scout-browser 4.91.1__py3-none-any.whl → 4.92__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.91.1"
+__version__ = "4.92"

scout/adapter/mongo/panel.py

@@ -501,7 +501,7 @@ class PanelHandler:
         new_panel["version"] = float(version)
 
         # Update same version or create new version
-        if version == panel_obj["version"]:
+        if new_panel["version"] == panel_obj["version"]:
             result = self.panel_collection.find_one_and_replace(
                 {"_id": panel_obj["_id"]}, new_panel, return_document=pymongo.ReturnDocument.AFTER
             )

scout/adapter/mongo/query.py

@@ -1,7 +1,7 @@
 import logging
 import re
 from datetime import datetime, timedelta
-from typing import Optional, Union
+from typing import List, Optional, Union
 
 from scout.constants import (
     CLINSIG_MAP,
@@ -19,23 +19,19 @@ LOG = logging.getLogger(__name__)
 
 class QueryHandler(object):
     def build_case_query(
-        self, case_id=None, status=None, older_than=None, analysis_type=[]
+        self,
+        case_ids: Optional[List[str]],
+        institute_id: Optional[List[str]],
+        status: Optional[List[str]],
+        older_than: Optional[int],
+        analysis_type: Optional[List[str]],
     ) -> dict:
-        """Build case query based on case id, status and analysis date
-
-        Args:
-            case_id(str): id of a case
-            status(list): one or more case status
-            older_than(int): to select cases older than a number of months
-            case_ids(list): a list of case _ids
-            analysis_type(list): a list of type of analysis ["wgs", "wes", "panel"]
-
-        Returns:
-            case_query(dict): query dictionary
-        """
+        """Build case query based on case id, status and analysis date."""
         case_query = {}
-        if case_id:
-            case_query["_id"] = case_id
+        if case_ids:
+            case_query["_id"] = {"$in": case_ids}
+        if institute_id:
+            case_query["owner"] = institute_id
         if analysis_type:
             case_query["individuals.analysis_type"] = {"$in": analysis_type}
         if older_than:
@@ -43,6 +39,7 @@ class QueryHandler(object):
             case_query["analysis_date"] = {"$lt": older_than_date}
         if status:
             case_query["status"] = {"$in": list(status)}
+
         return case_query
 
     def delete_variants_query(

scout/build/variant/clnsig.py

@@ -1,18 +1,13 @@
 import logging
+
 from scout.constants import REV_CLINSIG_MAP
 
 LOG = logging.getLogger(__name__)
 
 
-def build_clnsig(clnsig_info):
-    """Prepare clnsig information for database
-
-    Args:
-        clnsig_info(dict): Parsed information from clinvar annotation
+def build_clnsig(clnsig_info: dict) -> dict:
+    """Prepare clnsig information for database."""
 
-    Returns:
-        clnsig_obj(dict): Converted and prepared for database
-    """
     value = clnsig_info["value"]
     if value not in REV_CLINSIG_MAP:
         LOG.warning("Clinsig value %s does not have an internal representation", value)
@@ -24,4 +19,7 @@ def build_clnsig(clnsig_info):
         revstat=clnsig_info.get("revstat"),
     )
 
+    if isinstance(value, str) and "low_penetrance" in value:
+        clnsig_obj["low_penetrance"] = True
+
     return clnsig_obj

scout/commands/delete/delete_command.py

@@ -29,7 +29,14 @@ VARIANT_CATEGORIES = ["mei", "snv", "sv", "cancer", "cancer_sv", "str"]
 
 @click.command("variants", short_help="Delete variants for one or more cases")
 @click.option("-u", "--user", help="User running this command (email)", required=True)
-@click.option("-c", "--case-id", help="Case id")
+@click.option("-c", "--case-id", help="Case id", multiple=True)
+@click.option(
+    "-f",
+    "--case-file",
+    help="Path to file containing list of case IDs",
+    type=click.Path(exists=True),
+)
+@click.option("-i", "--institute", help="Restrict to cases with specified institute ID")
 @click.option(
     "--status",
     type=click.Choice(CASE_STATUSES),
@@ -42,7 +49,6 @@ VARIANT_CATEGORIES = ["mei", "snv", "sv", "cancer", "cancer_sv", "str"]
     "--analysis-type",
     type=click.Choice(["wgs", "wes", "panel"]),
     multiple=True,
-    default=["wgs"],
     help="Type of analysis",
 )
 @click.option("--rank-threshold", type=click.INT, default=5, help="With rank threshold lower than")
@@ -62,7 +68,9 @@ VARIANT_CATEGORIES = ["mei", "snv", "sv", "cancer", "cancer_sv", "str"]
 @with_appcontext
 def variants(
     user: str,
-    case_id: str,
+    case_id: list,
+    case_file: str,
+    institute: str,
     status: list,
     older_than: int,
     analysis_type: list,
@@ -73,6 +81,12 @@ def variants(
 ) -> None:
     """Delete variants for one or more cases"""
 
+    if case_file and case_id:
+        click.echo(
+            "You should specify either case ID (multiple times if needed) or the path to a text file containing a list of case IDs (one per line)."
+        )
+        return
+
     user_obj = store.user(user)
     if user_obj is None:
         click.echo(f"Could not find a user with email '{user}' in database")
@@ -86,7 +100,16 @@ def variants(
     else:
         click.confirm("Variants are going to be deleted from database. Continue?", abort=True)
 
-    case_query = store.build_case_query(case_id, status, older_than, analysis_type)
+    if case_file:
+        case_id = [line.strip() for line in open(case_file).readlines() if line.strip()]
+
+    case_query = store.build_case_query(
+        case_ids=case_id,
+        institute_id=institute,
+        status=status,
+        older_than=older_than,
+        analysis_type=analysis_type,
+    )
     # Estimate the average size of a variant document in database
     avg_var_size = store.collection_stats("variant").get("avgObjSize", 0)  # in bytes
 

scout/constants/clnsig.py

@@ -33,7 +33,9 @@ REV_CLINSIG_MAP = {
     "conflicting_classifications_of_pathogenicity": 8,
     "uncertain_significance": 0,
     "likely_pathogenic": 4,
+    "likely_pathogenic,low_penetrance": 4,
     "pathogenic": 5,
+    "pathogenic,low_penetrance": 5,
     # These are here so that the parsing function will work with the older clinvar format
     # Where significance where annotated with numbers
     0: 0,

scout/constants/indexes.py

@@ -8,6 +8,17 @@ INDEXES = {
             name="genes",
         )
     ],
+    "gene_panel": [
+        IndexModel(
+            [("panel_name", ASCENDING), ("version", ASCENDING)],
+            name="panel_name_version",
+            unique=True,
+        ),
+        IndexModel(
+            [("genes.hgnc_id", ASCENDING)],
+            name="genes.hgnc_id",
+        ),
+    ],
     "hgnc_gene": [
         IndexModel(
             [("build", ASCENDING), ("chromosome", ASCENDING)],

scout/parse/panelapp.py

@@ -1,12 +1,13 @@
 """Code to parse panel information"""
 
 import logging
-from typing import Dict, List, Optional
+from typing import Dict, Optional
 
 from scout.constants import INCOMPLETE_PENETRANCE_MAP, MODELS_MAP, PANELAPP_CONFIDENCE_EXCLUDE
 from scout.utils.date import get_date
 
 LOG = logging.getLogger(__name__)
+PANELAPP_PANELS_URL = "https://panelapp.genomicsengland.co.uk/panels/"
 
 
 def parse_panel_app_gene(
@@ -90,6 +91,7 @@ def parse_panelapp_panel(
     gene_panel["display_name"] = " - ".join([panel_info["name"], f"[{confidence.upper()}]"])
     gene_panel["institute"] = institute
     gene_panel["panel_type"] = ("clinical",)
+    gene_panel["description"] = f"{PANELAPP_PANELS_URL}{panel_id}"
 
     LOG.info("Parsing panel %s", gene_panel["display_name"])
 

scout/parse/variant/callers.py

@@ -1,11 +1,17 @@
 import logging
+from typing import Optional
+
+import cyvcf2
 
 from scout.constants import CALLERS
 
 LOG = logging.getLogger(__name__)
 
+PASS_STATUS = "Pass"
+FILTERED_STATUS = "Filtered"
+
 
-def parse_callers(variant, category="snv"):
+def parse_callers(variant: cyvcf2.Variant, category: str = "snv") -> dict:
     """Parse how the different variant callers have performed
 
     Caller information can be passed in one of three ways, in order of priority:
@@ -13,6 +19,10 @@ def parse_callers(variant, category="snv"):
     2. If a svdb_origin tag (pipe separated) is found, callers listed will be marked Pass
     3. If a set tag (dash separated, GATK CombineVariants) is found, callers will be marked Pass or Filtered accordingly
 
+    If the FILTER status is not PASS (e.g. None - cyvcf2 FILTER is None if VCF file column FILTER is "PASS"),
+    in all of these cases, if a single caller is found, the caller status is set to the filter status.
+    If there is more than one caller, we can't quite tell which one is which, so all caller statuses will be "Filtered" instead.
+
     Args:
         variant (cyvcf2.Variant): A variant object
 
@@ -20,47 +30,114 @@ def parse_callers(variant, category="snv"):
         callers (dict): A dictionary on the format
         {'gatk': <filter>,'freebayes': <filter>,'samtools': <filter>}
     """
+    FILTERED = "Filtered - {}"
+
     relevant_callers = CALLERS[category]
     callers = {caller["id"]: None for caller in relevant_callers}
     callers_keys = set(callers.keys())
 
-    other_info = variant.INFO.get("FOUND_IN")
-    svdb_origin = variant.INFO.get("svdb_origin")
-    raw_info = variant.INFO.get("set")
+    def get_callers_from_found_in(info_found_in: str, filter_status: Optional[str]) -> dict:
+        """If a FOUND_IN tag (comma separated) is found, callers listed will be marked Pass.
+        In case of a FILTER status, also set the caller status for a single caller to 'Filtered - status'.
+        If more than one caller, and FILTER status, we cant really tell which said what, and all will be
+        "Filtered".
+        """
+        found_ins: list = info_found_in.split(",")
+
+        call_status = PASS_STATUS
+        if filter_status is not None:
+            call_status = (
+                FILTERED.format(filter_status.replace(";", " - "))
+                if len(found_ins) == 1
+                else FILTERED_STATUS
+            )
 
-    if other_info:
-        for info in other_info.split(","):
-            called_by = info.split("|")[0]
+        for found_in in found_ins:
+            called_by = found_in.split("|")[0]
             if called_by in callers_keys:
-                callers[called_by] = "Pass"
-    elif svdb_origin:
-        for called_by in svdb_origin.split("|"):
+                callers[called_by] = call_status
+        return callers
+
+    info_found_in: str = variant.INFO.get("FOUND_IN")
+    if info_found_in:
+        return get_callers_from_found_in(info_found_in, variant.FILTER)
+
+    def get_callers_from_svdb_origin(svdb_origin: str, filter_status: Optional[str]) -> dict:
+        """If a svdb_origin tag (pipe separated) is found, callers listed will be marked Pass.
+        In case of a FILTER status, also set the caller status for a single caller to 'Filtered - status'.
+        """
+        svdb_callers: list = svdb_origin.split("|")
+
+        call_status = PASS_STATUS
+        if filter_status is not None:
+            call_status = (
+                FILTERED.format(filter_status.replace(";", " - "))
+                if len(svdb_callers) == 1
+                else FILTERED_STATUS
+            )
+
+        for called_by in svdb_callers:
             if called_by in callers_keys:
-                callers[called_by] = "Pass"
-    elif raw_info:
-        info = raw_info.split("-")
-        for call in info:
+                callers[called_by] = call_status
+        return callers
+
+    svdb_origin = variant.INFO.get("svdb_origin")
+    if svdb_origin:
+        return get_callers_from_svdb_origin(svdb_origin, variant.FILTER)
+
+    def get_callers_from_set(info_set: str, filter_status: str) -> dict:
+        """
+        If the FILTER status is not PASS (e.g. None - cyvcf2 FILTER is None if VCF file column FILTER is "PASS"),
+        in all of these cases, if a single caller is found, the "Pass" status is replaced with variant filter
+            status. If there is more than one caller, we can't quite tell which one is which, so all will be "Filtered"
+            without explicit status instead.
+
+        """
+
+        calls = info_set.split("-")
+
+        call_status = PASS_STATUS
+        if filter_status is not None:
+            call_status = (
+                FILTERED.format(filter_status.replace(";", " - "))
+                if len(calls) == 1
+                else FILTERED_STATUS
+            )
+
+        for call in calls:
             if call == "FilteredInAll":
                 for caller in callers:
-                    callers[caller] = "Filtered"
-            elif call == "Intersection":
+                    callers[caller] = FILTERED_STATUS
+                return callers
+            if call == "Intersection":
                 for caller in callers:
-                    callers[caller] = "Pass"
-            elif "filterIn" in call:
+                    callers[caller] = PASS_STATUS
+                return callers
+            if "filterIn" in call:
+                if "Filtered" not in call_status:
+                    call_status = FILTERED_STATUS
                 for caller in callers:
                     if caller in call:
-                        callers[caller] = "Filtered"
+                        callers[caller] = call_status
             elif call in callers_keys:
-                callers[call] = "Pass"
+                callers[call] = PASS_STATUS
+        return callers
+
+    info_set = variant.INFO.get("set")
+    if info_set:
+        return get_callers_from_set(info_set, variant.FILTER)
 
-    if raw_info or svdb_origin or other_info:
+    def get_callers_gatk_snv_fallback(filter_status: Optional[str]):
+        """As a final fallback, to accommodate a version range of MIP where no SNV caller was set for GATK,
+        if this is an SNV variant, and no other call was found, set as if it was a GATK call with Pass or filter status.
+        """
+        filter_status_default = "Pass"
+        if filter_status is not None:
+            filter_status_default = FILTERED.format(filter_status.replace(";", " - "))
+        callers["gatk"] = filter_status_default
         return callers
 
     if category == "snv":
-        # cyvcf2 FILTER is None if VCF file column FILTER is "PASS"
-        filter_status = "Pass"
-        if variant.FILTER is not None:
-            filter_status = "Filtered - {}".format(filter_status.replace(";", " - "))
-        callers["gatk"] = filter_status
+        return get_callers_gatk_snv_fallback(variant.FILTER)
 
     return callers

scout/parse/variant/clnsig.py

@@ -6,6 +6,17 @@ import cyvcf2
 LOG = logging.getLogger(__name__)
 
 
+def parse_clnsig_low_penetrance(sig_groups: List[str]) -> List[str]:
+    """If 'low_penetrance' is among the clnsig terms of an array, the term gets appended to the term immediately before in the array."""
+    result = []
+    for sig in sig_groups:
+        if sig == "low_penetrance" and result:
+            result[-1] += f",{sig}"
+        else:
+            result.append(sig)
+    return result
+
+
 def parse_clnsig(
     variant: cyvcf2.Variant, transcripts: Optional[dict] = None
 ) -> List[Dict[str, Union[str, int]]]:
@@ -58,6 +69,8 @@ def parse_clnsig(
             for term in significance.lstrip("_").split("/"):
                 sig_groups.append("_".join(term.split(" ")))
 
+        sig_groups: List[str] = parse_clnsig_low_penetrance(sig_groups)
+
         for sig_term in sig_groups:
             clnsig_accession = {
                 "value": sig_term,

scout/parse/variant/genotype.py

@@ -495,7 +495,7 @@ def _parse_format_entry_trgt_mc(variant: cyvcf2.Variant, pos: int):
                 if index in pathologic_mcs:
                     pathologic_counts += int(count)
         else:
-            pathologic_counts = int(allele)
+            pathologic_counts = 0 if allele == "." else int(allele)
 
         if ref_idx is not None and idx == ref_idx:
             mc_ref = pathologic_counts

scout/parse/variant/variant.py

@@ -92,6 +92,7 @@ def parse_variant(
 
     # cyvcf2 will set QUAL to None if '.' in vcf
     parsed_variant["quality"] = variant.QUAL
+
     parsed_variant["filters"] = get_filters(variant)
 
     # Add the dbsnp ids
@@ -235,6 +236,7 @@ def parse_variant(
 
     ###################### Add conservation ######################
     parsed_variant["conservation"] = parse_conservations(variant, parsed_transcripts)
+
     parsed_variant["callers"] = parse_callers(variant, category=category)
     set_rank_result(parsed_variant, variant, rank_results_header)
 

scout/server/blueprints/genes/templates/genes/gene.html

@@ -84,6 +84,12 @@
                       <a target="_blank" href={{ record.entrez_link }} referrerpolicy="no-referrer" rel="noopener" target="_blank"> {{ entrez_id }}</a>
                     </span>
                   </li>
+                  <li class="list-group-item">
+                    PanelApp
+                    <span class="float-end">
+                      <a target="_blank" href={{ record.panelapp_link }} referrerpolicy="no-referrer" rel="noopener" target="_blank"> {{ symbol }} </a>
+                    </span>
+                  </li>
                   {% if pli_score %}
                   <li class="list-group-item">
                     pLi Score (<a href={{ record.gnomad_link }} referrerpolicy="no-referrer" rel="noopener" target="_blank">GnomAD</a>)

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

@@ -79,17 +79,17 @@
                 {% endif %}
                   <div class="d-flex justify-content-center">
                   {% if case.vcf_files.vcf_snv %}
-                    <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
+                    <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}" target="_blank">
                     <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
                     <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-                    <span><button type="submit" class="btn btn-secondary btn-sm" style="float: right;" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SNVs</button></span>
+                    <span><button type="submit" class="btn btn-secondary btn-sm" style="float: right;" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SNVs</button></span>
                     </form>
                   {% endif %}
                   {% if case.vcf_files.vcf_sv %}
-                    <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
+                    <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}" target="_blank">
                     <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
                     <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-                    <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SV variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SVs</button></span>
+                    <button type="submit" class="btn btn-secondary btn-sm" data-bs-toggle="tooltip" title="SV variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SVs</button></span>
                   </form>
                   {% endif %}
                     </div>

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

@@ -26,6 +26,9 @@
     {{ new_panel() }}
     {{ search_gene_card() }}
     {% if panel_groups %}
+      <span class="float-end me-3 mt-3">
+        <input type="checkbox" name="hideLine" checked onclick="toggleRow(this)"> Hide removed panels</input>
+      </span>
       {% for institute,panels in panel_groups %}
         {{ panel_view(institute,panels) }}
       {% endfor %}
@@ -103,7 +106,7 @@
               <select name="institute" class="form-control" required>
                 <option value="">Choose institute...</option>
                 {% for institute in institutes %}
-                  <option value="{{ institute._id }}">{{ institute.display_name }}</option>
+                  <option value="{{ institute._id }}">{{ institute.display_name }} ({{institute._id}})</option>
                 {% endfor %}
               </select>
           </div>
@@ -141,10 +144,7 @@
 {% macro panel_view(institute, panels) %}
   <div class="card panel-default w-100 mt-3 justify-content-center">
     <div class="card-title d-flex justify-content-between">
-      <span><strong>{{ institute.display_name }}</strong> - Panels</span>
-      <span>
-        <input type="checkbox" name="hideLine" checked onclick="toggleRow(this)"> Hide removed panels</input>
-      </span>
+      <span><strong>{{ institute.display_name }} ({{institute._id}})</strong> - Panels</span>
     </div>
     <div class="card-body">
         <table class="table table-striped" id="panelTable" style="table-layout: fixed;">

scout/server/blueprints/variant/controllers.py

@@ -41,13 +41,14 @@ from scout.server.utils import (
 from .utils import (
     add_gene_info,
     associate_variant_genes_with_case_panels,
-    callers,
     clinsig_human,
     default_panels,
     end_position,
     evaluation,
     frequencies,
     frequency,
+    get_callers,
+    get_filters,
     is_affected,
     predictions,
 )
@@ -315,7 +316,10 @@ def variant(
     update_representative_gene(variant_obj, variant_genes)
 
     # Add display information about callers
-    variant_obj["callers"] = callers(variant_obj)
+    variant_obj["callers"] = get_callers(variant_obj)
+
+    # annotate filters
+    variant_obj["filters"] = get_filters(variant_obj)
 
     # Convert affection status to strings for the template
     is_affected(variant_obj, case_obj)

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

@@ -17,7 +17,7 @@
       <tbody>
         {% for clinsig in variant.clinsig_human %}
           <tr>
-            <td>{{ clinsig.human }}</td>
+            <td>{{ clinsig.human }} {% if clinsig.low_penetrance %}(low penetrance){% endif %}</td>
             {% if clinsig.accession %}
               <td><a href="{{ clinsig.link }}" target="_blank">{{ clinsig.accession }}</a></td>
             {% else %}

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

@@ -97,8 +97,15 @@
       </table>
     </div>
     <div class="panel-footer">
+       {% for filter in variant.filters %} <!-- collect info from variant's filters (PASS) -->
+        <span class="badge bg-{{ filter.label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="{{ filter.description }}">
+          {{ filter.label }}
+        </span>
+      {% endfor %}
       {% for name, caller in variant.callers %}
-        <span class="badge bg-secondary">{{ name }}: {{ caller }}</span>
+        <span class="badge {% if caller == 'Pass' %}bg-success{% elif 'Filtered' in caller %}bg-secondary{% else %}bg-black{% endif %}">
+        {{ name }}: {{ caller }}
+        </span>
       {% endfor %}
     </div>
     </div>

scout/server/blueprints/variant/utils.py

@@ -2,7 +2,7 @@ import logging
 from typing import Dict, List, Optional, Tuple
 
 from scout.adapter import MongoAdapter
-from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS
+from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS, VARIANT_FILTERS
 from scout.server.links import add_gene_links, add_tx_links
 
 LOG = logging.getLogger(__name__)
@@ -592,14 +592,15 @@ def clinsig_human(variant_obj):
         yield clinsig_obj
 
 
-def callers(variant_obj):
+def get_callers(variant_obj: dict) -> List[Tuple]:
     """Return info about callers.
 
-    Args:
-        variant_obj(scout.models.Variant)
+    Given a scout.models.Variant compliant variant obj dict,
+    return a list of the callers that identified the variant.
 
-    Returns:
-        calls(list(str)): A list of the callers that identified the variant
+    Finds calls in the CALLERS constant for the variant category,
+    directly on the variant object, gathers them in a set of tuples
+    of caller name and status, and returns as a list of tuples.
     """
     category = variant_obj.get("category", "snv")
     calls = set()
@@ -610,6 +611,37 @@ def callers(variant_obj):
     return list(calls)
 
 
+def get_filters(variant_obj: dict) -> List[Dict[str, str]]:
+    """Return a list with richer format descriptions about filter status,
+    if available. Fall back to display the filter status in a "danger" badge
+    if it is not known from the VARIANT_FILTERS constant.
+
+    Currently, the controller may be applied repeatedly to the same variant object
+    for redecoration. Check if the filter strings have already been converted
+    to dicts before attemting to convert them.
+    """
+    variant_filters = variant_obj.get("filters", [])
+
+    filters: List[Dict[str, str]] = []
+
+    for f in variant_filters:
+        if isinstance(f, str):
+            if f.lower() in VARIANT_FILTERS:
+                filters.append(VARIANT_FILTERS[f.lower()])
+            else:
+                filters.append(
+                    {
+                        "label": f.replace("_", " ").upper(),
+                        "description": f.replace("_", " "),
+                        "label_class": "danger",
+                    }
+                )
+        elif isinstance(f, dict):
+            filters.append(f)
+
+    return filters
+
+
 def associate_variant_genes_with_case_panels(case_obj: Dict, variant_obj: Dict) -> None:
     """Add associated gene panels to each gene in variant object"""
 

scout/server/blueprints/variants/controllers.py

@@ -27,12 +27,12 @@ from scout.constants import (
     MANUAL_RANK_OPTIONS,
     MOSAICISM_OPTIONS,
     SPIDEX_HUMAN,
-    VARIANT_FILTERS,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
 from scout.server.blueprints.variant.utils import (
-    callers,
     clinsig_human,
+    get_callers,
+    get_filters,
     predictions,
     update_representative_gene,
     update_variant_case_panels,
@@ -936,14 +936,10 @@ def parse_variant(
     update_representative_gene(variant_obj, variant_genes)
 
     # Add display information about callers
-    variant_obj["callers"] = callers(variant_obj)
+    variant_obj["callers"] = get_callers(variant_obj)
 
     # annotate filters
-    variant_obj["filters"] = [
-        VARIANT_FILTERS[f]
-        for f in map(lambda x: x.lower(), variant_obj["filters"])
-        if f in VARIANT_FILTERS
-    ]
+    variant_obj["filters"] = get_filters(variant_obj)
 
     return variant_obj
 
@@ -1082,7 +1078,7 @@ def variant_export_lines_common(store: MongoAdapter, variant: dict, case_obj: di
         else variant.get("category")
     )
     variant_line.append(cat.upper() if cat else "")
-    variant_line.append("  ".join([f"{name}:{caller}" for name, caller in callers(variant)]))
+    variant_line.append("  ".join([f"{name}:{caller}" for name, caller in get_callers(variant)]))
     variant_line.append(variant["chromosome"])
     variant_line.append(position)
     variant_line.append(change)

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

@@ -62,7 +62,7 @@
               <th title="Population frequency">Pop Freq</th>
               <th title="Observed" style="width:7%">Observed</th>
               <th title="Variant type">Type</th>
-              <th title="Callers" style="width:8%">Callers</th>
+              <th title="Callers" style="width:12%">Callers</th>
               <th title="Functional consequence annotation" style="width:10%">Consequence</th>
               <th data-bs-toggle="tooltip" data-bs-placement="top" title="Tumor alt. AF. &#013; Alt. allele count | Ref. allele count">Tumor</th>
               <th data-bs-toggle="tooltip" data-bs-placement="top" title="Normal alt. AF. &#013; Alt. allele count | Ref. allele count">Normal</th>
@@ -115,7 +115,7 @@
             <td>{{ position_cell(variant) }}</td>
             <td class="text-end">{{ frequency_cell_general(variant) }}</td>
             <td>{{ observed_cell_general(variant) }}</td>
-            <td>{{ variant.sub_category }}</td>
+            <td>{{ variant.sub_category|upper }}</td>
             <td>{{ callers_cell(variant) }}</td>
             <td>{{ variant_funct_anno_cell(variant) }}</td>
             <td>{{ allele_cell(variant.tumor or {}) }}</td>

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

@@ -56,7 +56,7 @@
       </span>
     {% endfor %}
   {% for name, caller in variant.callers %} <!-- Collect info for specific callers -->
-      <span class="badge {% if caller == 'Pass' %}bg-success{% elif caller == 'Filtered' %}bg-secondary{% else %}bg-black{% endif %}" data-bs-toggle="tooltip" data-bs-html="true" title="{{caller}}">
+      <span class="badge {% if caller == 'Pass' %}bg-success{% elif 'Filtered' in caller %}bg-secondary{% else %}bg-black{% endif %}" data-bs-toggle="tooltip" data-bs-html="true" title="{{caller}}">
         {{ name }}
       </span>
   {% endfor %}

scout/server/extensions/panelapp_extension.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Optional
+from typing import List, Optional
 
 import requests
 
@@ -41,7 +41,7 @@ class PanelAppClient:
             for type in panel.get("types", []):
                 self.panel_types.add(type["slug"])
 
-    def get_panel_ids(self, signed_off: bool) -> list[int]:
+    def get_panel_ids(self, signed_off: bool) -> List[int]:
         """Returns a list of panel ids contained in a json document with gene panels data."""
 
         def get_ids(json_panels):

{scout_browser-4.91.1.dist-info → scout_browser-4.92.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.91.1
+Version: 4.92
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

{scout_browser-4.91.1.dist-info → scout_browser-4.92.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=UEW2jG2n4LaWe4lbBdEuuVDJFg2ITmLfH-vIghRM4ms,23
+scout/__version__.py,sha256=ANcNj-w6TB4wETdZ9CZJYc1ZGU2Q1cA11Hzzi92m9BE,21
 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
@@ -20,9 +20,9 @@ scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTF
 scout/adapter/mongo/managed_variant.py,sha256=YFdnIhNVIawVhmlOxHOpe6sJyso0FCGdlXOXyhSWol8,8373
 scout/adapter/mongo/matchmaker.py,sha256=amTvFOlUbrt1RmecY_8hPY6bO3j79lc2UbmzlCQcRuk,6378
 scout/adapter/mongo/omics_variant.py,sha256=VdkNG_l6vcr3UF25EixEfvIdMGkSGeNaMjLRhQHS_lc,7521
-scout/adapter/mongo/panel.py,sha256=XbV_oh9II89OLsWm2BWxiYKkxMGU4HGKuG-8L-drWbk,20018
+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=MzeMUND_BPHgJLGDEbOVgwf4ic8M9ZXFcyroQd0LMJQ,33314
+scout/adapter/mongo/query.py,sha256=Zk5BV9GZYVlGoSRRjP88TpvB4teVpvHgHnSDV0W-kS0,33157
 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
@@ -44,7 +44,7 @@ scout/build/genes/exon.py,sha256=a0oyW69x0tTImu4rxce5pU3Cb_GLSIdbexU0ex_OH7Q,225
 scout/build/genes/hgnc_gene.py,sha256=3ckEc4jpwcN_bYeAbv_wJrjzWMthm0HJR1dSzAraM_A,678
 scout/build/genes/transcript.py,sha256=qXdS7bU1d-ikgN8UOSyW7u34y-qpgcpVuCccP2tKR80,2416
 scout/build/variant/__init__.py,sha256=Y70EK_8TS69seYSyIvL1Mek1FMo3XPeXcOnYVIOWggA,173
-scout/build/variant/clnsig.py,sha256=uAfrf4RSUGliIp13fW9XqJshodNWxjuAwUbBbNHgmCc,719
+scout/build/variant/clnsig.py,sha256=O3JmBsMXZhD0PCWvM-sAgAYzU1oZ-U6Xhv_Kh8nA5mU,680
 scout/build/variant/compound.py,sha256=tYikQ4PmgAH1_yrE9uYaUX4_EoAs_XEiT8JWAjrZuDg,816
 scout/build/variant/gene.py,sha256=Fj_ouJtNAZOvxYVo9oVXaYJE5_zx-mJqL-uOARD4ku8,3857
 scout/build/variant/genotype.py,sha256=QDTZWFB8ix9Zd1m9UPWgT008i6rC7gT-uFzRr9GniDU,1009
@@ -58,7 +58,7 @@ scout/commands/serve.py,sha256=fImJrgMBYQTD18xODjGqN6NgXjTe8seI_awd9vF04rU,1564
 scout/commands/utils.py,sha256=T29f-1wTq3uoxqtv6QOqBdMBl7tLeEn8DYXnnv3gowI,306
 scout/commands/wipe_database.py,sha256=TvCoXZCT-mvTqsZaFstV5u5FM8KAQstB3JxyGHYMLtg,1005
 scout/commands/delete/__init__.py,sha256=6Z97FsWMqyKqF64Anl1zwljVNTfjJUCI7yylxIEnsUY,35
-scout/commands/delete/delete_command.py,sha256=X3sH0pP51n1Gmv3e7EbgXggFp_yG4ZtziSNsIpcNu78,12584
+scout/commands/delete/delete_command.py,sha256=_x897Du0nTsYmSG_5LAIm6Z9sjKcaCrtAR7cwuNwl4I,13285
 scout/commands/download/__init__.py,sha256=mfDzxqKzJ0LgfPBN_fehkdX5BPy1FJ3rauA3ORLIjCM,39
 scout/commands/download/download_command.py,sha256=m5CKefst3qhs4urfNu1A2TERisUb_5WPn-wn9bGCDr0,736
 scout/commands/download/ensembl.py,sha256=CsTMjYihBtXyfofNIQ2riL9UBzydDbqoNZ7jJVQ15ak,2112
@@ -128,13 +128,13 @@ scout/constants/__init__.py,sha256=HZvAMX-37ugK0fRwa8xKGvnZkicyUJH-SH2pqw7rm-g,5
 scout/constants/acmg.py,sha256=hYPzoLUqpuTjGXfIN80Nb1njriesH9oAELu1scp-ByU,18083
 scout/constants/case_tags.py,sha256=EvLYtbZADyFEngeY8rvPsJ_1NdLmHrlnrGTlnj7tGGs,9336
 scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
-scout/constants/clnsig.py,sha256=5Z4fZU__ej9teXK4hD9vGhIGmaGL6PoJqK5GuzLWxpE,1414
+scout/constants/clnsig.py,sha256=TSeZjUno2jEvQTenrltZ900ZFYIRNoul_Wm2qRjvpPA,1493
 scout/constants/disease_parsing.py,sha256=M9_OgsN88oXwKH_XpxdDma0zuWPRoHFQjL19tzojBPo,686
 scout/constants/file_types.py,sha256=3BU2cw40cHMT5IzEGEF_SsIhgYUbnIlUCRmwmB01fzI,3046
 scout/constants/filters.py,sha256=1bcj-z7__yv5eQpjB60wqSHZ3U5U0CVyNbcYT-Wn-vc,957
 scout/constants/gene_tags.py,sha256=pRRsjn9zYGR3nLFKxe1gOYqWm4uQbpfxYzfRxcptxqA,3856
 scout/constants/igv_tracks.py,sha256=NbBBnM3s1S8cJM_S36qi7SU2ACW_lJVS6EP2W0kCTIQ,4697
-scout/constants/indexes.py,sha256=-rb5VP68Arl2t-bFDYWiQswAF3YxjrAJVuMtQWrT__8,5497
+scout/constants/indexes.py,sha256=mCj_ih9Sv7Qv4DrzLRH30EQZ-Tgyn_Sf6NYapCOlMOc,5793
 scout/constants/panels.py,sha256=X38XGPlNgOGhXHt5mSpryOS7gMeP-tUD1t1WIT2G5wM,785
 scout/constants/phenotype.py,sha256=MrbXirisR_7GPnxV3NOj3-BoM9CvtGgFZj7PfJu85RM,2331
 scout/constants/query_terms.py,sha256=2A4CuTgc7W_VMj4atkJdZFfvBATu7OQg51udFM0rMOo,1574
@@ -414,28 +414,28 @@ scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
 scout/parse/omim.py,sha256=nrCaFZgjUKZo9Jfku2-jcNjdsIYHsvjdWcydz4nCpZA,12465
 scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
 scout/parse/panel.py,sha256=J28e_MkKeB5r4hOutb3qimxUT7G5yg8x1Ca4bAs0I_c,9577
-scout/parse/panelapp.py,sha256=1UAKBm48tKlfDpNb_VH_kfqO8tgduXRSIQnWa61Fzrc,3944
+scout/parse/panelapp.py,sha256=Idz6cGvQnyI-nn6yCTc6EGSRp1gX-CXN6Y4ayAee-_A,4076
 scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
 scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
 scout/parse/omics_variant/__init__.py,sha256=vq8Ew4_Xr2vPy_3Fg0eTpPWsQpWnUXYBhjRndBUvtTw,422
 scout/parse/omics_variant/drop.py,sha256=SD98E9ksPPv62SFUuR4TfZHVIIIy1RXZRdMhm5Hu4RQ,478
 scout/parse/variant/__init__.py,sha256=5yqCQlAYMqosRabdipFUXqopSMBN4X6jwpNiKiYKlsE,35
-scout/parse/variant/callers.py,sha256=roTeQUMMNxOCeRHuL-TwJpIg5OwetMn4v-5E2xWvulU,2372
-scout/parse/variant/clnsig.py,sha256=p5YNF_H1x6h1lTJX0D06Z9G1NfwQJ1WjnLauK1Oli28,4951
+scout/parse/variant/callers.py,sha256=eA5o4Ov_v5ds__4xpif1ttj5yk2nK4GXwhYSWL4NTDg,5709
+scout/parse/variant/clnsig.py,sha256=dFIvV29cvMOFw7hSgbjBEXzWV5YVKpSGQqgLuHbMePk,5421
 scout/parse/variant/compound.py,sha256=zeRHBwobusCW-ylgurHrnPsc-edeJHeXj6xjXkrbFt8,1493
 scout/parse/variant/conservation.py,sha256=8eHXy57g6ng0eMo38LsIcQ8w_H5mpBSfiMuaXF7aBi4,2949
 scout/parse/variant/coordinates.py,sha256=CU-EyD8NVgTbyIdmYDO3k-zVaMN1EDONjorDwyUSnXU,4742
 scout/parse/variant/deleteriousness.py,sha256=zeFzx218GL-5pKniyci7MVHj3a1cep4nmvoSg7u0ogA,541
 scout/parse/variant/frequency.py,sha256=kpUNrXvg6IeLvf3TFmEni5lUfp1jFIMCKMrevJwUCNg,7854
 scout/parse/variant/gene.py,sha256=30SR2ck12HQW87LlRfchdgPVzOxb74aIXC2WzPL2BPk,4688
-scout/parse/variant/genotype.py,sha256=IqoH3UOd34ZrPE1xkDDmXavDEYe10D5mH9zf20E_BTA,16553
+scout/parse/variant/genotype.py,sha256=c53cRtC-9DH6kEb_F2n4fbXdKY3Zcq6srQC-2scqiaU,16577
 scout/parse/variant/headers.py,sha256=se3H4r22q30MIvtOyc5jWNXZLVnDx58X4h-eED7hkl4,2947
 scout/parse/variant/ids.py,sha256=N_2m7Hgdh7asHdWU4k2dMySsutxp16ODRE_OHy_Niwg,2628
 scout/parse/variant/managed_variant.py,sha256=qwmi2sPLwGZM5izSsMpvhQ9vfMHREiwiIzjDCuOdqQo,2288
 scout/parse/variant/models.py,sha256=NrqLXu7PxpIQ0NmjGRIEk4vS_y972VPiexLsZCZpOn0,507
 scout/parse/variant/rank_score.py,sha256=ipFxCTsQHMqObUbzLJlDAKUb3_lk_sqEYzH52myZVVk,486
 scout/parse/variant/transcript.py,sha256=0kxaXWrNAvSiU76ZdIl9PQFzUyj6go6u3BnNhnTk8pg,13359
-scout/parse/variant/variant.py,sha256=CTCaE07GqDg52ZhUPLpEOoEYLgr4y1mPtvRvAsxt5IM,24057
+scout/parse/variant/variant.py,sha256=nf_0q2J7TryWhB-Oz697HYSDJTPNmkXnPHmKtjhHQUU,24059
 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
@@ -500,7 +500,7 @@ scout/server/blueprints/diagnoses/templates/diagnoses/disease_term.html,sha256=8
 scout/server/blueprints/genes/__init__.py,sha256=LPHrbmfVhZpLGGdExFbJp_Du1NKCsVOO_eaevpsNLC8,52
 scout/server/blueprints/genes/controllers.py,sha256=LCuGPQymKxA7sES49z_j2_B3prKmNY-ME0VK892VoPs,3629
 scout/server/blueprints/genes/views.py,sha256=lFJ7izYu0CbUJo3j5TesrUhIwreZUYw9_dDqd6iG8m4,1512
-scout/server/blueprints/genes/templates/genes/gene.html,sha256=X1WR-sHYGnWyhQfgN77TqC3_yoweaqu7MjwUvAO9UBo,10872
+scout/server/blueprints/genes/templates/genes/gene.html,sha256=a--c-IjzNKN_JW7z9jbNCnk3bLD_oVeFvf5x8IAmynA,11197
 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
@@ -542,7 +542,7 @@ scout/server/blueprints/managed_variants/templates/managed_variants/managed_vari
 scout/server/blueprints/omics_variants/__init__.py,sha256=8UVXrChArhIvMxtgUcG-udvmlTn56q41iy-naOZw5us,37
 scout/server/blueprints/omics_variants/controllers.py,sha256=AnM70stvLniJIU3pFUX-InNjuT-7K0RpuAEYa7vM-jw,3912
 scout/server/blueprints/omics_variants/views.py,sha256=P-mo2S1RBGYxsNCFqSTNQNLvqiH9r6_AoZgsOWpopPE,3817
-scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html,sha256=hd8vxHY1hBqiyvgefLK3S_i_VnOgGwCJLmJUxiJhB4M,13733
+scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html,sha256=gv9llZzH-AKJ4i2XJKZFJi9IBgvF84WI7QCVuvFOhTA,13703
 scout/server/blueprints/panels/__init__.py,sha256=usxBF0O7zNX1d9jt-8DRoFZwcfHHS96Gv87LDr1AgG4,53
 scout/server/blueprints/panels/controllers.py,sha256=DHIIXp_kms4DkTX2mkSdWhW-b4mk0gsRX2XU-4JP3CM,12597
 scout/server/blueprints/panels/forms.py,sha256=DYlhYpnpv7ehf9JlY3HRFwy-TZ5QDHB0RIRaNTAW1jQ,696
@@ -551,7 +551,7 @@ scout/server/blueprints/panels/templates/panels/gene-edit.html,sha256=KqdUdu9370
 scout/server/blueprints/panels/templates/panels/panel.html,sha256=qMdyxia0Oei83ECR6TTxOn62hh447XuGFF_TD63NP6E,16527
 scout/server/blueprints/panels/templates/panels/panel_pdf_case_hits.html,sha256=uzfZJiMNQiTa_6u4uMuIbK3VXIs-8Rw-MjKujFttZG8,3438
 scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html,sha256=cpOnQzeKYnQwXosTKk9hkiBigJJLS3Q_y2oHDR3C8io,2744
-scout/server/blueprints/panels/templates/panels/panels.html,sha256=zjVzfgsapjlZBZ8Kz2zRz0oShg1msXTkkoENy9jF4Tc,14038
+scout/server/blueprints/panels/templates/panels/panels.html,sha256=2IEZFbXzp4MKbx-9UZTW8rZt8pl3iZXPlkvppS3sj0Q,14106
 scout/server/blueprints/phenomodels/__init__.py,sha256=Kb1fqfCn-QsH5mz6hiuQ2DiC7icTClD4HLey6QN4GD4,34
 scout/server/blueprints/phenomodels/controllers.py,sha256=g5-BxlaHN7JBuQHEcOtQMUDEO9U9iy9HICaIaIEn3vk,11019
 scout/server/blueprints/phenomodels/forms.py,sha256=Z7dMIJml5xZ1cQV1jh_-IGVxhxk4lVhcUTvFa6ArbJo,740
@@ -600,14 +600,14 @@ scout/server/blueprints/public/static/ideograms/chromosome-X.png,sha256=Dj7npcW_
 scout/server/blueprints/public/static/ideograms/chromosome-Y.png,sha256=KlOsBLZYFVHRvXvTioT-XE57zSWoYeIwIEXo_rzLBR0,1524
 scout/server/blueprints/public/templates/public/index.html,sha256=-c6-r2G6-cdE9PLV126V8zTwYmApI88UIQKWuVP6HP4,4268
 scout/server/blueprints/variant/__init__.py,sha256=SlD8-Aoj9Jq9aVTJjtFfsu-0sUVfkzpiEXcH8z9q6dI,54
-scout/server/blueprints/variant/controllers.py,sha256=9pojsGPszRn61XHQg4OwCXxqniyJgTGdZvMz4_4rNxQ,25406
-scout/server/blueprints/variant/utils.py,sha256=fsX_PHBOHloypjtKx9LPKxjyH-HW3ERxnQl-8NOP8Sw,23127
+scout/server/blueprints/variant/controllers.py,sha256=yCna3EoYG-KwfPy4k9Z-p0cMeMO-EAB4YwUt3MyBYN0,25509
+scout/server/blueprints/variant/utils.py,sha256=XMnsgIzOSG2z1mXlBoWZpNvFr-Ocx860AKlKXnOJ0oI,24463
 scout/server/blueprints/variant/verification_controllers.py,sha256=eKzP222e7xuFOaQaI9MLOrD9RWtI8uGB1cJYbcXLzF0,10972
 scout/server/blueprints/variant/views.py,sha256=XAAIE35SXsGLLphUK4mQ6Kl8wpxwDEEo5kXLh6KD83w,14957
 scout/server/blueprints/variant/templates/variant/acmg.html,sha256=Fk4vL1Pu4G3wZsfiUO2jBlFLFoRgFAeqChlIyas5Bb4,8758
 scout/server/blueprints/variant/templates/variant/buttons.html,sha256=4vlnvJKhr28qqzevlecAIvumvOgLZhGyPYQm68AnKzU,7608
 scout/server/blueprints/variant/templates/variant/cancer-variant.html,sha256=1D9uLIgb06qfhcbl0wB5mRrgARVgfCJfRZhf4wEA2tc,13971
-scout/server/blueprints/variant/templates/variant/components.html,sha256=dINgA52b2kZ3g0DKzimVu21jmhZL2BVzEDNfMibQA_M,21507
+scout/server/blueprints/variant/templates/variant/components.html,sha256=wBBrIMtEvkSX2lzFnkBB8gj--vETJ55cHtAC21aZG2s,21566
 scout/server/blueprints/variant/templates/variant/gene_disease_relations.html,sha256=1U77akxqbb4AS2GSyvFwGD6D7rP68L3KXKLUmP73664,7256
 scout/server/blueprints/variant/templates/variant/rank_score_results.html,sha256=32RfBrpZ_J-1WYE01Bdd5IC9i1MAzXT7GF27OlElk94,2040
 scout/server/blueprints/variant/templates/variant/sanger.html,sha256=0kVnscTw3KUwjR4QOEuNJMOK9eADGEn9qGNtGx2ST7Y,4507
@@ -616,22 +616,22 @@ scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=8199JLl
 scout/server/blueprints/variant/templates/variant/tx_overview.html,sha256=turyCoOCCd_N80FakxXfIl7q_WViysz1fwx3j312_Lg,6737
 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=saZzZ-ppdjE_4hSfW3MqMGyu5l_L8upyXS1uzwhbMiM,17844
-scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=J-pF8LRXFnCxIbNfL7klTLj172rlpWF8PznO4ie9Igc,19921
+scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=a-_DgccaehxiAQaBeTv9PXubwjHOGVqH1fj7WQMWWqM,20332
 scout/server/blueprints/variants/__init__.py,sha256=W1KCz9kEbVlNO0o3NvLitYLQoP_3JSJ5KSjhpcjlUBQ,55
-scout/server/blueprints/variants/controllers.py,sha256=OOBoemjmuOAADLv3wgKZU2OHiuH2CaK8bO3-mMhRV3M,72924
+scout/server/blueprints/variants/controllers.py,sha256=xUxBgVe7sns5FzsjS1Z0VOgnRMTNSpIcotFzSjW9wwU,72824
 scout/server/blueprints/variants/forms.py,sha256=w4Woeek6gpZfPM_9e1E_n-gpVvNxXPU_ria7cvP1HSo,10750
 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=6t1ZKUm2f6l5NJKDQvo9RBc4DBZgkWBXiePoIFkm6OY,9789
+scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=CTZyD1nne-w8EwcO6_ugnS6eMndLAzomlCNKJ1MM6VU,9796
 scout/server/blueprints/variants/templates/variants/components.html,sha256=xXa0ndN42htflWDYsbKhMwIYdk8hBJ0znyinVfLCU2o,17815
 scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
 scout/server/blueprints/variants/templates/variants/indicators.html,sha256=BX6Wg8OpsALCGGozR1eXT57D0Ixrf-OFXVg6G20Wjr0,4400
 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/utils.html,sha256=3jixwVolEzf7-mmV8e7AgDLoMrQlJfucKa877FF5SUg,50042
+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
 scout/server/extensions/beacon_extension.py,sha256=YDXQQl5kFcsA4OFHDMVurIKLw_3Gl6yWfcy3lYHl9RE,9904
@@ -644,7 +644,7 @@ scout/server/extensions/ldap_extension.py,sha256=nVgJ6YhSyvpg8J4bSYzJwoEvKhP0faW
 scout/server/extensions/loqus_extension.py,sha256=uiqUXQ7Q7DCj6C20TKgL8yLu9DXov95vrJfhq0tvbTM,12602
 scout/server/extensions/matchmaker_extension.py,sha256=mNytCYnZX1hgdq1otkvnyOkh4dj9SVgQthJAfKb8TMI,5024
 scout/server/extensions/mongo_extension.py,sha256=bKB0K5ibp-BWynOTgzBJd5qIYO0S9zRtEyDUw7EoxSQ,1029
-scout/server/extensions/panelapp_extension.py,sha256=UoPFGKqXJtAfbw3WRTxvHZweNI4jVgYgrhWkgVJouRo,2732
+scout/server/extensions/panelapp_extension.py,sha256=UnHhyG7iSMy3ERQg5Sl3DOkmKjsLPgAEfPkzlfn2BrY,2738
 scout/server/extensions/phenopacket_extension.py,sha256=kcEUIOSfkQAlAmUm07hQS1BeUjeN4lBc-InvaNtbFxo,7295
 scout/server/extensions/rerunner_extension.py,sha256=SEwQi5BZR5X70BoD0U7TfyGgGv2WbJbas0v1efuv_r8,1104
 scout/server/static/bs_styles.css,sha256=Y7aq8Es3NHj1OaLPX0eiY5485C8gENptpuYmf7W3o1w,6421
@@ -677,9 +677,9 @@ 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-4.91.1.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.91.1.dist-info/METADATA,sha256=b8Nefs04nnQtwP5Auh5mCb4ZMX909osa6b7rnp9iEkU,14262
-scout_browser-4.91.1.dist-info/WHEEL,sha256=bFJAMchF8aTQGUgMZzHJyDDMPTO3ToJ7x23SLJa1SVo,92
-scout_browser-4.91.1.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.91.1.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.91.1.dist-info/RECORD,,
+scout_browser-4.92.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.92.dist-info/METADATA,sha256=Z78U2w0_9MMsAmsc1pLdjEAkA2k2J06aUwZ2R6VIbJM,14260
+scout_browser-4.92.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+scout_browser-4.92.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.92.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.92.dist-info/RECORD,,

{scout_browser-4.91.1.dist-info → scout_browser-4.92.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.45.0)
+Generator: bdist_wheel (0.45.1)
 Root-Is-Purelib: true
 Tag: py3-none-any