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

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/blueprints/variants/templates/variants/utils.html

@@ -36,12 +36,18 @@
       the_form.submit();
     }}
 
-    var show_unaffected =document.getElementById('show_unaffected');
+    var show_unaffected = document.getElementById('show_unaffected');
     if (show_unaffected) {
       show_unaffected.onchange = function() {
       the_form.submit();
     }}
 
+    var show_soft_filtered = document.getElementById('show_soft_filtered');
+    if (show_soft_filtered) {
+      show_soft_filtered.onchange = function() {
+      the_form.submit();
+    }}
+
     function resetPage(){
       document.getElementById('page').value = "1";
     }
@@ -102,6 +108,18 @@
         {{ form.hide_dismissed(class="form-check-input") }}
         {{ form.hide_dismissed.label(class="form-check-label ms-2") }}
       </div>
+      {% if institute.soft_filters %} <!-- Available only for institutes with soft filters in settings -->
+        <div class="form-check d-flex justify-content-start">
+          {{ form.show_soft_filtered(class="form-check-input") }}
+          {{ form.show_soft_filtered.label(
+              class="form-check-label ms-2",
+              data_bs_toggle="tooltip",
+              title="Filters are defined by an admin in the institute settings. Current filters are: " ~
+                form.institute_soft_filters.data|safe
+          ) }}
+          {{ form.institute_soft_filters() }}
+        </div>
+      {% endif %}
       <div class="form-check d-flex justify-content-start">
         {% if institute.check_show_all_vars %}
           <input type="checkbox" class="form-check-input" name="show_unaffected" id="show_unaffected" checked disabled>
@@ -275,6 +293,16 @@
 </div>
 {% endmacro %}
 
+{% macro variant_size_filter(form) %}
+<div class="col-2">
+  {{ form.size_selector.label(class="control-label") }}
+  <div class="input-group">
+    {{ form.size_selector(class="form-select") }}
+    {{ form.size(class="form-control") }}
+  </div>
+</div>
+{% endmacro %}
+
 {% macro snv_filters(form, institute, case, filters)%}
 <input type="hidden" name="variant_type" value="{{ form.variant_type.data }}">
   {{ variants_common_filters(form, "snv") }}
@@ -308,16 +336,28 @@
       {{ form.spidex_human(class="selectpicker", data_style="btn-secondary") }}
     </div>
     <div class="col-2">
-      {{ form.clinsig.label(class="control-label") }}
+      <span>{{ form.clinsig.label(class="control-label") }}</span>
+      <span style="float:right;">{{ form.clinsig_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Exclude variants with clinical significance among the selected categories.") }} {{form.clinsig_exclude}}</span>
       {{ form.clinsig(class="selectpicker", data_style="btn-secondary") }}
     </div>
-    <div class="col-1">
-      {{ form.clinsig_confident_always_returned.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Always show selected CLINSIG entries with trusted revision status levels.") }}
-      <div>{{ form.clinsig_confident_always_returned() }}</div>
-    </div>
-    <div class="col-1">
-      {{ form.clinvar_tag() }}
-      {{ form.clinvar_tag.label(class="ms-2") }}
+    <div class="col-2">
+      <div class="row">
+        <div class="class="form-check">
+          {{ form.clinvar_trusted_revstat(class="form-check-input") }}
+          {{ form.clinvar_trusted_revstat.label(class="form-check-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Limit search to variants with trusted ClinVar revision status levels: mult, multiple_submitters, single, single_submitter, exp, reviewed_by_expert_panel, guideline, practice_guideline.") }}
+        </div>
+      </div>
+      <div class="row">
+        <div class="class="form-check">
+        {{ form.clinvar_tag(class="form-check-input") }}
+        {{ form.clinvar_tag.label(class="form-check-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Return only variants with annotated ClinVar significance.") }}
+        </div>
+      </div>
+      <div class="row">
+        <div class="class="form-check">
+        {{ form.prioritise_clinvar(class="form-check-input") }}
+        {{ form.prioritise_clinvar.label(class="form-check-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Include variants matching the selected ClinVar conditions, in addition to those found using the other search criteria (broadens the search). Note that variants excluded using ClinVar tags will still be returned when found using the other search criteria.") }}
+      </div>
     </div>
   </div>
   <div class="row mb-2">
@@ -336,10 +376,10 @@
         </div>
       </div>
     </div>
-    <div class="col-2">
+    <div class="col-1">
       {{ wtf.form_field(form.start) }}
     </div>
-    <div class="col-2">
+    <div class="col-1">
       {{ wtf.form_field(form.end) }}
     </div>
     <div class="col-2">
@@ -348,6 +388,7 @@
     <div class="col-2">
       {{ wtf.form_field(form.cytoband_end) }}
     </div>
+     {{ variant_size_filter(form) }}
   </div>
   <div class="row">
     <div class="col-2">
@@ -577,16 +618,6 @@
         gene_panels=['hpo']) }}">HPO gene list</a>
     </div>
   </div>
-  <div class="col-2">
-    {{ form.size.label(class="control-label") }}
-    {{ form.size(class="form-control", type="number") }}
-  </div>
-  <div class="col-2 d-flex align-items-end">
-    <div class="mb-2 form-check">
-      {{ form.size_shorter.label(class="form-check-label") }}
-      {{ form.size_shorter(class="form-check-input",type="checkbox") }}
-    </div>
-  </div>
   <div class="col-1 d-flex align-items-end">
     <div class="mb-2 form-check">
       {{ form.decipher.label(class="form-check-label") }}
@@ -622,10 +653,10 @@
       </div>
     </div>
   </div>
-  <div class="col-2">
+  <div class="col-1">
     {{ wtf.form_field(form.start) }}
   </div>
-  <div class="col-2">
+  <div class="col-1">
     {{ wtf.form_field(form.end) }}
   </div>
   <div class="col-1">
@@ -634,6 +665,7 @@
   <div class="col-1">
     {{ wtf.form_field(form.cytoband_end) }}
   </div>
+  {{ variant_size_filter(form) }}
 </div>
 <div class="row mb-3">
   <div class="col-2">
@@ -694,7 +726,8 @@
         {{ form.genetic_models(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
-        {{ form.clinsig.label(class="control-label") }}
+        <span>{{ form.clinsig.label(class="control-label") }}</span>
+        <span style="float:right;">{{ form.clinsig_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Exclude variants with clinical significance among the selected categories.") }} {{form.clinsig_exclude}}</span>
         {{ form.clinsig(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
@@ -765,9 +798,9 @@
         <div class="col">
           {{ wtf.form_field(form.cytoband_end) }}
         </div>
+        {{ variant_size_filter(form) }}
       </div>
       <div class="row" style="margin-top:10px;">
-        <div class="col-2"></div>
         <div class="col-2">
           <a class="btn btn-secondary btn-sm form-control" data-bs-toggle="collapse" href="#stringcoords" aria-expanded="false" aria-controls="stringcoords">
             String coordinates
@@ -841,16 +874,6 @@
         {{ form.hgnc_symbols.label(class="control-label") }}
         {{ form.hgnc_symbols(class="form-control") }}
       </div>
-      <div class="col-2">
-        {{ form.size.label(class="control-label") }}
-        {{ form.size(class="form-control", type="number") }}
-      </div>
-      <div class="col-2 d-flex align-items-end">
-        <div class="form-check mb-2">
-          {{ form.size_shorter.label(class="form-check-label") }}
-          {{ form.size_shorter(class="form-check-input",type="checkbox") }}
-        </div>
-      </div>
       <div class="col-1">
       </div>
       <div class="col-1">
@@ -889,9 +912,9 @@
         <div class="col">
           {{ wtf.form_field(form.cytoband_end) }}
         </div>
+        {{ variant_size_filter(form) }}
       </div>
       <div class="row" style="margin-top:10px;">
-        <div class="col-2"></div>
         <div class="col-2">
           <a class="btn btn-secondary btn-sm form-control" data-bs-toggle="collapse" href="#stringcoords" aria-expanded="false" aria-controls="stringcoords">
             String coordinates

scout/server/blueprints/variants/views.py

@@ -67,8 +67,7 @@ def variants(institute_id, case_name):
 
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    controllers.set_hpo_clinical_filter(case_obj, request.form)
 
     user_obj = store.user(current_user.email)
     if request.method == "POST":
@@ -97,14 +96,12 @@ def variants(institute_id, case_name):
 
     controllers.populate_force_show_unaffected_vars(institute_obj, form)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_id, category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
@@ -161,7 +158,9 @@ def variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         genetic_models_palette=GENETIC_MODELS_PALETTE,
         inherit_palette=INHERITANCE_PALETTE,
@@ -210,15 +209,12 @@ def str_variants(institute_id, case_name):
     controllers.populate_force_show_unaffected_vars(institute_obj, form)
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_id, category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
@@ -254,7 +250,9 @@ def str_variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -282,8 +280,7 @@ def sv_variants(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    controllers.set_hpo_clinical_filter(case_obj, request.form)
 
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
@@ -299,15 +296,12 @@ def sv_variants(institute_id, case_name):
     controllers.activate_case(store, institute_obj, case_obj, current_user)
     form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
@@ -334,7 +328,9 @@ def sv_variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -361,8 +357,7 @@ def mei_variants(institute_id, case_name):
     )
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    controllers.set_hpo_clinical_filter(case_obj, request.form)
 
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
@@ -393,15 +388,12 @@ def mei_variants(institute_id, case_name):
         # set chromosome to all chromosomes
         form.chrom.data = request.args.get("chrom", "")
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
@@ -431,7 +423,9 @@ def mei_variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -507,15 +501,12 @@ def cancer_variants(institute_id, case_name):
     # update status of case if visited for the first time
     controllers.activate_case(store, institute_obj, case_obj, current_user)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_id, category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
@@ -550,7 +541,9 @@ def cancer_variants(institute_id, case_name):
             **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
         },
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         result_size=result_size,
         show_dismiss_block=controllers.get_show_dismiss_block(),
         total_variants=variants_stats.get(variant_type, {}).get(category, "NA"),
@@ -574,9 +567,6 @@ def cancer_sv_variants(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
-
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
             store,
@@ -591,15 +581,12 @@ def cancer_sv_variants(institute_id, case_name):
     controllers.activate_case(store, institute_obj, case_obj, current_user)
     form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
@@ -630,7 +617,9 @@ def cancer_sv_variants(institute_id, case_name):
             **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
         },
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -660,9 +649,6 @@ def fusion_variants(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
-
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
             store,
@@ -679,15 +665,12 @@ def fusion_variants(institute_id, case_name):
         store, institute_obj, case_obj, category, request
     )
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
@@ -717,7 +700,9 @@ def fusion_variants(institute_id, case_name):
             **DISMISS_VARIANT_OPTIONS,
         },
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,

scout/server/extensions/beacon_extension.py

@@ -1,5 +1,5 @@
 """Scout supports integration with the Clinical Genomics SciLifeLab Beacon
-   cgbeacon2: https://github.com/Clinical-Genomics/cgbeacon2
+cgbeacon2: https://github.com/Clinical-Genomics/cgbeacon2
 """
 
 import datetime

scout/server/extensions/bionano_extension.py

@@ -1,10 +1,10 @@
 """
-    Connect to BioNano Access server via its API.
+Connect to BioNano Access server via its API.
 
-    The server API we connect to is described in the following document:
-    https://bionano.com/wp-content/uploads/2023/01/30462-Bionano-Access-API-Guide-1.pdf
-    For further development, the server has a Swagger-like demo interface at https://bionano-access.scilifelab.se/Bnx/
-    which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
+The server API we connect to is described in the following document:
+https://bionano.com/wp-content/uploads/2023/01/30462-Bionano-Access-API-Guide-1.pdf
+For further development, the server has a Swagger-like demo interface at https://bionano-access.scilifelab.se/Bnx/
+which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
 """
 
 import json

scout/server/extensions/chanjo2_extension.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Dict
+from typing import Dict, List
 
 import requests
 from flask import current_app
@@ -8,6 +8,9 @@ REF_CHROM = "14"
 MT_CHROM = "MT"
 LOG = logging.getLogger(__name__)
 
+CHANJO_BUILD_37 = "GRCh37"
+CHANJO_BUILD_38 = "GRCh38"
+
 
 class Chanjo2Client:
     """Runs requests to chanjo2 and returns results in the expected format."""
@@ -44,3 +47,39 @@ class Chanjo2Client:
             coverage_stats[ind["individual_id"]] = coverage_info
 
         return coverage_stats
+
+    def get_gene_complete_coverage(
+        self, hgnc_id: int, threshold: int = 15, individuals: dict = {}, build: str = "38"
+    ) -> bool:
+        """
+        Return complete coverage for hgnc_id at a coverage threshold.
+        """
+        chanjo_build = CHANJO_BUILD_37 if "37" in build else CHANJO_BUILD_38
+        chanjo2_gene_cov_url: str = "/".join(
+            [current_app.config.get("CHANJO2_URL"), "coverage/d4/genes/summary"]
+        )
+
+        gene_cov_query = {
+            "build": chanjo_build,
+            "coverage_threshold": threshold,
+            "hgnc_gene_ids": [hgnc_id],
+            "interval_type": "genes",
+            "samples": [],
+        }
+        for ind in individuals:
+            if not ind.get("d4_file"):
+                continue
+
+            gene_cov_query["samples"].append(
+                {"coverage_file_path": ind["d4_file"], "name": ind["individual_id"]}
+            )
+
+        resp = requests.post(chanjo2_gene_cov_url, json=gene_cov_query)
+        gene_cov = resp.json()
+
+        full_coverage = bool(gene_cov)
+        for sample in gene_cov.keys():
+            if gene_cov[sample]["coverage_completeness_percent"] < 100:
+                full_coverage = False
+
+        return full_coverage

scout/server/extensions/chanjo_extension.py

@@ -1,5 +1,5 @@
 """
-    Generate coverage reports using chanjo and chanjo-report. Documentation under -> `docs/admin-guide/chanjo_coverage_integration.md`
+Generate coverage reports using chanjo and chanjo-report. Documentation under -> `docs/admin-guide/chanjo_coverage_integration.md`
 """
 
 import json

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)