def _type_shape(self, iri: URIRef):
try:
shape = self._sg.lookup_shape_from_node(iri)
except KeyError:
self._load_shape(self._shapes_to_resources[iri])
# reloads the shapes graph
self._sg = ShapesGraphWrapper(self._graph)
shape = self._sg.lookup_shape_from_node(iri)
return shape
def __init__(self,
default_store: Store,
context_iri: Optional[str] = None,
context_store: Optional[Store] = None) -> None:
self.default_store = default_store
self.context_store = context_store or default_store
self.NXV = Namespace("https://bluebrain.github.io/nexus/vocabulary/")
self.store_metadata_iri = "https://bluebrain.github.io/nexus/contexts/resource.json"
self._shapes_to_resources: Dict
self._imported = list()
self._graph = Graph()
self._sg = ShapesGraphWrapper(self._graph)
super().__init__(self._graph, context_iri)
def __init__(self, default_store: Store, context_iri: Optional[str] = None,
context_store: Optional[Store] = None) -> None:
self.default_store = default_store
self.context_store = context_store or default_store
# FIXME: define a store independent strategy
self.NXV = Namespace(self.default_store.service.namespace) if hasattr(self.default_store.service, "namespace") \
else Namespace(Service.NEXUS_NAMESPACE_FALLBACK)
self.store_metadata_iri = self.default_store.service.store_context if hasattr(self.default_store.service, "store_context") \
else Namespace(Service.NEXUS_CONTEXT_FALLBACK)
self._shapes_to_resources: Dict
self._imported = list()
self._graph = Graph()
self._sg = ShapesGraphWrapper(self._graph)
super().__init__(self._graph, context_iri)
class DirectoryService(RdfService):
def __init__(self, dirpath: Path, context_iri: str) -> None:
self._graph = load_rdf_files(dirpath)
self._sg = ShapesGraphWrapper(self._graph)
super().__init__(self._graph, context_iri)
def schema_source_id(self, schema_iri: str) -> str:
# FIXME should return the file path where the schema is in
return schema_iri
def materialize(self, iri: URIRef) -> NodeProperties:
sh = self._sg.lookup_shape_from_node(iri)
predecessors = set()
props, attrs = sh.traverse(predecessors)
if props:
attrs["properties"] = props
return NodeProperties(**attrs)
def _validate(self, iri: str,
data_graph: Graph) -> Tuple[bool, Graph, str]:
validator = Validator(data_graph, shacl_graph=self._graph)
return validator.run()
def resolve_context(self, iri: str) -> Dict:
if iri in self._context_cache:
return self._context_cache[iri]
else:
try:
context = Context(iri)
except FileNotFoundError as e:
raise ValueError(e)
else:
self._context_cache.update({iri: context.document})
return context.document
def generate_context(self) -> Dict:
return self._generate_context()
def _build_shapes_map(self) -> Dict:
query = """
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sh: <http://www.w3.org/ns/shacl#>
SELECT ?type ?shape WHERE {
{ ?shape sh:targetClass ?type .}
UNION {
SELECT (?shape as ?type) ?shape WHERE {
?shape a sh:NodeShape .
?shape a rdfs:Class
}
}
} ORDER BY ?type"""
res = self._graph.query(query)
return {row["type"]: row["shape"] for row in res}
def generate_context(self) -> Dict:
for v in self._shapes_to_resources.values():
self._load_shape(v)
# reloads the shapes graph
self._sg = ShapesGraphWrapper(self._graph)
return self._generate_context()
class StoreService(RdfService):
def __init__(self,
default_store: Store,
context_iri: Optional[str] = None,
context_store: Optional[Store] = None) -> None:
self.default_store = default_store
self.context_store = context_store or default_store
# FIXME: define a store independent strategy
self.NXV = Namespace(self.default_store.service.namespace) if hasattr(self.default_store.service, "namespace") \
else Namespace(Service.NEXUS_NAMESPACE_FALLBACK)
self.store_metadata_iri = self.default_store.service.store_context if hasattr(self.default_store.service, "store_context") \
else Namespace(Service.NEXUS_CONTEXT_FALLBACK)
self._shapes_to_resources: Dict
self._imported = list()
self._graph = Graph()
self._sg = ShapesGraphWrapper(self._graph)
super().__init__(self._graph, context_iri)
def schema_source_id(self, schema_iri: str) -> str:
return self._shapes_to_resources[schema_iri]
def materialize(self, iri: URIRef) -> NodeProperties:
shape = self._type_shape(iri)
predecessors = set()
props, attrs = shape.traverse(predecessors)
if props:
attrs["properties"] = props
return NodeProperties(**attrs)
def _validate(self, iri: str,
data_graph: Graph) -> Tuple[bool, Graph, str]:
# _type_shape will make sure all the shapes for this type are in the graph
self._type_shape(iri)
validator = Validator(data_graph, shacl_graph=self._graph)
return validator.run()
def resolve_context(self, iri: str) -> Dict:
if iri in self._context_cache:
return self._context_cache[iri]
document = self.recursive_resolve(iri)
self._context_cache.update({iri: document})
return document
def generate_context(self) -> Dict:
for v in self._shapes_to_resources.values():
self._load_shape(v)
# reloads the shapes graph
self._sg = ShapesGraphWrapper(self._graph)
return self._generate_context()
def _build_shapes_map(self) -> Dict:
query = f"""
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sh: <http://www.w3.org/ns/shacl#>
SELECT ?type ?shape ?resource_id WHERE {{
{{ ?shape sh:targetClass ?type .
?resource_id <{self.NXV.shapes}> ?shape
}} UNION {{
SELECT (?shape as ?type) ?shape ?resource_id WHERE {{
?shape a sh:NodeShape .
?shape a rdfs:Class .
?resource_id <{self.NXV.shapes}> ?shape
}}
}}
}} ORDER BY ?type"""
# make sure to get all types
limit = 100
offset = 0
count = limit
class_to_shapes = dict()
shape_resource = dict()
while count == limit:
resources = self.context_store.sparql(query,
debug=False,
limit=limit,
offset=offset)
for r in resources:
shape_uri = URIRef(r.shape)
class_to_shapes[r.type] = shape_uri
shape_resource[shape_uri] = URIRef(r.resource_id)
count = len(resources)
offset += limit
self._shapes_to_resources = shape_resource
return class_to_shapes
def recursive_resolve(self, context: Union[Dict, List, str]) -> Dict:
document = dict()
if isinstance(context, list):
if self.store_metadata_iri in context:
context.remove(self.store_metadata_iri)
for x in context:
document.update(self.recursive_resolve(x))
elif isinstance(context, str):
try:
local_only = False if self.default_store == self.context_store else True
doc = self.default_store.service.resolve_context(
context, local_only=local_only)
except ValueError:
try:
doc = self.context_store.service.resolve_context(
context, local_only=False)
except ValueError as e:
raise e
document.update(self.recursive_resolve(doc))
elif isinstance(context, dict):
document.update(context)
return document
def _load_shape(self, resource_id):
if resource_id not in self._imported:
try:
shape = self.context_store.retrieve(resource_id,
version=None,
cross_bucket=False)
except RetrievalError as e:
print(e, resource_id)
# failed, don't try to load again
self._imported.append(resource_id)
else:
json_dict = as_jsonld(shape,
form="compacted",
store_metadata=False,
model_context=None,
metadata_context=None,
context_resolver=self.context_store.
service.resolve_context)
# this double conversion was due blank nodes were not "regenerated" with json-ld
temp_graph = Graph().parse(data=json.dumps(json_dict),
format="json-ld")
self._graph.parse(data=temp_graph.serialize(format="n3"),
format="n3")
self._imported.append(resource_id)
if hasattr(shape, "imports"):
for dependency in shape.imports:
self._load_shape(self.context.expand(dependency))
def _type_shape(self, iri: URIRef):
try:
shape = self._sg.lookup_shape_from_node(iri)
except KeyError:
self._load_shape(self._shapes_to_resources[iri])
# reloads the shapes graph
self._sg = ShapesGraphWrapper(self._graph)
shape = self._sg.lookup_shape_from_node(iri)
return shape
def __init__(self, dirpath: Path, context_iri: str) -> None:
self._graph = load_rdf_files(dirpath)
self._sg = ShapesGraphWrapper(self._graph)
super().__init__(self._graph, context_iri)