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Open Source Science

https://github.com/clinical-genomics/statina

https://github.com/clinical-genomics/statina

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.3%) to scientific vocabulary

Keywords from Contributors

genomics bioconda coverage sambamba
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: Clinical-Genomics
  • Language: Python
  • Default Branch: master
  • Size: 1.85 MB
Statistics
  • Stars: 2
  • Watchers: 9
  • Forks: 3
  • Open Issues: 20
  • Releases: 68
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Codeowners

README.md

Statina Coverage Status Build Status Latest Release

Statina is a visualisation tool for the data produced by the Fluffy pipeline running WisecondorX to analyze NIPT.

Installation

bash git clone https://github.com/Clinical-Genomics/statina cd statina pip install -r requirements.txt -e .

Usage

Demo

The CLI is intended for development/testing purpose only. To run in a production setting please refer to documentation for suggestions how.

Once installed, you can set up Statina 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 set up a fully working Statina demo:

bash statina load batch --result-file statina/tests/fixtures/valid_fluffy.csv

Settings can be used by exporting the environment variables: DB_NAME, DB_URI, HOST, PORT This will set up an instance of Statina with a database called statina-demo. Now run

bash statina serve --reload and play around with the interface.

Docker image

Statina can also run as a container. The image is available on Docker Hub or can be build using the Dockerfile provided in this repository.

To build a new image from the Dockerfile use the commands: docker build -t statina .

To run the image use the following command: docker run --name statina statina statina

To remove the container, type: docker rm statina

Release model

Statina is using github flow release model as described in our development manual.

Steps to make a new release:

1) Get you PR approved. 2) Append the version bump to PR title. Eg. Update README becomes Update Readme (patch) 3) Select squash and merge 4) Write a change log comment. 5) Merge.

Deploying to staging

Opening pull requests in Statina repository will enable a Github Action to build containers and publish to statina-stage dockerhub with each commit.

Two tags will be published: one with the name of the branch and another tagged "latest".

Steps to test current branch on staging:

ssh firstname.lastname@cg-vm1.scilifelab.se

sudo -iu hiseq.clinical

ssh localhost

If you made changes to internal app : systemctl --user restart statina.target

Your branch should be deployed to staging at https://statina-stage.scilifelab.se

If for some reason you cannot access the application at given address, check status of the container: systemctl --user status statinaApp.service

Deploying to production

Use update-statina.sh script to update production both on Hasta and CGVS. Please follow the development guide and servers repo when doing so. It is also important to keep those involved informed.

Back End

The Statina database is a Mongo database consisting of following collections:

  • batch - holds batch level information.
  • sample - holds sample level information.
  • user - holds user names, emails and roles.

The database is loaded through the CLI with data generated by the FluFFyPipe

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

GitHub Events

Total
  • Issues event: 1
  • Delete event: 1
  • Push event: 2
  • Pull request review event: 1
  • Pull request event: 1
  • Create event: 1
Last Year
  • Issues event: 1
  • Delete event: 1
  • Push event: 2
  • Pull request review event: 1
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 435
  • Total Committers: 10
  • Avg Commits per committer: 43.5
  • Development Distribution Score (DDS): 0.375
Top Committers
Name Email Commits
mayabrandi m****i@s****e 272
Mropat m****t@g****m 49
Clinical Genomics Bot c****m@g****m 46
Maria Ropat 3****t@u****m 35
moonso m****n@s****e 17
Github CI 4****]@u****m 7
northwestwitch r****a@g****m 5
Eleonora 6****u@u****m 2
Vincent Janvid 6****v@u****m 1
Patrik Grenfeldt p****t@s****e 1
Committer Domains (Top 20 + Academic)
scilifelab.se: 3

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 67
  • Total pull requests: 37
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 10
  • Total pull request authors: 5
  • Average comments per issue: 1.72
  • Average comments per pull request: 0.49
  • Merged pull requests: 35
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • alieden (38)
  • Mropat (12)
  • elevu (7)
  • mayabrandi (3)
  • moahaegglund (2)
  • pbiology (1)
  • NIPT-LabTech (1)
  • Smeds (1)
  • dnil (1)
  • J35P312 (1)
  • northwestwitch (1)
Pull Request Authors
  • Mropat (18)
  • mayabrandi (13)
  • Vince-janv (4)
  • elevu (2)
  • pbiology (1)
Top Labels
Issue Labels
backend (20) Low prio (16) frontend (11) High prio (8) discuss (3) Effort low (3) Decoupled Frontend (3) Medium prio (2) Effort high (2) refinement needed (1) bug (1) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 73 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 54
  • Total maintainers: 1
pypi.org: statina

NIPT data storage and visualisation

  • Versions: 54
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 73 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 16.9%
Dependent repos count: 21.6%
Average: 25.2%
Stargazers count: 31.9%
Downloads: 45.7%
Maintainers (1)
moamaya
Last synced: 11 months ago

Dependencies

requirements-dev.txt pypi
  • bump2version * development
  • coveralls * development
  • mongomock * development
  • pylint * development
  • pytest >=5.2 development
  • pytest-cov * development
requirements.txt pypi
  • aiofiles *
  • bcrypt *
  • bump2version *
  • cerberus *
  • click *
  • coloredlogs *
  • email-validator *
  • fastapi *
  • gunicorn *
  • httptools *
  • jinja2 *
  • mongo_adapter *
  • numpy *
  • passlib *
  • pymongo *
  • python-dotenv *
  • python-jose *
  • python-multipart *
  • pyyaml *
  • sendmail-container *
  • uvicorn *
  • uvloop *
setup.py pypi
  • x.strip *
.github/workflows/deploy_prod.yml actions
.github/workflows/deploy_stage.yml actions
.github/workflows/merge_master_ci.yml actions
  • Clinical-Genomics/bump2version-ci v3 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
.github/workflows/pull_request_ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
  • psf/black stable composite
.github/workflows/release_ci.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
Dockerfile docker
  • python 3.8-slim-bullseye build