statina 2.9.1

NIPT data storage and visualisation

Statina

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

Installation

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:

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

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 [e-mail]

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