scout-browser 4.102.0__py3-none-any.whl → 4.103.0__py3-none-any.whl

scout/server/blueprints/clinvar/views.py

@@ -1,10 +1,11 @@
 import logging
 from json import dumps
 from tempfile import NamedTemporaryFile
-from typing import List, Tuple
+from typing import List, Optional, Tuple
 
 from flask import (
     Blueprint,
+    Response,
     flash,
     redirect,
     render_template,
@@ -18,9 +19,10 @@ from scout.constants.clinvar import (
     CASEDATA_HEADER,
     CLINVAR_HEADER,
     GERMLINE_CLASSIF_TERMS,
+    ONCOGENIC_CLASSIF_TERMS,
 )
 from scout.server.extensions import clinvar_api, store
-from scout.server.utils import institute_and_case
+from scout.server.utils import institute_and_case, safe_redirect_back
 
 from . import controllers
 
@@ -40,8 +42,13 @@ def clinvar_submission_status(submission_id):
     """Sends a request to ClinVar to retrieve and display the status of a submission."""
 
     # flash a message with current submission status for a ClinVar submission
+    clinvar_resp_status = dict(
+        clinvar_api.json_submission_status(
+            submission_id=submission_id, api_key=request.form.get("apiKey")
+        )
+    )
     flash(
-        f'Response from ClinVar: {clinvar_api.json_submission_status( submission_id=submission_id, api_key=request.form.get("apiKey"))}',
+        f"Response from ClinVar: {clinvar_resp_status}",
         "primary",
     )
     return redirect(request.referrer)
@@ -76,8 +83,8 @@ def clinvar_add_variant(institute_id, case_name):
 
 
 @clinvar_bp.route("/<institute_id>/<case_name>/clinvar/save", methods=["POST"])
-def clinvar_save(institute_id, case_name):
-    """Adds one variant with eventual CaseData observations to an open (or new) ClinVar submission"""
+def clinvar_save(institute_id: str, case_name: str):
+    """Adds one germline variant with eventual CaseData observations to an open (or new) ClinVar submission."""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     controllers.add_variant_to_submission(
         institute_obj=institute_obj, case_obj=case_obj, form=request.form
@@ -85,14 +92,14 @@ def clinvar_save(institute_id, case_name):
     return redirect(url_for("cases.case", institute_id=institute_id, case_name=case_name))
 
 
-@clinvar_bp.route("/<institute_id>/clinvar_submissions", methods=["GET"])
-def clinvar_submissions(institute_id):
+@clinvar_bp.route("/<institute_id>/clinvar_germline_submissions", methods=["GET"])
+def clinvar_germline_submissions(institute_id):
     """Handle clinVar submission objects and files"""
 
     institute_obj = institute_and_case(store, institute_id)
     institute_clinvar_submitters: List[str] = institute_obj.get("clinvar_submitters", [])
     data = {
-        "submissions": store.clinvar_submissions(institute_id),
+        "submissions": store.get_clinvar_germline_submissions(institute_id),
         "institute": institute_obj,
         "variant_header_fields": CLINVAR_HEADER,
         "casedata_header_fields": CASEDATA_HEADER,
@@ -131,24 +138,94 @@ def clinvar_update_submission(institute_id, submission):
 
 
 @clinvar_bp.route("/<submission>/download/json/<clinvar_id>", methods=["GET"])
-def clinvar_download_json(submission, clinvar_id):
-    """Download a json for a clinVar submission"""
+def clinvar_download_json(submission: str, clinvar_id: Optional[str]) -> Response:
+    """Download a json for a clinVar submission.
+
+    Accepts:
+        submission:. It's the _id of the submission in the database
+        clinvar_id: It's the submission number (i.e. SUB123456). Might be available or not in the submission dictionary
+
+    """
+    filename = clinvar_id if clinvar_id != "None" else submission
 
     code, conversion_res = controllers.json_api_submission(submission_id=submission)
 
     if code in [200, 201]:
         # Write temp CSV file and serve it in response
-        tmp_json = NamedTemporaryFile(mode="a+", prefix=clinvar_id, suffix=".json")
+        tmp_json = NamedTemporaryFile(mode="a+", prefix=filename, suffix=".json")
         tmp_json.write(dumps(conversion_res, indent=4))
 
         tmp_json.flush()
         tmp_json.seek(0)
         return send_file(
             tmp_json.name,
-            download_name=f"{clinvar_id}.json",
+            download_name=f"{filename}.json",
             mimetype="application/json",
             as_attachment=True,
         )
     else:
-        flash(f"JSON file could not be crated for ClinVar submission: {clinvar_id} ", "warning")
+        flash(
+            f"JSON file could not be crated for ClinVar submission: {filename}: {conversion_res}",
+            "warning",
+        )
         return redirect(request.referrer)
+
+
+### ClinVar oncogenicity variants submissions views
+
+
+@clinvar_bp.route("/<institute_id>/clinvar_onc_submissions", methods=["GET"])
+def clinvar_onc_submissions(institute_id):
+    """Handle clinVar submission objects and files"""
+
+    institute_obj = institute_and_case(store, institute_id)
+    institute_clinvar_submitters: List[str] = institute_obj.get("clinvar_submitters", [])
+    data = {
+        "submissions": list(store.get_clinvar_onc_submissions(institute_id)),
+        "institute": institute_obj,
+        "show_submit": current_user.email in institute_clinvar_submitters
+        or not institute_clinvar_submitters,
+    }
+    return render_template("clinvar/clinvar_onc_submissions.html", **data)
+
+
+@clinvar_bp.route("/<institute_id>/<case_name>/clinvar/clinvar_add_onc_variant", methods=["POST"])
+def clinvar_add_onc_variant(institute_id: str, case_name: str):
+    """Create a ClinVar submission document in database for one or more variants from a case."""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+    data = {
+        "institute": institute_obj,
+        "case": case_obj,
+        "onc_classif_terms": ONCOGENIC_CLASSIF_TERMS,
+    }
+    controllers.set_onc_clinvar_form(request.form.get("var_id"), data)
+    return render_template("clinvar/multistep_add_onc_variant.html", **data)
+
+
+@clinvar_bp.route(
+    "/<institute_id>/<case_name>/clinvar_onc/clinvar_save_onc_variant", methods=["POST"]
+)
+def clinvar_onc_save(institute_id: str, case_name: str):
+    """Adds one somatic variant with eventual CaseData observations to an open (or new) ClinVar congenicity submission"""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+    controllers.add_onc_variant_to_submission(
+        institute_obj=institute_obj, case_obj=case_obj, form=request.form
+    )
+    return redirect(url_for("cases.case", institute_id=institute_id, case_name=case_name))
+
+
+@clinvar_bp.route("/<submission>/clinvar_onc/delete_variant", methods=["POST"])
+def clinvar_delete_onc_variant(submission: str):
+    """Delete a single variant (oncogenicitySubmission) from the ClinVar submissions collection."""
+    store.delete_clinvar_onc_var(
+        submission=submission,
+        variant_id=request.form.get("delete_object"),
+    )
+    return safe_redirect_back(request)
+
+
+@clinvar_bp.route("/<submission>/download", methods=["GET"])
+def clinvar_download(submission):
+    """Download a json file for a clinVar submission. This function is only used for oncogenocity submissions for the time being"""
+
+    return store.get_onc_submission_json(submission)

scout/server/blueprints/institutes/controllers.py

@@ -51,6 +51,11 @@ VAR_SPECIFIC_EVENTS = [
     "cancel_sanger",
 ]
 
+# Query terms in default, non-specific queries for cases
+NONSPECIFIC_QUERY_TERMS = [
+    "collaborators",
+]
+
 # Projection for fetching cases
 ALL_CASES_PROJECTION = {
     "analysis_date": 1,
@@ -566,6 +571,7 @@ def get_cases_by_query(
         has_clinvar_submission=request.form.get("clinvar_submitted"),
         projection=ALL_CASES_PROJECTION,
     )
+
     return all_cases
 
 
@@ -598,13 +604,42 @@ def get_and_set_cases_by_status(
             case_groups[status].append(case_obj)
             nr_cases_showall_statuses += 1
 
+    def get_specific_query(request: request) -> bool:
+        """Check if only non-specific query terms were used in query,
+        by yielding the query without actually executing it.
+
+        If so we assume this is a default query, and dim all cases
+        that match the "show_all_cases_status", highlighting the
+        (max limit number) other cases that were returned.
+
+        If this is a specific query, cases returned by this query part will be explicitly
+        highlighted even if they have a status that matches "show_all_cases_status".
+        """
+        cases_query: dict = store.cases(
+            collaborator=institute_obj["_id"],
+            name_query=request.form,
+            skip_assigned=request.form.get("skip_assigned"),
+            is_research=request.form.get("is_research"),
+            has_rna_data=request.form.get("has_rna"),
+            verification_pending=request.form.get("validation_ordered"),
+            has_clinvar_submission=request.form.get("clinvar_submitted"),
+            yield_query=True,
+        )
+        for key, value in cases_query.items():
+            if key not in NONSPECIFIC_QUERY_TERMS and value not in [None, ""]:
+                return True
+        return False
+
+    specific_query_asked = get_specific_query(request)
+
     nr_name_query_matching_displayed_cases = 0
     limit = int(request.form.get("search_limit", 100))
     for case_obj in previous_query_result_cases:
         if case_obj["status"] in status_show_all_cases:
-            for group_case in case_groups[status]:
-                if group_case["_id"] == case_obj["_id"]:
-                    group_case["dimmed_in_search"] = False
+            if specific_query_asked:
+                for group_case in case_groups[status]:
+                    if group_case["_id"] == case_obj["_id"]:
+                        group_case["dimmed_in_search"] = False
         elif nr_name_query_matching_displayed_cases == limit:
             break
         else:
@@ -668,7 +703,7 @@ def populate_case_obj(case_obj: dict, store: MongoAdapter):
         all_analyses_dates
     )
 
-    case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
+    case_obj["clinvar_variants"] = store.case_to_clinvars(case_obj["_id"])
     case_obj["display_track"] = TRACKS.get(case_obj.get("track", "rare"))
 
 
@@ -830,7 +865,9 @@ def export_gene_variants(
         )  # CADD score
         variant_line.append(" | ".join(variant.get("region_annotations", [])))  # Region
         variant_line.append(" | ".join(variant.get("functional_annotations", [])))  # Function
-        variant_line.append(variant.get("hgvs", "-"))  # HGVS
+        variant_line.append(
+            " | ".join(current_app.custom_filters.format_variant_canonical_transcripts(variant))
+        )
 
         export_lines.append(",".join(variant_line))
 
@@ -860,6 +897,8 @@ def gene_variants(store, pymongo_cursor, variant_count, page=1, per_page=50):
     for variant_obj in variant_res:
         # Populate variant case_display_name
         variant_case_obj = store.case(case_id=variant_obj["case_id"])
+        if variant_case_obj is None:
+            continue
         case_display_name = variant_case_obj.get("display_name")
         variant_obj["case_display_name"] = case_display_name
 

scout/server/blueprints/institutes/forms.py

@@ -152,6 +152,7 @@ class GeneVariantFiltersForm(FlaskForm):
         "HGNC Symbols (comma-separated, case sensitive)",
         validators=[validators.InputRequired()],
     )
+    institute = SelectMultipleField(choices=[])
     rank_score = IntegerField(default=15)
     phenotype_terms = TagListField("HPO terms (comma-separated)")
     phenotype_groups = TagListField("Phenotype groups")

scout/server/blueprints/institutes/templates/overview/gene_variants.html

@@ -2,7 +2,7 @@
 {% from "variants/components.html" import frequency_cell_general, variant_funct_anno_cell, variant_gene_symbols_cell %}
 {% from "utils.html" import comments_table %}
 {% from "overview/institute_sidebar.html" import institute_actionbar %}
-{% from "variants/utils.html" import pagination_footer, pagination_hidden_div %}
+{% from "variants/utils.html" import pagination_footer, pagination_hidden_div, variant_rank_score %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - All SNVs and INDELs
@@ -96,17 +96,22 @@
         {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
        {% endif %}
   {% else %}
-    <a href="{{ url_for('variant.variant', institute_id=variant.institute,
+      <a href="{{ url_for('variant.variant', institute_id=variant.institute,
             case_name=variant.case_display_name, variant_id=variant._id) }}" target="_blank">
-    {{ (variant.hgvs or '')|url_decode }}
-  {% endif %}
-  </a>
+      {% set lines = variant | format_variant_canonical_transcripts %}
+      {% if lines | length > 1 %}
+        {{ lines | join('<br>') | safe }}
+      {% elif lines %}
+        {{ lines[0] }}
+      {% endif %}
+   {% endif %}
+   </a>
 {% endmacro %}
 
 {% macro cell_rank(variant) %}
    {{ variant.case_display_name }}
     :
-    <span class="badge bg-info">{{ variant.rank_score|int }}</span>
+    <span class="badge bg-info">{{ variant_rank_score(variant) }}</span>
 {% endmacro %}
 
 {% macro cell_cadd(variant) %}
@@ -130,6 +135,10 @@
           {{ form.hgnc_symbols.label(class="control-label") }}
           {{ form.hgnc_symbols(class="form-control") }}
         </div>
+        <div class="col col-md-2">
+          {{ form.institute.label(class="control-label") }}
+          {{ form.institute(class="form-control", class="selectpicker", data_style="btn-secondary") }}
+        </div>
         <div class="col col-md-1">
           <label class="control-label" for="rank_score">Rank Score</label>
           <input type="number" class="form-control" id="rank_score" name="rank_score" min="5" value={{form.rank_score.data}}>

scout/server/blueprints/institutes/templates/overview/institute_sidebar.html

@@ -44,12 +44,38 @@
       </a>
 
       <!-- ClinVar data menu item -->
-      <a href="{{ url_for('clinvar.clinvar_submissions', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
+      <a href="#submenu1" aria-controls="submenu1" data-bs-toggle="collapse" aria-expanded="false" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
           <div class="d-flex w-100 justify-content-start align-items-center">
               <span class="fas fa-file-medical me-3"></span>
-              <span class="menu-collapsed">ClinVar submissions</span>
+              <span class="menu-collapsed text-nowrap flex-grow-1">ClinVar submissions</span>
+              <span class="submenu-icon ms-auto"></span>
           </div>
       </a>
+      <div id='submenu1' class="collapse sidebar-submenu">
+        <div href="#" class="bg-dark list-group-item text-white">
+
+          <div class="d-flex flex-row flex-fill bd-highlight">
+            <div>
+              <span class="menu-collapsed">Germline</span>
+            </div>
+            <div>
+              <a href="{{ url_for('clinvar.clinvar_germline_submissions', institute_id=institute._id) }}" target="_blank" rel="noopener">
+                    <span class="fa fa-link"></span></a>
+            </div>
+          </div>
+
+          <div class="d-flex flex-row flex-fill bd-highlight">
+            <div>
+              <span class="menu-collapsed">Oncogenic</span>
+            </div>
+            <div>
+              <a href="{{ url_for('clinvar.clinvar_onc_submissions', institute_id=institute._id) }}" target="_blank" rel="noopener">
+                    <span class="fa fa-link"></span></a>
+            </div>
+          </div>
+
+         </div>
+      </div>
 
      <!-- MME data menu item -->
       <a href="{{ url_for('mme.mme_submissions', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">

scout/server/blueprints/institutes/templates/overview/utils.html

@@ -25,7 +25,7 @@
         </div>
         <div class="col-md-1 mb-3">
             {{ form.search_limit.label(class="form-label") }}
-            {{ form.search_limit(class="form-control") }}
+            {{ form.search_limit(class="form-control", type="number", min="1", step="1", required=True) }}
         </div>
         <div class="btn-sm mb-2 col-md-3 mx-auto">
           {{ form.search(class="btn btn-primary mt-4") }}

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/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/variant/controllers.py

@@ -365,7 +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"]

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/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%})
@@ -352,13 +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"
@@ -386,23 +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/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 %}