# pyDataPipeline
[![PyPI](https://img.shields.io/pypi/v/data-pipeline-api)](https://pypi.org/project/data-pipeline-api/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/data-pipeline-api)](https://pypi.org/project/data-pipeline-api/)
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Welcome to pyDataPipeline a Python api to interact with the Fair Data Pipeline.
Full documention of the pyDataPipeline is avaialable at [https://www.fairdatapipeline.org/pyDataPipeline/](https://www.fairdatapipeline.org/pyDataPipeline/)
## Installation
pyDataPipeline can be installed from PyPi:
```
pip3 install data-pipeline-api
```
Or from the Repository:
```
git clone https://github.com/FAIRDataPipeline/pythonFDP.git
git checkout dev
pip3 install -e .
```
**NB. PyDataPipeline requires Python3.**
## Example submission_script
Assume FDP_CONFIG_DIR, storage_locations and objects have been set by CLI tool
```
import os
import fairdatapipeline as pipeline
token = os.environ['FDP_LOCAL_TOKEN']
config_dir = os.environ['FDP_CONFIG_DIR']
config_path = os.path.join(config_dir, 'config.yaml')
script_path = os.path.join(config_dir, 'script.sh')
handle = pipeline.initialise(token, config_path, script_path)
pipeline.finalise(token, handle)
```
## SEIRS Model Example
The SEIRS Model Example is available at: [https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html](https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html)
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"description": "# pyDataPipeline\n\n[![PyPI](https://img.shields.io/pypi/v/data-pipeline-api)](https://pypi.org/project/data-pipeline-api/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/data-pipeline-api)](https://pypi.org/project/data-pipeline-api/)\n[![pyDataPipeline](https://github.com/FAIRDataPipeline/pyDataPipeline/actions/workflows/pyDataPipeline.yaml/badge.svg?branch=dev)](https://github.com/FAIRDataPipeline/pyDataPipeline/actions/workflows/pyDataPipeline.yaml)\n[![codecov](https://codecov.io/gh/FAIRDataPipeline/pyDataPipeline/branch/dev/graph/badge.svg?token=Eax5AmrDxx)](https://codecov.io/gh/FAIRDataPipeline/pyDataPipeline)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5562602.svg)](https://doi.org/10.5281/zenodo.5562602)\n[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/5461/badge)](https://bestpractices.coreinfrastructure.org/projects/5461)\n\nWelcome to pyDataPipeline a Python api to interact with the Fair Data Pipeline.\n\nFull documention of the pyDataPipeline is avaialable at [https://www.fairdatapipeline.org/pyDataPipeline/](https://www.fairdatapipeline.org/pyDataPipeline/)\n\n## Installation\npyDataPipeline can be installed from PyPi:\n```\npip3 install data-pipeline-api\n```\n\nOr from the Repository:\n```\ngit clone https://github.com/FAIRDataPipeline/pythonFDP.git\n\ngit checkout dev\n\npip3 install -e .\n```\n**NB. PyDataPipeline requires Python3.**\n\n## Example submission_script\n\nAssume FDP_CONFIG_DIR, storage_locations and objects have been set by CLI tool\n\n```\nimport os\nimport fairdatapipeline as pipeline\n\ntoken = os.environ['FDP_LOCAL_TOKEN']\nconfig_dir = os.environ['FDP_CONFIG_DIR']\nconfig_path = os.path.join(config_dir, 'config.yaml')\nscript_path = os.path.join(config_dir, 'script.sh')\n\nhandle = pipeline.initialise(token, config_path, script_path)\n\npipeline.finalise(token, handle)\n\n```\n\n## SEIRS Model Example\n\nThe SEIRS Model Example is available at: [https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html](https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html)\n",
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