scout-browser 4.90.1__tar.gz → 4.91__tar.gz

{scout-browser-4.90.1 → scout-browser-4.91}/CHANGELOG.md

@@ -4,6 +4,44 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+
+## [4.91]
+### Added
+- Variant link to Franklin in database buttons (different depending on rare or cancer track)
+- MANE badges on list of variant's Genes/Transcripts/Proteins table, this way also SVs will display MANE annotations
+- Export variant type and callers-related info fields when exporting variants from variantS pages
+- Cases advanced search on the dashboard page
+- Possibility to use only signed off panels when building the PanelApp GREEN panel
+### Changed
+- On genes panel page and gene panel PDF export, it's more evident which genes were newly introduced into the panel
+- WTS outlier position copy button on WTS outliers page
+- Update IGV.js to v3.0.9
+- Managed variants VCF export more verbose on SVs
+- `/api/v1/hpo-terms` returns pymongo OperationFailure errors when provided query string contains problematic characters
+- When parsing variants, prioritise caller AF if set in FORMAT over recalculation from AD
+- Expand the submissions information section on the ClinVar submissions page to fully display long text entries
+- Jarvik et al for PP1 added to ACMG modification guidelines
+- Display institute `_id` + display name on dashboard filters
+- ClinVar category 8 has changed to "Conflicting classifications of pathogenicity" instead of "interpretations"
+- Simplify always loading ClinVar `CLNSIG` P, LP and conflicting annotations slightly
+- Increased visibility of variant callers's "Pass" or "Filtered" on the following pages: SNV variants (cancer cases), SV variants (both RD and cancer cases)
+- Names on IGV buttons, including an overview level IGV MT button
+- Cases query no longer accepts strings for the `name_query` parameter, only ImmutableMultiDict (form data)
+- Refactor the loading of PanelApp panels to use the maintained API - Customised PanelApp GREEN panels
+- Better layout for Consequence cell on cancer SNVs page
+- Merged `Qual` and `Callers` cell on cancer SNVs page
+### Fixed
+- Empty custom_images dicts in case load config do not crash
+- Tracks missing alignment files are skipped on generating IGV views
+- ClinVar form to accept MedGen phenotypes
+- Cancer SV variantS page spinner on variant export
+- STRs variants export (do not allow null estimated variant size and repeat locus ID)
+- STRs variants page when one or more variants have SweGen mean frequency but lack Short Tandem Repeat motif count
+- ClinVar submission enquiry status for all submissions after the latest
+- CLI scout update type hint error when running commands using Python 3.9
+- Missing alignment files but present index files could crash the function creating alignment tracks for IGV display
+- Fix missing "Repeat locus" info on STRs export
+
 ## [4.90.1]
 ### Fixed
 - Parsing Matchmaker Exchange's matches dates
@@ -26,6 +64,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - VariantS page local observation badges have counts visible also without hover
 - On Matchmaker page, show number of matches together with matching attempt date
 - Display all custom inheritance models, both standard and non-standard, as gathered from the gene panel information on the variant page
+- Moved PanelApp-related code to distinct modules/extension
 ### Fixed
 - Make BA1 fully stand-alone to Benign prediction
 - Modifying Benign terms to "Moderate" has no effect under Richards. Ignored completely before, will retain unmodified significance now

{scout-browser-4.90.1/scout_browser.egg-info → scout-browser-4.91}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.90.1
+Version: 4.91
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.91/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.91"

{scout-browser-4.90.1 → scout-browser-4.91}/scout/adapter/mongo/case.py

@@ -4,7 +4,7 @@ import logging
 import operator
 import re
 from copy import deepcopy
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional
 
 import pymongo
 from bson import ObjectId
@@ -219,7 +219,7 @@ class CaseHandler(object):
         query.setdefault("$or", []).extend(or_options)
 
     def populate_case_query(
-        self, query: dict, name_query: Union[str, ImmutableMultiDict], owner=None, collaborator=None
+        self, query: dict, name_query: ImmutableMultiDict, owner=None, collaborator=None
     ):
         """Parses and adds query parameters provided by users in cases search filter."""
 
@@ -306,36 +306,29 @@ class CaseHandler(object):
             users = self.user_collection.find(user_query)
             query["assignees"] = {"$in": [user["_id"] for user in users]}
 
-        if isinstance(name_query, str):
-            # Example: status -> Comes from a GET request from dashboard cases
-            query_field, query_value = name_query.split(":", 1)
-            set_case_item_query(
-                query=query, query_field=query_field.strip(), query_value=query_value.strip()
-            )
-        else:
-            # POST request form from more advanced case search from cases page
-            for query_field in [
-                "case",
-                "exact_pheno",
-                "exact_dia",
-                "synopsis",
-                "panel",
-                "status",
-                "tags",
-                "track",
-                "pheno_group",
-                "cohort",
-                "pinned",
-                "causative",
-                "user",
-                "similar_case",  # In order to be able to sort results by phenotype similarity, keep this at the bottom
-                "similar_pheno",  # In order to be able to sort results by phenotype similarity, keep this at the bottom
-            ]:
-                query_value = name_query.get(query_field)
-                if query_value not in ["", None]:
-                    set_case_item_query(
-                        query=query, query_field=query_field, query_value=query_value.strip()
-                    )
+        # POST request form from more advanced case search from cases page
+        for query_field in [
+            "case",
+            "exact_pheno",
+            "exact_dia",
+            "synopsis",
+            "panel",
+            "status",
+            "tags",
+            "track",
+            "pheno_group",
+            "cohort",
+            "pinned",
+            "causative",
+            "user",
+            "similar_case",  # In order to be able to sort results by phenotype similarity, keep this at the bottom
+            "similar_pheno",  # In order to be able to sort results by phenotype similarity, keep this at the bottom
+        ]:
+            query_value = name_query.get(query_field)
+            if query_value not in ["", None]:
+                set_case_item_query(
+                    query=query, query_field=query_field, query_value=query_value.strip()
+                )
 
     def _update_case_id_query(self, query, id_list):
         """Update a case query ["_id"]["$in"] values using an additional list of case _ids
@@ -371,7 +364,7 @@ class CaseHandler(object):
         group: Optional[ObjectId] = None,
         pinned: bool = False,
         cohort: bool = False,
-        name_query: Optional[str] = None,
+        name_query: Optional[ImmutableMultiDict] = None,
         yield_query: bool = False,
         within_days: Optional[int] = None,
         assignee: Optional[str] = None,
@@ -564,13 +557,9 @@ class CaseHandler(object):
 
         return self.case_collection.find(query, projection).sort("updated_at", -1)
 
-    def is_pheno_similarity_query(self, name_query: Union[str, ImmutableMultiDict]) -> bool:
+    def is_pheno_similarity_query(self, name_query: ImmutableMultiDict) -> bool:
         """Return True if the user query contains 'similar_case' or 'similar_pheno' fields."""
         similar_pheno_keys = ["similar_case", "similar_pheno"]
-
-        if isinstance(name_query, str):
-            return any(key in name_query for key in similar_pheno_keys)
-
         return any(name_query.get(key) not in [None, ""] for key in similar_pheno_keys)
 
     def rna_cases(self, owner):

{scout-browser-4.90.1 → scout-browser-4.91}/scout/commands/export/variant.py

@@ -191,7 +191,7 @@ def get_vcf_entry(variant_obj, case_id=None):
     Returns:
         variant_string(str): string representing variant in vcf format
     """
-    if variant_obj["category"] == "snv":
+    if variant_obj["category"] in ["snv", "cancer"]:
         var_type = "TYPE"
     else:
         var_type = "SVTYPE"
@@ -203,14 +203,24 @@ def get_vcf_entry(variant_obj, case_id=None):
         ]
     )
 
+    reference = variant_obj["reference"]
+    if reference in [".", ""]:
+        reference = "N"
+
+    alternative = variant_obj["alternative"]
+    if alternative in ["", ".", "-", variant_obj["sub_category"]]:
+        alternative = "N"
+        if variant_obj["category"] == "sv":
+            alternative = f"<{variant_obj['sub_category'].upper()}>"
+
     variant_string = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}".format(
         variant_obj["chromosome"],
         variant_obj["position"],
         variant_obj.get("dbsnp_id", "."),
-        variant_obj["reference"],
-        variant_obj["alternative"],
+        reference,
+        alternative,
         variant_obj.get("quality", "."),
-        ";".join(variant_obj.get("filters", [])),
+        ";".join(variant_obj.get("filters", [])) or ".",
         info_field,
     )
 

{scout-browser-4.90.1 → scout-browser-4.91}/scout/commands/load/panel.py

@@ -5,7 +5,8 @@ import logging
 import click
 from flask.cli import current_app, with_appcontext
 
-from scout.load.panel import load_omim_panel, load_panel, load_panelapp_panel
+from scout.load.panel import load_omim_panel, load_panel
+from scout.load.panelapp import load_panelapp_panel
 from scout.server.extensions import store
 
 LOG = logging.getLogger(__name__)

{scout-browser-4.90.1 → scout-browser-4.91}/scout/commands/update/panelapp.py

@@ -5,7 +5,7 @@ import logging
 import click
 from flask.cli import current_app, with_appcontext
 
-from scout.load.panel import load_panelapp_green_panel
+from scout.load.panelapp import load_panelapp_green_panel
 from scout.server.extensions import store
 
 LOG = logging.getLogger(__name__)
@@ -19,6 +19,12 @@ LOG = logging.getLogger(__name__)
     default="cust002",
     show_default=True,
 )
+@click.option(
+    "-s",
+    "--signed-off",
+    is_flag=True,
+    help="Collect genes from signed-off panels only",
+)
 @click.option(
     "-f",
     "--force",
@@ -26,7 +32,7 @@ LOG = logging.getLogger(__name__)
     help="Force update even if updated panel contains less genes",
 )
 @with_appcontext
-def panelapp_green(institute, force):
+def panelapp_green(institute, force, signed_off):
     """
     Update the automatically generated PanelApp Green Genes panel in the database.
     """
@@ -40,7 +46,9 @@ def panelapp_green(institute, force):
         raise click.Abort()
 
     try:
-        load_panelapp_green_panel(adapter=store, institute=institute, force=force)
+        load_panelapp_green_panel(
+            adapter=store, institute=institute, force=force, signed_off=signed_off
+        )
     except Exception as err:
         LOG.error(err)
         raise click.Abort()

{scout-browser-4.90.1 → scout-browser-4.91}/scout/commands/view/case.py

@@ -1,8 +1,8 @@
 import logging
-from pprint import pprint as pp
 
 import click
 from flask.cli import with_appcontext
+from werkzeug.datastructures import ImmutableMultiDict
 
 from scout.server.extensions import store
 
@@ -52,7 +52,7 @@ def cases(institute, display_name, case_id, nr_variants, variants_treshold, simi
 
     else:
         if display_name:
-            name_query = f"case:{display_name}"
+            name_query = ImmutableMultiDict({"case": display_name})
         models = adapter.cases(collaborator=institute, name_query=name_query)
         models = [case_obj for case_obj in models]
 

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/__init__.py

@@ -12,7 +12,6 @@ from .case_tags import (
     ANALYSIS_TYPES,
     CANCER_PHENOTYPE_MAP,
     CASE_REPORT_VARIANT_TYPES,
-    CASE_SEARCH_TERMS,
     CASE_STATUSES,
     CASE_TAGS,
     CUSTOM_CASE_REPORTS,
@@ -62,11 +61,11 @@ from .gene_tags import (
     MODELS_MAP,
     PANEL_GENE_INFO_MODELS,
     PANEL_GENE_INFO_TRANSCRIPTS,
-    PANELAPP_CONFIDENCE_EXCLUDE,
     UPDATE_GENES_RESOURCES,
 )
 from .igv_tracks import CASE_SPECIFIC_TRACKS, HUMAN_REFERENCE, IGV_TRACKS, USER_DEFAULT_TRACKS
 from .indexes import ID_PROJECTION, INDEXES
+from .panels import PANELAPP_CONFIDENCE_EXCLUDE
 from .phenotype import (
     COHORT_TAGS,
     HPO_URL,

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/acmg.py

@@ -47,7 +47,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Null variant",
                             "description": "Null variant (nonsense, frameshift, canonical +/- 2 bp splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease.",
-                            "documentation": 'Strength can be modified based on <a href="https://pubmed.ncbi.nlm.nih.gov/30192042/" target="_blank">Tayoun et al</a> and <a href="http://autopvs1.genetics.bgi.com/" target="_blank">AutoPVS1</a>, or for RNA <a href="https://www.clinicalgenome.org/docs/application-of-the-acmg-amp-framework-to-capture-evidence-relevant-to-predicted-and-observed-impact-on-splicing-recommendations/" target="_blank">Walker et al</a>.',
+                            "documentation": 'Strength can be modified based on <a href="https://pubmed.ncbi.nlm.nih.gov/30192042/" rel="noopener noreferrer" target="_blank">Tayoun et al</a> and <a href="http://autopvs1.genetics.bgi.com/" rel="noopener noreferrer" target="_blank">AutoPVS1</a>, or for RNA <a href="https://www.clinicalgenome.org/docs/application-of-the-acmg-amp-framework-to-capture-evidence-relevant-to-predicted-and-observed-impact-on-splicing-recommendations/" target="_blank">Walker et al</a>.',
                         },
                     )
                 ]
@@ -69,7 +69,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "<i>De novo</i> (confirmed)",
                             "description": "De novo (both maternity and paternity confirmed) in a patient with the disease and no family history",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/site/assets/files/3461/svi_proposal_for_de_novo_criteria_v1_1.pdf" target="_blank">SVI <i>de novo</i></a>.',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/site/assets/files/3461/svi_proposal_for_de_novo_criteria_v1_1.pdf" rel="noopener noreferrer" target="_blank">SVI <i>de novo</i></a>.',
                         },
                     ),
                     (
@@ -77,7 +77,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Functional damage",
                             "description": "Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product, and the evidence is strong",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/recommendations-for-application-of-the-functional-evidence-ps3-bs3-criterion-using-the-acmg-amp-sequence-variant-interpretation/" target="_blank">Brnich 2019</a>.',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/recommendations-for-application-of-the-functional-evidence-ps3-bs3-criterion-using-the-acmg-amp-sequence-variant-interpretation/" rel="noopener noreferrer" target="_blank">Brnich 2019</a>.',
                         },
                     ),
                     (
@@ -85,7 +85,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "In >=4 unrelated patients, not controls",
                             "description": "The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls; 4 or more unrelated patients",
-                            "documentation": '<a href="https://www.acgs.uk.com/media/11631/uk-practice-guidelines-for-variant-classification-v4-01-2020.pdf" target="_blank">ACGS (Ellard et al 2020)</a> suggest <a href="https://www.medcalc.org/calc/odds_ratio.php" target="_blank">Odds ratio calculator</a>, '
+                            "documentation": '<a href="https://www.acgs.uk.com/media/11631/uk-practice-guidelines-for-variant-classification-v4-01-2020.pdf" rel="noopener noreferrer" target="_blank">ACGS (Ellard et al 2020)</a> suggest <a href="https://www.medcalc.org/calc/odds_ratio.php" target="_blank">Odds ratio calculator</a>, '
                             "and application with strength modification for fewer unrelated affected individuals or gnomAD controls.",
                         },
                     ),
@@ -108,7 +108,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Not in matched controls",
                             "description": "Absent from controls (or at extremely low frequency if recessive), in ethnically matched population",
-                            "documentation": 'Apply only if variant is expected to be detected in large population datasets - see e.g. <a href="https://pubmed.ncbi.nlm.nih.gov/31479589/" target="_blank">Harrison et al 2019</a>.',
+                            "documentation": 'Apply only if variant is expected to be detected in large population datasets - see e.g. <a href="https://pubmed.ncbi.nlm.nih.gov/31479589/" rel="noopener noreferrer" target="_blank">Harrison et al 2019</a>.',
                         },
                     ),
                     (
@@ -116,7 +116,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "In trans pathogenic & AR",
                             "description": "For recessive disorders, detected in trans with a pathogenic variant",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf" target="_blank">SVI in <i>trans</i></a>.',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf" rel="noopener noreferrer" target="_blank">SVI in <i>trans</i></a>.',
                         },
                     ),
                     (
@@ -138,7 +138,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "<i>De novo</i> (unconfirmed)",
                             "description": "Assumed de novo, but without confirmation of paternity and maternity",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/site/assets/files/3461/svi_proposal_for_de_novo_criteria_v1_1.pdf" target="_blank">SVI <i>de novo</i></a>.',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/site/assets/files/3461/svi_proposal_for_de_novo_criteria_v1_1.pdf" rel="noopener noreferrer" target="_blank">SVI <i>de novo</i></a>.',
                         },
                     ),
                 ]
@@ -153,7 +153,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Cosegregation",
                             "description": "Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease, and the evidence is weak",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/clingen-guidance-for-use-of-the-pp1-bs4-co-segregation-and-pp4-phenotype-specificity-criteria-for-sequence-variant/" target="_blank">Biesecker et al 2023</a>',
+                            "documentation": 'Strength can be modified <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4908147/" target="_blank" rel="noopener noreferrer">Jarvik 2016</a>, <a href="https://clinicalgenome.org/docs/clingen-guidance-for-use-of-the-pp1-bs4-co-segregation-and-pp4-phenotype-specificity-criteria-for-sequence-variant/" rel="noopener noreferrer" target="_blank">Biesecker et al 2023</a>',
                         },
                     ),
                     (
@@ -168,7 +168,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Predicted pathogenic",
                             "description": "Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc)",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/calibration-of-computational-tools-for-missense-variant-pathogenicity-classification-and-clingen-recommendations-for-pp3-bp4-cri/" target="_blank">Pejaver et al</a>',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/calibration-of-computational-tools-for-missense-variant-pathogenicity-classification-and-clingen-recommendations-for-pp3-bp4-cri/" rel="noopener noreferrer" target="_blank">Pejaver et al</a>',
                         },
                     ),
                     (
@@ -176,7 +176,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Phenotype: single gene",
                             "description": "Patient's phenotype or family history is highly specific for a disease with a single genetic etiology",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/clingen-guidance-for-use-of-the-pp1-bs4-co-segregation-and-pp4-phenotype-specificity-criteria-for-sequence-variant/" target="_blank">Biesecker et al 2023</a>',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/clingen-guidance-for-use-of-the-pp1-bs4-co-segregation-and-pp4-phenotype-specificity-criteria-for-sequence-variant/" target="_blank" rel="noopener noreferrer">Biesecker et al 2023</a>',
                         },
                     ),
                     (
@@ -184,7 +184,7 @@ ACMG_CRITERIA["pathogenicity"] = OrderedDict(
                         {
                             "short": "Reported pathogenic, evidence unavailable",
                             "description": "Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation",
-                            "documentation": 'Deprecated by ClinGen SVI <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709533/" target="_blank">Biesecker et al 2018</a>.',
+                            "documentation": 'Deprecated by ClinGen SVI <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709533/" target="_blank" rel="noopener noreferrer">Biesecker et al 2018</a>.',
                         },
                     ),
                 ]
@@ -204,7 +204,7 @@ ACMG_CRITERIA["benign impact"] = OrderedDict(
                         {
                             "short": "Frequency >=0.05",
                             "description": "Allele frequency is >=0.05 in a general continental population dataset",
-                            "documentation": 'For clarification and exceptions see <a href="https://clinicalgenome.org/docs/updated-recommendation-for-the-benign-stand-alone-acmg-amp-criterion/" target="_blank">Ghosh et al</a>',
+                            "documentation": 'For clarification and exceptions see <a href="https://clinicalgenome.org/docs/updated-recommendation-for-the-benign-stand-alone-acmg-amp-criterion/" target="_blank" rel="noopener noreferrer">Ghosh et al</a>',
                         },
                     )
                 ]
@@ -233,7 +233,7 @@ ACMG_CRITERIA["benign impact"] = OrderedDict(
                         {
                             "short": "No functional damage",
                             "description": "Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing, and the evidence is strong",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/recommendations-for-application-of-the-functional-evidence-ps3-bs3-criterion-using-the-acmg-amp-sequence-variant-interpretation/" target="_blank">Brnich 2019</a>.',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/recommendations-for-application-of-the-functional-evidence-ps3-bs3-criterion-using-the-acmg-amp-sequence-variant-interpretation/" rel="noopener noreferrer" target="_blank">Brnich 2019</a>.',
                         },
                     ),
                     (
@@ -241,7 +241,7 @@ ACMG_CRITERIA["benign impact"] = OrderedDict(
                         {
                             "short": "Non-segregation",
                             "description": "Lack of segregation in affected members of a family, and the evidence is strong",
-                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/clingen-guidance-for-use-of-the-pp1-bs4-co-segregation-and-pp4-phenotype-specificity-criteria-for-sequence-variant/" target="_blank">Biesecker et al 2023</a>',
+                            "documentation": 'Strength can be modified based on <a href="https://clinicalgenome.org/docs/clingen-guidance-for-use-of-the-pp1-bs4-co-segregation-and-pp4-phenotype-specificity-criteria-for-sequence-variant/" target="_blank" rel="noopener noreferrer">Biesecker et al 2023</a>',
                         },
                     ),
                 ]
@@ -291,7 +291,7 @@ ACMG_CRITERIA["benign impact"] = OrderedDict(
                         {
                             "short": "Reported benign, evidence unavailable",
                             "description": "Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation",
-                            "documentation": 'Deprecated by ClinGen SVI <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709533/" target="_blank">Biesecker et al</a>.',
+                            "documentation": 'Deprecated by ClinGen SVI <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709533/" rel="noopener noreferrer" target="_blank">Biesecker et al</a>.',
                         },
                     ),
                     (

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/case_tags.py

@@ -245,49 +245,3 @@ SOURCES = [
 ]
 
 SAMPLE_SOURCE = dict((i, el) for i, el in enumerate(SOURCES))
-
-CASE_SEARCH_TERMS = {
-    "case": {"label": "Case or Individual Name", "prefix": "case:", "placeholder": "example:18201"},
-    "exact_pheno": {
-        "label": "HPO Terms",
-        "prefix": "exact_pheno:",
-        "placeholder": "example:HP:0001166,HP:0001250,...",
-    },
-    "exact_dia": {
-        "label": "OMIM Terms",
-        "prefix": "exact_dia:",
-        "placeholder": "example:OMIM:616538,OMIM:607681,...",
-    },
-    "synopsis": {
-        "label": "Search Synopsis",
-        "prefix": "synopsis:",
-        "placeholder": "example:epilepsy",
-    },
-    "panel": {"label": "Gene Panel", "prefix": "panel:", "placeholder": "example:NMD"},
-    "status": {"label": "Case Status", "prefix": "status:", "placeholder": "example:active"},
-    "tags": {"label": "Tags", "prefix": "tags:", "placeholder": "example:medical"},
-    "track": {"label": "Analysis Track", "prefix": "track:", "placeholder": "rare or cancer"},
-    "pheno_group": {
-        "label": "Phenotype Group",
-        "prefix": "pheno_group:",
-        "placeholder": "example:HP:0001166",
-    },
-    "cohort": {"label": "Patient Cohort", "prefix": "cohort:", "placeholder": "example:pedhep"},
-    "similar_case": {
-        "label": "Similar Case",
-        "prefix": "similar_case:",
-        "placeholder": "example:18201",
-    },
-    "similar_pheno": {
-        "label": "Similar Phenotype",
-        "prefix": "similar_pheno:",
-        "placeholder": "example:HP:0001166,HP:0001250,..",
-    },
-    "pinned": {"label": "Pinned Gene", "prefix": "pinned:", "placeholder": "example:POT1"},
-    "causative": {"label": "Causative Gene", "prefix": "causative:", "placeholder": "example:POT1"},
-    "user": {
-        "label": "Assigned User",
-        "prefix": "user:",
-        "placeholder": "example:John Doe",
-    },
-}

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/clnsig.py

@@ -7,7 +7,7 @@ CLINSIG_MAP = {
     5: "Pathogenic",
     6: "drug response",
     7: "histocompatibility",
-    8: "Conflicting interpretations of pathogenicity",
+    8: "Conflicting classifications of pathogenicity",
     9: "affects",
     10: "association",
     11: "protective",
@@ -30,6 +30,7 @@ REV_CLINSIG_MAP = {
     "likely_benign": 3,
     "conflicting_interpretations_of_pathogenicity": 8,
     "conflicting_interpretations": 8,
+    "conflicting_classifications_of_pathogenicity": 8,
     "uncertain_significance": 0,
     "likely_pathogenic": 4,
     "pathogenic": 5,

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/gene_tags.py

@@ -84,12 +84,6 @@ UPDATE_GENES_RESOURCES = {
     ],
 }
 
-PANELAPP_CONFIDENCE_EXCLUDE = {
-    "green": ["ModerateEvidence", "LowEvidence"],
-    "amber": ["LowEvidence"],
-    "red": [],
-}
-
 GNOMAD_CONSTRAINT_FILENAME = "gnomad.v4.0.constraint_metrics.tsv"
 
 GENE_CONSTRAINT_LABELS = {

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/panels.py

@@ -9,3 +9,19 @@ EXPORT_PANEL_FIELDS = [
     ("custom_inheritance_models", "custom_inheritance_models"),
     ("comment", "comment"),
 ]
+
+PANELAPP_CONFIDENCE_EXCLUDE = {
+    "green": ["0", "1", "2"],
+    "amber": ["0", "1"],
+    "red": ["0"],
+}
+
+PRESELECTED_PANELAPP_PANEL_TYPE_SLUGS = [
+    "cancer-germline-100k",
+    "clingen-curated-genes",
+    "gms-cancer-germline-virtual",
+    "gms-rare-disease",
+    "gms-rare-disease-virtual",
+    "gms-signed-off",
+    "rare-disease-100k",
+]

{scout-browser-4.90.1 → scout-browser-4.91}/scout/constants/variants_export.py

@@ -1,5 +1,7 @@
 EXPORT_HEADER = [
     "Rank_score",
+    "Type",
+    "Callers",
     "Chromosome",
     "Position",
     "Change",

{scout-browser-4.90.1 → scout-browser-4.91}/scout/demo/__init__.py

@@ -5,7 +5,10 @@ BASE_PATH = "scout.demo"
 ###### Paths ######
 # Panel paths
 panel_path = str(files(BASE_PATH).joinpath("panel_1.txt"))
-panelapp_panel_path = str(files(BASE_PATH).joinpath("panelapp_test_panel.json"))
+
+# PanelApp json files
+panelapp_panels_reduced_path = str(files(BASE_PATH).joinpath("panelapp_panels_reduced.json"))
+panelapp_panel_path = str(files(BASE_PATH).joinpath("panelapp_panel.json"))
 
 # Case paths
 ped_path = str(files(BASE_PATH).joinpath("643594.ped"))