o2r-project / o2r-meta

Metadata toolsuite for an extract-map-validate workflow supporting reproducible research

o2r meta

This is python library with a set of tools for extract-map-validate workflows as part of the o2r project:

0. schema & documentation of the o2r metadata
1. extract - collect meta information from files in a workspace
2. broker - translate metadata from o2r to third party schemas
3. validate - check if metadata set is valid to the schema
4. harvest - collect metadata from external sources via OAI-PMH
5. adding new parsers to the program

For their role within o2r, please refer to o2r-architecture.

Getting started

The full functionality of o2r-meta, including building the documentation and running the tests, requires Python >= 3.7.

Installation from source code

git clone https://github.com/o2r-project/o2r-meta.git
cd o2r-meta
pip install -r requirements.txt
pip install -e .

Common pitfall: pygdal version has to match the system GDAL version. Verify the system GDAL version like this:

gdal-config --version

and, if necessary, force pygdal version to be installed as following:

pip install pygdal==x.x.x.x

Installation with Docker

Another way of installation is provided by the Dockerfile. Build it like this:

git clone https://github.com/o2r-project/o2r-meta.git
cd o2r-meta
docker build -t meta .

And start a tool of o2r-meta like this:

docker run --rm -v $(pwd)/extract/tests/:/testdata:ro meta -debug extract -i /testdata -s

Build the documentation

To familiarise with the use of o2r-meta and get access to the How-to guide, we recommend the installation of the documentation before using the tool.

cd docs/
pip install -r requirements-docs.txt
make html

This will create directory build/html under docs, which contains the documentation. The entry point is file index.html.

Run the tests

The o2r-meta tests use pytest. To install the necessary packages:

pip install -U pytest
pip install -U pytest-console-scripts

To run the tests:

cd tests
pytest

How to cite

To cite this software please use

Nüst, Daniel, 2018. Reproducibility Service for Executable Research Compendia: Technical Specifications and Reference Implementation. Zenodo. doi:10.5281/zenodo.2203843

License

o2r-meta is licensed under Apache License, Version 2.0, see file LICENSE. Copyright (C) 2016-2020 - o2r project