A Java library to create and modify RO-Crates. The aim of this implementation is to not require too deep knowledge of the specification, and avoiding crates which do not fully comply to the specification, at the same time.
- Instructions for your build manager (e.g., Gradle, Maven, etc.)
- Quick-Start
- Adapting Specification Examples
- Related Publications
Build and run tests: ./gradlew build
Build documentation: ./gradlew javadoc
On Windows, replace ./gradlew with gradlew.bat.
- âś… Version 1.1
- 🛠️ Version 1.2-DRAFT
- âś… Reading and writing crates with additional profiles or specifications (examples for reading, examples for writing)
- âś… Adding profiles or other specifications to a crate (examples)
Example for a basic crate from RO-Crate website
RoCrate roCrate = new RoCrateBuilder("name", "description").build();RoCrate roCrate = new RoCrateBuilder("name", "description")
.addValuePairToContext("Station", "www.station.com")
.addUrlToContext("contextUrl")
.addDataEntity(
new FileEntity.FileEntityBuilder()
.setId("survey-responses-2019.csv")
.addProperty("name", "Survey responses")
.addProperty("contentSize", "26452")
.addProperty("encodingFormat", "text/csv")
.build()
)
.addDataEntity(...)
...
.addContextualEntity(...)
...
.build();Note: Adding an entity with an ID ("@id") which is already being used by another entity in the crate, the old entity will be overwritten.
The library currently comes with three specialized DataEntities:
DataSetEntityFileEntity(used in the example above)WorkflowEntity
If another type of DataEntity is required, the base class DataEntity can be used. Example:
new DataEntity.DataEntityBuilder()
.addType("CreativeWork")
.setId("ID")
.addProperty("property from schema.org/Creativework", "value")
.build();Note that here you are supposed to add the type of your DataEntity because it is not known.
A DataEntity and its subclasses can have a local file associated with them,
instead of one located on the web (which link is the ID of the data entity). Example:
Example adding file:
new FileEntity.FileEntityBuilder()
.setId("new_file.txt")
.setSource(new File("file"))
.addProperty("description", "my new file that I added")
.build();Contextual entities cannot be associated with a file (they are pure metadata).
To add a contextual entity to a crate you use the function .addContextualEntity(ContextualEntity entity).
Some types of derived/specializes entities are:
OrganizationEntityPersonEntityPlaceEntity
If you need another type of contextual entity, use the base class ContextualEntity.
The library provides a way to automatically create contextual entities from external providers. Currently, support for ORCID and ROR is implemented. Example:
PersonEntity person = ORCIDProvider.getPerson("https://orcid.org/*")
OrganizationEntity organization = RORProvider.getOrganization("https://ror.org/*");Writing to folder:
RoCrateWriter folderRoCrateWriter = new RoCrateWriter(new FolderWriter());
folderRoCrateWriter.save(roCrate, "destination");Writing to zip file:
RoCrateWriter roCrateZipWriter = new RoCrateWriter(new ZipWriter());
roCrateZipWriter.save(roCrate, "destination");More writing strategies can be implemented, if required.
Reading from folder:
RoCrateReader roCrateFolderReader = new RoCrateReader(new FolderReader());
RoCrate res = roCrateFolderReader.readCrate("source");Reading from zip file:
RoCrateReader roCrateFolderReader = new RoCrateReader(new ZipReader());
RoCrate crate = roCrateFolderReader.readCrate("source");By setting the preview to an AutomaticPreview, the library will automatically create a preview using the ro-crate-html-js tool.
It has to be installed using npm install --global ro-crate-html-js in order to use it.
If you want to use a custom-made preview, you can set it using the CustomPreview class. AutomaticPreview is currently not set by default.
RoCrate roCrate = new RoCrateBuilder("name", "description")
.setPreview(new AutomaticPreview())
.build();Right now, the only implemented way of validating a RO-crate is to use a JSON-Schema that the crates metadata JSON file should match. JSON-Schema is an established standard and therefore a good choice for a crate profile. Example:
Validator validator = new Validator(new JsonSchemaValidation("./schema.json"));
boolean valid = validator.validate(crate);This section describes how to generate the official specifications examples. Each example first shows the ro-crate-metadata.json and, below that, the required Java code to generate it.
{ "@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
"about": {"@id": "./"}
},
{
"@id": "./",
"identifier": "https://doi.org/10.4225/59/59672c09f4a4b",
"@type": "Dataset",
"datePublished": "2017",
"name": "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...",
"description": "Palliative care planning for nursing home residents with advanced dementia ...",
"license": {"@id": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/"}
},
{
"@id": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/",
"@type": "CreativeWork",
"description": "This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.",
"identifier": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/",
"name": "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)"
}
]
}Here, everything is created manually. For the following examples, more convenient creation methods are used.
RoCrate crate = new RoCrate();
ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
.addType("CreativeWork")
.setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
.addProperty("description", "This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
.addProperty("identifier", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
.addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
.build();
crate.setRootDataEntity(new RootDataEntity.RootDataEntityBuilder()
.addProperty("identifier", "https://doi.org/10.4225/59/59672c09f4a4b")
.addProperty("datePublished", "2017")
.addProperty("name", "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...")
.addProperty("description", "Palliative care planning for nursing home residents with advanced dementia ...")
.setLicense(license)
.build());
crate.setJsonDescriptor(new ContextualEntity.ContextualEntityBuilder()
.setId("ro-crate-metadata.json")
.addType("CreativeWork")
.addIdProperty("about", "./")
.addIdProperty("conformsTo", "https://w3id.org/ro/crate/1.1")
.build()
);
crate.addContextualEntity(license);{ "@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
"about": {"@id": "./"}
},
{
"@id": "./",
"@type": [
"Dataset"
],
"hasPart": [
{
"@id": "cp7glop.ai"
},
{
"@id": "lots_of_little_files/"
}
]
},
{
"@id": "cp7glop.ai",
"@type": "File",
"name": "Diagram showing trend to increase",
"contentSize": "383766",
"description": "Illustrator file for Glop Pot",
"encodingFormat": "application/pdf"
},
{
"@id": "lots_of_little_files/",
"@type": "Dataset",
"name": "Too many files",
"description": "This directory contains many small files, that we're not going to describe in detail."
}
]
}Here we use the inner builder classes for the construction of the crate.
Doing so, the Metadata File Descriptor and the Root Data Entity entities are added automatically.
setSource() is used to provide the actual location of these Data Entities (if they are not remote).
The Data Entity file in the crate will have the name of the entity's ID.
RoCrate crate = new RoCrate.RoCrateBuilder()
.addDataEntity(
new FileEntity.FileEntityBuilder()
.setId("cp7glop.ai")
.setSource(new File("path to file"))
.addProperty("name", "Diagram showing trend to increase")
.addProperty("contentSize", "383766")
.addProperty("description", "Illustrator file for Glop Pot")
.setEncodingFormat("application/pdf")
.build()
)
.addDataEntity(
new DataSetEntity.DataSetBuilder()
.setId("lots_of_little_files/")
.setSource(new File("path_to_files"))
.addProperty("name", "Too many files")
.addProperty("description", "This directory contains many small files, that we're not going to describe in detail.")
.build()
)
.build();{ "@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
"about": {"@id": "./"}
},
{
"@id": "./",
"@type": [
"Dataset"
],
"hasPart": [
{
"@id": "survey-responses-2019.csv"
},
{
"@id": "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf"
},
]
},
{
"@id": "survey-responses-2019.csv",
"@type": "File",
"name": "Survey responses",
"contentSize": "26452",
"encodingFormat": "text/csv"
},
{
"@id": "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf",
"@type": "File",
"name": "RO-Crate specification",
"contentSize": "310691",
"description": "RO-Crate specification",
"encodingFormat": "application/pdf"
}
]
}The web resource does not use .setSource(), but uses the ID to indicate the file's location.
RoCrate crate = new RoCrate.RoCrateBuilder()
.addDataEntity(
new FileEntity.FileEntityBuilder()
.setId("survey-responses-2019.csv")
.setSource(new File("README.md"))
.addProperty("name", "Survey responses")
.addProperty("contentSize", "26452")
.setEncodingFormat("text/csv")
.build()
)
.addDataEntity(
new FileEntity.FileEntityBuilder()
.setId("https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf")
.addProperty("name", "RO-Crate specification")
.addProperty("contentSize", "310691")
.addProperty("description", "RO-Crate specification")
.setEncodingFormat("application/pdf")
.build()
)
.build();{ "@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
"about": {"@id": "./"},
"description": "RO-Crate Metadata File Descriptor (this file)"
},
{
"@id": "./",
"@type": "Dataset",
"name": "Example RO-Crate",
"description": "The RO-Crate Root Data Entity",
"hasPart": [
{"@id": "data1.txt"},
{"@id": "data2.txt"}
]
},
{
"@id": "data1.txt",
"@type": "File",
"description": "One of hopefully many Data Entities",
"author": {"@id": "#alice"},
"contentLocation": {"@id": "http://sws.geonames.org/8152662/"}
},
{
"@id": "data2.txt",
"@type": "File"
},
{
"@id": "#alice",
"@type": "Person",
"name": "Alice",
"description": "One of hopefully many Contextual Entities"
},
{
"@id": "http://sws.geonames.org/8152662/",
"@type": "Place",
"name": "Catalina Park"
}
]
}If there is no special method for including relative entities (ID properties) one can use .addIdProperty("key","value").
PersonEntity alice = new PersonEntity.PersonEntityBuilder()
.setId("#alice")
.addProperty("name", "Alice")
.addProperty("description", "One of hopefully many Contextual Entities")
.build();
PlaceEntity park = new PlaceEntity.PlaceEntityBuilder()
.setId("http://sws.geonames.org/8152662/")
.addProperty("name", "Catalina Park")
.build();
RoCrate crate = new RoCrate.RoCrateBuilder("Example RO-Crate", "The RO-Crate Root Data Entity")
.addContextualEntity(park)
.addContextualEntity(alice)
.addDataEntity(
new FileEntity.FileEntityBuilder()
.setId("data2.txt")
.setSource(new File(.......))
.build()
)
.addDataEntity(
new FileEntity.FileEntityBuilder()
.setId("data1.txt")
.setSource(new File(.......))
.addProperty("description", "One of hopefully many Data Entities")
.addAuthor(alice.getId())
.addIdProperty("contentLocation", park)
.build()
)
.build();{ "@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
"about": {"@id": "./"}
},
{
"@id": "./",
"@type": "Dataset",
"hasPart": [
{ "@id": "workflow/alignment.knime" }
]
},
{
"@id": "workflow/alignment.knime",
"@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
"conformsTo":
{"@id": "https://bioschemas.org/profiles/ComputationalWorkflow/0.5-DRAFT-2020_07_21/"},
"name": "Sequence alignment workflow",
"programmingLanguage": {"@id": "#knime"},
"creator": {"@id": "#alice"},
"dateCreated": "2020-05-23",
"license": { "@id": "https://spdx.org/licenses/CC-BY-NC-SA-4.0"},
"input": [
{ "@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b"}
],
"output": [
{ "@id": "#6c703fee-6af7-4fdb-a57d-9e8bc4486044"},
{ "@id": "#2f32b861-e43c-401f-8c42-04fd84273bdf"}
],
"sdPublisher": {"@id": "#workflow-hub"},
"url": "http://example.com/workflows/alignment",
"version": "0.5.0"
},
{
"@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b",
"@type": "FormalParameter",
"conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
"name": "genome_sequence",
"valueRequired": true,
"additionalType": {"@id": "http://edamontology.org/data_2977"},
"format": {"@id": "http://edamontology.org/format_1929"}
},
{
"@id": "#6c703fee-6af7-4fdb-a57d-9e8bc4486044",
"@type": "FormalParameter",
"conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
"name": "cleaned_sequence",
"additionalType": {"@id": "http://edamontology.org/data_2977"},
"encodingFormat": {"@id": "http://edamontology.org/format_2572"}
},
{
"@id": "#2f32b861-e43c-401f-8c42-04fd84273bdf",
"@type": "FormalParameter",
"conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
"name": "sequence_alignment",
"additionalType": {"@id": "http://edamontology.org/data_1383"},
"encodingFormat": {"@id": "http://edamontology.org/format_1982"}
},
{
"@id": "https://spdx.org/licenses/CC-BY-NC-SA-4.0",
"@type": "CreativeWork",
"name": "Creative Commons Attribution Non Commercial Share Alike 4.0 International",
"alternateName": "CC-BY-NC-SA-4.0"
},
{
"@id": "#knime",
"@type": "ProgrammingLanguage",
"name": "KNIME Analytics Platform",
"alternateName": "KNIME",
"url": "https://www.knime.com/whats-new-in-knime-41",
"version": "4.1.3"
},
{
"@id": "#alice",
"@type": "Person",
"name": "Alice Brown"
},
{
"@id": "#workflow-hub",
"@type": "Organization",
"name": "Example Workflow Hub",
"url":"http://example.com/workflows/"
},
{
"@id": "http://edamontology.org/format_1929",
"@type": "Thing",
"name": "FASTA sequence format"
},
{
"@id": "http://edamontology.org/format_1982",
"@type": "Thing",
"name": "ClustalW alignment format"
},
{
"@id": "http://edamontology.org/format_2572",
"@type": "Thing",
"name": "BAM format"
},
{
"@id": "http://edamontology.org/data_2977",
"@type": "Thing",
"name": "Nucleic acid sequence"
},
{
"@id": "http://edamontology.org/data_1383",
"@type": "Thing",
"name": "Nucleic acid sequence alignment"
}
]
} ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
.addType("CreativeWork")
.setId("https://spdx.org/licenses/CC-BY-NC-SA-4.0")
.addProperty("name", "Creative Commons Attribution Non Commercial Share Alike 4.0 International")
.addProperty("alternateName", "CC-BY-NC-SA-4.0")
.build();
ContextualEntity knime = new ContextualEntity.ContextualEntityBuilder()
.setId("#knime")
.addType("ProgrammingLanguage")
.addProperty("name", "KNIME Analytics Platform")
.addProperty("alternateName", "KNIME")
.addProperty("url", "https://www.knime.com/whats-new-in-knime-41")
.addProperty("version", "4.1.3")
.build();
OrganizationEntity workflowHub = new OrganizationEntity.OrganizationEntityBuilder()
.setId("#workflow-hub")
.addProperty("name", "Example Workflow Hub")
.addProperty("url", "http://example.com/workflows/")
.build();
ContextualEntity fasta = new ContextualEntity.ContextualEntityBuilder()
.setId("http://edamontology.org/format_1929")
.addType("Thing")
.addProperty("name", "FASTA sequence format")
.build();
ContextualEntity clustalW = new ContextualEntity.ContextualEntityBuilder()
.setId("http://edamontology.org/format_1982")
.addType("Thing")
.addProperty("name", "ClustalW alignment format")
.build();
ContextualEntity ban = new ContextualEntity.ContextualEntityBuilder()
.setId("http://edamontology.org/format_2572")
.addType("Thing")
.addProperty("name", "BAM format")
.build();
ContextualEntity nucSec = new ContextualEntity.ContextualEntityBuilder()
.setId("http://edamontology.org/data_2977")
.addType("Thing")
.addProperty("name", "Nucleic acid sequence")
.build();
ContextualEntity nucAlign = new ContextualEntity.ContextualEntityBuilder()
.setId("http://edamontology.org/data_1383")
.addType("Thing")
.addProperty("name", "Nucleic acid sequence alignment")
.build();
PersonEntity alice = new PersonEntity.PersonEntityBuilder()
.setId("#alice")
.addProperty("name", "Alice Brown")
.build();
ContextualEntity requiredParam = new ContextualEntity.ContextualEntityBuilder()
.addType("FormalParameter")
.setId("#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b")
.addProperty("name", "genome_sequence")
.addProperty("valueRequired", true)
.addIdProperty("conformsTo", "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/")
.addIdProperty("additionalType", nucSec)
.addIdProperty("encodingFormat", fasta)
.build();
ContextualEntity clnParam = new ContextualEntity.ContextualEntityBuilder()
.addType("FormalParameter")
.setId("#6c703fee-6af7-4fdb-a57d-9e8bc4486044")
.addProperty("name", "cleaned_sequence")
.addIdProperty("conformsTo", "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/")
.addIdProperty("additionalType", nucSec)
.addIdProperty("encodingFormat", ban)
.build();
ContextualEntity alignParam = new ContextualEntity.ContextualEntityBuilder()
.addType("FormalParameter")
.setId("#2f32b861-e43c-401f-8c42-04fd84273bdf")
.addProperty("name", "sequence_alignment")
.addIdProperty("conformsTo", "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/")
.addIdProperty("additionalType", nucAlign)
.addIdProperty("encodingFormat", clustalW)
.build();
RoCrate crate = new RoCrate.RoCrateBuilder("Example RO-Crate", "The RO-Crate Root Data Entity")
.addContextualEntity(license)
.addContextualEntity(knime)
.addContextualEntity(workflowHub)
.addContextualEntity(fasta)
.addContextualEntity(clustalW)
.addContextualEntity(ban)
.addContextualEntity(nucSec)
.addContextualEntity(nucAlign)
.addContextualEntity(alice)
.addContextualEntity(requiredParam)
.addContextualEntity(clnParam)
.addContextualEntity(alignParam)
.addDataEntity(
new WorkflowEntity.WorkflowEntityBuilder()
.setId("workflow/alignment.knime")
.setSource(new File("src"))
.addIdProperty("conformsTo", "https://bioschemas.org/profiles/ComputationalWorkflow/0.5-DRAFT-2020_07_21/")
.addProperty("name", "Sequence alignment workflow")
.addIdProperty("programmingLanguage", "#knime")
.addAuthor("#alice")
.addProperty("dateCreated", "2020-05-23")
.setLicense("https://spdx.org/licenses/CC-BY-NC-SA-4.0")
.addInput("#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b")
.addOutput("#6c703fee-6af7-4fdb-a57d-9e8bc4486044")
.addOutput("#2f32b861-e43c-401f-8c42-04fd84273bdf")
.addProperty("url", "http://example.com/workflows/alignment")
.addProperty("version", "0.5.0")
.addIdProperty("sdPublisher", "#workflow-hub")
.build()
)
.build();