move attrsdef to rdf[].definition

h5rdmtoolbox/_repr.py

@@ -298,7 +298,7 @@ def __attrs__(self, name, h5obj) -> str:
             use_attr_name = name
         else:
             pred = h5obj.rdf[name].get(RDF_PREDICATE_ATTR_NAME, None)
-            attrsdef = h5obj.attrsdef.get(name, None)
+            attrsdef = h5obj.rdf[name].definition
             if pred and attrsdef:
                 use_attr_name = f'{name} (p={pred}, def={attrsdef})'
             elif pred:
@@ -576,7 +576,7 @@ def __attrs__(self, name, h5obj):
         if rdf_predicate is not None:
             disp_name += get_iri_icon_href(rdf_predicate, icon_url=IRI_ICON)
 
-        attrs_def = h5obj.attrsdef.get(name, None)
+        attrs_def = h5obj.rdf[name].definition
         if attrs_def is not None:
             disp_name += get_def_icon_href(attrs_def)
 

h5rdmtoolbox/wrapper/core.py

@@ -28,7 +28,6 @@
 from .. import get_ureg
 from .. import protocols
 from .._repr import H5Repr, H5PY_SPECIAL_ATTRIBUTES
-from ..convention import definition
 from ..convention.consts import DefaultValue
 
 logger = logging.getLogger('h5rdmtoolbox')
@@ -406,10 +405,10 @@ def iri(self):
         warnings.warn('Property "iri" is deprecated. Use "rdf" instead.', DeprecationWarning)
         return rdf.RDFManager(self.attrs)
 
-    @property
-    def attrsdef(self) -> definition.DefinitionManager:
-        """Return DefinitionManager"""
-        return definition.DefinitionManager(self.attrs)
+    # @property
+    # def attrsdef(self) -> definition.DefinitionManager:
+    #     """Return DefinitionManager"""
+    #     return definition.DefinitionManager(self.attrs)
 
     def get_tree_structure(self, recursive=True, ignore_attrs: List[str] = None):
         """Return the tree (attributes, names, shapes) of the group and subgroups"""
@@ -1411,11 +1410,6 @@ def iri(self):
         warnings.warn('Property "iri" is deprecated. Use "rdf" instead.', DeprecationWarning)
         return rdf.RDFManager(self.attrs)
 
-    @property
-    def attrsdef(self) -> definition.DefinitionManager:
-        """Return DefinitionManager"""
-        return definition.DefinitionManager(self.attrs)
-
     @property
     def hdf_filename(self) -> pathlib.Path:
         """The filename of the file, even if the HDF5 file is closed."""
@@ -1515,11 +1509,6 @@ def attach_ancillary_dataset(self, ancillary_dataset: Union[str, h5py.Dataset]):
         self.attrs[consts.ANCILLARY_DATASET] = ancillary_datasets
         return self
 
-    # @property
-    # def has_flag_data(self):
-    #     """Check if the dataset has a flag dataset attached."""
-    #     return ANCILLARY_DATASET in self.attrs and self.attrs[FLAG_DATASET_CONST] in self.parent
-
     def detach_data_scale(self):
         """Remove the attached data scale dataset from this dataset."""
         warnings.warn('Note, that detaching data scale may influence the correctness and traceability of your data',
@@ -2171,10 +2160,10 @@ def iri(self):
         warnings.warn('Property "iri" is deprecated. Use "rdf" instead.', DeprecationWarning)
         return rdf.RDFManager(self.attrs)
 
-    @property
-    def attrsdef(self) -> definition.DefinitionManager:
-        """Return DefinitionManager"""
-        return definition.DefinitionManager(self.attrs)
+    # @property
+    # def attrsdef(self) -> definition.DefinitionManager:
+    #     """Return DefinitionManager"""
+    #     return definition.DefinitionManager(self.attrs)
 
     def moveto(self, destination: Path, overwrite: bool = False) -> Path:
         """Move the opened file to a new destination.

h5rdmtoolbox/wrapper/h5attr.py

@@ -1,20 +1,19 @@
 """Attribute module"""
 import ast
+import h5py
 import json
 import logging
-import warnings
-from datetime import datetime
-from typing import Dict, Union, Tuple, Optional, Any
-
-import h5py
 import numpy as np
 import pint
 import pydantic
 import rdflib
+import warnings
+from datetime import datetime
 from h5py._hl.attrs import AttributeManager
 from h5py._hl.base import with_phil
 from h5py._objects import ObjectID, phil
 from pydantic import HttpUrl
+from typing import Dict, Union, Tuple, Optional, Any
 
 from .h5utils import get_rootparent
 from .. import errors
@@ -265,7 +264,7 @@ def create(self,
         if rdf_object is not None:
             self._parent.rdf.object[name] = rdf_object
         if definition is not None:
-            self._parent.attrsdef[name] = definition
+            self._parent.rdf[name].definition = definition
         return r
 
     @with_phil

h5rdmtoolbox/wrapper/jsonld.py

@@ -1,18 +1,17 @@
+import h5py
 import json
 import logging
-import pathlib
-import warnings
-from itertools import count
-from typing import Dict, List
-from typing import Optional, Union, Iterable, Tuple, Any
-
-import h5py
 import numpy as np
 import ontolutils
+import pathlib
 import rdflib
+import warnings
+from itertools import count
 from ontolutils.classes.utils import split_URIRef
-from rdflib import Graph, URIRef, Literal, BNode, XSD, RDF, SKOS
+from rdflib import Graph, URIRef, BNode, XSD, RDF, SKOS
 from rdflib.plugins.shared.jsonld.context import Context
+from typing import Dict, List
+from typing import Optional, Union, Iterable, Tuple, Any
 
 from h5rdmtoolbox.convention import hdf_ontology
 from .core import Dataset, File
@@ -94,7 +93,8 @@ def build_node_list(g: Graph, data: List, use_simple_bnode_value: bool = True) -
         if i == n - 1:
             flag_list_rest = RDF.nil
         else:
-            flag_list_rest = rdflib.BNode(value=f'N{next(_bnode_counter)}') if use_simple_bnode_value else rdflib.BNode()
+            flag_list_rest = rdflib.BNode(
+                value=f'N{next(_bnode_counter)}') if use_simple_bnode_value else rdflib.BNode()
         g.add((flag_list, RDF.rest, flag_list_rest))
         flag_list = flag_list_rest
 
@@ -149,7 +149,7 @@ def resolve_iri(key_or_iri: str, context: Context) -> str:
 #         return Literal(_av)
 
 
-def _get_id(_node, use_simple_bnode_value:bool=True) -> Union[URIRef, BNode]:
+def _get_id(_node, use_simple_bnode_value: bool = True) -> Union[URIRef, BNode]:
     """if an attribute in the node is called "@id", use that, otherwise use the node name"""
     _id = _node.rdf.subject  # _node.attrs.get('@id', None)
     # if local is not None:
@@ -638,7 +638,8 @@ def _add_hdf_node(name, obj, ctx) -> Dict:
 
             if structural:  # add hdf type and name nodes
                 _add_node(g, (attr_node, RDF.type, HDF5.Attribute))
-                attr_def: str = obj.attrsdef.get(ak, None)
+                # attr_def: str = obj.attrsdef.get(ak, None)
+                attr_def: str = obj.rdf[ak].definition# .get(ak, None)
                 if attr_def:
                     _add_node(g, (attr_node, HDF5.name, rdflib.Literal(ak)))
                     _add_node(g, (attr_node, SKOS.definition, rdflib.Literal(attr_def)))
@@ -741,8 +742,8 @@ def _parse_val(_k, _v):
 
                 attr_object = None
 
-
-            attr_def = obj.attrsdef.get(ak, None)
+            # attr_def = obj.attrsdef.get(ak, None)
+            attr_def = obj.rdf[ak].definition#.get(ak, None)
             if attr_def:
                 _add_node(g, (attr_node, SKOS.definition, rdflib.Literal(attr_def)))
 

h5rdmtoolbox/wrapper/rdf.py

@@ -1,16 +1,17 @@
 """RDF (Resource Description Framework) module for use with HDF5 files"""
 import abc
-from typing import Dict, Union, Optional, List
-
 import h5py
 import pydantic
 from pydantic import HttpUrl
+from typing import Dict, Union, Optional, List
 
 RDF_OBJECT_ATTR_NAME = 'RDF_OBJECT'
 RDF_PREDICATE_ATTR_NAME = 'RDF_PREDICATE'
 RDF_SUBJECT_ATTR_NAME = '@ID'  # equivalent to @ID in JSON-LD, thus can only be one value!!!
 RDF_TYPE_ATTR_NAME = '@TYPE'  # equivalent to @type in JSON-LD, thus can be multiple values.
 
+DEFINITION_ATTR_NAME = 'ATTR_DEFINITION'
+
 
 class RDFError(Exception):
     """Generic RDF error"""
@@ -154,6 +155,18 @@ def object(self, value):
         else:
             set_object(self._attr, self._attr_name, value)
 
+    @property
+    def definition(self):
+        """Return the definition of the attribute"""
+        return self._attr.get(DEFINITION_ATTR_NAME, {}).get(self._attr_name, None)
+
+    @definition.setter
+    def definition(self, definition: str):
+        """Define the attribute. JSON-LD export will interpret this as SKOS.definition."""
+        attr_def = self._attr.get(DEFINITION_ATTR_NAME, {})
+        attr_def.update({self._attr_name: definition})
+        self._attr[DEFINITION_ATTR_NAME] = attr_def
+
 
 class _RDFPO(abc.ABC):
     """Abstract class for predicate (P) and object (O)"""

tests/test_repr.py

@@ -68,7 +68,7 @@ def test_dump_orcid(self):
         def test_repr_def(self):
             with File() as h5:
                 h5.attrs['orcid'] = h5tbx.__author_orcid__
-                h5.attrsdef['orcid'] = 'https://example.com/hasOrcid'
+                h5.rdf['orcid'].definition = 'https://example.com/hasOrcid'
 
                 ssr = _repr.HDF5StructureStrRepr()
                 ssr(h5)

tests/wrapper/test_rdf.py

@@ -365,18 +365,14 @@ def test_find_object(self):
 
             self.assertEqual(len(res), 1)
 
-
-
     def test_definition(self):
         with h5tbx.File() as h5:
             h5.attrs['title'] = 'test'
-            h5.attrsdef['title'] = 'This is the title of the dataset'
-            self.assertEqual(h5.attrsdef['title'], 'This is the title of the dataset')
+            h5.rdf['title'].definition = 'This is the title of the dataset'
+            # h5.attrsdef['title'] = 'This is the title of the dataset'
+            self.assertEqual(h5.rdf['title'].definition, 'This is the title of the dataset')
 
             h5.attrs['name'] = h5tbx.Attribute('Matthias', definition='This is the name of the person to contact')
-            self.assertEqual(h5.attrsdef['name'], 'This is the name of the person to contact')
+            self.assertEqual(h5.rdf['name'].definition, 'This is the name of the person to contact')
 
             h5.dumps()
-
-            with self.assertRaises(KeyError):
-                h5.attrsdef['test'] = 'This should not work!'