scout-browser 4.84__py3-none-any.whl → 4.86__py3-none-any.whl

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

@@ -100,7 +100,7 @@
             <div class="col-3">Show tracks:</div>
             <div class="col-6">
               <select name="user_tracks" class="selectpicker" data-width="90%" data-style="btn-secondary" multiple>
-                {% for track in igv_tracks %}
+                {% for track in igv_tracks|sort %}
                   <!--pre-select option if user has saved it in preferences or select all options if user has no preferences yet-->
                   <option value="{{ track }}" {{ "selected" if current_user.igv_tracks and track in current_user.igv_tracks or current_user.igv_tracks is not defined }}>{{ track }}</option>
                 {% endfor %}

scout/server/blueprints/variant/utils.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Tuple
 
 from scout.adapter import MongoAdapter
 from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS
@@ -333,122 +333,72 @@ def predictions(genes):
     return data
 
 
-def frequencies(variant_obj):
-    """Add frequencies in the correct way for the template
-
-    This function converts the raw annotations to something better to visualize.
-    GnomAD is mandatory and will always be shown.
+def frequencies(variant_obj: dict) -> list[Tuple]:
+    """Convert raw annotations to a more visual format with frequencies.
 
     Args:
         variant_obj(scout.models.Variant)
 
     Returns:
-        frequencies(list(tuple)): A list of frequencies to display
+        list of tuple: A list of frequencies to display.
     """
     is_mitochondrial_variant = variant_obj.get("chromosome") == "MT"
+    category = variant_obj["category"]
+
+    # Define frequency mappings for each category
+    frequency_mappings = {
+        "sv": {
+            "gnomad_frequency": ("GnomAD", variant_obj.get("gnomad_sv_link")),
+            "clingen_cgh_benign": ("ClinGen CGH (benign)", None),
+            "clingen_cgh_pathogenic": ("ClinGen CGH (pathogenic)", None),
+            "clingen_ngi": ("ClinGen NGI", None),
+            "clingen_mip": ("ClinGen MIP", None),
+            "swegen": ("SweGen", None),
+            "decipher": ("Decipher", None),
+            "thousand_genomes_frequency": ("1000G", None),
+            "thousand_genomes_frequency_left": ("1000G(left)", None),
+            "thousand_genomes_frequency_right": ("1000G(right)", None),
+            "colorsdb_af": ("CoLoRSdb", None),
+        },
+        "mei": {
+            "swegen_alu": ("SweGen ALU", None),
+            "swegen_herv": ("SweGen HERV", None),
+            "swegen_l1": ("SweGen L1", None),
+            "swegen_sva": ("SweGen SVA", None),
+            "swegen_mei_max": ("SweGen MEI(max)", None),
+        },
+        "snv": {
+            "gnomad_frequency": ("GnomAD", variant_obj.get("gnomad_link")),
+            "thousand_genomes_frequency": ("1000G", variant_obj.get("thousandg_link")),
+            "max_thousand_genomes_frequency": ("1000G(max)", variant_obj.get("thousandg_link")),
+            "exac_frequency": ("ExAC", variant_obj.get("exac_link")),
+            "max_exac_frequency": ("ExAC(max)", variant_obj.get("exac_link")),
+            "swegen": ("SweGen", variant_obj.get("swegen_link")),
+            "gnomad_mt_homoplasmic_frequency": (
+                "GnomAD MT, homoplasmic",
+                variant_obj.get("gnomad_link"),
+            ),
+            "gnomad_mt_heteroplasmic_frequency": (
+                "GnomAD MT, heteroplasmic",
+                variant_obj.get("gnomad_link"),
+            ),
+            "colorsdb_af": ("CoLoRSdb", None),
+        },
+    }
+
+    # Select the appropriate frequency dictionary
+    freqs = frequency_mappings.get(category, frequency_mappings["snv"])
 
-    if variant_obj["category"] == "sv":
-        freqs = {
-            "gnomad_frequency": {
-                "display_name": "GnomAD",
-                "link": variant_obj.get("gnomad_sv_link"),
-            },
-            "clingen_cgh_benign": {
-                "display_name": "ClinGen CGH (benign)",
-                "link": None,
-            },
-            "clingen_cgh_pathogenic": {
-                "display_name": "ClinGen CGH (pathogenic)",
-                "link": None,
-            },
-            "clingen_ngi": {"display_name": "ClinGen NGI", "link": None},
-            "clingen_mip": {"display_name": "ClinGen MIP", "link": None},
-            "swegen": {"display_name": "SweGen", "link": None},
-            "decipher": {"display_name": "Decipher", "link": None},
-            "thousand_genomes_frequency": {"display_name": "1000G", "link": None},
-            "thousand_genomes_frequency_left": {
-                "display_name": "1000G(left)",
-                "link": None,
-            },
-            "thousand_genomes_frequency_right": {
-                "display_name": "1000G(right)",
-                "link": None,
-            },
-        }
-    elif variant_obj["category"] == "mei":
-        freqs = {
-            "swegen_alu": {
-                "display_name": "SweGen ALU",
-                "link": None,
-            },
-            "swegen_herv": {
-                "display_name": "SweGen HERV",
-                "link": None,
-            },
-            "swegen_l1": {
-                "display_name": "SweGen L1",
-                "link": None,
-            },
-            "swegen_sva": {
-                "display_name": "SweGen SVA",
-                "link": None,
-            },
-            "swegen_mei_max": {
-                "display_name": "SweGen MEI(max)",
-                "link": None,
-            },
-        }
-    else:
-        freqs = {
-            "gnomad_frequency": {
-                "display_name": "GnomAD",
-                "link": variant_obj.get("gnomad_link"),
-            },
-            "thousand_genomes_frequency": {
-                "display_name": "1000G",
-                "link": variant_obj.get("thousandg_link"),
-            },
-            "max_thousand_genomes_frequency": {
-                "display_name": "1000G(max)",
-                "link": variant_obj.get("thousandg_link"),
-            },
-            "exac_frequency": {
-                "display_name": "ExAC",
-                "link": variant_obj.get("exac_link"),
-            },
-            "max_exac_frequency": {
-                "display_name": "ExAC(max)",
-                "link": variant_obj.get("exac_link"),
-            },
-            "swegen": {
-                "display_name": "SweGen",
-                "link": variant_obj.get("swegen_link"),
-            },
-            "gnomad_mt_homoplasmic_frequency": {
-                "display_name": "GnomAD MT, homoplasmic",
-                "link": variant_obj.get("gnomad_link"),
-            },
-            "gnomad_mt_heteroplasmic_frequency": {
-                "display_name": "GnomAD MT, heteroplasmic",
-                "link": variant_obj.get("gnomad_link"),
-            },
-        }
     frequency_list = []
-    for freq_key in freqs:
-        display_name = freqs[freq_key]["display_name"]
+    for freq_key, (display_name, link) in freqs.items():
         value = variant_obj.get(freq_key)
-        link = freqs[freq_key]["link"]
-        # Always add gnomad for non-mitochondrial variants
+
         if freq_key == "gnomad_frequency":
             if is_mitochondrial_variant:
                 continue
-            # If gnomad not found search for exac
-            if not value:
-                value = variant_obj.get("exac_frequency")
-            value = value or "NA"
+            value = value or variant_obj.get("exac_frequency") or "NA"
 
-        # Always add gnomad MT frequencies for mitochondrial variants
-        elif freq_key.startswith("gnomad_mt_") and is_mitochondrial_variant:
+        if freq_key.startswith("gnomad_mt_") and is_mitochondrial_variant:
             value = value or "NA"
 
         if value:
@@ -474,6 +424,7 @@ def frequency(variant_obj):
         variant_obj.get("gnomad_frequency") or 0,
         variant_obj.get("gnomad_mt_homoplasmic_frequency") or 0,
         variant_obj.get("swegen_mei_max") or 0,
+        variant_obj.get("colorsdb_af") or 0,
     )
 
     if most_common_frequency > 0.05:

scout/server/blueprints/variant/views.py

@@ -47,6 +47,7 @@ def update_tracks_settings():
     # update user in database with custom tracks info
     user_obj["igv_tracks"] = selected_tracks
     store.update_user(user_obj)
+    setattr(current_user, "igv_tracks", selected_tracks)
     return redirect(request.referrer)
 
 

scout/server/blueprints/variants/controllers.py

@@ -1496,9 +1496,6 @@ def populate_filters_form(store, institute_obj, case_obj, user_obj, category, re
     Returns:
         form: FiltersForm
     """
-    form = None
-    clinical_filter_panels = []
-
     default_panels = []
     for panel in case_obj.get("panels", []):
         if panel.get("is_default"):
@@ -1520,7 +1517,7 @@ def populate_filters_form(store, institute_obj, case_obj, user_obj, category, re
             }
         )
         clinical_filter = MultiDict(clinical_filter_dict)
-    elif category in ("sv", "cancer", "cancer_sv", "mei"):
+    elif category in ("sv", "cancer", "cancer_sv", "mei", "outlier"):
         clinical_filter_dict = FiltersFormClass.clinical_filter_base
         clinical_filter_dict.update(
             {

scout/server/blueprints/variants/forms.py

@@ -23,10 +23,12 @@ from scout.constants import (
     CLINICAL_FILTER_BASE,
     CLINICAL_FILTER_BASE_CANCER,
     CLINICAL_FILTER_BASE_MEI,
+    CLINICAL_FILTER_BASE_OUTLIER,
     CLINICAL_FILTER_BASE_SV,
     CLINSIG_MAP,
     FEATURE_TYPES,
     GENETIC_MODELS,
+    OUTLIER_TYPES,
     SO_TERMS,
     SPIDEX_LEVELS,
     SV_TYPES,
@@ -39,6 +41,7 @@ CLINSIG_OPTIONS = list(CLINSIG_MAP.items())
 FUNC_ANNOTATIONS = [(term, term.replace("_", " ")) for term in SO_TERMS]
 REGION_ANNOTATIONS = [(term, term.replace("_", " ")) for term in FEATURE_TYPES]
 SV_TYPE_CHOICES = [(term, term.replace("_", " ").upper()) for term in SV_TYPES]
+OUTLIER_TYPE_CHOICES = [(term, term.replace("_", " ").upper()) for term in OUTLIER_TYPES]
 SPIDEX_CHOICES = [(term, term.replace("_", " ")) for term in SPIDEX_LEVELS]
 FUSION_CALLER_CHOICES = [(term.get("id"), term.get("name")) for term in CALLERS.get("fusion")]
 
@@ -236,6 +239,44 @@ class FusionFiltersForm(VariantFiltersForm):
     fusion_caller = SelectMultipleField("Fusion Caller", choices=FUSION_CALLER_CHOICES, default=[])
 
 
+class OutlierFiltersForm(FlaskForm):
+    variant_type = HiddenField(default="clinical")
+
+    gene_panels = NonValidatingSelectMultipleField(choices=[])
+    gene_panels_exclude = BooleanField("Exclude genes")
+    hgnc_symbols = TagListField("HGNC Symbols/Ids (case sensitive)")
+
+    svtype = SelectMultipleField("Type", choices=OUTLIER_TYPE_CHOICES)
+
+    filters = NonValidatingSelectField(choices=[], validators=[validators.Optional()])
+    filter_display_name = StringField(default="")
+    save_filter = SubmitField(label="Save filter")
+    load_filter = SubmitField(label="Load filter")
+    lock_filter = SubmitField(label="Lock filter")
+    delete_filter = SubmitField(label="Delete filter")
+    audit_filter = SubmitField(label="Audit filter")
+    clinical_filter = SubmitField(label="Clinical filter")
+
+    chrom_pos = StringField(
+        "Chromosome position",
+        [validators.Optional()],
+        render_kw={"placeholder": "<chr>:<start pos>-<end pos>[optional +/-<span>]"},
+    )
+
+    chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
+    start = IntegerField("Start position", [validators.Optional()])
+    end = IntegerField("End position", [validators.Optional()])
+    cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
+    cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
+
+    filter_variants = SubmitField(label="Filter variants")
+    export = SubmitField(label="Filter and export")
+
+    clinical_filter_base = CLINICAL_FILTER_BASE_OUTLIER
+
+    show_unaffected = BooleanField("Show also variants present only in unaffected", default=False)
+
+
 FILTERSFORMCLASS = {
     "snv": FiltersForm,
     "str": StrFiltersForm,
@@ -244,4 +285,5 @@ FILTERSFORMCLASS = {
     "cancer": CancerFiltersForm,
     "mei": MeiFiltersForm,
     "fusion": FusionFiltersForm,
+    "outlier": OutlierFiltersForm,
 }

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

@@ -30,13 +30,17 @@
 
     var the_form = document.forms['filters_form'];
 
-    document.getElementById('hide_dismissed').onchange = function() {
+    var hide_dismissed = document.getElementById('hide_dismissed');
+    if (hide_dismissed) {
+      hide_dismissed.onchange = function() {
       the_form.submit();
-    };
+    }}
 
-    document.getElementById('show_unaffected').onchange = function() {
+    var show_unaffected =document.getElementById('show_unaffected');
+    if (show_unaffected) {
+      show_unaffected.onchange = function() {
       the_form.submit();
-    };
+    }}
 
     function resetPage(){
       document.getElementById('page').value = "1";

scout/server/blueprints/variants/views.py

@@ -137,7 +137,9 @@ def variants(institute_id, case_name):
     variants_query = store.variants(
         case_obj["_id"], query=form.data, category=category, build=genome_build
     )
-    result_size = store.count_variants(case_obj["_id"], form.data, None, category)
+    result_size = store.count_variants(
+        case_obj["_id"], form.data, None, category, build=genome_build
+    )
 
     if request.form.get("export"):
         return controllers.download_variants(store, case_obj, variants_query)
@@ -236,7 +238,7 @@ def str_variants(institute_id, case_name):
         ]
     )
 
-    result_size = store.count_variants(case_obj["_id"], query, None, category)
+    result_size = store.count_variants(case_obj["_id"], query, None, category, build=genome_build)
 
     if request.form.get("export"):
         return controllers.download_str_variants(case_obj, variants_query)
@@ -312,7 +314,9 @@ def sv_variants(institute_id, case_name):
         case_obj["_id"], category=category, query=form.data, build=genome_build
     )
 
-    result_size = store.count_variants(case_obj["_id"], form.data, None, category)
+    result_size = store.count_variants(
+        case_obj["_id"], form.data, None, category, build=genome_build
+    )
 
     # if variants should be exported
     if request.form.get("export"):
@@ -406,7 +410,9 @@ def mei_variants(institute_id, case_name):
         case_obj["_id"], category=category, query=form.data, build=genome_build
     )
 
-    result_size = store.count_variants(case_obj["_id"], form.data, None, category)
+    result_size = store.count_variants(
+        case_obj["_id"], form.data, None, category, build=genome_build
+    )
 
     # if variants should be exported
     if request.form.get("export"):
@@ -515,7 +521,9 @@ def cancer_variants(institute_id, case_name):
     variants_query = store.variants(
         case_obj["_id"], category="cancer", query=form.data, build=genome_build
     )
-    result_size = store.count_variants(case_obj["_id"], form.data, None, category)
+    result_size = store.count_variants(
+        case_obj["_id"], form.data, None, category, build=genome_build
+    )
 
     if request.form.get("export"):
         return controllers.download_variants(store, case_obj, variants_query)
@@ -596,7 +604,9 @@ def cancer_sv_variants(institute_id, case_name):
         case_obj["_id"], category=category, query=form.data, build=genome_build
     )
 
-    result_size = store.count_variants(case_obj["_id"], form.data, None, category)
+    result_size = store.count_variants(
+        case_obj["_id"], form.data, None, category, build=genome_build
+    )
 
     # if variants should be exported
     if request.form.get("export"):
@@ -681,7 +691,9 @@ def fusion_variants(institute_id, case_name):
         case_obj["_id"], category=category, query=form.data, build=genome_build
     )
 
-    result_size = store.count_variants(case_obj["_id"], form.data, None, category)
+    result_size = store.count_variants(
+        case_obj["_id"], form.data, None, category, build=genome_build
+    )
 
     # if variants should be exported
     if request.form.get("export"):
@@ -765,3 +777,12 @@ def toggle_show_dismiss_block():
     """Endpoint to toggle the show dismiss block session variable."""
     session["show_dismiss_block"] = not session.get("show_dismiss_block")
     return f"Toggled to {session['show_dismiss_block']}"
+
+
+@variants_bp.route("/variants/un-audit_filter", methods=["GET"])
+def unaudit_filter():
+    """Un-audit an audited filter."""
+    store.unaudit_filter(
+        audit_id=request.args.get("audit_id"), user_obj=store.user(current_user.email)
+    )
+    return redirect(request.referrer)

scout/server/config.py

@@ -64,6 +64,10 @@ ACCREDITATION_BADGE = "swedac-1926-iso17025.png"
 # BEACON_URL = "http://localhost:6000/apiv1.0"
 # BEACON_TOKEN = "DEMO"
 
+# ClinVar API URL
+# An alternative URL that will be used to send ClinVar submissions to. Just uncomment the line below to use the test API
+# CLINVAR_API_URL = "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions/"
+
 # connection details for LoqusDB MongoDB database
 # Example with 2 instances of LoqusDB, one using a binary file and one instance connected via REST API
 # When multiple instances are available, admin users can modify which one is in use for a given institute from the admin settings page

scout/server/extensions/clinvar_extension.py

@@ -4,7 +4,7 @@ import logging
 import requests
 from flask import flash
 
-from scout.constants.clinvar import CLINVAR_API_URL, PRECLINVAR_URL
+from scout.constants.clinvar import CLINVAR_API_URL_DEFAULT, PRECLINVAR_URL
 
 LOG = logging.getLogger(__name__)
 
@@ -15,9 +15,9 @@ class ClinVarApi:
     the ClinVar submission schema (https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/) and if valid, can be directly submitted to ClinVar.
     """
 
-    def __init__(self):
+    def init_app(self, app):
         self.convert_service = "/".join([PRECLINVAR_URL, "csv_2_json"])
-        self.submit_service = CLINVAR_API_URL
+        self.submit_service_url = app.config.get("CLINVAR_API_URL") or CLINVAR_API_URL_DEFAULT
 
     def set_header(self, api_key) -> dict:
         """Creates a header to be submitted a in a POST rquest to the CLinVar API
@@ -71,16 +71,16 @@ class ClinVarApi:
             "actions": [{"type": "AddData", "targetDb": "clinvar", "data": {"content": json_data}}]
         }
         try:
-            resp = requests.post(self.submit_service, data=json.dumps(data), headers=header)
-            return resp.status_code, resp
+            resp = requests.post(self.submit_service_url, data=json.dumps(data), headers=header)
+            return self.submit_service_url, resp.status_code, resp
 
         except Exception as ex:
-            return None, ex
+            return self.submit_service_url, None, ex
 
     def show_submission_status(self, submission_id: str, api_key=None):
         """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)
-        actions_url = f"{CLINVAR_API_URL}{submission_id}/actions/"
+        actions_url = f"{self.submit_service_url}{submission_id}/actions/"
         actions_resp: requests.models.Response = requests.get(actions_url, headers=header)
         flash(f"Response from ClinVar: {actions_resp.json()}", "primary")

scout/server/links.py

@@ -563,9 +563,9 @@ def decipher_link(variant_obj, build=37):
 def exac_link(variant_obj):
     """Compose link to ExAC website for a variant position."""
     url_template = (
-        "https://exac.broadinstitute.org/variant/"
+        "https://gnomad.broadinstitute.org/variant/"
         "{this[chromosome]}-{this[position]}-{this[reference]}"
-        "-{this[alternative]}"
+        "-{this[alternative]}?dataset=exac"
     )
     return url_template.format(this=variant_obj)
 

scout/server/templates/bootstrap_global.html

@@ -10,16 +10,13 @@
 
 	{% block css %}
     <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/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+    <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 %}
 
 	{% block css_style %}
   {% endblock %}
 
-	<!-- Adding support for Font Awesome icons version 6 -->
-  <script src="https://kit.fontawesome.com/bff7dad824.js" integrity="sha512-+ohxkrmvsgaa299uNunuNiobFRMBGoAVR3t/fpqBmZdObzKnfBMKVyIqxrXtHMZDrwQS73ZuOVj8hUqxoJt+Ww==" crossorigin="anonymous"></script>
-
 	<style>
 
 		.spinner {

scout/server/templates/utils.html

@@ -12,7 +12,7 @@
       	<td>
       	  <small>
       	    <strong> {{ comment.user_name }} </strong>
-      	    on {{ comment.created_at.date() }}
+      	    on {{ comment.created_at.strftime('%y-%m-%d %H:%M') }}
       	    {% if comment.level == 'global' %}
                     <span class='badge bg-info text-white'>GLOBAL</span>
             {% endif %}
@@ -134,7 +134,7 @@
             <form method="POST" action="{{ url_for('cases.events', institute_id=institute._id, case_name=case.display_name, event_id=comment._id,_anchor='comments') }}">
               <small>
                 <strong>{{ comment.user_name }}</strong>
-                on {{ comment.created_at.date() }}
+                on {{ comment.created_at.strftime('%y-%m-%d %H:%M') }}
                 {% if comment.level == 'global' %}
                   <span class="badge bg-info">GLOBAL</span>
                 {% endif %}
@@ -145,7 +145,7 @@
                   <span class='badge bg-secondary'>edited</span>
                 {% endif %}
                 {% if comment.user_id == current_user.email %}
-                  <button class="btn btn-link btn-sm" type="submit" name="remove"><i class="fa fa-remove"></i></button>
+                  <button class="btn btn-link btn-sm" type="submit" name="remove"><i class="fa fa-times"></i></button>
                   <button class="btn btn-link btn-sm" type="button" data-bs-toggle="modal" data-bs-target="#editComment_{{index}}"><i class="fa fa-edit"></i></button>
                 {% endif %}
               </small>
@@ -208,7 +208,7 @@
             ({{ event.hpo_term }})
           {%- endif %}
           {%-if event.individuals %}, individuals: {{event.individuals|join(', ')}}{% endif %}
-          at <span class="timestamp">{{ event.created_at.date() }}</span>
+          at <span class="timestamp">{{ event.created_at.strftime('%y-%m-%d %H:%M') }}</span>
         </li>
       {% else %}
         <li class="list-group-item">No activity yet</li>

scout/server/utils.py

@@ -269,7 +269,8 @@ def case_has_mt_alignments(case_obj: dict):
 
 
 def case_has_rna_tracks(case_obj: Dict) -> bool:
-    """Returns True if one of more individuals of the case contain RNA-seq data
+    """Returns True if one or more individuals of the case contain RNA-seq data
+    Add this info to the case obj dict.
 
     Args:
         case_obj(dict)
@@ -277,10 +278,12 @@ def case_has_rna_tracks(case_obj: Dict) -> bool:
         True or False (bool)
     """
     # Display junctions track if available for any of the individuals
+    case_obj["has_rna_tracks"] = False
     for ind in case_obj.get("individuals", []):
         # RNA can have three different aln track files
         for path_name in ["splice_junctions_bed", "rna_coverage_bigwig", "rna_alignment_path"]:
             if _check_path_name(ind, path_name):
+                case_obj["has_rna_tracks"] = True
                 return True
     return False
 

{scout_browser-4.84.dist-info → scout_browser-4.86.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.84
+Version: 4.86
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson
@@ -15,8 +15,8 @@ Classifier: Topic :: Software Development :: Libraries
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug <3
-Requires-Dist: Flask >=2.0
+Requires-Dist: werkzeug
+Requires-Dist: Flask>=2.0
 Requires-Dist: Flask-Bootstrap
 Requires-Dist: Flask-CORS
 Requires-Dist: path.py
@@ -26,9 +26,9 @@ Requires-Dist: Flask-WTF
 Requires-Dist: Flask-Mail
 Requires-Dist: coloredlogs
 Requires-Dist: query-phenomizer
-Requires-Dist: Flask-Babel >=3
-Requires-Dist: livereload
-Requires-Dist: tornado <6.3
+Requires-Dist: Flask-Babel>=3
+Requires-Dist: livereload>=2.7
+Requires-Dist: tornado>=6.4.1
 Requires-Dist: python-dateutil
 Requires-Dist: pymongo
 Requires-Dist: pathlib
@@ -47,14 +47,14 @@ Requires-Dist: flask-ldapconn
 Requires-Dist: cyvcf2
 Requires-Dist: configobj
 Requires-Dist: ped-parser
-Requires-Dist: pydantic >=2
-Requires-Dist: PyYaml >=5.1
-Requires-Dist: intervaltree ==3.0.2
+Requires-Dist: pydantic>=2
+Requires-Dist: PyYaml>=5.1
+Requires-Dist: intervaltree==3.0.2
 Requires-Dist: anytree
 Requires-Dist: tabulate
 Provides-Extra: coverage
-Requires-Dist: chanjo-report ; extra == 'coverage'
-Requires-Dist: pymysql ; extra == 'coverage'
+Requires-Dist: chanjo-report; extra == "coverage"
+Requires-Dist: pymysql; extra == "coverage"
 
 
 <p align="center">