Metadata-Version: 2.1
Name: statina
Version: 1.7.2
Summary: NIPT data storage and visualisation
Home-page: https://github.com/Clinical-Genomics/statina
Author: Maya Brandi
Author-email: maya.brandi@scilifelab.se
License: UNKNOWN
Description: # Statina  [![Coverage Status](https://coveralls.io/repos/github/Clinical-Genomics/statina/badge.svg?branch=master)](https://coveralls.io/github/Clinical-Genomics/statina?branch=master) [![Build Status](https://travis-ci.org/Clinical-Genomics/statina.svg?branch=master)](https://travis-ci.org/Clinical-Genomics/statina) ![Latest Release](https://img.shields.io/github/v/release/clinical-genomics/statina)
        
        
        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][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](https://hub.docker.com/repository/docker/clinicalgenomics/statina-stage) 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][Fluffy]
        
        
        [Fluffy]: https://github.com/Clinical-Genomics/fluffy
        [WisecondorX]: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX
        [docker-hub]: https://hub.docker.com/repository/docker/clinicalgenomics/statina
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
