scout-browser 4.101.0__py3-none-any.whl → 4.102.0__py3-none-any.whl

scout/server/blueprints/login/views.py

@@ -13,7 +13,7 @@ from flask import (
     session,
     url_for,
 )
-from flask_login import login_user, logout_user
+from flask_login import logout_user
 
 from scout.server.extensions import login_manager, oauth_client, store
 from scout.server.utils import public_endpoint
@@ -102,11 +102,14 @@ def authorized():
 
 @login_bp.route("/logout")
 def logout():
+    session.pop("email", None)
+    session.pop("name", None)
+    session.pop("locale", None)
+    session.pop("consent_given", None)
     logout_user()  # logs out user from scout
     for provider in ["GOOGLE", "KEYCLOAK"]:
         if current_app.config.get(provider):
             controllers.logout_oidc_user(session, provider)
-    session.clear()
     flash("you logged out", "success")
     return redirect(url_for("public.index"))
 

scout/server/blueprints/omics_variants/views.py

@@ -17,7 +17,7 @@ from scout.server.blueprints.variants.controllers import (
 )
 from scout.server.blueprints.variants.forms import OutlierFiltersForm
 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
 
@@ -71,7 +71,7 @@ def outliers(institute_id, case_name):
     # Populate chromosome select choices
     populate_chrom_choices(form, 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)
 
     update_form_hgnc_symbols(store, case_obj, form)

scout/server/blueprints/phenotypes/controllers.py

@@ -1,7 +1,17 @@
 # -*- coding: utf-8 -*-
 
+from typing import Optional
 
-def hpo_terms(store, query=None, limit=None, page=None):
+from scout.adapter import MongoAdapter
+from scout.constants import HPO_LINK_URL
+
+
+def hpo_terms(
+    store: MongoAdapter,
+    query: Optional[str] = None,
+    limit: Optional[str] = None,
+    page: Optional[str] = None,
+) -> dict:
     """Retrieves a list of HPO terms from scout database
 
     Args:
@@ -29,4 +39,7 @@ def hpo_terms(store, query=None, limit=None, page=None):
         hpo_phenotypes["phenotypes"] = list(store.hpo_terms(query=query, limit=limit, skip=skip))
     else:
         hpo_phenotypes["phenotypes"] = list(store.hpo_terms(limit=limit, skip=skip))
-    return hpo_phenotypes
+
+    data = hpo_phenotypes
+    data["hpo_link_url"] = HPO_LINK_URL
+    return data

scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html

@@ -34,7 +34,7 @@
                 </thead>
                 {% for pheno in phenotypes %}
                 <tr>
-                  <td><a href="http://hpo.jax.org/app/browse/term/{{pheno.hpo_id}}" referrerpolicy="no-referrer" target="_blank">{{ pheno.hpo_id }}</a></td>
+                  <td><a href="{{hpo_link_url}}{{pheno.hpo_id}}" referrerpolicy="no-referrer" target="_blank">{{ pheno.hpo_id }}</a></td>
                   <td><span class="text-body">{{ pheno.description }}</span></td>
                   <td><span class="text-body">{{pheno.genes|length}}</span></td>
                 </tr>

scout/server/blueprints/variant/controllers.py

@@ -28,6 +28,7 @@ from scout.constants import (
     VERBS_MAP,
 )
 from scout.server.blueprints.variant.utils import (
+    get_str_mc,
     update_representative_gene,
     update_variant_case_panels,
 )
@@ -40,6 +41,7 @@ from scout.server.utils import (
     case_has_chanjo_coverage,
     case_has_mt_alignments,
     case_has_rna_tracks,
+    get_case_genome_build,
     user_institutes,
     variant_institute_and_case,
 )
@@ -232,9 +234,7 @@ def variant(
 
     variant_id = variant_obj["variant_id"]
 
-    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)
 
     # is variant located on the mitochondria
     variant_obj["is_mitochondrial"] = any(
@@ -314,6 +314,9 @@ def variant(
 
     variant_obj["end_position"] = end_position(variant_obj)
 
+    # common motif count for STR variants
+    variant_obj["str_mc"] = get_str_mc(variant_obj)
+
     # Add general variant links
     variant_obj.update(get_variant_links(institute_obj, variant_obj, int(genome_build)))
     variant_obj["frequencies"] = frequencies(variant_obj)
@@ -425,9 +428,7 @@ def get_gene_has_full_coverage(institute_obj, case_obj, variant_obj) -> Dict[int
     if not case_obj.get("chanjo2_coverage"):
         return {}
 
-    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)
 
     gene_has_full_coverage: dict = {
         hgnc_id: chanjo2.get_gene_complete_coverage(
@@ -436,7 +437,7 @@ def get_gene_has_full_coverage(institute_obj, case_obj, variant_obj) -> Dict[int
             individuals=case_obj.get("individuals"),
             build=genome_build,
         )
-        for hgnc_id in [gene.get("hgnc_id") for gene in variant_obj.get("genes")]
+        for hgnc_id in [gene.get("hgnc_id") for gene in variant_obj.get("genes", [])]
     }
     return gene_has_full_coverage
 
@@ -555,7 +556,7 @@ def observations(store: MongoAdapter, loqusdb: LoqusDB, variant_obj: dict) -> Di
                 f"Could not find a Loqus instance with id:{loqus_id}",
                 "warning",
             )
-            obs_data[loqus_id]["observations"] = "N/A"
+            obs_data[loqus_id] = {"observations": "N/A"}
             continue
 
         if obs_data[loqus_id] == {}:  # Variant was not found
@@ -656,9 +657,7 @@ def variant_acmg(store: MongoAdapter, institute_id: str, case_name: str, variant
         store, variant_obj, institute_id, case_name
     )
 
-    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)
 
     add_gene_info(store, variant_obj, genome_build=genome_build)
 

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

@@ -396,7 +396,7 @@
     <div class="col-1">
       <!--Define build variable to be used in the UCSC link-->
       {% set build = "hg19" %}
-      {% if case.genome_build == 38 or variant.chromosome == "MT" %}
+      {% if case.genome_build == "38" or variant.chromosome == "MT" %}
         {% set build = "hg38" %}
       {% endif %}
 

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

@@ -164,38 +164,42 @@
   </div>
 {% endmacro %}
 
+{% macro frequencies_table(variant) %}
+<table class="table table-sm align-middle mb-1" style="font-size: 0.875rem;">
+  <thead class="table-light">
+    <tr>
+      <th scope="col" class="py-1 px-2">Source</th>
+      <th scope="col" class="py-1 px-2">Frequency</th>
+    </tr>
+  </thead>
+  <tbody>
+    {% for freq_name, value, link in variant.frequencies %}
+      <tr>
+        <td class="py-1 px-2">
+          {% if link %}
+            <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
+          {% else %}
+            {{ freq_name }}
+          {% endif %}
+        </td>
+        <td class="py-1 px-2">
+          {% if value %}
+            <span class="badge bg-secondary" style="font-size: 0.75rem;">{{ value|human_decimal }}</span>
+          {% else %}
+            -
+          {% endif %}
+        </td>
+      </tr>
+    {% endfor %}
+  </tbody>
+</table>
+{% endmacro %}
+
 {% macro frequencies(variant) %}
   <div class="card panel-default">
     <div class="panel-heading">Frequencies</div>
     <div class="card-body">
-      <table class="table">
-          <thead class="thead table-light">
-            <tr>
-              <th scope="col">Source</th>
-              <th scope="col">Frequency</th>
-            </tr>
-          </thead>
-          <tbody>
-            {% for freq_name, value, link in variant.frequencies %}
-              <tr>
-                <td>
-                  {% if link %}
-                    <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
-                  {% else %}
-                    {{ freq_name }}
-                  {% endif %}
-                </td>
-                <td>
-                  {% if value %}
-                    <span class="badge bg-secondary">{{ value|human_decimal }}</span>
-                  {% else %}
-                    -
-                  {% endif %}
-                </td>
-              </tr>
-            {% endfor %}
-          </tbody>
-      </table>
+      {{ frequencies_table(variant) }}
     </div>
   </div>
 {% endmacro %}
@@ -282,6 +286,41 @@
   </div>
 {% endmacro %}
 
+{% macro old_observations_table(variant) %}
+<table class="table">
+  <thead class="thead table-light">
+    <tr>
+      <th scope="col">Local archive</th>
+      <th scope="col">Nr obs.</th>
+      <th scope="col">Nr homo.</th>
+      <th scope="col">Frequency</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>RD</td>
+      <td>{{ variant.local_obs_old|default('N/A') }}</td>
+      <td>{{ variant.local_obs_hom_old|default('N/A') }}</td>
+      <td>{% if variant.local_obs_old_freq %} {{variant.local_obs_old_freq|round(6)}} {% elif variant.local_obs_old_nr_cases and variant.local_obs_old %} {{ (variant.local_obs_old/variant.local_obs_old_nr_cases)|round(5) }} {% elif variant.local_obs_old_nr_cases %} 0 / {{variant.local_obs_old_nr_cases}} {% else %} N/A {% endif %}</td>
+    </tr>
+    {% if variant.category in ['cancer', 'cancer_sv'] %}
+      <tr>
+        <td>Cancer Germline</td>
+        <td>{{ variant.local_obs_cancer_germline_old|default('N/A') }}</td>
+        <td>{{ variant.local_obs_cancer_germline_hom_old|default('N/A') }}</td>
+        <td>{% if variant.local_obs_cancer_germline_old_freq %} {{variant.local_obs_cancer_germline_old_freq|round(6)}} {% elif variant.local_obs_cancer_germline_old_nr_cases and variant.local_obs_cancer_germline_old %} {{ (variant.local_obs_cancer_germline_old/variant.local_obs_cancer_germline_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_germline_old_nr_cases %} 0 / {{variant.local_obs_cancer_germline_old_nr_cases}} {% else %} N/A {% endif %}</td>
+      </tr>
+      <tr>
+        <td>Cancer Somatic</td>
+        <td>{{ variant.local_obs_cancer_somatic_old|default('N/A') }}</td>
+        <td>{{ variant.local_obs_cancer_somatic_hom_old|default('N/A') }}</td>
+        <td>{% if variant.local_obs_cancer_somatic_old_freq %} {{variant.local_obs_cancer_somatic_old_freq|round(6)}} {% elif variant.local_obs_cancer_somatic_old_nr_cases and variant.local_obs_cancer_somatic_old %} {{ (variant.local_obs_cancer_somatic_old/variant.local_obs_cancer_somatic_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_somatic_old_nr_cases %} 0 / {{variant.local_obs_cancer_somatic_old_nr_cases}} {% else %} N/A {% endif %}</td>
+      </tr>
+    {% endif %}
+  </tbody>
+</table>
+{% endmacro %}
+
 {% macro old_observations(variant, obs_date) %}
 {% if "SHOW_OBSERVED_VARIANT_ARCHIVE" in config and config["SHOW_OBSERVED_VARIANT_ARCHIVE"] == true %}
   <div class="card panel-default">
@@ -289,38 +328,7 @@
       <a href="https://github.com/moonso/loqusdb" target="_blank" data-bs-toggle="tooltip" title="Local observations annotated from an archive copy of the loqusdb local frequency database. Only variants above a quality threshold are included, and each case is included only once. {% if variant.local_obs_old_desc %} {{variant.local_obs_old_desc}} {% endif %}">Local observations (archive {{ obs_date or variant.local_obs_old_date or "version"}})</a>
     </div>
     <div class="card-body">
-      <table class="table">
-        <thead class="thead table-light">
-          <tr>
-            <th scope="col">Archive</th>
-            <th scope="col">Nr obs.</th>
-            <th scope="col">Nr homo.</th>
-            <th scope="col">Frequency</th>
-          </tr>
-        </thead>
-        <tbody>
-          <tr>
-            <td>RD</td>
-            <td>{{ variant.local_obs_old|default('N/A') }}</td>
-            <td>{{ variant.local_obs_hom_old|default('N/A') }}</td>
-            <td>{% if variant.local_obs_old_freq %} {{variant.local_obs_old_freq|round(6)}} {% elif variant.local_obs_old_nr_cases and variant.local_obs_old %} {{ (variant.local_obs_old/variant.local_obs_old_nr_cases)|round(5) }} {% elif variant.local_obs_old_nr_cases %} 0 / {{variant.local_obs_old_nr_cases}} {% else %} N/A {% endif %}</td>
-          </tr>
-          {% if variant.category in ['cancer', 'cancer_sv'] %}
-            <tr>
-              <td>Cancer Germline</td>
-              <td>{{ variant.local_obs_cancer_germline_old|default('N/A') }}</td>
-              <td>{{ variant.local_obs_cancer_germline_hom_old|default('N/A') }}</td>
-              <td>{% if variant.local_obs_cancer_germline_old_freq %} {{variant.local_obs_cancer_germline_old_freq|round(6)}} {% elif variant.local_obs_cancer_germline_old_nr_cases and variant.local_obs_cancer_germline_old %} {{ (variant.local_obs_cancer_germline_old/variant.local_obs_cancer_germline_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_germline_old_nr_cases %} 0 / {{variant.local_obs_cancer_germline_old_nr_cases}} {% else %} N/A {% endif %}</td>
-            </tr>
-            <tr>
-              <td>Cancer Somatic</td>
-              <td>{{ variant.local_obs_cancer_somatic_old|default('N/A') }}</td>
-              <td>{{ variant.local_obs_cancer_somatic_hom_old|default('N/A') }}</td>
-              <td>{% if variant.local_obs_cancer_somatic_old_freq %} {{variant.local_obs_cancer_somatic_old_freq|round(6)}} {% elif variant.local_obs_cancer_somatic_old_nr_cases and variant.local_obs_cancer_somatic_old %} {{ (variant.local_obs_cancer_somatic_old/variant.local_obs_cancer_somatic_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_somatic_old_nr_cases %} 0 / {{variant.local_obs_cancer_somatic_old_nr_cases}} {% else %} N/A {% endif %}</td>
-            </tr>
-          {% endif %}
-        </tbody>
-      </table>
+      {{ old_observations_table(variant) }}
     </div>
   </div>
 {% endif %}

scout/server/blueprints/variant/utils.py

@@ -1,4 +1,5 @@
 import logging
+import re
 from typing import Dict, List, Optional, Tuple
 
 from scout.adapter import MongoAdapter
@@ -683,3 +684,27 @@ def associate_variant_genes_with_case_panels(case_obj: Dict, variant_obj: Dict)
             geneid_gene[hgnc_id]["associated_gene_panels"] = matching_panels
 
     variant_obj["genes"] = list(geneid_gene.values())
+
+
+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>'.
+    """
+    NUM = re.compile(r"\d+")
+
+    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

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/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/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="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>