scout-browser 4.83__tar.gz → 4.85__tar.gz

{scout-browser-4.83 → scout-browser-4.85}/CHANGELOG.md

@@ -4,6 +4,31 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.85]
+### Added
+- Load also genes which are missing Ensembl gene ID (72 in both builds), including immunoglobulins and fragile sites
+### Changed
+- Unfreeze werkzeug again
+- Show "(Removed)" after removed panels in dropdown
+- The REVEL score is collected as the maximum REVEL score from all of the variant's transcripts
+- Parse GNOMAD POPMAX values only if they are numerical when loading variants
+### Fixed
+- Alphabetically sort "select default panels" dropdown menu options on case page
+- Show gene panel removed status on case page
+- Fixed visibility of the following buttons: remove assignee, remove pinned/causative, remove comment, remove case from group
+
+## [4.84]
+### Changed
+- Clearer error message when a loqusdb query fails for an instance that initially connected
+- Do not load chanjo-report module if not needed and more visible message when it fails loading
+- Converted the HgncGene class into a Pydantic class
+- Swap menu open and collapse indicator chevrons - down is now displayed-open, right hidden-closed
+- Linters and actions now all use python 3.11
+### Fixed
+- Safer way to update variant genes and compounds that avoids saving temporary decorators into variants' database documents
+- Link to HGNC gene report on gene page
+- Case file load priority so that e.g. SNV get loaded before SV, or clinical before research, for consistent variant_id collisions
+
 ## [4.83]
 ### Added
 - Edit ACMG classifications from variant page (only for classifications with criteria)

scout-browser-4.85/PKG-INFO

@@ -0,0 +1,300 @@
+Metadata-Version: 2.1
+Name: scout-browser
+Version: 4.85
+Summary: Clinical DNA variant visualizer and browser.
+Home-page: https://github.com/Clinical-Genomics/scout
+Author: Måns Magnusson
+Author-email: mans.magnusson@scilifelab.se
+Classifier: Environment :: Web Environment
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Programming Language :: Python :: 3.6
+Description-Content-Type: text/markdown
+Provides-Extra: coverage
+License-File: LICENSE
+
+
+<p align="center">
+	<a href="https://Clinical-Genomics.github.io/scout/">
+		<img height="165" width="637" src="artwork/logo-display.png">
+	</a>
+	<h3 align="center">Analyze VCFs and collaborate on solving rare diseases quicker</h3>
+</p>
+
+![Build Status - GitHub][actions-build-status]
+[![PyPI Version][pypi-img]][pypi-url]
+![GitHub Release Date][github-release-date]
+[![GitHub commits latest](https://img.shields.io/github/commits-since/Clinical-Genomics/scout/latest)](https://GitHub.com/Clinical-Genomics/scout/commit/)
+[![GitHub commit rate](https://img.shields.io/github/commit-activity/w/Clinical-Genomics/scout)](https://GitHub.com/Clinical-Genomics/scout/pulse/)
+[![GitHub commits](https://img.shields.io/github/commits-since/Clinical-Genomics/scout/v4.0.0.svg)](https://GitHub.com/Clinical-Genomics/scout/commit/)
+[![GitHub issues-closed][closed-issues-img]][closed-issues-url]
+[![Average time to resolve an issue][ismaintained-resolve-img]][ismaintained-resolve-url]
+[![Percentage of issues still open][ismaintained-open-rate-img]][ismaintained-open-rate-url]
+[![Coverage Status][codecov-img]][codecov-url]
+[![CodeFactor](https://www.codefactor.io/repository/github/clinical-genomics/scout/badge)](https://www.codefactor.io/repository/github/clinical-genomics/scout)
+[![Code style: black][black-image]][black-url]
+[![Woke][woke-image]][woke-url]
+
+
+## What is Scout?
+
+- **Simple** - Analyze variants in a simple to use web interface.
+- **Aggregation** - Combine results from multiple analyses and VCFs into a centralized database.
+- **Collaboration** - Write comments and share cases between users and institutes.
+
+## Documentation
+
+This README only gives a brief overview of Scout, for a more complete reference, please check out our docs: https://clinical-genomics.github.io/scout .
+
+## Runnable demo image - does not require installing of software and database
+
+A simple demo instance of Scout requires the installation of Docker and can be launched either by using the command:
+`docker-compose up -d` or `make up`.
+
+The repository includes a Makefile with common shortcuts to simplify setting up and working with Scout. To see a full list and description of these shortcuts run: `make help`.
+
+This demo is consisting of 3 containers:
+- a MongoDB instance, on the default port 27017 in the container, mapped to host port 27013
+- scout-cli --> the Scout command line, connected to the database. Populates the database with demo data
+- scout-web --> the Scout web app, that serves the app on localhost, port 8000.
+
+Once the server has started you and open the app in the web browser at the following address: http://localhost:8000/
+
+The command to stop the demo are either `docker-compose down` or `make down`.
+
+Instructions on how to run a Scout image connected to your local database or a custom database are present [on this page](docs/admin-guide/containers/container-deploy.md).
+
+## Installation
+
+<!-- You can install the latest release of Scout using `pip`:
+
+```bash
+pip install scout-browser
+
+# ... to include optional coverage tools you would use:
+pip install scout-browser[coverage]
+```
+
+If you would like to install Scout for local development: -->
+
+```bash
+git clone https://github.com/Clinical-Genomics/scout
+cd scout
+pip install --editable .
+```
+
+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/).
+
+You also need to have an instance of MongoDB running. I've found that it's easiest to do using the official Docker image:
+
+```bash
+docker run --name mongo -p 27017:27017 mongo
+```
+
+## Usage
+
+### Demo - requires pip-installing the app in a container and a running instance of mongodb
+
+Once installed, you can setup Scout by running a few commands using the included command line interface. Given you have a MongoDB server listening on the default port (27017), this is how you would setup a fully working Scout demo:
+
+```bash
+scout setup demo
+```
+
+This will setup an instance of scout with a database called `scout-demo`. Now run
+
+```bash
+scout --demo serve
+```
+And play around with the interface. A user has been created with email clark.kent@mail.com so use that address to get access
+
+### Initialize scout
+
+To initialize a working instance with all genes, diseases etc run
+
+```bash
+scout setup database
+```
+
+for more info, run `scout --help`
+
+The previous command initializes the database with a curated collection of gene definitions with links to OMIM along with HPO phenotype terms. Now we will load some example data. Scout expects the analysis to be accomplished using various gene panels so let's load one and then our first analysis case:
+
+```bash
+scout load panel scout/demo/panel_1.txt
+scout load case scout/demo/643594.config.yaml
+```
+
+## Integration with chanjo and chanjo2 for coverage report visualization
+
+Scout may be configured to visualize coverage reports produced by [Chanjo][chanjo] or [chanjo2][chanjo2]. Instructions on
+how to enable this feature can be found in the document [chanjo_coverage_integration][chanjo-scout].
+
+## Integration with loqusdb for integrating local variant frequencies
+
+Scout may be configured to visualize local variant frequencies monitored by [Loqusdb][loqusdb].
+Instructions on how to enable this feature can be found in the document
+[loqusdb integration][loqusdb-scout].
+
+## Integration with Gens for displaying copy number profiles for variants
+
+Scout may be configured to link to a local [Gens][gens] installation.
+Instructions on how to enable this feature can be found in the document
+[Gens integration][gens-scout].
+
+## Server setup
+
+Scout needs a server config to know which databases to connect to etc. Depending on which
+information you provide you activate different parts of the interface automatically,
+including user authentication, coverage, and local observations.
+
+This is an example of the config file:
+
+```python
+# scoutconfig.py
+
+# list of email addresses to send errors to in production
+ADMINS = ['paul.anderson@magnolia.com']
+
+MONGO_HOST = 'localhost'
+MONGO_PORT = 27017
+MONGO_DBNAME = 'scout'
+MONGO_USERNAME = 'testUser'
+MONGO_PASSWORD = 'testPass'
+
+# enable user authentication using Google OAuth 2.0
+GOOGLE = dict(
+   client_id="client_id_string.apps.googleusercontent.com",
+   client_secret="client_secret_string",
+   discovery_url="https://accounts.google.com/.well-known/openid-configuration"
+)
+
+# enable Phenomizer gene predictions from phenotype terms
+PHENOMIZER_USERNAME = '???'
+PHENOMIZER_PASSWORD = '???'
+
+# enable Chanjo coverage integration
+SQLALCHEMY_DATABASE_URI = '???'
+REPORT_LANGUAGE = 'en'  # or 'sv'
+
+# other interesting settings
+SQLALCHEMY_TRACK_MODIFICATIONS = False  # this is essential in production
+TEMPLATES_AUTO_RELOAD = False  			# consider turning off in production
+SECRET_KEY = 'secret key'               # override in production!
+```
+
+Most of the config settings are optional. A minimal config would consist of SECRET_KEY and MONGO_DBNAME.
+
+Starting the server in now really easy, for the demo and local development we will use the CLI:
+
+```bash
+scout --flask-config config.py serve
+```
+
+![Scout Interface demo](artwork/scout-variant-demo.png)
+
+### Hosting a production server
+
+When running the server in production you will likely want to use a proper Python server solution
+such as Gunicorn.
+This is also how we can multiprocess the server and use encrypted HTTPS connections.
+
+```bash
+SCOUT_CONFIG=./config.py gunicorn --workers 4 --bind 0.0.0.0:8080 scout.server.auto:app
+```
+
+For added security and flexibility, we recommend a reverse proxy solution like NGINX.
+
+### Setting up a user login system
+Scout currently supports 3 mutually exclusive types of login:
+- Google authentication via OpenID Connect (OAuth 2.0)
+- LDAP authentication
+- Simple authentication using userid and password
+
+The first 2 solutions are both suitable for a production server. A description on how to set up an advanced login system is available in the [admin guide](docs/admin-guide/login-system.md)
+
+
+### Integration with Matchmaker Exchange
+
+Starting from release 4.4, Scout offers integration for patient data sharing via Matchmaker
+Exchange.
+General info about Matchmaker and patient matching could be found in [this paper][matchmaker-pub].
+For a technical guideline of our implementation of Matchmaker Exchange at Clinical Genomics and its
+integration with Scout check scouts [matchmaker docs][matchmaker-scout].
+A user-oriented guide describing how to share case and variant data to Matchmaker using Scout can
+be found [here][matchmaker-scout-sharing].
+
+
+## Development
+
+To keep the code base consistent, formatting with [Black](https://github.com/psf/black) is always applied as part of the PR submission process via GitHub Actions. While not strictly required, to avoid confusion, it is suggested that developers apply Black locally.
+Black defaults to 88 characters per line, we use 100.
+
+To format all the files in the project run:
+
+```bash
+black --line-length 100 .
+```
+
+We recommend using Black with [pre-commit](https://github.com/pre-commit/pre-commit).
+In `.pre-commit-config.yaml` you can find the pre-commit configuration.
+To enable this configuration run:
+
+```bash
+pre-commit install
+```
+
+### Test
+
+To run unit tests:
+
+```bash
+pytest
+```
+
+
+### Contributing to Scout
+
+If you want to contribute and make Scout better, you help is very appreciated! Bug reports or
+feature requests are really helpful and can be submitted via github issues.
+Feel free to open a pull request to add a new functionality or fixing a bug, we welcome any help,
+regardless of the amount of code provided or your skills as a programmer.
+More info on how to contribute to the project and a description of the Scout branching workflow can
+be found in [CONTRIBUTING](CONTRIBUTING.md).
+
+
+
+[chanjo]: https://github.com/Clinical-Genomics/chanjo
+[chanjo2]: https://github.com/Clinical-Genomics/chanjo2
+[chanjo-scout]: docs/admin-guide/chanjo_coverage_integration.md
+[loqusdb]: https://github.com/moonso/loqusdb
+[loqusdb-scout]: docs/admin-guide/loqusdb_integration.md
+[gens]: https://github.com/Clinical-Genomics-Lund/gens
+[gens-scout]: docs/admin-guide/gens_integration.md
+[github-release-date]: https://img.shields.io/github/release-date/Clinical-Genomics/scout
+[matchmaker-pub]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016856/
+[matchmaker-scout]: docs/admin-guide/matchmaker_exchange_integration.md
+[matchmaker-scout-sharing]: docs/user-guide/cases.md#matchmaker-exchange-integration
+[travis-img]: https://img.shields.io/travis/Clinical-Genomics/scout/develop.svg?style=flat-square
+[travis-url]: https://travis-ci.org/Clinical-Genomics/scout
+[pypi-img]: https://img.shields.io/pypi/v/scout-browser.svg?style=flat-square
+[pypi-url]: https://pypi.python.org/pypi/scout-browser/
+[ismaintained-resolve-img]: http://isitmaintained.com/badge/resolution/Clinical-Genomics/scout.svg
+[ismaintained-resolve-url]: http://isitmaintained.com/project/Clinical-Genomics/scout
+[ismaintained-open-rate-img]: http://isitmaintained.com/badge/open/Clinical-Genomics/scout.svg
+[ismaintained-open-rate-url]: http://isitmaintained.com/project/Clinical-Genomics/scout
+[closed-issues-img]: https://img.shields.io/github/issues-closed/Clinical-Genomics/scout.svg
+[closed-issues-url]: https://GitHub.com/Clinical-Genomics/scout/issues?q=is%3Aissue+is%3Aclosed
+[codecov-img]: https://codecov.io/gh/Clinical-Genomics/scout/branch/main/graph/badge.svg?token=BOhMTZ4T3c
+[codecov-url]: https://codecov.io/gh/Clinical-Genomics/scout
+[actions-build-status]: https://github.com/Clinical-Genomics/scout/actions/workflows/build_and_publish.yml/badge.svg
+[black-image]: https://img.shields.io/badge/code%20style-black-000000.svg
+[black-url]: https://github.com/psf/black
+[woke-image]: https://github.com/Clinical-Genomics/scout/actions/workflows/woke.yml/badge.svg
+[woke-url]: https://github.com/Clinical-Genomics/scout/actions/workflows/woke.yml

{scout-browser-4.83 → scout-browser-4.85}/requirements.txt

@@ -1,5 +1,5 @@
 # Everything needed in production
-werkzeug<3
+werkzeug
 Flask>=2.0
 Flask-Bootstrap
 Flask-CORS

scout-browser-4.85/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.85"

{scout-browser-4.83 → scout-browser-4.85}/scout/adapter/mongo/case.py

@@ -14,6 +14,7 @@ from scout.constants import ACMG_MAP, FILE_TYPE_MAP, ID_PROJECTION
 from scout.exceptions import ConfigError, IntegrityError
 from scout.parse.variant.ids import parse_document_id
 from scout.utils.algorithms import ui_score
+from scout.utils.sort import get_load_priority
 
 LOG = logging.getLogger(__name__)
 
@@ -904,7 +905,10 @@ class CaseHandler(object):
                     continue
                 load_variants.add((vcf_file["variant_type"], vcf_file["category"]))
 
-            for variant_type, category in load_variants:
+            for variant_type, category in sorted(
+                load_variants,
+                key=lambda tup: get_load_priority(variant_type=tup[0], category=tup[1]),
+            ):
                 if update:
                     self.delete_variants(
                         case_id=case_obj["_id"],

{scout-browser-4.83 → scout-browser-4.85}/scout/adapter/mongo/cytoband.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import logging
+from typing import Dict
 
 import pymongo
 
@@ -20,6 +21,18 @@ class CytobandHandler(object):
         result = self.cytoband_collection.insert_many(cytobands)
         LOG.debug(f"Number of inserted documents:{len(result.inserted_ids)}")
 
+    def cytoband_to_coordinates(self, build: str) -> Dict[str, dict]:
+        """Returns a dictionary with cytoband name as key and its coordinates as value."""
+        cytobands = self.cytoband_collection.find({"build": build})
+        return {
+            "".join([cytoband["chrom"], cytoband["band"]]): {
+                "chromosome": cytoband["chrom"],
+                "start": int(cytoband["start"]),
+                "stop": int(cytoband["stop"]),
+            }
+            for cytoband in cytobands
+        }
+
     def cytoband_by_chrom(self, build="37"):
         """Returns a dictionary of cytobands with chromosomes as keys
 

{scout-browser-4.83 → scout-browser-4.85}/scout/adapter/mongo/hgnc.py

@@ -405,7 +405,7 @@ class GeneHandler(object):
             add_transcripts = True
 
         for gene_obj in self.all_genes(build=build, add_transcripts=add_transcripts):
-            ensg_id = gene_obj["ensembl_id"]
+            ensg_id = gene_obj.get("ensembl_id")
             hgnc_id = gene_obj["hgnc_id"]
             transcript_objs = gene_obj.get("ens_transcripts")
             if id_transcripts and transcript_objs:

{scout-browser-4.83 → scout-browser-4.85}/scout/adapter/mongo/variant.py

@@ -2,6 +2,7 @@
 # stdlib modules
 import logging
 import re
+from typing import Any
 
 # Third party modules
 import pymongo
@@ -221,6 +222,14 @@ class VariantHandler(VariantLoader):
         query = self.build_query(case_id, query=query, variant_ids=variant_ids, category=category)
         return self.variant_collection.count_documents(query)
 
+    def variant_update_field(self, variant_id: str, field_name: str, field_value: Any) -> dict:
+        """Updates the value of the given key(field_name) in the variant document in the database."""
+        return self.variant_collection.find_one_and_update(
+            {"_id": variant_id},
+            {"$set": {field_name: field_value}},
+            return_document=pymongo.ReturnDocument.AFTER,
+        )
+
     def variant(
         self,
         document_id=None,

{scout-browser-4.83 → scout-browser-4.85}/scout/adapter/mongo/variant_loader.py

@@ -27,6 +27,7 @@ from scout.parse.variant.headers import (
 from scout.parse.variant.ids import parse_simple_id
 from scout.parse.variant.managed_variant import parse_managed_variant_id
 from scout.parse.variant.rank_score import parse_rank_score
+from scout.utils.sort import get_load_priority
 
 LOG = logging.getLogger(__name__)
 
@@ -200,87 +201,88 @@ class VariantLoader(object):
         """
 
         case_id = case_obj["_id"]
-        # Possible categories 'snv', 'sv', 'str', 'cancer', 'cancer_sv':
-        categories = set()
-        # Possible variant types 'clinical', 'research':
-        variant_types = set()
-
-        for file_type in FILE_TYPE_MAP:
-            if case_obj.get("vcf_files", {}).get(file_type):
-                categories.add(FILE_TYPE_MAP[file_type]["category"])
-                variant_types.add(FILE_TYPE_MAP[file_type]["variant_type"])
+        # Possible categories 'snv', 'sv', 'str', 'cancer', 'cancer_sv'. Sort according to load order to ensure Cancer SNVs before
+        # Cancer SVs, in particular, and keep a consistent variant_id collision resolution order.
+        # Possible variant types are 'clinical', 'research'.
+        load_variants = {
+            (FILE_TYPE_MAP[file_type]["variant_type"], FILE_TYPE_MAP[file_type]["category"])
+            for file_type in FILE_TYPE_MAP
+            if case_obj.get("vcf_files", {}).get(file_type)
+        }
 
         coding_intervals = self.get_coding_intervals(build=build)
         # Loop over all intervals
         for chrom in CHROMOSOMES:
             intervals = coding_intervals.get(chrom, IntervalTree())
-            for var_type in variant_types:
-                for category in categories:
-                    LOG.info(
-                        "Updating compounds on chromosome:{0}, type:{1}, category:{2} for case:{3}".format(
-                            chrom, var_type, category, case_id
-                        )
+            for var_type, category in sorted(
+                list(load_variants),
+                key=lambda tup: get_load_priority(variant_type=tup[0], category=tup[1]),
+            ):
+                LOG.info(
+                    "Updating compounds on chromosome:{0}, type:{1}, category:{2} for case:{3}".format(
+                        chrom, var_type, category, case_id
                     )
+                )
+
+                # Fetch all variants from a chromosome
+                query = {"variant_type": var_type, "chrom": chrom}
+
+                # Get all variants from the database of the specific type
+                variant_objs = self.variants(
+                    case_id=case_id,
+                    query=query,
+                    category=category,
+                    nr_of_variants=-1,
+                    sort_key="position",
+                )
+
+                # Initiate a bulk
+                bulk = {}
+                current_region = None
+                special = False
 
-                    # Fetch all variants from a chromosome
-                    query = {"variant_type": var_type, "chrom": chrom}
+                # Loop over the variants and check if they are in a coding region
+                for var_obj in variant_objs:
+                    var_id = var_obj["_id"]
+                    var_chrom = var_obj["chromosome"]
+                    var_start = var_obj["position"]
+                    var_end = var_obj["end"] + 1
 
-                    # Get all variants from the database of the specific type
-                    variant_objs = self.variants(
-                        case_id=case_id,
-                        query=query,
-                        category=category,
-                        nr_of_variants=-1,
-                        sort_key="position",
+                    update_bulk = True
+                    new_region = None
+
+                    # Check if the variant is in a coding region
+                    genomic_regions = coding_intervals.get(var_chrom, IntervalTree()).overlap(
+                        var_start, var_end
                     )
 
-                    # Initiate a bulk
-                    bulk = {}
-                    current_region = None
-                    special = False
-
-                    # Loop over the variants and check if they are in a coding region
-                    for var_obj in variant_objs:
-                        var_id = var_obj["_id"]
-                        var_chrom = var_obj["chromosome"]
-                        var_start = var_obj["position"]
-                        var_end = var_obj["end"] + 1
-
-                        update_bulk = True
-                        new_region = None
-
-                        # Check if the variant is in a coding region
-                        genomic_regions = coding_intervals.get(var_chrom, IntervalTree()).overlap(
-                            var_start, var_end
-                        )
-
-                        # If the variant is in a coding region
-                        if genomic_regions:
-                            # We know there is data here so get the interval id
-                            new_region = genomic_regions.pop().data
-
-                        if new_region and (new_region == current_region):
-                            # If the variant is in the same region as previous
-                            # we add it to the same bulk
-                            update_bulk = False
-
-                        current_region = new_region
-
-                        # If the variant is not in a current region we update the compounds
-                        # from the previous region, if any. Otherwise continue
-                        if update_bulk and bulk:
-                            self.update_compounds(bulk)
-                            self.update_mongo_compound_variants(bulk)
-                            bulk = {}
-
-                        if new_region:
-                            bulk[var_id] = var_obj
-
-                    if not bulk:
-                        continue
-
-                    self.update_compounds(bulk)
-                    self.update_mongo_compound_variants(bulk)
+                    # If the variant is in a coding region
+                    if genomic_regions:
+                        # We know there is data here so get the interval id
+                        new_region = genomic_regions.pop().data
+
+                    if new_region and (new_region == current_region):
+                        # If the variant is in the same region as previous
+                        # we add it to the same bulk
+                        update_bulk = False
+
+                    current_region = new_region
+
+                    # If the variant is not in a current region we update the compounds
+                    # from the previous region, if any. Otherwise continue
+                    if update_bulk and bulk:
+                        self.update_compounds(bulk)
+                        self.update_mongo_compound_variants(bulk)
+                        bulk = {}
+
+                    if new_region:
+                        bulk[var_id] = var_obj
+
+                if not bulk:
+                    continue
+
+                self.update_compounds(bulk)
+                self.update_mongo_compound_variants(bulk)
 
         LOG.info("All compounds updated")
 

scout-browser-4.85/scout/build/genes/hgnc_gene.py

@@ -0,0 +1,23 @@
+import logging
+
+from scout.models.hgnc_map import HgncGene
+
+LOG = logging.getLogger(__name__)
+
+
+def build_phenotype(phenotype_info):
+    phenotype_obj = {}
+    phenotype_obj["mim_number"] = phenotype_info["mim_number"]
+    phenotype_obj["description"] = phenotype_info["description"]
+    phenotype_obj["inheritance_models"] = list(phenotype_info.get("inheritance", set()))
+    phenotype_obj["status"] = phenotype_info["status"]
+
+    return phenotype_obj
+
+
+def build_hgnc_gene(gene_info: dict, build: bool = "37") -> dict:
+    """Build a HGNC gene object"""
+
+    gene_info["build"] = build
+    hgnc_gene = HgncGene(**gene_info)
+    return hgnc_gene.model_dump(exclude_none=True)

{scout-browser-4.83 → scout-browser-4.85}/scout/commands/download/ensembl.py

@@ -1,4 +1,5 @@
 """Code for handling downloading of ensembl files used by scout from CLI"""
+
 import logging
 import pathlib
 from typing import List, Optional

{scout-browser-4.83 → scout-browser-4.85}/scout/commands/download/everything.py

@@ -1,6 +1,7 @@
 """Code for handling downloading Download all necessary resources for scout used by scout from
 CLI
 """
+
 import logging
 import pathlib
 

{scout-browser-4.83 → scout-browser-4.85}/scout/commands/download/exac.py

@@ -1,4 +1,5 @@
 """Code for handling downloading of the ExAC genes file used by scout from CLI"""
+
 import logging
 import pathlib
 

{scout-browser-4.83 → scout-browser-4.85}/scout/commands/download/hgnc.py

@@ -1,4 +1,5 @@
 """Code for handling downloading of HPO files used by scout from CLI"""
+
 import logging
 import pathlib
 

{scout-browser-4.83 → scout-browser-4.85}/scout/commands/download/hpo.py

@@ -1,4 +1,5 @@
 """Code for handling downloading of HPO files used by scout from CLI"""
+
 import logging
 import pathlib
 

{scout-browser-4.83 → scout-browser-4.85}/scout/commands/download/omim.py

@@ -1,4 +1,5 @@
 """Code for handling downloading of HPO files used by scout from CLI"""
+
 import logging
 from pathlib import Path
 from typing import Dict