h5rdmtoolbox 2.7.0__tar.gz → 2.7.2__tar.gz

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5rdmtoolbox
-Version: 2.7.0
+Version: 2.7.2
 Summary: Supporting a FAIR Research Data lifecycle using Python and HDF5.
 Author-email: Matthias Probst <matth.probst@gmail.com>
 License-Expression: MIT

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/h5rdmtoolbox/catalog/abstracts.py

@@ -80,7 +80,8 @@ class DataStore(Store, ABC):
 class MetadataStore(Store, ABC):
     """Metadata database interface using."""
 
-    __populate_on_init__ = False
+    __supports_named_graphs__: bool
+    __populate_on_init__: bool = False
     __shacl_shapes__: Dict[str, rdflib.Graph] = {}
 
     @abstractmethod

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/h5rdmtoolbox/catalog/core.py

@@ -121,6 +121,8 @@ class RemoteSparqlStore(MetadataStore):
 
 class GraphDB(RemoteSparqlStore):
     """GraphDB RDF database store."""
+
+    __supports_named_graphs__: bool=True
     __supported_file_extensions__ = {".ttl", ".rdf", ".jsonld"}
 
     def __init__(self,
@@ -401,7 +403,7 @@ class GraphDB(RemoteSparqlStore):
 
 class InMemoryRDFStore(RDFStore):
     """In-memory RDF database that can upload files and return a combined graph."""
-
+    __supports_named_graphs__=False
     __default_expected_file_extensions__ = {".ttl", ".rdf", ".jsonld", ".nt", ".xml", ".n3"}
     __populate_on_init__ = True
 
@@ -786,6 +788,10 @@ class HDF5SqlDB(DataStore):
 class MetadataStoreQuery(Query, ABC):
     """RDF Store Query interface."""
 
+    @abstractmethod
+    def execute(self, store: "Store", named_graph: Optional[str]=None) -> "QueryResult":
+        """Executes the query against the given metadata store with optional named graph."""
+
 
 class SparqlQuery(MetadataStoreQuery):
     """A SPARQL query interface for RDF stores."""

h5rdmtoolbox-2.7.2/h5rdmtoolbox/ld/user/datasets.py

@@ -0,0 +1,45 @@
+import rdflib
+from ontolutils.namespacelib import SCHEMA
+
+from h5rdmtoolbox.ld.rdf import PROTECTED_ATTRIBUTE_NAMES
+from h5rdmtoolbox.ld.user.attributes import process_attribute
+from h5rdmtoolbox.ld.utils import get_obj_bnode
+from .utils import apply_rdf_mappings
+from ..rdf import RDFManager
+import json
+
+def process_dataset(*, dataset, graph, rdf_mappings, blank_node_iri_base=None):
+    dataset_uri = get_obj_bnode(dataset, blank_node_iri_base=blank_node_iri_base)
+    for ak, av in dataset.attrs.items():
+        if ak not in PROTECTED_ATTRIBUTE_NAMES:
+            process_attribute(dataset, ak, av, graph, blank_node_iri_base=blank_node_iri_base)
+        apply_rdf_mappings(dataset, dataset_uri, graph, rdf_mappings)
+
+    rdf_type = RDFManager(dataset.attrs).type
+    if rdf_type is not None:
+        graph.add((dataset_uri, rdflib.RDF.type, rdflib.URIRef(rdf_type)))
+
+    rdf_subject = RDFManager(dataset.attrs).subject
+    if rdf_subject:
+        graph.add((dataset_uri, SCHEMA.about, rdflib.URIRef(rdf_subject)))
+
+    rdf_predicate = RDFManager(dataset.attrs).predicate
+    if rdf_predicate:
+        _predicates = dataset.attrs.get("RDF_PREDICATE", None)
+        if _predicates:
+            self_predicate = json.loads(dataset.attrs["RDF_PREDICATE"]).get("SELF", None)
+            if self_predicate:
+                parent_uri = get_obj_bnode(dataset.parent, blank_node_iri_base=blank_node_iri_base)
+
+                _parent_subject = RDFManager(dataset.parent.attrs).subject
+
+                if _parent_subject:
+                    if rdf_subject:
+                        graph.add((rdflib.URIRef(_parent_subject), rdflib.URIRef(self_predicate), rdflib.URIRef(rdf_subject)))
+                    else:
+                        graph.add((rdflib.URIRef(_parent_subject), rdflib.URIRef(self_predicate), dataset_uri))
+                else:
+                    if rdf_subject:
+                        graph.add((parent_uri, rdflib.URIRef(self_predicate), rdflib.URIRef(rdf_subject)))
+                    else:
+                        graph.add((parent_uri, rdflib.URIRef(self_predicate), dataset_uri))

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/h5rdmtoolbox/ld/utils.py

@@ -132,9 +132,9 @@ def get_property_node(
     """Get a property node for an HDF5 object."""
     _file_id = _get_file_id(obj.file)
     if obj.name == "/":
-        _id = f"{_file_id}@{name}"
+        _id = f"{_file_id}@{_parse_obj_name(name)}"
     else:
-        _id = f"{_file_id}{_parse_obj_name(obj.name)}__{name}"
+        _id = f"{_file_id}{_parse_obj_name(obj.name)}__{_parse_obj_name(name)}"
     if blank_node_iri_base:
         return rdflib.URIRef(f'{blank_node_iri_base}{_id}')
     return rdflib.BNode(_id)
@@ -146,9 +146,9 @@ def get_attr_node(
         blank_node_iri_base: str) -> Union[rdflib.URIRef, rdflib.BNode]:
     _file_id = _get_file_id(obj.file)
     if obj.name == "/":
-        _id = f"{_file_id}@{name}"
+        _id = f"{_file_id}@{_parse_obj_name(name)}"
     else:
-        _id = f"{_file_id}{_parse_obj_name(obj.name)}@{name}"
+        _id = f"{_file_id}{_parse_obj_name(obj.name)}@{_parse_obj_name(name)}"
     if blank_node_iri_base:
         return rdflib.URIRef(f'{blank_node_iri_base}{_id}')
     return rdflib.BNode(f"{_id}")

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/h5rdmtoolbox/wrapper/core.py

@@ -2513,6 +2513,7 @@ class File(h5py.File, Group):
                        contextual=contextual,
                        file_uri=file_uri,
                        skipND=skipND,
+                       context=context,
                        rdf_mappings=rdf_mappings)
         if prefix:
             graph.bind(prefix, file_uri)

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/h5rdmtoolbox.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5rdmtoolbox
-Version: 2.7.0
+Version: 2.7.2
 Summary: Supporting a FAIR Research Data lifecycle using Python and HDF5.
 Author-email: Matthias Probst <matth.probst@gmail.com>
 License-Expression: MIT

{h5rdmtoolbox-2.7.0 → h5rdmtoolbox-2.7.2}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "h5rdmtoolbox"
-version = "2.7.0"
+version = "2.7.2"
 description = "Supporting a FAIR Research Data lifecycle using Python and HDF5."
 readme = "README.md"
 requires-python = ">=3.9, <3.14"

h5rdmtoolbox-2.7.0/h5rdmtoolbox/ld/user/datasets.py

@@ -1,24 +0,0 @@
-import rdflib
-from ontolutils.namespacelib import SCHEMA
-
-from h5rdmtoolbox.ld.rdf import PROTECTED_ATTRIBUTE_NAMES
-from h5rdmtoolbox.ld.user.attributes import process_attribute
-from h5rdmtoolbox.ld.utils import get_obj_bnode
-from .utils import apply_rdf_mappings
-from ..rdf import RDFManager
-
-
-def process_dataset(*, dataset, graph, rdf_mappings, blank_node_iri_base=None):
-    dataset_uri = get_obj_bnode(dataset, blank_node_iri_base=blank_node_iri_base)
-    for ak, av in dataset.attrs.items():
-        if ak not in PROTECTED_ATTRIBUTE_NAMES:
-            process_attribute(dataset, ak, av, graph, blank_node_iri_base=blank_node_iri_base)
-        apply_rdf_mappings(dataset, dataset_uri, graph, rdf_mappings)
-
-    rdf_type = RDFManager(dataset.attrs).type
-    if rdf_type is not None:
-        graph.add((dataset_uri, rdflib.RDF.type, rdflib.URIRef(rdf_type)))
-
-    rdf_subject = RDFManager(dataset.attrs).subject
-    if rdf_subject:
-        graph.add((dataset_uri, SCHEMA.about, rdflib.URIRef(rdf_subject)))