Python library to create/parse RO-Crate (Research Object Crate) metadata.
Supports specification: RO-Crate 1.1
Status: Alpha
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
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 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 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 ]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"
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(out_path)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.
# 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'
- 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.
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.
You may also be interested in the paper Packaging research artefacts with RO-Crate to appear in Data Science.