scout-browser 4.97.0__tar.gz → 4.99.0__tar.gz

{scout_browser-4.97.0 → scout_browser-4.99.0}/CHANGELOG.md

@@ -4,6 +4,45 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.99]
+### Added
+- De novo assembly alignment file load and display (#5284)
+- Paraphase bam-let alignment file load and display (#5284)
+- Parsing and showing ClinVar somatic oncogenicity anontations, when available (#5304)
+- Gene overlapping variants (superset of compounds) for SVs (#5332)
+- Gene overlapping variants for MEIs (#5332)
+- Gene overlapping variants for cancer (and cancer_sv) (#5332)
+- Tests for the Google login functionality (#5335)
+- Support for login using Keycloak (#5337)
+- Documentation on Keycloak login system integration (#5342)
+- Integrity check for genes/transcripts/exons files downloaded from Ensembl (#5353)
+- Options for custom ID/display name for PanelApp Green updates (#5355)
+### Changed
+- Allow ACMG criteria strength modification to Very strong/Stand-alone (#5297)
+- Mocked the Ensembl liftover service in igv tracks tests (#5319)
+- Refactored the login function into smaller functions, handling respectively: user consent, LDAP login, Google login, database login and user validation (#5331)
+- Allow loading of mixed analysis type cases where some individuals are fully WTS and do not appear in DNA VCFs (#5327)
+- Documentation available in dark mode, and expanded installation instructions (#5343)
+### Fixed
+- Re-enable display of case and individual specific tracks (pre-computed coverage, UPD, zygosity) (#5300)
+- Disable 2-color mode in IGV.js by default, since it obscures variant proportion of reads. Can be manually enabled (#5311)
+- Institute settings reset (#5309)
+- Updated color scheme for variant assessment badges that were hard to see in light mode, notably Risk Factor (#5318)
+- Avoid page timeout by skipping HGVS validations in ClinVar multistep submission for non-MANE transcripts from variants in build 38 (#5302)
+- Sashimi view page displaying an error message when Ensembl REST API (LiftOver) is not available (#5322)
+- Refactored the liftover functionality to avoid using the old Ensembl REST API (#5326)
+- Downloading of Ensembl resources by fixing the URL to the schug server, pointing to the production instance instead of the staging one (#5348)
+- Missing MT genes from the IGV track (#5339)
+- Paraphase and de novo assembly tracks could mismatch alignment sample labels - refactor to case specific tracks (#5357)
+
+## [4.98]
+### Added
+- Documentation on how to delete variants for one or more cases
+- Document the option to collect green genes from any panel when updating the PanelApp green genes panel
+- On the institute's filters page, display also any soft filters applied to institute's variants
+### Fixed
+- Case page patch for research cases without WTS outliers
+
 ## [4.97]
 ### Added
 - Software version and link to the relative release on GitHub on the top left dropdown menu

{scout_browser-4.97.0 → scout_browser-4.99.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.97.0
+Version: 4.99.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
@@ -124,29 +124,25 @@ Instructions on how to run a Scout image connected to your local database or a c
 
 ## 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: -->
+Here is a quick start. Please see e.g. the [Installation instructions](docs/install.md) for more details.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --editable .
 ```
 
-Scout is configured to use `uv` if you like; either run, install, install as a tool or
-```
+Scout is configured to use `uv`; either run, install, or install as a tool.
+
+```bash
 uv sync --frozen
 uv run scout
 ```
 
+You can also install using pip:
+
+```
+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).
 

{scout_browser-4.97.0 → scout_browser-4.99.0}/README.md

@@ -50,29 +50,25 @@ Instructions on how to run a Scout image connected to your local database or a c
 
 ## 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: -->
+Here is a quick start. Please see e.g. the [Installation instructions](docs/install.md) for more details.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --editable .
 ```
 
-Scout is configured to use `uv` if you like; either run, install, install as a tool or
-```
+Scout is configured to use `uv`; either run, install, or install as a tool.
+
+```bash
 uv sync --frozen
 uv run scout
 ```
 
+You can also install using pip:
+
+```
+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).
 

scout_browser-4.99.0/docs/admin-guide/deleting-variants.md

@@ -0,0 +1,78 @@
+# Deleting Variants
+
+The Scout command line provides instructions to remove variants from one or more cases using the `scout delete variants` command.
+
+## Usage
+
+To view available options, run:
+
+```shell
+scout delete variants --help
+```
+
+This will display:
+
+```shell
+Usage: scout delete variants [OPTIONS]
+
+  Delete variants for one or more cases.
+
+Options:
+  -u, --user TEXT                 User running this command (email) [required]
+  -c, --case-id TEXT              Case ID (e.g., expertpoodle or helpedgoat)
+  -f, --case-file PATH            Path to file containing a list of case IDs
+  -i, --institute TEXT            Restrict to cases with the specified institute ID
+  --status [prioritized|inactive|active|solved|archived|ignored]
+                                  Restrict to cases with the specified status
+  --older-than INTEGER            Remove variants from cases older than (months)
+  --analysis-type [external|mixed|ogm|panel|panel-umi|unknown|wes|wgs|wts]
+                                  Restrict to cases with the specified analysis type
+  --rank-threshold INTEGER        Remove only variants with a rank lower than this threshold
+  --variants-threshold INTEGER    Remove variants only from cases containing at least this number of variants
+  --rm-ctg [cancer|cancer_sv|fusion|mei|outlier|snv|str|sv]
+                                  Remove only the specified variant categories
+  --keep-ctg [cancer|cancer_sv|fusion|mei|outlier|snv|str|sv]
+                                  Keep only the specified variant categories
+  --dry-run                       Perform a simulation without removing any variants
+  --help                          Show this message and exit.
+```
+
+### Parameter Descriptions
+
+| Option                 | Description                                                                                                                                              |
+| ---------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `--user (-u)`          | **Required.** The email of the user executing the command. The user must exist in the Scout database.                                                    |
+| `--case-id (-c)`       | **Optional.** The case ID (e.g., `expertpoodle` or `helpedgoat`).                                                                                        |
+| `--case-file (-f)`     | **Optional.** Path to a file containing a list of case IDs.                                                                                              |
+| `--institute (-i)`     | **Optional.** Institute ID. Not required if a case ID is provided.                                                                                       |
+| `--status`             | **Optional.** Restrict removal to cases with the specified status (e.g., `solved`).                                                                      |
+| `--older-than`         | **Optional.** Remove variants from cases older than the specified number of months (e.g., `12` for cases older than a year).                             |
+| `--analysis-type`      | **Optional.** Restrict removal to cases with the specified analysis type.                                                                                |
+| `--rank-threshold`     | **Optional.** Remove only variants with a rank lower than this threshold.                                                                                |
+| `--variants-threshold` | **Optional.** Remove variants only from cases containing at least this number of variants.                                                               |
+| `--rm-ctg`             | **Optional.** Remove only the specified variant categories. Example: `--rm-ctg snv --rm-ctg sv`.                                                         |
+| `--keep-ctg`           | **Optional.** Keep only the specified variant categories. Cannot be used together with `--rm-ctg`. Use multiple times to specify more than one category. |
+| `--dry-run`            | **Optional.** Runs a simulation, showing an estimate of the number of variants to be removed without actually deleting anything.                                   |
+
+> **Note:** If you are removing variants from Scout for the first time, it is strongly recommended to run a simulation first using the `--dry-run` option.
+
+### Example Command
+
+To simulate the deletion of variants that:
+
+-   Have a rank lower than `5`
+-   Belong to cases with `wgs` analysis type
+-   Contain at least `100,000` variants
+-   Are older than `24` months
+
+Run:
+
+```shell
+scout delete variants --loglevel WARNING \
+  -u youremail \
+  --rank-threshold 5 \
+  --analysis-type wgs \
+  --variants-threshold 100000 \
+  --older-than 24 \
+  --dry-run
+```

{scout_browser-4.97.0 → scout_browser-4.99.0}/docs/admin-guide/load-config.md

@@ -51,6 +51,7 @@ Below are available configuration parameters for a Scout case. Names marked with
 - **samples** _List_ List of samples included in the case:
     - **alignment_path** _String_ Path to BAM/CRAM file to view alignments.
     - **analysis_type** _String_ Specifies the analysis type for the sample. Options: {wgs, wes, panel, unknown, external}.
+    - **assembly_alignment_path** _String_ Path to BAM/CRAM file to view de novo assembly alignments.
     - **bam_file** _String_ Path to BAM/CRAM file to view alignments **WARNING:** Soon to be deprecated, use *alignment_path*.
     - **bam_path** _String_ Path to BAM/CRAM file to view alignments **WARNING:** Soon to be deprecated, use *alignment_path*.
     - **capture_kit** _String_ Exome specifies the capture kit.
@@ -70,6 +71,7 @@ Below are available configuration parameters for a Scout case. Names marked with
     - **mother** _String/Int_ Sample ID for mother or 0.
     - **msi** _Int_ Microsatellite instability [0-60].
     - **mt_bam** _String_ Path to the reduced mitochondrial BAM/CRAM alignment file.
+    - **paraphase_alignment_path** _String_ Path to BAM/CRAM file to view Paraphase alignments.
     - **phenotype(*)** _String_ Specifies the affection status {affected, unaffected, unknown}.
     - **reviewer** _List_ [Reference][srs]
       - **alignment** _String_ Path to BAM/CRAM file to view STR alignments

{scout_browser-4.97.0 → scout_browser-4.99.0}/docs/admin-guide/login-system.md

@@ -1,6 +1,7 @@
 # Setting up a user login system
 
-Scout currently supports 3 types of login systems:
+Scout currently supports 4 types of login systems:
+  - [keycloak authentication via OpenID Connect](#keycloak-openid-connect-login-system)
   - [Google authentication via OpenID Connect](#google-openid-connect-login-system)
   - [LDAP authentication](#login-using-lightweight-directory-access-protocol)
   - [Simple authentication using userid](#simple-login-with-userid)
@@ -8,6 +9,30 @@ Scout currently supports 3 types of login systems:
 **Login systems are mutually exclusive so when you choose a system, it will become be the only way all users will have access to the Scout app.**
 
 
+## Keycloak OpenID Connect Login System
+
+If your organization uses Keycloak as a login provider, Scout can be configured to authenticate users (who are already registered in the Scout database) using Keycloak in a few simple steps.
+
+A small tutorial with basic settings (intended for testing only, not for production) is available [on this page](https://github.com/northwestwitch/keycloak_flask_auth?tab=readme-ov-file#keycloak_flask_auth).
+
+Assuming a Keycloak realm containing users is available, you can edit the Scout configuration file to enable this authentication method:
+
+```python
+KEYCLOAK = dict(
+    client_id="<name_of_client>",
+    client_secret="secret", # available on Keycloak's admin console, under client credentials
+    discovery_url="http://<url_to_keycloak_instance>/realms/<name_of_realm>/.well-known/openid-configuration",
+    logout_url="http://<url_to_keycloak_instance>/realms/<name_of_realm>/protocol/openid-connect/logout",
+)
+```
+
+**Please note**: For this setup to work, the Keycloak client must include the following parameter:
+
+`Valid redirect URIs: "http://<scout-uri>/authorized"`
+
+
+Users attempting to log in to Scout will be redirected to the Keycloak instance for authentication.
+
 ## Google OpenID Connect login system
 
 Scout supports Google account login via OpenID Connect. Before setting up the Google authentication system in Scout it is necessary to register the Scout application in the Google API console and obtain OAuth 2.0 credentials. A detailed guide on how to do this is available [at this link](https://developers.google.com/identity/protocols/oauth2/openid-connect).

{scout_browser-4.97.0 → scout_browser-4.99.0}/docs/admin-guide/panelapp_panels.md

@@ -68,10 +68,14 @@ At the time of writing, the following panel types are available:
 12. **Research**
 13. **Submitted List**
 14. **Superpanel**
+15. **all** - all types above
 
 #### Default Behavior
 If no panel type is selected (i.e., the user presses Enter without input), Green Genes will be selected from the following default panel types: `3`, `4`, `6`, `7`, `8`, `9`, `10`.
 
+### Include all available panels
+By typing `all` at the prompt, green genes will be collected from any panel available in PanelApp
+
 #### Important Note
 The `--force` or (`-f`) parameter is required to create a new version of the gene panel if the number of green genes retrieved from the PanelApp server is lower than the number of genes in the older version of the panel. This ensures the panel is updated despite the reduction in gene count.
 

{scout_browser-4.97.0 → scout_browser-4.99.0}/docs/admin-guide/updating-individuals.md

@@ -22,11 +22,13 @@ Options:
   --help              Show this message and exit.
 ```
 And the tracks that can be updated are the following:
+- assembly_alignment_path
 - bam_file
 - d4_file
 - rna_alignment_path
 - mt_bam
 - vcf2cytosure
+- paraphase_alignment_path
 - rhocall_bed
 - rhocall_wig
 - tiddit_coverage_wig

scout_browser-4.99.0/docs/faq.md

@@ -0,0 +1,25 @@
+# FAQ
+
+## My email is white listed but I can't log into Scout
+
+You can be logged into multiple Google accounts at the same time. If you are only logged into
+one account, it will automatically be used when you click "Login with Google".
+
+Visit [Google][google] and click your avatar in the top right corner and "Add account" and log with your Scout connected account. Next time you access Scout you will be presented with an option of which Google account to use.
+
+
+## What should my VCF format look like in detail?
+
+Scout will work to some degree with many a generic (ideally VEP annotated) VCF as input, but, if you have a choice, for best results out of the box, use an already well integrated pipeline.
+The most well tested pipelines for Scout viewing currently are [MIP](https://github.com/Clinical-Genomics/MIP) (RD SR) or [Nextflow-wgs](https://github.com/Clinical-Genomics-Lund/nextflow_wgs) (RD SR),
+[Balsamic](https://github.com/Clinical-Genomics/BALSAMIC) (somatic), [nf-core/RNAfusion](https://github.com/nf-core/rnafusion) (RNA fusion) and [tomte](https://github.com/genomic-medicine-sweden/tomte) (RNA expression)
+We fully support [nf-core/raredisease](https://github.com/nf-core/raredisease) and [nf-core/Nallo](https://github.com/genomic-medicine-sweden/nallo) (RD LRS). We also
+have compatibility with at least earlier versions of other pipelines e.g. [sarek](https://github.com/nf-core/sarek) (somatic) and [poorpipe](https://github.com/J35P312/poorpipe) (RD LRS).
+
+To use the full features of Scout, try to load pre-ranked variants (see [genmod](https://github.com/Clinical-Genomics/genmod)).
+An important take home for variant triage, especially of SVs, is that you need to get good local database frequency annotation going. We use [SVDB](https://github.com/J35P312/SVDB) and/or [loqusdb](https://github.com/Clinical-Genomics/loqusdb).
+
+Say hi to the developers in a GitHub issue or discussion, describe your pipeline and situation and we may be able to direct you.
+
+
+[google]: https://www.google.com

{scout_browser-4.97.0 → scout_browser-4.99.0}/docs/install.md

@@ -9,34 +9,53 @@ Make sure you have a `mongod` process running. First install [mongodb][mongodb]
 
 
 ## 1. Install
-Installation of Scout is possible via pip or GitHub.
+Installation of Scout is possible via PyPi, GitHub or Dockerhub.
 Let's start by pulling down the GitHub repository with the source code.
 
 ### GitHub
 
+Use `git` to clone from [GitHub](https://github.com/Clinical-Genomics/scout), either the `https` or `ssh` route.
+Scout is configured to use `uv`: either run, install, or install as a tool.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --requirement requirements.txt --editable .
+
+uv sync --frozen
+uv run scout
+```
+Or if you rather, the project definition is compatible with pip, so instead of the `uv` statement above you can just
+
+```
+pip install --editable .
 ```
 
 ### Pip
 
-To get the latest version, use the above. When using pip the latest stable release will be installed.
+To get the latest development (`main`) version, use the above. When using pip the latest stable release will be installed.
 
 ```bash
 pip install scout-browser
 ```
 
 
-<!-- ## 2. Configure
-You need to sign up for access to a few web APIs like Google OAuth and
-OMIM to make full use of Scout. The keys and secrets should be added to
+## 2. Configure
+In order to make full use of Scout, you will want to integrate with both external resources and a number of available extensions,
+e.g. `chanjo` for coverage analysis and `gens` for seamless visualisation and triage of larger CNVs.
+
+You will want to sign up for access to a few web APIs like Google OAuth and
+OMIM. The keys and secrets should be added to
 the Flask instance config. To learn more about possible settings, take a
 look in the ``scout/settings.py`` module.
 
-### Google OAuth
+
+### Autentication
+If you intend to use authentication, which you should, there are several options!
+
+OAuth2 via an ODIC provider (we have good experience with Google) or a KeyCloak server of you own. Scout also supports LDAP.
+See the [admin-guide][admin-guide] for details.
+
+#### Google OAuth
 Create a new project in your [Google Developer console][google-console].
 Under your project, click "APIs & auth" > "Credentials". Here you will
 find your "CLIENT ID" and "CLIENT SECRET". You also need to add some
@@ -66,40 +85,45 @@ account should work so you don't need to sign up for any special access.
 If you are using a password protected Mongo database you also need to add
 the authentication details to the instance config.
 
+## 2. Setup
 
-## 3. Boostrap
-We use gulp.js to compile the statis assets (CSS, JS, etc.)
-
-```bash
-$ gulp build --production
-```
-
+### Demo setup
 
-## 4. Develop
-You are now ready to start the development server and complete the setup
-in the admin interface.
+This option is used to quickly get a operating instance with some example data
 
-```bash
-$ python manage.py -c "$(pwd)/configs/boilerplate.cfg" vagrant
 ```
-
-That's it! Go and explore Scout. -->
-
-## 2. Setup
+scout setup demo
+scout --demo serve
+```
+The previous command setup the database with a truncated collection of gene definitions with links to OMIM along with HPO phenotype terms.
 
 ### Full setup
 
-To initialize a working instance with all genes, diseases etc run
+For more info, run `scout --help`!
+
+To initialize a working instance - a database where you store genes, diseases, cases, variants etc run
 
 ```bash
 scout setup database
 ```
+You will want to make sure you have a full complement of these genes, diseases etc before you start working on cases.
 
-for more info, run `scout --help`
+```
+scout download everything --api-key YOUR_OMIM_API_KEY
+scout update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt
+scout update diseases -f .
+scout update genes -f .
+```
 
-> If you intent to use authentication, make sure you are using a Google email!
+A common task is to have a couple of broad screening panels for rare disease genomics set up. We provide automation for two such in silico panels
+out of the box, one with OMIM morbid genes, and one with all PanelApp ``Green`` genes. Here you provide the name of an institute you created that
+will serve as responsible for these panels (`cust002` below):
+```
+scout update omim --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt
+scout update panelapp-green -i cust002 --force
+```
 
-The previous command setup 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:
+For more information about populating and updating the database, please see [admin-guide][admin-guide].
 
 ```
 scout load panel scout/demo/panel_1.txt
@@ -107,21 +131,9 @@ scout load case scout/demo/643594.config.yaml
 ```
 
 
-For more information about populating the database, please see [admin-guide][admin-guide].
-
-### Demo
-
-This option is used to quickly get a operating instance with some example data
-
-```
-scout setup demo
-scout --demo serve
-```
-
 
 [google-console]: https://console.developers.google.com/project
 [omim-register]: http://omim.org/api
-[vagrant]: https://www.vagrantup.com/
 [mongodb]: https://docs.mongodb.com/manual/installation/
 [admin-guide]: admin-guide/README.md
 [containers]: admin-guide/containers/container-deploy.md

scout_browser-4.99.0/docs/stylesheets/extra.css

@@ -0,0 +1,15 @@
+[data-md-color-scheme="slate"][data-md-color-primary="black"] {
+    --md-cg-color:       27;
+    --md-typeset-a-color: hsl(var(--md-cg-color), 92%, 64%);
+    --md-default-fg-color--light: hsla(var(--md-cg-color), 92%, 56%, 1);
+
+}
+
+[data-md-color-scheme="slate"] {
+    --md-typeset-table-color: hsla(var(--md-cg-color), 92%, 64%, 0.24);
+}
+
+[data-md-color-accent="cg-accent"] {
+    --md-accent-fg-color:              hsla(var(--md-cg-color), 92%, 56%, 1);
+    --md-accent-fg-color--transparent: hsla(var(--md-cg-color), 92%, 60%, 0.1);
+}

{scout_browser-4.97.0 → scout_browser-4.99.0}/mkdocs.yml

@@ -22,9 +22,25 @@ theme:
   name: 'material'
   logo: 'img/logo-only.png'
   palette:
-    primary: 'blue grey'
-    accent: 'cyan'
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      primary: 'blue grey'
+      accent: 'cyan'
+      toggle:
+          icon: material/toggle-switch
+          name: Switch to dark mode
 
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: "slate"
+      primary: "black"
+      accent: "cg-accent"
+      toggle:
+          icon: material/toggle-switch-off-outline
+          name: Switch to light mode
+
+extra_css:
+    - stylesheets/extra.css
 
 nav:
   - Introduction: 'README.md'
@@ -67,6 +83,7 @@ nav:
       - Updating a case without a new config: 'admin-guide/updating-case.md'
       - Updating case individuals tracks: 'admin-guide/updating-individuals.md'
       - Loading variants: 'admin-guide/loading-variants.md'
+      - Removing variants: 'admin-guide/deleting-variants.md'
       - Gene definitions: 'admin-guide/genes.md'
       - PanelApp gene panels: 'admin-guide/panelapp_panels.md'
       - HPO terms: 'admin-guide/hpo.md'

{scout_browser-4.97.0 → scout_browser-4.99.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "scout-browser"
-version = "4.97.0"
+version = "4.99.0"
 description = "Clinical DNA variant visualizer and browser"
 authors = [{name="Chiara Rasi", email="chiara.rasi@scilifelab.se"}, {name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Robin Andeer", email="robin.andeer@gmail.com"}, {name="Mans Magnuson", email="monsunas@gmail.com"}]
 license = {text = "MIT License"}