vO.4.0 Release Notes¶

This release adds incremental features to both Nexus Forge core and specializations modules. This release also implemented many fixes to various issues raised by users.

New Features¶

Querying¶

Add cross-bucket search feature #71 #74 (issue:#63)(usage: 04 - Querying notebook on Github or on )

If cross_bucket is set to True, resources could be retrieved by identifier from multiple buckets. In such case, a specific bucket can be target using the bucket argument.

Usage:

resource = forge.search(<resource_id>, cross_bucket=True, bucket=<str>)

Note

The configured store should support cross bucket search.

Add support for targeting specific search endpoint when searching data. Currently only SPARQL endpoints are supported #71 (issue:#63)(usage: 04 - Querying notebook on Github or on )

A searchendpoints configuration can be added to the Store configuration.

"Store": {
        "name": <str>,
        "endpoint": <str>,
        "bucket": <str>,
        "token": <str>,
        "searchendpoints": {
             "<querytype>": { # <a query paradigm supported by the store (e.g. sparql)>
             "endpoint": <str> #<an IRI of a query endpoint>
         }
        },
        "versioned_id_template": <str>,
        "file_resource_mapping": <str>
}

Enhancements¶

Forge¶

Add creating a forge session from a configuration URL #91 (issue:#65)

forge = KnowledgeGraphForge(configuration="https://...config.json") # or config.yml

Querying¶

Add query param support when retrieving a resource #79

resource = forge.retrieve(id="https://..?rev=1&p=aparam")

Specifically, when the version argument is provided like in:

resource = forge.retrieve(id="https://..?rev=1&p=aparam, version=2")

then it supersedes the rev query param while the other query params (e.g p=aparam) are kept as they are.

Dataset¶

Dataset provenance assertion methods are now all aligned to accept either a Resource object of identifier. #88 (usage: 02 - Dataset notebook on Github or on )

Dataset(forge: KnowledgeGraphForge, type: str = "Dataset", **properties)
  add_contribution(resource: Union[str, Resource], versioned: bool = True, **kwargs) -> None
  add_generation(resource: Union[str, Resource], versioned: bool = True, **kwargs) -> None
  add_derivation(resource: Union[str, Resource], versioned: bool = True, **kwargs) -> None
  add_invalidation(resource: Union[str, Resource], versioned: bool = True, **kwargs) -> None

When a Resourcce is provided, forge.freeze will add the resource’s version to its reference within the dataset enabling immutable identifier. forge.freeze is not supported when a resource identifier (str) is provided.

Bug Fixes¶

Forge¶

Fix has no attribute ‘_rev’ error when calling forge.freeze on a Dataset object. #81 #88 (issue:#80)
Fix RuntimeError occuring when calling nest_asyncio.apply() outside a Jupyter notebook session #62 (issue:#60)
Fix failing forge.download when the provided path (e.g. distribution.contentUrl) is no longer present in all distributions json objects #85 (issue:#84)(usage: 02 - Dataset notebook on Github or on ). This is to cope with schema.org/distribution specification which supports distribution.contentUrl or distribution.url when recording the location of a dataset.

Resolving¶

Fix OntologyResolver to resolve ontology terms when notation and prefLabel properties are missing #76 (issue:#69)(usage: 09 - Resolving notebook on Github or on )

Querying¶

Fix BlueBrainNexus store file retrieval support #75 (issue:#64)

Converting¶

Fix turning a list of Resource elements to RDFlib Graph using forge.as_graph while avoiding graph merge resulting from using graph set operation (such as +) #87