scout-browser 4.90.1__py3-none-any.whl → 4.91__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scout/__version__.py +1 -1
- scout/adapter/mongo/case.py +27 -38
- scout/commands/export/variant.py +14 -4
- scout/commands/load/panel.py +2 -1
- scout/commands/update/panelapp.py +11 -3
- scout/commands/view/case.py +2 -2
- scout/constants/__init__.py +1 -2
- scout/constants/acmg.py +15 -15
- scout/constants/case_tags.py +0 -46
- scout/constants/clnsig.py +2 -1
- scout/constants/gene_tags.py +0 -6
- scout/constants/panels.py +16 -0
- scout/constants/variants_export.py +2 -0
- scout/demo/__init__.py +4 -1
- scout/demo/panelapp_panel.json +463 -0
- scout/demo/panelapp_panels_reduced.json +37 -0
- scout/load/panel.py +3 -142
- scout/load/panelapp.py +138 -0
- scout/models/case/case_loading_models.py +5 -4
- scout/parse/panel.py +3 -117
- scout/parse/panelapp.py +112 -0
- scout/parse/variant/clnsig.py +26 -21
- scout/parse/variant/genotype.py +6 -5
- scout/server/blueprints/alignviewers/controllers.py +7 -5
- scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
- scout/server/blueprints/cases/templates/cases/case_sma.html +49 -42
- scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +27 -12
- scout/server/blueprints/cases/views.py +18 -7
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +7 -7
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +2 -2
- scout/server/blueprints/dashboard/controllers.py +128 -165
- scout/server/blueprints/dashboard/forms.py +3 -13
- scout/server/blueprints/dashboard/templates/dashboard/dashboard_general.html +17 -22
- scout/server/blueprints/institutes/forms.py +1 -2
- scout/server/blueprints/institutes/templates/overview/cases.html +2 -133
- scout/server/blueprints/institutes/templates/overview/utils.html +135 -0
- scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +5 -0
- scout/server/blueprints/panels/templates/panels/panel.html +5 -1
- scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html +5 -1
- scout/server/blueprints/variant/controllers.py +6 -1
- scout/server/blueprints/variant/templates/variant/buttons.html +11 -10
- scout/server/blueprints/variant/templates/variant/components.html +63 -44
- scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html +1 -1
- scout/server/blueprints/variant/templates/variant/utils.html +38 -10
- scout/server/blueprints/variant/templates/variant/variant.html +1 -1
- scout/server/blueprints/variants/controllers.py +9 -4
- scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html +9 -5
- scout/server/blueprints/variants/templates/variants/cancer-variants.html +6 -17
- scout/server/blueprints/variants/templates/variants/str-variants.html +2 -2
- scout/server/blueprints/variants/templates/variants/sv-variants.html +8 -1
- scout/server/blueprints/variants/templates/variants/utils.html +14 -0
- scout/server/extensions/__init__.py +2 -0
- scout/server/extensions/panelapp_extension.py +75 -0
- scout/server/links.py +19 -1
- scout/server/utils.py +25 -33
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/METADATA +1 -1
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/RECORD +61 -57
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/WHEEL +1 -1
- scout/demo/panelapp_test_panel.json +0 -79
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/LICENSE +0 -0
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/top_level.txt +0 -0
@@ -1,4 +1,5 @@
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{% extends "layout.html" %}
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{% from "overview/utils.html" import cases_search_form %}
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{% block top_nav %}
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{{ super() }}
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<div class="container-float mt-3">
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<!--filter panel -->
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<div>
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{{
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{{ cases_search_form(dashboard_form, url_for('dashboard.index'), url_for('dashboard.index'), urlnone) }}
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{% if total_cases == 0 %}
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<div class="alert alert-danger mt-3">Your search didn't return any results!</div>
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{% elif not total_cases %}
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<script src="{{ url_for('dashboard.static', filename='charts.js') }}"></script>
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<script type="text/javascript">
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//
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var searchTerm = document.getElementById('search_term'); // Case search term label
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var sel = document.getElementById('search_type'); // Case search term select
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document.getElementById("search_type").onchange = function() {
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// Change case search term placeholder
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selectedKey = sel.options[sel.selectedIndex].value.slice(0, -1);
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if(selectedKey){
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searchTerm.placeholder=caseSearchTerms[selectedKey]["placeholder"];
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searchTerm.disabled = false;
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}
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else{
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searchTerm.disabled = (sel.value == "");
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searchTerm.placeholder="Search term";
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}
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// Reset search
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searchTerm.value="";
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};
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// Show/hide advanced search options
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let advSearchBlock = $('#advancesSearchOptions');
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$(
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searchTerm.disabled = (sel.value == "");
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});
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let advBlockCheckbox = $('#advanced_search');
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window.onload = function(){
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if(!advBlockCheckbox.is(':checked'))
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advSearchBlock.hide();
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}
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advBlockCheckbox.on('click', function() {
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if($(this).is(':checked')) {
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advSearchBlock.show();
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} else {
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advSearchBlock.hide();
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}
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})
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{% if cases %}
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//create analysis type chart ===> general stats
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@@ -13,10 +13,9 @@ from wtforms import (
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)
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from wtforms.widgets import PasswordInput, TextInput
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from scout.constants import
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from scout.constants import PHENOTYPE_GROUPS
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from scout.models.case import STATUS
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CASE_SEARCH_KEY = [(value["prefix"], value["label"]) for key, value in CASE_SEARCH_TERMS.items()]
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CATEGORY_CHOICES = [("snv", "SNV"), ("sv", "SV")]
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{% import "bootstrap/wtf.html" as wtf %}
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{% extends "layout.html" %}
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{% from "overview/institute_sidebar.html" import institute_actionbar %}
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{% from "overview/utils.html" import analysis_type %}
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{% from "overview/utils.html" import analysis_type, cases_search_form %}
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{% block title %}
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{{ super() }} - {{ institute.display_name }} - Cases
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</li>
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{% endblock %}
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{% macro search_form() %}
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<!-- Collect advanced search key/values -->
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{% set search = {} %}
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{% for field in form._fields %}
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{% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
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{% do search.update({field: form._fields[field].data}) %}
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{% endif %}
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{% endfor %}
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<form action="{{ url_for('overview.cases', institute_id=institute._id) }}" method="POST" accept-charset="utf-8">
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{{ form.hidden_tag() }}
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<div class="row">
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<div class="col-md-3 mb-3">
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{{ form.case.label(class="form-label") }}
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{{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-1 mb-3">
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{{ form.search_limit.label(class="form-label") }}
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{{ form.search_limit(class="form-control") }}
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</div>
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<div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
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{{ form.search(class="btn btn-lg btn-primary mt-4") }}
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</div>
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<div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
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<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>
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</div>
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<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.">
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{{ form.advanced_search(class="form-check-input") }}
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{{ form.advanced_search.label(class="form-check-label") }}
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</div>
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</div>
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<div class="row">
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<div class="col-md-2 mb-3 form-check ms-3">
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{{ form.skip_assigned(class="form-check-input") }}
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{{ form.skip_assigned.label(class="form-check-label") }}
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</div>
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<div class="col-md-2 mb-3 form-check">
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{{ form.is_research(class="form-check-input") }}
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{{ form.is_research.label(class="form-check-label") }}
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</div>
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<div class="col-md-2 mb-3 form-check">
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{{ form.clinvar_submitted(class="form-check-input") }}
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{{ form.clinvar_submitted.label(class="form-check-label") }}
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</div>
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<div class="col-md-2 mb-3 form-check">
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{{ form.has_rna(class="form-check-input") }}
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{{ form.has_rna.label(class="form-check-label") }}
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</div>
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<div class="col-md-2 mb-3 form-check">
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{{ form.validation_ordered(class="form-check-input") }}
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{{ form.validation_ordered.label(class="form-check-label") }}
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</div>
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</div>
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<!-- This div contains the advances search options -->
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<div id="advancesSearchOptions">
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<div class="row">
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<div class="col-md-4 mb-3">
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{{ form.exact_pheno.label(class="form-label") }}
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{{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.exact_dia.label(class="form-label") }}
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{{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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</div>
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<div class="row">
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<div class="col-md-4 mb-3">
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{{ form.synopsis.label(class="form-label") }}
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{{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.panel.label(class="form-label") }}
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{{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.status.label(class="form-label") }}
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{{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="row">
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<div class="col-md-4 mb-3">
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{{ form.tags.label(class="form-label") }}
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{{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.track.label(class="form-label") }}
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{{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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{{ form.pheno_group.label(class="form-label") }}
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{{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="row">
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<div class="col-md-4 mb-3">
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{{ form.cohort.label(class="form-label") }}
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{{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.similar_case.label(class="form-label") }}
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{{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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{{ form.similar_pheno.label(class="form-label") }}
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{{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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</div>
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<div class="row">
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<div class="col-md-4 mb-3">
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{{ form.pinned.label(class="form-label") }}
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{{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.causative.label(class="form-label") }}
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{{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-4 mb-3">
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{{ form.user.label(class="form-label") }}
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{{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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</div>
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</div> <!--End of advancedSearchOptions div -->
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</form>
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<div>
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<span class="text-muted">The following search criteria were used: {{search}}</span>
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</div>
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{% endmacro %}
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{% macro cases_table(group_name, cases) %}
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{% if sort_order == 'asc' %}
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{% set sort_option = 'desc'%}
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<div class="container-float">
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<div class="card panel-default">
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<div class="card-body">
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{{
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{{ cases_search_form(form, url_for('overview.cases', institute_id=institute._id), url_for('overview.cases', institute_id=institute._id), institute) }}
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</div>
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<div class="card-footer text-center">
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Showing {{ found_cases }} / {{ nr_cases }} cases
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{% from "variants/components.html" import variant_gene_symbols_cell, variant_funct_anno_cell, fusion_variant_gene_symbols_cell %}
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{% macro cases_search_form(form, form_action, reset_action, institute = none) %}
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<!-- Collect advanced search key/values -->
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{% set search = {} %}
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{% for field in form._fields %}
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{% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
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{% do search.update({field: form._fields[field].data}) %}
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{% endif %}
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{% endfor %}
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<form action="{{ form_action }}" method="POST" accept-charset="utf-8">
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{{ form.hidden_tag() }}
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<div class="row">
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{% if not institute %} <!-- used only on dashboard page, when search might return results from many institutes -->
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<div class="col-md-2 mb-3">
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{{ form.search_institute.label(class="form-label") }}
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{{ form.search_institute(class="form-control") }}
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</div>
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{% endif %}
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<div class="col-md-3 mb-3">
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{{ form.case.label(class="form-label") }}
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{{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
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</div>
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<div class="col-md-1 mb-3">
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{{ form.search_limit.label(class="form-label") }}
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{{ form.search_limit(class="form-control") }}
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</div>
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<div class="btn-sm mb-2 col-md-2 mx-auto">
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31
|
+
{{ form.search(class="btn btn-lg btn-primary mt-4") }}
|
32
|
+
<a href="{{ reset_action }}" class="btn btn-lg btn-secondary mt-4 text-white">Reset search</a>
|
33
|
+
</div>
|
34
|
+
<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.">
|
35
|
+
{{ form.advanced_search(class="form-check-input") }}
|
36
|
+
{{ form.advanced_search.label(class="form-check-label") }}
|
37
|
+
</div>
|
38
|
+
</div>
|
39
|
+
{% if institute %} <!-- The following checkboxes will be displayed when the form is used on institute caseS page only, not on the dashboard -->
|
40
|
+
<div class="row">
|
41
|
+
<div class="col-md-2 mb-3 form-check ms-3">
|
42
|
+
{{ form.skip_assigned(class="form-check-input") }}
|
43
|
+
{{ form.skip_assigned.label(class="form-check-label") }}
|
44
|
+
</div>
|
45
|
+
<div class="col-md-2 mb-3 form-check">
|
46
|
+
{{ form.is_research(class="form-check-input") }}
|
47
|
+
{{ form.is_research.label(class="form-check-label") }}
|
48
|
+
</div>
|
49
|
+
<div class="col-md-2 mb-3 form-check">
|
50
|
+
{{ form.clinvar_submitted(class="form-check-input") }}
|
51
|
+
{{ form.clinvar_submitted.label(class="form-check-label") }}
|
52
|
+
</div>
|
53
|
+
<div class="col-md-2 mb-3 form-check">
|
54
|
+
{{ form.has_rna(class="form-check-input") }}
|
55
|
+
{{ form.has_rna.label(class="form-check-label") }}
|
56
|
+
</div>
|
57
|
+
<div class="col-md-2 mb-3 form-check">
|
58
|
+
{{ form.validation_ordered(class="form-check-input") }}
|
59
|
+
{{ form.validation_ordered.label(class="form-check-label") }}
|
60
|
+
</div>
|
61
|
+
</div>
|
62
|
+
{% endif %}
|
63
|
+
<!-- This div contains the advances search options -->
|
64
|
+
<div id="advancesSearchOptions">
|
65
|
+
<div class="row">
|
66
|
+
<div class="col-md-4 mb-3">
|
67
|
+
{{ form.exact_pheno.label(class="form-label") }}
|
68
|
+
{{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
69
|
+
</div>
|
70
|
+
<div class="col-md-4 mb-3">
|
71
|
+
{{ form.exact_dia.label(class="form-label") }}
|
72
|
+
{{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
73
|
+
</div>
|
74
|
+
</div>
|
75
|
+
<div class="row">
|
76
|
+
<div class="col-md-4 mb-3">
|
77
|
+
{{ form.synopsis.label(class="form-label") }}
|
78
|
+
{{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
79
|
+
</div>
|
80
|
+
<div class="col-md-4 mb-3">
|
81
|
+
{{ form.panel.label(class="form-label") }}
|
82
|
+
{{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
83
|
+
</div>
|
84
|
+
<div class="col-md-4 mb-3">
|
85
|
+
{{ form.status.label(class="form-label") }}
|
86
|
+
{{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
87
|
+
</div>
|
88
|
+
</div>
|
89
|
+
<div class="row">
|
90
|
+
<div class="col-md-4 mb-3">
|
91
|
+
{{ form.tags.label(class="form-label") }}
|
92
|
+
{{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
93
|
+
</div>
|
94
|
+
<div class="col-md-4 mb-3">
|
95
|
+
{{ form.track.label(class="form-label") }}
|
96
|
+
{{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
97
|
+
</div>
|
98
|
+
<div class="col-md-4 mb-3">
|
99
|
+
{{ form.pheno_group.label(class="form-label") }}
|
100
|
+
{{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
101
|
+
</div>
|
102
|
+
</div>
|
103
|
+
<div class="row">
|
104
|
+
<div class="col-md-4 mb-3">
|
105
|
+
{{ form.cohort.label(class="form-label") }}
|
106
|
+
{{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
107
|
+
</div>
|
108
|
+
<div class="col-md-4 mb-3">
|
109
|
+
{{ form.similar_case.label(class="form-label") }}
|
110
|
+
{{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
111
|
+
</div>
|
112
|
+
<div class="col-md-4 mb-3">
|
113
|
+
{{ form.similar_pheno.label(class="form-label") }}
|
114
|
+
{{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
115
|
+
</div>
|
116
|
+
</div>
|
117
|
+
<div class="row">
|
118
|
+
<div class="col-md-4 mb-3">
|
119
|
+
{{ form.pinned.label(class="form-label") }}
|
120
|
+
{{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
121
|
+
</div>
|
122
|
+
<div class="col-md-4 mb-3">
|
123
|
+
{{ form.causative.label(class="form-label") }}
|
124
|
+
{{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
125
|
+
</div>
|
126
|
+
<div class="col-md-4 mb-3">
|
127
|
+
{{ form.user.label(class="form-label") }}
|
128
|
+
{{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
|
129
|
+
</div>
|
130
|
+
</div>
|
131
|
+
</div> <!--End of advancedSearchOptions div -->
|
132
|
+
</form>
|
133
|
+
<div>
|
134
|
+
<span class="text-muted">The following search criteria were used: {{search}}</span>
|
135
|
+
</div>
|
136
|
+
{% endmacro %}
|
137
|
+
|
3
138
|
{% macro analysis_type(analysis_types) %}
|
4
139
|
{% for analysis_type in analysis_types %}
|
5
140
|
{% if analysis_type == 'wgs' %}
|
@@ -5,6 +5,7 @@
|
|
5
5
|
{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell %}
|
6
6
|
{% from "variant/buttons.html" import splice_junctions_button %}
|
7
7
|
{% from "variants/utils.html" import filter_script_main, pagination_footer, pagination_hidden_div, stash_filter_buttons, update_stash_filter_button_status%}
|
8
|
+
{% from "variant/components.html" import variant_scripts %}
|
8
9
|
|
9
10
|
{% block title %}
|
10
11
|
{{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ form.variant_type.data|capitalize }} omics outlier variants
|
@@ -117,6 +118,9 @@
|
|
117
118
|
</td>
|
118
119
|
<td class="text-end">{{ variant.chromosome }}</td>
|
119
120
|
<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>
|
121
|
+
<button type="button" class="fa fa-copy btn-xs js-tooltip js-copy"
|
122
|
+
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">
|
123
|
+
</button>
|
120
124
|
{% if case.has_rna_tracks %}
|
121
125
|
{{ splice_junctions_button(institute._id, case, None, variant.omics_variant_id) }}
|
122
126
|
{% endif %}
|
@@ -142,6 +146,7 @@
|
|
142
146
|
{% block scripts %}
|
143
147
|
{{ super() }}
|
144
148
|
{{ external_scripts() }}
|
149
|
+
{{ variant_scripts() }}
|
145
150
|
<script src="{{ url_for('variants.static', filename='form_scripts.js') }}"></script>
|
146
151
|
{{ filter_script_main(cytobands) }}
|
147
152
|
<script type="text/javascript">
|
@@ -180,7 +180,11 @@
|
|
180
180
|
<td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
|
181
181
|
<td>{{ 'Yes' if gene.reduced_penetrance }}</td>
|
182
182
|
<td>{{ 'Yes' if gene.mosaicism }}</td>
|
183
|
-
<td
|
183
|
+
<td class="d-flex justify-content-center">
|
184
|
+
{% if gene.database_entry_version and gene.database_entry_version|string == panel.version|string %}
|
185
|
+
<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>
|
186
|
+
{% endif %}
|
187
|
+
</td>
|
184
188
|
<td>{{ gene.inheritance_models|join(', ') }}</td>
|
185
189
|
<td>{{ gene.custom_inheritance_models|join(', ') }}</td>
|
186
190
|
<td>{{ gene.comment }}</td>
|
@@ -69,7 +69,11 @@
|
|
69
69
|
<td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
|
70
70
|
<td>{{ 'Reduced penetrance' if gene.reduced_penetrance }}</td>
|
71
71
|
<td>{{ 'Mosaicism' if gene.mosaicism }}</td>
|
72
|
-
<td>
|
72
|
+
<td>
|
73
|
+
{% if gene.database_entry_version and gene.database_entry_version|string == panel.version|string %}
|
74
|
+
<span class="badge bg-success rounded-pill">new</span>
|
75
|
+
{% endif %}
|
76
|
+
</td>
|
73
77
|
<td>{{ gene.inheritance_models|join(', ') }}</td>
|
74
78
|
<td>{{ gene.custom_inheritance_models|join(', ') }}</td>
|
75
79
|
<td>{{ gene.comment }}</td>
|
@@ -63,6 +63,7 @@ def tx_overview(variant_obj: dict):
|
|
63
63
|
variant_obj(dict)
|
64
64
|
"""
|
65
65
|
overview_txs = [] # transcripts to be shown in transcripts overview
|
66
|
+
ensembl_txid_mane_transcripts = {}
|
66
67
|
if variant_obj.get("genes") is None:
|
67
68
|
variant_obj["overview_transcripts"] = []
|
68
69
|
return
|
@@ -89,7 +90,6 @@ def tx_overview(variant_obj: dict):
|
|
89
90
|
ovw_tx["muted_refseq_ids"] = []
|
90
91
|
|
91
92
|
for refseq_id in tx.get("refseq_identifiers", []):
|
92
|
-
decorated_tx = None
|
93
93
|
if ovw_tx["mane"] and ovw_tx["mane"].startswith(refseq_id):
|
94
94
|
decorated_tx = ovw_tx["mane"]
|
95
95
|
elif ovw_tx["mane_plus"] and ovw_tx["mane_plus"].startswith(refseq_id):
|
@@ -121,12 +121,17 @@ def tx_overview(variant_obj: dict):
|
|
121
121
|
ovw_tx["cbioportal_link"] = tx.get("cbioportal_link")
|
122
122
|
ovw_tx["mycancergenome_link"] = tx.get("mycancergenome_link")
|
123
123
|
|
124
|
+
ensembl_txid_mane_transcripts[tx.get("transcript_id")] = {
|
125
|
+
"mane": ovw_tx["mane"],
|
126
|
+
"mane_plus": ovw_tx["mane_plus"],
|
127
|
+
}
|
124
128
|
overview_txs.append(ovw_tx)
|
125
129
|
|
126
130
|
# sort txs for the presence of "mane_select_transcript" and "mane_plus_clinical_transcript"
|
127
131
|
variant_obj["overview_transcripts"] = sorted(
|
128
132
|
overview_txs, key=lambda tx: (tx["mane"], tx["mane_plus"]), reverse=True
|
129
133
|
)
|
134
|
+
variant_obj["mane_transcripts"] = ensembl_txid_mane_transcripts
|
130
135
|
|
131
136
|
|
132
137
|
def get_igv_tracks(build: str = "37") -> set:
|
@@ -1,33 +1,34 @@
|
|
1
1
|
{% macro database_buttons(variant) %}
|
2
2
|
<div class="mt-3">
|
3
|
-
<a class="btn btn-sm btn-info text-white me-1 mb-1"
|
4
|
-
<a class="btn btn-sm btn-info text-white me-1 mb-1"
|
3
|
+
<a class="btn btn-sm btn-info text-white me-1 mb-1" href="{{ variant.swegen_link }}" rel="noreferrer noopener" target="_blank">SweGen</a>
|
4
|
+
<a class="btn btn-sm btn-info text-white me-1 mb-1" href="{{ variant.beacon_link }}" rel="noreferrer noopener" target="_blank">Beacon</a>
|
5
|
+
<a class="btn btn-sm btn-info text-white me-1 mb-1" href="{{ variant.franklin_link }}" rel="noreferrer noopener" target="_blank">Franklin</a>
|
5
6
|
{% if variant.cosmic_links %} <!-- This is a list of tuples : [(id1, link1), (id2, link2), ..] -->
|
6
7
|
{% for cosmic_link in variant.cosmic_links %}
|
7
|
-
<a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1"
|
8
|
+
<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>
|
8
9
|
{% endfor %}
|
9
10
|
{% endif %}
|
10
11
|
{% if variant.dbsnp_id %}
|
11
12
|
{% for snp in variant.dbsnp_id.split(';') %}
|
12
|
-
<a class="btn btn-sm btn-info text-white me-1 mb-1"
|
13
|
+
<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>
|
13
14
|
{% endfor %}
|
14
15
|
{% endif %}
|
15
16
|
</div>
|
16
17
|
<div class="btn-group">
|
17
18
|
{% if primary_transcript and primary_transcript.varsome_link %}
|
18
|
-
<a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"
|
19
|
+
<a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
|
19
20
|
data-bs-toggle="tooltip" title="Varsome">V</a>
|
20
21
|
{% endif %}
|
21
22
|
{% if primary_transcript and primary_transcript.tp53_link %}
|
22
|
-
<a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"
|
23
|
+
<a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
|
23
24
|
data-bs-toggle="tooltip" title="MutanTP53">TP53</a>
|
24
25
|
{% endif %}
|
25
26
|
{% if primary_transcript and primary_transcript.cbioportal_link %}
|
26
|
-
<a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"
|
27
|
+
<a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
|
27
28
|
data-bs-toggle="tooltip" title="cBioPortal">CBP</a>
|
28
29
|
{% endif %}
|
29
30
|
{% if primary_transcript and primary_transcript.mycancergenome_link %}
|
30
|
-
<a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"
|
31
|
+
<a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
|
31
32
|
data-bs-toggle="tooltip" title="MyCancerGenome">MCG</a>
|
32
33
|
{% endif %}
|
33
34
|
</div>
|
@@ -36,10 +37,10 @@
|
|
36
37
|
{% macro splice_junctions_button(institute_id, case, variant_id, omics_variant_id) %}
|
37
38
|
{% if omics_variant_id %}
|
38
39
|
<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"
|
39
|
-
data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA
|
40
|
+
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>
|
40
41
|
{% else %}
|
41
42
|
<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"
|
42
|
-
data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA
|
43
|
+
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>
|
43
44
|
{% endif %}
|
44
45
|
{% endmacro %}
|
45
46
|
|