scout-browser 4.93.1__py3-none-any.whl → 4.94.1__py3-none-any.whl

scout/adapter/mongo/query.py

@@ -474,63 +474,98 @@ class QueryHandler(object):
 
         return mongo_query
 
-    def sv_coordinate_query(self, query):
-        """Adds genomic coordinated-related filters to the query object
-            This method is called to buid coordinate query for sv variants
-
-        Args:
-            query(dict): a dictionary of query filters specified by the users
-            mongo_query(dict): the query that is going to be submitted to the database
+    def get_position_query(self, chrom: str, start: int, end: int) -> dict:
+        """Helper function that returns a dictionary containing start and stop coordinates.
+
+        The position query consists of 3 parts, each of them elements of the $or
+        First part applies to searches when chromosome and end_chrom are the same.
+        Here are the possible overlapping search scenarios:
+        # Case 1
+        # filter                 xxxxxxxxx
+        # Variant           xxxxxxxx
+
+        # Case 2
+        # filter                 xxxxxxxxx
+        # Variant                    xxxxxxxx
+
+        # Case 3
+        # filter                 xxxxxxxxx
+        # Variant                   xx
+
+        # Case 4
+        # filter                 xxxxxxxxx
+        # Variant             xxxxxxxxxxxxxx
+
+        Second and third elements of the $or cover queries for variants where chromosome != end_chrom.
+        In this situation there are the following scenarios:
+        - Case chromosome != end_chrom, position matching 'chromosome'
+        - Case chromosome != end_chrom, position matching 'end_chrom'
+        """
 
-        Returns:
-            coordinate_query(dict): returned object contains coordinate filters for sv variant
+        return {
+            "$or": [
+                # Case chromosome == end_chrom
+                {
+                    "$and": [
+                        {"chromosome": chrom},
+                        {"end_chrom": chrom},
+                        {
+                            "$or": [
+                                # Overlapping cases 1-4 (chromosome == end_chrom)
+                                {"end": {"$gte": start, "$lte": end}},  # Case 1
+                                {"position": {"$gte": start, "$lte": end}},  # Case 2
+                                {
+                                    "$and": [
+                                        {"position": {"$lte": start}},
+                                        {"end": {"$gte": end}},
+                                    ]
+                                },  # Case 3
+                                {
+                                    "$and": [
+                                        {"position": {"$gte": start}},
+                                        {"end": {"$lte": end}},
+                                    ]
+                                },  # Case 4
+                            ]
+                        },
+                    ]
+                },
+                # Case chromosome != end_chrom, position matching 'chromosome'
+                {
+                    "$and": [
+                        {"chromosome": chrom},
+                        {"end_chrom": {"$ne": chrom}},
+                        {"position": {"$gte": start}},
+                        {"position": {"$lte": end}},
+                    ]
+                },
+                # Case chromosome != end_chrom, position matching 'end_chrom'
+                {
+                    "$and": [
+                        {"chromosome": {"$ne": chrom}},
+                        {"end_chrom": chrom},
+                        {"end": {"$gte": start}},
+                        {"end": {"$lte": end}},
+                    ]
+                },
+            ]
+        }
 
+    def sv_coordinate_query(self, query: dict) -> dict:
+        """Adds genomic coordinated-related filters to the query object
+        This method is called to build coordinate query for sv variants
         """
-        coordinate_query = None
-        chromosome_query = {"$or": [{"chromosome": query["chrom"]}, {"end_chrom": query["chrom"]}]}
-        if query.get("start") and query.get("end"):
-            # Query for overlapping intervals. Taking into account these cases:
-            # 1
-            # filter                 xxxxxxxxx
-            # Variant           xxxxxxxx
-
-            # 2
-            # filter                 xxxxxxxxx
-            # Variant                    xxxxxxxx
-
-            # 3
-            # filter                 xxxxxxxxx
-            # Variant                   xx
-
-            # 4
-            # filter                 xxxxxxxxx
-            # Variant             xxxxxxxxxxxxxx
-            position_query = {
-                "$or": [
-                    {"end": {"$gte": int(query["start"]), "$lte": int(query["end"])}},  # 1
-                    {
-                        "position": {
-                            "$lte": int(query["end"]),
-                            "$gte": int(query["start"]),
-                        }
-                    },  # 2
-                    {
-                        "$and": [
-                            {"position": {"$gte": int(query["start"])}},
-                            {"end": {"$lte": int(query["end"])}},
-                        ]
-                    },  # 3
-                    {
-                        "$and": [
-                            {"position": {"$lte": int(query["start"])}},
-                            {"end": {"$gte": int(query["end"])}},
-                        ]
-                    },  # 4
-                ]
+        if (
+            query.get("start") is not None and query.get("end") is not None
+        ):  # query contains full coordinates
+            chrom = query["chrom"]
+            start = int(query["start"])
+            end = int(query["end"])
+            coordinate_query = self.get_position_query(chrom=chrom, start=start, end=end)
+        else:  # query contains only chromosome info
+            coordinate_query = {
+                "$or": [{"chromosome": query["chrom"]}, {"end_chrom": query["chrom"]}]
             }
-            coordinate_query = {"$and": [chromosome_query, position_query]}
-        else:
-            coordinate_query = chromosome_query
         return coordinate_query
 
     def gene_filter(self, query, build="37"):

scout/adapter/mongo/variant.py

@@ -311,14 +311,14 @@ class VariantHandler(VariantLoader):
             "category": variant_obj["category"],  # sv
             "variant_type": variant_obj["variant_type"],  # clinical or research
             "sub_category": variant_obj["sub_category"],  # example -> "del"
-            "$and": coordinate_query["$and"],  # query for overlapping SV variants
+            "$or": coordinate_query["$or"],  # query for overlapping SV variants
         }
-
         overlapping_svs = list(
             self.variant_collection.find(
                 query,
             )
         )
+
         if not overlapping_svs:
             return None
         if len(overlapping_svs) == 1:

scout/server/blueprints/cases/controllers.py

@@ -62,6 +62,7 @@ from scout.server.utils import (
     case_has_rna_tracks,
     institute_and_case,
 )
+from scout.utils.acmg import get_acmg_temperature
 
 LOG = logging.getLogger(__name__)
 
@@ -611,6 +612,22 @@ def check_outdated_gene_panel(panel_obj, latest_panel):
     return extra_genes, missing_genes
 
 
+def add_bayesian_acmg_classification(variant_obj: dict):
+    """Append info to display the ACMG VUS Bayesian score / temperature."""
+    variant_acmg_classifications = list(
+        store.get_evaluations_case_specific(document_id=variant_obj["_id"])
+    )
+    if variant_acmg_classifications:
+        variant_obj["bayesian_acmg"] = get_acmg_temperature(
+            set(
+                [
+                    criterium.get("term")
+                    for criterium in variant_acmg_classifications[0].get("criteria", [])
+                ]
+            )
+        )
+
+
 def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dict, data: dict):
     """Gather evaluated variants info to include in case report."""
 
@@ -624,6 +641,7 @@ def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dic
                 continue
             if case_key == "partial_causatives":
                 var_obj["phenotypes"] = case_obj["partial_causatives"][var_id]
+            add_bayesian_acmg_classification(var_obj)
             evaluated_variants_by_type[eval_category].append(
                 _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
             )
@@ -663,6 +681,9 @@ def _append_evaluated_variant_by_type(
     """
     for eval_category, variant_key in CASE_REPORT_VARIANT_TYPES.items():
         if variant_key in var_obj and var_obj[variant_key] is not None:
+
+            add_bayesian_acmg_classification(var_obj)
+
             evaluated_variants_by_type[eval_category].append(
                 _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
             )

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -668,6 +668,7 @@
               <th>Inheritance models</th>
             {% endif %}
             <th>ACMG classification</th>
+            <th>Bayesian classification</th>
             {% if cancer %}
             <th>ClinGen-CGC-VICC classification</th>
             {% endif %}
@@ -718,6 +719,13 @@
               {% else %}
                 -
               {% endif %}
+            <td>
+              {% if variant.bayesian_acmg %}
+                <span class="badge rounded-pill bg-{{variant.bayesian_acmg.temperature_class}}">Score {{variant.bayesian_acmg.points|string}} <span class='fa {{variant.bayesian_acmg.temperature_icon}}'></span> {{variant.bayesian_acmg.temperature}} ({{variant.bayesian_acmg.point_classification}})</span>
+              {% else %}
+                -
+              {% endif %}
+            </td>
             </td>
             {% if cancer %}
             <td>

scout/server/blueprints/cases/views.py

@@ -7,6 +7,7 @@ import shutil
 from ast import literal_eval
 from io import BytesIO
 from operator import itemgetter
+from tempfile import NamedTemporaryFile, mkdtemp
 from typing import Generator, Optional, Union
 
 from cairosvg import svg2png
@@ -286,7 +287,9 @@ def pdf_case_report(institute_id, case_name):
     # Workaround to be able to print the case pedigree to pdf
     if case_obj.get("madeline_info") and case_obj.get("madeline_info") != "":
         try:
-            write_to = os.path.join(cases_bp.static_folder, "madeline.png")
+            write_to = NamedTemporaryFile(
+                mode="a+", prefix=case_obj.get("_id"), suffix="madeline.png"
+            )
             svg2png(
                 bytestring=case_obj["madeline_info"],
                 write_to=write_to,
@@ -322,11 +325,8 @@ def mt_report(institute_id, case_name):
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
 
     # create a temp folder to write excel files into
-    temp_excel_dir = os.path.join(
-        cases_bp.static_folder, "_".join([case_obj["display_name"], "mt_reports"])
-    )
-    os.makedirs(temp_excel_dir, exist_ok=True)
 
+    temp_excel_dir = mkdtemp(suffix="_".join([case_obj["display_name"], "mt_reports"]))
     if controllers.mt_excel_files(store, case_obj, temp_excel_dir):
         data = zip_dir_to_obj(temp_excel_dir)
 

scout/server/blueprints/clinvar/controllers.py

@@ -399,11 +399,10 @@ def json_api_submission(submission_id):
         afile.flush()
         afile.seek(0)
 
-    with NamedTemporaryFile(
-        mode="a+", prefix="Variant", suffix=".csv"
-    ) as variant_file, NamedTemporaryFile(
-        mode="a+", prefix="CaseData", suffix=".csv"
-    ) as casedata_file:
+    with (
+        NamedTemporaryFile(mode="a+", prefix="Variant", suffix=".csv") as variant_file,
+        NamedTemporaryFile(mode="a+", prefix="CaseData", suffix=".csv") as casedata_file,
+    ):
         # Write temp Variant CSV file
         _, variants_header, variants_lines = clinvar_submission_file(
             submission_id, "variant_data", "SUB000"

scout/server/blueprints/institutes/controllers.py

@@ -3,7 +3,7 @@ import datetime
 import logging
 from typing import Dict, List, Optional, Tuple
 
-from flask import Response, current_app, flash, url_for
+from flask import Response, current_app, flash, request, url_for
 from flask_login import current_user
 from pymongo import ASCENDING, DESCENDING
 from pymongo.cursor import Cursor
@@ -11,10 +11,13 @@ from werkzeug.datastructures import Headers, MultiDict
 
 from scout.adapter.mongo.base import MongoAdapter
 from scout.constants import (
+    CANCER_PHENOTYPE_MAP,
     CASE_STATUSES,
     DATE_DAY_FORMATTER,
     ID_PROJECTION,
     PHENOTYPE_GROUPS,
+    PHENOTYPE_MAP,
+    SEX_MAP,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
 from scout.server.blueprints.variant.utils import predictions, update_representative_gene
@@ -422,97 +425,129 @@ def _sort_cases(data, request, all_cases):
     return all_cases
 
 
-def cases(store, request, institute_id):
-    """Preprocess case objects.
+def export_case_samples(institute_id, filtered_cases) -> Response:
+    """Export to CSV file a list of samples from selected cases."""
+    EXPORT_HEADER = [
+        "Sample ID",
+        "Sample Name",
+        "Analysis",
+        "Affected status",
+        "Sex",
+        "Sex confirmed",
+        "Parenthood confirmed",
+        "Predicted ancestry",
+        "Tissue",
+        "Case Name",
+        "Case ID",
+        "Analysis date",
+        "Case Status",
+        "Case phenotypes",
+        "Research",
+        "Track",
+        "Default panels",
+        "Genome build",
+        "SNV/SV rank models",
+    ]
+    export_lines = []
+    export_lines.append("\t".join(EXPORT_HEADER))  # Use tab-separated values
+    for case in filtered_cases:
+        for individual in case.get("individuals", []):
+            export_line = [
+                individual["individual_id"],
+                individual["display_name"],
+                individual.get("analysis_type").upper(),
+                (
+                    CANCER_PHENOTYPE_MAP[individual.get("phenotype", 0)]
+                    if case.get("track") == "cancer"
+                    else PHENOTYPE_MAP[individual.get("phenotype", 0)]
+                ),
+                SEX_MAP[individual.get("sex", 0)],
+                individual.get("confirmed_sex") or "-",
+                individual.get("confirmed_parent") or "-",
+                individual.get("predicted_ancestry") or "-",
+                individual.get("tissue_type") or "-",
+                case["display_name"],
+                case["_id"],
+                case["analysis_date"].strftime("%Y-%m-%d %H:%M:%S"),
+                case["status"],
+                ", ".join(hpo["phenotype_id"] for hpo in case.get("phenotype_terms", [])),
+                case.get("is_research"),
+                case.get("track"),
+                ", ".join(
+                    panel["panel_name"] for panel in case.get("panels") if panel.get("is_default")
+                ),
+                case.get("genome_build"),
+                f"{case.get('rank_model_version', '-')}/{case.get('sv_rank_model_version', '-')}",
+            ]
+            export_lines.append("\t".join(str(item) for item in export_line))
 
-    Add all the necessary information to display the 'cases' view
+    file_content = "\n".join(export_lines)
 
-    Args:
-        store(adapter.MongoAdapter)
-        request(flask.request) request sent by browser to the api_institutes endpoint
-        institute_id(str): An _id of an institute
+    return Response(
+        file_content,
+        mimetype="text/plain",
+        headers={
+            "Content-Disposition": f"attachment;filename={institute_id}_cases_{datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')}.txt"
+        },
+    )
 
-    Returns:
-        data(dict): includes the cases, how many there are and the limit.
-    """
+
+def cases(store: MongoAdapter, request: request, institute_id: str) -> dict:
+    """Preprocess case objects for the 'cases' view."""
     data = {}
+
+    # Initialize data (institute info, filters, and case counts)
     institute_obj = institute_and_case(store, institute_id)
     data["institute"] = institute_obj
-
-    name_query = request.form
-    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
-
     data["form"] = CaseFilterForm(request.form)
+    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
+    data["nr_cases"] = sum(data["status_ncases"].values())
+
+    # Fetch Sanger unevaluated and validated cases
+    sanger_ordered_not_validated = get_sanger_unevaluated(store, institute_id, current_user.email)
+    data["sanger_unevaluated"], data["sanger_validated_by_others"] = sanger_ordered_not_validated
 
+    # Projection for fetching cases
     ALL_CASES_PROJECTION = {
         "analysis_date": 1,
         "assignees": 1,
         "beacon": 1,
         "case_id": 1,
         "display_name": 1,
+        "genome_build": 1,
         "individuals": 1,
         "is_rerun": 1,
         "is_research": 1,
         "mme_submission": 1,
         "owner": 1,
         "panels": 1,
+        "phenotype_terms": 1,
+        "rank_model_version": 1,
         "status": 1,
+        "sv_rank_model_version": 1,
         "track": 1,
         "vcf_files": 1,
     }
 
-    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
-    data["nr_cases"] = sum(data["status_ncases"].values())
-
-    sanger_ordered_not_validated: Tuple[Dict[str, list]] = get_sanger_unevaluated(
-        store, institute_id, current_user.email
-    )
-    data["sanger_unevaluated"]: Dict[str, list] = sanger_ordered_not_validated[0]
-    data["sanger_validated_by_others"]: Dict[str, list] = sanger_ordered_not_validated[1]
-
-    # local function to add info to case obj
-    def populate_case_obj(case_obj):
-        analysis_types = set(ind["analysis_type"] for ind in case_obj["individuals"])
-        if len(analysis_types) > 1:
-            LOG.debug("Set analysis types to {'mixed'}")
-            analysis_types = set(["mixed"])
-
-        case_obj["analysis_types"] = list(analysis_types)
-        case_obj["assignees"] = [
-            store.user(user_email) for user_email in case_obj.get("assignees", [])
-        ]
-        # Check if case was re-runned
-        last_analysis_date = case_obj.get("analysis_date", datetime.datetime.now())
-        all_analyses_dates = set()
-        for analysis in case_obj.get("analyses", [{"date": last_analysis_date}]):
-            all_analyses_dates.add(analysis.get("date", last_analysis_date))
-
-        case_obj["is_rerun"] = len(all_analyses_dates) > 1 or last_analysis_date > max(
-            all_analyses_dates
-        )
-
-        case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
-        case_obj["display_track"] = TRACKS[case_obj.get("track", "rare")]
-        return case_obj
-
+    # Group cases by status
     case_groups = {status: [] for status in CASE_STATUSES}
+    nr_cases_showall_statuses = 0
+    status_show_all_cases = institute_obj.get("show_all_cases_status") or ["prioritized"]
 
-    nr_cases_showall_statuses = (
-        0  # Nr of cases for the case statuses where all cases should be shown
-    )
-    # In institute settings, retrieve all case status categories for which all cases should be displayed
-    status_show_all_cases: List[str] = institute_obj.get("show_all_cases_status") or ["prioritized"]
+    # Process cases for statuses that require all cases to be shown
     for status in status_show_all_cases:
         cases_in_status = store.cases_by_status(
             institute_id=institute_id, status=status, projection=ALL_CASES_PROJECTION
         )
         cases_in_status = _sort_cases(data, request, cases_in_status)
         for case_obj in cases_in_status:
-            populate_case_obj(case_obj)
-            nr_cases_showall_statuses += 1
+            populate_case_obj(case_obj, store)
             case_groups[status].append(case_obj)
+            nr_cases_showall_statuses += 1
 
-    # Retrieve cases for the remaining status categories
+    # Fetch additional cases based on filters
+    name_query = request.form
+    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
     all_cases = store.cases(
         collaborator=institute_id,
         name_query=name_query,
@@ -525,17 +560,20 @@ def cases(store, request, institute_id):
     )
     all_cases = _sort_cases(data, request, all_cases)
 
+    if request.form.get("export"):
+        return export_case_samples(institute_id, all_cases)
+
+    # Process additional cases for the remaining statuses
     nr_cases = 0
     for case_obj in all_cases:
-        case_status = case_obj["status"]
-        if case_status in status_show_all_cases:
-            continue
-        if nr_cases == limit:
-            break
-        populate_case_obj(case_obj)
-        case_groups[case_status].append(case_obj)
-        nr_cases += 1
-
+        if case_obj["status"] not in status_show_all_cases:
+            if nr_cases == limit:
+                break
+            populate_case_obj(case_obj, store)
+            case_groups[case_obj["status"]].append(case_obj)
+            nr_cases += 1
+
+    # Compile the final data
     data["cases"] = [(status, case_groups[status]) for status in CASE_STATUSES]
     data["found_cases"] = nr_cases + nr_cases_showall_statuses
     data["limit"] = limit
@@ -543,8 +581,32 @@ def cases(store, request, institute_id):
     return data
 
 
+def populate_case_obj(case_obj: dict, store: MongoAdapter):
+    """Helper function to populate additional case information."""
+    analysis_types = set(ind["analysis_type"] for ind in case_obj["individuals"])
+    if len(analysis_types) > 1:
+        analysis_types = set(["mixed"])
+    case_obj["analysis_types"] = list(analysis_types)
+
+    case_obj["assignees"] = [store.user(user_email) for user_email in case_obj.get("assignees", [])]
+
+    last_analysis_date = case_obj.get("analysis_date", datetime.datetime.now())
+    all_analyses_dates = {
+        analysis.get("date", last_analysis_date)
+        for analysis in case_obj.get("analyses", [{"date": last_analysis_date}])
+    }
+    case_obj["is_rerun"] = len(all_analyses_dates) > 1 or last_analysis_date > max(
+        all_analyses_dates
+    )
+
+    case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
+    case_obj["display_track"] = TRACKS.get(case_obj.get("track", "rare"))
+
+
 def _get_unevaluated_variants_for_case(
-    case_obj: dict, var_ids_list: List[str], sanger_validated_by_user_by_case: Dict[str, List[str]]
+    case_obj: dict,
+    var_ids_list: List[str],
+    sanger_validated_by_user_by_case: Dict[str, List[str]],
 ) -> Tuple[Dict[str, list]]:
     """Returns the variants with Sanger ordered by a user that need validation or are validated by another user."""
 

scout/server/blueprints/institutes/forms.py

@@ -73,7 +73,8 @@ class InstituteForm(FlaskForm):
     pheno_abbrev = StringField("Abbreviation", validators=[validators.Optional()])
 
     gene_panels = NonValidatingSelectMultipleField(
-        "Gene panels available for variants filtering", validators=[validators.Optional()]
+        "Gene panels available for variants filtering",
+        validators=[validators.Optional()],
     )
 
     gene_panels_matching = NonValidatingSelectMultipleField(
@@ -144,7 +145,8 @@ class GeneVariantFiltersForm(FlaskForm):
     variant_type = SelectMultipleField(choices=[("clinical", "clinical"), ("research", "research")])
     category = SelectMultipleField(choices=CATEGORY_CHOICES)
     hgnc_symbols = TagListField(
-        "HGNC Symbols (comma-separated, case sensitive)", validators=[validators.InputRequired()]
+        "HGNC Symbols (comma-separated, case sensitive)",
+        validators=[validators.InputRequired()],
     )
     rank_score = IntegerField(default=15)
     phenotype_terms = TagListField("HPO terms (comma-separated)")
@@ -181,3 +183,4 @@ class CaseFilterForm(FlaskForm):
     has_rna = BooleanField("Has RNA-seq data")
     validation_ordered = BooleanField("Validation pending")
     search = SubmitField(label="Search")
+    export = SubmitField(label="Filter and export")

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

@@ -249,6 +249,12 @@
     advSearchBlock.hide();
   }
 
+  function StopSpinner() {
+    // Avoid page spinner being stuck on file download
+    $(window).unbind('beforeunload');
+    return true;
+  }
+
   advBlockCheckbox.on('click', function() {
     if($(this).is(':checked')) {
       advSearchBlock.show();

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

@@ -9,7 +9,7 @@
   {% endif %}
 {% endfor %}
 
-<form action="{{ form_action }}" method="POST" accept-charset="utf-8">
+<form action="{{ form_action }}" method="POST" accept-charset="utf-8" onsubmit="return StopSpinner()">
     {{ form.hidden_tag() }}
 
     <div class="row">
@@ -19,7 +19,7 @@
             {{ form.search_institute(class="form-control") }}
         </div>
       {% endif %}
-        <div class="col-md-3 mb-3">
+        <div class="col-md-2 mb-3">
             {{ form.case.label(class="form-label") }}
             {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
         </div>
@@ -27,9 +27,10 @@
             {{ form.search_limit.label(class="form-label") }}
             {{ form.search_limit(class="form-control") }}
         </div>
-        <div class="btn-sm mb-2 col-md-2 mx-auto">
-          {{ form.search(class="btn btn-lg btn-primary mt-4") }}
-          <a href="{{ reset_action }}" class="btn btn-lg btn-secondary mt-4 text-white">Reset search</a>
+        <div class="btn-sm mb-2 col-md-3 mx-auto">
+          {{ form.search(class="btn btn-primary mt-4") }}
+          {{ form.export(class="btn btn-primary mt-4") }}
+          <a href="{{ reset_action }}" class="btn btn-secondary mt-4 text-white">Reset search</a>
         </div>
         <div class="col-md-2 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
           {{ form.advanced_search(class="form-check-input") }}

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

@@ -76,15 +76,15 @@
               </td> <!-- end of ID col-->
 
               <td> <!-- HGVS Description col -->
-                {% set hgvs_c = (tx.coding_sequence_name or '')|truncate(20, True) %}
+                {% set hgvs_c = (tx.coding_sequence_name or '')|truncate(30, True) %}
                 {% if variant.chromosome in ["MT","M"] %}
                   {% set mt_notation = "m." ~ variant.position ~ variant.reference ~ ">" ~ variant.alternative %}
-                  {{ mt_notation|truncate(20,True) }} <span class="text-muted">({{ hgvs_c }})</span>
+                  {{ mt_notation|truncate(30,True) }} <span class="text-muted">({{ hgvs_c }})</span>
                 {% else %}
                   {{ hgvs_c }}
                 {% endif %}
                 <span class="text-muted float-end">
-                  {{ (tx.protein_sequence_name or '')|url_decode }}
+                  {{ (tx.protein_sequence_name or '')|url_decode|truncate(30, True) }}
                 </span>
               </td> <!-- end of HGVS Description col -->
 

scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import cancer_sv_filters,cell_rank, pagination_footer, pagination_hidden_div, filter_form_footer, filter_script_main, update_stash_filter_button_status, dismiss_variants_block, callers_cell %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
+{% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - SV variants
@@ -111,8 +111,8 @@
       {{ variant.sub_category|upper }}
     </td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
-    <td class="col-2"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
-    <td class="col-2"><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
+    <td class="col-2">{% if variant.chromosome != variant.end_chrom %}<span class="text-body"></span><b>{{ variant.chromosome }}</b>:</span>{% endif %}<span class="text-body" style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
+    <td class="col-2">{% if variant.chromosome != variant.end_chrom %}<span class="text-body"><b>{{ variant.end_chrom }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
     <td class="col-2"><span style="white-space: nowrap;">{{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe }}</span></td>
     <td class="text-end">{{ frequency_cell_general(variant) }}</td>
     <td>{{observed_cell_general(variant)}}</td>
@@ -122,25 +122,11 @@
     <td>
       {{ variant_funct_anno_cell(variant) }}
     </td>
-    <td>{{ allele_cell(variant.tumor or {}) }}{% if variant.somatic_score %}<small class="text-muted">[{{ variant.somatic_score }}]</small>{% endif %}</td>
+    <td>{{ allele_cell(variant.tumor or {}) }}{% if variant.somatic_score %}<small class="text-body" data-bs-toggle="tooltip" data-bs-placement="top" title="SV caller (Manta) somatic score">[{{ variant.somatic_score }}]</small>{% endif %}</td>
     <td>{{ allele_cell(variant.normal or {}) }}</td>
   </tr>
 {% endmacro %}
 
-{% macro allele_cell(allele) %}
-  {% if 'alt_freq' in allele %}
-    {% if allele.alt_freq == -1 %}
-      <span class="text-muted">.</span>
-    {% else %}
-      {{ allele.alt_freq|round(4) }}
-    {% endif %}
-    <br>
-    <small class="text-muted">{% if allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}</small>
-  {% else %}
-    <span class="text-muted">N/A</span>
-  {% endif %}
-{% endmacro %}
-
 
 {% block scripts %}
   {{ super() }}

scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 
-{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
+{% 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/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, ccv_evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
 
@@ -175,17 +175,7 @@
 {% endmacro %}
 
 {% macro position_cell(variant) %}
-  {{ variant.chromosome }}<span class="text-muted">:{{ variant.position }}</span>
-{% endmacro %}
-
-{% macro allele_cell(allele) %}
-  {% if 'alt_freq' in allele %}
-    {{ allele.alt_freq|round(4)  }}
-    <br>
-    <small class="text-muted">{{ allele.alt_depth }} | {{ allele.ref_depth }}</small>
-  {% else %}
-    <span class="text-muted">N/A</span>
-  {% endif %}
+  <span class="text-body"><b>{{ variant.chromosome }}</b>:{{ variant.position }}</span>
 {% endmacro %}
 
 {% block scripts %}

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

@@ -211,7 +211,7 @@
         title="Overlapping gene panels"
         data-bs-content="{% for panel in matching_panels %}
           {{ panel.panel_name|safe }}<br>
-        {% endfor %}"
+        {% else %} No ovelapping gene panels {% endfor %}"
       >{{ panel_count }}</a>
     {% endmacro %}
 
@@ -403,3 +403,17 @@
   <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 src="https://cdn.datatables.net/1.12.0/js/dataTables.bootstrap5.min.js" integrity="sha512-nfoMMJ2SPcUdaoGdaRVA1XZpBVyDGhKQ/DCedW2k93MTRphPVXgaDoYV1M/AJQLCiw/cl2Nbf9pbISGqIEQRmQ==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
 {% endmacro %}
+
+{% macro allele_cell(allele) %}
+  {% if 'alt_freq' in allele %}
+    {% if allele.alt_freq == -1 %}
+      <span class="text-body">.</span>
+    {% else %}
+      <span class="text-body"><b>{{ allele.alt_freq|round(4) }}</b></span>
+    {% endif %}
+    <br>
+    <small class="text-body">{% if 'alt_depth' in allele and allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if 'ref_depth' in allele and allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}</small>
+  {% else %}
+    <span class="text-body">N/A</span>
+  {% endif %}
+{% endmacro %}

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

@@ -108,8 +108,8 @@ onsubmit="return validateForm()">
     </td>
     <td>{{ variant.sub_category|upper }}</td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
-    <td><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
-<td><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
+    <td>{% if variant.chromosome != variant.end_chrom %}<span class="text-body"></span><b>{{ variant.chromosome }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
+    <td>{% if variant.chromosome != variant.end_chrom %}<span class="text-body"><b>{{ variant.end_chrom }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
     <td class="text-end"><span style="white-space: nowrap;">{{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe}}</span></td>
     <td>
       {{ frequency_cell_general(variant) }}

scout/server/links.py

@@ -714,7 +714,7 @@ def ucsc_link(variant_obj, build=None):
     )
     if build == 38:
         url_template = (
-            "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg20&"
+            "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&"
             "position=chr{this[chromosome]}:{this[position]}"
             "-{this[position]}&dgv=pack&knownGene=pack&omimGene=pack"
         )

scout/utils/acmg.py

@@ -1,6 +1,5 @@
 # coding=UTF-8
 
-
 from typing import Optional
 
 from scout.constants import ACMG_COMPLETE_MAP

{scout_browser-4.93.1.dist-info → scout_browser-4.94.1.dist-info}/METADATA

@@ -1,62 +1,76 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.93.1
-Summary: Clinical DNA variant visualizer and browser.
-Home-page: https://github.com/Clinical-Genomics/scout
-Author: Måns Magnusson
-Author-email: mans.magnusson@scilifelab.se
+Version: 4.94.1
+Summary: Clinical DNA variant visualizer and browser
+Project-URL: Repository, https://github.com/Clinical-Genomics/scout
+Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
+Project-URL: Documentation, https://clinical-genomics.github.io/scout/
+Project-URL: Bug Tracker, https://github.com/Clinical-Genomics/scout/issues
+Project-URL: Issues, https://github.com/Clinical-Genomics/scout/issues
+Author-email: Chiara Rasi <chiara.rasi@scilifelab.se>, Daniel Nilsson <daniel.nilsson@ki.se>, Robin Andeer <robin.andeer@gmail.com>, Mans Magnuson <monsunas@gmail.com>
+License: MIT License
+License-File: LICENSE
+Keywords: acmg,beacon,cancer,clingen-cgc-vicc,clinvar,cnv,coverage,dna,fusion,genome visualisation,lrs,matchmaker exchange,ogm,outliers,panel,panelapp,phenopacket,rna,sma,snv,str,sv,variant ranking,variant triage,variants,vcf,wes,wgs,wts
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Web Environment
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Programming Language :: Python :: 3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: werkzeug
-Requires-Dist: Flask>=2.0
-Requires-Dist: Flask-Bootstrap
-Requires-Dist: Flask-CORS
-Requires-Dist: path.py
-Requires-Dist: markdown
-Requires-Dist: WTForms
-Requires-Dist: Flask-WTF
-Requires-Dist: Flask-Mail
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Requires-Dist: anytree
+Requires-Dist: authlib
+Requires-Dist: cairosvg
+Requires-Dist: click
 Requires-Dist: coloredlogs
-Requires-Dist: query_phenomizer
-Requires-Dist: Flask-Babel>=3
+Requires-Dist: configobj
+Requires-Dist: cryptography
+Requires-Dist: cyvcf2
+Requires-Dist: defusedxml
+Requires-Dist: flask-babel>=3
+Requires-Dist: flask-bootstrap
+Requires-Dist: flask-cors
+Requires-Dist: flask-ldapconn
+Requires-Dist: flask-login
+Requires-Dist: flask-mail
+Requires-Dist: flask-wtf
+Requires-Dist: flask>=2.0
+Requires-Dist: importlib-resources
+Requires-Dist: intervaltree==3.0.2
 Requires-Dist: livereload>=2.7
-Requires-Dist: tornado>=6.4.1
-Requires-Dist: python-dateutil
-Requires-Dist: pymongo
+Requires-Dist: markdown
+Requires-Dist: path-py
 Requires-Dist: pathlib
 Requires-Dist: pdfkit
+Requires-Dist: ped-parser
 Requires-Dist: phenopackets
-Requires-Dist: xlsxwriter
-Requires-Dist: click
-Requires-Dist: cryptography
-Requires-Dist: defusedxml
-Requires-Dist: svglib
-Requires-Dist: cairosvg
-Requires-Dist: importlib_resources
-Requires-Dist: authlib
-Requires-Dist: flask_login
-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: anytree
+Requires-Dist: pymongo
 Requires-Dist: python-dateutil
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: query-phenomizer
+Requires-Dist: svglib
 Requires-Dist: tabulate
+Requires-Dist: tornado>=6.4.1
+Requires-Dist: werkzeug
+Requires-Dist: wtforms
+Requires-Dist: xlsxwriter
 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'
+Requires-Dist: python-dateutil; extra == 'coverage'
+Description-Content-Type: text/markdown
 
 <p align="center">
 	<a href="https://Clinical-Genomics.github.io/scout/">
@@ -127,6 +141,13 @@ cd scout
 pip install --editable .
 ```
 
+Scout is configured to use `uv` if you like; either run, install, install as a tool or
+```
+uv sync --frozen
+uv run scout
+```
+
+
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).
 
 <b>NB</b>: in order to convert HTML reports into PDF reports, we have recently switched from the WeasyPrint lib to [python-pdfkit](https://github.com/JazzCore/python-pdfkit). For this reason, when upgrading to a Scout version >4.47, you need to install an additional [wkhtmltopdf system library](https://wkhtmltopdf.org/).

{scout_browser-4.93.1.dist-info → scout_browser-4.94.1.dist-info}/RECORD

@@ -1,5 +1,4 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=QvBUfmeaghMXRYxQv7CLutqQ8EWHp4OXnrEJdYtEKgU,23
 scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
 scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -23,11 +22,11 @@ scout/adapter/mongo/matchmaker.py,sha256=amTvFOlUbrt1RmecY_8hPY6bO3j79lc2UbmzlCQ
 scout/adapter/mongo/omics_variant.py,sha256=VdkNG_l6vcr3UF25EixEfvIdMGkSGeNaMjLRhQHS_lc,7521
 scout/adapter/mongo/panel.py,sha256=d1oMEYAiDGybLmlbbf3-fQdCdU0-T7x2XdIUwZGthYk,20031
 scout/adapter/mongo/phenomodel.py,sha256=cypSS8YRzu98Bf1kC0orfrLNn_ZQSYCK8e4mNR5PaPY,2572
-scout/adapter/mongo/query.py,sha256=Zk5BV9GZYVlGoSRRjP88TpvB4teVpvHgHnSDV0W-kS0,33157
+scout/adapter/mongo/query.py,sha256=rF4WjVaH0x1vupJkYMj0c_p8TQbApmZ1t8LgH8MsZwA,34777
 scout/adapter/mongo/rank_model.py,sha256=wvDNI4OLf-f7ZYZ_Q_6qi0myxOJCNNJR_-2-_0u2K2M,5712
 scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt8NMY,7417
 scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
-scout/adapter/mongo/variant.py,sha256=4kGyJn6kitOQ68-zp5bkT6koUP7WbZ3SLl2NXll6dOE,34928
+scout/adapter/mongo/variant.py,sha256=Mwu-2N2ziXSR4lQEFXegbftH2nTskAWL_vpAdeu-i2M,34926
 scout/adapter/mongo/variant_events.py,sha256=yNnMM58P1LbYFw73rWzti6l2zWa_G93ozUTbVkcz4_I,33475
 scout/adapter/mongo/variant_loader.py,sha256=C05StRMFVChopcolPYXFIbh_S-FhYHu4NvBCpiBLOeE,28327
 scout/build/__init__.py,sha256=GUWEaXTpwsJil_KtrXBQJpZIwCQFSgo8NlK49R9IkA8,521
@@ -443,11 +442,12 @@ scout/parse/variant/variant.py,sha256=nf_0q2J7TryWhB-Oz697HYSDJTPNmkXnPHmKtjhHQU
 scout/resources/__init__.py,sha256=i9UVG651subgmOZ-Gm-JKPsXBqr5-50QUDfSpbwmwIw,443
 scout/resources/cytoBand_hg19.txt.gz,sha256=pheUD5b9NlVuvwwnbKwDc2FG80Yg70gvPxVXP-Sqd3k,6147
 scout/resources/cytoBand_hg38.txt.gz,sha256=sqSVmvPlktQ-0hTiTapJM-5UgyV6xDoYZuTF0kPuETs,6105
+scout/resources/custom_igv_tracks/mane.bb,sha256=flEexDxHmbX7IwwrMM0P5DWOxcSCjmHxGNlyg_WqElQ,3519360
 scout/server/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 scout/server/app.py,sha256=70YdN9eWL1ySEYkuAHKOk_WA4Fm5dcIwtIZEcEf-xA0,10836
 scout/server/auto.py,sha256=8B6GwfOaUChkTLuLgYQDFMWlxGuHkEegF1argH2G2Ik,401
 scout/server/config.py,sha256=BFx6ix8D3KM90FqmaHLxv_feudO2kN2CkX1UWBGTjXE,5923
-scout/server/links.py,sha256=UdYqYyRHh7v1gGtP-F3UYBdT3-49ySqiv9VkCnHX5ZU,28115
+scout/server/links.py,sha256=f2h_zUFt4Tm_383ZmdIGsA6mUVQbpQmJ199ZTzUWemE,28115
 scout/server/utils.py,sha256=d1fGdSwo-XjNHVjHd-uT3mGmUJ8yYB6weT7VgHo9nxM,12592
 scout/server/blueprints/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 scout/server/blueprints/alignviewers/__init__.py,sha256=XMVed2ekVUAvroqENDHSr2pwM8otqau8ZA-rbH1T2U8,59
@@ -460,15 +460,15 @@ scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=x2
 scout/server/blueprints/api/__init__.py,sha256=HR6HjS7ot1K_8Lt5eQdNT154z_FCdHGSigy8r2LpNCI,26
 scout/server/blueprints/api/views.py,sha256=pbl78wfhrm1T8JmiJDYF3BbTbfFrlF-hQRbuv2GWI0s,3729
 scout/server/blueprints/cases/__init__.py,sha256=_c17kPFITFYcIVphF4V9bf0PZBer8bU3rtVWQnljKDU,52
-scout/server/blueprints/cases/controllers.py,sha256=gDnjRYzc-z4SZro0Q7q8AQT0muyEUIfOY16hMaT-ZlE,53638
-scout/server/blueprints/cases/views.py,sha256=NCBYZl56jrdmwip4-UXq0-1oH9Y0EddTVDXdCVpmCws,43141
+scout/server/blueprints/cases/controllers.py,sha256=Nn2MrlqAHzDfm8RSkjrWpeCD4W7DoPp_8Gm8Eu4l44Q,54362
+scout/server/blueprints/cases/views.py,sha256=MQDOnLuywAQkVBgYaZAbaj9f6tps18bpo4nDFm77S4s,43165
 scout/server/blueprints/cases/static/case_images.js,sha256=pb_gG7DNQc-1lADqSII8YvjBwmHyeQWYVtuu2jyrTlU,14997
 scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAjaRWhjL-bK5bsQnLpH54HZak,541
 scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkke1UHxjiYWY_gBzWcIkGpdJUA,2978
 scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
 scout/server/blueprints/cases/templates/cases/case.html,sha256=9Fcn-OFA1yIHchD0PjDs7-Y8I7Qqr8o6cavN0eOi5rI,37183
 scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
-scout/server/blueprints/cases/templates/cases/case_report.html,sha256=ZhxBrEXq1jmjqeJPGgCRtN-dVo10d5SWK7GAIjbO80A,65341
+scout/server/blueprints/cases/templates/cases/case_report.html,sha256=BFEJdsIgPCBQdZUqi7XyXgh_j0kMaYbxfVvrzh1wX8w,65839
 scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=99rmRyDXFXjooB52TI5_ebJKv1ZAJbVXEw4deHfSVMA,7285
 scout/server/blueprints/cases/templates/cases/case_tabular_view.html,sha256=ko-LDUKmIoTazMZ2nFWvPEZsgObU07RwqIkDYFjokoY,4317
 scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=5Wmk7DM8LI3MynqzxeTzAr_EoEBwVVo31djcI5ZlTdo,2164
@@ -482,7 +482,7 @@ scout/server/blueprints/cases/templates/cases/matchmaker.html,sha256=kPYnmcZJ1gm
 scout/server/blueprints/cases/templates/cases/phenotype.html,sha256=7vz5XPUExD6vc-wdijLKnPzaOFm9mQxOZ_ITAL3y7U8,16420
 scout/server/blueprints/cases/templates/cases/utils.html,sha256=gHcxf3DOGcJJZMfjKY4NgvU_tjta5OnyWrKZy9pfGyY,35981
 scout/server/blueprints/clinvar/__init__.py,sha256=BV3aH2AbiA2WWrUEMbGd0H9MefFd2eTsRE9ShywbzpI,30
-scout/server/blueprints/clinvar/controllers.py,sha256=EZv6cwmg2pYwLFq5SPskrARrjjf3Az7GN23lcZn52vg,24254
+scout/server/blueprints/clinvar/controllers.py,sha256=lCrVlokjnSURvsYkm6sTMxrZOL1Xj3VQAWbYr1o_mEY,24251
 scout/server/blueprints/clinvar/form.py,sha256=2h42YJzaOtsdEglxqt7F1i2ncjSU_IHNt-m4QOJytK4,5148
 scout/server/blueprints/clinvar/views.py,sha256=hPyTJA7Qy6QOL-ENSG1N0atnQXuYCb-iiO8fuNDjJns,6036
 scout/server/blueprints/clinvar/static/form_style.css,sha256=Tro2w0Su9st2ZRpt8PjF7qXYet-0n6Eyol4oh94JafU,4073
@@ -508,14 +508,14 @@ scout/server/blueprints/genes/templates/genes/gene.html,sha256=a--c-IjzNKN_JW7z9
 scout/server/blueprints/genes/templates/genes/genes.html,sha256=x6jXKijvuEX9GvIedHW4O_BerYXiWEmAdYT0HTiGnhI,1130
 scout/server/blueprints/genes/templates/genes/layout.html,sha256=cZMLe2cInq24z0sZpPxDm_kEiAe5VQbOR-8XWn6wlvI,1601
 scout/server/blueprints/institutes/__init__.py,sha256=kGSyYrBC1QaEQBDdoMkMLfaowV7roaV5DowICi_0RSQ,65
-scout/server/blueprints/institutes/controllers.py,sha256=Fv57oJ96VsOaYGtQb-0m96bb7ospNGRBPiVX9QsMJZw,31720
-scout/server/blueprints/institutes/forms.py,sha256=gjVNdKt7hIrNk_JOwCDRuOXiOrE9kS41VZQuTkkmkk8,6615
+scout/server/blueprints/institutes/controllers.py,sha256=qu8bonz74Ff-nTevOy4BaLhYrXbgD4rZEc81NvBkK_w,34055
+scout/server/blueprints/institutes/forms.py,sha256=7ixKPYewR24lnM9vwGNS9EcBHR6072kPRuvE0jk6acE,6685
 scout/server/blueprints/institutes/views.py,sha256=PSpf82kW0EKZc24CPhBhuE-wXXGyIz-R6IJu7IM0IrM,9052
 scout/server/blueprints/institutes/static/form_scripts.js,sha256=8Sn7omeXeeUbiXJPfT0Qb4CaBJ_KtZZWw7N2he7EDx0,747
 scout/server/blueprints/institutes/static/select2_darktheme.css,sha256=Nq_va597W_e5y-52B4ClwSJzACq0WFbPU8SIp3DtKIo,1818
 scout/server/blueprints/institutes/static/timeline_styles.css,sha256=Vq48ffIidpQmDQhAzfW47O9mGQZEWdlbMtOE8AK-ZEU,2122
 scout/server/blueprints/institutes/static/variants_list_scripts.js,sha256=gO_ZuJC2jj7Y9x6CEVEVhN1oIE4bIWrTY0_zVcsbRbY,236
-scout/server/blueprints/institutes/templates/overview/cases.html,sha256=7-9nUomP6iaqXGtf6GemVECYMG2nD-h64RKTAmLkof0,12758
+scout/server/blueprints/institutes/templates/overview/cases.html,sha256=GOt1Y2PZLVigL3wqi5NAJFqIjQHgaocrbJzFcCUzOfY,12900
 scout/server/blueprints/institutes/templates/overview/causatives.html,sha256=192pgqUSXQF4qhC933qsYtTwvmlqDctxwHcArERkHc8,1619
 scout/server/blueprints/institutes/templates/overview/filters.html,sha256=Dzu5YicmdjW_zGqbCUrb8TMbSUuRaG47itTMwwX7Bm8,3102
 scout/server/blueprints/institutes/templates/overview/gene_variants.html,sha256=EyhBZEdMZQBaJWR_FDeabuWXRSd4Xcqh0teaxVyNvAE,8442
@@ -523,7 +523,7 @@ scout/server/blueprints/institutes/templates/overview/institute_settings.html,sh
 scout/server/blueprints/institutes/templates/overview/institute_sidebar.html,sha256=vQQunXH2Cr8-z2Kc7uTCzsSqIX14Xld44NWqdhpw-Hs,4304
 scout/server/blueprints/institutes/templates/overview/timeline.html,sha256=upTv7v4sUwxGfJDSyk8F5zPb61dedG66zgfvh_SMR4M,2289
 scout/server/blueprints/institutes/templates/overview/users.html,sha256=6dkbDBNLw2b97M2Pd8JImpPoT3FLTcl84oBN3inLJRg,1134
-scout/server/blueprints/institutes/templates/overview/utils.html,sha256=Z66aFcrEXzgo0FyPc1tfFA_VYJdfG58QWLgJuXG2l1Y,33123
+scout/server/blueprints/institutes/templates/overview/utils.html,sha256=9W60kUmIRPsu_JX0kDMg0hkz8CUY8vn2MdoegRAMqFc,33199
 scout/server/blueprints/institutes/templates/overview/verified.html,sha256=qxZ8mIPX00ZXIy_5eLO2QmLrjJZrhw97kdXBZxpRj38,3363
 scout/server/blueprints/login/__init__.py,sha256=uDzQjNNrMloZ4-i-1cEW7d59FZ--Xy89b-Xn5SvyC1U,52
 scout/server/blueprints/login/controllers.py,sha256=bg0me00OvwYJiTm4dZnbl8eyRRRDquBMs5U7_YV4xWI,1883
@@ -618,7 +618,7 @@ scout/server/blueprints/variant/templates/variant/rank_score_results.html,sha256
 scout/server/blueprints/variant/templates/variant/sanger.html,sha256=0kVnscTw3KUwjR4QOEuNJMOK9eADGEn9qGNtGx2ST7Y,4507
 scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html,sha256=p0nWqo71GJ8ACLEzXuZbJAzDXoCHZLvH6f7yLi3JslI,2208
 scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=8199JLlkuNOLI88hSwgtPxKjk9SDyhNS-WJR1S7mnFs,16978
-scout/server/blueprints/variant/templates/variant/tx_overview.html,sha256=turyCoOCCd_N80FakxXfIl7q_WViysz1fwx3j312_Lg,6737
+scout/server/blueprints/variant/templates/variant/tx_overview.html,sha256=EXLBDh_SgNVEO7MPMjlmfO6MDhtDcj0JyvZdRgxbwSM,6756
 scout/server/blueprints/variant/templates/variant/utils.html,sha256=lF-w3400plEn0gVpHG-9k7N9L_p1U-PFGitcT_YlZw8,25414
 scout/server/blueprints/variant/templates/variant/variant.html,sha256=JA0jI1ITvKamJY88U6-uBXYrHRZa3H2oyBUROtX9TKw,17874
 scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=KAdrLo8UTxO1Nr5ggfdn663E7xMq1rK0A2PrKXCJGjM,21049
@@ -628,14 +628,14 @@ scout/server/blueprints/variants/forms.py,sha256=w4Woeek6gpZfPM_9e1E_n-gpVvNxXPU
 scout/server/blueprints/variants/utils.py,sha256=ifFBoyigx0A5KPE4iz9NSpyuUeF1bElrb4ohQLD2GlU,919
 scout/server/blueprints/variants/views.py,sha256=skUGpZyRDzW4BEDIqWKajHBLF3qBUSP-UYSZYxbv3l8,28895
 scout/server/blueprints/variants/static/form_scripts.js,sha256=o3GCboaesA9Sm1HgejS_yQwt0I-NTkvcl56jiBdLqZs,8319
-scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html,sha256=rLASILYRFwTIA3S0WtfN3QS7JbL_VvXKYJOoa-1yQJQ,7389
-scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=N2AM-uqgRTwHo5Ep0GNNzm_kqG0hTnYTdWU2Ox2Ocs4,9870
-scout/server/blueprints/variants/templates/variants/components.html,sha256=b2LKVE5vkKy8bgHbScCnGyL9xQzMuQYeBpOl5h8IR_E,16820
+scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html,sha256=QlGmUEdUQ7gCq7tMMUFAlGqqC9jFB78Q0h6tSp3QUas,7271
+scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=LnybOzNu4RkbighdIcV6okJwQWiO5ixOhTev_-QaQII,9611
+scout/server/blueprints/variants/templates/variants/components.html,sha256=PGtcPGVbd3gcdG_6ozA66LDo3ZJ8VoehaDMUZjwyA5Q,17431
 scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
 scout/server/blueprints/variants/templates/variants/indicators.html,sha256=5aSXytiWvaU87cqcR9GcB7U5jP8t-PVnor8FpKLl_k0,4847
 scout/server/blueprints/variants/templates/variants/mei-variants.html,sha256=2Tb0vfzM--kJa5mVbT7L32h4E8nKYRSb245g6O5JIUU,5860
 scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=bjjeyoEO1aScqIDLtCh3xexZfvf1906yusPGJTyeNLU,10644
-scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=V_3hTZXmI_VEcQ6DpxVrTYnM3cBDGWtPri8cDVIsR9A,6153
+scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=fRDnB9wXago2OB2mthp0rD_Es4kxnj9YKRlOKCGVW3s,6407
 scout/server/blueprints/variants/templates/variants/utils.html,sha256=MNDc2JwumU9ukISizSAraxIY06rHXR2Ze32RNnDEBI4,50042
 scout/server/blueprints/variants/templates/variants/variants.html,sha256=KnCcsA1VaRdsbRCCw9Rg0TJTUvq03X9S24QgCqVToUk,9328
 scout/server/extensions/__init__.py,sha256=s6qkGSFNRi_tP7yoeoXB5UarvLHidaK1Yw2Pae7Py90,1366
@@ -666,7 +666,7 @@ scout/server/translations/sv/LC_MESSAGES/messages.po,sha256=Wp7Mx4LoiFNtzsV1tpAo
 scout/update/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scout/update/panel.py,sha256=4z-vQ7GVIJXtlIub9pubFcQ-I9mLX5fRXKNPBdpuhJw,1649
 scout/utils/__init__.py,sha256=DHCMH05dxkyD7m9QSs0WXsQQPgVRFQ9XvyNeNpHjjvg,74
-scout/utils/acmg.py,sha256=UCyvfg3Wx4-janh4L7LPRtFI6oigwlPAzns-aydPy8U,11540
+scout/utils/acmg.py,sha256=IkWWmHxc0YvoSurzXimKkH_Vf8C0bncywVUVu8m-YlY,11539
 scout/utils/algorithms.py,sha256=w--NauXbQohZis7obr39a8bS57C4NRelYXn79V7m1dU,800
 scout/utils/ccv.py,sha256=85lY7uSjHg3VAfWOfrx9jnaDUQXSa5hDQcRIqZ_Ikas,6025
 scout/utils/convert.py,sha256=asrsis3zkt9jXzseRmCqSa4_t1UT73HPPQRW-DKDdqE,1794
@@ -683,9 +683,8 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=lgPumNI_EikBZR1m9ztZI_mZAfV29y1KGoiBv9kejzQ,12797
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.93.1.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.93.1.dist-info/METADATA,sha256=OKsRo0nvHP2tVP3vzUfhPN5T34XvOwXA3u4n_dVPjLM,14293
-scout_browser-4.93.1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-scout_browser-4.93.1.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.93.1.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.93.1.dist-info/RECORD,,
+scout_browser-4.94.1.dist-info/METADATA,sha256=GokLVy4fCW8zv-7QwERH1vldMGvaOn0iIstTGd4KoGA,15642
+scout_browser-4.94.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scout_browser-4.94.1.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.94.1.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.94.1.dist-info/RECORD,,

{scout_browser-4.93.1.dist-info → scout_browser-4.94.1.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any
-

scout/__version__.py

@@ -1 +0,0 @@
-__version__ = "4.93.1"

scout_browser-4.93.1.dist-info/top_level.txt

@@ -1 +0,0 @@
-scout