scout-browser 4.80__py3-none-any.whl → 4.82.1__py3-none-any.whl

scout/server/blueprints/variants/forms.py

@@ -95,6 +95,7 @@ class VariantFiltersForm(FlaskForm):
     variant_type = HiddenField(default="clinical")
 
     gene_panels = NonValidatingSelectMultipleField(choices=[])
+    gene_panels_exclude = BooleanField("Exclude genes")
     hgnc_symbols = TagListField("HGNC Symbols/Ids (case sensitive)")
 
     region_annotations = SelectMultipleField(choices=REGION_ANNOTATIONS)
@@ -111,7 +112,7 @@ class VariantFiltersForm(FlaskForm):
     clinsig = NonValidatingSelectMultipleField("ClinVar CLINSIG", choices=CLINSIG_OPTIONS)
 
     gnomad_frequency = BetterDecimalField("gnomadAF", validators=[validators.Optional()])
-    local_obs = IntegerField("Local obs. (archive)", validators=[validators.Optional()])
+    local_obs_old = IntegerField("Local obs. (archive)", validators=[validators.Optional()])
 
     filters = NonValidatingSelectField(choices=[], validators=[validators.Optional()])
     filter_display_name = StringField(default="")
@@ -165,6 +166,12 @@ class CancerFiltersForm(VariantFiltersForm):
     clinvar_tag = BooleanField("ClinVar hits")
     cosmic_tag = BooleanField("Cosmic hits")
     mvl_tag = BooleanField("Managed Variants hits")
+    local_obs_cancer_somatic_old = IntegerField(
+        "Local somatic obs. (archive)", validators=[validators.Optional()]
+    )
+    local_obs_cancer_germline_old = IntegerField(
+        "Local germline obs. (archive)", validators=[validators.Optional()]
+    )
 
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE_CANCER
@@ -196,6 +203,13 @@ class SvFiltersForm(VariantFiltersForm):
     swegen = IntegerField("SweGen obs")
     clinical_filter = SubmitField(label="Clinical filter")
 
+    local_obs_cancer_somatic_old = IntegerField(
+        "Local somatic obs. (archive)", validators=[validators.Optional()]
+    )
+    local_obs_cancer_germline_old = IntegerField(
+        "Local germline obs. (archive)", validators=[validators.Optional()]
+    )
+
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE_SV
 

scout/server/blueprints/variants/templates/variants/components.html

@@ -23,6 +23,61 @@
   </div>
 {% endmacro %}
 
+{% macro fusion_variants_header() %}
+  <thead class="table-light">
+    <tr>
+      <th id="checkbox" style="width:1%"></th>
+      <th id="rank" style="width:3%;" title="Beta version. Currently testing" class="text-left">Rank (beta)</th>
+      <th id="genes" style="width:6%" title="Genes">Fusion Genes</th>
+      <th id="callers" style="width:4%" title="Number of callers detecting a given event">Callers</th>
+      <th id="observed" style="width:4%" title="Observed database matches">Observed</th>
+      <th id="score" style="width:4%" title="Beta version. Currently testing">Score (beta)</th>
+      <th id="junction_reads" style="width:6%" title="Number of paired-ends that support the event">Junction Reads</th>
+      <th id="split_reads" style="width:6%" title="Number of split reads that support the event">Split Reads</th>
+      <th id="ffpm" style="width:6%" title="Fusion fragments per million total RNA-seq fragments">FFPM</th>
+      <th id="frame_status" style="width:8%" title="Frame status of the fusion">Frame Status</th>
+      <th id="transcripts" style="width:8%" title="Transcript ID">Transcript ID</th>
+      <th id="exons" style="width:4%" title="Exon Number">Exon Number</th>
+      <th id="brealpoints" style="width:4%" title="Breakpoints">Breakpoints</th>
+      <th id="oriantation" style="width:4%" title="Orientation">Orientation</th>
+    </tr>
+  </thead>
+{% endmacro %}
+
+{% macro default_fusion_variant_cells(institute, case, variant) %}
+  <td>
+    {{ fusion_variant_gene_symbols_cell(variant) }}
+  </td>
+  <td class="text-center"><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
+    {{ variant.tool_hits|int }}</span></td>
+  <td>{{variant.found_db|join(", ") if variant.found_db else "-"}}</td>
+  <td class="text-center">{{ variant.fusion_score|float|round(3) }}</td>
+  <td class="text-center">{{ variant.samples[0].read_depth }}</td>
+  <td class="text-center">{{ variant.samples[0].split_read }}</td>
+  <td class="text-center">{{ variant.samples[0].ffpm }}</td>
+  <td>{{ variant.frame_status }}</td>
+  <td>
+    {% if variant.genes %}
+      {% for gene in variant.genes %}
+        {% for transcript in gene.transcripts %}
+          <div>{{ transcript.transcript_id }} </div>
+        {% endfor %}
+      {% endfor %}
+    {% endif %}
+  </td>
+  <td>
+    {% if variant.genes %}
+      {% for gene in variant.genes %}
+        {% for transcript in gene.transcripts %}
+          <div>{% if "exon" in transcript %}{{ transcript.exon|int }}{% endif %} </div>
+        {% endfor %}
+      {% endfor %}
+    {% endif %}
+  </td>
+  <td> {{ variant.chromosome }}:{{ variant.position }}  <br> {{ variant.end_chrom }}:{{ variant.end }} </td>
+  <td class="text-center">{{ variant.orientation }}</td>
+{% endmacro %}
+
 {% macro fusion_variant_gene_symbols_cell(variant) %}
 <div class="align-items-center">
   {% if variant.genes %}

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

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import fusion_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, fusion_variant_gene_symbols_cell %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, fusion_variant_gene_symbols_cell, fusion_variants_header, default_fusion_variant_cells %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - Fusion variants
@@ -54,24 +54,7 @@ onsubmit="return validateForm()">
 
     <div class="card mt-3">
       <table id="variantsTable" class="table table-hover table-bordered" aria-label="Fusion variants table">
-        <thead class="table-light thead">
-          <tr>
-            <th style="width:3%"></th>
-            <th style="width:4%" title="Beta version. Currently testing">Rank (beta)</th>
-            <th style="width:6%" title="Genes">Fusion Genes</th>
-            <th style="width:4%" title="Number of callers detecting a given event">Callers</th>
-            <th style="width:4%" title="Observed database matches">Observed</th>
-            <th style="width:4%" title="Beta version. Currently testing">Score (beta)</th>
-            <th style="width:6%" title="Number of paired-ends that support the event">Junction Reads</th>
-            <th style="width:6%" title="Number of split reads that support the event">Split Reads</th>
-            <th style="width:6%" title="Fusion fragments per million total RNA-seq fragments">FFPM</th>
-            <th style="width:8%" title="Frame status of the fusion">Frame Status</th>
-            <th style="width:8%" title="Transcript ID">Transcript ID</th>
-            <th style="width:4%" title="Exon Number">Exon Number</th>
-            <th style="width:4%" title="Breakpoints">Breakpoints</th>
-            <th style="width:4%" title="Orientation">Orientation</th>
-          </tr>
-        </thead>
+        {{ fusion_variants_header() }}
         <tbody>
           {% for variant in variants %}
             {{ variant_row(variant) }}
@@ -103,37 +86,7 @@ onsubmit="return validateForm()">
     <td class="text-start">
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
-    <td>
-      {{ fusion_variant_gene_symbols_cell(variant) }}
-    </td>
-    <td><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
-      {{ variant.tool_hits|int }}</span></td>
-    <td>{{variant.found_db|join(", ") if variant.found_db else "-"}}</td>
-    <td class="text-end">{{ variant.fusion_score|float|round(3) }}</td>
-    <td>{{ variant.samples[0].read_depth }}</td>
-    <td>{{ variant.samples[0].split_read }}</td>
-    <td>{{ variant.samples[0].ffpm }}</td>
-    <td>{{ variant.frame_status }}</td>
-    <td>
-      {% if variant.genes %}
-        {% for gene in variant.genes %}
-          {% for transcript in gene.transcripts %}
-            <div>{{ transcript.transcript_id }} </div>
-          {% endfor %}
-        {% endfor %}
-      {% endif %}
-    </td>
-    <td>
-      {% if variant.genes %}
-        {% for gene in variant.genes %}
-          {% for transcript in gene.transcripts %}
-            <div>{% if "exon" in transcript %}{{ transcript.exon|int }}{% endif %} </div>
-          {% endfor %}
-        {% endfor %}
-      {% endif %}
-    </td>
-    <td> {{ variant.chromosome }}:{{ variant.position }}  <br> {{ variant.end_chrom }}:{{ variant.end }} </td>
-    <td>{{ variant.orientation }}</td>
+    {{ default_fusion_variant_cells(institute, case, variant) }}
   </tr>
 {% endmacro %}
 

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

@@ -91,9 +91,9 @@
 	        {% endif %}
             <td class="str-link">{{ cell_rank(variant, institute, case, form, manual_rank_options) }}</td>
             <td class="str-link">{{ str_locus_info(variant) }}</td>
-	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru  }}</td>
-            <td class="text-end"><b>{{ variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "") }}</b></td>
-            <td class="text-end">{{ variant.str_ref }}</td>
+	          <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>{{ str_status(variant) }}</td>
             <td>{% for sample in variant.samples %}
                   {% if sample.genotype_call != "./." %}
@@ -187,7 +187,9 @@
       <tr><td colspan=2>&nbsp;</td></tr>
       {% if variant.str_swegen_mean %}
         <tr><td>SweGen Z-score</td><td>
-          {{ ((variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "")|int - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
+          {% if variant.str_mc %}
+            {{ ((variant.str_mc - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
+          {% endif %}
         </td></tr>
         <tr><td>SweGen mean</td><td>{{variant.str_swegen_mean|round(2)}}</td></tr>
         <tr><td>SweGen std</td><td>{{variant.str_swegen_std|round(2)}}</td></tr>
@@ -233,7 +235,8 @@
       {% endfor %}
     {%endif%}
   </div>"
-  title="">{{ variant.str_repid }}
+  title="">{% if variant.str_repid %} {{ variant.str_repid }} {% elif variant.str_trid %} {{ variant.str_trid  }} {% else %}
+  {% for gene in variant.genes %} {{ gene.symbol }} {% endfor %} {% endif %}
   </a>
   {% for gene in variant.genes %}
     <span class="badge bg-secondary"><a href="{{ gene.stripy_link }}" class="text-white" referrerpolicy="no-referrer" rel="noopener" target="_blank">S</a></span>

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

@@ -55,6 +55,27 @@
   {% endfor %}
 {% endmacro %}
 
+{% macro archived_observations_filter(form) %}
+  {% if config.SHOW_OBSERVED_VARIANT_ARCHIVE and config.SHOW_OBSERVED_VARIANT_ARCHIVE is true %}
+    {{ form.local_obs_old.label(class="control-label") }}
+    {{ form.local_obs_old(class="form-control") }}
+  {% endif %}
+{% endmacro %}
+
+{% macro archived_observations_cancer_filters(form) %}
+  {% if config.SHOW_OBSERVED_VARIANT_ARCHIVE and config.SHOW_OBSERVED_VARIANT_ARCHIVE is true %}
+    <div class="col">
+      {{ wtf.form_field(form.local_obs_old) }}
+    </div>
+    <div class="col">
+      {{ wtf.form_field(form.local_obs_cancer_somatic_old) }}
+    </div>
+    <div class="col">
+      {{ wtf.form_field(form.local_obs_cancer_germline_old) }}
+    </div>
+  {% endif %}
+{% endmacro %}
+
 {% macro filter_form_footer(form, result_size, total_variants, more_variants, page, nvars, institute) %}
 <div class="card-footer text-center">
   <div class="row">
@@ -110,12 +131,17 @@
 {% endmacro %}
 
 
-{% macro compounds_table(institute, case, compounds) %}
+{% macro compounds_table(institute, case, compounds, is_popover) %}
+  {% set is_popover = is_popover|default(false) %}
   <table class='table table-condensed table-bordered table-sm'>
     <thead class='thead table-light'>
       <tr>
         <th>Variant</th>
-        <th>Combined score</th>
+        <th>Combined score
+          {% if not is_popover %}
+            <span data-bs-toggle='tooltip' data-bs-title='Combined score is the sum of variants´s score and compound variant´s score'>?</span>
+        </th>
+          {% endif %}
         <th>Rank score</th>
         <th>Gene annotation</th>
         <th>Func. annotation</th>
@@ -131,6 +157,8 @@
           <td>
               {% if compound.not_loaded %}
                 {{ compound.display_name }} <small>(not loaded)</small>
+              {% elif is_popover %}
+                {{ compound.display_name }}
               {% else %}
                 <a href='{{ url_for("variant.variant",
                 institute_id=institute._id,
@@ -194,7 +222,8 @@
 {% macro variants_common_filters(form, type) %}
 <div class="row mb-2">
   <div class="col-2">
-    {{ form.gene_panels.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}
+    <span>{{ form.gene_panels.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}</span>
+    <span style="float:right;">{{ form.gene_panels_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Check this box to exclude from the search any gene listed in selected 'Gene Panels', 'Symbol file' or provided in the 'HGNC Symbols/Ids' field.") }} {{form.gene_panels_exclude}}</span>
     {{ form.gene_panels(class="selectpicker", data_style="btn-secondary") }}
   </div>
   <div class="col-2">
@@ -281,8 +310,7 @@
           {{ form.gnomad_frequency(class="form-control") }}
         </div>
         <div class="col-4">
-          {{ form.local_obs.label(class="control-label") }}
-          {{ form.local_obs(class="form-control") }}
+          {{ archived_observations_filter(form) }}
         </div>
         <div class="col-4">
           {{ form.chrom.label(class="control-label") }}
@@ -382,8 +410,7 @@
           {{ form.swegen_freq(class="form-control") }}
          </div>
         <div class="col-4">
-          {{ form.local_obs.label(class="control-label") }}
-          {{ form.local_obs(class="form-control") }}
+          {{ archived_observations_filter(form) }}
         </div>
         <div class="col-4">
           {{ form.chrom.label(class="control-label") }}
@@ -459,7 +486,8 @@
 <input type="hidden" name="variant_type" value="{{ form.variant_type.data }}">
 <div class="row">
   <div class="col-2">
-    {{ form.gene_panels.label(class="control-label", data_toggle="tooltip", data_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}
+    <span>{{ form.gene_panels.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}</span>
+    <span style="float:right;">{{ form.gene_panels_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Check this box to exclude from the search any gene listed in selected 'Gene Panels', 'Symbol file' or provided in the 'HGNC Symbols/Ids' field.") }} {{form.gene_panels_exclude}}</span>
     {{ form.gene_panels(class="selectpicker", data_style="btn-secondary") }}
   </div>
   <div class="col-3">
@@ -560,8 +588,7 @@
   <div class="col-6">
     <div class="row">
       <div class="col-3">
-        {{ form.local_obs.label(class="control-label") }}
-        {{ form.local_obs(class="form-control") }}
+        {{ archived_observations_filter(form) }}
       </div>
       <div class="col-3">
          {{ form.clingen_ngi.label(class="control-label") }}
@@ -632,7 +659,8 @@
     {{ form.variant_type() }}
     <div class="row">
       <div class="col-2">
-        {{ form.gene_panels.label(data_toggle="tooltip", data_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}
+        <span>{{ form.gene_panels.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}</span>
+    <span style="float:right;">{{ form.gene_panels_exclude.label(class="control-label",  data_bs_toggle="tooltip", data_bs_placement="left", title="Check this box to exclude from the search any gene listed in selected 'Gene Panels', 'Symbol file' or provided in the 'HGNC Symbols/Ids' field.") }} {{form.gene_panels_exclude}}</span>
         {{ form.gene_panels(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
@@ -698,27 +726,25 @@
     </div>
     <div class="form" id="chromosome_search">
       <div class="row" style="margin-top:20px;">
-        <div class="col-1">
+        <div class="col">
           {{ form.gnomad_frequency.label(class="control-label") }}
           {{ form.gnomad_frequency(class="form-control") }}
         </div>
-        <div class="col-1">
-          {{ wtf.form_field(form.local_obs) }}
-        </div>
-        <div class="col-2">
+        {{ archived_observations_cancer_filters(form) }}
+        <div class="col">
           {{ form.chrom.label(class="control-label") }}
           {{ form.chrom(class="selectpicker", data_actions_box="true", data_style="btn-secondary") }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.start) }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.end) }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.cytoband_start) }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.cytoband_end) }}
         </div>
       </div>
@@ -767,7 +793,8 @@
     {{ form.variant_type() }}
     <div class="row mb-3">
       <div class="col-2">
-        {{ form.gene_panels.label(class="control-label", data_toggle="tooltip", data_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}
+        <span>{{ form.gene_panels.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}</span>
+        <span style="float:right;">{{ form.gene_panels_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Check this box to exclude from the search any gene listed in selected 'Gene Panels', 'Symbol file' or provided in the 'HGNC Symbols/Ids' field.") }} {{form.gene_panels_exclude}}</span>
         {{ form.gene_panels(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
@@ -823,27 +850,25 @@
     </div>
     <div id="chromosome_search">
       <div class="row" style="margin-top:20px;">
-        <div class="col-1">
+        <div class="col">
          {{ form.gnomad_frequency.label(class="control-label") }}
          {{ form.gnomad_frequency(class="form-control") }}
         </div>
-        <div class="col-1">
-          {{ wtf.form_field(form.local_obs) }}
-        </div>
-        <div class="col-2">
+        {{ archived_observations_cancer_filters(form) }}
+        <div class="col">
           {{ form.chrom.label(class="control-label") }}
           {{ form.chrom(class="selectpicker", data_actions_box="true", data_style="btn-secondary") }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.start) }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.end) }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.cytoband_start) }}
         </div>
-        <div class="col-2">
+        <div class="col">
           {{ wtf.form_field(form.cytoband_end) }}
         </div>
       </div>
@@ -892,7 +917,8 @@
 <input type="hidden" name="variant_type" value="{{ form.variant_type.data }}">
 <div class="row">
   <div class="col-2">
-    {{ form.gene_panels.label(class="control-label", data_toggle="tooltip", data_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}
+    <span>{{ form.gene_panels.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="This list can be modified from the institute settings page. Latest panel version is used in variants filtering.") }}</span>
+    <span style="float:right;">{{ form.gene_panels_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Check this box to exclude from the search any gene listed in selected 'Gene Panels', 'Symbol file' or provided in the 'HGNC Symbols/Ids' field.") }} {{form.gene_panels_exclude}}</span>
     {{ form.gene_panels(class="selectpicker", data_style="btn-secondary") }}
   </div>
   <div class="col-3">

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

@@ -164,7 +164,7 @@
     {% if ns.show_compounds %}
       <a href="#" class="badge bg-primary text-white" data-bs-toggle="popover" data-bs-placement="left"
         data-bs-html="true" data-bs-trigger="hover click"
-        data-bs-content="{{ compounds_table(institute, case, variant.compounds[:20]) }}">Compounds</a>
+        data-bs-content="{{ compounds_table(institute, case, variant.compounds[:20], is_popover=true) }}">Compounds</a>
     {% endif %}
   {% endif %}
 

scout/server/blueprints/variants/utils.py

@@ -1,23 +1,20 @@
 # -*- coding: utf-8 -*-
+from scout.adapter import MongoAdapter
 
 
-def update_case_panels(store, case_obj):
+def update_case_panels(store: MongoAdapter, case_obj: dict):
     """Refresh case gene panels with info on if a panel was removed.
+    Also sets the key "latest_panels" for a case where the value is the latest version of the case panels
 
-    Also return these more populated panels for optional storage on the variant_obj.
     If you do not use the returned variants, but rely on the update, please remember
     to call this function before updating the variants.
-
-    store(adapter.MongoAdapter)
-    case_obj(dict)
-
-    Returns:
-        list(panel_info)
     """
+    case_obj["latest_panels"] = []
 
     for panel_info in case_obj.get("panels", []):
         panel_name = panel_info["panel_name"]
         latest_panel = store.gene_panel(panel_name)
         panel_info["removed"] = False if latest_panel is None else latest_panel.get("hidden", False)
-
-    return case_obj.get("panels", [])
+        if latest_panel:
+            latest_panel["hgnc_ids"] = [gene["hgnc_id"] for gene in latest_panel.get("genes", [])]
+            case_obj["latest_panels"].append(latest_panel)

scout/server/extensions/clinvar_extension.py

@@ -1,8 +1,8 @@
 import json
 import logging
-from tempfile import NamedTemporaryFile
 
 import requests
+from flask import flash
 
 from scout.constants.clinvar import CLINVAR_API_URL, PRECLINVAR_URL
 
@@ -19,7 +19,7 @@ class ClinVarApi:
         self.convert_service = "/".join([PRECLINVAR_URL, "csv_2_json"])
         self.submit_service = CLINVAR_API_URL
 
-    def set_header(self, api_key):
+    def set_header(self, api_key) -> dict:
         """Creates a header to be submitted a in a POST rquest to the CLinVar API
         Args:
             api_key(str): API key to be used to submit to ClinVar (64 alphanumeric characters)
@@ -76,3 +76,11 @@ class ClinVarApi:
 
         except Exception as ex:
             return None, ex
+
+    def show_submission_status(self, submission_id: str, api_key=None):
+        """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"{CLINVAR_API_URL}{submission_id}/actions/"
+        actions_resp: requests.models.Response = requests.get(actions_url, headers=header)
+        flash(f"Response from ClinVar: {actions_resp.json()}", "primary")

scout/server/templates/report_base.html

@@ -4,7 +4,7 @@
 	<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
 
 	{% block css %}
-	<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css">
+  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
   <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
     <style>
 		tr.light-grey td{
@@ -22,8 +22,8 @@
 	{% endblock %}
 
 	{% block scripts %}
-	<script src="https://code.jquery.com/jquery-3.1.1.min.js"></script>
-	<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"></script>
+  <script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
+	<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.min.js" integrity="sha384-QJHtvGhmr9XOIpI6YVutG+2QOK9T+ZnN4kzFN1RtK3zEFEIsxhlmWl5/YESvpZ13" crossorigin="anonymous"></script>
 	{% endblock %}
 </body>
 </html>

scout/server/templates/utils.html

@@ -78,7 +78,7 @@
                     {{ single_comment(institute, case, current_user, comment, item_index) }}
                     {% endfor %}
                     {% if expandable_comments|length >0 %}
-                    <div class="accordion-item">
+                    <div class="accordion-item border-0">
                       <div id="expandable-comments-content" class="accordion-collapse collapse" aria-labelledby="expandable-comments-heading">
                         <div class="" >
                           {% for comment in expandable_comments %}
@@ -87,7 +87,7 @@
                           {% endfor %}
                         </div>
                       </div>
-                      <button id="expandable-comments-control" class="accordion-button collapsed" style="color:#0c63e4; background-color:#e7f1ff;" type="button" data-bs-toggle="collapse" data-bs-target="#expandable-comments-content" aria-expanded="false" aria-controls="expandable-comments-content"
+                      <button id="expandable-comments-control" class="accordion-button collapsed" style="background-color:var(--bs-body-bg);color:var(--bs-body-color)" type="button" data-bs-toggle="collapse" data-bs-target="#expandable-comments-content" aria-expanded="false" aria-controls="expandable-comments-content"
                               onclick="{let thisElement=event.currentTarget; let children= thisElement.querySelectorAll('span'); Array.from(children).forEach(child=> child.classList.toggle('d-none'));}">
                         <span>See more comments...</span>
                         <span class="d-none">Minimise comments</span>

{scout_browser-4.80.dist-info → scout_browser-4.82.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.80
+Version: 4.82.1
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson
@@ -16,12 +16,12 @@ Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
-Requires-Dist: werkzeug <2.3
+Requires-Dist: werkzeug <3
 Requires-Dist: Flask >=2.0
 Requires-Dist: Flask-Bootstrap
 Requires-Dist: Flask-CORS
 Requires-Dist: path.py
-Requires-Dist: Flask-Markdown
+Requires-Dist: markdown
 Requires-Dist: WTForms
 Requires-Dist: Flask-WTF
 Requires-Dist: Flask-Mail
@@ -171,9 +171,9 @@ scout load panel scout/demo/panel_1.txt
 scout load case scout/demo/643594.config.yaml
 ```
 
-## Integration with chanjo for coverage report visualization
+## Integration with chanjo and chanjo2 for coverage report visualization
 
-Scout may be configured to visualize coverage reports produced by [Chanjo][chanjo]. Instructions on
+Scout may be configured to visualize coverage reports produced by [Chanjo][chanjo] or [chanjo2][chanjo2]. Instructions on
 how to enable this feature can be found in the document [chanjo_coverage_integration][chanjo-scout].
 
 ## Integration with loqusdb for integrating local variant frequencies
@@ -311,6 +311,7 @@ be found in [CONTRIBUTING](CONTRIBUTING.md).
 
 
 [chanjo]: https://github.com/Clinical-Genomics/chanjo
+[chanjo2]: https://github.com/Clinical-Genomics/chanjo2
 [chanjo-scout]: docs/admin-guide/chanjo_coverage_integration.md
 [loqusdb]: https://github.com/moonso/loqusdb
 [loqusdb-scout]: docs/admin-guide/loqusdb_integration.md