https://github.com/Senckenberg-DCBiodivIT/FAIR-workflow-platform-cordra-schema
Cordra schema for the FAIR workflow platform. Modeled after RO-Crate.
https://github.com/Senckenberg-DCBiodivIT/FAIR-workflow-platform-cordra-schema
Last synced: 11 months ago
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Cordra schema for the FAIR workflow platform. Modeled after RO-Crate.
- Host: GitHub
- URL: https://github.com/Senckenberg-DCBiodivIT/FAIR-workflow-platform-cordra-schema
- Owner: dnlbauer
- License: mit
- Created: 2024-11-13T09:12:29.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-11-26T10:39:32.000Z (over 1 year ago)
- Last Synced: 2024-11-26T11:38:47.831Z (over 1 year ago)
- Language: Kotlin
- Size: 631 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](https://github.com/dnlbauer/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](https://www.cordra.org/documentation/design/java-hooks-and-methods.html)).
## 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`:
```bash
gradle clean build
(...snip...)
BUILD SUCCESSFUL in 10s
7 actionable tasks: 7 execute
```
Then update Cordra using the script:
```bash
# 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) License