* load local configuration when configuration tests

* keep commons imports together

* fix duplicate keyword argument issue

* use context path from default config in test_to_resource test

* rm extra store_config.pop

* refactor store config

* pass view when sparql, elastic call, todo search

* rm unless constants from store

* turn view to endpoint

* endpoint to view param

* rename param

* rename param2

* keyword param from forge call

* missing underscore

* git status

* make endpoint refac

* edit querying notebook to showcase feature, todo set up better view

* refac notebook edit

* change view creation mapping

* check filters not provided as keyword arg

* fix querying notebook, retrieve using resource url

* test make endpoint function

* use *filters for the store interface and implementations

* added timeouts to every requests. call

* centralise default request timeout

* rm import

* use constant in file get

…ething it raises an error

* change signatures to allow for boolean change_schema on update

* change_schema implemented for single resource update

* refactor batch actions

* lint

* began batch update schema

* change schema many

* progress

* rm / join

* rm useless change

* fix

* change schema to update schema

* update instead of change

* example notebook for schema method, todo update

* notebook example with update

* lint

* improve notebook

* fix one test

* keep unconstrained schema only for update endpoint else _

* same url building in one and many

* add timeout

* schema id optional in update

* rename local parse

* rename keep_unconstrained to use_unconstrained_id

* rm extra docstring param

* change signatures to allow for boolean change_schema on update

* change_schema implemented for single resource update

* refactor batch actions

* lint

* began batch update schema

* change schema many

* progress

* rm / join

* rm useless change

* fix

* change schema to update schema

* update instead of change

* example notebook for schema method, todo update

* notebook example with update

* lint

* improve notebook

* fix one test

* keep unconstrained schema only for update endpoint else _

* same url building in one and many

* add timeout

* schema id optional in update

* rename local parse

* rm second request for metadata

* add query param annotate only if retrieve source is true

* retrieval error if issue creating resource from response

* rm cross bucket check with source

* add todo

* separate metadata call if cross bucket and source

* refac

* fixes and notebook update

* check deployment endpoint self, may need to be checking multiple values

* revert to self.endpoint

* updated notebook to show retrieval

* fix response name

* add query param annotate only if retrieve source is true

* separate metadata call if cross bucket and source

* rename keep_unconstrained to use_unconstrained_id

* rm extra docstring

* better comments

* clarify comment

* comment fix

* improve markdown

* re-do metadata fetch until endpoint is fixed

* better notebook

* rename variables

* code style

* fix replace in comments

* update comments

…False (#382)

* return resource as_json optionally when forge.elastic

* as_resource instead of as_json, default True

* skeleton to enable building resources from different values in the es response payload

* example of forge.elastic as_resource = False in getting started Querying notebook

* Set jsonld context version to 1.1
* this enables non IRI-delimiting character not present in rdflib.plugins.shared.jsonld.context.URI_GEN_DELIMS (e.g '_' in "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_") to be used when defining jsonld context prefix

…gregated (#392)

Currently the pySHACL throws a ReportableRuntimeError("Evaluation path too deep!\n{}".format(path_str)) exception when evaluating a shape if the length of its transitive closure of the sh:node property is bigger or equal to 30.

Give a node shape, this PR addresses this by:

* Fixes pyshacl deep nodeshape path eval error by first recursively collecting all the property shapes directly defined (through sh:property) by the node shape or inherited from the node shape parents then link those collected property shapes to the node shape through sh:property
and finally remove the node shape <-> parent shape relatioinships
* Aligned the expected data model for a shacl shape between the RDF StoreService and DirectoryService:

* Fixed coupled of issues:
* forge.prefixes() was raising pandas.Dataframe error "if using all scalar values, you must pass an index"
* fixed forge.types() to properly collect types from rdfsercice.class_to_shape
* fixed forge.template() when using an rdf  model based on a store service: Unable to generate template:'tuple' object has no attribute 'traverse'

* Added support for inference when using the RdfModel:
     * support for importing ontologies from schemas using owl:imports
     * use forge.validate(resource, inference="inference_value", type_='AType') with inference_value as in https://github.com/RDFLib/pySHACL/blob/v0.25.0/pyshacl/validate.py#L81. inference_value="rdfs" seems to be enough to extend the resource with the transitive closures of type subClassOf and/or property subPropertyOf relations as per the
                          RDFS entailment rules (https://www.w3.org/TR/rdf-mt/).

* Validation now fails when a type not in the resource is provided as value of the type_ argument unless inference is enabled (with inference='rdfs' for example) and the resource type is a subClassOf of type_

…cursive_resolve when resolving a str jsonld context (#402)

* Add alternateName to agent resolver

* Added property also to the agent-to-resource mapping

* Make add_image method of a Dataset, and not of KnowledgeGraphForge

* Update notebooks with example of dataset.add_image method

resolve with target species returns only species and strain returns strains

…able (#406)

* Add method when initializing forge to export environment variable

* Remove addition in setup.py and try os.environ instead of os.system

…-file-content-length` to header (#403)

* Remove nexus_sdk from nexus store when uploading files

* Change content length header to be

* split file get call and property access

* split prepare download one

* lint

---------

Co-authored-by: Leonardo Cristella <[email protected]>

* rm sdk usage from bluebrainexus store file

* rm sdk usage from utils

* rm sdk usage from service

* rm nexussdk from test

* lint

* fix patch

* change usage of project_fetch function for successful patching in tests

* rename module of sdk methods

* remove leftover image from store

* missing file

* restore config

* remove s from file name

* missing the file, again

---------

Co-authored-by: Cristina E. González-Espinoza <[email protected]>

…Literal value (#397)

* Added batched retrieval

* Check for schema id to use schema endpoint

* Add example in unit test

* Add missing  parameter inside _register_one. Add notebook example of schema handling

* check if resource_id is given