forms.py,sha256=nxsZGHOr2M9GyQob8_8CK5qFgPgxZ3wBdFT69PkVVJc,11447
@@ -629,12 +629,12 @@ scout/server/blueprints/variants/utils.py,sha256=ifFBoyigx0A5KPE4iz9NSpyuUeF1bEl
 scout/server/blueprints/variants/views.py,sha256=skUGpZyRDzW4BEDIqWKajHBLF3qBUSP-UYSZYxbv3l8,28895
 scout/server/blueprints/variants/static/form_scripts.js,sha256=o3GCboaesA9Sm1HgejS_yQwt0I-NTkvcl56jiBdLqZs,8319
 scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html,sha256=QlGmUEdUQ7gCq7tMMUFAlGqqC9jFB78Q0h6tSp3QUas,7271
-scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=LnybOzNu4RkbighdIcV6okJwQWiO5ixOhTev_-QaQII,9611
+scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=nqJ1q23arq4yJokMJpsyf8-ayzZkD2zgwH7j-Y9bpfE,9688
 scout/server/blueprints/variants/templates/variants/components.html,sha256=PGtcPGVbd3gcdG_6ozA66LDo3ZJ8VoehaDMUZjwyA5Q,17431
 scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
 scout/server/blueprints/variants/templates/variants/indicators.html,sha256=5aSXytiWvaU87cqcR9GcB7U5jP8t-PVnor8FpKLl_k0,4847
 scout/server/blueprints/variants/templates/variants/mei-variants.html,sha256=2Tb0vfzM--kJa5mVbT7L32h4E8nKYRSb245g6O5JIUU,5860
-scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=bjjeyoEO1aScqIDLtCh3xexZfvf1906yusPGJTyeNLU,10644
+scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=n424D8xV76bCKDSFzzIsWfFAoU2dAYE-PPZyTtQeMdM,10924
 scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=fRDnB9wXago2OB2mthp0rD_Es4kxnj9YKRlOKCGVW3s,6407
 scout/server/blueprints/variants/templates/variants/utils.html,sha256=MNDc2JwumU9ukISizSAraxIY06rHXR2Ze32RNnDEBI4,50042
 scout/server/blueprints/variants/templates/variants/variants.html,sha256=KnCcsA1VaRdsbRCCw9Rg0TJTUvq03X9S24QgCqVToUk,9328
@@ -643,7 +643,7 @@ scout/server/extensions/beacon_extension.py,sha256=YDXQQl5kFcsA4OFHDMVurIKLw_3Gl
 scout/server/extensions/bionano_extension.py,sha256=0rWPLMSCRP8uK4_yozo6HTPR6V-oITF492vrGA3wSj0,7129
 scout/server/extensions/chanjo2_extension.py,sha256=ZKCIv8muR9bzCV0_rM277ePvxdWC3wuPIwY4VppH7lY,1530
 scout/server/extensions/chanjo_extension.py,sha256=JtKAgT6ASnCcKYbgKMWGwflISLzHuyDKpcyljzCV_aY,4045
-scout/server/extensions/clinvar_extension.py,sha256=w1fOzGKRhxmIlZkAqqd_rdGD49qE_nn-tgZsEMTrZNw,3870
+scout/server/extensions/clinvar_extension.py,sha256=X3LsJZ4XL8hr8FyqhW1Zn4OmXEG0_edCZRHtWhTuLVk,6332
 scout/server/extensions/gens_extension.py,sha256=KOF-pP4DiRVQkygthAq6XCHnZwAGHo1kjIxmvW7ItYI,1003
 scout/server/extensions/ldap_extension.py,sha256=nVgJ6YhSyvpg8J4bSYzJwoEvKhP0faWazt3Xk0ixE2U,2746
 scout/server/extensions/loqus_extension.py,sha256=uiqUXQ7Q7DCj6C20TKgL8yLu9DXov95vrJfhq0tvbTM,12602
@@ -666,7 +666,7 @@ scout/server/translations/sv/LC_MESSAGES/messages.po,sha256=Wp7Mx4LoiFNtzsV1tpAo
 scout/update/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scout/update/panel.py,sha256=4z-vQ7GVIJXtlIub9pubFcQ-I9mLX5fRXKNPBdpuhJw,1649
 scout/utils/__init__.py,sha256=DHCMH05dxkyD7m9QSs0WXsQQPgVRFQ9XvyNeNpHjjvg,74
-scout/utils/acmg.py,sha256=IkWWmHxc0YvoSurzXimKkH_Vf8C0bncywVUVu8m-YlY,11539
+scout/utils/acmg.py,sha256=b2WLE2-s0pijXWBdwfrGE3SFogYMDoeVVKQd9d7pBQA,11576
 scout/utils/algorithms.py,sha256=w--NauXbQohZis7obr39a8bS57C4NRelYXn79V7m1dU,800
 scout/utils/ccv.py,sha256=WhVyIzNW0ttfT4ZegOPGFR1xqqjRFNgnJSY7DPfXGNQ,5605
 scout/utils/convert.py,sha256=asrsis3zkt9jXzseRmCqSa4_t1UT73HPPQRW-DKDdqE,1794
@@ -683,8 +683,8 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=lgPumNI_EikBZR1m9ztZI_mZAfV29y1KGoiBv9kejzQ,12797
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.95.0.dist-info/METADATA,sha256=IbeBpNPEf-Th3spPxj1Jjt1KXYuLBgWig8t7CWb6-dY,15642
-scout_browser-4.95.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scout_browser-4.95.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.95.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.95.0.dist-info/RECORD,,
+scout_browser-4.96.0.dist-info/METADATA,sha256=Jipku15t2ek-OH7TQfUdgEIM1yieNz1hpRoOrcBkr-U,15642
+scout_browser-4.96.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scout_browser-4.96.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.96.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.96.0.dist-info/RECORD,,