ro-crate-py

Create/parse rocrate_ (Research Object Crate) metadata.

Note: Under development

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.

Installing

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

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

.. _rocrate: https://w3id.org/ro/crate .. _pip: https://docs.python.org/3/installing/

General usage

The package contains a The standard use case is by instantiating ROCrate class. This can be a new one: crate = ROCrate() or an existing RO-crate package can be load 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)

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

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

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 are used in a ro-crate to adequately describe a Data Entity. The following example shows how to add them to the RO-Crate root:

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

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

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