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

scout/server/blueprints/institutes/views.py

@@ -18,7 +18,12 @@ from scout.constants import (
 )
 from scout.server.blueprints.variants.controllers import update_form_hgnc_symbols
 from scout.server.extensions import beacon, loqusdb, store
-from scout.server.utils import institute_and_case, jsonconverter, templated, user_institutes
+from scout.server.utils import (
+    institute_and_case,
+    jsonconverter,
+    templated,
+    user_institutes,
+)
 
 from . import controllers
 from .forms import GeneVariantFiltersForm, InstituteForm
@@ -138,10 +143,18 @@ def gene_variants(institute_id):
 
     data = {}
 
+    institute_choices = [
+        (inst["_id"], f"{inst['display_name']} ({inst['_id']})")
+        for inst in user_institutes(store, current_user)
+    ]
+    form = GeneVariantFiltersForm()
+    form.institute.choices = institute_choices
+    users_institute_ids = [choice[0] for choice in institute_choices]
+
     if request.method == "GET":
-        form = GeneVariantFiltersForm(request.args)
+        form.process(request.args)
     else:  # POST
-        form = GeneVariantFiltersForm(request.form)
+        form.process(request.form)
 
         if form.variant_type.data == []:
             form.variant_type.data = ["clinical"]
@@ -158,7 +171,7 @@ def gene_variants(institute_id):
 
         variants_query = store.build_variant_query(
             query=form.data,
-            institute_ids=[inst["_id"] for inst in user_institutes(store, current_user)],
+            institute_ids=[inst for inst in form.institute.data if inst in users_institute_ids],
             category=category,
             variant_type=variant_type,
         )  # This is the actual query dictionary, not the cursor with results

scout/server/blueprints/login/controllers.py

@@ -98,7 +98,7 @@ def google_login() -> Optional[Response]:
 
     redirect_uri: str = url_for("login.authorized", _external=True)
     try:
-        return oauth_client.google.authorize_redirect(redirect_uri)
+        return oauth_client.google.authorize_redirect(redirect_uri, prompt="select_account")
     except Exception:
         flash("An error has occurred while logging in user using Google OAuth", "warning")
         return None
@@ -151,6 +151,7 @@ def perform_flask_login(user_dict: "LoginUser") -> Response:
 
 def logout_oidc_user(session, provider: str):
     """Log out a user from an OIDC login provider-"""
+
     logout_url = current_app.config[provider].get("logout_url")
     if not logout_url or not session.get("token_response"):
         return

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/mme/templates/mme/mme_submissions.html

@@ -60,7 +60,7 @@
           {% set collapse_id = 'collapse-' + case._id %}
           {% set max_chars = 300 %}
 
-          {% if case.synopsis|length > max_chars %}
+          {% if case.synopsis and case.synopsis|length > max_chars %}
             <div>
               {{ case.synopsis[:max_chars] }}…
             </div>
@@ -80,7 +80,7 @@
               </div>
             </div>
           {% else %}
-            {{ case.synopsis }}
+            {{ case.synopsis or 'NA' }}
           {% endif %}
         </td>
         <td>{{ case.status }}</td>

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

@@ -100,8 +100,8 @@
                   <span data-bs-toggle="tooltip" data-bs-html="true" title='The ∆ψ-value, which is the difference between the actual observed ψ (intron Jaccard Index splice metric) and the expected ψ - see FRASER vignette for details.'>
                   {{ variant.delta_psi }}&nbsp;<a target="_blank" href="https://www.bioconductor.org/packages/devel/bioc/vignettes/FRASER/inst/doc/FRASER.pdf" rel="noopener noreferrer">&Delta;&psi;</a></span>
                 {% else %}
-                  <span data-bs-toggle="tooltip" data-bs-html="true" title='The log2 fold change - click to see OUTRIDER vignette for details.'>
-                  {{ variant.l2fc }}&nbsp;&nbsp;<a target="_blank" href="https://www.bioconductor.org/packages/devel/bioc/vignettes/OUTRIDER/inst/doc/OUTRIDER.pdf" rel="noopener noreferrer">{% if variant.l2fc > 0 %}&uarr;{% elif variant.l2fc < 0 %}&darr;{% endif %}</a></span>
+                  <span data-bs-toggle="tooltip" data-bs-html="true" title='The log2 fold change (fold change) - click to see OUTRIDER vignette for details.'>
+                  {{ variant.l2fc }} ({{variant.l2fc|l2fc_2_fc|round(2)}}x) &nbsp;&nbsp;<a target="_blank" href="https://www.bioconductor.org/packages/devel/bioc/vignettes/OUTRIDER/inst/doc/OUTRIDER.pdf" rel="noopener noreferrer">{% if variant.l2fc > 0 %}&uarr;{% elif variant.l2fc < 0 %}&darr;{% endif %}</a></span>
                 {% endif %}
               </td>
               <td>

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)
@@ -362,7 +365,7 @@ def variant(
         ccv_evaluation(store, evaluation_obj)
         ccv_evaluations.append(evaluation_obj)
 
-    case_clinvars = store.case_to_clinVars(case_obj.get("display_name"))
+    case_clinvars = store.case_to_clinvars(case_obj.get("display_name"))
 
     if variant_id in case_clinvars:
         variant_obj["clinvar_clinsig"] = case_clinvars.get(variant_id)["clinsig"]
@@ -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/cancer-variant.html

@@ -8,6 +8,7 @@
 {% from "variant/sanger.html" import modal_cancel_sanger, modal_sanger, sanger_button %}
 {% from "variant/gene_disease_relations.html" import orpha_omim_phenotypes %}
 {% from "variant/rank_score_results.html" import rankscore_panel %}
+{% from "variants/utils.html" import variant_rank_score %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }}
@@ -282,7 +283,7 @@
             <strong>{{ variant.alternative }}</strong>
           {%- endif -%}
         </li>
-        <li class="list-group-item">Rank score: <span class="font-weight-bold">{{ variant.rank_score }}</span>
+        <li class="list-group-item">Rank score: <span class="font-weight-bold">{{ variant_rank_score(variant) }}</span>
         </li>
         <li class="list-group-item">
           {{ clinsig_table(variant) }}

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

@@ -1,7 +1,6 @@
 {% from "cases/chanjo2_form.html" import chanjo2_report_form %}
 {% from "variant/buttons.html" import variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button %}
 {% from "variants/utils.html" import compounds_table %}
-{% from "variant/variant_details.html" import severity_list %}
 {% from "variant/buttons.html" import reviewer_button, splice_junctions_button %}
 {% from "variant/utils.html" import igv_track_selection  %}
 

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

@@ -7,6 +7,7 @@
 {% from "variant/gene_disease_relations.html" import orpha_omim_phenotypes %}
 {% from "variant/variant_details.html" import frequencies, gtcall_panel, observations_panel %}
 {% from "variant/buttons.html" import dismiss_variant_button, splice_junctions_button, variant_tag_button %}
+{% from "variants/utils.html" import variant_rank_score %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }}
@@ -174,7 +175,7 @@
         <li class="list-group-item">Rank <span class="badge rounded-pill bg-secondary float-end">{{ variant.variant_rank }}</span></li>
         <li class="list-group-item">
           Rank score
-          <span class="badge rounded-pill bg-secondary float-end">{{ variant.rank_score }}</span>
+          <span class="badge rounded-pill bg-secondary float-end">{{variant_rank_score(variant)}}</span>
         </li>
 
         <li class="list-group-item">

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.html

@@ -1,7 +1,7 @@
 {% extends "layout.html" %}
 {% from "variant/buttons.html" import database_buttons %}
 {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %}
-{% from "variants/utils.html" import compounds_table %}
+{% from "variants/utils.html" import compounds_table, variant_rank_score %}
 {% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel, custom_annotations, gene_panels %}
 {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %}
 {% from "variant/gene_disease_relations.html" import autozygosity_panel, genemodels_panel, inheritance_panel, orpha_omim_phenotypes %}
@@ -263,7 +263,7 @@
             </td>
             <td>
               Rank score
-              <span><strong>{{ variant.rank_score }}</strong></span>
+              <span><strong>{{variant_rank_score(variant)}}</strong></span>
             </td>
             <td>
               CADD score

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

@@ -19,7 +19,7 @@
             {% elif variant.category == "sv" %}
               <th rowspan="2" colspan="1" title="SV caller specific quality score. Note different scales for different callers.">SV quality</th>
             {% elif variant.category == "str" %}
-              <th rowspan="2" colspan="1">ExpansionHunter support</th>
+              <th rowspan="2" colspan="1">Expansion support</th>
             {% else %}
 	      {% if variant.chromosome in ["MT","M"] %}
                 <th rowspan="2" colspan="1" title="Variant Allele Frequency.">Variant Allele Frequency (VAF)</th>
@@ -54,7 +54,8 @@
 
               {% if variant.category == "snv" and variant.chromosome in ["MT","M"] %}
                 <td>
-                  {% if sample.alt_frequency and sample.alt_frequency != -1 %}
+                  {# Using number == number as a test for NaN value numbers here. Given that they exist, NaN values are the only time a number is not considered equal to itself. #}
+                  {% if sample.alt_frequency and sample.alt_frequency != -1 and sample.alt_frequency == sample.alt_frequency %}
                     {{ (100*sample.alt_frequency)|round(2) }}%
                   {% else %}
 		    N/A
@@ -80,7 +81,7 @@
                     <small>N/A</small>
                   {% endif %} (<small>VQ</small>
                   {% if variant.quality not in ["None", None, "-1", -1] %}
-                    {{variant.quality}}
+                    {{variant.quality|round(1)}}
                   {% else %}
                     <small>N/A</small>
                   {% endif%})
@@ -164,38 +165,42 @@
   </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 +287,41 @@
   </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 +329,7 @@
       <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 %}
@@ -344,13 +353,15 @@
         <li class="list-group-item">
           <a href="https://sites.google.com/site/revelgenomics/about" target="_blank" data-bs-toggle="tooltip"
             title="An ensemble score based on 13 individual scores for predicting the pathogenicity of missense variants. Scores range from 0 to 1. The larger the score the more likely the SNP has damaging effect">REVEL score</a>
-          <span class="float-end">
-          {% if variant.revel  %}
-             {{ variant.revel }}
+          {% if variant.revel and variant.revel != "-" %}
+            <span class="badge float-end bg-{{variant.revel|get_label_or_color_by_score('revel', 'color')}}" data-bs-toggle="tooltip" title="{{variant.revel|get_label_or_color_by_score('revel', 'label')}}">
+              {{ variant.revel }}
+            </span>
           {% else %}
-             {{ "-" }}
+            <span class="float-end">
+              {{ "-" }}
+            </span>
           {% endif %}
-          </span>
         </li>
         <li class="list-group-item">
           <a href="http://database.liulab.science/dbNSFP" target="_blank" data-bs-toggle="tooltip"
@@ -378,23 +389,28 @@
           <span class="float-end">{{ variant.spidex|spidex_human if variant.spidex else none|spidex_human }}</span>
         </li>
         <li class="list-group-item">
+          {% set spliceai_highest = variant.spliceai_scores | spliceai_max %}
           <a href="{{ variant.spliceai_link }}" target="_blank" rel="noopener">SpliceAI</a> <a href="https://github.com/Illumina/SpliceAI" target="_blank" rel="noopener">DS max</a>
-          <span class="float-end control-label" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="bottom"
-              title="<strong>
-                {% for entry in variant.spliceai_scores %}
-                  {% if entry is not none %}
-                    SpliceAI highest delta score {{ entry }} </strong> at position {{ variant.spliceai_positions[loop.index0]}} relative to this variant.
-                    {% if variant.spliceai_predictions[loop.index0] %}
-                      <br>All scores and positions(relative to variant):<br>
-                      {{ variant.spliceai_predictions[loop.index0] }} <br>
-                    {%  endif %}
-                    <br>
-                  {% else %}
-                    No SpliceAI positions annotated for this variant.
-                  {% endif %}
-                {% endfor %}
-              ">
-            {{ variant.spliceai_scores|join(', ') or "-"}}
+          {% if spliceai_highest %}
+            <span class="badge bg-{{ spliceai_highest | get_label_or_color_by_score('spliceai', 'color') }} float-end" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="bottom"
+                title="<strong>
+                  {% for entry in variant.spliceai_scores %}
+                    {% if entry is not none %}
+                      SpliceAI highest delta score {{ entry }} </strong> at position {{ variant.spliceai_positions[loop.index0]}} relative to this variant. {{ spliceai_highest | get_label_or_color_by_score('spliceai', 'label')}} according to Walker et al 2023.
+                      {% if variant.spliceai_predictions[loop.index0] %}
+                        <br>All scores and positions(relative to variant):<br>
+                        {{ variant.spliceai_predictions[loop.index0] }} <br>
+                      {%  endif %}
+                      <br>
+                    {% else %}
+                      No SpliceAI positions annotated for this variant.
+                    {% endif %}
+                  {% endfor %}
+                ">
+                {{ variant.spliceai_scores|join(', ') }}
+            {% else %}
+              <span class="float-end">{{ "-" }}
+            {% endif %}
           </span>
         </li>
       </ul>

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