introduce Attribute class

matthiasprobst · Apr 19, 2024 · 403e507 · 403e507
1 parent 40b8103
commit 403e507
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Showing 8 changed files with 260 additions and 76 deletions.
diff --git a/h5rdmtoolbox/__init__.py b/h5rdmtoolbox/__init__.py
@@ -1,10 +1,11 @@
 """h5rdtoolbox repository"""
 
-import appdirs
 import logging
 import pathlib
 from logging.handlers import RotatingFileHandler
 
+import appdirs
+
 _logdir = pathlib.Path(appdirs.user_log_dir('h5rdmtoolbox'))
 _logdir.mkdir(parents=True, exist_ok=True)
 
@@ -38,14 +39,14 @@
 
 from . import convention
 from .convention.core import Convention
-from .convention.rdf import RDFAttribute
 from . import wrapper
 from ._user import UserDir
 from ._version import __version__
 from . import utils
 from .wrapper.core import lower, Lower, File, Group, Dataset
 from . import warnings, errors
 from .wrapper import jsonld
+from .wrapper.h5attr import Attribute
 from .wrapper.accessory import register_special_dataset
 import json
 
@@ -232,7 +233,7 @@ def clean_temp_data(full: bool = False):
 
 __all__ = ('__version__', '__author__', '__author_orcid__',
            'UserDir', 'use',
-           'File', 'Group', 'Dataset', 'RDFAttribute',
+           'File', 'Group', 'Dataset', 'Attribute',
            'dump', 'dumps', 'cv_h5py', 'lower', 'Lower',
            'set_config', 'get_config', 'get_ureg',
            'Convention', 'jsonld')
diff --git a/h5rdmtoolbox/_repr.py b/h5rdmtoolbox/_repr.py
@@ -1,17 +1,18 @@
-import h5py
-import importlib_resources
-import numpy as np
 import os
 import re
 import typing
 import warnings
-import xarray as xr
-from IPython.display import HTML, display
 from abc import abstractmethod
-from numpy import ndarray
 from time import perf_counter_ns
 
+import h5py
+import importlib_resources
+import numpy as np
+import xarray as xr
+from IPython.display import HTML, display
+from numpy import ndarray
 from ontolutils import M4I, Thing
+
 from . import get_config, identifiers, protected_attributes
 from .convention.rdf import RDF_SUBJECT_ATTR_NAME, RDF_PREDICATE_ATTR_NAME, RDF_OBJECT_ATTR_NAME
 
@@ -28,6 +29,7 @@
 # if IRI_ICON.exists():
 #     IRI_ICON = rf'file:///{IRI_ICON}'
 # else:
+DEF_ICON = "https://github.com/matthiasprobst/h5RDMtoolbox/blob/dev-FAIRattrs/h5rdmtoolbox/data/def_icon.png?raw=true"
 IRI_ICON = "https://github.com/matthiasprobst/h5RDMtoolbox/blob/dev/h5rdmtoolbox/data/iri_icon.png?raw=true"
 hasUnitIRI = str(M4I.hasUnit)
 """
@@ -165,6 +167,12 @@ def get_iri_icon_href(iri: typing.Union[str, typing.Dict], tooltiptext=None) ->
            f'<img class="size_of_img" src="{IRI_ICON}" alt="IRI_ICON" width="16" height="16" />' \
            f' <span class="tooltiptext">{tooltiptext or iri}</span></a>'
 
+def get_def_icon_href(def_text: str) -> str:
+    """get html representation of an attribute definition with icon"""
+    return f'<div class="tooltip">' \
+           f'<img class="size_of_img" src="{DEF_ICON}" alt="D" width="16" height="16" />' \
+           f'<span class="tooltiptext">{def_text}</span></div>'
+
 
 class _HDF5StructureRepr:
 
@@ -283,19 +291,20 @@ def __attrs__(self, name, h5obj) -> str:
             use_attr_name = name
         else:
             pred = h5obj.rdf[name].get(RDF_PREDICATE_ATTR_NAME, None)
-            if pred:
+            attrsdef = h5obj.attrsdef.get(name, None)
+            if pred and attrsdef:
+                use_attr_name = f'{name} (p={pred}, def={attrsdef})'
+            elif pred:
                 use_attr_name = f'{name} (p={pred})'
+            elif attrsdef:
+                use_attr_name = f'{name} (def={attrsdef})'
             else:
                 use_attr_name = name
 
             obj_iri = h5obj.rdf[name].get(RDF_OBJECT_ATTR_NAME, None)
             if obj_iri:
                 attr_value = f'{attr_value} (o={obj_iri})'
 
-            attrsdef = h5obj.attrsdef.get(name, None)
-            if attrsdef:
-                attr_value = f'{attr_value} (def={attrsdef})'
-
         # if isinstance(attr_value, h5py.Group):
         #     attr_value = f'grp:{attr_value.name}'
         # elif isinstance(attr_value, h5py.Dataset):
@@ -547,6 +556,10 @@ def __attrs__(self, name, h5obj):
         if rdf_predicate is not None:
             name += get_iri_icon_href(rdf_predicate)
 
+        attrs_def = h5obj.attrsdef.get(name, None)
+        if attrs_def is not None:
+            name += get_def_icon_href(attrs_def)
+
         rdf_object = rdf.object
 
         if isinstance(attr_value, ndarray):

diff --git a/h5rdmtoolbox/convention/definition.py b/h5rdmtoolbox/convention/definition.py
@@ -21,10 +21,9 @@ def __getitem__(self, item) -> Optional[str]:
         return self.get(item)
 
     def __setitem__(self, key, value):
-        if DEFINITION_ATTR_NAME not in self._attr:
-            attrdef = self._attr.get(DEFINITION_ATTR_NAME, {})
-        attrdef.update({key: value})
-        self._attr[DEFINITION_ATTR_NAME] = attrdef
+        attr_def = self._attr.get(DEFINITION_ATTR_NAME, {})
+        attr_def.update({key: value})
+        self._attr[DEFINITION_ATTR_NAME] = attr_def
 
     def get(self, item, default=None) -> Optional[str]:
         if DEFINITION_ATTR_NAME not in self._attr:

diff --git a/h5rdmtoolbox/convention/rdf.py b/h5rdmtoolbox/convention/rdf.py
@@ -18,49 +18,49 @@ class RDFError(Exception):
     pass
 
 
-class RDFAttribute:
-    """Helper class for quick assignment of RDF attributes to the HDF5 file.
-
-    Examples
-    --------
-    >>> import h5rdmtoolbox as h5tbx
-    >>> from ontolutils import M4I
-    >>> rdf_attr = h5tbx.RDFAttribute('0000-0001-8729-0482', rdf_predicate=M4I.orcidId,
-    ...                                rdf_object='https://orcid.org/0000-0001-8729-0482')
-    >>> with h5tbx.File('test.h5', 'w') as h5:
-    ...     grp = h5.create_group('person')
-    ...     grp.attrs['orcid'] = rdf_attr
-    ...     # equal to:
-    ...     # grp.attrs['orcid'] = '0000-0001-8729-0482'
-    ...     # grp.rdf.predicate['orcid'] = str(M4I.orcidId)
-    ...     # grp.rdf.object['orcid'] = 'https://orcid.org/0000-0001-8729-0482'
-    """
-
-    def __init__(self, value, rdf_predicate: str = None, rdf_object: str = None):
-        self.value = value
-
-        if rdf_predicate:
-            try:
-                str(HttpUrl(rdf_predicate))
-            except pydantic.ValidationError as e:
-                raise RDFError(f'Invalid predicate IRI: "{rdf_predicate}". '
-                               f'Expecting a valid URL. This was validated with pydantic. Pydantic error: {e}')
-
-        if rdf_object:
-            try:
-                str(HttpUrl(rdf_object))
-            except pydantic.ValidationError as e:
-                raise RDFError(f'Invalid object IRI: "{rdf_object}". '
-                               f'Expecting a valid URL. This was validated with pydantic. Pydantic error: {e}')
-
-        self.rdf_predicate = rdf_predicate
-        self.rdf_object = rdf_object
-
-    def __repr__(self) -> str:
-        return f'{self.__class__.__name__}({self.value}, rdf_predicate={self.rdf_predicate}, rdf_object={self.rdf_object})'
-
-    def __str__(self) -> str:
-        return self.__repr__()
+# class RDFAttribute:
+#     """Helper class for quick assignment of RDF attributes to the HDF5 file.
+#
+#     Examples
+#     --------
+#     >>> import h5rdmtoolbox as h5tbx
+#     >>> from ontolutils import M4I
+#     >>> rdf_attr = h5tbx.RDFAttribute('0000-0001-8729-0482', rdf_predicate=M4I.orcidId,
+#     ...                                rdf_object='https://orcid.org/0000-0001-8729-0482')
+#     >>> with h5tbx.File('test.h5', 'w') as h5:
+#     ...     grp = h5.create_group('person')
+#     ...     grp.attrs['orcid'] = rdf_attr
+#     ...     # equal to:
+#     ...     # grp.attrs['orcid'] = '0000-0001-8729-0482'
+#     ...     # grp.rdf.predicate['orcid'] = str(M4I.orcidId)
+#     ...     # grp.rdf.object['orcid'] = 'https://orcid.org/0000-0001-8729-0482'
+#     """
+#
+#     def __init__(self, value, rdf_predicate: str = None, rdf_object: str = None):
+#         self.value = value
+#
+#         if rdf_predicate:
+#             try:
+#                 str(HttpUrl(rdf_predicate))
+#             except pydantic.ValidationError as e:
+#                 raise RDFError(f'Invalid predicate IRI: "{rdf_predicate}". '
+#                                f'Expecting a valid URL. This was validated with pydantic. Pydantic error: {e}')
+#
+#         if rdf_object:
+#             try:
+#                 str(HttpUrl(rdf_object))
+#             except pydantic.ValidationError as e:
+#                 raise RDFError(f'Invalid object IRI: "{rdf_object}". '
+#                                f'Expecting a valid URL. This was validated with pydantic. Pydantic error: {e}')
+#
+#         self.rdf_predicate = rdf_predicate
+#         self.rdf_object = rdf_object
+#
+#     def __repr__(self) -> str:
+#         return f'{self.__class__.__name__}({self.value}, rdf_predicate={self.rdf_predicate}, rdf_object={self.rdf_object})'
+#
+#     def __str__(self) -> str:
+#         return self.__repr__()
 
 
 def set_predicate(attr: h5py.AttributeManager, attr_name: str, value: str) -> None:

diff --git a/h5rdmtoolbox/data/def_icon.png b/h5rdmtoolbox/data/def_icon.png
diff --git a/h5rdmtoolbox/data/def_icon.svg b/h5rdmtoolbox/data/def_icon.svg