scout-browser 4.85__py3-none-any.whl → 4.86__py3-none-any.whl

scout/server/blueprints/omics_variants/views.py

@@ -0,0 +1,106 @@
+from flask import Blueprint, request
+from flask_login import current_user
+from markupsafe import Markup
+
+from scout.server.blueprints.variants.controllers import (
+    activate_case,
+    case_default_panels,
+    gene_panel_choices,
+    get_expand_search,
+    get_variants_page,
+    populate_chrom_choices,
+    populate_filters_form,
+)
+from scout.server.blueprints.variants.forms import OutlierFiltersForm
+from scout.server.extensions import store
+from scout.server.utils import institute_and_case, templated
+
+from . import controllers
+
+omics_variants_bp = Blueprint(
+    "omics_variants",
+    __name__,
+    template_folder="templates",
+)
+
+
+@omics_variants_bp.route(
+    "/<institute_id>/<case_name>/omics_variants/outliers", methods=["GET", "POST"]
+)
+@templated("omics_variants/outliers.html")
+def outliers(institute_id, case_name):
+    """Display a list of outlier omics variants."""
+
+    page = get_variants_page(request.form)
+    category = "outlier"
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+
+    variant_type = Markup.escape(
+        request.args.get("variant_type", request.form.get("variant_type", "clinical"))
+    )
+    if variant_type not in ["clinical", "research"]:
+        variant_type = "clinical"
+    variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
+
+    if request.form.get("hpo_clinical_filter"):
+        case_obj["hpo_clinical_filter"] = True
+
+    # update status of case if visited for the first time
+    activate_case(store, institute_obj, case_obj, current_user)
+
+    if request.method == "GET":
+        form = OutlierFiltersForm(request.args)
+        variant_type = request.args.get("variant_type", "clinical")
+        form.variant_type.data = variant_type
+        # set chromosome to all chromosomes
+        form.chrom.data = request.args.get("chrom", "")
+        if form.gene_panels.data == [] and variant_type == "clinical":
+            form.gene_panels.data = case_default_panels(case_obj)
+    else:  # POST
+        user_obj = store.user(current_user.email)
+        form = populate_filters_form(
+            store, institute_obj, case_obj, user_obj, category, request.form
+        )
+
+    # populate filters dropdown
+    available_filters = list(store.filters(institute_obj["_id"], category))
+    form.filters.choices = [
+        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
+    ]
+
+    # populate available panel choices
+    form.gene_panels.choices = gene_panel_choices(store, institute_obj, case_obj)
+
+    # 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"
+    cytobands = store.cytoband_by_chrom(genome_build)
+
+    # controllers.update_form_hgnc_symbols(store, case_obj, form)
+    variants_query = store.omics_variants(
+        case_obj["_id"], query=form.data, category=category, build=genome_build
+    )
+
+    if request.form.get("export"):
+        return controllers.download_omics_variants(case_obj, variants_query)
+
+    result_size = store.count_omics_variants(
+        case_id=case_obj["_id"], query=form.data, category=category, build=genome_build
+    )
+
+    data = controllers.outliers(store, institute_obj, case_obj, variants_query, result_size, page)
+
+    return dict(
+        case=case_obj,
+        cytobands=cytobands,
+        expand_search=get_expand_search(request.form),
+        filters=available_filters,
+        form=form,
+        institute=institute_obj,
+        page=page,
+        result_size=result_size,
+        total_variants=variants_stats.get(variant_type, {}).get(category, "NA"),
+        variant_type=variant_type,
+        **data,
+    )

scout/server/blueprints/panels/controllers.py

@@ -16,13 +16,7 @@ LOG = logging.getLogger(__name__)
 INHERITANCE_MODELS = ["ar", "ad", "mt", "xr", "xd", "x", "y"]
 
 
-def shall_display_panel(panel_obj, user):
-    """Check if panel shall be displayed based on display status and user previleges."""
-    is_visible = not panel_obj.get("hidden", False)
-    return is_visible or panel_write_granted(panel_obj, user)
-
-
-def panel_write_granted(panel_obj, user):
+def panel_write_granted(panel_obj, user) -> bool:
     return any(
         ["maintainer" not in panel_obj, user.is_admin, user._id in panel_obj.get("maintainer", [])]
     )

scout/server/blueprints/panels/templates/panels/panels.html

@@ -150,7 +150,7 @@
         <table class="table table-striped" id="panelTable" style="table-layout: fixed;">
         <thead>
           <tr>
-            <th>Name</th>
+            <th style="width: 30%">Name</th>
             <th>Version</th>
             <th>Number of genes</th>
             <th>History</th>
@@ -163,8 +163,11 @@
           <tr {% if panel.hidden %} class="hidableRow collapse" {% endif %}>
             <td>
               <a href="{{ url_for('panels.panel', panel_id=panel._id) }}">{{ panel.display_name }}</a>
+              {% if current_user.email in panel.maintainer %}
+                <span class="badge bg-dark" data-bs-toggle="tooltip" title="You are a maintainer of this panel"><span class="fa fa-tools"></span></span>
+              {% endif %}
               {% if panel.hidden %}
-                <span class="badge bg-danger">Removed</span>
+                <span class="badge bg-danger" data-bs-toggle="tooltip" title="This panel was removed">Removed</span>
               {% endif %}
             </td>
             <td>{{ panel.version }} ({{ panel.date.date()}})</td>
@@ -174,10 +177,10 @@
             <td>
               {% if panel.hidden %}
                 <form action="{{ url_for('panels.panel_restore', panel_id=panel._id) }}" method="POST">
-                  <button id="{{panel._id}}" type="submit" title="Restore panel" class="btn btn-success btn-xs"><span class="fa fa-undo"></span></button>
+                  <button {{panel.writable}} id="{{panel._id}}" type="submit" title="Restore panel" class="btn btn-success btn-xs"><span class="fa fa-undo"></span></button>
                 </form>
               {% else %}
-              <button id="{{panel._id}}" type="button" data-bs-toggle="modal" data-bs-target="#remove-gene-panel-modal-{{ panel._id }}" class="btn btn-danger btn-xs"><span class="fa fa-trash"></span></button>
+              <button {{panel.writable}} id="{{panel._id}}" type="button" data-bs-toggle="modal" data-bs-target="#remove-gene-panel-modal-{{ panel._id }}" class="btn btn-danger btn-xs"><span class="fa fa-trash"></span></button>
               {% endif %}
             </td>
           </tr>
@@ -269,6 +272,11 @@
 <script src="https://cdn.datatables.net/1.12.0/js/jquery.dataTables.min.js" integrity="sha512-fu0WiDG5xqtX2iWk7cp17Q9so54SC+5lk/z/glzwlKFdEOwGG6piUseP2Sik9hlvlmyOJ0lKXRSuv1ltdVk9Jg==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
 <script type="text/javascript">
 
+var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'))
+tooltipTriggerList.map(function (tooltipTriggerEl) {
+  return new bootstrap.Tooltip(tooltipTriggerEl)
+})
+
 $('.history_btn').on('click', function(){
     var bid = $(this)[0].id;
     var sel = '#paneldiv_' + bid;

scout/server/blueprints/panels/views.py

@@ -52,7 +52,6 @@ def panels():
     if request.method == "POST" and request.form.get("search_for"):
         # Query db for panels containing the search string. This is done with autocompletion
         # therefor only one(1) hgnc_id will be received from the form.
-        hgnc_symbols = []
         search_string = escape(request.form.get("search_for"))
         try:
             hgnc_symbols = parse_raw_gene_ids([search_string])
@@ -84,18 +83,17 @@ def panels():
     panel_versions = {}
     for name in panel_names:
         panels = store.gene_panels(panel_id=name, include_hidden=True)
-        panel_versions[name] = [
-            panel_obj
-            for panel_obj in panels
-            if controllers.shall_display_panel(panel_obj, current_user)
-        ]
+        panel_versions[name] = [panel_obj for panel_obj in panels]
+
     panel_groups = []
     for institute_obj in institutes:
-        institute_panels = (
-            panel_obj
-            for panel_obj in store.latest_panels(institute_obj["_id"], include_hidden=True)
-            if controllers.shall_display_panel(panel_obj, current_user)
-        )
+        institute_panels = []
+        for panel in store.latest_panels(institute_obj["_id"], include_hidden=True):
+            panel["writable"] = (
+                "" if controllers.panel_write_granted(panel, current_user) else "disabled"
+            )
+            institute_panels.append(panel)
+
         panel_groups.append((institute_obj, institute_panels))
     return dict(
         panel_groups=panel_groups,

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

@@ -33,9 +33,14 @@
 </div>
 {% endmacro %}
 
-{% macro splice_junctions_button(institute_id, case_name, variant_id) %}
-  <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case_name, variant_id=variant_id)}}" target="_blank"
+{% macro splice_junctions_button(institute_id, case_name, variant_id, omics_variant_id) %}
+  {% if omics_variant_id %}
+    <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case_name, omics_variant_id=omics_variant_id)}}" target="_blank"
     data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh38">RNA splicing</a>
+  {% else %}
+    <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case_name, variant_id=variant_id)}}" target="_blank"
+    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh38">RNA splicing</a>
+  {%  endif  %}
 {% endmacro %}
 
 {% macro variant_tag_button(variant, institute, case, manual_rank_options) %}

scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "utils.html" import comments_table, pedigree_panel %}
-{% from "variants/components.html" import gene_cell, frequency_cell_general %}
+{% from "variants/components.html" import frequency_cell_general %}
 {% from "variants/utils.html" import cell_rank, dismiss_variants_block, filter_form_footer, update_stash_filter_button_status, pagination_footer, pagination_hidden_div, str_filters %}
 {% from "variant/buttons.html" import igv_button, reviewer_button%}
 

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