scout-browser 4.95.0__py3-none-any.whl → 4.97.0__py3-none-any.whl

scout/server/blueprints/alignviewers/controllers.py

@@ -305,6 +305,7 @@ def set_sample_tracks(display_obj: dict, case_groups: list, chromosome: str):
 
     A missing file is indicated with the string "missing", and no track is made for such entries.
     """
+
     sample_tracks = []
 
     track_items = "mt_bams" if chromosome == "M" else "bam_files"
@@ -330,6 +331,7 @@ def set_sample_tracks(display_obj: dict, case_groups: list, chromosome: str):
                     "indexURL": case[track_index_items][count],
                     "format": case[track_items][count].split(".")[-1],  # "bam" or "cram"
                     "height": 700,
+                    "show_soft_clips": case["track_items_soft_clips_settings"][count],
                 }
             )
         display_obj["sample_tracks"] = sample_tracks

scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html

@@ -116,6 +116,9 @@
                         url: "{{ url_for('alignviewers.remote_static', file=track.url) }}",
                         indexURL: "{{ url_for('alignviewers.remote_static', file=track.indexURL) }}",
                         sourceType: "file",
+                        groupBy: "tag:HP",
+                        colorBy: "basemod2:m",
+                        showSoftClips: {{track.show_soft_clips | lower }},
                         format: "{{ track.format }}",
                         height: "{{track.height}}"
                       },

scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -1,5 +1,5 @@
 {% macro igv_script() %}
   <link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
   <!-- IGV JS-->
-  <script src="https://cdn.jsdelivr.net/npm/igv@3.1.0/dist/igv.min.js" integrity="sha512-GqDTDFFltqWxc3IeSMcVcPNenhJE/OZnaMk7hkTk/shtC5bejPWstJF5AY8TsVpJWfK2HOzXYKUk95fS51Warw==" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.2.0/dist/igv.min.js" integrity="sha512-MHnbGQeONlQXyEs6PgiW2bhwywJW5IwUnRKfQKrPaVSrzopctBTU1VtOiEXMf/ZPBk47eFimlVRxdff+sdsyAg==" crossorigin="anonymous"></script>
 {% endmacro %}

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)
 
@@ -1086,11 +1088,12 @@ def update_default_panels(store, current_user, institute_id, case_name, panel_id
     store.update_default_panels(institute_obj, case_obj, user_obj, link, panel_objs)
 
 
-def update_clinical_filter_hpo(store, current_user, institute_id, case_name, hpo_clinical_filter):
+def update_clinical_filter_hpo(store, current_user, institute_obj, case_obj, hpo_clinical_filter):
     """Update HPO clinical filter use for a case."""
-    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     user_obj = store.user(current_user.email)
-    link = url_for("cases.case", institute_id=institute_id, case_name=case_name)
+    link = url_for(
+        "cases.case", institute_id=institute_obj["_id"], case_name=case_obj["display_name"]
+    )
     store.update_clinical_filter_hpo(institute_obj, case_obj, user_obj, link, hpo_clinical_filter)
 
 
@@ -1491,3 +1494,22 @@ def add_link_for_disease(case_obj: dict):
         for diagnosis in case_diagnoses:
             #: Add link
             diagnosis.update({"disease_link": disease_link(disease_id=diagnosis["disease_id"])})
+
+
+def remove_dynamic_genes(store: dict, case_obj: dict, institute_obj: dict, request_form: dict):
+    """Remove one or more genes from the dynamic gene list. If there are no more
+    genes on the list, also stop using the HPO panel for clinical filter."""
+    case_dynamic_genes = [dyn_gene["hgnc_id"] for dyn_gene in case_obj.get("dynamic_gene_list")]
+    genes_to_remove = [int(gene_id) for gene_id in request_form.getlist("dynamicGene")]
+    hgnc_ids = list(set(case_dynamic_genes) - set(genes_to_remove))
+    store.update_dynamic_gene_list(
+        case_obj,
+        hgnc_ids=hgnc_ids,
+        delete_only=True,
+    )
+    if not hgnc_ids:
+        hpo_clinical_filter = False
+        case_obj["hpo_clinical_filter"] = hpo_clinical_filter
+        update_clinical_filter_hpo(
+            store, current_user, institute_obj, case_obj, hpo_clinical_filter
+        )

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

@@ -295,6 +295,9 @@
         {% if case.vcf_files.vcf_fusion_research %}
           <a class="btn btn-dark btn-sm text-white" href="{{ url_for('variants.fusion_variants', institute_id=institute._id, case_name=case.display_name, variant_type='research') }}">Research fusion variants</a>
         {% endif %}
+        {% if case.omics_files.fraser_research or case.omics_files.outrider_research %}
+          <a class="btn btn-dark btn-sm text-white" href="{{ url_for('omics_variants.outliers', institute_id=institute._id, case_name=case.display_name, variant_type='research') }}">Research WTS variants</a>
+        {% endif %}
       </div>
     </div>
   </div>

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/chanjo2_form.html

@@ -1,4 +1,4 @@
-{% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text) %}
+{% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text, link_class = "link-primary") %}
 
   {% set form_name = "chanjo2_"+panel_name+"_"+report_type %}
   {% set form_action = config.CHANJO2_URL+"/"+report_type %}
@@ -40,7 +40,7 @@
     {% if panel_name == "HPO Panel" %}
       <button type="submit" class="btn btn-secondary btn-sm text-white"> Coverage {{report_type}} (Chanjo2) </button>
     {% else %}
-      <a class="link-primary" onclick="this.closest('form').submit();return false;">{{link_text}}</a>
+      <a class="{{ link_class }}" onclick="this.closest('form').submit();return false;">{{link_text}}</a>
     {% endif %}
   </form>
 

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/cases/templates/cases/gene_panel.html

@@ -79,8 +79,7 @@
           <span class="mr-3" data-bs-toggle="tooltip" data-bs-placement="bottom" title="{{ case.dynamic_panel_phenotypes|join(', ') }}">
               {{ case.dynamic_panel_phenotypes|length }} phenotypes
           </span>
-        {% endif %}
-        )
+        {% endif %})
         {% if case.dynamic_gene_list_edited %} <span class="text-danger ml-3"> (edited) </span> {% endif %}
       </h6>
     </div>
@@ -119,6 +118,7 @@
       </div>
 
       <div>
+        {% if case.track == 'rare' %}
         <div class="row"> <!-- Show variants in dynamic gene list -->
           <form action="{{ url_for('cases.update_clinical_filter_hpo', institute_id=institute._id, case_name=case.display_name)+'#hpo_clinical_filter' }}" method="POST">
             <div class="form-check form-switch">
@@ -128,6 +128,7 @@
             </div>
           </form>
         </div>
+        {% endif %}
         <div class="row mt-3">
           <div class="btn-group btn-group-sm">
           {% if case.track == 'cancer' %}
@@ -180,7 +181,12 @@
                Clinical HPO MEIs
              </a>
             {% endif %}
-           {% endif %}
+            {% if case.has_outliers %}
+              <a class="btn btn-secondary btn-sm text-white" href="{{ url_for('omics_variants.outliers',
+                institute_id=institute._id, case_name=case.display_name, variant_type='clinical',
+                gene_panels=['hpo']) }}" target="_blank" rel="noopener">Clinical HPO WTS</a>
+            {% endif %}
+          {% endif %}
           </div>
         </div>
         {% if case.chanjo_coverage or case.chanjo2_coverage and case.dynamic_gene_list|length > 0 %}

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

@@ -17,7 +17,9 @@
              title="Measure of the tumor mutational burden">TMB</th>
             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
              title="Measure of microsatellite instability">MSI</th>
-            <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
+             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
+             title="Homologous Recombination Deficiency">HRD</th>
+             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
              title="Measure of tumor purity">Tumor Purity</th>
             <th data-bs-toggle='tooltip' data-bs-container='body' class="col-xs-1"
              title="Downloadable CytoSure file">CGH</th>
@@ -41,6 +43,7 @@
               <td>{{ ind.analysis_type|upper }}</td>
               <td>{{ ind.tmb or 'N/A' }}</td>
               <td>{{ ind.msi or 'N/A' }}</td>
+              <td>{{ ind.hrd or 'N/A' }}</td>
               {% if ind.phenotype_human == "tumor" %}
                 <td>
                   <div class="d-flex align-items-center">

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

@@ -291,29 +291,33 @@
 
 {% macro pretty_variant(variant) %}
 
-  {% if variant.category in "str" %}
-        {{ variant.str_repid }} {{ variant.alternative | replace("<", " ") | replace(">", "")}}
-
-  {% elif variant.category in ("snv", "cancer") %}
-    {% set display_genes = [] %}
-    {% for gene in variant.genes %}
-      {% if gene.hgvs_identifier and gene.hgnc_symbol  %}
-        {{ "" if display_genes.append(gene.hgnc_symbol + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
-      {% elif gene.hgnc_symbol %}
-        {{ "" if display_genes.append(gene.hgnc_symbol) }}
-      {% elif gene.hgvs_identifier and gene.hgnc_id %}
-        {{ "" if display_genes.append( gene.hgnc_id|string + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
+  {% if variant.category %}
+    {% if variant.category in "str" %}
+      {{ variant.str_repid }} {{ variant.alternative | replace("<", " ") | replace(">", "")}}
+
+    {% elif variant.category in ("snv", "cancer") %}
+      {% set display_genes = [] %}
+      {% for gene in variant.genes %}
+        {% if gene.hgvs_identifier and gene.hgnc_symbol  %}
+          {{ "" if display_genes.append(gene.hgnc_symbol + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
+        {% elif gene.hgnc_symbol %}
+          {{ "" if display_genes.append(gene.hgnc_symbol) }}
+        {% elif gene.hgvs_identifier and gene.hgnc_id %}
+          {{ "" if display_genes.append( gene.hgnc_id|string + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
+        {% endif %}
+      {% endfor %}
+
+      {% if not display_genes %}
+          {{ "" if display_genes.append( variant.simple_id|truncate(40,True) ) }}
       {% endif %}
-    {% endfor %}
 
-    {% if not display_genes %}
-        {{ "" if display_genes.append( variant.simple_id|truncate(40,True) ) }}
-    {% endif %}
+      {{ display_genes|join(", ") }}
 
-    {{ display_genes|join(", ") }}
-  {% else %} <!-- structural variants -->
-    {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
+    {% else %} <!-- structural variants -->
+      {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
+    {% endif %}
   {% endif %}
+
 {% endmacro %}
 
 {% macro pretty_link_variant(variant, case) %}

scout/server/blueprints/cases/views.py

@@ -486,6 +486,7 @@ def phenotypes_actions(institute_id, case_name):
     hpo_ids = request.form.getlist("hpo_id")
     user_obj = store.user(current_user.email)
 
+    ### match action for 3.10
     if action == "PHENOMIZER":
         diseases = controllers.phenomizer_diseases(hpo_ids, case_obj)
         if diseases:
@@ -511,14 +512,8 @@ def phenotypes_actions(institute_id, case_name):
             )
         store.update_dynamic_gene_list(case_obj, hgnc_ids=list(hgnc_ids), add_only=True)
 
-    if action == "REMOVEGENES":  # Remove one or more genes from the dynamic gene list
-        case_dynamic_genes = [dyn_gene["hgnc_id"] for dyn_gene in case_obj.get("dynamic_gene_list")]
-        genes_to_remove = [int(gene_id) for gene_id in request.form.getlist("dynamicGene")]
-        store.update_dynamic_gene_list(
-            case_obj,
-            hgnc_ids=list(set(case_dynamic_genes) - set(genes_to_remove)),
-            delete_only=True,
-        )
+    if action == "REMOVEGENES":
+        controllers.remove_dynamic_genes(store, case_obj, institute_obj, request.form)
 
     if action == "GENES":
         hgnc_symbols = parse_raw_gene_symbols(request.form.getlist("genes"))
@@ -928,9 +923,10 @@ def default_panels(institute_id, case_name):
 @cases_bp.route("/<institute_id>/<case_name>/update-clinical-filter-hpo", methods=["POST"])
 def update_clinical_filter_hpo(institute_id, case_name):
     """Update default panels for a case."""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     hpo_clinical_filter = request.form.get("hpo_clinical_filter")
     controllers.update_clinical_filter_hpo(
-        store, current_user, institute_id, case_name, hpo_clinical_filter
+        store, current_user, institute_obj, case_obj, hpo_clinical_filter
     )
     return redirect(request.referrer)
 

scout/server/blueprints/clinvar/controllers.py

@@ -2,7 +2,7 @@ import csv
 import logging
 from datetime import datetime
 from tempfile import NamedTemporaryFile
-from typing import List, Optional
+from typing import List, Optional, Tuple
 
 from flask import flash
 from flask_login import current_user
@@ -17,6 +17,7 @@ from scout.constants.clinvar import (
 )
 from scout.constants.variant_tags import MANUAL_RANK_OPTIONS
 from scout.models.clinvar import clinvar_variant
+from scout.server.blueprints.variant.utils import add_gene_info
 from scout.server.extensions import clinvar_api, store
 from scout.utils.hgvs import validate_hgvs
 from scout.utils.scout_requests import fetch_refseq_version
@@ -26,18 +27,15 @@ from .form import CaseDataForm, SNVariantForm, SVariantForm
 LOG = logging.getLogger(__name__)
 
 
-def _get_var_tx_hgvs(case_obj, variant_obj):
-    """Retrieve all transcripts / hgvs for a given variant
-    Args:
-        case_obj(scout.models.Case)
-        variant_obj(scout.models.Variant)
-    Returns:
-        list of tuples. example: [("NM_002340.6:c.1840C>T", "NM_002340.6:c.1840C>T (validated)" ), ("NM_001145436.2:c.1840C>T", "NM_001145436.2:c.1840C>T"), .. ]
-    """
+def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]:
+    """Retrieve all transcripts / hgvs for a given variant."""
+
     build = str(case_obj.get("genome_build", "37"))
     tx_hgvs_list = [("", "Do not specify")]
+    add_gene_info(store, variant_obj, genome_build=build)
     for gene in variant_obj.get("genes", []):
         for tx in gene.get("transcripts", []):
+            mane_select = tx.get("mane_select_transcript")
             if all([tx.get("refseq_id"), tx.get("coding_sequence_name")]):
                 for refseq in tx.get("refseq_identifiers"):
                     refseq_version = fetch_refseq_version(refseq)  # adds version to a refseq ID
@@ -48,10 +46,12 @@ def _get_var_tx_hgvs(case_obj, variant_obj):
 
                     label = hgvs_simple
                     if validated:
-                        label += " (validated)"
+                        label += "_validated_"
 
-                    tx_hgvs_list.append((hgvs_simple, label))
+                    if mane_select and mane_select == refseq_version:
+                        label += "_mane-select_"
 
+                    tx_hgvs_list.append((hgvs_simple, label))
     return tx_hgvs_list
 
 
@@ -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/templates/clinvar/multistep_add_variant.html

@@ -110,26 +110,34 @@
                     <table style="width:100%; table-layout: auto; border-collapse: collapse;">
                       <caption></caption>
                       <tr><th></th></tr>
-                    {% set ns = namespace(label='', validated=false) %}
                     {% for item_row in variant_data.var_form.tx_hgvs | batch(3) %}
                       <tr>
                       {% for item in item_row %}
-                        <td style="width: 3%; text-align: right; vertical-align: baseline;">{{item}}</td>
+                        {% set ns = namespace(label='', validated=false, mane_select=false) %}
 
-                        {% if "(validated)" in item.label.text %}
+                        {% if "_validated_" in item.label.text %}
                           {% set ns.validated = true %}
-                        {% else %}
-                          {% set ns.validated = false %}
                         {% endif %}
-                        {% set ns.label = item.label.text | replace(" (validated)", "") %}
+                        {% if "_mane-select_" in item.label.text %}
+                          {% set ns.mane_select = true %}
+                        {% endif %}
+                        {% set ns.label = item.label.text | replace("_validated_", "") | replace("_mane-select_", "")  %}
+
+                        <td style="width: 3%; text-align: right; vertical-align: baseline;">
+                          <input type="radio" name="tx_hgvs" value="{{ ns.label }}"
+                            {% if ns.mane_select %}checked{% endif %}>
+                        </td>
 
                         <td style="width: 30%; text-align: left; ">
                           <p class="text-dark"
-                          {% if ns.label|length > 25 %}
+                          {% if ns.label|length > 50 %}
                            data-bs-toggle="tooltip" title="{{ns.label}}">{{ ns.label|truncate(25,true,'..') }}
                           {% else %}
                             >{{ ns.label }}
                           {% endif %}
+                          {% if ns.mane_select %}
+                            <span class='badge bg-dark'>MANE SELECT</span>
+                          {% endif %}
                           {% if ns.validated %}
                             <em class="fa fa-check text-success" aria-hidden="true" data-bs-toggle="tooltip" title="Verified by VariantValidator"></em>
                           {% endif %}

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/institutes/controllers.py

@@ -20,7 +20,10 @@ from scout.constants import (
     SEX_MAP,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
-from scout.server.blueprints.variant.utils import predictions, update_representative_gene
+from scout.server.blueprints.variant.utils import (
+    predictions,
+    update_representative_gene,
+)
 from scout.server.extensions import beacon, store
 from scout.server.utils import institute_and_case, user_institutes
 
@@ -328,6 +331,21 @@ def get_clinvar_submitters(form: MultiDict) -> Optional[List[str]]:
     return clinvar_submitters
 
 
+def get_soft_filters(form: MultiDict) -> Optional[list]:
+    """
+    Return a list with custom soft filters or None.
+    This is not available on the form for unprivileged users, only admin.
+    """
+    if current_user.is_admin is False:
+        return None
+
+    soft_filters = []
+    for filter in form.getlist("soft_filters"):
+        soft_filters.append(filter)
+
+    return soft_filters
+
+
 def get_loqusdb_ids(form: MultiDict) -> Optional[List[str]]:
     """
     Return loqusdb ids from the form multiselect.
@@ -390,6 +408,7 @@ def update_institute_settings(store: MongoAdapter, institute_obj: Dict, form: Mu
         check_show_all_vars=form.get("check_show_all_vars"),
         clinvar_key=form.get("clinvar_key"),
         clinvar_submitters=get_clinvar_submitters(form),
+        soft_filters=get_soft_filters(form),
     )
     return updated_institute