pylode 3.0.0__tar.gz → 3.0.1__tar.gz

{pyLODE-3.0.0 → pyLODE-3.0.1}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: pyLODE
-Version: 3.0.0
+Version: 3.0.1
 Summary: An OWL ontology documentation tool using Python and templating, based on LODE.
 Home-page: https://github.com/rdflib/pyLODE
 Author: Nicholas J. Car
 Author-email: nicholas.car@surroundaustralia.com
 License: LICENSE
-Download-URL: https://github.com/RDFLib/pyLODE/releases/tag/3.0.0
+Download-URL: https://github.com/RDFLib/pyLODE/releases/tag/3.0.1
 Project-URL: Bug Reports, https://github.com/rdflib/pyLODE/issues
 Project-URL: Source, https://github.com/rdflib/pyLODE/
 Keywords: Semantic Web,OWL,ontology,template,HTML,documentation
@@ -41,12 +41,17 @@ In addition to making web page, human-readable forms of ontologies, pyLODE encou
 practice* by only producing good results for well documented inputs! pyLODE defines what it considers 'well documented'
 in sections below, e.g. `What pyLODE understands`_.
 
-.. note::
+----
 
-    This is pyLODE version 3.0.0 and it's vastly different from pyLODE < 3.0.0. It doesn't yet handle all the various "profiles" that pyLODE 2.13.2 does, such as SKOS _vocabularies_ & Profiles Vocabulary _profiles, it only handles OWL _ontologies_ nor all the special data types, such as JSON literals, BUT, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it's been made. v 3.x will eventually catch up to all of v 2.13.2's features.
+**A note on the v 3.x change**
 
-    To access v 2.13.2 of pyLODE, either `download it from PyPI <https://pypi.org/project/pyLODE/2.13.2/>`_, `check it out from GitHub <https://github.com/RDFLib/pyLODE/releases/tag/2.13.2>`_ or access it via the `online service <http://pylode.surroundaustralia.com/>`_.
+*This is pyLODE version 3.0.1 and it's vastly different from pyLODE 2.x. It doesn't yet handle all the various "profiles" that pyLODE 2.13.2 does, such as SKOS 'vocabularies' & Profiles Vocabulary 'profiles', it only handles OWL 'ontologies', nor all the special data types, such as JSON literals, BUT, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it's been made.*
 
+*v 3.x will eventually catch up to all of v 2.13.2's features.*
+
+*To access v 2.13.2 of pyLODE, either `download it from PyPI <https://pypi.org/project/pyLODE/2.13.2/>`_, `check it out from GitHub <https://github.com/RDFLib/pyLODE/releases/tag/2.13.2>`_ or access it via the `online service <http://pylode.surroundaustralia.com/>`_.*
+
+----
 
 Contents
 ========
@@ -257,7 +262,7 @@ and change/add development priorities.
 Current Release
 ---------------
 
-The current release, as of December, 2021, is **2.13.2**.
+The current release, as of January, 2022, is **3.0.1**.
 
 Release Schedule
 ----------------
@@ -266,7 +271,7 @@ Release Schedule
    :header: "Version", "Date", "Description"
    :widths: 15, 10, 30
 
-   **3.0.0**, **6 Jan 2022**, "Direct HTML generation using dominate; easier to maintain and extend"
+   **3.0.1**, **6 Jan 2022**, "**Direct HTML generation using dominate; easier to maintain and extend**"
    2.13.2, 21 December 2021, "Updated RDFlib to 6.1.1, improved test to properly use pytest"
    2.10.0, 24 May 2021, "Update Windows EXE build process, simplified versioning"
    2.9.1, 28 Apr 2021, "Support for ASCIIDOC format (OntDoc profile only)"

{pyLODE-3.0.0 → pyLODE-3.0.1}/README.rst

@@ -11,12 +11,17 @@ In addition to making web page, human-readable forms of ontologies, pyLODE encou
 practice* by only producing good results for well documented inputs! pyLODE defines what it considers 'well documented'
 in sections below, e.g. `What pyLODE understands`_.
 
-.. note::
+----
 
-    This is pyLODE version 3.0.0 and it's vastly different from pyLODE < 3.0.0. It doesn't yet handle all the various "profiles" that pyLODE 2.13.2 does, such as SKOS _vocabularies_ & Profiles Vocabulary _profiles, it only handles OWL _ontologies_ nor all the special data types, such as JSON literals, BUT, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it's been made. v 3.x will eventually catch up to all of v 2.13.2's features.
+**A note on the v 3.x change**
 
-    To access v 2.13.2 of pyLODE, either `download it from PyPI <https://pypi.org/project/pyLODE/2.13.2/>`_, `check it out from GitHub <https://github.com/RDFLib/pyLODE/releases/tag/2.13.2>`_ or access it via the `online service <http://pylode.surroundaustralia.com/>`_.
+*This is pyLODE version 3.0.1 and it's vastly different from pyLODE 2.x. It doesn't yet handle all the various "profiles" that pyLODE 2.13.2 does, such as SKOS 'vocabularies' & Profiles Vocabulary 'profiles', it only handles OWL 'ontologies', nor all the special data types, such as JSON literals, BUT, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it's been made.*
 
+*v 3.x will eventually catch up to all of v 2.13.2's features.*
+
+*To access v 2.13.2 of pyLODE, either `download it from PyPI <https://pypi.org/project/pyLODE/2.13.2/>`_, `check it out from GitHub <https://github.com/RDFLib/pyLODE/releases/tag/2.13.2>`_ or access it via the `online service <http://pylode.surroundaustralia.com/>`_.*
+
+----
 
 Contents
 ========
@@ -227,7 +232,7 @@ and change/add development priorities.
 Current Release
 ---------------
 
-The current release, as of December, 2021, is **2.13.2**.
+The current release, as of January, 2022, is **3.0.1**.
 
 Release Schedule
 ----------------
@@ -236,7 +241,7 @@ Release Schedule
    :header: "Version", "Date", "Description"
    :widths: 15, 10, 30
 
-   **3.0.0**, **6 Jan 2022**, "Direct HTML generation using dominate; easier to maintain and extend"
+   **3.0.1**, **6 Jan 2022**, "**Direct HTML generation using dominate; easier to maintain and extend**"
    2.13.2, 21 December 2021, "Updated RDFlib to 6.1.1, improved test to properly use pytest"
    2.10.0, 24 May 2021, "Update Windows EXE build process, simplified versioning"
    2.9.1, 28 Apr 2021, "Support for ASCIIDOC format (OntDoc profile only)"

{pyLODE-3.0.0 → pyLODE-3.0.1}/pyLODE.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: pyLODE
-Version: 3.0.0
+Version: 3.0.1
 Summary: An OWL ontology documentation tool using Python and templating, based on LODE.
 Home-page: https://github.com/rdflib/pyLODE
 Author: Nicholas J. Car
 Author-email: nicholas.car@surroundaustralia.com
 License: LICENSE
-Download-URL: https://github.com/RDFLib/pyLODE/releases/tag/3.0.0
+Download-URL: https://github.com/RDFLib/pyLODE/releases/tag/3.0.1
 Project-URL: Bug Reports, https://github.com/rdflib/pyLODE/issues
 Project-URL: Source, https://github.com/rdflib/pyLODE/
 Keywords: Semantic Web,OWL,ontology,template,HTML,documentation
@@ -41,12 +41,17 @@ In addition to making web page, human-readable forms of ontologies, pyLODE encou
 practice* by only producing good results for well documented inputs! pyLODE defines what it considers 'well documented'
 in sections below, e.g. `What pyLODE understands`_.
 
-.. note::
+----
 
-    This is pyLODE version 3.0.0 and it's vastly different from pyLODE < 3.0.0. It doesn't yet handle all the various "profiles" that pyLODE 2.13.2 does, such as SKOS _vocabularies_ & Profiles Vocabulary _profiles, it only handles OWL _ontologies_ nor all the special data types, such as JSON literals, BUT, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it's been made. v 3.x will eventually catch up to all of v 2.13.2's features.
+**A note on the v 3.x change**
 
-    To access v 2.13.2 of pyLODE, either `download it from PyPI <https://pypi.org/project/pyLODE/2.13.2/>`_, `check it out from GitHub <https://github.com/RDFLib/pyLODE/releases/tag/2.13.2>`_ or access it via the `online service <http://pylode.surroundaustralia.com/>`_.
+*This is pyLODE version 3.0.1 and it's vastly different from pyLODE 2.x. It doesn't yet handle all the various "profiles" that pyLODE 2.13.2 does, such as SKOS 'vocabularies' & Profiles Vocabulary 'profiles', it only handles OWL 'ontologies', nor all the special data types, such as JSON literals, BUT, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it's been made.*
 
+*v 3.x will eventually catch up to all of v 2.13.2's features.*
+
+*To access v 2.13.2 of pyLODE, either `download it from PyPI <https://pypi.org/project/pyLODE/2.13.2/>`_, `check it out from GitHub <https://github.com/RDFLib/pyLODE/releases/tag/2.13.2>`_ or access it via the `online service <http://pylode.surroundaustralia.com/>`_.*
+
+----
 
 Contents
 ========
@@ -257,7 +262,7 @@ and change/add development priorities.
 Current Release
 ---------------
 
-The current release, as of December, 2021, is **2.13.2**.
+The current release, as of January, 2022, is **3.0.1**.
 
 Release Schedule
 ----------------
@@ -266,7 +271,7 @@ Release Schedule
    :header: "Version", "Date", "Description"
    :widths: 15, 10, 30
 
-   **3.0.0**, **6 Jan 2022**, "Direct HTML generation using dominate; easier to maintain and extend"
+   **3.0.1**, **6 Jan 2022**, "**Direct HTML generation using dominate; easier to maintain and extend**"
    2.13.2, 21 December 2021, "Updated RDFlib to 6.1.1, improved test to properly use pytest"
    2.10.0, 24 May 2021, "Update Windows EXE build process, simplified versioning"
    2.9.1, 28 Apr 2021, "Support for ASCIIDOC format (OntDoc profile only)"

{pyLODE-3.0.0 → pyLODE-3.0.1}/pyLODE.egg-info/SOURCES.txt

@@ -11,7 +11,6 @@ pyLODE.egg-info/top_level.txt
 pylode/__init__.py
 pylode/__main__.py
 pylode/cli.py
-pylode/extra.py
 pylode/ontdoc.py
 pylode/pylode.css
 pylode/rdf_elements.py

{pyLODE-3.0.0 → pyLODE-3.0.1}/pylode/cli.py

@@ -10,7 +10,10 @@ from pylode import OntDoc, PylodeError
 parser = argparse.ArgumentParser()
 
 parser.add_argument(
-    "-v", "--version", action="version", version="{version}".format(version=__version__)
+    "-v",
+    "--version",
+    action="version",
+    version="{version}".format(version=__version__)
 )
 
 parser.add_argument(
@@ -21,15 +24,17 @@ parser.add_argument(
 parser.add_argument(
     "-o",
     "--outputfile",
-    help="A name you wish to assign to the output file. Will be postfixed with .html if not already "
-    "added. If no output file is given, output will be printed to screen",
+    help="A name you wish to assign to the output file. Will be postfixed "
+         "with .html if not already added. If no output file is given, "
+         "output will be printed to screen",
     default=None,
 )
 
 parser.add_argument(
     "-c",
     "--css",
-    help="Whether (true) or not (false) to include CSS within an output HTML file.",
+    help="Whether (true) or not (false) to include CSS within an output "
+         "HTML file.",
     choices=["true", "false"],
     default="true",
 )

{pyLODE-3.0.0 → pyLODE-3.0.1}/pylode/ontdoc.py

@@ -56,7 +56,12 @@ try:
         prop_obj_pair_html,
         section_html,
     )
-except:
+
+    from .rdf_elements import ONTDOC, AGENT_PROPS, \
+        ONT_PROPS, CLASS_PROPS, PROP_PROPS
+
+    from .version import __version__
+except ImportError:
     from utils import (
         load_ontology,
         load_background_onts,
@@ -67,14 +72,9 @@ except:
         section_html,
     )
 
-try:
-    from .rdf_elements import ONTDOC, AGENT_PROPS, ONT_PROPS, CLASS_PROPS, PROP_PROPS
-except:
-    from rdf_elements import ONTDOC, AGENT_PROPS, ONT_PROPS, CLASS_PROPS, PROP_PROPS
+    from rdf_elements import ONTDOC, AGENT_PROPS, \
+        ONT_PROPS, CLASS_PROPS, PROP_PROPS
 
-try:
-    from .version import __version__
-except:
     from version import __version__
 
 RDF_FOLDER = Path(__file__).parent / "rdf"
@@ -85,7 +85,8 @@ class PylodeError(Exception):
 
 
 class OntDoc:
-    """Ontology Document class used to create HTML documentation from OWL Ontologies.
+    """Ontology Document class used to create HTML documentation
+    from OWL Ontologies.
 
     Use:
         # initialise
@@ -120,7 +121,8 @@ class OntDoc:
                 t = str(o2)
         if t is None:
             raise PylodeError(
-                "You MUST supply a title property (dcterms:title, rdf:label or sdo:name) for your ontology"
+                "You MUST supply a title property "
+                "(dcterms:title, rdf:label or sdo:name) for your ontology"
             )
         self.doc = dominate.document(title=t)
 
@@ -132,7 +134,9 @@ class OntDoc:
 
         Either writes to a file or returns a string"""
         self._make_head(
-            self._make_schema_org(), include_css=include_css, destination=destination
+            self._make_schema_org(),
+            include_css=include_css,
+            destination=destination
         )
         self._make_body()
 
@@ -188,12 +192,12 @@ class OntDoc:
             g.add((s_, RDF.type, OWL.Restriction))
 
         for s_ in chain(
-            g.subjects(OWL.unionOf, None),
-            g.subjects(OWL.intersectionOf, None)
+            g.subjects(OWL.unionOf, None), g.subjects(OWL.intersectionOf, None)
         ):
             g.add((s_, RDF.type, OWL.Class))
 
-        # we do these next few so we only need to loop through Class & Property properties once: single subject
+        # we do these next few so we only need to loop through
+        # Class & Property properties once: single subject
         for s_, o in g.subject_objects(RDFS.subClassOf):
             g.add((o, ONTDOC.superClassOf, s_))
 
@@ -222,7 +226,7 @@ class OntDoc:
         for s_, o in chain(
             g.subject_objects(DC.creator),
             g.subject_objects(SDO.creator),
-            g.subject_objects(SDO.author),  # conflate SDO.author with DCTERMS.creator
+            g.subject_objects(SDO.author),
         ):
             g.remove((s_, DC.creator, o))
             g.remove((s_, SDO.creator, o))
@@ -265,7 +269,10 @@ class OntDoc:
             g.add((s_, SDO.affiliation, o))
 
     def _make_head(
-        self, schema_org: Graph, include_css: bool = True, destination: Path = None
+        self,
+        schema_org: Graph,
+        include_css: bool = True,
+        destination: Path = None
     ):
         """Healper function for make_html(). Makes <head>???</head> content"""
         with self.doc.head:
@@ -280,7 +287,9 @@ class OntDoc:
                 )
             else:
                 link(href="pylode.css", rel="stylesheet", type="text/css")
-                shutil.copy(Path("pylode.css"), destination.parent / "pylode.css")
+                shutil.copy(
+                    Path("pylode.css"),
+                    destination.parent / "pylode.css")
             link(
                 rel="icon",
                 type="image/png",
@@ -297,7 +306,7 @@ class OntDoc:
             script(
                 raw("\n" + schema_org.serialize(format="json-ld") + "\n\t"),
                 type="application/ld+json",
-                id="schema.org"
+                id="schema.org",
             )
 
     def _make_body(self):
@@ -321,7 +330,8 @@ class OntDoc:
                         span("LODE")
                     a(
                         __version__,
-                        href="https://github.com/rdflib/pyLODE/release/" + __version__,
+                        href="https://github.com/rdflib/pyLODE/release/"
+                             + __version__,
                         id="version",
                     )
 
@@ -339,7 +349,10 @@ class OntDoc:
                     this_onts_props[p_].append(o)
 
         # make HTML for all props in order of ONT_PROPS
-        sec = div(h1(this_onts_props[DCTERMS.title]), id="metadata", _class="section")
+        sec = div(
+            h1(this_onts_props[DCTERMS.title]),
+            id="metadata",
+            _class="section")
         sec.appendChild(h2("Metadata"))
         d = dl(div(dt(strong("IRI")), dd(code(str(iri)))))
         for prop in ONT_PROPS:
@@ -369,38 +382,38 @@ class OntDoc:
             self.ont.subjects(predicate=RDF.type, object=PROF.Profile),
         ):
             sdo.add((ont_iri, RDF.type, SDO.DefinedTermSet))
-            for p, o in self.ont.predicate_objects(ont_iri):
-                if p == DCTERMS.title:
+            for p_, o in self.ont.predicate_objects(ont_iri):
+                if p_ == DCTERMS.title:
                     sdo.add((ont_iri, SDO.name, o))
-                elif p == DCTERMS.description:
+                elif p_ == DCTERMS.description:
                     sdo.add((ont_iri, SDO.description, o))
-                elif p == DCTERMS.publisher:
+                elif p_ == DCTERMS.publisher:
                     sdo.add((ont_iri, SDO.publisher, o))
                     if not isinstance(o, Literal):
                         for p2, o2 in self.ont.predicate_objects(o):
                             if p2 in AGENT_PROPS:
                                 sdo.add((o, p2, o2))
-                elif p == DCTERMS.creator:
+                elif p_ == DCTERMS.creator:
                     sdo.add((ont_iri, SDO.creator, o))
                     if not isinstance(o, Literal):
                         for p2, o2 in self.ont.predicate_objects(o):
                             if p2 in AGENT_PROPS:
                                 sdo.add((o, p2, o2))
-                elif p == DCTERMS.contributor:
+                elif p_ == DCTERMS.contributor:
                     sdo.add((ont_iri, SDO.contributor, o))
                     if not isinstance(o, Literal):
                         for p2, o2 in self.ont.predicate_objects(o):
                             if p2 in AGENT_PROPS:
                                 sdo.add((o, p2, o2))
-                elif p == DCTERMS.created:
+                elif p_ == DCTERMS.created:
                     sdo.add((ont_iri, SDO.dateCreated, o))
-                elif p == DCTERMS.modified:
+                elif p_ == DCTERMS.modified:
                     sdo.add((ont_iri, SDO.dateModified, o))
-                elif p == DCTERMS.issued:
+                elif p_ == DCTERMS.issued:
                     sdo.add((ont_iri, SDO.dateIssued, o))
-                elif p == DCTERMS.license:
+                elif p_ == DCTERMS.license:
                     sdo.add((ont_iri, SDO.license, o))
-                elif p == DCTERMS.rights:
+                elif p_ == DCTERMS.rights:
                     sdo.add((ont_iri, SDO.copyrightNotice, o))
 
         return sdo
@@ -505,7 +518,10 @@ class OntDoc:
 
                     if self.toc.get("classes") is not None:
                         with tr():
-                            td(sup("c", _class="sup-c", title="OWL/RDFS Class"))
+                            td(sup(
+                                "c",
+                                _class="sup-c",
+                                title="OWL/RDFS Class"))
                             td("Classes")
                     if self.toc.get("properties") is not None:
                         with tr():
@@ -513,7 +529,10 @@ class OntDoc:
                             td("Properties")
                     if self.toc.get("objectproperties") is not None:
                         with tr():
-                            td(sup("op", _class="sup-op", title="OWL Object Property"))
+                            td(sup(
+                                "op",
+                                _class="sup-op",
+                                title="OWL Object Property"))
                             td("Object Properties")
                     if self.toc.get("datatypeproperties") is not None:
                         with tr():
@@ -547,13 +566,21 @@ class OntDoc:
                             td("Functional Properties")
                     if self.toc.get("named_individuals") is not None:
                         with tr():
-                            td(sup("ni", _class="sup-ni", title="OWL Named Individual"))
+                            td(sup(
+                                "ni",
+                                _class="sup-ni",
+                                title="OWL Named Individual"
+                            ))
                             td("Named Individuals")
 
     def _make_namespaces(self):
         # get only namespaces used in ont
         nses = {}
-        for n in chain(self.ont.subjects(), self.ont.predicates(), self.ont.objects()):
+        for n in chain(
+                self.ont.subjects(),
+                self.ont.predicates(),
+                self.ont.objects()
+        ):
             for prefix, ns in self.ont.namespaces():
                 if str(n).startswith(ns):
                     nses[prefix] = ns
@@ -602,7 +629,10 @@ class OntDoc:
                         and len(self.toc["objectproperties"]) > 0
                     ):
                         with li():
-                            h4(a("Object Properties", href="#objectproperties"))
+                            h4(a(
+                                "Object Properties",
+                                href="#objectproperties"
+                            ))
                             with ul(_class="second"):
                                 for c in self.toc["objectproperties"]:
                                     li(a(c[1], href=c[0]))
@@ -612,7 +642,10 @@ class OntDoc:
                         and len(self.toc["datatypeproperties"]) > 0
                     ):
                         with li():
-                            h4(a("Datatype Properties", href="#datatypeproperties"))
+                            h4(a(
+                                "Datatype Properties",
+                                href="#datatypeproperties"
+                            ))
                             with ul(_class="second"):
                                 for c in self.toc["datatypeproperties"]:
                                     li(a(c[1], href=c[0]))
@@ -622,7 +655,10 @@ class OntDoc:
                         and len(self.toc["annotationproperties"]) > 0
                     ):
                         with li():
-                            h4(a("Annotation Properties", href="#annotationproperties"))
+                            h4(a(
+                                "Annotation Properties",
+                                href="#annotationproperties"
+                            ))
                             with ul(_class="second"):
                                 for c in self.toc["annotationproperties"]:
                                     li(a(c[1], href=c[0]))
@@ -632,7 +668,10 @@ class OntDoc:
                         and len(self.toc["functionalproperties"]) > 0
                     ):
                         with li():
-                            h4(a("Functional Properties", href="#functionalproperties"))
+                            h4(a(
+                                "Functional Properties",
+                                href="#functionalproperties"
+                            ))
                             with ul(_class="second"):
                                 for c in self.toc["functionalproperties"]:
                                     li(a(c[1], href=c[0]))
@@ -644,28 +683,3 @@ class OntDoc:
                                 li(a(n[1], href="#" + n[1]))
 
                     li(h4(a("Legend", href="#legend")), ul(_class="second"))
-
-
-if __name__ == "__main__":
-    # TODO: schema.org generation from ont
-    # TODO: move background ont into Dataset
-    # TODO: cli UI
-
-    logging.basicConfig(
-        level=logging.INFO,
-        format="%(asctime)s [%(levelname)s] %(message)s",
-        handlers=[logging.StreamHandler()],
-    )
-
-    od = OntDoc(ontology="https://data.surroundaustralia.com/def/exem")
-    od.make_html(destination="some.html")
-
-    # import cProfile
-    #
-    # pr = cProfile.Profile()
-    # pr.enable()
-    #
-    # check_all_props_are_known()
-    #
-    # pr.disable()
-    # pr.print_stats(sort='time')

{pyLODE-3.0.0 → pyLODE-3.0.1}/pylode/rdf_elements.py

@@ -1,12 +1,7 @@
 from rdflib import Namespace
 from rdflib.namespace import (
-    DC,
     DCTERMS,
-    FOAF,
-    ORG,
     OWL,
-    PROF,
-    PROV,
     RDF,
     RDFS,
     SDO,
@@ -62,7 +57,8 @@ CLASS_PROPS = [
     ONTDOC.superClassOf,
 ]
 
-# properties for instances of RDF Property and OWL specialised forms, such as ObjectProperty etc.
+# properties for instances of RDF Property and OWL specialised
+# forms, such as ObjectProperty etc.
 PROP_PROPS = [
     RDFS.isDefinedBy,
     DCTERMS.title,
@@ -106,7 +102,9 @@ RESTRICTION_PROPS = [
 ]
 
 # all known properties
-PROPS = set(ONT_PROPS + CLASS_PROPS + PROP_PROPS + AGENT_PROPS + RESTRICTION_PROPS)
+PROPS = set(
+    ONT_PROPS + CLASS_PROPS + PROP_PROPS +
+    AGENT_PROPS + RESTRICTION_PROPS)
 
 ONT_TYPES = {
     OWL.Class: ("c", "OWL/RDFS Class"),
@@ -131,7 +129,4 @@ RESTRICTION_TYPES = [
     OWL.hasValue,
 ]
 
-OWL_SET_TYPES = [
-    OWL.unionOf,
-    OWL.intersectionOf
-]
+OWL_SET_TYPES = [OWL.unionOf, OWL.intersectionOf]

{pyLODE-3.0.0 → pyLODE-3.0.1}/pylode/utils.py

@@ -26,24 +26,37 @@ from dominate.tags import (
     dd,
     h2,
 )
-from dominate.util import raw, text
+from dominate.util import raw
 from rdflib import BNode, Literal, Graph, URIRef
 from rdflib.paths import ZeroOrMore
-from rdflib.paths import Path as PropertyPath
-from rdflib.namespace import DC, DCTERMS, FOAF, ORG, OWL, PROF, PROV, RDF, RDFS, SDO, SKOS, VANN
+from rdflib.namespace import (
+    DC,
+    DCTERMS,
+    PROF,
+    PROV,
+    OWL,
+    RDF,
+    RDFS,
+    SDO,
+    SKOS,
+    VANN
+)
 
 try:
-    from .rdf_elements import *
-except:
-    from rdf_elements import *
+    from .rdf_elements import AGENT_PROPS, ONTDOC, ONT_TYPES, \
+        OWL_SET_TYPES, PROPS, RESTRICTION_TYPES
+except ImportError:
+    from rdf_elements import AGENT_PROPS, ONTDOC, ONT_TYPES, \
+        OWL_SET_TYPES, PROPS, RESTRICTION_TYPES
 
 RDF_FOLDER = Path(__file__).parent / "rdf"
 
 
 def check_all_props_are_known():
-    """Check all properties listed in the combined property lists in properties.py to see if
-    their titles and descriptions are present in the background ontologies in the folder rdf/.
-    Run after performing labelling inferencing."""
+    """Check all properties listed in the combined property lists in
+    properties.py to see if their titles and descriptions are present in the
+    background ontologies in the folder rdf/. Run after performing labelling
+    inferencing."""
     bg = load_background_onts()
     for prop in PROPS:
         if (prop, RDF.type, None) not in bg:
@@ -84,9 +97,11 @@ def get_ns(ont: Graph) -> Tuple[str, str]:
             if prefix is not None:
                 return prefix, default_iri
         else:
-            # can't find either a declared or default namespace so we have an error
+            # can't find either a declared or default namespace
+            # so we have an error
             raise Exception(
-                "pyLODE can't detect a URI for an owl:Ontology, a skos:ConceptScheme or a prof:Profile"
+                "pyLODE can't detect a URI for an owl:Ontology, "
+                "a skos:ConceptScheme or a prof:Profile"
             )
 
 
@@ -126,7 +141,8 @@ def make_title_from_iri(iri: URIRef):
 
 
 def generate_fid(title_: Union[Literal, None], iri: URIRef, fids: dict):
-    """Makes an HTML fragment ID for an RDF resource, based on title (preferred) or IRI"""
+    """Makes an HTML fragment ID for an RDF resource,
+    based on title (preferred) or IRI"""
     s_iri = str(iri) if iri is not None else None
     s_title_ = str(title_) if title_ is not None else None
 
@@ -149,7 +165,8 @@ def generate_fid(title_: Union[Literal, None], iri: URIRef, fids: dict):
             fids[s_iri] = fid
             return fid
 
-        # this fid is already present so generate a new one from the URI instead
+        # this fid is already present
+        # so generate a new one from the URI instead
 
     # split URI for last slash segment
     segments = s_iri.split("/")
@@ -158,7 +175,8 @@ def generate_fid(title_: Union[Literal, None], iri: URIRef, fids: dict):
     if len(segments[-1]) < 1:
         return None
 
-    # return None for domains, i.e. ['http:', '', '{domain}'] - no path segments
+    # return None for domains, i.e. ['http:', '', '{domain}'],
+    # no path segments
     if len(segments) < 4:
         return None
 
@@ -180,13 +198,16 @@ def generate_fid(title_: Union[Literal, None], iri: URIRef, fids: dict):
         fids[s_iri] = fid
         return fid
     else:
-        # since it's in use but we've exhausted generation options, just add 1 to existing fid name
+        # since it's in use but we've exhausted generation options,
+        # just add 1 to existing fid name
         fids[s_iri] = fid + "1"
-        return fid + "1"  # yeah yeah, there could be more than one but unlikely
+        return fid + "1"
+        # yeah yeah, there could be more than one but unlikely
 
 
 def back_onts_label_props(back_onts: Graph):
-    """Gets titles and descriptions for all properties in the background ontologies"""
+    """Gets titles and descriptions for all properties
+    in the background ontologies"""
     back_onts_titles = load_background_onts_titles(back_onts)
 
     def _get_prop_label(prop_iri: URIRef, back_onts: Graph) -> dict:
@@ -234,9 +255,9 @@ def load_ontology(ontology: Union[Graph, Path, str]) -> Graph:
                 if ontology.startswith("[") or ontology.startswith("{"):
                     input_format = "json-ld"
                 elif (
-                    ontology.startswith("<?xml")
-                    or ontology.startswith("<!--")
-                    or ontology.startswith("<rdf:RDF")
+                        ontology.startswith("<?xml")
+                        or ontology.startswith("<!--")
+                        or ontology.startswith("<rdf:RDF")
                 ):
                     input_format = "xml"
                 else:
@@ -248,21 +269,21 @@ def load_ontology(ontology: Union[Graph, Path, str]) -> Graph:
             return Graph().parse(ontology)
         else:
             raise ValueError(
-                "The ontology you supply to OntDoc must be either an RDFlib Graph, a Path (to an RDF file) "
-                "or a string (of RDF data)"
+                "The ontology you supply to OntDoc must be either "
+                "an RDFlib Graph, a Path (to an RDF file) or a string "
+                "(of RDF data)"
             )
     except Exception as e:
         print(f"{type(e).__name__} Error {e}")
         exit()
-        # raise ParserError(f"Could not parse supplied ontology.\n\n {type(e).__name__} error with message: {str(e)}")
 
 
 def load_background_onts():
-    """Loads background ontology files into an RDFLib graph from either RDF source
-    files or a pickled Graph.
+    """Loads background ontology files into an RDFLib graph from either
+    RDF source files or a pickled Graph.
 
-    Performs title and description inference and stores a pickle if generating from
-    RDF source files."""
+    Performs title and description inference and stores a pickle if
+    generating from RDF source files."""
 
     def _parse_background_onts():
         g_ = Graph()
@@ -274,19 +295,19 @@ def load_background_onts():
     def _expand_background_onts_graph(back_ont: Graph):
         # make regular titles
         for s_, o in chain(
-            back_ont.subject_objects(DC.title),
-            back_ont.subject_objects(RDFS.label),
-            back_ont.subject_objects(SKOS.prefLabel),
-            back_ont.subject_objects(SDO.name),
+                back_ont.subject_objects(DC.title),
+                back_ont.subject_objects(RDFS.label),
+                back_ont.subject_objects(SKOS.prefLabel),
+                back_ont.subject_objects(SDO.name),
         ):
             back_ont.add((s_, DCTERMS.title, o))
 
         # make regular descriptions
         for s_, o in chain(
-            back_ont.subject_objects(DC.description),
-            back_ont.subject_objects(RDFS.comment),
-            back_ont.subject_objects(SKOS.definition),
-            back_ont.subject_objects(SDO.description),
+                back_ont.subject_objects(DC.description),
+                back_ont.subject_objects(RDFS.comment),
+                back_ont.subject_objects(SKOS.definition),
+                back_ont.subject_objects(SDO.description),
         ):
             back_ont.add((s_, DCTERMS.description, o))
 
@@ -295,7 +316,7 @@ def load_background_onts():
             with open(RDF_FOLDER / "refs.pickle", "wb") as f_:
                 pickle.dump(back_ont, f_)
         except FileNotFoundError:
-            print("Could not cache background ontologies graph")
+            logging.warning("Could not cache background ontologies graph")
 
     if Path(RDF_FOLDER / "refs.pickle").is_file():
         logging.info("Loading background ontologies from a pickle file")
@@ -310,7 +331,8 @@ def load_background_onts():
 
 
 def load_background_onts_titles(ont: Graph):
-    """Loads the titles of background ontologies into a discionary of Ontology IRI / title"""
+    """Loads the titles of background ontologies
+    into a dictionary of Ontology IRI / title"""
 
     def _get_background_ontology_titles(back_ont: Graph):
         onts_titles = {}
@@ -318,14 +340,22 @@ def load_background_onts_titles(ont: Graph):
             for o in back_ont.objects(subject=s_, predicate=DCTERMS.title):
                 onts_titles[str(s_)] = str(o)
 
-        return {k: v for k, v in sorted(onts_titles.items(), key=lambda item: item[1])}
+        return {
+            k: v
+            for k, v
+            in sorted(
+                onts_titles.items(),
+                key=lambda item: item[1]
+            )
+        }
 
     def _pickle_background_onts_titles(ont_titles: dict):
         try:
             with open(RDF_FOLDER / "refs_titles.pickle", "wb") as f_:
                 pickle.dump(ont_titles, f_)
         except FileNotFoundError:
-            print("Could not cache background ontologies' titles graph")
+            logging.warning(
+                "Could not cache background ontologies' titles graph")
 
     if Path(RDF_FOLDER / "refs_titles.pickle").is_file():
         with open(RDF_FOLDER / "refs_titles.pickle", "rb") as f:
@@ -337,24 +367,24 @@ def load_background_onts_titles(ont: Graph):
 
 
 def rdf_obj_html(
-    ont: Graph,
-    back_onts: Graph,
-    ns: Tuple[str, str],
-    obj: List[Union[URIRef, BNode, Literal]],
-    fids,
-    rdf_type=None,
+        ont: Graph,
+        back_onts: Graph,
+        ns: Tuple[str, str],
+        obj: List[Union[URIRef, BNode, Literal]],
+        fids,
+        rdf_type=None,
 ):
     """Makes a sensible HTML rendering of an RDF resource.
 
     Can handle IRIs, Blank Nodes of Agents or OWL Restrictions or Literals"""
 
     def _rdf_obj_single_html(
-        ont_: Graph,
-        back_onts_: Graph,
-        ns_: Tuple[str, str],
-        obj_: Union[URIRef, BNode, Literal],
-        fids_,
-        rdf_type_=None,
+            ont_: Graph,
+            back_onts_: Graph,
+            ns_: Tuple[str, str],
+            obj_: Union[URIRef, BNode, Literal],
+            fids_,
+            rdf_type_=None,
     ):
         def _hyperlink_html(
                 ont__: Graph,
@@ -391,17 +421,18 @@ def rdf_obj_html(
                     if x_ in this_objects_types:
                         return x_
 
+            # find type
+            if rdf_type__ is None:
+                rdf_type__ = _get_ont_type(ont__, back_onts__, iri__)
+
             try:
                 qname = ont__.compute_qname(iri__, True)
             except ValueError:
                 qname = iri__
 
-            # find type
-            if rdf_type__ is None:
-                rdf_type__ = _get_ont_type(ont__, back_onts__, iri__)
-
             prefix = "" if qname[0] == "" else f"{qname[0]}:"
-            if str(iri__).startswith(ns__):
+
+            if ns__ is not None and str(iri__).startswith(ns__):
                 fid = generate_fid(None, iri__, fids__)
                 if fid is not None:
                     iri__ = "#" + fid
@@ -424,7 +455,9 @@ def rdf_obj_html(
 
         def _literal_html(obj__):
             if str(obj__).startswith("http"):
-                return _hyperlink_html(ont_, back_onts_, ns_, cast(URIRef, obj__), fids_)
+                return _hyperlink_html(
+                    ont_, back_onts_, ns_, cast(URIRef, obj__), fids_
+                )
             else:
                 return raw(markdown.markdown(str(obj__)))
 
@@ -516,7 +549,8 @@ def rdf_obj_html(
 
                 if email is not None:
                     email = email.replace("mailto:", "")
-                    sp.appendChild(span("(", a(email, href="mailto:" + email), ")"))
+                    sp.appendChild(
+                        span("(", a(email, href="mailto:" + email), ")"))
 
                 if affiliation is not None:
                     sp.appendChild(_affiliation_html(ont__, affiliation))
@@ -530,7 +564,13 @@ def rdf_obj_html(
             for px, o in ont__.predicate_objects(obj__):
                 if px != RDF.type:
                     if px == OWL.onProperty:
-                        prop = _hyperlink_html(ont__, back_onts_, ns__, o, fids_)
+                        prop = _hyperlink_html(
+                            ont__,
+                            back_onts_,
+                            ns__,
+                            o,
+                            fids_
+                        )
                     elif px in RESTRICTION_TYPES + OWL_SET_TYPES:
                         if px in [
                             OWL.minCardinality,
@@ -540,14 +580,25 @@ def rdf_obj_html(
                             OWL.cardinality,
                             OWL.qualifiedCardinality,
                         ]:
-                            if px in [OWL.minCardinality, OWL.minQualifiedCardinality]:
+                            if px in [
+                                OWL.minCardinality,
+                                OWL.minQualifiedCardinality
+                            ]:
                                 card = "min"
-                            elif px in [OWL.maxCardinality, OWL.maxQualifiedCardinality]:
+                            elif px in [
+                                OWL.maxCardinality,
+                                OWL.maxQualifiedCardinality,
+                            ]:
                                 card = "max"
-                            elif px in [OWL.cardinality, OWL.qualifiedCardinality]:
+                            elif px in [
+                                OWL.cardinality,
+                                OWL.qualifiedCardinality
+                            ]:
                                 card = "exactly"
 
-                            card = span(span(card, _class="cardinality"), span(str(o)))
+                            card = span(
+                                span(card, _class="cardinality"),
+                                span(str(o)))
                         else:
                             if px == OWL.allValuesFrom:
                                 card = "only"
@@ -560,20 +611,29 @@ def rdf_obj_html(
                             elif px == OWL.intersectionOf:
                                 card = "intersection"
 
-                                card = span(span(card, _class="cardinality"), raw(_rdf_obj_single_html))
+                                card = span(
+                                    span(card, _class="cardinality"),
+                                    raw(_rdf_obj_single_html),
+                                )
                             else:
                                 card = span(
                                     span(card, _class="cardinality"),
                                     span(
                                         _hyperlink_html(
-                                            ont__, back_onts_, ns__, o, fids_, OWL.Class
+                                            ont__,
+                                            back_onts_,
+                                            ns__,
+                                            o,
+                                            fids_,
+                                            OWL.Class
                                         )
                                     ),
                                 )
 
             restriction = span(prop, card, br()) if card is not None else prop
             restriction = (
-                span(restriction, cls, br()) if cls is not None else restriction
+                span(restriction, cls, br())
+                if cls is not None else restriction
             )
 
             return span(restriction) if restriction is not None else "None"
@@ -589,17 +649,21 @@ def rdf_obj_html(
                 joining_word = ' <span class="cardinality">,</span> '
 
             class_set = set()
-            for o in ont__.objects(obj__, OWL.unionOf|OWL.intersectionOf):
+            for o in ont__.objects(obj__, OWL.unionOf | OWL.intersectionOf):
                 for o2 in ont__.objects(o, RDF.rest * ZeroOrMore / RDF.first):
-                    class_set.add(_rdf_obj_single_html(ont__, back_onts__, ns__, o2, fids__, OWL.Class))
+                    class_set.add(
+                        _rdf_obj_single_html(
+                            ont__, back_onts__, ns__, o2, fids__, OWL.Class
+                        )
+                    )
 
             return raw(joining_word.join([mem.render() for mem in class_set]))
 
         def _bn_html(ont__, back_onts__, ns__, fids__, obj__: BNode):
             # TODO: remove back_onts and fids if not needed by subfunctions
             # What kind of BN is it?
-            # An Agent, a Restriction or a Set Class (union/intersection) handled
-            # all typing added in OntDoc inferencing
+            # An Agent, a Restriction or a Set Class (union/intersection)
+            # handled all typing added in OntDoc inferencing
             if (obj__, RDF.type, PROV.Agent) in ont__:
                 return _agent_html(ont__, obj__)
             elif (obj__, RDF.type, OWL.Restriction) in ont__:
@@ -608,44 +672,52 @@ def rdf_obj_html(
                 return _setclass_html(ont__, obj__, back_onts__, ns__, fids__)
 
         if isinstance(obj_, URIRef):
-            ret = _hyperlink_html(ont_, back_onts_, ns_, obj_, fids_, rdf_type__=rdf_type_)
+            ret = _hyperlink_html(
+                ont_, back_onts_, ns_, obj_, fids_, rdf_type__=rdf_type_
+            )
         elif isinstance(obj_, BNode):
             ret = _bn_html(ont_, back_onts_, ns_, fids_, obj_)
         else:  # isinstance(obj, Literal):
             ret = _literal_html(obj_)
 
-        # TODO: replace this filler-inner when all subfunctions are returning fine
-        return ret if ret is not None else span("xxx")
+        return ret if ret is not None else span()
 
     if len(obj) == 1:
-        return _rdf_obj_single_html(ont, back_onts, ns, obj[0], fids, rdf_type_=rdf_type)
+        return _rdf_obj_single_html(
+            ont, back_onts, ns, obj[0], fids, rdf_type_=rdf_type
+        )
     else:
         u_ = ul()
         for x in obj:
             u_.appendChild(
-                li(_rdf_obj_single_html(ont, back_onts, ns, x, fids, rdf_type_=rdf_type))
+                li(
+                    _rdf_obj_single_html(
+                        ont, back_onts, ns, x, fids, rdf_type_=rdf_type
+                    )
+                )
             )
         return u_
 
 
 def prop_obj_pair_html(
-    ont: Graph,
-    back_onts: Graph,
-    ns: Tuple[str, str],
-    table_or_dl: str,
-    prop_iri: URIRef,
-    property_title: Literal,
-    property_description: Literal,
-    ont_title: Literal,
-    fids,
-    obj: List[Union[URIRef, BNode, Literal]],
-    obj_type: Optional[str] = None,
+        ont: Graph,
+        back_onts: Graph,
+        ns: Tuple[str, str],
+        table_or_dl: str,
+        prop_iri: URIRef,
+        property_title: Literal,
+        property_description: Literal,
+        ont_title: Literal,
+        fids,
+        obj: List[Union[URIRef, BNode, Literal]],
+        obj_type: Optional[str] = None,
 ):
     """Makes an HTML Definition list dt & dd pair or a Table tr, th & td set,
     for a given RDF property & resource pair"""
     prop = a(
         str(property_title).title(),
-        title=str(property_description).rstrip(".") + ". Defined in " + str(ont_title),
+        title=str(property_description).rstrip(".") +
+        ". Defined in " + str(ont_title),
         _class="hover_property",
         href=str(prop_iri),
     )
@@ -660,32 +732,32 @@ def prop_obj_pair_html(
 
 
 def section_html(
-    section_title: str,
-    ont: Graph,
-    back_onts: Graph,
-    ns: Tuple[str, str],
-    obj_class: URIRef,
-    prop_list: list,
-    toc,
-    toc_ul_id: str,
-    fids: dict,
-    props_labeled,
+        section_title: str,
+        ont: Graph,
+        back_onts: Graph,
+        ns: Tuple[str, str],
+        obj_class: URIRef,
+        prop_list: list,
+        toc,
+        toc_ul_id: str,
+        fids: dict,
+        props_labeled,
 ):
     """Makes all the HTML (div, title & table) for all instances of a
     given RDF class, e.g. owl:Class or owl:ObjectProperty"""
 
     def _element_html(
-        ont_: Graph,
-        back_onts_: Graph,
-        ns_: Tuple[str, str],
-        iri: URIRef,
-        fid: str,
-        title_: str,
-        ont_type: URIRef,
-        props_list,
-        this_props_,
-        fids_: dict,
-        props_labeled_,
+            ont_: Graph,
+            back_onts_: Graph,
+            ns_: Tuple[str, str],
+            iri: URIRef,
+            fid: str,
+            title_: str,
+            ont_type: URIRef,
+            props_list,
+            this_props_,
+            fids_: dict,
+            props_labeled_,
     ):
         """Makes all the HTML (div, title & table) for one instance of a
         given RDF class, e.g. owl:Class or owl:ObjectProperty"""
@@ -743,14 +815,15 @@ def section_html(
             if any(x in ont for x in specialised_props):
                 continue
         if isinstance(
-            s_, URIRef
+                s_, URIRef
         ):  # ignore blank nodes for things like [ owl:unionOf ( ... ) ]
             this_props = defaultdict(list)
             # get all properties of this object
             for p_, o in ont.predicate_objects(subject=s_):
                 # ... in the property list for this class
                 if p_ in prop_list:
-                    if p_ == RDFS.subClassOf and (o, RDF.type, OWL.Restriction) in ont:
+                    if p_ == RDFS.subClassOf \
+                            and (o, RDF.type, OWL.Restriction) in ont:
                         this_props[ONTDOC.restriction].append(o)
                     else:
                         this_props[p_].append(o)
@@ -788,8 +861,3 @@ def section_html(
 
 def de_space_html(html):
     return "".join([l_.strip().replace("\n", "") for l_ in html.split("\n")])
-
-
-if __name__ == "__main__":
-    # ("http://example.com/thing/FiveFive", "Five 5", "Five5"),
-    print(generate_fid("Five 5", "http://example.com/thing/FiveFive", {}))

pyLODE-3.0.1/pylode/version.py

@@ -0,0 +1 @@
+__version__ = "3.0.1"

pyLODE-3.0.0/pylode/extra.py

@@ -1,6 +0,0 @@
-from typing import Union
-from rdflib import Dataset, URIRef, Graph
-
-
-def get_graph_from_dataset(d: Dataset, graph_identifier: URIRef) -> Union[Graph, None]:
-    return [x for x in d.contexts() if x.identifier == graph_identifier][0]

pyLODE-3.0.0/pylode/version.py

@@ -1 +0,0 @@
-__version__ = "3.0.0"