pylode 3.4.4__tar.gz → 3.5.1__tar.gz

{pylode-3.4.4 → pylode-3.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylode
-Version: 3.4.4
+Version: 3.5.1
 Summary: An OWL ontology documentation tool using Python, based on LODE.
 Author: Nicholas Car
 Author-email: Nicholas Car <nick@kurrawong.ai>
@@ -13,7 +13,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: rdflib>=7.6.0,<8.0.0
 Requires-Dist: markdown>=3.3.7,<4
-Requires-Dist: dominate>=2.6.0,<3
+Requires-Dist: dominate>=2.9.1,<3
 Requires-Dist: html5lib>=1.1,<2
 Requires-Dist: httpx>=0.25.0,<1.0.0
 Requires-Dist: tqdm>=4.67.3
@@ -38,25 +38,7 @@ An OWL ontology documentation tool using Python, based on LODE.
 
 In addition to making web page, human-readable forms of ontologies, pyLODE encourages ontology annotation *best 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](#what-pylode-understands).
 
-**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` mode. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
-
----
-
-## A note on the v 3.x change
-
-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.
-
-However, 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)
-- Access it via the [online service](http://tools.kurrawong.ai/pylode)
-
----
+**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` & `vocpub` modes. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
 
 ## Contents
 
@@ -101,20 +83,23 @@ The tool can be used in multiple ways:
 ### Command line arguments
 
 ```text
-usage: cli.py [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] input
+usage: pylode [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] [-s] [-p {ontpub,vocpub,supermodel}] [-l {error,warning,info,debug}] input
 
 positional arguments:
-    input                 Input file location or URL
-
-optional arguments:
-    -h, --help            show this help message and exit
-    -v, --version         show program's version number and exit
-    -o OUTPUTFILE,
-    --outputfile OUTPUTFILE
-                          Output file name (postfixed with .html if needed)
-    -c {true,false},
-    --css {true,false}
-                          Include CSS in the output HTML
+  input                 Input file location or URL
+
+options:
+  -h, --help            show this help message and exit
+  -v, --version         show program's version number and exit
+  -o, --outputfile OUTPUTFILE
+                        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
+  -c, --css {true,false}
+                        Whether (true) or not (false) to include CSS within an output HTML file.
+  -s, --sort            Enables sorting of the subjects in the ontology in the output
+  -p, --profile {ontpub,vocpub,supermodel}
+                        Which profile to use to generate HTML. Must be one of 'ontpub' (https://linked.data.gov.au/def/ontpub) - for ontologies, 'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies, 'supermodel' - for profiles of profiles
+  -l, --loglevel {error,warning,info,debug}
+                        Set the logging level
 ```
 
 ### Basic Use
@@ -125,6 +110,12 @@ optional arguments:
 python pylode examples/ontpub/minimal.ttl -o minimal.html
 ```
 
+for a SKOS vocabulary, indicate the `vocpub` profile:
+
+```bash
+python pylode examples/vocpub/GeologicSpecimenMaterialTypes.ttl -o GeologicSpecimenMaterialTypes.html -p vocpub
+```
+
 #### As a Docker container
 
 ```bash
@@ -246,6 +237,9 @@ pyLODE deliberately does **not** translate everything in RDF to HTML, enforcing
 pyLODE supports simple and complex Agent objects, including ORCIDs, affiliations, and contact details.
 
 ```turtle
+PREFIX schema: <https://schema.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
 <ontology_x>
     schema:creator [
         schema:name "Nicholas J. Car" ;
@@ -302,9 +296,6 @@ Older releases
 
 | Version | Date             | Description                                                                     |
 |---------|------------------|---------------------------------------------------------------------------------|
-| 3.0.5   | 27 April 2023    | Minor patching                                                                  |
-| 3.0.4   | 24 May 2022      | Use of Poetry                                                                   |
-| 3.0.2   | 24 May 2022      | Support for preformatted skos:example literals                                  |
 | 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                         |
@@ -355,7 +346,7 @@ Nicholas Car
 5. tag with version number: `$git tag ...`
 6. push changes `$ git push`
 7. push version `git push --tags`
-8make a GitHub release
+8. make a GitHub release
     * PyPI release is automated from this in `pypi.yml`
 9. increment version number to next release alpha in `pyproject.toml`
 10. commit all changes `$ git commit -a "..."`

{pylode-3.4.4 → pylode-3.5.1}/README.md

@@ -7,25 +7,7 @@ An OWL ontology documentation tool using Python, based on LODE.
 
 In addition to making web page, human-readable forms of ontologies, pyLODE encourages ontology annotation *best 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](#what-pylode-understands).
 
-**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` mode. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
-
----
-
-## A note on the v 3.x change
-
-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.
-
-However, 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)
-- Access it via the [online service](http://tools.kurrawong.ai/pylode)
-
----
+**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` & `vocpub` modes. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
 
 ## Contents
 
@@ -70,20 +52,23 @@ The tool can be used in multiple ways:
 ### Command line arguments
 
 ```text
-usage: cli.py [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] input
+usage: pylode [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] [-s] [-p {ontpub,vocpub,supermodel}] [-l {error,warning,info,debug}] input
 
 positional arguments:
-    input                 Input file location or URL
-
-optional arguments:
-    -h, --help            show this help message and exit
-    -v, --version         show program's version number and exit
-    -o OUTPUTFILE,
-    --outputfile OUTPUTFILE
-                          Output file name (postfixed with .html if needed)
-    -c {true,false},
-    --css {true,false}
-                          Include CSS in the output HTML
+  input                 Input file location or URL
+
+options:
+  -h, --help            show this help message and exit
+  -v, --version         show program's version number and exit
+  -o, --outputfile OUTPUTFILE
+                        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
+  -c, --css {true,false}
+                        Whether (true) or not (false) to include CSS within an output HTML file.
+  -s, --sort            Enables sorting of the subjects in the ontology in the output
+  -p, --profile {ontpub,vocpub,supermodel}
+                        Which profile to use to generate HTML. Must be one of 'ontpub' (https://linked.data.gov.au/def/ontpub) - for ontologies, 'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies, 'supermodel' - for profiles of profiles
+  -l, --loglevel {error,warning,info,debug}
+                        Set the logging level
 ```
 
 ### Basic Use
@@ -94,6 +79,12 @@ optional arguments:
 python pylode examples/ontpub/minimal.ttl -o minimal.html
 ```
 
+for a SKOS vocabulary, indicate the `vocpub` profile:
+
+```bash
+python pylode examples/vocpub/GeologicSpecimenMaterialTypes.ttl -o GeologicSpecimenMaterialTypes.html -p vocpub
+```
+
 #### As a Docker container
 
 ```bash
@@ -215,6 +206,9 @@ pyLODE deliberately does **not** translate everything in RDF to HTML, enforcing
 pyLODE supports simple and complex Agent objects, including ORCIDs, affiliations, and contact details.
 
 ```turtle
+PREFIX schema: <https://schema.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
 <ontology_x>
     schema:creator [
         schema:name "Nicholas J. Car" ;
@@ -271,9 +265,6 @@ Older releases
 
 | Version | Date             | Description                                                                     |
 |---------|------------------|---------------------------------------------------------------------------------|
-| 3.0.5   | 27 April 2023    | Minor patching                                                                  |
-| 3.0.4   | 24 May 2022      | Use of Poetry                                                                   |
-| 3.0.2   | 24 May 2022      | Support for preformatted skos:example literals                                  |
 | 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                         |
@@ -324,7 +315,7 @@ Nicholas Car
 5. tag with version number: `$git tag ...`
 6. push changes `$ git push`
 7. push version `git push --tags`
-8make a GitHub release
+8. make a GitHub release
     * PyPI release is automated from this in `pypi.yml`
 9. increment version number to next release alpha in `pyproject.toml`
 10. commit all changes `$ git commit -a "..."`

{pylode-3.4.4 → pylode-3.5.1}/pylode/cli.py

@@ -46,7 +46,7 @@ parser.add_argument(
     "--profile",
     help="Which profile to use to generate HTML. Must be one of "
     "'ontpub' (https://linked.data.gov.au/def/ontpub) - for ontologies, "
-    "'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies"
+    "'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies, "
     "'supermodel' - for profiles of profiles",
     choices=["ontpub", "vocpub", "supermodel"],
     default="ontpub",

{pylode-3.4.4 → pylode-3.5.1}/pylode/profiles/ontpub.py

@@ -16,10 +16,12 @@ from dominate.tags import (
     h2,
     h3,
     h4,
+    h5,
     li,
     link,
     meta,
     script,
+    section,
     strong,
     style,
     sup,
@@ -132,6 +134,9 @@ class OntPub:
         for s_ in g.subjects(RDF.type, OWL.Class):
             g.add((s_, RDF.type, RDFS.Class))
 
+        for s_ in g.subjects(RDF.type, RDFS.Class):
+            g.add((s_, RDF.type, OWL.Class))
+
         # # property types
         # for s_ in chain(
         #     g.subjects(RDF.type, OWL.ObjectProperty),
@@ -474,6 +479,21 @@ class OntPub:
                 )
                 d.render()
 
+            if (None, RDF.type, RDFS.Datatype) in self.ont:
+                d = section_html(
+                    "Custom Datatypes",
+                    self.ont,
+                    self.back_onts,
+                    self.ns,
+                    RDFS.Datatype,
+                    PROP_PROPS,
+                    self.toc,
+                    "datatypes",
+                    self.fids,
+                    self.props_labeled,
+                )
+                d.render()
+
     def _make_legend(self):
         with self.content:
             with div(id="legend"):
@@ -573,9 +593,23 @@ class OntPub:
                     ):
                         with li():
                             h4(a("Classes", href="#classes"))
+                            h5(
+                                a(
+                                    "Class Hierarchy",
+                                    href="#class-hierarchy",
+                                    style="margin-left:10px;",
+                                )
+                            )
+                            h5(
+                                a(
+                                    "Class Definitions",
+                                    href="#class-definitions",
+                                    style="margin-left:10px;",
+                                )
+                            )
                             with ul(_class="second"):
                                 for c in self.toc["classes"]:
-                                    li(a(c[1], href=c[0]))
+                                    li(a(c[1], href=c[0]), style="margin-left:10px;")
 
                     if (
                         self.toc.get("properties") is not None
@@ -593,9 +627,23 @@ class OntPub:
                     ):
                         with li():
                             h4(a("Object Properties", href="#objectproperties"))
+                            h5(
+                                a(
+                                    "Object Property Hierarchy",
+                                    href="#object-property-hierarchy",
+                                    style="margin-left:10px;",
+                                )
+                            )
+                            h5(
+                                a(
+                                    "Object Property Definitions",
+                                    href="#object-property-definitions",
+                                    style="margin-left:10px;",
+                                )
+                            )
                             with ul(_class="second"):
                                 for c in self.toc["objectproperties"]:
-                                    li(a(c[1], href=c[0]))
+                                    li(a(c[1], href=c[0]), style="margin-left:10px;")
 
                     if (
                         self.toc.get("datatypeproperties") is not None
@@ -627,6 +675,16 @@ class OntPub:
                                 for c in self.toc["functionalproperties"]:
                                     li(a(c[1], href=c[0]))
 
+                    if (
+                        self.toc.get("datatypes") is not None
+                        and len(self.toc["datatypes"]) > 0
+                    ):
+                        with li():
+                            h4(a("Custom Datatypes", href="#datatypes"))
+                            with ul(_class="second"):
+                                for c in self.toc["datatypes"]:
+                                    li(a(c[1], href=c[0]))
+
                     with li():
                         h4(a("Namespaces", href="#namespaces"))
                         with ul(_class="second"):

{pylode-3.4.4 → pylode-3.5.1}/pylode/profiles/vocpub.py

@@ -50,7 +50,7 @@ from rdflib.namespace import (
 
 from pylode.rdf_elements import AGENT_PROPS, CONCEPT_SCHEME_PROPS, ONT_PROPS, ONTDOC
 from pylode.utils import (
-    PylodeError,
+    _make_hierarchy_html,
     back_onts_label_props,
     get_ns,
     load_background_onts,
@@ -302,7 +302,7 @@ class VocPub:
             )
 
     def _make_body(self):
-        """Healper function for make_html(). Makes <body>???</body> content.
+        """Helper function for make_html(). Makes <body>???</body> content.
 
         Just calls other helper functions in order"""
         make_pylode_logo(
@@ -450,53 +450,11 @@ class VocPub:
     def _make_concept_hierarchy(self):
         with self.content:
             if (None, RDF.type, SKOS.Concept) in self.ont:
-                concepts = []
-                for s in self.ont.subjects(RDF.type, SKOS.Concept):
-                    for o in self.ont.objects(s, SDO.name):
-                        c = {"iri": str(s), "prefLabel": str(o)}
-                        for o2 in self.ont.objects(s, SKOS.broader):
-                            c["broader"] = str(o2)
-                    concepts.append(c)
-
-                def build_html_tree(items):
-                    # Index items by id
-                    by_id = {item["iri"]: dict(item, children=[]) for item in items}
-
-                    roots = []
-
-                    # Build tree structure
-                    for item in by_id.values():
-                        broader = item.get("broader")
-                        if broader and broader in by_id:
-                            by_id[broader]["children"].append(item)
-                        else:
-                            roots.append(item)
-
-                    # Recursive renderer
-                    def render_nodes(nodes):
-                        container = ul()
-                        for node in nodes:
-                            node_li = li(
-                                a(
-                                    node["prefLabel"],
-                                    href="#"
-                                    + str(
-                                        self.ont.namespace_manager.qname(
-                                            node["iri"]
-                                        ).replace(":", "_")
-                                    ),
-                                )
-                            )
-                            if node["children"]:
-                                node_li.add(render_nodes(node["children"]))
-                            container.add(node_li)
-                        return container
-
-                    return render_nodes(roots)
-
                 d = div(
                     h2("Concept Hierarchy"),
-                    build_html_tree(concepts),
+                    _make_hierarchy_html(
+                        self.ont, SKOS.Concept, SKOS.broader, self.fids
+                    ),
                     id="concept-hierarchy",
                 )
 
@@ -516,7 +474,7 @@ class VocPub:
                 remaining = {k: v for k, v in d.items() if k not in ordered}
                 return ordered | remaining
 
-            d = div(h2("Concepts"), id="concepts")
+            d = div(h2("Concept Definitions"), id="concepts")
             for iri, concept in dict(
                 sorted(concepts.items(), key=lambda item: item[1][SDO.name])
             ).items():  # order by Concept's label
@@ -601,7 +559,7 @@ class VocPub:
 
                     li(h4(a("Concepts Hierarchy", href="#concept-hierarchy")))
 
-                    li(h4(a("Concepts", href="#concepts")))
+                    li(h4(a("Concept Definitions", href="#concepts")))
 
                     with li():
                         h4(a("Namespaces", href="#namespaces"))

{pylode-3.4.4 → pylode-3.5.1}/pylode/pylode.css

@@ -51,17 +51,18 @@
             padding-top: 7px;
         }
 
-        #metadata ul,
-        #classes ul {
+        ul.pylodelitlist {
             list-style-type: none;
+            margin-left: -40px;
         }
 
         #metadata ul li,
         #classes ul li {
-            margin-left: -40px;
+            margin-bottom: 10px;
         }
+
         #metadata dd p {
-          margin: 0;
+          margin: 0 0 1em 0;
         }
 
         ul.hlist {
@@ -71,12 +72,19 @@
             background-color: #F4FFFF;
         }
 
-        ul.hierarchy {
-            border: 1px solid navy;
-            padding: 5px 25px 5px 25px;
+        div.hierarchy {
+            margin-bottom: 30px;
             background-color: #F4FFFF;
+            padding: 10px;
         }
 
+        ul.hierarchy {=
+            padding: 5px 25px 5px 25px;
+        }
+
+        ul.hierarchy li {
+            margin-top:5px;
+        }
 
         ul.hlist li {
             display: inline;
@@ -128,7 +136,10 @@
             border-bottom: 1px solid navy;
         }
         h4 { font: bold 100% sans-serif }
-        h5 { font: italic 100% sans-serif }
+        h5 {
+            font: italic 100% sans-serif;
+            margin-bottom: 10px;
+        }
         h6 { font: small-caps 100% sans-serif }
 
         body {
@@ -217,60 +228,60 @@
             text-decoration: none;
         }
 
-#toc {
-    position: fixed;
-    top: 0;
-    right: 0;
-    z-index: 2;
-    height: 100%;
-    overflow-y: auto;
-    padding: 10px;
-    border: solid 1px navy;
-    font-size: small;
-    width: 180px;
-}
-#toc h3 {
-    margin-top: 5px;
-}
-
-#toc ul {
-    list-style: none;
-    padding-left: 0;
-}
-
-#toc .first > li {
-    margin-top: 5px;
-}
-
-#toc .second,
-#toc .third {
-    padding-left: 10px;
-}
-
-#content {
-    width: calc(100% - 150px);
-}
-
-.hover_property {
-    cursor: help;
-    text-decoration: none;
-    border-bottom: dashed 1px;
-}
-
-.setclass {
-    list-style-type: none;
-}
-
-code{
-    word-wrap: break-word;
-  }
-table {
-    table-layout: fixed;
-    width: 100%;
-}
-td {
-    word-wrap: break-word;
-}
-#legend table.entity {
-    width: 25%;
-}
+        #toc {
+            position: fixed;
+            top: 0;
+            right: 0;
+            z-index: 2;
+            height: 100%;
+            overflow-y: auto;
+            padding: 10px;
+            border: solid 1px navy;
+            font-size: small;
+            width: 180px;
+        }
+        #toc h3 {
+            margin-top: 5px;
+        }
+
+        #toc ul {
+            list-style: none;
+            padding-left: 0;
+        }
+
+        #toc .first > li {
+            margin-top: 5px;
+        }
+
+        #toc .second,
+        #toc .third {
+            padding-left: 10px;
+        }
+
+        #content {
+            width: calc(100% - 150px);
+        }
+
+        .hover_property {
+            cursor: help;
+            text-decoration: none;
+            border-bottom: dashed 1px;
+        }
+
+        .setclass {
+            list-style-type: none;
+        }
+
+        code{
+            word-wrap: break-word;
+          }
+        table {
+            table-layout: fixed;
+            width: 100%;
+        }
+        td {
+            word-wrap: break-word;
+        }
+        #legend table.entity {
+            width: 25%;
+        }

{pylode-3.4.4 → pylode-3.5.1}/pylode/rdf/sdo-mod.ttl

@@ -1715,7 +1715,7 @@ schema:code a rdf:Property ;
     schema:rangeIncludes schema:MedicalCode .
 
 schema:codeRepository a rdf:Property ;
-    rdfs:label "codeRepository" ;
+    rdfs:label "code repository" ;
     rdfs:comment "Link to the repository where the un-compiled, human readable code and related code is located (SVN, github, CodePlex)." ;
     schema:domainIncludes schema:SoftwareSourceCode ;
     schema:rangeIncludes schema:URL .

{pylode-3.4.4 → pylode-3.5.1}/pylode/rdf_elements.py

@@ -1,13 +1,5 @@
 from rdflib import Namespace
-from rdflib.namespace import (
-    DCTERMS,
-    OWL,
-    RDF,
-    RDFS,
-    SDO,
-    SKOS,
-    VANN,
-)
+from rdflib.namespace import DCTERMS, OWL, RDF, RDFS, SDO, SKOS, VANN, XSD
 
 ONTDOC = Namespace("https://w3id.org/profile/ontdoc/")
 
@@ -160,6 +152,7 @@ ONT_TYPES = {
     OWL.AnnotationProperty: ("ap", "OWL Annotation Property"),
     OWL.FunctionalProperty: ("fp", "OWL Functional Property"),
     OWL.InverseFunctionalProperty: ("ifp", "OWL Inverse Functional Property"),
+    RDFS.Datatype: ("dt", "RDFS Datatypes"),
     OWL.NamedIndividual: ("ni", "OWL Named Individual"),
 }
 
@@ -176,3 +169,10 @@ RESTRICTION_TYPES = [
 ]
 
 OWL_SET_TYPES = [OWL.unionOf, OWL.intersectionOf]
+
+DATATYPE_CARDINALITIES = {
+    XSD.minInclusive: ">=",
+    XSD.minExclusive: ">",
+    XSD.maxInclusive: "<=",
+    XSD.maxExclusive: "<",
+}

{pylode-3.4.4 → pylode-3.5.1}/pylode/utils.py

@@ -36,6 +36,7 @@ from rdflib.paths import ZeroOrMore
 try:
     from .rdf_elements import (
         AGENT_PROPS,
+        DATATYPE_CARDINALITIES,
         ONT_TYPES,
         ONTDOC,
         OWL_SET_TYPES,
@@ -410,9 +411,9 @@ def rdf_obj_html(
     ):
         def _hyperlink_html(
             ont__: Graph,
+            iri__: URIRef,
             back_onts__: Graph,
             ns__: Tuple[str, str],
-            iri__: URIRef,
             fids__,
             rdf_type__: Optional[URIRef] = None,
         ):
@@ -470,8 +471,6 @@ def rdf_obj_html(
             else:
                 try:
                     qname = ont__.compute_qname(iri__, False)
-                    if "ASGS" in qname[2]:
-                        print(qname)
                 except Exception:
                     qname = iri__
                 prefix = "" if qname[0] == "" else f"{qname[0]}:"
@@ -503,11 +502,13 @@ def rdf_obj_html(
         def _literal_html(obj__):
             if str(obj__).startswith("http"):
                 return _hyperlink_html(
-                    ont_, back_onts_, ns_, cast(URIRef, obj__), fids_
+                    ont_, cast(URIRef, obj__), back_onts_, ns_, fids_
                 )
             else:
                 if prop == SKOS.example:
                     return pre(str(obj__))
+                elif obj__.datatype == RDF.HTML:
+                    return raw(str(obj__))
                 else:
                     return raw(markdown.markdown(str(obj__)))
 
@@ -559,18 +560,47 @@ def rdf_obj_html(
                         </g>
                     </svg>"""
 
+            def _ror_logo_svg(id):
+                id = id if ("http" in id) else f"https://ror.org/{id}"
+                return f"""
+                    <svg 
+                        width="20px" 
+                        height="20px" 
+                        viewBox="0 0 164 118" 
+                        version="1.1" 
+                        xmlns="http://www.w3.org/2000/svg" 
+                        xmlns:xlink="http://www.w3.org/1999/xlink" 
+                        xml:space="preserve" 
+                        xmlns:serif="http://www.serif.com/" 
+                        style="fill-rule:evenodd;clip-rule:evenodd;stroke-linejoin:round;stroke-miterlimit:2;">
+                        <title>{id}</title>
+                        <g transform="matrix(0.994301,0,0,0.989352,0,0)">
+                            <rect x="0" y="0" width="164.94" height="119.27" style="fill:white;"/>
+                        </g>
+                        <g transform="matrix(1,0,0,1,-0.945,-0.815)">
+                            <path d="M68.65,4.16L56.52,22.74L44.38,4.16L68.65,4.16Z" style="fill:rgb(83,186,161);fill-rule:nonzero;"/>
+                            <path d="M119.41,4.16L107.28,22.74L95.14,4.16L119.41,4.16Z" style="fill:rgb(83,186,161);fill-rule:nonzero;"/>
+                            <path d="M44.38,115.47L56.52,96.88L68.65,115.47L44.38,115.47Z" style="fill:rgb(83,186,161);fill-rule:nonzero;"/>
+                            <path d="M95.14,115.47L107.28,96.88L119.41,115.47L95.14,115.47Z" style="fill:rgb(83,186,161);fill-rule:nonzero;"/>
+                            <path d="M145.53,63.71C149.83,62.91 153.1,61 155.33,57.99C157.57,54.98 158.68,51.32 158.68,47.03C158.68,43.47 158.06,40.51 156.83,38.13C155.6,35.75 153.93,33.86 151.84,32.45C149.75,31.05 147.31,30.04 144.53,29.44C141.75,28.84 138.81,28.54 135.72,28.54L112.16,28.54L112.16,47.37C111.97,46.82 111.77,46.28 111.55,45.74C109.92,41.79 107.64,38.42 104.71,35.64C101.78,32.86 98.32,30.72 94.3,29.23C90.29,27.74 85.9,26.99 81.14,26.99C76.38,26.99 72,27.74 67.98,29.23C63.97,30.72 60.5,32.86 57.57,35.64C54.95,38.13 52.85,41.1 51.27,44.54C51.04,42.07 50.46,39.93 49.53,38.13C48.3,35.75 46.63,33.86 44.54,32.45C42.45,31.05 40.01,30.04 37.23,29.44C34.45,28.84 31.51,28.54 28.42,28.54L4.87,28.54L4.87,89.42L18.28,89.42L18.28,65.08L24.9,65.08L37.63,89.42L53.71,89.42L38.24,63.71C42.54,62.91 45.81,61 48.04,57.99C48.14,57.85 48.23,57.7 48.33,57.56C48.31,58.03 48.3,58.5 48.3,58.98C48.3,63.85 49.12,68.27 50.75,72.22C52.38,76.17 54.66,79.54 57.59,82.32C60.51,85.1 63.98,87.24 68,88.73C72.01,90.22 76.4,90.97 81.16,90.97C85.92,90.97 90.3,90.22 94.32,88.73C98.33,87.24 101.8,85.1 104.73,82.32C107.65,79.54 109.93,76.17 111.57,72.22C111.79,71.69 111.99,71.14 112.18,70.59L112.18,89.42L125.59,89.42L125.59,65.08L132.21,65.08L144.94,89.42L161.02,89.42L145.53,63.71ZM36.39,50.81C35.67,51.73 34.77,52.4 33.68,52.83C32.59,53.26 31.37,53.52 30.03,53.6C28.68,53.69 27.41,53.73 26.2,53.73L18.29,53.73L18.29,39.89L27.06,39.89C28.26,39.89 29.5,39.98 30.76,40.15C32.02,40.32 33.14,40.65 34.11,41.14C35.08,41.63 35.89,42.33 36.52,43.25C37.15,44.17 37.47,45.4 37.47,46.95C37.47,48.6 37.11,49.89 36.39,50.81ZM98.74,66.85C97.85,69.23 96.58,71.29 94.91,73.04C93.25,74.79 91.26,76.15 88.93,77.13C86.61,78.11 84.01,78.59 81.15,78.59C78.28,78.59 75.69,78.1 73.37,77.13C71.05,76.16 69.06,74.79 67.39,73.04C65.73,71.29 64.45,69.23 63.56,66.85C62.67,64.47 62.23,61.85 62.23,58.98C62.23,56.17 62.67,53.56 63.56,51.15C64.45,48.74 65.72,46.67 67.39,44.92C69.05,43.17 71.04,41.81 73.37,40.83C75.69,39.86 78.28,39.37 81.15,39.37C84.02,39.37 86.61,39.86 88.93,40.83C91.25,41.8 93.24,43.17 94.91,44.92C96.57,46.67 97.85,48.75 98.74,51.15C99.63,53.56 100.07,56.17 100.07,58.98C100.07,61.85 99.63,64.47 98.74,66.85ZM143.68,50.81C142.96,51.73 142.06,52.4 140.97,52.83C139.88,53.26 138.66,53.52 137.32,53.6C135.97,53.69 134.7,53.73 133.49,53.73L125.58,53.73L125.58,39.89L134.35,39.89C135.55,39.89 136.79,39.98 138.05,40.15C139.31,40.32 140.43,40.65 141.4,41.14C142.37,41.63 143.18,42.33 143.81,43.25C144.44,44.17 144.76,45.4 144.76,46.95C144.76,48.6 144.4,49.89 143.68,50.81Z" style="fill:rgb(32,40,38);fill-rule:nonzero;"/>
+                        </g>
+                    </svg>"""
+
             if isinstance(obj__, Literal):
                 return span(str(obj__))
             honorific_prefix = None
             name = None
             identifier = None
             orcid = None
+            ror = None
             url = None
             email = None
             affiliation = None
 
             if "orcid.org" in str(obj__):
                 orcid = True
+            elif "ror.org" in str(obj__):
+                ror = True
 
             for px, o in ont__.predicate_objects(obj__):
                 if px in AGENT_PROPS:
@@ -607,6 +637,13 @@ def rdf_obj_html(
                         sp.appendChild(
                             a(raw(_orcid_logo_svg(identifier)), href=identifier)
                         )
+                elif ror:
+                    if "ror.org" in obj__:
+                        sp.appendChild(a(raw(_ror_logo_svg(obj__)), href=obj__))
+                    else:
+                        sp.appendChild(
+                            a(raw(_ror_logo_svg(identifier)), href=identifier)
+                        )
                 elif identifier is not None:
                     sp.appendChild(a(identifier, href=identifier))
                 if email is not None:
@@ -629,10 +666,15 @@ 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_)
-                    #Added the onClass restriction otherwise the class name is ignored in the HTML output. 
+                        prop = _hyperlink_html(ont__, o, back_onts_, ns__, fids_)
+                    # Added the onClass restriction otherwise the class name is ignored in the HTML output.
                     elif px == OWL.onClass:
-                        cls = _hyperlink_html(ont__, back_onts_, ns__, o, fids_, OWL.Class)
+                        if (o, OWL.unionOf | OWL.intersectionOf, None) in ont__:
+                            cls = _setclass_html(ont__, o, back_onts_, ns__, fids_)
+                        else:
+                            cls = _hyperlink_html(
+                                ont__, o, back_onts_, ns__, fids_, OWL.Class
+                            )
                     elif px in RESTRICTION_TYPES + OWL_SET_TYPES:
                         if px in [
                             OWL.minCardinality,
@@ -674,12 +716,35 @@ def rdf_obj_html(
                                 span(card, _class="cardinality"),
                                 span(
                                     _hyperlink_html(
-                                        ont__, back_onts_, ns__, o, fids_, OWL.Class
+                                        ont__, o, back_onts_, ns__, fids_, OWL.Class
                                     )
                                 ),
                             )
-
-            #Combined the check for card and cls so that only one br is added.
+                    elif px == ONTDOC.inRangeOf:  # rdfs:range
+                        for o2 in ont__.objects(o, RDFS.range):
+                            for rp, ro in ont__.predicate_objects(o2):
+                                if rp == OWL.onDatatype:
+                                    prop = _hyperlink_html(
+                                        ont__, ro, back_onts_, ns__, fids_
+                                    )
+                                if rp == OWL.withRestrictions:
+                                    cards = []
+                                    for ro2 in ont__.objects(o2, OWL.withRestrictions):
+                                        for ro3 in ont__.objects(
+                                            ro2, RDF.rest * ZeroOrMore / RDF.first
+                                        ):
+                                            for rp4, ro4 in ont__.predicate_objects(
+                                                ro3
+                                            ):
+                                                if rp4 in DATATYPE_CARDINALITIES.keys():
+                                                    cards.append(
+                                                        f"{DATATYPE_CARDINALITIES[rp4]}{ro4}"
+                                                    )
+                                    if len(cards) > 0:
+                                        card = " [" + ", ".join(cards) + "]"
+                                        # XXX
+
+            # Combined the check for card and cls so that only one br is added.
             if card is not None and cls is not None:
                 restriction = span(prop, card, cls, br())
             elif card is not None:
@@ -699,18 +764,18 @@ def rdf_obj_html(
             else:
                 joining_word = span(",", _class="cardinality")
 
-            class_set = set()
+            class_set = []
             for o in ont__.objects(obj__, OWL.unionOf | OWL.intersectionOf):
                 for o2 in ont__.objects(o, RDF.rest * ZeroOrMore / RDF.first):
-                    class_set.add(
+                    class_set.append(
                         _rdf_obj_single_html(
-                            ont__, back_onts__, ns__, o2, fids__, OWL.Class
+                            ont__, back_onts__, ns__, o2, fids__, OWL.Class, prop=prop
                         )
                     )
 
             return intersperse(class_set, joining_word)
 
-        def _bn_html(ont__, back_onts__, ns__, fids__, obj__: BNode):
+        def _bn_html(ont__, obj__, back_onts__, ns__, fids__: 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)
@@ -719,15 +784,17 @@ def rdf_obj_html(
                 return _agent_html(ont__, obj__)
             elif (obj__, RDF.type, OWL.Restriction) in ont__:
                 return _restriction_html(ont__, obj__, ns__)
+            elif (obj__, RDF.type, RDFS.Datatype) in ont__:
+                return _restriction_html(ont__, obj__, ns__)
             else:  # (obj, RDF.type, OWL.Class) in ont:  # Set Class
                 return _setclass_html(ont__, obj__, back_onts__, ns__, fids__)
 
         if isinstance(obj_, Tuple) or isinstance(obj_, URIRef):
             ret = _hyperlink_html(
-                ont_, back_onts_, ns_, obj_, fids_, rdf_type__=rdf_type_
+                ont_, obj_, back_onts_, ns_, fids_, rdf_type__=rdf_type_
             )
         elif isinstance(obj_, BNode):
-            ret = _bn_html(ont_, back_onts_, ns_, fids_, obj_)
+            ret = _bn_html(ont_, obj_, back_onts_, ns_, fids_)
         else:  # isinstance(obj, Literal):
             ret = _literal_html(obj_)
 
@@ -738,7 +805,7 @@ def rdf_obj_html(
             ont, back_onts, ns, obj[0], fids, rdf_type_=rdf_type, prop=prop
         )
     else:
-        u_ = ul()
+        u_ = ul(_class="pylodelitlist")
         for x in obj:
             u_.appendChild(
                 li(
@@ -781,6 +848,68 @@ def prop_obj_pair_html(
     return t
 
 
+def _make_hierarchy_html(
+    ont: Graph, obj_class: URIRef, parent_indicator: URIRef, fids: dict
+):
+    if (None, RDF.type, obj_class) in ont:
+        items = []
+        for s in ont.subjects(RDF.type, obj_class):
+            if not isinstance(s, BNode):
+                name = ont.value(s, DCTERMS.title | SDO.name)
+                if name is None:
+                    name = make_title_from_iri(s)
+                c = {
+                    "iri": str(s),
+                    "name": str(
+                        name
+                    ),  # need 2 x for OntPub (title) and VocPub (prefLabel) profiles
+                }
+                for o2 in ont.objects(s, parent_indicator):
+                    if not isinstance(o2, BNode):
+                        c["parent"] = str(o2)
+                items.append(c)
+
+        def build_html_tree(items):
+            # Index items by id
+            by_id = {item["iri"]: dict(item, children=[]) for item in items}
+
+            roots = []
+
+            # Build tree structure
+            for item in by_id.values():
+                parent = item.get("parent")
+                if parent and parent in by_id:
+                    by_id[parent]["children"].append(item)
+                else:
+                    roots.append(item)
+
+            # Recursive renderer
+            def render_nodes(nodes):
+                container = ul(_class="hierarchy")
+                for node in sorted(
+                    nodes,
+                    key=lambda node: (
+                        node["name"].casefold(),
+                        node["name"],
+                        node["iri"],
+                    ),
+                ):
+                    node_li = li(
+                        a(
+                            node["name"],
+                            href="#" + generate_fid(None, node["iri"], fids),
+                        )
+                    )
+                    if node["children"]:
+                        node_li.add(render_nodes(node["children"]))
+                    container.add(node_li)
+                return container
+
+            return render_nodes(roots)
+
+        return div(build_html_tree(items), _class="hierarchy")
+
+
 def section_html(
     section_title: str,
     ont: Graph,
@@ -853,6 +982,22 @@ def section_html(
 
     elems = div(id=toc_ul_id, _class="section")
     elems.appendChild(h2(section_title))
+
+    if obj_class == OWL.Class:
+        elems.appendChild(h3("Class Hierarchy", id="class-hierarchy"))
+        elems.appendChild(_make_hierarchy_html(ont, OWL.Class, RDFS.subClassOf, fids))
+        elems.appendChild(h3("Class Definitions", id="class-definitions"))
+    elif obj_class == OWL.ObjectProperty:
+        elems.appendChild(
+            h3("Object Property Hierarchy", id="object-property-hierarchy")
+        )
+        elems.appendChild(
+            _make_hierarchy_html(ont, OWL.ObjectProperty, RDFS.subPropertyOf, fids)
+        )
+        elems.appendChild(
+            h3("Object Property Definitions", id="object-property-definitions")
+        )
+
     # get all objects of this class
     for s_ in ont.subjects(predicate=RDF.type, object=obj_class):
         if obj_class == RDF.Property:
@@ -918,7 +1063,7 @@ def de_space_html(html):
     # s = "".join([l_.strip().replace("\n", " ") for l_ in html.split("\n")])
     # return re.sub(" +", " ", s)
     s = re.sub(r">\s+<", "><", html)
-    return re.sub(r"\s+", " ", s)
+    return re.sub(r"\s+", " ", s).strip()
 
 
 def make_pylode_logo(doc, version, profile_name, profile_iri):

{pylode-3.4.4 → pylode-3.5.1}/pyproject.toml

@@ -7,7 +7,7 @@ Changelog = "https://github.com/RDFLib/pyLODE/releases"
 
 [project]
 name = "pylode"
-version = "3.4.4"
+version = "3.5.1"
 description = "An OWL ontology documentation tool using Python, based on LODE."
 authors = [{ name = "Nicholas Car", email = "nick@kurrawong.ai" }]
 requires-python = ">=3.12,<4"
@@ -24,7 +24,7 @@ classifiers = [
 dependencies = [
     "rdflib>=7.6.0,<8.0.0",
     "Markdown>=3.3.7,<4",
-    "dominate>=2.6.0,<3",
+    "dominate>=2.9.1,<3",
     "html5lib>=1.1,<2",
     "httpx>=0.25.0,<1.0.0",
     "tqdm>=4.67.3",