Commit 45620b4b authored by BorjaEst's avatar BorjaEst
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Update readme

parent 1fea437f
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<div align="center">
[![Build Status](https://jenkins.eosc-synergy.eu/buildStatus/icon?job=eosc-synergy-org%2Fo3skim%2Ftest)](https://jenkins.eosc-synergy.eu/job/eosc-synergy-org/job/o3skim/job/master)
[![Build Status](https://jenkins.eosc-synergy.eu/buildStatus/icon?job=eosc-synergy-org%2Fo3skim%2Fmaster)](https://jenkins.eosc-synergy.eu/job/eosc-synergy-org/job/o3skim/job/master)
[![Documentation Status](https://readthedocs.org/projects/o3as/badge/?version=latest)](https://o3as.readthedocs.io/en/latest/?badge=latest)
[![pipeline status](https://git.scc.kit.edu/synergy.o3as/o3skim/badges/master/pipeline.svg)](https://git.scc.kit.edu/synergy.o3as/o3skim/-/commits/master)
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# 📝 Table of Contents
- [About](#about)
- [Build using docker](#build)
- [Run using udocker](#deployment)
- [Testing](#testing)
- [Documentation](https://o3as.readthedocs.io/en/latest)
- [Authors](#authors)
- [TODO](https://git.scc.kit.edu/synergy.o3as/o3skim/-/issues)
- [Issues & ToDo](https://git.scc.kit.edu/synergy.o3as/o3skim/-/issues)
# About <a name = "about"></a>
This project provides the tools to preprocess, standardize and reduce ozone data for later transfer and plot.
## Prerequisites
To run the project as container, you need the following systems and container technologies:
- __Build machine__ with [docker](https://docs.docker.com/engine/install/)
- __Runtime machine__ with [udocker](https://indigo-dc.gitbook.io/udocker/installation_manual)
This software is shipped as python3 package, therefore you need to have python3
and pip installed. If not, please check [pip documentation](https://pip.pypa.io/en/stable/installing/) to find out how to run it in your system.
> Note udocker cannot be used to build containers, only to run them.
> Non admin rights? Check how to run [conda](https://docs.conda.io/en/latest/) in your machine.
# Built using docker <a name = "build"></a>
Download the repository at the __Build machine__ using git.
```sh
$ git clone git@git.scc.kit.edu:synergy.o3as/o3skim.git
Cloning into 'o3skim'...
...
```
Build the docker image at the __Build machine__ using docker.
```sh
$ docker build --tag o3skim .
...
Successfully built 69587025a70a
Successfully tagged o3skim:latest
```
If the build process succeeded, you can list the image on the docker image list:
```sh
$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
o3skim latest 69587025a70a xx seconds ago 557MB
...
```
# Run using udocker <a name = "deployment"></a>
To deploy the the application using __udocker__ at the __Runtime machine__ you need:
- Input path with data to skim, to be mounter on `/app/data` inside the container.
- Output path for skimmed results, to be mounted on `/app/output` inside the container.
- Configuration file with a data structure description at the input path in [YAML](https://yaml.org/) format.
This configuration file has to be mounted on `/app/sources.yaml` inside the container.
Once the requirement are completed, pull the image from the image registry.
For example, to pull it from the synergy-imk official registry use:
```sh
$ udocker pull synergyimk/o3skim
...
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
...
```
Once the repository is added and the image downloaded, create the local container:
```sh
$ udocker create --name=o3skim synergyimk/o3skim
fa42a912-b0d4-3bfb-987f-1c243863802d
```
Finally, run the container. Note the described _data_, _output_ and _sources.yaml_ have to be provided. Also it is needed to specify the user _application_ should run inside the container:
```sh
$ udocker run \
--user=application \
--volume=${PWD}/sources.yaml:/app/sources.yaml \
--volume=${PWD}/data:/app/data \
--volume=${PWD}/output:/app/output \
o3skim --verbosity INFO ${action1} ${action2}
...
executing: main
...
2020-08-25 12:42:34,151 - INFO - Configuration found at: './sources.yaml'
2020-08-25 12:42:34,152 - INFO - Loading data from './data'
2020-08-25 12:42:34,261 - INFO - Skimming data to './output'
```
For the main function description and commands help you can call:
```sh
$ udocker run --user=application o3skim --help
...
```
# Testing <a name = "testing"></a>
Testing is based on [sqa-baseline](https://indigo-dc.github.io/sqa-baseline/) criteria. On top, [tox](https://tox.readthedocs.io/en/latest/) automation is used to simplify the testing process.
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