ro-crate-py

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

Supports specification: RO-Crate 1.1

Status: Alpha

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:

from rocrate.rocrate import ROCrate

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:

from rocrate.model.person import Person

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

# wf_crate example
publisher = Person(crate, '001', {'name': 'Bert Verlinden'})
creator = Person(crate, '002', {'name': 'Lee Ritenour'})
wf_crate.add(publisher, creator)

# 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)

Command Line Interface

ro-crate-py includes a hierarchical command line interface: the rocrate tool. rocrate is the top-level command, while specific functionalities are provided via sub-commands. Currently, the tool allows to initialize a directory tree as an RO-Crate (rocrate init) and to modify the metadata of an existing RO-Crate (rocrate add).

$ rocrate --help
Usage: rocrate [OPTIONS] COMMAND [ARGS]...

Options:
  -c, --crate-dir PATH
  --help                Show this message and exit.

Commands:
  add
  init

Commands act on the current directory, unless the -c option is specified.

The rocrate init command explores a directory tree and generates an RO-Crate metadata file (ro-crate-metadata.json) listing all files and directories as File and Dataset entities, respectively. The metadata file is added (overwritten if present) to the directory at the top-level, turning it into an RO-Crate.

The rocrate add command allows to add workflows and other entity types (currently testing-related metadata) to an RO-Crate. The entity type is specified via another sub-command level:

# rocrate add --help
Usage: rocrate add [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  test-definition
  test-instance
  test-suite
  workflow

Note that data entities (e.g., workflows) must already be present in the directory tree: the effect of the command is to register them in the metadata file.

Example

# From the ro-crate-py repository root
cd test/test-data/ro-crate-galaxy-sortchangecase

This directory is already an ro-crate. Delete the metadata file to get a plain directory tree:

rm ro-crate-metadata.json

Now the directory tree contains several files and directories, including a Galaxy workflow and a Planemo test file, but it's not an RO-Crate since there is no metadata file. Initialize the crate:

rocrate init

This creates an ro-crate-metadata.json file that lists files and directories rooted at the current directory. Note that the Galaxy workflow is listed as a plain File:

        {
            "@id": "sort-and-change-case.ga",
            "@type": "File"
        }

To register the workflow as a ComputationalWorkflow:

rocrate add workflow -l galaxy sort-and-change-case.ga

Now the workflow has a type of ["File", "SoftwareSourceCode", "ComputationalWorkflow"] and points to a ComputerLanguage entity that represents the Galaxy workflow language. Also, the workflow is listed as the crate's mainEntity (see https://about.workflowhub.eu/Workflow-RO-Crate).

To add workflow testing metadata to the crate:

rocrate add test-suite -i \#test1
rocrate add test-instance \#test1 http://example.com -r jobs -i \#test1_1
rocrate add test-definition \#test1 test/test1/sort-and-change-case-test.yml  -e planemo -v '>=0.70'

License

• Copyright 2019-2021 The University of Manchester, UK
• Copyright 2021 Vlaams Instituut voor Biotechnologie (VIB), BE
• Copyright 2021 Barcelona Supercomputing Center (BSC), ES
• Copyright 2021 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.