%global _empty_manifest_terminate_build 0 Name: python-statina Version: 2.9.1 Release: 1 Summary: NIPT data storage and visualisation License: MIT License URL: https://github.com/Clinical-Genomics/statina Source0: https://mirrors.nju.edu.cn/pypi/web/packages/1b/a5/489b48765904ef7f2160b7ea655282cb6188fc86551f99a278012ba14758/statina-2.9.1.tar.gz BuildArch: noarch Requires: python3-click Requires: python3-bump2version Requires: python3-pymongo Requires: python3-mongo-adapter Requires: python3-coloredlogs Requires: python3-pyyaml Requires: python3-cerberus Requires: python3-multipart Requires: python3-dotenv Requires: python3-email-validator Requires: python3-jinja2 Requires: python3-passlib Requires: python3-fastapi Requires: python3-uvicorn Requires: python3-uvloop Requires: python3-httptools Requires: python3-gunicorn Requires: python3-jose[cryptography] Requires: python3-bcrypt Requires: python3-numpy Requires: python3-aiofiles Requires: python3-sendmail-container %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 %package -n python3-statina Summary: NIPT data storage and visualisation Provides: python-statina BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-statina # 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 %package help Summary: Development documents and examples for statina Provides: python3-statina-doc %description help # 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 %prep %autosetup -n statina-2.9.1 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-statina -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Fri May 05 2023 Python_Bot - 2.9.1-1 - Package Spec generated