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|
%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 [](https://coveralls.io/github/Clinical-Genomics/statina?branch=master) [](https://travis-ci.org/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 [](https://coveralls.io/github/Clinical-Genomics/statina?branch=master) [](https://travis-ci.org/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 [](https://coveralls.io/github/Clinical-Genomics/statina?branch=master) [](https://travis-ci.org/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 <Python_Bot@openeuler.org> - 2.9.1-1
- Package Spec generated
|
