h5rdmtoolbox 2.5.2__tar.gz → 2.5.3__tar.gz

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5rdmtoolbox
-Version: 2.5.2
+Version: 2.5.3
 Summary: Supporting a FAIR Research Data lifecycle using Python and HDF5.
 Home-page: https://h5rdmtoolbox.readthedocs.io/en/latest/
 Author: Matthias Probst
@@ -54,7 +54,7 @@ Provides-Extra: test
 Requires-Dist: pytest>=8.3.3; extra == "test"
 Requires-Dist: pytest-cov>=5.0.0; extra == "test"
 Requires-Dist: pylint; extra == "test"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "test"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "test"
 Requires-Dist: mongomock==4.1.2; extra == "test"
 Requires-Dist: xmltodict<=0.13.0; extra == "test"
 Requires-Dist: scipy>=1.10.1; extra == "test"
@@ -76,7 +76,7 @@ Requires-Dist: pymongo<=4.10.1,>=4.2.0; extra == "docs"
 Requires-Dist: pytest>=8.3.3; extra == "docs"
 Requires-Dist: pytest-cov>=5.0.0; extra == "docs"
 Requires-Dist: pylint; extra == "docs"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "docs"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "docs"
 Requires-Dist: mongomock==4.1.2; extra == "docs"
 Requires-Dist: xmltodict<=0.13.0; extra == "docs"
 Requires-Dist: scipy>=1.10.1; extra == "docs"
@@ -102,7 +102,7 @@ Requires-Dist: PyQt5==5.15.10; extra == "complete"
 Requires-Dist: pytest>=8.3.3; extra == "complete"
 Requires-Dist: pytest-cov>=5.0.0; extra == "complete"
 Requires-Dist: pylint; extra == "complete"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "complete"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "complete"
 Requires-Dist: mongomock==4.1.2; extra == "complete"
 Requires-Dist: xmltodict<=0.13.0; extra == "complete"
 Requires-Dist: scipy>=1.10.1; extra == "complete"
@@ -120,7 +120,7 @@ Requires-Dist: PyQt5==5.15.10; extra == "complete-with-docs"
 Requires-Dist: pytest>=8.3.3; extra == "complete-with-docs"
 Requires-Dist: pytest-cov>=5.0.0; extra == "complete-with-docs"
 Requires-Dist: pylint; extra == "complete-with-docs"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "complete-with-docs"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "complete-with-docs"
 Requires-Dist: mongomock==4.1.2; extra == "complete-with-docs"
 Requires-Dist: xmltodict<=0.13.0; extra == "complete-with-docs"
 Requires-Dist: scipy>=1.10.1; extra == "complete-with-docs"
@@ -141,7 +141,7 @@ Requires-Dist: pymongo<=4.10.1,>=4.2.0; extra == "complete-with-docs"
 Requires-Dist: pytest>=8.3.3; extra == "complete-with-docs"
 Requires-Dist: pytest-cov>=5.0.0; extra == "complete-with-docs"
 Requires-Dist: pylint; extra == "complete-with-docs"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "complete-with-docs"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "complete-with-docs"
 Requires-Dist: mongomock==4.1.2; extra == "complete-with-docs"
 Requires-Dist: xmltodict<=0.13.0; extra == "complete-with-docs"
 Requires-Dist: scipy>=1.10.1; extra == "complete-with-docs"

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/h5rdmtoolbox/ld/rdf.py

@@ -729,6 +729,14 @@ class FileIRIDict(Dict):
     def object(self):
         return self[RDF_FILE_OBJECT_ATTR_NAME]
 
+    @object.deleter
+    def object(self):
+        iri_data_data = self._attr.get(RDF_FILE_OBJECT_ATTR_NAME, None)
+        if iri_data_data is None:
+            iri_data_data = {}
+        iri_data_data.pop(self._attr_name, None)
+        self._attr[RDF_FILE_OBJECT_ATTR_NAME] = iri_data_data
+
     @object.setter
     def object(self, value):
         set_object(attr=self._attr,

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/h5rdmtoolbox/ld/user/attributes.py

@@ -25,7 +25,7 @@ def _is_date_str(value: str):
     # quick check, that first character is a digit
     if not re.match(r"^\d", value):
         return None
-    # reject version-like strings composed only of digits and dots, e.g. "2.5.2"
+    # reject version-like strings composed only of digits and dots, e.g. "2.5.3"
     if re.match(r"^\d+(?:\.\d+)+$", value):
         return None
     try:
@@ -94,14 +94,35 @@ def process_file_attribute(parent_obj, name, data, graph, file_uri: Union[URIRef
 
             elif isinstance(rdf_user_object, dict):
                 try:
-                    obj_graph = Graph().parse(data=json.loads(json.dumps(rdf_user_object)), format="json-ld")
-                    # relate the obj_graph with the predicate:
-                    _subjects = set(obj_graph.subjects())
-                    if len(_subjects) != 1:
-                        warnings.warn(f"Error parsing JSON-LD object for attribute. name={name}, data={data}. "
-                                      f"Expected exactly one subject, found {len(_subjects)}")
-                    obj_graph.add((file_uri, to_uriref(rdf_user_predicate, blank_node_iri_base),
-                                   to_uriref(list(_subjects)[0], blank_node_iri_base)))
+                    jsonld_dict = json.loads(json.dumps(rdf_user_object))
+                    obj_graph = Graph().parse(data=jsonld_dict,
+                                              format="json-ld")
+
+                    if "@graph" not in jsonld_dict:
+                        use_subject = jsonld_dict.get("@id")
+                        obj_graph.add((file_uri, to_uriref(rdf_user_predicate, blank_node_iri_base),
+                                       to_uriref(use_subject, blank_node_iri_base)))
+                    else:
+                        _graph_entities = jsonld_dict["@graph"]
+                        if len(_graph_entities) == 1:
+                            use_subject = _graph_entities[0].get("@id")
+                            obj_graph.add((file_uri, to_uriref(rdf_user_predicate, blank_node_iri_base),
+                                           to_uriref(use_subject, blank_node_iri_base)))
+                        else:
+                            for _entity in _graph_entities:
+                                if RDF.type in _entity and _entity[RDF.type] == str(SCHEMA.PropertyValue):
+                                    use_subject = _entity.get("@id")
+                                    obj_graph.add((file_uri, to_uriref(rdf_user_predicate, blank_node_iri_base),
+                                                   to_uriref(use_subject, blank_node_iri_base)))
+
+                    # obj_graph = Graph().parse(data=json.loads(json.dumps(rdf_user_object)), format="json-ld")
+                    # # relate the obj_graph with the predicate:
+                    # _subjects = set(obj_graph.subjects())
+                    # if len(_subjects) != 1:
+                    #     warnings.warn(f"Error parsing JSON-LD object for attribute. name={name}, data={data}. "
+                    #                   f"Expected exactly one subject, found {len(_subjects)}")
+                    # obj_graph.add((file_uri, to_uriref(rdf_user_predicate, blank_node_iri_base),
+                    #                to_uriref(list(_subjects)[0], blank_node_iri_base)))
                     graph += obj_graph
                 except Exception as e:
                     warnings.warn(

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/h5rdmtoolbox/ld/user/file.py

@@ -2,6 +2,7 @@ from typing import Optional
 from typing import Union
 
 import h5py
+import numpy as np
 import rdflib
 from ontolutils.namespacelib.hdf5 import HDF5
 from rdflib import Graph
@@ -38,16 +39,16 @@ def get_ld(
         file_node = get_file_bnode(source, file_uri=file_uri)
 
     if source.name == "/":
-        file_rdf = file_frdf_manager.type
+        file_rdf_type = file_frdf_manager.type
     else:
-        file_rdf = None
+        file_rdf_type = None
 
-    if file_rdf:
-        if isinstance(file_rdf, list):
-            for rdf_type in file_rdf:
+    if file_rdf_type is not None:
+        if isinstance(file_rdf_type, list) or isinstance(file_rdf_type, np.ndarray):
+            for rdf_type in file_rdf_type:
                 graph.add((file_node, rdflib.RDF.type, to_uriref(rdf_type, file_uri)))
         else:
-            graph.add((file_node, rdflib.RDF.type, to_uriref(file_rdf, file_uri)))
+            graph.add((file_node, rdflib.RDF.type, to_uriref(file_rdf_type, file_uri)))
 
     for ak, av in source.attrs.items():
         process_file_attribute(source, ak, av, graph, file_node, blank_node_iri_base=file_uri)

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/h5rdmtoolbox.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5rdmtoolbox
-Version: 2.5.2
+Version: 2.5.3
 Summary: Supporting a FAIR Research Data lifecycle using Python and HDF5.
 Home-page: https://h5rdmtoolbox.readthedocs.io/en/latest/
 Author: Matthias Probst
@@ -54,7 +54,7 @@ Provides-Extra: test
 Requires-Dist: pytest>=8.3.3; extra == "test"
 Requires-Dist: pytest-cov>=5.0.0; extra == "test"
 Requires-Dist: pylint; extra == "test"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "test"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "test"
 Requires-Dist: mongomock==4.1.2; extra == "test"
 Requires-Dist: xmltodict<=0.13.0; extra == "test"
 Requires-Dist: scipy>=1.10.1; extra == "test"
@@ -76,7 +76,7 @@ Requires-Dist: pymongo<=4.10.1,>=4.2.0; extra == "docs"
 Requires-Dist: pytest>=8.3.3; extra == "docs"
 Requires-Dist: pytest-cov>=5.0.0; extra == "docs"
 Requires-Dist: pylint; extra == "docs"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "docs"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "docs"
 Requires-Dist: mongomock==4.1.2; extra == "docs"
 Requires-Dist: xmltodict<=0.13.0; extra == "docs"
 Requires-Dist: scipy>=1.10.1; extra == "docs"
@@ -102,7 +102,7 @@ Requires-Dist: PyQt5==5.15.10; extra == "complete"
 Requires-Dist: pytest>=8.3.3; extra == "complete"
 Requires-Dist: pytest-cov>=5.0.0; extra == "complete"
 Requires-Dist: pylint; extra == "complete"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "complete"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "complete"
 Requires-Dist: mongomock==4.1.2; extra == "complete"
 Requires-Dist: xmltodict<=0.13.0; extra == "complete"
 Requires-Dist: scipy>=1.10.1; extra == "complete"
@@ -120,7 +120,7 @@ Requires-Dist: PyQt5==5.15.10; extra == "complete-with-docs"
 Requires-Dist: pytest>=8.3.3; extra == "complete-with-docs"
 Requires-Dist: pytest-cov>=5.0.0; extra == "complete-with-docs"
 Requires-Dist: pylint; extra == "complete-with-docs"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "complete-with-docs"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "complete-with-docs"
 Requires-Dist: mongomock==4.1.2; extra == "complete-with-docs"
 Requires-Dist: xmltodict<=0.13.0; extra == "complete-with-docs"
 Requires-Dist: scipy>=1.10.1; extra == "complete-with-docs"
@@ -141,7 +141,7 @@ Requires-Dist: pymongo<=4.10.1,>=4.2.0; extra == "complete-with-docs"
 Requires-Dist: pytest>=8.3.3; extra == "complete-with-docs"
 Requires-Dist: pytest-cov>=5.0.0; extra == "complete-with-docs"
 Requires-Dist: pylint; extra == "complete-with-docs"
-Requires-Dist: ssnolib<3.0.0,>=2.1.0.2; extra == "complete-with-docs"
+Requires-Dist: ssnolib<3.0.0,>=2.2.0.0; extra == "complete-with-docs"
 Requires-Dist: mongomock==4.1.2; extra == "complete-with-docs"
 Requires-Dist: xmltodict<=0.13.0; extra == "complete-with-docs"
 Requires-Dist: scipy>=1.10.1; extra == "complete-with-docs"

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/h5rdmtoolbox.egg-info/requires.txt

@@ -25,7 +25,7 @@ PyQt5==5.15.10
 pytest>=8.3.3
 pytest-cov>=5.0.0
 pylint
-ssnolib<3.0.0,>=2.1.0.2
+ssnolib<3.0.0,>=2.2.0.0
 mongomock==4.1.2
 xmltodict<=0.13.0
 scipy>=1.10.1
@@ -42,7 +42,7 @@ PyQt5==5.15.10
 pytest>=8.3.3
 pytest-cov>=5.0.0
 pylint
-ssnolib<3.0.0,>=2.1.0.2
+ssnolib<3.0.0,>=2.2.0.0
 mongomock==4.1.2
 xmltodict<=0.13.0
 scipy>=1.10.1
@@ -75,7 +75,7 @@ pymongo<=4.10.1,>=4.2.0
 pytest>=8.3.3
 pytest-cov>=5.0.0
 pylint
-ssnolib<3.0.0,>=2.1.0.2
+ssnolib<3.0.0,>=2.2.0.0
 mongomock==4.1.2
 scipy>=1.10.1
 scikit-image>=0.21.0
@@ -103,7 +103,7 @@ pypandoc>=1.11
 pytest>=8.3.3
 pytest-cov>=5.0.0
 pylint
-ssnolib<3.0.0,>=2.1.0.2
+ssnolib<3.0.0,>=2.2.0.0
 mongomock==4.1.2
 xmltodict<=0.13.0
 scipy>=1.10.1

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = h5rdmtoolbox
-version = 2.5.2
+version = 2.5.3
 author = Matthias Probst
 author_email = matth.probst@gmail.com
 description = Supporting a FAIR Research Data lifecycle using Python and HDF5.
@@ -62,7 +62,7 @@ test =
 	pytest>=8.3.3
 	pytest-cov>=5.0.0
 	pylint
-	ssnolib >= 2.1.0.2, < 3.0.0
+	ssnolib >= 2.2.0.0, < 3.0.0
 	mongomock==4.1.2
 	xmltodict<=0.13.0
 	scipy>=1.10.1  # provides netcdf4

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/tests/ld/test_ld.py

@@ -7,7 +7,9 @@ import ontolutils
 import rdflib
 import ssnolib
 from ontolutils import namespaces, urirefs, Thing
+from ontolutils.ex import dcat
 from ontolutils.namespacelib import M4I
+from ontolutils.namespacelib import SCHEMA
 from rdflib import DCAT
 
 import h5rdmtoolbox as h5tbx
@@ -477,7 +479,7 @@ WHERE {
             h5.create_dataset('test_dataset', shape=(3,))
             grp = h5.create_group('grp')
             grp.attrs['test', sn_iri] = 'test'
-            grp.attrs['description', ontolutils.SCHEMA.commentCount] = 5.3
+            grp.attrs['description', SCHEMA.commentCount] = 5.3
             self.assertIsInstance(grp.attrs['description'], np.floating)
 
             sub_grp = grp.create_group('Fan')
@@ -826,6 +828,17 @@ WHERE {
                 sorted("dcat:Dataset")
             )
 
+    def test_frdf_multiple_object(self):
+        with h5tbx.File() as h5:
+            h5.attrs["thing"] = "Thing"
+            h5.frdf["thing"].predicate = SCHEMA.about
+            h5.frdf["thing"].object = "https://example.org/Thing1"
+            h5.attrs["another_thing"] = "Thing 2"
+            h5.frdf["another_thing"].predicate = SCHEMA.about
+            h5.frdf["another_thing"].object = "https://example.org/Thing2"
+
+            print(h5.serialize("ttl", structural=False))
+
     def test_only_subject(self):
         with h5tbx.File() as h5:
             g = h5.create_group("contact")
@@ -849,3 +862,43 @@ WHERE {
             bindings = res.bindings
             self.assertEqual(len(bindings), 1)
             self.assertEqual(str(bindings[0][rdflib.Variable("relation")]), "https://orcid.org/0000-0001-8729-0482")
+
+    def test_setting_nested_objects(self):
+        filename = h5tbx.utils.generate_temporary_filename(suffix=".hdf")
+        with h5tbx.File(filename, "w") as h5:
+            h5.attrs["snt"] = "123"
+            h5.frdf["snt"].predicate = "https://matthiasprobst.github.io/ssno#usesStandardNameTable"
+            h5.frdf["snt"].object = "https://zenodo.org/records/17572275/files/opencefadb_standard_name_table.jsonld"
+            del h5.frdf["snt"].object
+            h5.frdf["snt"].object = ssnolib.StandardNameTable(
+                id="https://doi.org/10.5281/zenodo.17572275#StandardNameTable",
+                dataset=dcat.Dataset(
+                    id="https://doi.org/10.5281/zenodo.17572275",
+                    distribution=dcat.Distribution(
+                        id="https://doi.org/10.5281/zenodo.17572275#Distribution",
+                        download_URL="https://zenodo.org/records/17572275/files/opencefadb_standard_name_table.jsonld"
+                    )
+                )
+            )
+            ttl = f"""@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix ssno: <https://matthiasprobst.github.io/ssno#> .
+
+<https://example.org#{filename.name}> ssno:usesStandardNameTable <https://doi.org/10.5281/zenodo.17572275#StandardNameTable> .
+
+<https://doi.org/10.5281/zenodo.17572275> a dcat:Dataset ;
+    dcat:distribution <https://doi.org/10.5281/zenodo.17572275#Distribution> .
+
+<https://doi.org/10.5281/zenodo.17572275#Distribution> a dcat:Distribution ;
+    dcat:downloadURL <https://zenodo.org/records/17572275/files/opencefadb_standard_name_table.jsonld> .
+
+<https://doi.org/10.5281/zenodo.17572275#StandardNameTable> a ssno:StandardNameTable ;
+    ssno:dataset <https://doi.org/10.5281/zenodo.17572275> .
+
+"""
+            g1 = rdflib.Graph().parse(data=ttl, format="ttl")
+            actual_ttl = h5.serialize("ttl", structural=False, file_uri=f"https://example.org#")
+            g2 = rdflib.Graph().parse(data=actual_ttl,
+                                      format="ttl")
+            g1ttl = g1.serialize(format="ttl")
+            g2ttl = g2.serialize(format="ttl")
+            self.assertEqual(g1ttl, g2ttl)

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/tests/ld/test_rdf.py

@@ -309,6 +309,16 @@ local:SubjectNode a local:BNodeType1,
 
             h5.rdf.type = ['https://example.org/validURI', 'https://example.org/validURI2']
             self.assertEqual(h5.rdf.type, ['https://example.org/validURI', 'https://example.org/validURI2'])
+            self.assertEqual("""@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix schema: <https://schema.org/> .
+
+<https://example.org/validURI> a <https://example.org/validURI>,
+        <https://example.org/validURI2> ;
+    foaf:title "test" .
+
+[] schema:about <https://example.org/validURI> .
+
+""", h5.serialize("ttl", structural=False))
 
             # note, that the following will not overwrite, but append the value:
             h5.rdf.type = 'https://example.org/validURI3'

{h5rdmtoolbox-2.5.2 → h5rdmtoolbox-2.5.3}/tests/wrapper/test_core.py

@@ -56,14 +56,14 @@ class TestCore(unittest.TestCase):
             hdf:member [ a hdf:Group,
                         schema:SoftwareSourceCode ;
                     hdf:attribute [ a hdf:StringAttribute ;
-                            hdf:data "2.5.2" ;
+                            hdf:data "2.5.3" ;
                             hdf:name "__h5rdmtoolbox_version__" ],
                         [ a hdf:StringAttribute ;
                             hdf:data "https://github.com/matthiasprobst/h5RDMtoolbox" ;
                             hdf:name "code_repository" ] ;
                     hdf:name "/h5rdmtoolbox" ;
                     schema:codeRepository <https://github.com/matthiasprobst/h5RDMtoolbox> ;
-                    schema:softwareVersion "2.5.2" ] ;
+                    schema:softwareVersion "2.5.3" ] ;
             hdf:name "/" ] .
 
 """)