h5rdmtoolbox 2.7.3__tar.gz → 2.7.4__tar.gz

{h5rdmtoolbox-2.7.3 → h5rdmtoolbox-2.7.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5rdmtoolbox
-Version: 2.7.3
+Version: 2.7.4
 Summary: Supporting a FAIR Research Data lifecycle using Python and HDF5.
 Author-email: Matthias Probst <matth.probst@gmail.com>
 License-Expression: MIT
@@ -61,7 +61,7 @@ Requires-Dist: pytest>=8.3.3; extra == "test-core"
 Requires-Dist: pytest-cov>=5.0.0; extra == "test-core"
 Requires-Dist: pylint; extra == "test-core"
 Requires-Dist: ssnolib<3.0.0,>=2.2.0.2; extra == "test-core"
-Requires-Dist: mongomock==4.1.2; extra == "test-core"
+Requires-Dist: mongomock==4.3.0; extra == "test-core"
 Requires-Dist: scipy>=1.10.1; extra == "test-core"
 Requires-Dist: scikit-image>=0.21.0; extra == "test-core"
 Requires-Dist: scikit-learn; extra == "test-core"
@@ -75,7 +75,7 @@ Requires-Dist: sphinx_design==0.6.1; extra == "docs"
 Requires-Dist: myst_nb==1.2.0; extra == "docs"
 Requires-Dist: sphinxcontrib_bibtex==2.6.3; extra == "docs"
 Provides-Extra: complete
-Requires-Dist: h5rdmtoolbox[catalog,csv,database,gui,layout_validation,snt,test]; extra == "complete"
+Requires-Dist: h5rdmtoolbox[gui,test]; extra == "complete"
 Provides-Extra: complete-with-docs
 Requires-Dist: h5rdmtoolbox[complete,docs]; extra == "complete-with-docs"
 Dynamic: license-file

{h5rdmtoolbox-2.7.3 → h5rdmtoolbox-2.7.4}/h5rdmtoolbox/__init__.py

@@ -2,7 +2,6 @@
 
 import logging
 import pathlib
-import warnings
 from logging.handlers import RotatingFileHandler
 from typing import Optional, Dict
 
@@ -136,13 +135,24 @@ def get_ld(
         context: Optional[Dict] = None
 ) -> rdflib.Graph:
     """Return the HDF file content as a rdflib.Graph object."""
-    from h5rdmtoolbox.ld import get_ld
-    return get_ld(hdf_filename,
-                  structural=structural,
-                  contextual=contextual,
-                  skipND=skipND,
-                  file_uri=file_uri,
-                  context=context)
+    from . import ld
+    return ld.get_ld(
+        hdf_filename,
+        structural=structural,
+        contextual=contextual,
+        skipND=skipND,
+        file_uri=file_uri,
+        context=context,
+    )
+
+
+def _optimize_ld_context(graph: rdflib.Graph, context: Optional[Dict]) -> Dict:
+    from .ld import optimize_context
+    return optimize_context(graph, context or {})
+
+
+def _resolve_serialize_format(fmt: str, kwargs: Dict) -> str:
+    return kwargs.pop("format", fmt)
 
 
 def dump_jsonld(
@@ -155,19 +165,16 @@ def dump_jsonld(
         file_uri: Optional[str] = None
 ):
     """Return the file content as a JSON-LD string."""
-    from .ld import optimize_context
-    context = context or {}
     graph = get_ld(hdf_filename,
                    structural=structural,
                    contextual=contextual,
                    file_uri=file_uri,
                    skipND=skipND)
-    context = optimize_context(graph, context)
     return graph.serialize(
         format="json-ld",
         indent=indent,
         auto_compact=True,
-        context=context
+        context=_optimize_ld_context(graph, context)
     )
 
 
@@ -286,7 +293,7 @@ def serialize(hdf_filename,
               rdf_mappings: Dict[str, RDFMappingEntry] = None,
               **kwargs):
     """Alternative to json-ld but allows multiple serialization options"""
-    fmt = kwargs.pop("format", fmt)
+    fmt = _resolve_serialize_format(fmt, kwargs)
     with File(hdf_filename) as h5:
         return h5.serialize(fmt=fmt,
                             skipND=skipND,
@@ -296,6 +303,32 @@ def serialize(hdf_filename,
                             rdf_mappings=rdf_mappings)
 
 
+def sparql(
+        hdf_filename: Union[str, pathlib.Path],
+        query: str,
+        structural: bool = True,
+        contextual: bool = True,
+        skipND: int = 1,
+        file_uri: Optional[Union[str, Dict[str, str]]] = None,
+        rdf_mappings: Dict[str, RDFMappingEntry] = None,
+        as_dataframe: bool = False,
+        **kwargs
+) -> rdflib.query.Result:
+    """Run a SPARQL query on the HDF5 file content. Returns a rdflib.query.Result object."""
+    from .ld import sparql
+    return sparql(
+        source=hdf_filename,
+        query=query,
+        structural=structural,
+        contextual=contextual,
+        skipND=skipND,
+        file_uri=file_uri,
+        rdf_mappings=rdf_mappings,
+        as_dataframe=as_dataframe,
+        **kwargs
+    )
+
+
 def build_pyvis_graph(hdf_filename, output_filename="kg-graph.html", notebook=False,
                       structural: bool = True,
                       contextual: bool = True,