scout-browser 4.89.1__py3-none-any.whl → 4.90__py3-none-any.whl

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

@@ -72,7 +72,7 @@
               <td class="text-end">
                 <div class="d-flex flex-row justify-content-between">
                 {% if variant.genes %}
-                  {{ gene_cell(variant) }}
+                  {{ gene_cell(variant, inherit_palette) }}
                 {% else %}
                   {{ variant.gene_name_orig }}
                 {% endif %}

scout/server/blueprints/omics_variants/views.py

@@ -2,6 +2,7 @@ from flask import Blueprint, request
 from flask_login import current_user
 from markupsafe import Markup
 
+from scout.constants import INHERITANCE_PALETTE
 from scout.server.blueprints.variants.controllers import (
     activate_case,
     case_default_panels,
@@ -97,6 +98,7 @@ def outliers(institute_id, case_name):
         expand_search=get_expand_search(request.form),
         filters=available_filters,
         form=form,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         page=page,
         result_size=result_size,

scout/server/blueprints/panels/controllers.py

@@ -2,10 +2,13 @@
 import datetime as dt
 import logging
 import re
+from typing import List, Optional, Union
 
-from flask import flash, redirect
+from flask import Response, flash, redirect
 from flask_login import current_user
+from werkzeug.local import LocalProxy
 
+from scout.adapter import MongoAdapter
 from scout.build.panel import build_panel
 from scout.constants import DATE_DAY_FORMATTER
 from scout.parse.panel import parse_genes
@@ -45,14 +48,8 @@ def panel_decode_lines(panel_file):
     return lines
 
 
-def create_new_panel(store, request, lines):
+def create_new_panel(store: MongoAdapter, request: LocalProxy, lines: List[str]) -> Optional[str]:
     """Create a new gene panel with the data provided using the form
-
-    Args:
-        store(scout.adapter.MongoAdapter)
-        request(flask.request) request sent by browser form to the /panels endpoint
-        lines(list): list of lines containing gene data
-
     Returns:
         new_panel_id(str): the _id a newly created panel
     """
@@ -107,17 +104,12 @@ def update_existing_panel(store, request, lines):
         )
 
 
-def panel_create_or_update(store, request):
+def panel_create_or_update(store: MongoAdapter, request: LocalProxy) -> Union[str, Response]:
     """Process a user request to create a new gene panel
 
-    Args:
-        store(scout.adapter.MongoAdapter)
-        request(flask.request) request sent by browser form to the /panels endpoint
-
     Returns:
         redirect_id(str): the ID of the panel to redirect the page to
     """
-    redirect_id = None
     panel_file = request.files["panel_file"]
     lines = panel_decode_lines(panel_file)
 
@@ -324,9 +316,9 @@ def downloaded_panel_name(panel_obj, format) -> str:
 
 def panel_data(store, panel_obj):
     """Preprocess a panel of genes."""
+
     panel_obj["institute"] = store.institute(panel_obj["institute"])
-    full_name = "{}({})".format(panel_obj["display_name"], panel_obj["version"])
-    panel_obj["name_and_version"] = full_name
+    panel_obj["name_and_version"] = "{}({})".format(panel_obj["display_name"], panel_obj["version"])
 
     return dict(panel=panel_obj)
 

scout/server/blueprints/panels/templates/panels/gene-edit.html

@@ -28,13 +28,13 @@
               </select>
             </div>
             <div class="col-md-4">
+              {{ form.reduced_penetrance() }}
               {{ form.reduced_penetrance.label(class="control-label") }}
               (OMIM: {{ 'Yes' if gene.incomplete_penetrance else 'unknown' }})
-              <div>{{ form.reduced_penetrance() }}</div>
             </div>
             <div class="col-md-4">
+              {{ form.mosaicism() }}
               {{ form.mosaicism.label(class="control-label") }}
-              <div>{{ form.mosaicism() }}</div>
             </div>
           </div>
           <div class="row">

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

@@ -107,16 +107,24 @@
       {% if case and case.chanjo2_coverage and panel.genes %}
         <li class="list-group-item">
           <label for="coverage_report">Coverage report (chanjo2)</label>
-          <span class="float-end">
+          <span class="float-end" style="cursor: pointer;">
           {{ chanjo2_report_form(panel.institute, case, panel.name_and_version, 'report', panel.genes|map(attribute='hgnc_id')|join(','), case.display_name) }} <!--chanjo2 report-->
           </span>
         </li>
         <li class="list-group-item">
           <label for="coverage_report">Coverage overview (chanjo2)</label>
-          <span class="float-end">
+          <span class="float-end" style="cursor: pointer;">
           {{ chanjo2_report_form(panel.institute, case, panel.name_and_version, 'overview', panel.genes|map(attribute='hgnc_id')|join(','), case.display_name) }} <!--chanjo2 genes overview -->
           </span>
         </li>
+        {% if "38" in case.genome_build %}
+          <li class="list-group-item">
+          <label for="coverage_report">MANE coverage overview (chanjo2)</label>
+          <span class="float-end" style="cursor: pointer;">
+          {{ chanjo2_report_form(panel.institute, case, panel.name_and_version, 'mane_overview', panel.genes|map(attribute='hgnc_id')|join(','), case.display_name) }} <!--chanjo2 MANE overview -->
+          </span>
+        </li>
+        {% endif %}
       {% endif %}
       <li class="list-group-item">
         <div class="d-flex justify-content-between">
@@ -138,21 +146,30 @@
       <table class="table table-bordered" aria-label="Included genes">
         <thead class="table-light thead">
           <tr>
+            <th></th>
             <th>Gene</th>
             <th>HGNC ID</th>
-            <th>Transcripts</th>
+            <th>Disease-associated transcripts</th>
             <th>Reduced penetrance</th>
             <th>Mosaicism</th>
             <th>Entry version</th>
             <th>Manual inheritance (pre-set terms)</th>
             <th>Manual inheritance (free text terms)</th>
             <th>Comment</th>
-            <th>Action</th>
           </tr>
         </thead>
         <tbody>
           {% for gene in panel.genes|sort(attribute='symbol') %}
             <tr>
+              <td>
+                {% if not panel.is_archived %}
+                  <form class="float-start" action="{{ url_for('panels.panel', panel_id=panel._id) }}" method="POST">
+                    <input type="hidden" name="hgnc_id" value="{{ gene.hgnc_id }}">
+                    <button name="action" type="submit" value="delete" class="btn btn-danger btn-xs">Delete</button>
+                  </form>
+                  <a class="btn btn-secondary text-white btn-xs ms-1" href="{{ url_for('panels.gene_edit', panel_id=panel._id, hgnc_id=gene.hgnc_id) }}">Edit</a>
+                {% endif %}
+              </td>
               <td>
                 <a href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">
                   {{ gene.symbol }}
@@ -167,15 +184,6 @@
               <td>{{ gene.inheritance_models|join(', ') }}</td>
               <td>{{ gene.custom_inheritance_models|join(', ') }}</td>
               <td>{{ gene.comment }}</td>
-              <td>
-                {% if not panel.is_archived %}
-                  <a class="btn btn-secondary btn-xs" href="{{ url_for('panels.gene_edit', panel_id=panel._id, hgnc_id=gene.hgnc_id) }}">Edit</a>
-                  <form class="float-end" action="{{ url_for('panels.panel', panel_id=panel._id) }}" method="POST">
-                    <input type="hidden" name="hgnc_id" value="{{ gene.hgnc_id }}">
-                    <button name="action" type="submit" value="delete" class="btn btn-danger btn-xs">Delete</button>
-                  </form>
-                {% endif %}
-              </td>
             </tr>
           {% endfor %}
         </tbody>

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

@@ -18,25 +18,28 @@
   <div class="card-body">
     <table class="table table-sm">
       <tr>
-        <td>Updated:<span class="badge bg-secondary rounded-pill text-white">{{ panel.date.strftime('%Y-%m-%d') }}</span></td>
+        <td>Updated:{{ panel.date.strftime('%Y-%m-%d') }}</td>
       </tr>
       <tr>
-        <td>Number of genes:<span class="badge bg-secondary rounded-pill text-white">{{ panel.genes|length }}</span></td>
+        <td>Number of genes:{{ panel.genes|length }}</td>
       </tr>
       <tr>
-        <td>Institute: <span class="badge bg-secondary rounded-pill text-white">{{ panel.institute.display_name }}</span></td>
+        <td>Institute:{{ panel.institute.display_name }}</td>
       </tr>
       <tr>
         <td>Panel archived:
           {% if panel.is_archived %}
-            <span class="badge bg-danger rounded-pill">True</span>
+            True
           {% else %}
-            <span class="badge bg-secondary rounded-pill text-white">False</span>
+            False
           {% endif %}
         </td>
       </tr>
       <tr>
-        <td>Panel database ID: <span class="badge bg-secondary rounded-pill text-white">{{ panel._id }}</span></td>
+        <td>Panel database ID: {{ panel._id }}</td>
+      </tr>
+      <tr>
+        <td>Maintainers: {{ panel.maintainer|join(", ") }}</td>
       </tr>
     </table>
   </div>
@@ -45,27 +48,31 @@
   <div>
     <table class="table table-sm">
       <tr>
-        <td></td>
-        <td>HGNC id</td>
-        <td>Gene name</td>
-        <td>Disease associated transcripts</td>
-        <td>Reduced penetrance</td>
-        <td>Mosaicism</td>
-        <td>Entry version</td>
-        <td>Inheritance</td>
+        <th></th>
+        <th>Gene</th>
+        <th>HGNC ID</th>
+        <th>Disease-associated transcripts</th>
+        <th>Reduced penetrance</th>
+        <th>Mosaicism</th>
+        <th>Entry version</th>
+        <th>Manual inheritance (pre-set terms)</th>
+        <th>Manual inheritance (free text terms)</th>
+        <th>Comment</th>
       </tr>
       {% for gene in panel.genes|sort(attribute='symbol') %}
         <tr>
           <td>{{loop.index}}</td>
+          <td>{{ gene.symbol }}</td>
           <td>
-            <a style="text-decoration:none;" href="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id={{gene.hgnc_id}}" target="_blank">{{gene.hgnc_id}}</a>
+            <a style="text-decoration:none;" href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:{{gene.hgnc_id}}" target="_blank">{{gene.hgnc_id}}</a>
           </td>
-          <td>{{ gene.symbol }}</td>
           <td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
           <td>{{ 'Reduced penetrance' if gene.reduced_penetrance }}</td>
-          <td>{{ 'Mosaicism' if gene.mosaicism}}</td>
-          <td><span class="badge bg-secondary">{{ gene.database_entry_version }}</span></td>
+          <td>{{ 'Mosaicism' if gene.mosaicism }}</td>
+          <td>{{ gene.database_entry_version }}</td>
           <td>{{ gene.inheritance_models|join(', ') }}</td>
+          <td>{{ gene.custom_inheritance_models|join(', ') }}</td>
+          <td>{{ gene.comment }}</td>
         </tr>
       {% endfor %}
     </table>

scout/server/blueprints/panels/views.py

@@ -384,12 +384,14 @@ def gene_edit(panel_id, hgnc_id):
     form.disease_associated_transcripts.choices = tx_choices(hgnc_id, panel_obj)
     if form.validate_on_submit():
         action = "edit" if panel_gene else "add"
-        info_data = form.data.copy()
-        if "csrf_token" in info_data:
-            del info_data["csrf_token"]
-        if info_data["custom_inheritance_models"] != "":
-            info_data["custom_inheritance_models"] = info_data["custom_inheritance_models"].split(
-                ","
+        info_data: dict = {
+            k: v for k, v in form.data.copy().items() if v
+        }  # Update only fields edited by user
+        info_data.pop("csrf_token", None)
+
+        if info_data.get("custom_inheritance_models", ""):
+            info_data["custom_inheritance_models"] = (
+                info_data["custom_inheritance_models"].replace(" ", "").split(",")
             )
         store.add_pending(panel_obj, hgnc_gene, action=action, info=info_data)
         return redirect(url_for(".panel", panel_id=panel_id))
@@ -416,4 +418,5 @@ def gene_edit(panel_id, hgnc_id):
                 panel_value = panel_gene.get(field_key)
                 if panel_value is not None:
                     form_field.process_data(panel_value)
+
     return dict(panel=panel_obj, form=form, gene=hgnc_gene, panel_gene=panel_gene)

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

@@ -32,7 +32,7 @@
           {% if evaluation %}
              <h4>
               {{ evaluation.classification.label }}
-              <span class="badge bg-info">{{ evaluation.classification.short }}</span>
+              <span class="badge bg-info">{{ evaluation.classification.short|safe }}</span>
             </h4>
             By {{ evaluation.user_name }} on {{ evaluation.created_at.date() }}
             {% if edit %}
@@ -42,14 +42,7 @@
           {% elif not evaluation %}
             <button class="btn btn-primary form-control">Submit</button>
           {% endif %}
-          <!-- classification preview in the footer-->
-          <div class="mt-3 fixed-bottom bg-light border">
-              <div class="text-center">
-                {% for option in ACMG_OPTIONS %}
-                  <a id="acmg-{{ option.code }}" class="btn acmg-preview">{{ option.label }}</a>
-                {% endfor %}
-              </div>
-          </div>
+          <div id="conflicts_div" class="bg-warning"></div>
         </div>
       </div>
 
@@ -72,23 +65,23 @@
                   {% endif %}
                   <div class="list-group-item">
                     <div class="d-flex justify-content-between">
-                      <div data-bs-toggle="tooltip" data-bs-placement="top" title="{{ criterion.description }}">
+                      <div data-bs-toggle="tooltip" data-bs-placement="top" title="{{ criterion.description|safe }}">
                         <span class="badge bg-info me-1">{{ criterion_code }}</span>
-                        {{ criterion.short }}
+                        {{ criterion.short|safe}}
                       </div>
                       <div class="form-check form-switch">
-                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.criteria }} {{ 'disabled' if evaluation and edit is false}}>
+                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.criteria }} {{ 'disabled' if evaluation and edit is false }}>
                         <label class="form-check-label" for="checkbox-{{ criterion_code }}"></label>
                       </div>
                     </div>
                     <div id="comment-{{ criterion_code }}" class="{{ 'collapse' if not (comment or link or modifier) }} mt-2">
-                      {% if criterion.documentation %}<div class="row"><span class="me-1 fw-light text-wrap">{{ criterion.documentation | safe}}</span></div>{% endif %}
+                      {% if criterion.documentation %}<div class="row"><span class="me-1 fw-light text-wrap">{{ criterion.documentation | safe }}</span></div>{% endif %}
                       <div class="row">
                         <select {{ 'disabled' if evaluation and edit is false}} id="modifier-{{ criterion_code }}" name="modifier-{{ criterion_code }}" class="form-control form-select">
                           <option value="" {% if not modifier %}selected{% endif %}>Strength modifier...</option>
                           {% for level in "Strong", "Moderate", "Supporting" %}
                             {% if(level != evidence) %}
-                              <option id="{{criterion_code}}-{{level}}" value="{{level}}" {% if modifier == level %}selected{% endif%}>{{ level }}</option>
+                              <option id="{{ criterion_code }}-{{ level }}" value="{{ level }}" {% if modifier == level %}selected{% endif %}>{{ level }}</option>
                             {% endif %}
                           {% endfor %}
                         </select>
@@ -108,19 +101,23 @@
           </div>
         {% endfor %}
       </div>
+    <!-- classification preview in the footer-->
+      <div class="mt-3 fixed-bottom bg-light border">
+        <div class="row">
+          <div class="col-3" style="font-size:1.5em">
+            <a href="https://clinicalgenome.org/docs/modeling-the-acmg-amp-variant-classification-gudielines-as-a-bayesian-classification-framework/" data-bs-toggle="tooltip" title="Classification based on the Bayesian score model in Tavtigian et al." rel="noopener noreferrer" target="_blank"><span id="temperature_span" class="badge"></span></a>
+          </div>
+          <div class="col-6 text-center">
+          {% for option in ACMG_OPTIONS %}
+            <a id="acmg-{{ option.code }}" href="https://www.acmg.net/docs/standards_guidelines_for_the_interpretation_of_sequence_variants.pdf" class="btn acmg-preview" data-bs-toggle="tooltip" title="Suggested classification based on Richards et al 2015.">{{ option.label }}</a>
+          {% endfor %}
+          </div>
+        </div>
+      </div>
     </form>
   </div>
 {% endblock %}
 
-{% macro preview() %}
-  <div class="card panel-default">
-    <div class="card-body">
-      <span class="text-muted">Classification</span>
-      <h5>Likely Pathogenic</h5>
-    </div>
-  </div>
-{% endmacro %}
-
 {% block scripts %}
   {{ super() }}
 
@@ -166,12 +163,19 @@
         return 'criterion=' + elem.value
       });
 
-
       $.getJSON('/api/v1/acmg?' + criteria.toArray().join('&'), function(data) {
         // reset the selection
         $('.acmg-preview').removeClass('btn-primary');
         // add new selection
         $('#acmg-' + data.classification).addClass('btn-primary');
+
+        var temperature_span = document.getElementById("temperature_span");
+        temperature_span.innerHTML = 'Score ' + data.points + ' <span class="fa ' + data.temperature_icon + '"></span> ' + data.temperature + ' (' + data.point_classification + ')'
+        temperature_span.className = 'badge bg-' + data.temperature_class
+
+        // Update any classification conflicts
+        var conflicts_div = document.getElementById("conflicts_div");
+        conflicts_div.innerHTML = data.conflicts.join("<br>");
       });
     }
   </script>

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

@@ -42,7 +42,6 @@
             <tr>
               <th>Gene</th>
               <th>ORPHA Phenotype</th>
-              <th>Inheritance model</th>
             </tr>
           </thead>
           <tbody>
@@ -50,7 +49,7 @@
               {% if gene.common and gene.disease_terms %}
                 {% for disease_term in gene.disease_terms %}
                   {% if disease_term.source == 'ORPHA' %}
-                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily modes of inheritance known for this gene. ORPHA inheritance modes will not be shown on the general case report.">
+                    <tr data-bs-toggle="tooltip" title="We are not displaying inheritance models associated to ORPHANET terms. This is because some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily modes of inheritance known for this gene.">
                       <td>
                           <a href="http://omim.org/entry/{{ gene.common.omim_id }}" rel="noopener" target="_blank">
                             {{ gene.common.hgnc_symbol }}
@@ -62,7 +61,6 @@
                             {{ disease_term.description }}
                           </a>
                       </td>
-                      <td>{{ disease_term.inheritance|join(', ') }}</td>
                     </tr>
                   {% endif %}
                 {% endfor %}

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

@@ -451,7 +451,7 @@
   {% set symbol_genes_counter = namespace(value=0) %}
   {% set nosymbol_genes_counter = namespace(value=0) %}
   <a
-    href="{{ url_for('panels.panel', panel_id=panel.panel_id) }}"
+    href="{{ url_for('panels.panel', panel_id=panel._id) }}"
     {#
     Add hovertip listing occurence of each gene on selected panels, in the case
     where variant covers multiple genes.

scout/server/blueprints/variant/utils.py

@@ -50,6 +50,7 @@ def add_panel_specific_gene_info(panel_info: List[dict]) -> dict:
                 comment.append(panel_gene_comment)
 
         manual_inheritance.update(gene_info.get("inheritance_models", []))
+        manual_inheritance.update(gene_info.get("custom_inheritance_models", []))
 
     panel_specific["disease_associated_transcripts"] = list(disease_associated)
     panel_specific["disease_associated_no_version"] = disease_associated_no_version

scout/server/blueprints/variant/views.py

@@ -26,7 +26,7 @@ from scout.server.blueprints.variant.verification_controllers import (
 )
 from scout.server.extensions import loqusdb, store
 from scout.server.utils import institute_and_case, public_endpoint, templated
-from scout.utils.acmg import get_acmg
+from scout.utils.acmg import get_acmg, get_acmg_conflicts, get_acmg_temperature
 from scout.utils.ensembl_rest_clients import EnsemblRestApiClient
 
 LOG = logging.getLogger(__name__)
@@ -347,7 +347,10 @@ def acmg():
     """Calculate an ACMG classification from submitted criteria."""
     criteria = request.args.getlist("criterion")
     classification = get_acmg(criteria)
-    return jsonify(dict(classification=classification))
+
+    acmg_bayesian = get_acmg_temperature(criteria)
+    acmg_conflicts = get_acmg_conflicts(criteria)
+    return jsonify({"classification": classification, "conflicts": acmg_conflicts, **acmg_bayesian})
 
 
 @variant_bp.route(

scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import cancer_sv_filters,cell_rank, pagination_footer, pagination_hidden_div, filter_form_footer, filter_script_main, update_stash_filter_button_status, dismiss_variants_block %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell, variant_region_anno_cell %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - SV variants
@@ -56,18 +56,17 @@
       <table id="variantsTable" class="table table-hover table-bordered" aria-label="Somatic SV variants table">
         <thead class="thead table-light">
           <tr>
-            <th style="width:3%"></th>
+            <th style="width:2%"></th>
             <th style="width:9%">Index</th>
             <th>Type</th>
-            <th>Chr</th>
+            <th style="width:5%">Chr</th>
             <th>Start</th>
             <th>End</th>
             <th>Length</th>
             <th>Pop Freq</th>
             <th>Observed</th>
-            <th>Gene(s)</th>
-            <th>Region</th>
-            <th style="width:12%">Function</th>
+            <th style="width:12%">Gene(s)</th>
+            <th style="width:16%">Function</th>
             <th style="width:9%" data-bs-toggle="tooltip" data-bs-placement="top" title="Tumor alt. AF not computed as it varies with variant type and caller. &#013; Alt. allele support | Ref. allele support. [Somatic score if available from caller].">Tumor</th>
             <th style="width:6%" data-bs-toggle="tooltip" data-bs-placement="top" title="Normal alt. AF not computed as it varies with variant type and caller. &#013; Alt. allele support | Ref. allele support">Normal</th>
           </tr>
@@ -77,7 +76,7 @@
             {{ variant_row(variant) }}
           {% else %}
             <tr>
-                <td colspan="10">No matching variants</td>
+                <td colspan="13">No matching variants</td>
             </tr>
           {% endfor %}
         </tbody>
@@ -114,10 +113,7 @@
     <td class="text-end">{{ frequency_cell_general(variant) }}</td>
     <td>{{observed_cell_general(variant)}}</td>
     <td>
-      {{ variant_gene_symbols_cell(variant) }}
-    </td>
-    <td>
-      {{ variant_region_anno_cell(variant) }}
+      {{ variant_gene_symbols_cell(variant, inherit_palette) }}
     </td>
     <td>
       {{ variant_funct_anno_cell(variant) }}