tripper 0.5.2__tar.gz → 0.5.4__tar.gz

{tripper-0.5.2 → tripper-0.5.4}/PKG-INFO

@@ -1,16 +1,14 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: tripper
-Version: 0.5.2
+Version: 0.5.4
 Summary: A triplestore wrapper for Python.
 Keywords: triplestore,ontology,RDF
 Author-email: SINTEF <TEAM4.0@sintef.no>
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -20,38 +18,39 @@ Classifier: Environment :: Plugins
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: typing-extensions>=4.7.0,<4.13.1; python_version < '3.9'
 Requires-Dist: dlite-python>=0.5.27 ; extra == "backends"
-Requires-Dist: emmontopy>=0.5.0,<=0.8.1 ; extra == "backends"
-Requires-Dist: graphviz>=0.20.1,<0.20.2 ; extra == "backends"
+Requires-Dist: emmontopy>=0.5.0,<=0.11.3 ; extra == "backends"
+Requires-Dist: graphviz>=0.20.1,<0.20.4 ; extra == "backends"
 Requires-Dist: numpy<2.1.0 ; extra == "backends" and ( python_version=='3.13')
-Requires-Dist: rdflib>=6.3.0,<7.0.0 ; extra == "backends"
+Requires-Dist: rdflib>=6.3.0,<=7.6.0 ; extra == "backends"
 Requires-Dist: tripper[mappings] ; extra == "datadoc"
 Requires-Dist: keyring>=22.0.0,<25.6.1 ; extra == "datadoc"
-Requires-Dist: PyLD>=2.0.0,<2.0.5 ; extra == "datadoc"
-Requires-Dist: PyYaml>=3.0.0,<6.0.3 ; extra == "datadoc"
+Requires-Dist: PyLD>=2.0.0,<3.0.0 ; extra == "datadoc" and ( python_version<'3.10')
+Requires-Dist: PyLD>=2.0.0,<3.0.1 ; extra == "datadoc" and ( python_version>='3.10')
+Requires-Dist: PyYaml>=3.0.0,<6.0.4 ; extra == "datadoc"
 Requires-Dist: requests>=2.0.0,<3.4.1 ; extra == "datadoc"
 Requires-Dist: sparqlwrapper>=2.0.0,<2.0.1 ; extra == "datadoc"
+Requires-Dist: openpyxl ~= 3.0 ; extra == "datadoc"
 Requires-Dist: tripper[pre-commit, docs] ; extra == "dev"
 Requires-Dist: virtualenvwrapper>=4.0.0 ; extra == "dev"
 Requires-Dist: tripper[testing] ; extra == "docs"
-Requires-Dist: mike==2.1.3 ; extra == "docs"
+Requires-Dist: mike==2.2.0 ; extra == "docs"
 Requires-Dist: mkdocs==1.6.1 ; extra == "docs"
-Requires-Dist: mkdocs-autorefs==1.4.1 ; extra == "docs"
+Requires-Dist: mkdocs-autorefs==1.4.4 ; extra == "docs"
 Requires-Dist: mkdocs-awesome-pages-plugin==2.10.1 ; extra == "docs"
-Requires-Dist: mkdocs-github-admonitions-plugin==0.0.3 ; extra == "docs"
-Requires-Dist: mkdocs-material==9.6.11 ; extra == "docs"
-Requires-Dist: mkdocstrings==0.27.0 ; extra == "docs"
-Requires-Dist: mkdocstrings-python-legacy==0.2.4 ; extra == "docs"
+Requires-Dist: mkdocs-get-deps==0.2.0 ; extra == "docs"
+Requires-Dist: mkdocs-github-admonitions-plugin==0.1.1 ; extra == "docs"
+Requires-Dist: mkdocs-material==9.7.7 ; extra == "docs"
+Requires-Dist: mkdocs-material-extensions==1.3.1 ; extra == "docs"
+Requires-Dist: mkdocstrings==1.0.6 ; extra == "docs"
+Requires-Dist: mkdocstrings-python-legacy==0.2.7 ; extra == "docs"
 Requires-Dist: tripper[units] ; extra == "mappings"
 Requires-Dist: pre-commit==4.0.1 ; extra == "pre-commit"
-Requires-Dist: pylint==3.3.4 ; extra == "pre-commit" and ( python_version>='3.9')
+Requires-Dist: pylint==3.3.4 ; extra == "pre-commit"
 Requires-Dist: tripper[datadoc, backends, testing-core] ; extra == "testing"
-Requires-Dist: pytest==8.3.4 ; extra == "testing-core"
-Requires-Dist: pytest-cov==5.0.0 ; extra == "testing-core" and ( python_version<'3.9')
-Requires-Dist: pytest-cov==6.0.0 ; extra == "testing-core" and ( python_version>='3.9')
-Requires-Dist: pint>=0.21.1,<0.26 ; extra == "units" and ( python_version<'3.9')
-Requires-Dist: pint>=0.24.1,<0.26 ; extra == "units" and ( python_version>='3.9')
+Requires-Dist: pytest==9.1.1 ; extra == "testing-core"
+Requires-Dist: pytest-cov==6.0.0 ; extra == "testing-core"
+Requires-Dist: pint>=0.24.1,<0.26 ; extra == "units"
 Requires-Dist: rdflib>=6.3.0,<=7.6.0 ; extra == "units"
 Project-URL: Changelog, https://github.com/EMMC-ASBL/tripper/blob/master/CHANGELOG.md
 Project-URL: Documentation, https://EMMC-ASBL.github.io/tripper
@@ -68,6 +67,7 @@ Provides-Extra: pre-commit
 Provides-Extra: testing
 Provides-Extra: testing-core
 Provides-Extra: units
+Import-Name: tripper
 
 <img src="docs/figs/tripper_logo.svg" alt="Tripper logo" align="right" width="96" height="96">
 

{tripper-0.5.2 → tripper-0.5.4}/pyproject.toml

@@ -14,8 +14,6 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -26,17 +24,15 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 keywords = ["triplestore", "ontology", "RDF"]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dynamic = ["version"]
 
 dependencies = [
-    "typing-extensions>=4.7.0,<4.13.1; python_version < '3.9'",
 ]
 
 [project.optional-dependencies]
 units = [
-    "pint>=0.21.1,<0.26; python_version<'3.9'",
-    "pint>=0.24.1,<0.26; python_version>='3.9'",
+    "pint>=0.24.1,<0.26",
     "rdflib>=6.3.0,<=7.6.0",
 ]
 mappings = [
@@ -45,40 +41,43 @@ mappings = [
 datadoc = [
     "tripper[mappings]",
     "keyring>=22.0.0,<25.6.1",
-    "PyLD>=2.0.0,<2.0.5",
-    "PyYaml>=3.0.0,<6.0.3",  # todo: check lower version
-    "requests>=2.0.0,<3.4.1",  # todo: check lower version
+    "PyLD>=2.0.0,<3.0.0; python_version<'3.10'",
+    "PyLD>=2.0.0,<3.0.1; python_version>='3.10'",
+    "PyYaml>=3.0.0,<6.0.4",
+    "requests>=2.0.0,<3.4.1",
     "sparqlwrapper>=2.0.0,<2.0.1",
+    "openpyxl ~= 3.0"
 ]
 backends = [
     "dlite-python>=0.5.27",
-    "emmontopy>=0.5.0,<=0.8.1",
-    "graphviz>=0.20.1,<0.20.2",
-    "numpy<2.1.0; python_version=='3.13'",  # todo: relax versions
-    "rdflib>=6.3.0,<7.0.0",
+    "emmontopy>=0.5.0,<=0.11.3",
+    "graphviz>=0.20.1,<0.20.4",
+    "numpy<2.1.0; python_version=='3.13'",
+    "rdflib>=6.3.0,<=7.6.0",
 ]
 testing-core = [
-    "pytest==8.3.4",
-    "pytest-cov==5.0.0; python_version<'3.9'",
-    "pytest-cov==6.0.0; python_version>='3.9'",
+    "pytest==9.1.1",
+    "pytest-cov==6.0.0",
 ]
 testing = [
     "tripper[datadoc,backends,testing-core]",
 ]
 docs = [
     "tripper[testing]",
-    "mike==2.1.3",
+    "mike==2.2.0",
     "mkdocs==1.6.1",
-    "mkdocs-autorefs==1.4.1",
+    "mkdocs-autorefs==1.4.4",
     "mkdocs-awesome-pages-plugin==2.10.1",
-    "mkdocs-github-admonitions-plugin==0.0.3",
-    "mkdocs-material==9.6.11",
-    "mkdocstrings==0.27.0",
-    "mkdocstrings-python-legacy==0.2.4",
+    "mkdocs-get-deps==0.2.0",
+    "mkdocs-github-admonitions-plugin==0.1.1",
+    "mkdocs-material==9.7.7",
+    "mkdocs-material-extensions==1.3.1",
+    "mkdocstrings==1.0.6",
+    "mkdocstrings-python-legacy==0.2.7",
 ]
 pre-commit = [
     "pre-commit==4.0.1",
-    "pylint==3.3.4; python_version>='3.9'",
+    "pylint==3.3.4",
 ]
 dev = [
     "tripper[pre-commit,docs]",

{tripper-0.5.2 → tripper-0.5.4}/tripper/__init__.py

@@ -43,7 +43,7 @@ from .session import Session
 from .triplestore import Triplestore, backend_packages
 from .triplestore_extend import Tripper
 
-__version__ = "0.5.2"
+__version__ = "0.5.4"
 
 # Pre-defined namespaces
 EMMO = Namespace(

{tripper-0.5.2 → tripper-0.5.4}/tripper/backends/rdflib.py

@@ -55,13 +55,15 @@ def totriple(triple: "Triple"):
 
 
 def fromrdflib(
-    value: "Union[URIRef, rdflibLiteral, BNode]",
-) -> "Union[str, Literal]":
+    value: "Union[URIRef, rdflibLiteral, BNode, None]",
+) -> "Union[str, Literal, None]":
     """Help function converting an rdflib value to corresponding tripper value."""
     if isinstance(value, rdflibLiteral):
         return parse_literal(value)
     if isinstance(value, BNode) and not value.startswith("_:"):
         return f"_:{value}"
+    if value is None:
+        return value
     return str(value)
 
 
@@ -184,7 +186,7 @@ class RdflibStrategy:
 
     def query(
         self, query_object, **kwargs
-    ) -> "Union[List[Tuple[str, ...]], bool, Generator[Triple, None, None]]":
+    ) -> "Union[List[tuple], bool, Generator[Triple, None, None]]":
         """SPARQL query.
 
         Parameters:
@@ -271,4 +273,4 @@ def _convert_triples_to_tripper(triples) -> "Generator[Triple, None, None]":
     """Help function that converts a iterator/generator of rdflib triples
     to tripper triples."""
     for s, p, o in triples:  # pylint: disable=not-an-iterable
-        yield (fromrdflib(s), str(p), fromrdflib(o))
+        yield (fromrdflib(s), str(p), fromrdflib(o))  # type: ignore

{tripper-0.5.2 → tripper-0.5.4}/tripper/convert/convert.py

@@ -279,7 +279,7 @@ def load_container(
         return value.value if isinstance(value, Literal) else value
 
     if OTEIO.Dictionary in parents:
-        container = {}
+        container: "Dict[str, Any]" = {}
         for pred, obj in ts.predicate_objects(iri):
             if pred == OTEIO.hasKeyValuePair:
                 key_iri = ts.value(obj, OTEIO.hasDictionaryKey)

{tripper-0.5.2 → tripper-0.5.4}/tripper/datadoc/clitool.py

@@ -10,6 +10,7 @@ from pathlib import Path
 
 from tripper import Session, Triplestore
 from tripper.datadoc import (
+    Context,
     TableDoc,
     acquire,
     delete,
@@ -29,6 +30,9 @@ def subcommand_add(ts, args):
     if fmt in ("yml", "yaml"):
         save_datadoc(ts, infile)
     elif fmt in ("csv",):
+        context = Context(theme=args.theme)
+        for ctx in args.context:
+            context.add_context(ctx)
         kw = {}
         if args.csv_option:
             for token in args.csv_option:
@@ -38,7 +42,7 @@ def subcommand_add(ts, args):
             infile,
             type=args.type,
             keywords=args.keywords if args.keywords else None,
-            context=args.context,
+            context=context,
             redefine=args.redefine,
             baseiri=args.base_iri,
             **kw,
@@ -182,7 +186,15 @@ def maincommand(argv=None):
     )
     parser_add.add_argument(
         "--context",
-        help="Path or URL to custom JSON-LD context for the input.",
+        action="append",
+        help=(
+            "Path or URL to custom JSON-LD context for the input. "
+            "This option may be provided multiple times."
+        ),
+    )
+    parser_add.add_argument(
+        "--theme",
+        help="Initialise context from a theme (e.g. ddoc:datadoc).",
     )
     parser_add.add_argument(
         "--dump",
@@ -211,7 +223,6 @@ def maincommand(argv=None):
         choices=["raise", "allow", "skip"],
         help="How to handle redifinition of existing keywords.",
     )
-
     parser_add.add_argument(
         "--base-iri",
         help=(

{tripper-0.5.2 → tripper-0.5.4}/tripper/datadoc/context.py

@@ -11,11 +11,17 @@ from typing import TYPE_CHECKING, Sequence
 
 from pyld import jsonld
 
-from tripper import OWL, RDF, RDFS, Triplestore
+from tripper import OWL, RDF, RDFS, Namespace, Triplestore
 from tripper.datadoc.errors import InvalidContextError, PrefixMismatchError
 from tripper.datadoc.utils import asseq
 from tripper.errors import NamespaceError, NamespaceWarning
-from tripper.utils import MATCH_IRI, MATCH_PREFIXED_IRI, openfile, prefix_iri
+from tripper.utils import (
+    MATCH_IRI,
+    MATCH_PREFIXED_IRI,
+    expand_iri,
+    openfile,
+    prefix_iri,
+)
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import IO, Optional, Union
@@ -23,7 +29,9 @@ if TYPE_CHECKING:  # pragma: no cover
     from tripper.datadoc.keywords import Keywords
 
     # Possible types for a JSON-LD context
-    ContextType = Union[str, dict, Sequence[Union[str, dict]], "Context"]
+    ContextType = Union[
+        str, dict, Path, Sequence[Union[str, dict, Path]], "Context"
+    ]
 
 
 def get_context(
@@ -36,7 +44,7 @@ def get_context(
     copy: bool = False,
     timeout: float = 3,
 ) -> "Context":
-    """A convinient function that returns an Context instance.
+    """A convenience function that returns a Context instance.
 
     Arguments:
         context: Input context.  Several types are supported:
@@ -46,9 +54,12 @@ def get_context(
             - str: If a valid URI, the context is loaded from this URI,
               otherwise it is assumed to be a file path to load.
             - sequence: A sequence of the above.
-        theme: Load initial context for this theme.
-        default_theme: Initialise context for this theme if neither
-            `context` nor `theme` are provided.
+        theme: IRI (or list of IRIs) of theme(s) to load initial context
+            for.  Built-in themes:
+            - ``"ddoc:datadoc"`` (default) — basic data documentation.
+            - ``"ddoc:process"`` — basic documentation of processes.
+        default_theme: Theme used when neither `context`, `theme`, nor
+            `keywords` are provided.  Defaults to ``"ddoc:datadoc"``.
         keywords: Initialise from this keywords instance.
         prefixes: Optional dict with additional prefixes.
         processingMode: Either "json-ld-1.0" or "json-ld-1.1".
@@ -76,7 +87,7 @@ def get_context(
             timeout=timeout,
         )
     if prefixes:
-        context.add_context({k: str(v) for k, v in prefixes.items()})
+        context.add_prefixes(prefixes)
     return context
 
 
@@ -101,7 +112,12 @@ class Context:
                 - str: If a valid URI, the context is loaded from this URI,
                   otherwise it is assumed to be a file path to load.
                 - sequence: A sequence of the above.
-            theme: Load initial context for this theme.
+            theme: IRI (or list of IRIs) of theme(s) to load initial
+                context for.  Built-in themes:
+                - ``"ddoc:datadoc"`` (default) — basic data documentation.
+                - ``"ddoc:process"`` — basic documentation of processes.
+                Additional themes can be registered by third-party packages
+                via the ``tripper.keywords`` entry-point group.
             keywords: Initialise from this keywords instance.
             processingMode: Either "json-ld-1.0" or "json-ld-1.1".
             timeout: Timeout when accessing remote files.
@@ -118,6 +134,7 @@ class Context:
         self._expanded: dict = {}
         self._prefixed: dict = {}
         self._shortnamed: dict = {}
+        self._namespace_prefixes: dict = {}
 
         if keywords is not None:
             if theme:
@@ -157,13 +174,28 @@ class Context:
         """Return a copy of this context."""
         copy = Context(theme=None)
         copy.ctx = self.ctx  # frozendict - no need to copy
+        # pylint: disable=protected-access
+        copy._namespace_prefixes = self._namespace_prefixes.copy()
         return copy
 
+    def add_prefixes(self, prefixes: dict) -> None:
+        """Add prefixes, retaining Namespace objects for label lookup."""
+        self._namespace_prefixes.update(
+            {
+                prefix: namespace
+                for prefix, namespace in prefixes.items()
+                if isinstance(namespace, Namespace)
+            }
+        )
+        self.add_context(
+            {prefix: str(namespace) for prefix, namespace in prefixes.items()}
+        )
+
     def add_context(self, context: "ContextType") -> None:
         """Add a context to this object."""
         if isinstance(context, Context):
             context = context.get_context_dict()
-        elif isinstance(context, str):
+        elif isinstance(context, (Path, str)):
             with openfile(context, "rt", timeout=self.timeout) as f:
                 context = json.load(f)
         elif isinstance(context, Sequence):
@@ -174,8 +206,8 @@ class Context:
             pass
         else:
             raise TypeError(
-                "`context` should be a dict, str, Context or a sequence of "
-                f"these.  Got: {type(context)}"
+                "`context` should be a dict, str, Path, Context or a sequence "
+                f"of these.  Got: {type(context)}"
             )
 
         if "@id" in context:
@@ -351,6 +383,13 @@ class Context:
         'http://www.w3.org/ns/dcat#Dataset'
 
         """
+        expanded = expand_iri(
+            name,
+            {**self.get_prefixes(), **self._namespace_prefixes},
+            strict=strict,
+        )
+        if expanded != name:
+            return expanded
         # Check cache
         if self._expanded and name in self._expanded:
             return self._expanded[name]
@@ -385,6 +424,7 @@ class Context:
         'dcat:Dataset'
 
         """
+        name = self.expand(name, strict=False)
         if not self._prefixed:
             self._create_caches()
         if name in self._prefixed:
@@ -446,10 +486,16 @@ class Context:
         except NamespaceError:
             return default
 
-    def getdef(self, name: str) -> dict:
-        """Return JSON-LD definition of `name`."""
-        shortname = self.shortname(name)
-        return self.ctx["mappings"][shortname]
+    def getdef(self, name: str, strict: bool = True) -> dict:
+        """Return JSON-LD definition of `name`.
+
+        If strict is true, a `NamespaceError` will be raised if `name` is not
+        defined in the context. Otherwise, an empty dict will be returned.
+        """
+        shortname = self.shortname(name, strict=strict)
+        if shortname in self.ctx["mappings"]:
+            return self.ctx["mappings"][shortname]
+        return {}
 
     def isref(self, name: str) -> bool:
         """Return wheter `name` is an object property that refers to a node."""
@@ -495,6 +541,7 @@ class Context:
 
     def is_class(self, name: str) -> bool:
         """Returns whether `name` appears to be a class."""
+        name = self.expand(name)
         return name in self and self.getdef(name).get("@type") in (
             RDFS.Class,
             OWL.Class,
@@ -624,9 +671,25 @@ class Context:
         self._shortnamed[RDF.type] = "@type"
         self._shortnamed["rdf:type"] = "@type"
         self._shortnamed["@type"] = "@type"
+        # Build a reverse map: IRI -> all prefixed aliases (e.g. both
+        # "dcterms:license" and "term:license" when two prefixes share an IRI)
+        aliases: "dict[str, list[str]]" = {}
+        for pfx, ns in prefixes.items():
+            for expanded in mappings.values():
+                if expanded.startswith(ns):
+                    local = expanded[len(ns) :]
+                    aliases.setdefault(expanded, []).append(f"{pfx}:{local}")
+
         for key, expanded in mappings.items():
             prefixed = prefix_iri(expanded, prefixes)
             self._update_caches(key, prefixed, expanded)
+            # Also register every alias prefixed form so that e.g.
+            # "dcterms:license" is found even when "term" is the canonical
+            # prefix for http://purl.org/dc/terms/.
+            for alias in aliases.get(expanded, []):
+                if alias not in self._shortnamed:
+                    self._shortnamed[alias] = key
+                    self._expanded[alias] = expanded
 
     def _update_caches(self, shortname, prefixed, expanded):
         self._expanded[shortname] = expanded

{tripper-0.5.2 → tripper-0.5.4}/tripper/datadoc/dataaccess.py

@@ -111,7 +111,6 @@ def save(
         raise TypeError(
             "if given, `dataset` should be either a string or dict"
         )
-    dataset: dict  # Tell mypy that this now is a dict
 
     if distribution is None:
         if "distribution" in dataset:
@@ -146,7 +145,6 @@ def save(
         raise TypeError(
             "if given, `distribution` should be either a string or dict"
         )
-    distribution: dict  # Tell mypy that this now is a dict
 
     if isinstance(generator, str):
         gen = get(distribution, "generator")
@@ -154,7 +152,7 @@ def save(
             gen = [gen]
         for g in gen:
             if isinstance(g, dict):
-                if gen.get("@id") == generator:
+                if g.get("@id") == generator:
                     break
             else:
                 break  # ???
@@ -186,7 +184,11 @@ def save(
         f"{scheme}://{p.netloc}{p.path}" if p.netloc else f"{scheme}:{p.path}"
     )
     options = [p.query] if p.query else []
-    if gen and "configuration" in gen and "options" in gen.configuration:
+    if (
+        isinstance(gen, AttrDict)
+        and "configuration" in gen
+        and "options" in gen.configuration
+    ):
         # __TODO__: allow options to also be a dict
         options.append(gen.configuration["options"])
     id = (