scout-browser 4.81__py3-none-any.whl → 4.82.1__py3-none-any.whl

scout/server/blueprints/cases/controllers.py

@@ -4,7 +4,7 @@ import itertools
 import json
 import logging
 import os
-from typing import Dict, List, Optional, Set
+from typing import Dict, List, Set
 
 import query_phenomizer
 import requests
@@ -85,61 +85,6 @@ def phenomizer_diseases(hpo_ids, case_obj, p_value_treshold=1):
         flash("Could not establish a conection to Phenomizer", "danger")
 
 
-def chanjo2_coverage_report_contents(
-    institute_obj: dict, case_obj: dict, panel_name: str, panel_id: Optional[str], report_type: str
-) -> Optional[str]:
-    """Retrieve the HTML contents of the Chanjo2 coverage report/overview for a case."""
-
-    if panel_id:
-        hgnc_gene_ids: List[int] = store.panel_to_genes(panel_id=panel_id, gene_format="hgnc_id")
-    elif panel_name == "HPO Panel":
-        hgnc_gene_ids: List[int] = [
-            gene["hgnc_id"] for gene in case_obj.get("dynamic_gene_list", [])
-        ]
-    else:
-        hgnc_gene_ids: List[int] = _get_default_panel_genes(store, case_obj)
-
-    if not hgnc_gene_ids:
-        flash("Case should have at least one default gene panel containing genes", "warning")
-        return
-
-    query_samples: List[dict] = []
-    analysis_types: List[str] = []
-
-    for ind in case_obj.get("individuals", []):
-        if not ind.get("d4_file"):
-            continue
-        query_samples.append(
-            {
-                "name": ind.get("display_name"),
-                "coverage_file_path": ind.get("d4_file"),
-                "case_name": case_obj["display_name"],
-                "analysis_date": case_obj["analysis_date"].isoformat(),
-            }
-        )
-        analysis_types.append(ind.get("analysis_type"))
-
-    interval_type = "genes"
-    if "wes" in analysis_types:
-        interval_type = "transcripts"
-    elif "wts" in analysis_types:
-        interval_type = "exons"
-
-    report_query: dict = {
-        "build": "GRCh38" if "38" in case_obj.get("genome_build", "37") else "GRCh37",
-        "default_level": institute_obj.get("coverage_cutoff"),
-        "interval_type": interval_type,
-        "panel_name": panel_name,
-        "case_display_name": case_obj["display_name"],
-        "hgnc_gene_ids": hgnc_gene_ids,
-        "samples": query_samples,
-    }
-
-    report_url: str = "/".join([current_app.config.get("CHANJO2_URL"), report_type])
-    response = requests.post(report_url, json=report_query)
-    return response.text
-
-
 def coverage_report_contents(base_url, institute_obj, case_obj):
     """Capture the contents of a case coverage report (chanjo-report), to be displayed in the general case report
 
@@ -389,7 +334,7 @@ def case(store, institute_obj, case_obj):
     clinvar_variants_not_in_suspects = [
         store.variant(variant_id) or variant_id
         for variant_id in case_obj["clinvar_variants"]
-        if variant_id not in [entry.get("_id") for entry in suspects]
+        if variant_id not in case_obj.get("suspects", [])
     ]
 
     case_obj["clinvar_variants_not_in_suspects"] = clinvar_variants_not_in_suspects

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

@@ -1,5 +1,6 @@
 {% from "cases/utils.html" import variant_transcripts %}
 {% from "utils.html" import comments_table, variant_related_comments_table %}
+{% from "variants/components.html" import fusion_variants_header, default_fusion_variant_cells %}
 
 {% extends "report_base.html" %}
 
@@ -174,27 +175,30 @@
 	          {% endif %}
 	        </td>
 	        <td class="ms-3 d-flex align-items-start flex-column" style="border-bottom:none;">
-            <strong>Associated phenotypes:</strong><br>
-  	          {% if case.phenotype_terms %}
-  	            <ul>
-  	              {% for pheno in case.phenotype_terms %}
-  	                <li>
-  	                {{pheno.feature}} - (<a style="text-decoration:none;" href="https://hpo.jax.org/app/browse/term/{{pheno.phenotype_id}}" target="_blank">{{pheno.phenotype_id}})</a>
-                    {% for feature_ind in pheno.individuals %} <!-- display eventual individual-level HPO terms -->
-                      {% for case_ind in case.individuals %}
-                        {% if feature_ind.individual_name == case_ind.display_name %}
-                          <span class="ms-1 {% if case_ind.phenotype == 2 %} text-danger {% endif %}">{{case_ind.display_name}}</span>
-                        {% endif %}
+              <strong>Associated phenotypes:</strong>
+  	            {% if case.phenotype_terms %}
+  	              <ul>
+  	                {% for pheno in case.phenotype_terms %}
+  	                  <li>
+  	                  {{pheno.feature}} - (<a style="text-decoration:none;" href="https://hpo.jax.org/app/browse/term/{{pheno.phenotype_id}}" target="_blank">{{pheno.phenotype_id}})</a>
+                      {% for feature_ind in pheno.individuals %} <!-- display eventual individual-level HPO terms -->
+                        {% for case_ind in case.individuals %}
+                          {% if feature_ind.individual_name == case_ind.display_name %}
+                            <span class="ms-1 {% if case_ind.phenotype == 2 %} text-danger {% endif %}">{{case_ind.display_name}}</span>
+                          {% endif %}
+                        {% endfor %}
                       {% endfor %}
-                    {% endfor %}
-  	                </li>
-  	              {% endfor %}
-  	            </ul>
-  	          {% else %}
-  	            No associated HPO terms.
-  	          {% endif %}
-              <br>
-              <strong>Associated diagnoses:</strong><br>
+  	                  </li>
+  	                {% endfor %}
+  	              </ul>
+  	            {% else %}
+                  <ul style="list-style-type: none; padding-left:0;">
+                    <li>
+  	                  No associated HPO terms.
+                    </li>
+                  </ul>
+  	            {% endif %}
+              <strong>Associated diagnoses:</strong>
               {% if case.diagnosis_phenotypes %}
                 <ul>
                   {% for dia in case.diagnosis_phenotypes %}
@@ -211,7 +215,11 @@
                   {% endfor %}
                 </ul>
               {% else %}
-                No associated diagnoses.
+                <ul style="list-style-type: none;padding-left:0;">
+                  <li>
+                    No associated diagnoses.
+                  </li>
+                </ul>
               {% endif %}
 	        </td>
 	      </tr>
@@ -354,10 +362,10 @@
           {% do printed_vars.append(pinned['_id']) %}
           {% do pinned_not_causative_variants.append(pinned['_id']) %}
           {{ variant_content(pinned, loop.index) }}
+          <br>
         {% else %}
           {% do duplicated_variants.append(pinned['_id']) %}
         {% endif %}
-        <br>
       {% endfor %}
     {% else %}
       No pinned variants available for this case
@@ -381,10 +389,10 @@
         {% if variant['_id'] not in printed_vars %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
+          <br>
         {% else %}
           {% do duplicated_variants.append(variant['_id']) %}
         {% endif %}
-        <br>
       {% endfor %}
     {% else %}
       No ACMG-classified variants available for this case
@@ -408,10 +416,10 @@
         {% if variant['_id'] not in printed_vars %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
+          <br>
         {% else %}
           {% do duplicated_variants.append(variant['_id']) %}
         {% endif %}
-        <br>
       {% endfor %}
     {% endif %}
     {% if variants.tier_detailed %}
@@ -419,10 +427,10 @@
         {% if variant['_id'] not in printed_vars %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
+          <br>
         {% else %}
           {% do duplicated_variants.append(variant['_id']) %}
         {% endif %}
-        <br>
       {% endfor %}
     {% endif %}
     {% if not (variants.tagged_detailed or variants.tier_detailed) %}
@@ -435,6 +443,18 @@
 </div>
 {% endmacro %}
 
+{% macro overlapping_panels(variant) %}
+{% if variant.case_panels %}
+  {% if variant.case_panels|length <= 3 %}
+    {% for panel in variant.case_panels %}
+      <a style="text-decoration:none;" href="{{ url_for('panels.panel', panel_id=panel_id) }}" target="_blank" rel="noopener" class="badge bg-secondary">{{ panel.panel_name }}</a><br>
+    {% endfor %}
+  {% else %}
+    {{ variant.case_panels|length }} panels
+  {% endif %}
+{% endif %}
+{% endmacro %}
+
 {% macro variant_content(variant, index) %}
   {% if variant.category == 'snv' %}
     {{ sn_variant_content(variant, index) }}
@@ -467,10 +487,10 @@
           {% else %}
             {{ sv_variant_content(variant, loop.index) }}
           {% endif %}
+          <br>
         {% else %}
           {% do duplicated_variants.append(variant['_id']) %}
         {% endif %}
-        <br>
       {% endfor %}
     {% else %}
       No commented variants for this case
@@ -536,22 +556,14 @@
               {% endif %}
             </td>
             <td>
-              {% if variant.panels%}
-                {% if variant.panels|length <= 3 %}
-                  {% for panel_id in variant.panels %}
-                   <a style="text-decoration:none;" href="{{ url_for('panels.panel', panel_id=panel_id) }}" rel="noopener" target="_blank" class="badge bg-secondary">{{ panel_id }}</a><br>
-                  {% endfor %}
-                {% else %}
-                  {{ variant.panels|length }} panels
-                {% endif %}
-              {% endif %}
+              {{ overlapping_panels(variant) }}
             </td>
           </tr>
         </tbody>
       </table>
       <table class="table table-sm">
         <tr>
-          <td style="width=45%">
+          <td style="width:60%;">
             {{ genotype_table(variant) }}
           </td>
           <td style="width:3%"></td>
@@ -627,8 +639,8 @@
       <table id="panel-table" class="table table-sm" style="background-color: transparent">
         <thead>
           <tr>
-            <th>Scout Rank</th>
-            <th>Scout score</th>
+            <th>Rank</th>
+            <th>Score</th>
             <th>Manual rank</th>
             <th>CADD score</th>
             {% if not cancer %}
@@ -763,8 +775,8 @@
           </thead>
           {% for variant in variants.dismissed_detailed|sort(attribute='variant_rank') %}
             <tr{% if loop.index0 % 2 %} class="light-grey" {% endif %}>
-              <td width="5%">#{{loop.index}}</td>
-              <td width="25%">
+              <td style="width:5%,">#{{loop.index}}</td>
+              <td style="width:25%;">
                 {% if variant.category == 'snv' %}
                   <a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" target="_blank"><strong>{{variant.display_name[:30]}}</strong></a>
                 {% elif variant.category == 'cancer' %}
@@ -775,8 +787,8 @@
                   <a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" target="_blank"><strong>rep. {{variant.str_repid}}</strong></a>
                 {% endif %}
               </td>
-              <td width="5%">{{variant.category|upper}}</td>
-              <td width="15%">
+              <td style="width:5%;">{{variant.category|upper}}</td>
+              <td style="width:15%;"
                 {{ dismissed_gene_list(variant) }}
               </td>
 
@@ -957,15 +969,7 @@
             <td>-</td>
           {% endif %}
           <td>
-            {% if variant.panels %}
-              {% if variant.panels|length <= 3 %}
-                {% for panel_id in variant.panels %}
-                  <a style="text-decoration:none;" href="{{ url_for('panels.panel', panel_id=panel_id) }}" rel="noopener" target="_blank" class="badge bg-secondary">{{ panel_id }}</a><br>
-                {% endfor %}
-              {% else %}
-                {{ variant.panels|length }} panels
-              {% endif %}
-            {% endif %}
+            {{ overlapping_panels(variant) }}
           </td>
           <td>
             {% if variant.callers %}
@@ -981,7 +985,7 @@
     </table>
     <table id="panel-table" class="table table-sm" style="background-color: transparent">
       <tr>
-        <td>
+        <td style="width:60%;">
           {{genotype_table(variant)}}
         </td>
         <td style="width:3%"></td>
@@ -1008,11 +1012,30 @@
         </td>
       </tr>
     </table>
+    {% if variant.category == "fusion" %}
+    <table id="panel-table" class="table table-sm" style="background-color: transparent">
+      {{ fusion_variants_header() }}
+      <tbody>
+        <tr>
+          <td class="text-center">{{variant.variant_rank}}</td>
+          <td>
+            {% if variant.cancer_tier %}
+              <span class="badge rounded-pill bg-secondary" title="Tier">{{ cancer_tier_options[variant.cancer_tier]['label'] }}</span>
+            {% endif %}
+            {% if variant.acmg_classification %}
+              <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['code'] }}</span>
+            {% endif %}
+          </td>
+          {{ default_fusion_variant_cells(institute, case, variant) }}
+        </tr>
+      </tbody>
+    </table>
+    {% else %}
     <table id="panel-table" class="table table-sm" style="background-color: transparent">
       <thead>
         <tr>
-          <th>Scout Rank</th>
-          <th>Scout score</th>
+          <th>Rank</th>
+          <th>Score</th>
           <th>Manual rank</th>
           {% if not cancer %}
             <th>Inheritance models</th>
@@ -1058,6 +1081,7 @@
         </tr>
       </tbody>
     </table>
+    {% endif %}
     <table id="panel-table" class="table table-sm" style="background-color: transparent">
       {% if variant.genes and variant.genes|length <= 3 %}
         <thead>
@@ -1145,7 +1169,7 @@
           <tr class="bg-warning">
         {% endif %}
           <td><span class="badge bg-info">{{variant.category | upper}}</span></td>
-          <td>{{ variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "") }}</td>
+          <td>{{ variant.str_mc }}</td>
           <td>{{ variant.str_ref }}</td>
           <td>
             {% if variant.chromosome == variant.end_chrom %}
@@ -1155,15 +1179,7 @@
             {% endif %}
           </td>
           <td>
-            {% if variant.panels %}
-              {% if variant.panels|length <= 3 %}
-                {% for panel_id in variant.panels %}
-                  <a style="text-decoration:none;" href="{{ url_for('panels.panel', panel_id=panel_id) }}" target="_blank" class="badge bg-secondary">{{ panel_id }}</a><br>
-                {% endfor %}
-              {% else %}
-                {{ variant.panels|length }} panels
-              {% endif %}
-            {% endif %}
+            {{ overlapping_panels(variant) }}
           </td>
         </tr>
       </tbody>
@@ -1214,8 +1230,8 @@
     <table id="panel-table" class="table table-sm table-bordered" style="background-color: transparent; margin-left:-.3rem;">
       <thead>
         <tr class="table-secondary">
-          <th>Scout Rank</th>
-          <th>Scout score</th>
+          <th>Rank</th>
+          <th>Score</th>
           <th>Manual rank</th>
         </tr>
       </thead>

scout/server/blueprints/cases/templates/cases/chanjo2_form.html

@@ -0,0 +1,47 @@
+{% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text) %}
+
+  {% set form_name = "chanjo2_"+panel_name+"_"+report_type %}
+  {% set form_action = config.CHANJO2_URL+"/"+report_type %}
+  {% set build = "GRCh38" if "38" in case_obj.get("genome_build", "37") else "GRCh37" %}
+  {% set default_level = institute_obj.coverage_cutoff %}
+  {% set interval_type = "genes" %} <!-- wgs analysis as default -->
+  {% set samples = [] %}
+  {% set analysis_types = [] %}
+
+  <!-- set sample dictionaries -->
+
+  {% for ind in case_obj.individuals %}
+    {% if ind.d4_file %}
+      {% set sample = {
+        "name" : ind.display_name,
+        "coverage_file_path" : ind.d4_file,
+        "case_name" : case_obj.display_name,
+        "analysis_date" : case_obj.analysis_date.strftime("%FT%T.%f")[:-3] ~ "Z" }
+      %}
+      {% do samples.append( sample ) %}
+      {% do analysis_types.append( ind.analysis_type ) %}
+    {% endif %}
+  {% endfor %}
+
+  {% if "wes" in analysis_types %}
+    {% set interval_type = "exons" %}
+  {% elif "wts" in analysis_types %}
+    {% set interval_type = "transcripts" %}
+  {% endif %}
+
+  <form name="{{form_name}}" method="post" action="{{form_action}}" target="_blank" rel="noopener">
+    <input type="hidden" id="build" name="build" value="{{build}}">
+    <input type="hidden" id="default_level" name="default_level" value="{{default_level}}">
+    <input type="hidden" id="interval_type" name="interval_type" value="{{interval_type}}">
+    <input type="hidden" id="panel_name" name="panel_name" value="{{panel_name}}">
+    <input type="hidden" id="case_display_name" name="case_display_name" value="{{case_obj.display_name}}">
+    <input type="hidden" id="hgnc_gene_ids" name="hgnc_gene_ids" value={{hgnc_ids}}>
+    <input type="hidden" id="samples" name="samples" value="{{samples|safe}}">
+    {% 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>
+    {% endif %}
+  </form>
+
+{% endmacro %}

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

@@ -1,3 +1,5 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
+
 {% macro action_bar(institute, case, causatives, collaborators, current_user, report_types, has_rna_tracks) %}
 <!-- Collapsible Sidebar, Based on https://www.codeply.com/go/LFd2SEMECH -->
   <div id="sidebar-container" class="sidebar-expanded d-none d-md-block"><!-- d-* hiddens the Sidebar in smaller devices. Its itens can be kept on the Navbar 'Menu' -->
@@ -84,13 +86,11 @@
     </div>
 
     <!-- If connected to a chanjo or chanjo2 instance, display coverage report -->
-    {% if case.chanjo2_coverage %}
+    {% if case.chanjo2_coverage and case.default_genes %}
       <div href="#" class="bg-dark list-group-item text-white">
         <div class="d-flex flex-row flex-fill bd-highlight">
           <span class="menu-collapsed">Coverage (chanjo2)</span>
-          <a href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id, case_name=case.display_name, panel_name=case.panel_names|join(', '), report_type='report') }}" target="_blank" rel="noopener">
-            <span class="fa fa-link"></span>
-          </a>
+          {{ chanjo2_report_form(institute, case, case.panel_names|join(', '), 'report', case.default_genes|join(','), "<span class='fa fa-link'></span>"|safe ) }} <!--chanjo2 report-->
         </div>
       </div>
     {% endif %}

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

@@ -1,3 +1,5 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
+
 {% macro genepanels_table(case, institute) %}
   <div class="card panel-default">
     <div class="panel-heading">Gene panels</div>
@@ -211,17 +213,8 @@
             {% endif %}
 
             {% if case.chanjo2_coverage %}
-              <a class="btn btn-secondary btn-sm text-white"
-                href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id,
-                                 case_name=case.display_name, panel_name='HPO Panel', report_type='report') }}" target="_blank" rel="noopener">
-                  Coverage report (Chanjo2)
-              </a>
-
-              <a class="btn btn-secondary btn-sm text-white"
-                href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id,
-                                 case_name=case.display_name, panel_name='HPO Panel', report_type='overview') }}" target="_blank" rel="noopener">
-                  Coverage overview (Chanjo2)
-              </a>
+              {{ chanjo2_report_form(institute, case, "HPO Panel", 'report', case.dynamic_gene_list|map(attribute='hgnc_id')|join(',')) }} <!--chanjo2 report-->
+              {{ chanjo2_report_form(institute, case, "HPO Panel", 'overview', case.dynamic_gene_list|map(attribute='hgnc_id')|join(',')) }} <!--chanjo2 genes overview -->
             {% endif %}
 
           </div>

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

@@ -268,7 +268,7 @@
 
         <!-- show transcript info only if it's canonical, disease-associated or primary (print max 5 primary transcripts) -->
       {% if transcript.refseq_identifiers and n_primary_txs.count <= 5 or transcript.is_canonical or transcript.is_disease_associated or transcript.is_primary %}
-        <li>{{transcript.transcript_id}}, RefSeq:[{{ transcript.refseq_identifiers|join(", ") or "-" }}], {{ (transcript.coding_sequence_name or '')|truncate(20, True) }},  {{ (transcript.protein_sequence_name or '')|url_decode|truncate(20, True) }}
+        <li class="mb-1">{{transcript.transcript_id}}, RefSeq:[{{ transcript.refseq_identifiers|join(", ") or "-" }}], {{ (transcript.coding_sequence_name or '')|truncate(20, True) }},  {{ (transcript.protein_sequence_name or '')|url_decode|truncate(20, True) }}
           {% if transcript.is_canonical %}
             <span class="badge rounded-pill bg-info text-white" title="canonical">C</span>
           {% endif %}
@@ -602,6 +602,8 @@
         <form id="clinvar_submit" class="d-flex justify-content-center" action="{{ url_for('clinvar.clinvar_add_variant', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
             {% if case.clinvar_variants and variant._id in case.clinvar_variants.keys() %}
                 (included in ClinVar submission)
+            {% elif variant.category in ('cancer', 'cancer_sv') %}
+                <button data-bs-toggle='tooltip' data-bs-placement="bottom" title="Submission of somatic variants from Scout is temporarily suspended. We are working to harmonize submissions with changes introduced by ClinVar for this variant category." disabled >Add to ClinVar submission</button>
             {% else %}
                 <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
             {% endif %}

scout/server/blueprints/cases/views.py

@@ -313,28 +313,6 @@ def pdf_case_report(institute_id, case_name):
     )
 
 
-@cases_bp.route("/<institute_id>/<case_name>/chanjo2_report/<report_type>", methods=["GET"])
-def chanjo2_coverage_report(institute_id: str, case_name: str, report_type: str):
-    """Return the HTML coverage report or coverage overview created by chanjo2."""
-
-    REPORT_TYPES = ["report", "overview"]
-    if report_type not in REPORT_TYPES:
-        flash(f"Wrong value for report_type parameter. Accepted values: {REPORT_TYPES}", "warning")
-        return redirect(request.referrer)
-
-    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
-    report_html_content: str = controllers.chanjo2_coverage_report_contents(
-        institute_obj=institute_obj,
-        case_obj=case_obj,
-        panel_name=request.args.get("panel_name"),
-        panel_id=request.args.get("panel_id"),
-        report_type=report_type,
-    )
-    if report_html_content is None:
-        return redirect(request.referrer)
-    return report_html_content
-
-
 @cases_bp.route("/<institute_id>/<case_name>/mt_report", methods=["GET"])
 def mt_report(institute_id, case_name):
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)

scout/server/blueprints/clinvar/controllers.py

@@ -107,7 +107,7 @@ def _get_snv_var_form(variant_obj, case_obj):
     var_form.variations_ids.data = var_ids.split(";")[0]
     var_form.chromosome.data = variant_obj.get("chromosome")
     var_form.start.data = variant_obj.get("position")
-    var_form.stop.data = variant_obj.get("position")
+    var_form.stop.data = variant_obj.get("end")
     return var_form
 
 
@@ -276,7 +276,7 @@ def parse_variant_form_fields(form):
         clinvar_var["variations_ids"] = form["dbsnp_id"]
 
     if clinvar_var.get("ref_seq") and clinvar_var.get("hgvs"):
-        # Variant is described by RefSeq and HGVS already, remove redundanti fields from submission
+        # Variant is described by RefSeq and HGVS already, remove redundant fields from submission
         for item in ["chromosome", "start", "stop", "ref", "alt"]:
             clinvar_var.pop(item)
 
@@ -437,7 +437,7 @@ def send_api_submission(institute_id, submission_id, key):
 
     clinvar_id = store.get_clinvar_id(
         submission_id
-    )  # This is the official ID associated with this submission in Clinvar ((ex: SUB999999)
+    )  # This is the official ID associated with this submission in Clinvar (ex: SUB999999)
 
     if clinvar_id:  # Check if submission object has already an associated ClinVar ID
         conversion_res["submissionName"] = clinvar_id

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

@@ -95,10 +95,16 @@
               </form>
               {% if subm_obj.status == 'open' and show_submit  %}
                 <form id="useApi_{{subm_obj._id}}" action="{{ url_for('clinvar.clinvar_update_submission', institute_id=institute._id, submission=subm_obj._id) }}" method="POST">
-                {{ submit_modal(subm_obj) }}
+                {{ submit_modal() }}
                   <td style="width: 20%"><button type="button" class="btn btn-sm btn-success form-control" name="update_submission" value="api_submit" data-bs-toggle="modal" data-bs-target="#submitModal">Submit to ClinVar</button></td>
                 </form>
               {% 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() }}
+                   <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">Submission status enquiry</button></td>
+                 </form>
+              {% endif %}
             </tr>
           </table>
         </div>
@@ -240,7 +246,28 @@
 </div>
 {% endmacro %}
 
-{% macro submit_modal(subm_obj) %}
+{% macro status_modal() %}
+<div class="modal fade" id="statusModal" tabindex="-1">
+  <div class="modal-dialog">
+    <div class="modal-content">
+      <div class="modal-header">
+        <h5 class="modal-title">Submission status</h5>
+        <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
+      </div>
+      <div class="modal-body">
+        <label for="apiKey">Submitter's <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/" target="_blank" rel="noopener">API key</a></label>
+        <input type="password" class="form-control" name="apiKey" id="apiKey" placeholder="64 alphanumeric characters" value="{{institute.clinvar_key or ''}}" required>
+      </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>
+      </div>
+    </div>
+  </div>
+</div>
+{% endmacro %}
+
+{% macro submit_modal() %}
 <div class="modal fade" id="submitModal" tabindex="-1">
   <div class="modal-dialog">
     <div class="modal-content">