rocrate 0.2.2

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.