Corda Data Schema for Crop wild relatives

Corda types and hooks for representing workflows and their results as FAIR Digital Objects. This is part of the FAIR workflow platform.

The data model closely resembles the RO-Crate data schema. All digital objects are intended to also represent valid JSON-LD objects, and therefore provide their own JSON-LD @context.

Schema

Hooks and Methods

• All Types extend JsonLdType, which patches objects before schema validation to add a @context and @type.
• The Dataset type deletes all of it's linked objects in afterDelete to clean the repository if a dataset is removed.

Type Methods

• asNestedGraph is a custom method on the Dataset type that returns a dataset and all linked objects in a single jsonld graph {"@graph": [dataset, relatedObject1, relatedObject2, ...]}
• asGraph is similar to asNestedGraph, but does not return objects linked by a nested Dataset (i.e. Files that are not part of the root dataset, but of a dataset that is included in that dataset)

Build

Lifecycle hooks and type methods are written in Kotlin. Gradle is used as a build system to create a "fat jar" which can be used with Cordra (see Cordra Java hooks).

Deployment/Installation

The provided script [schemas/updateSchemas.py] can be used to update a running Cordra instance with all types and the hook library. It takes care of uploading all schemas and attaches the library jar file to the dataset schema object:

To install, first build the library with gradle build:

gradle clean build
(...snip...)
BUILD SUCCESSFUL in 10s
7 actionable tasks: 7 execute

Then update Cordra using the script:

# install requirements for update script
python -m virtualenv venv
source venv/bin/activate
pip install -r schemas/requirements.txt

# run script
./schemas/updateSchemas.py https://example.com/cordra -u user -p password
Found schemas: ['Dataset.schema.json', 'FileObject.schema.json', 'PropertyValue.schema.json', 'FormalParameter.schema.json', 'Person.schema.json', 'Workflow.schema.json', 'Organization.schema.json', 'SoftwareApplication.schema.json', 'CreateAction.schema.json']
Patches for all schemas: [PosixPath('/home/dbauer/projects/destine_sdm/cordra-schema/schemas/AuthConfig.mergepatch.json')]
Processing  Dataset.schema.json ...
attach library /home/dbauer/projects/destine_sdm/cordra-schema/schemas/../lib/build/libs/lib.jar to schema Dataset
Schema known under id test/1052689464e38f5066d8. Updating...
Processing  FileObject.schema.json ...
Schema known under id test/d4c3554875c2b918da2d. Updating...
Processing  PropertyValue.schema.json ...
Schema known under id test/fcf8f76dda223261a8d8. Updating...
Processing  FormalParameter.schema.json ...
Schema known under id test/497954f5a6f4f66ce6f7. Updating...
Processing  Person.schema.json ...
Schema known under id test/8c41ae88467fe5bbad09. Updating...
Processing  Workflow.schema.json ...
Schema known under id test/d7a484140f5f9f7f5427. Updating...
Processing  Organization.schema.json ...
Schema known under id test/519255ae1f74ffc5ddd2. Updating...
Processing  SoftwareApplication.schema.json ...
Schema known under id test/ca05d5aed1fb0fa6b2c0. Updating...
Processing  CreateAction.schema.json ...
Schema known under id test/64b34dfa733ba2401298. Updating...

There is also an utility script [./schemas/deleteAllObjects.py] which can be used to delete all objects from a running Cordra instance.

LICENSE

Licensed under the MIT License