scout-browser 4.95.0__tar.gz → 4.96.0__tar.gz

{scout_browser-4.95.0 → scout_browser-4.96.0}/CHANGELOG.md

@@ -4,6 +4,27 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.96]
+### Added
+- Support case status assignment upon loading (by providing case status in the case config file)
+- Severity predictions on general case report for SNVs and cancer SNVs
+- Variant functional annotation on general case report for SNVs and cancer SNVs
+- Version of Scout used when the case was loaded is displayed on case page and general report
+### Removed
+- Discontinue ClinVar submissions via CSV files and support only submission via API: removed buttons for downloading ClinVar submission objects as CSV files
+### Changed
+- Display STR variant filter status on corresponding variantS page
+- Warning and reference to Biesecker et al when using PP1/BS4 and PP4 together in ACMG classifications
+- Warning to not use PP4 criterion together with PS2/PM6 in ACMG classifications with reference to the SVI Recommendation for _de novo_ Criteria (PS2 & PM6)
+- Button to directly remove accepted submissions from ClinVar
+- Upgraded libs in uv.lock file
+### Fixed
+- Release docs to include instructions for upgrading dependencies
+- Truncated long HGVS descriptions on cancer SNV and SNVs pages
+- Avoid recurrent error by removing variant ranking settings in unranked demo case
+- Actually re-raise exception after load aborts and has rolled back variant insertion
+
+
 ## [4.95]
 ### Added
 - CCV score / temperature on case reports

{scout_browser-4.95.0 → scout_browser-4.96.0}/PKG-INFO

@@ -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 → scout_browser-4.96.0}/RELEASE.md

@@ -10,6 +10,13 @@
 
    - in `scout/pyproject.toml`
 
+1. Upgrade dependencies that are not frozen to their latest compatible version e.g.
+   ```bash
+   uv lock --upgrade
+   git add uv.lock
+   git commit -m 'Upgrade dependencies'
+   ```
+
 1. Make sure CHANGELOG.md is up to date for the release
 
 1. Create a new blog post for the documentation

{scout_browser-4.95.0 → scout_browser-4.96.0}/docs/admin-guide/load-config.md

@@ -98,6 +98,7 @@ Below are available configuration parameters for a Scout case. Names marked with
     - **upd_sites_bed** _String_ Path to BED file to view alignments [Reference][upd].
     - **vcf2cytosure** _String_ Path to CGH file to allow download per individual. Such SV files can be visualized using standard arrayCGH analysis tools. See [vcf2cytosure](https://github.com/NBISweden/vcf2cytosure/blob/master/README.md).
 - **smn_tsv** _String_ Path to an SMN TSV file.
+- **status** _String_ Any of the following strings: 'prioritized', 'inactive', 'ignored', 'active', 'solved' or 'archived'.
 - **synopsis** _String_ Synopsis of case.
 - **sv_rank_model_version** _String_ Rank model that was used when scoring the variants.
 - **track** _String_ Type of track: {"rare", "cancer"}. Default: "rare".

{scout_browser-4.95.0 → scout_browser-4.96.0}/docs/admin-guide/loading-case.md

@@ -55,7 +55,7 @@ madeline: scout/demo/madeline.xml
 default_gene_panels: [panel1]
 gene_panels: [panel1]
 
-# meta data
+# metadata
 rank_model_version: '1.12'
 sv_rank_model_version: '1.5'
 rank_score_threshold: -100

{scout_browser-4.95.0 → scout_browser-4.96.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "scout-browser"
-version = "4.95.0"
+version = "4.96.0"
 description = "Clinical DNA variant visualizer and browser"
 authors = [{name="Chiara Rasi", email="chiara.rasi@scilifelab.se"}, {name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Robin Andeer", email="robin.andeer@gmail.com"}, {name="Mans Magnuson", email="monsunas@gmail.com"}]
 license = {text = "MIT License"}

{scout_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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_browser-4.95.0 → scout_browser-4.96.0}/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,