Release Notes¶
This release introduces new features and enhancements to Nexus Forge while fixing a couple of bugs.
New Features¶
Resolving¶
and to try.
It is now possible to configure a property path filter for a SPARQL based Resolver (OntologyResolver and AgentResolver) target to better narrow down data to resolve to within a given bucket #290, #312 . This allows for example a user to target a specific ontology to resolve a string from. Here is the complete configuration of a Resolver:
Resolvers: <scope>: - resolver: <a class name of a Resolver> origin: <'directory', 'web_service', or 'store'> source: <a directory path, a web service endpoint, or the class name of a Store> targets: - identifier: <a name, or an IRI> bucket: <a file name, an URL path, or a Store bucket> filters: - path: <a resource property path> - value: <a resource property value to filter with> searchendpoints: sparql: endpoint: <A SPARQL endpoint to send resolving query to. Only used for resolvers based on SPARQL> result_resource_mapping: <an Hjson string, a file path, or an URL> endpoint: <when 'origin' is 'store', a Store endpoint, default to Store:endpoint> token: <when 'origin' is 'store', a Store token, default to the token provided in the configured Store>
An example of configuration for an OntologyResolver is:
config = """
Resolvers:
ontology:
- resolver: OntologyResolver
origin: store
source: BlueBrainNexus
targets:
- identifier: terms
bucket: neurosciencegraph/datamodels
- identifier: CellType
bucket: neurosciencegraph/datamodels
filters:
- path: subClassOf*.id
value: BrainCellType
- identifier: BrainRegion
bucket: neurosciencegraph/datamodels
filters:
- path: subClassOf*.id
value: BrainRegion
- identifier: Species
bucket: neurosciencegraph/datamodels
filters:
- path: subClassOf*.id
value: Species
searchendpoints:
sparql:
endpoint: "https://bluebrain.github.io/nexus/vocabulary/defaultSparqlIndex"
result_resource_mapping: https://raw.githubusercontent.com/BlueBrain/nexus-forge/master/examples/configurations/nexus-resolver/term-to-resource-mapping.hjson
"""
forge.resolve(text="Chapter", scope="schemaorg_CreativeWork", target="CreativeWork", strategy=ResolvingStrategy.EXACT_MATCH)
A specific configured target can be specified as usual when resolving:
# forge.resolvers() lists configured resolvers
forge.resolve(text="MC", scope="ontology", target="CellType", strategy=ResolvingStrategy.EXACT_MATCH)
Enhancements¶
Resource¶
to try the enhancements.
Querying¶
to try the enhancements.
Added more SPARQL clauses (such as optional, as or describe) to ignore when rewriting (using Store.rewrite_sparql()) a SPARQL query #288, #292, #297.
Added support for specifying a content-type when downloading data #265 (issue #251).
Updated SPARQL query statement builder to consider the values of resource properties @id and @type as URIs (so that the values get correctly rewritten as follows: <uri>) when used with the NOT_EQUAL search operator #265.
Introduced core/commons/sparql_query_builder.SPARQLQueryBuilder for building SPARQL select query statements and filters #290.
BlueBrainNexus store: added resource retrieval by _self value (Resource._store_metadata._self) in addition to Resource.id #271.
Added support for chaining multiple json properties using / as keys when calling searching using the filter dict syntax #305.
# Filter by type using a dictionary. affiliation and id are chained as a single json key using '/'.
# This syntax is equivalent to {"type":"Person", "affiliation": {"id":"https://www.grid.ac/institutes/grid.5333.6"}}
filters = {"type":"Person", "affiliation/id": "https://www.grid.ac/institutes/grid.5333.6"}
forge.search(filters)
Added ElasticSearch Terms query support when filter values are provided as a list and when ElasticSearch is used as a search endpoint #306.
# Filter by type using a dictionary
filters = {"type":"Person", "affiliation/id": ["https://www.grid.ac/institutes/grid.5333.6","https://ror.org/02mrd0686"]}
forge.search(filters, search_endpoint="elastic")
Set “distribution.contentUrl” as default resource json property path to follow when collecting downloadable file urls. Set the current folder as the default download path #265.
# By default and when files downloads are described as distributions (https://nexus-forge.readthedocs.io/en/latest/interaction.html#dataset),
# this release allows a client to move from:
forge.download(Resource, follow="distribution.contentUrl", path=".")
Dataset.download(forge, follow="distribution.contentUrl", path=".")
# to simply:
forge.download(Resource)
Dataset.download()
Formattting¶
to try the enhancements.
Updated forge.format() to know support URI rewriting. The specifiic rewriting logic is delegated to the configured Store. Two formatters are now supported:
Formatter.STR: corresponds to configured (in the forge config file) str formatter
Formatter.URI_REWRITER: URI rewriter. Using BlueBrainNexus store, this formatter will build a fully expanded _self rom a resource or file id
forge.format(uri=resource.id, formatter=Formatter.URI_REWRITER, is_file=False, encoding=None)
Bug Fixes¶
Modeling¶
Querying¶
BlueBrainNexus store: fixed failing resource download when the downloadble URL is a _self #283 (issue #282) .
BlueBrainNexus store: fixed download of a list of resources which were failing if at least one resource in the list did not have the requested content-type. Now only resources in the list with the requested content-type are downloaded #283 .
Resolving¶
Storing¶
Store.upload() was failing when a configured file-to-resource-mapping.hjson file was definining a transformation rule based on a forge method because of an incorrect instanciation of a Mapper object (a None Forge object was provided) was provided #315 .