rocrate 0.3.0

RO-Crate metadata generator/parser

ro-crate-py

Python library to create/parse RO-Crate (Research Object Crate) metadata.

Supports specification: RO-Crate 1.1

Status: Alpha

Contribute

Source code: https://github.com/researchobject/ro-crate-py

Feel free to raise a pull request at https://github.com/researchobject/ro-crate-py/pulls or an issue at https://github.com/researchobject/ro-crate-py/issues.

Submitted contributions are assumed to be covered by section 5 of the Apache License 2.0.

For development, you can build a Docker image with:

docker build -t ro-crate-py .

And then run it interactively with:

docker run --rm -it --name ro-crate-py ro-crate-py bash

Installing

You will need Python 3.6 or later (Recommended: 3.7).

This library is easiest to install using pip:

pip install rocrate

If you want to install manually from this code base, then try:

pip install .

..or if you use don't use pip:

python setup.py install

General usage

The RO-crate object

In general you will want to start by instantiating the ROCrate object. This can be a new one:

crate = ROCrate() 

or an existing RO-Crate package can be loaded from a directory or zip file:

crate = ROCrate('/path/to/crate/')

crate = ROCrate('/path/to/crate/file.zip')

In addition, there is a set of higher level functions in the form of an interface to help users create some predefined types of crates. As an example here is the code to create a workflow RO-Crate, containing a workflow template. This is a good starting point if you want to wrap up a workflow template to register at workflowhub.eu:

from rocrate import rocrate_api

wf_path = "test/test-data/test_galaxy_wf.ga"
files_list = ["test/test-data/test_file_galaxy.txt"]

# Create base package
wf_crate = rocrate_api.make_workflow_rocrate(workflow_path=wf_path,wf_type="Galaxy",include_files=files_list)

Independently of the initialization method, once an instance of ROCrate is created it can be manipulated to extend the content and metadata.

Data entities

Data entities can be added with:

## adding a File entity:
sample_file = '/path/to/sample_file.txt'
file_entity = crate.add_file(sample_file)

# Adding a File entity with a reference to an external (absolute) URI
remote_file = crate.add_file('https://github.com/ResearchObject/ro-crate-py/blob/master/test/test-data/test_galaxy_wf.ga', fetch_remote = False)

# adding a Dataset
sample_dir = '/path/to/dir'
dataset_entity = crate.add_directory(sample_dir, 'relative/rocrate/path')

Contextual entities

Contextual entities are used in an RO-Crate to adequately describe a Data Entity. The following example shows how to add the person contextual entity to the RO-Crate root:

# Add authors info
crate.add_person('#joe', {'name': 'Joe Bloggs'})

# wf_crate example
publisher = wf_crate.add_person('001', {'name': 'Bert Verlinden'})

creator = wf_crate.add_person('002', {'name': 'Lee Ritenour'})

# These contextual entities can be assigned to other metadata properties:

wf_crate.publisher = publisher
wf_crate.creator = [ creator, publisher ]

Other metadata

Several metadata fields on root level are supported for the workflow RO-crate:

wf_crate.license = 'MIT'
wf_crate.isBasedOn = "https://climate.usegalaxy.eu/u/annefou/w/workflow-constructed-from-history-climate-101"
wf_crate.name = 'Climate 101'
wf_crate.keywords = ['GTN', 'climate']
wf_crate.image = "climate_101_workflow.svg"
wf_crate.description = "The tutorial for this workflow can be found on Galaxy Training Network"
wf_crate.CreativeWorkStatus = "Stable"

Writing the RO-crate file

In order to write the crate object contents to a zip file package or a decompressed directory, there are 2 write methods that can be used:

# Write to zip file
out_path = "/home/test_user/crate"
crate.write_zip(out_path)

# write crate to disk
out_path = "/home/test_user/crate_base"
crate.write_crate(out_path)

License

• © 2019-2020 The University of Manchester, UK
• © 2020 Vlaams Instituut voor Biotechnologie (VIB), BE
• © 2020 Barcelona Supercomputing Center (BSC), ES
• © 2020 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT

Licensed under the Apache License, version 2.0 https://www.apache.org/licenses/LICENSE-2.0, see the file LICENSE.txt for details.

Cite as

The above DOI corresponds to the latest versioned release as published to Zenodo, where you will find all earlier releases. To cite ro-crate-py independent of version, use https://doi.org/10.5281/zenodo.3956493, which will always redirect to the latest release.