scout-browser 4.90__py3-none-any.whl → 4.91__py3-none-any.whl

scout/server/blueprints/institutes/templates/overview/cases.html

@@ -1,7 +1,7 @@
 {% import "bootstrap/wtf.html" as wtf %}
 {% extends "layout.html" %}
 {% from "overview/institute_sidebar.html" import institute_actionbar %}
-{% from "overview/utils.html" import analysis_type %}
+{% from "overview/utils.html" import analysis_type, cases_search_form %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - Cases
@@ -20,137 +20,6 @@
   </li>
 {% endblock %}
 
-
-{% macro search_form() %}
-
-<!-- Collect advanced search key/values -->
-{% set search = {} %}
-{% for field in form._fields %}
-  {% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
-    {% do search.update({field: form._fields[field].data}) %}
-  {% endif %}
-{% endfor %}
-
-<form action="{{ url_for('overview.cases', institute_id=institute._id) }}" method="POST" accept-charset="utf-8">
-    {{ form.hidden_tag() }}
-
-    <div class="row">
-        <div class="col-md-3 mb-3">
-            {{ form.case.label(class="form-label") }}
-            {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-        </div>
-        <div class="col-md-1 mb-3">
-            {{ form.search_limit.label(class="form-label") }}
-            {{ form.search_limit(class="form-control") }}
-        </div>
-        <div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
-          {{ form.search(class="btn btn-lg btn-primary mt-4") }}
-        </div>
-        <div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
-          <a href="{{ url_for('overview.cases', institute_id=institute._id) }}" class="btn btn-lg btn-secondary mt-4 text-white" role="button">Reset search</a>
-        </div>
-        <div class="col-md-3 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
-          {{ form.advanced_search(class="form-check-input") }}
-          {{ form.advanced_search.label(class="form-check-label") }}
-        </div>
-    </div>
-    <div class="row">
-        <div class="col-md-2 mb-3 form-check ms-3">
-            {{ form.skip_assigned(class="form-check-input") }}
-            {{ form.skip_assigned.label(class="form-check-label") }}
-        </div>
-        <div class="col-md-2 mb-3 form-check">
-            {{ form.is_research(class="form-check-input") }}
-            {{ form.is_research.label(class="form-check-label") }}
-        </div>
-        <div class="col-md-2 mb-3 form-check">
-            {{ form.clinvar_submitted(class="form-check-input") }}
-            {{ form.clinvar_submitted.label(class="form-check-label") }}
-        </div>
-        <div class="col-md-2 mb-3 form-check">
-            {{ form.has_rna(class="form-check-input") }}
-            {{ form.has_rna.label(class="form-check-label") }}
-        </div>
-        <div class="col-md-2 mb-3 form-check">
-            {{ form.validation_ordered(class="form-check-input") }}
-            {{ form.validation_ordered.label(class="form-check-label") }}
-        </div>
-    </div>
-    <!-- This div contains the advances search options -->
-    <div id="advancesSearchOptions">
-      <div class="row">
-          <div class="col-md-4 mb-3">
-              {{ form.exact_pheno.label(class="form-label") }}
-              {{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.exact_dia.label(class="form-label") }}
-              {{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-      </div>
-      <div class="row">
-          <div class="col-md-4 mb-3">
-              {{ form.synopsis.label(class="form-label") }}
-              {{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.panel.label(class="form-label") }}
-              {{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.status.label(class="form-label") }}
-              {{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-      </div>
-      <div class="row">
-          <div class="col-md-4 mb-3">
-              {{ form.tags.label(class="form-label") }}
-              {{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.track.label(class="form-label") }}
-              {{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.pheno_group.label(class="form-label") }}
-              {{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-      </div>
-      <div class="row">
-          <div class="col-md-4 mb-3">
-              {{ form.cohort.label(class="form-label") }}
-              {{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.similar_case.label(class="form-label") }}
-              {{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.similar_pheno.label(class="form-label") }}
-              {{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-      </div>
-      <div class="row">
-          <div class="col-md-4 mb-3">
-              {{ form.pinned.label(class="form-label") }}
-              {{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.causative.label(class="form-label") }}
-              {{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-          <div class="col-md-4 mb-3">
-              {{ form.user.label(class="form-label") }}
-              {{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
-          </div>
-      </div>
-    </div> <!--End of advancedSearchOptions div -->
-  </form>
-<div>
-  <span class="text-muted">The following search criteria were used: {{search}}</span>
-</div>
-{% endmacro %}
-
 {% macro cases_table(group_name, cases) %}
 {% if sort_order == 'asc' %}
   {% set sort_option = 'desc'%}
@@ -333,7 +202,7 @@
     <div class="container-float">
       <div class="card panel-default">
         <div class="card-body">
-          {{ search_form() }}
+          {{ cases_search_form(form, url_for('overview.cases', institute_id=institute._id), url_for('overview.cases', institute_id=institute._id), institute) }}
         </div>
         <div class="card-footer text-center">
           Showing {{ found_cases }} / {{ nr_cases }} cases

scout/server/blueprints/institutes/templates/overview/utils.html

@@ -1,5 +1,140 @@
 {% from "variants/components.html" import variant_gene_symbols_cell, variant_funct_anno_cell, fusion_variant_gene_symbols_cell %}
 
+{% macro cases_search_form(form, form_action, reset_action, institute = none) %}
+<!-- Collect advanced search key/values -->
+{% set search = {} %}
+{% for field in form._fields %}
+  {% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
+    {% do search.update({field: form._fields[field].data}) %}
+  {% endif %}
+{% endfor %}
+
+<form action="{{ form_action }}" method="POST" accept-charset="utf-8">
+    {{ form.hidden_tag() }}
+
+    <div class="row">
+      {% if not institute %} <!-- used only on dashboard page, when search might return results from many institutes -->
+        <div class="col-md-2 mb-3">
+            {{ form.search_institute.label(class="form-label") }}
+            {{ form.search_institute(class="form-control") }}
+        </div>
+      {% endif %}
+        <div class="col-md-3 mb-3">
+            {{ form.case.label(class="form-label") }}
+            {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+        </div>
+        <div class="col-md-1 mb-3">
+            {{ form.search_limit.label(class="form-label") }}
+            {{ form.search_limit(class="form-control") }}
+        </div>
+        <div class="btn-sm mb-2 col-md-2 mx-auto">
+          {{ form.search(class="btn btn-lg btn-primary mt-4") }}
+          <a href="{{ reset_action }}" class="btn btn-lg btn-secondary mt-4 text-white">Reset search</a>
+        </div>
+        <div class="col-md-2 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
+          {{ form.advanced_search(class="form-check-input") }}
+          {{ form.advanced_search.label(class="form-check-label") }}
+        </div>
+    </div>
+    {% if institute %} <!-- The following checkboxes will be displayed when the form is used on institute caseS page only, not on the dashboard -->
+    <div class="row">
+        <div class="col-md-2 mb-3 form-check ms-3">
+            {{ form.skip_assigned(class="form-check-input") }}
+            {{ form.skip_assigned.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.is_research(class="form-check-input") }}
+            {{ form.is_research.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.clinvar_submitted(class="form-check-input") }}
+            {{ form.clinvar_submitted.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.has_rna(class="form-check-input") }}
+            {{ form.has_rna.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.validation_ordered(class="form-check-input") }}
+            {{ form.validation_ordered.label(class="form-check-label") }}
+        </div>
+    </div>
+    {% endif %}
+    <!-- This div contains the advances search options -->
+    <div id="advancesSearchOptions">
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.exact_pheno.label(class="form-label") }}
+              {{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.exact_dia.label(class="form-label") }}
+              {{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.synopsis.label(class="form-label") }}
+              {{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.panel.label(class="form-label") }}
+              {{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.status.label(class="form-label") }}
+              {{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.tags.label(class="form-label") }}
+              {{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.track.label(class="form-label") }}
+              {{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.pheno_group.label(class="form-label") }}
+              {{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.cohort.label(class="form-label") }}
+              {{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.similar_case.label(class="form-label") }}
+              {{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.similar_pheno.label(class="form-label") }}
+              {{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.pinned.label(class="form-label") }}
+              {{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.causative.label(class="form-label") }}
+              {{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.user.label(class="form-label") }}
+              {{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+    </div> <!--End of advancedSearchOptions div -->
+  </form>
+<div>
+  <span class="text-muted">The following search criteria were used: {{search}}</span>
+</div>
+{% endmacro %}
+
 {% macro analysis_type(analysis_types) %}
   {% for analysis_type in analysis_types %}
     {% if analysis_type == 'wgs' %}

scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html

@@ -5,6 +5,7 @@
 {% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell %}
 {% from "variant/buttons.html" import splice_junctions_button %}
 {% from "variants/utils.html" import filter_script_main, pagination_footer, pagination_hidden_div, stash_filter_buttons, update_stash_filter_button_status%}
+{% from "variant/components.html" import variant_scripts %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ form.variant_type.data|capitalize }} omics outlier variants
@@ -117,6 +118,9 @@
               </td>
               <td class="text-end">{{ variant.chromosome }}</td>
                 <td class="text-end"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span>-<span style="white-space: nowrap;">{{ variant.end|human_longint|safe }}</span>
+                  <button type="button" class="fa fa-copy btn-xs js-tooltip js-copy"
+                    style="background-color: Transparent;outline:none; border: none;" data-bs-toggle="tooltip" data-bs-placement="bottom" data-copy="{{ variant.chromosome }}:{{ variant.position }}-{{ variant.end }}" title="Copy to clipboard">
+                  </button>
                 {% if case.has_rna_tracks %}
                   {{ splice_junctions_button(institute._id, case, None, variant.omics_variant_id) }}
                 {% endif %}
@@ -142,6 +146,7 @@
 {% block scripts %}
   {{ super() }}
   {{ external_scripts() }}
+  {{ variant_scripts() }}
   <script src="{{ url_for('variants.static', filename='form_scripts.js') }}"></script>
   {{ filter_script_main(cytobands) }}
   <script type="text/javascript">

scout/server/blueprints/panels/templates/panels/panel.html

@@ -180,7 +180,11 @@
               <td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
               <td>{{ 'Yes' if gene.reduced_penetrance }}</td>
               <td>{{ 'Yes' if gene.mosaicism }}</td>
-              <td>{{ gene.database_entry_version }}</td>
+              <td class="d-flex justify-content-center">
+                {% if gene.database_entry_version and gene.database_entry_version|string == panel.version|string %}
+                   <span class="badge bg-success rounded-pill" data-bs-toggle="tooltip" data-bs-placement="right" data-bs-html="true" title="This gene has been introduced in the panel starting from version {{gene.database_entry_version}}.">new</span>
+                {% endif %}
+              </td>
               <td>{{ gene.inheritance_models|join(', ') }}</td>
               <td>{{ gene.custom_inheritance_models|join(', ') }}</td>
               <td>{{ gene.comment }}</td>

scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html

@@ -69,7 +69,11 @@
           <td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
           <td>{{ 'Reduced penetrance' if gene.reduced_penetrance }}</td>
           <td>{{ 'Mosaicism' if gene.mosaicism }}</td>
-          <td>{{ gene.database_entry_version }}</td>
+          <td>
+            {% if gene.database_entry_version and gene.database_entry_version|string == panel.version|string %}
+              <span class="badge bg-success rounded-pill">new</span>
+            {% endif %}
+          </td>
           <td>{{ gene.inheritance_models|join(', ') }}</td>
           <td>{{ gene.custom_inheritance_models|join(', ') }}</td>
           <td>{{ gene.comment }}</td>

scout/server/blueprints/variant/controllers.py

@@ -63,6 +63,7 @@ def tx_overview(variant_obj: dict):
         variant_obj(dict)
     """
     overview_txs = []  # transcripts to be shown in transcripts overview
+    ensembl_txid_mane_transcripts = {}
     if variant_obj.get("genes") is None:
         variant_obj["overview_transcripts"] = []
         return
@@ -89,7 +90,6 @@ def tx_overview(variant_obj: dict):
             ovw_tx["muted_refseq_ids"] = []
 
             for refseq_id in tx.get("refseq_identifiers", []):
-                decorated_tx = None
                 if ovw_tx["mane"] and ovw_tx["mane"].startswith(refseq_id):
                     decorated_tx = ovw_tx["mane"]
                 elif ovw_tx["mane_plus"] and ovw_tx["mane_plus"].startswith(refseq_id):
@@ -121,12 +121,17 @@ def tx_overview(variant_obj: dict):
             ovw_tx["cbioportal_link"] = tx.get("cbioportal_link")
             ovw_tx["mycancergenome_link"] = tx.get("mycancergenome_link")
 
+            ensembl_txid_mane_transcripts[tx.get("transcript_id")] = {
+                "mane": ovw_tx["mane"],
+                "mane_plus": ovw_tx["mane_plus"],
+            }
             overview_txs.append(ovw_tx)
 
     # sort txs for the presence of "mane_select_transcript" and "mane_plus_clinical_transcript"
     variant_obj["overview_transcripts"] = sorted(
         overview_txs, key=lambda tx: (tx["mane"], tx["mane_plus"]), reverse=True
     )
+    variant_obj["mane_transcripts"] = ensembl_txid_mane_transcripts
 
 
 def get_igv_tracks(build: str = "37") -> set:

scout/server/blueprints/variant/templates/variant/buttons.html

@@ -1,33 +1,34 @@
 {% macro database_buttons(variant) %}
 <div class="mt-3">
-  <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{ variant.swegen_link }}" target="_blank">SweGen</a>
-  <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{ variant.beacon_link }}" target="_blank">Beacon</a>
+  <a class="btn btn-sm btn-info text-white me-1 mb-1"  href="{{ variant.swegen_link }}" rel="noreferrer noopener" target="_blank">SweGen</a>
+  <a class="btn btn-sm btn-info text-white me-1 mb-1"  href="{{ variant.beacon_link }}" rel="noreferrer noopener" target="_blank">Beacon</a>
+    <a class="btn btn-sm btn-info text-white me-1 mb-1"  href="{{ variant.franklin_link }}" rel="noreferrer noopener" target="_blank">Franklin</a>
   {% if variant.cosmic_links %} <!-- This is a list of tuples : [(id1, link1), (id2, link2), ..] -->
     {% for cosmic_link in variant.cosmic_links %}
-      <a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{cosmic_link[1]}}" target="_blank">{{cosmic_link[0]}}</a>
+      <a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" href="{{cosmic_link[1]}}" target="_blank">{{cosmic_link[0]}}</a>
     {% endfor %}
   {% endif %}
   {% if variant.dbsnp_id %}
     {% for snp in variant.dbsnp_id.split(';') %}
-      <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank" href="{{variant.snp_links[snp]}}">dbSNP ({{ snp }})</a>
+      <a class="btn btn-sm btn-info text-white me-1 mb-1"  target="_blank" rel="noreferrer noopener" href="{{variant.snp_links[snp]}}">dbSNP ({{ snp }})</a>
     {% endfor %}
   {% endif %}
 </div>
 <div class="btn-group">
   {% if primary_transcript and primary_transcript.varsome_link %}
-  <a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+  <a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
     data-bs-toggle="tooltip" title="Varsome">V</a>
   {% endif %}
   {% if primary_transcript and primary_transcript.tp53_link %}
-    <a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+    <a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
       data-bs-toggle="tooltip" title="MutanTP53">TP53</a>
   {% endif %}
   {% if primary_transcript and primary_transcript.cbioportal_link %}
-    <a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+    <a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
       data-bs-toggle="tooltip" title="cBioPortal">CBP</a>
   {% endif %}
   {% if primary_transcript and primary_transcript.mycancergenome_link %}
-    <a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+    <a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
       data-bs-toggle="tooltip" title="MyCancerGenome">MCG</a>
   {% endif %}
 </div>
@@ -36,10 +37,10 @@
 {% macro splice_junctions_button(institute_id, case, variant_id, omics_variant_id) %}
   {% if omics_variant_id %}
     <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case.display_name, omics_variant_id=omics_variant_id)}}" target="_blank"
-    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA splicing</a>
+    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}"><span class="fa fa-magnifying-glass fa-fw me-1"></span>IGV RNA</a>
   {% else %}
     <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case.display_name, variant_id=variant_id)}}" target="_blank"
-    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA splicing</a>
+    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}"><span class="fa fa-magnifying-glass fa-fw me-1"></span>IGV RNA</a>
   {%  endif  %}
 {% endmacro %}
 

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

@@ -66,51 +66,70 @@
 {% endmacro %}
 
 {% macro alignments(institute, case, variant, current_user, config, igv_tracks, has_rna_tracks=False) %}
-   <ul class="list-group">
-        <li class="list-group-item d-flex justify-content-between">
-          {% if variant.chromosome in ["MT","M"] and case.mt_bams or case.bam_files %}
-            <span><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}" target="_blank">IGV viewer</a></span>
-          {% else %}
-            <span class="text-muted">BAM file(s) missing</span>
-          {% endif %}
-          {% if variant.category == "str" %}
-            <div class="ms-1">
-              {{ reviewer_button(case,variant,case_groups,institute._id) }}
-            </div>
-          {% endif %}
-          {% if has_rna_tracks %}
-            <div class="ms-1">
-              {{ splice_junctions_button(institute._id, case, variant._id) }}
-            </div>
-          {% endif %}
-          {% if variant.alamut_link %}
-            <div class="ms-1">
-              <a href="{{ variant.alamut_link }}" class="btn btn-sm btn-secondary" role="button" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with genome g. coordinate">Alamut g.</a>
-            </div>
-          {% endif %}
+  <ul class="list-group">
+    <li class="list-group-item d-flex justify-content-between">
+      {% if variant.is_mitochondrial and not case.mt_bams %}
+        <span data-bs-toggle="tooltip" title="Alignment file(s) missing">
+          <a href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}"
+             target="_blank"
+             class="btn btn-secondary btn-sm text-white disabled" aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV mtDNA
+          </a>
+        </span>
+      {% elif not case.bam_files and not variant.is_mitochondrial %}
+        <span data-bs-toggle="tooltip" title="Alignment file(s) missing">
+          <a href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}"
+            target="_blank"
+            class="btn btn-secondary btn-sm text-white disabled"
+            aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV gDNA
+          </a>
+        </span>
+      {% else %}
+        <span>
+          <a href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}"
+            target="_blank"
+            class="btn btn-secondary btn-sm text-white"><span class="fa fa-magnifying-glass fa-fw me-1"></span>
+            IGV {% if variant.is_mitochondrial %}mt{% else %}g{% endif %}DNA
+          </a>
+        </span>
+      {% endif %}
+      {% if variant.category == "str" %}
+        <div class="ms-1">
+          {{ reviewer_button(case,variant,case_groups,institute._id) }}
+        </div>
+      {% endif %}
+      {% if has_rna_tracks %}
+        <div class="ms-1">
+          {{ splice_junctions_button(institute._id, case, variant._id) }}
+        </div>
+      {% endif %}
+      {% if variant.alamut_link %}
+        <div class="ms-1">
+          <a href="{{ variant.alamut_link }}" class="btn btn-sm btn-secondary" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with genome g. coordinate">Alamut g.</a>
+        </div>
+      {% endif %}
+      {% for gene in variant.genes %}
+        <div class="d-flex flex-wrap ms-1">
+        {% if gene.alamut_link %}
+          <a href="{{ gene.alamut_link }}" class="btn btn-sm btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate">Alamut {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} c.</a>
+        {% endif %}
+        </div>
+      {% endfor %}
+      {% if config.chanjo_report %}
+        <div class="d-flex flex-wrap ms-1">
           {% for gene in variant.genes %}
-            <div class="d-flex flex-wrap ms-1">
-            {% if gene.alamut_link %}
-              <a href="{{ gene.alamut_link }}" class="btn btn-sm btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate">Alamut {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} c.</a>
-            {% endif %}
-            </div>
+            <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}">
+              Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
+            </a>
           {% endfor %}
-          {% if config.chanjo_report %}
-            <div class="d-flex flex-wrap ms-1">
-              {% for gene in variant.genes %}
-                <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}">
-                  Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
-                </a>
-              {% endfor %}
-            </div>
-          {% endif %}
-        </li>
-        <li class="list-group-item">
-          <div>
-            {{ igv_track_selection(igv_tracks, current_user) }}
-          </div>
-        </li>
-      </ul>
+        </div>
+      {% endif %}
+    </li>
+    <li class="list-group-item">
+      <div>
+        {{ igv_track_selection(igv_tracks, current_user) }}
+      </div>
+    </li>
+  </ul>
 {% endmacro %}
 
 {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
@@ -224,7 +243,7 @@
       <div class="card-body mt-1 ms-3 mb-1" style="padding: 0;">
         Matching tiered:&nbsp;
         {% for tier, tiered_info in matching_tiered.items() %}
-          <a style="padding: 0;" class="btn btn-{{tiered_info.label}} btn-xs" data-bs-toggle="collapse" href="#collapse_{{tier}}" role="button" aria-expanded="false" aria-controls="collapseExample">
+          <a style="padding: 0;" class="btn btn-{{tiered_info.label}} btn-xs" data-bs-toggle="collapse" href="#collapse_{{tier}}" aria-expanded="false" aria-controls="collapseExample">
             {{tier}} ({{tiered_info.links|length}}x)
           </a>
           <div class="collapse" id="collapse_{{tier}}">

scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html

@@ -2,7 +2,7 @@
 {% from "utils.html" import comments_table, pedigree_panel %}
 {% from "variants/components.html" import 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 %}
-{% from "variant/buttons.html" import igv_button, reviewer_button%}
+{% from "variant/buttons.html" import reviewer_button%}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - STR variants