scout-browser 4.101.0__py3-none-any.whl → 4.103.0__py3-none-any.whl

scout/server/blueprints/variants/controllers.py

@@ -35,6 +35,7 @@ from scout.server.blueprints.variant.utils import (
     clinsig_human,
     get_callers,
     get_filters,
+    get_str_mc,
     predictions,
     update_representative_gene,
     update_variant_case_panels,
@@ -45,6 +46,7 @@ from scout.server.links import add_gene_links, cosmic_links, str_source_link
 from scout.server.utils import (
     case_has_alignments,
     case_has_mt_alignments,
+    get_case_genome_build,
     institute_and_case,
     user_institutes,
 )
@@ -57,8 +59,6 @@ from .forms import (
 )
 from .utils import update_case_panels
 
-NUM = re.compile(r"\d+")
-
 LOG = logging.getLogger(__name__)
 
 
@@ -106,7 +106,7 @@ def populate_persistent_filters_choices(
 def populate_chrom_choices(form, case_obj):
     """Populate the option of the chromosome select according to the case genome build"""
     # Populate chromosome choices
-    chromosomes = CHROMOSOMES if "37" in str(case_obj.get("genome_build")) else CHROMOSOMES_38
+    chromosomes = CHROMOSOMES if get_case_genome_build(case_obj) == "37" else CHROMOSOMES_38
     form.chrom.choices = [(chrom, chrom) for chrom in chromosomes]
 
 
@@ -139,9 +139,7 @@ def variants(
     more_variants = variant_count > (skip_count + per_page)
     variant_res = variants_query.skip(skip_count).limit(per_page)
 
-    genome_build = str(case_obj.get("genome_build", "37"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "37"
+    genome_build = get_case_genome_build(case_obj)
 
     case_dismissed_vars = store.case_dismissed_variants(institute_obj, case_obj)
 
@@ -237,9 +235,7 @@ def sv_variants(store, institute_obj, case_obj, variants_query, variant_count, p
 
     more_variants = variant_count > (skip_count + per_page)
     variants = []
-    genome_build = str(case_obj.get("genome_build", "37"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "37"
+    genome_build = get_case_genome_build(case_obj)
 
     case_dismissed_vars = store.case_dismissed_variants(institute_obj, case_obj)
 
@@ -285,9 +281,7 @@ def mei_variants(
 
     more_variants = variant_count > (skip_count + per_page)
     variants = []
-    genome_build = str(case_obj.get("genome_build", "37"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "37"
+    genome_build = get_case_genome_build(case_obj)
 
     case_dismissed_vars = store.case_dismissed_variants(institute_obj, case_obj)
 
@@ -353,9 +347,7 @@ def fusion_variants(
 
     more_variants = variant_count > (skip_count + per_page)
     variants = []
-    genome_build = str(case_obj.get("genome_build", "38"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "38"
+    genome_build = get_case_genome_build(case_obj)
 
     case_dismissed_vars = store.case_dismissed_variants(institute_obj, case_obj)
 
@@ -997,28 +989,6 @@ def parse_variant(
     return variant_obj
 
 
-def get_str_mc(variant_obj: dict) -> Optional[int]:
-    """Return variant Short Tandem Repeat motif count, either as given by its ALT MC value
-    from the variant FORMAT field, or as a number given in the ALT on the form
-    '<STR123>'.
-    """
-    alt_mc = None
-    if variant_obj["alternative"] == ".":
-        return alt_mc
-
-    for sample in variant_obj["samples"]:
-        if sample["genotype_call"] in ["./.", ".|", "0/0", "0|0"]:
-            continue
-        alt_mc = sample.get("alt_mc")
-    if alt_mc:
-        return alt_mc
-
-    alt_num = NUM.search(variant_obj["alternative"])
-    if alt_num:
-        alt_mc = int(alt_num.group())
-        return alt_mc
-
-
 def download_str_variants(case_obj, variant_objs):
     """Download filtered STR variants for a case to a CSV file
 
@@ -1502,7 +1472,9 @@ def upload_panel(store, institute_id, case_name, stream):
     hgnc_symbols = set()
     for raw_symbol in raw_symbols:
         matching_genes = list(
-            store.gene_by_symbol_or_aliases(symbol=raw_symbol, build=case_obj.get("genome_build"))
+            store.gene_by_symbol_or_aliases(
+                symbol=raw_symbol, build=get_case_genome_build(case_obj)
+            )
         )
         if not matching_genes:
             flash("HGNC symbol not found: {}".format(raw_symbol), "warning")
@@ -1983,10 +1955,7 @@ def update_form_hgnc_symbols(store, case_obj, form):
     genome_build = None
     case_obj = case_obj or {}
 
-    for build in ["37", "38"]:
-        if build in str(case_obj.get("genome_build", "")):
-            genome_build = build
-            break
+    genome_build = get_case_genome_build(case_obj)
 
     # retrieve current symbols from form
     if form.hgnc_symbols.data:

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

@@ -1,7 +1,7 @@
 {% extends "layout.html" %}
 
 {% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
-{% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
+{% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell, variant_rank_score %}
 {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
 
 {% block title %}
@@ -56,7 +56,7 @@
               <th title="Gene">Gene</th>
               <th title="Variant" style="width:12%">HGVS[c/p]</th>
               <th title="Assessments including variant tier" style="width:8%">Assessment</th>
-              <th title="Rank scores" style="width:4%">Rank</th>
+              <th data-bs-toggle="tooltip" title="Rank score (normalized rank score in the range 0-1)" style="width:5%">Rank</th>
               <th title="CADD scores" style="width:4%">CADD</th>
               <th title="Genomic coordinate" style="width:8%">Chr pos</th>
               <th title="Population frequency">Pop Freq</th>
@@ -156,7 +156,9 @@
     {% elif variant.rank_score > 8 %}
       {% set label_class = 'danger' %}
     {% endif %}
-    <div class="badge bg-{{ label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="Rank score">{{ variant.rank_score }}</div>
+    <div class="badge bg-{{ label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="Rank score">
+      {{ variant_rank_score(variant) }}
+    </div>
   {% endif %}
 {% endmacro %}
 

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

@@ -93,7 +93,10 @@
 	        {% endif %}
             <td class="str-link">{{ cell_rank(variant, institute, case, form, manual_rank_options) }}</td>
             <td class="str-link">{{ str_locus_info(variant) }}</td>
-	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru or variant.reference }}</td>
+        <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.str_display_ru or variant.str_ru or variant.reference }}">
+          {% if variant.str_display_ru %}{{variant.str_display_ru | truncate(12, True)}}
+          {% elif variant.str_ru %}{{ variant.str_ru | truncate(12, True) }}
+          {% else %}{{ variant.reference | truncate(12, True) }}{% endif %}</span></td>
             <td class="text-end"><b><span data-bs-toggle="tooltip" title="{{ variant.alternative }}">{{ variant.str_mc }}</span></b></td>
             <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
             <td>{{ callers_cell(variant) }}</td>

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

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
+{% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell, variant_rank_score %}
 {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, overlapping_cell, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
@@ -58,7 +58,7 @@ onsubmit="return validateForm()">
           <tr>
             <th style="width:3%"></th>
             <th title="Rank position">Rank</th>
-            <th title="Rank score">Score</th>
+            <th data-bs-toggle="tooltip" title="Rank score (normalized rank score in the range 0-1)">Score</th>
             <th>Callers</th>
             <th>Type</th>
             <th title="Chromosome">Chr</th>
@@ -103,7 +103,7 @@ onsubmit="return validateForm()">
     <td class="text-start">
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
-    <td class="text-end">{{ variant.rank_score|int }}</td>
+    <td class="text-start">{{variant_rank_score(variant)}}</td>
     <td>
       {{ callers_cell(variant) }}
     </td>

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

@@ -3,6 +3,10 @@
 {% from "cases/utils.html" import pretty_link_variant %}
 {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, research_assessments_badge %}
 
+{% macro variant_rank_score(variant) %}
+  {% if variant.rank_score %}{{ variant.rank_score|int }} {% endif %} {% if variant.norm_rank_score %} ({{variant.norm_rank_score|round(2)}}) {% endif %}
+{% endmacro %}
+
 {% macro filter_script_main(cytobands) %}
   <script type="text/javascript">
     var startElem = document.getElementById("start");

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

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/utils.html" import snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt %}
+{% from "variants/utils.html" import snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt, variant_rank_score %}
 {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, gene_cell, observed_cell_general, overlapping_cell  %}
 
 {% block title %}
@@ -55,8 +55,8 @@
          <thead class="thead table-light">
             <tr>
               <th style="width:2%"></th>
-              <th style="width:12%" title="Rank position">Rank</th>
-              <th style="width:5%" title="Rank score">Score</th>
+              <th style="width:7%" title="Rank position">Rank</th>
+              <th style="width:10%" data-bs-toggle="tooltip" title="Rank score (normalized rank score in the range 0-1)">Score</th>
               <th style="width:4%" title="Chromosome">Chr.</th>
               <th style="width:12%" title="HGNC symbols">Gene</th>
               <th style="width:6%" title="Population Frequency">Pop Freq</th>
@@ -78,7 +78,7 @@
               {% endif %}
                 <td><input type="checkbox" value="{{variant._id}}" name="dismiss" onclick="enableDismiss()"></td>
                 <td class="text-start">{{ cell_rank(variant, institute, case, form, manual_rank_options) }}</td>
-                <td class="text-end">{{ variant.rank_score|int }}</td>
+                <td class="text-start">{{variant_rank_score(variant)}}</td>
                 <td>
                   {{ variant.chromosome }}
                   {% if variant.chromosome in ["MT","M"] %}

scout/server/blueprints/variants/views.py

@@ -19,7 +19,7 @@ from scout.constants import (
     SEVERE_SO_TERMS_SV,
 )
 from scout.server.extensions import store
-from scout.server.utils import institute_and_case, templated
+from scout.server.utils import get_case_genome_build, institute_and_case, templated
 
 from . import controllers
 from .forms import (
@@ -129,7 +129,7 @@ def variants(institute_id, case_name):
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     variants_query = store.variants(
@@ -220,7 +220,7 @@ def str_variants(institute_id, case_name):
 
     controllers.activate_case(store, institute_obj, case_obj, current_user)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     query = form.data
@@ -231,6 +231,7 @@ def str_variants(institute_id, case_name):
     ).sort(
         [
             ("str_repid", pymongo.ASCENDING),
+            ("str_trid", pymongo.ASCENDING),
             ("chromosome", pymongo.ASCENDING),
             ("position", pymongo.ASCENDING),
         ]
@@ -302,7 +303,7 @@ def sv_variants(institute_id, case_name):
     # Populate custom soft filters
     controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
@@ -397,7 +398,7 @@ def mei_variants(institute_id, case_name):
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
@@ -509,7 +510,7 @@ def cancer_variants(institute_id, case_name):
 
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
@@ -587,7 +588,7 @@ def cancer_sv_variants(institute_id, case_name):
     # Populate custom soft filters
     controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
@@ -671,7 +672,7 @@ def fusion_variants(institute_id, case_name):
     # Populate custom soft filters
     controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)

scout/server/config.py

@@ -1,6 +1,9 @@
 # -*- coding: utf-8 -*-
 SECRET_KEY = "this is not secret..."
 REMEMBER_COOKIE_NAME = "scout_remember_me"  # Prevent session timeout when user closes browser
+# INSTANCE_NAME = "Development" # Name will be displayed on the top navigation menu
+# INSTANCE_COLOR = "#800000" # Color of the top navigation menu
+
 # SESSION_TIMEOUT_MINUTES = 60  # Minutes of inactivity before session times out
 
 # MONGO_URI = "mongodb://127.0.0.1:27011,127.0.0.1:27012,127.0.0.1:27013/?replicaSet=rs0&readPreference=primary"

scout/server/extensions/beacon_extension.py

@@ -8,7 +8,12 @@ import logging
 from flask import flash, url_for
 from flask_login import current_user
 
-from scout.utils.scout_requests import delete_request_json, get_request_json, post_request_json
+from scout.server.utils import get_case_genome_build
+from scout.utils.scout_requests import (
+    delete_request_json,
+    get_request_json,
+    post_request_json,
+)
 
 LOG = logging.getLogger(__name__)
 DATASET_BUILDS = ["GRCh37", "GRCh38"]
@@ -58,7 +63,7 @@ class Beacon:
             data(dict): a dictionary with base info to be used as json data in beacon add request (lacks path to VCF file to extract variants from)
         """
         # Initialize key/values to be sent in request:
-        assembly = "GRCh38" if "38" in str(case_obj.get("genome_build", "37")) else "GRCh37"
+        assembly = "GRCh38" if get_case_genome_build(case_obj) == "38" else "GRCh37"
         dataset_id = "_".join([case_obj["owner"], case_obj.get("build", assembly)])
 
         samples = []

scout/server/extensions/clinvar_extension.py

@@ -1,7 +1,7 @@
 import json
 import logging
 from io import StringIO
-from typing import Optional, Tuple
+from typing import Any, Optional, Tuple
 
 import requests
 from flask import flash
@@ -80,7 +80,7 @@ class ClinVarApi:
         except Exception as ex:
             return self.submit_service_url, None, ex
 
-    def json_submission_status(self, submission_id: str, api_key=None) -> dict:
+    def json_submission_status(self, submission_id: str, api_key=None) -> Any:
         """Retrieve the status of a ClinVar submission using the https://submit.ncbi.nlm.nih.gov/api/v1/submissions/SUBnnnnnn/actions/ endpoint."""
 
         header: dict = self.set_header(api_key)

scout/server/templates/bootstrap_global.html

@@ -12,7 +12,17 @@
     <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-dark-5@1.1.3/dist/css/bootstrap-dark.min.css" integrity="sha384-pZAJcuaxKZEGkzXV5bYqUcSwBfMZPdQS/+JXdYOu9ScyZJMnGHD5Xi6HVHfZuULH" crossorigin="anonymous">
     <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.6.0/css/all.min.css" integrity="sha512-Kc323vGBEqzTmouAECnVceyQqyqdsSiqLQISBL29aUW4U/M7pSPA/gEUZQqv1cwx4OnYxTxve5UMg5GT6L4JJg==" crossorigin="anonymous" referrerpolicy="no-referrer" />
     <link rel="stylesheet" href="{{ url_for('static', filename='bs_styles.css') }}">
-	{% endblock %}
+
+   {% if config.INSTANCE_COLOR %}
+    <style>
+      /* Override Scout's bg-primary with color set on app config, if available */
+      nav.navbar.bg-primary {
+        background-color: {{ config.INSTANCE_COLOR }} !important;
+      }
+    </style>
+  {% endif %}
+
+  {% endblock %}
 
 	{% block css_style %}
   {% endblock %}

scout/server/templates/layout.html

@@ -18,9 +18,14 @@
 
 {% block navbar %}
     <nav class="navbar navbar-expand-lg nav-pills navbar-dark bg-primary sticky-top" >
-      <div class="container-fluid bg-primary rounded-bottom">
+      <div class="container-fluid rounded-bottom">
         <a class="navbar-brand" href="{{ url_for('cases.index') }}">
           <img src="{{ url_for('public.static', filename='scout-logo.png') }}" width="30" height="30" class="d-inline-block align-top text-white" alt="">Scout</a>
+          {% if config.INSTANCE_NAME %}
+            <span class="navbar-text badge bg-light text-dark">
+              {{ config.INSTANCE_NAME }}
+            </span>
+          {% endif %}
         <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
           <span class="navbar-toggler-icon"></span>
         </button>

scout/server/utils.py

@@ -8,11 +8,21 @@ import zipfile
 from functools import wraps
 from io import BytesIO
 from typing import Dict, Optional, Tuple
+from urllib.parse import urlparse
 
 import pdfkit
 from bson.objectid import ObjectId
-from flask import abort, current_app, flash, render_template, request
+from flask import (
+    Response,
+    abort,
+    current_app,
+    flash,
+    redirect,
+    render_template,
+    request,
+)
 from flask_login import current_user
+from werkzeug.local import LocalProxy
 
 LOG = logging.getLogger(__name__)
 
@@ -102,6 +112,17 @@ def public_endpoint(function):
     return function
 
 
+def safe_redirect_back(request: LocalProxy, link: Optional[str] = None) -> Response:
+    """Safely redirects the user back to the referring URL, if it originates from the same host.
+    Otherwise, the user is redirected to a default '/'."""
+    referrer = request.referrer
+    if referrer:
+        parsed_referrer = urlparse(referrer)
+        if parsed_referrer.netloc == request.host:
+            return redirect(link or referrer)
+    return redirect("/")
+
+
 def variant_institute_and_case(
     store, variant_obj: dict, institute_id: Optional[str], case_name: Optional[str]
 ) -> Tuple[dict, dict]:
@@ -145,7 +166,7 @@ def institute_and_case(store, institute_id, case_name=None):
             return abort(404)
 
         # Make sure build is either "37" or "38"
-        case_obj["genome_build"] = "38" if "38" in str(case_obj.get("genome_build")) else "37"
+        case_obj["genome_build"] = get_case_genome_build(case_obj)
 
     # validate that user has access to the institute
 
@@ -208,7 +229,7 @@ def user_institutes(store, login_user):
 
 def get_case_genome_build(case_obj: dict) -> str:
     """returns the genome build of a case, as a string."""
-    return "38" if "38" in case_obj.get("genome_build", "37") else "37"
+    return "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
 
 
 def get_case_mito_chromosome(case_obj: dict) -> str:

{scout_browser-4.101.0.dist-info → scout_browser-4.103.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.101.0
+Version: 4.103.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md