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ontpub.py
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ontpub.py
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import shutil
from collections import defaultdict
from itertools import chain
from pathlib import Path
from typing import Dict
from typing import Union
import dominate
from dominate.tags import (
h2,
h1,
h4,
style,
link,
meta,
script,
dl,
strong,
a,
sup,
tr,
td,
ul,
li,
code,
table,
h3,
div,
dt,
dd,
)
from dominate.util import raw
from rdflib import Literal, Graph
from rdflib.namespace import (
DC,
DCTERMS,
FOAF,
ORG,
OWL,
PROF,
PROV,
RDF,
RDFS,
SDO,
SKOS,
)
from pylode.utils import PylodeError
try:
from .utils import (
load_ontology,
load_background_onts,
load_background_onts_titles,
back_onts_label_props,
get_ns,
prop_obj_pair_html,
section_html,
sort_ontology,
make_pylode_logo,
)
from .rdf_elements import ONTDOC, AGENT_PROPS, ONT_PROPS, CLASS_PROPS, PROP_PROPS
from .version import __version__
except ImportError:
from pylode.utils import (
load_ontology,
load_background_onts,
load_background_onts_titles,
back_onts_label_props,
get_ns,
prop_obj_pair_html,
section_html,
sort_ontology,
make_pylode_logo,
)
from pylode.rdf_elements import (
ONTDOC,
AGENT_PROPS,
ONT_PROPS,
CLASS_PROPS,
PROP_PROPS,
)
from pylode.version import __version__
RDF_FOLDER = Path(__file__).parent / "rdf"
class OntPub:
"""Ontology Document class used to create HTML documentation
from OWL Ontologies.
Use:
# initialise
od = OntDoc(ontology="some-ontology-file.ttl")
# produce HTML
html = od.make_html()
# or save HTML to a file
od.make_html(destination="some-resulting-html-file.html")
"""
def __init__(self, ontology: Union[Graph, Path, str], sort_subjects: bool = False):
self.ont = load_ontology(ontology)
if sort_subjects:
self.ont = sort_ontology(self.ont)
self._ontdoc_inference(self.ont)
self.back_onts = load_background_onts()
self.back_onts_titles = load_background_onts_titles(self.back_onts)
self.props_labeled = back_onts_label_props(self.back_onts)
self.toc: Dict[str, str] = {}
self.fids: Dict[str, str] = {}
self.ns = get_ns(self.ont)
# make HTML doc with title
t = None
for s in chain(
self.ont.subjects(RDF.type, OWL.Ontology),
self.ont.subjects(RDF.type, PROF.Profile),
self.ont.subjects(RDF.type, SKOS.ConceptScheme),
):
for o2 in self.ont.objects(s, DCTERMS.title):
t = str(o2)
if t is None:
raise PylodeError(
"You MUST supply a title property "
"(dcterms:title, rdfs:label or sdo:name) for your ontology"
)
self.doc = dominate.document(title=t)
with self.doc:
self.content = div(id="content")
def make_html(self, destination: Path = None, include_css: bool = True):
"""Makes the complete OntDoc HTML document.
Either writes to a file or returns a string"""
self._make_head(
self._make_schema_org(), include_css=include_css, destination=destination
)
self._make_body()
if destination is not None:
open(destination, "w", encoding="utf8").write(self.doc.render())
else:
return self.doc.render()
def _ontdoc_inference(self, g):
"""Expands the ontology's graph to make OntDoc querying easier.
Uses axioms made up for OntDoc, but they are simple and obvious
and don't collide with well-known ontologies"""
# class types
for s_ in g.subjects(RDF.type, OWL.Class):
g.add((s_, RDF.type, RDFS.Class))
# # property types
# for s_ in chain(
# g.subjects(RDF.type, OWL.ObjectProperty),
# g.subjects(RDF.type, OWL.FunctionalProperty),
# g.subjects(RDF.type, OWL.DatatypeProperty),
# g.subjects(RDF.type, OWL.AnnotationProperty),
# ):
# g.add((s_, RDF.type, RDF.Property))
# name
for s_, o in chain(
g.subject_objects(DC.title),
g.subject_objects(RDFS.label),
g.subject_objects(SKOS.prefLabel),
g.subject_objects(SDO.name),
):
g.add((s_, DCTERMS.title, o))
# description
for s_, o in chain(
g.subject_objects(DC.description),
g.subject_objects(RDFS.comment),
g.subject_objects(SKOS.definition),
g.subject_objects(SDO.description),
):
g.add((s_, DCTERMS.description, o))
# source
for s_, o in g.subject_objects(DC.source):
g.add((s_, DCTERMS.source, o))
# license
for s_, o in g.subject_objects(SDO.license):
g.add((s_, DCTERMS.license, o))
#
# Blank Node Types
#
for s_ in g.subjects(OWL.onProperty, None):
g.add((s_, RDF.type, OWL.Restriction))
for s_ in chain(
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
for s_, o in g.subject_objects(RDFS.subClassOf):
g.add((o, ONTDOC.superClassOf, s_))
for s_, o in g.subject_objects(RDFS.subPropertyOf):
g.add((o, ONTDOC.superPropertyOf, s_))
for s_, o in g.subject_objects(RDFS.domain):
g.add((o, ONTDOC.inDomainOf, s_))
for s_, o in g.subject_objects(SDO.domainIncludes):
g.add((o, ONTDOC.inDomainIncludesOf, s_))
for s_, o in g.subject_objects(RDFS.range):
g.add((o, ONTDOC.inRangeOf, s_))
for s_, o in g.subject_objects(SDO.rangeIncludes):
g.add((o, ONTDOC.inRangeIncludesOf, s_))
for s_, o in g.subject_objects(RDF.type):
g.add((o, ONTDOC.hasMember, s_))
#
# Agents
#
# creator
for s_, o in chain(
g.subject_objects(DC.creator),
g.subject_objects(SDO.creator),
g.subject_objects(SDO.author),
):
g.remove((s_, DC.creator, o))
g.remove((s_, SDO.creator, o))
g.remove((s_, SDO.author, o))
g.add((s_, DCTERMS.creator, o))
# contributor
for s_, o in chain(
g.subject_objects(DC.contributor),
g.subject_objects(SDO.contributor),
):
g.remove((s_, DC.contributor, o))
g.remove((s_, SDO.contributor, o))
g.add((s_, DCTERMS.contributor, o))
# publisher
for s_, o in chain(
g.subject_objects(DC.publisher), g.subject_objects(SDO.publisher)
):
g.remove((s_, DC.publisher, o))
g.remove((s_, SDO.publisher, o))
g.add((s_, DCTERMS.publisher, o))
# indicate Agent instances from properties
for o in chain(
g.objects(None, DCTERMS.publisher),
g.objects(None, DCTERMS.creator),
g.objects(None, DCTERMS.contributor),
):
g.add((o, RDF.type, PROV.Agent))
# Agent annotations
for s_, o in g.subject_objects(FOAF.name):
g.add((s_, SDO.name, o))
for s_, o in g.subject_objects(FOAF.mbox):
g.add((s_, SDO.email, o))
for s_, o in g.subject_objects(ORG.memberOf):
g.add((s_, SDO.affiliation, o))
def _make_head(
self, schema_org: Graph, include_css: bool = True, destination: Path = None
):
"""Healper function for make_html(). Makes <head>???</head> content"""
with self.doc.head:
# use standard pyLODE stylesheet
if include_css:
style(
raw(
"\n"
+ open(Path(__file__).parent.parent / "pylode.css").read()
+ "\n\t"
)
)
else:
link(href="pylode.css", rel="stylesheet", type="text/css")
shutil.copy(
Path(__file__).parent.parent / "pylode.css",
destination.parent / "pylode.css",
)
link(
rel="icon",
type="image/png",
sizes="16x16",
href="data:image/png;base64,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",
)
link(
rel="icon",
type="image/png",
sizes="32x32",
href="data:image/png;base64,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",
)
meta(http_equiv="Content-Type", content="text/html; charset=utf-8")
script(
raw("\n" + schema_org.serialize(format="json-ld") + "\n\t"),
type="application/ld+json",
id="schema.org",
)
def _make_body(self):
"""Healper function for make_html(). Makes <body>???</body> content.
Just calls other helper functions in order"""
make_pylode_logo(
self.doc, __version__, "OntPub", "https://w3id.org/profile/ontpub"
)
self._make_metadata()
self._make_main_sections()
self._make_namespaces()
self._make_legend()
self._make_toc()
def _make_metadata(self):
# get all ONT_PROPS props and their (multiple) values
this_onts_props = defaultdict(list)
for s_ in chain(
self.ont.subjects(predicate=RDF.type, object=OWL.Ontology),
self.ont.subjects(predicate=RDF.type, object=SKOS.ConceptScheme),
self.ont.subjects(predicate=RDF.type, object=PROF.Profile),
):
iri = s_
for p_, o in self.ont.predicate_objects(s_):
if p_ in ONT_PROPS:
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.appendChild(h2("Metadata"))
d = dl(div(dt(strong("IRI")), dd(code(str(iri)))))
for prop in ONT_PROPS:
if prop in this_onts_props.keys():
d.appendChild(
prop_obj_pair_html(
self.ont,
self.back_onts,
self.ns,
"dl",
prop,
self.props_labeled[prop]["title"],
self.props_labeled[prop]["description"],
self.props_labeled[prop]["ont_title"],
self.fids,
this_onts_props[prop],
)
)
sec.appendChild(d)
self.content.appendChild(sec)
def _make_schema_org(self):
sdo = Graph()
for ont_iri in chain(
self.ont.subjects(predicate=RDF.type, object=OWL.Ontology),
self.ont.subjects(predicate=RDF.type, object=SKOS.ConceptScheme),
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:
sdo.add((ont_iri, SDO.name, o))
elif p_ == DCTERMS.description:
sdo.add((ont_iri, SDO.description, o))
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:
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:
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:
sdo.add((ont_iri, SDO.dateCreated, o))
elif p_ == DCTERMS.modified:
sdo.add((ont_iri, SDO.dateModified, o))
elif p_ == DCTERMS.issued:
sdo.add((ont_iri, SDO.dateIssued, o))
elif p_ == DCTERMS.license:
sdo.add((ont_iri, SDO.license, o))
elif p_ == DCTERMS.rights:
sdo.add((ont_iri, SDO.copyrightNotice, o))
return sdo
def _make_main_sections(self):
with self.content:
if (None, RDF.type, OWL.Class) in self.ont:
d = section_html(
"Classes",
self.ont,
self.back_onts,
self.ns,
OWL.Class,
CLASS_PROPS,
self.toc,
"classes",
self.fids,
self.props_labeled,
)
d.render()
if (None, RDF.type, RDF.Property) in self.ont:
d = section_html(
"Properties",
self.ont,
self.back_onts,
self.ns,
RDF.Property,
PROP_PROPS,
self.toc,
"properties",
self.fids,
self.props_labeled,
)
d.render()
if (None, RDF.type, OWL.ObjectProperty) in self.ont:
d = section_html(
"Object Properties",
self.ont,
self.back_onts,
self.ns,
OWL.ObjectProperty,
PROP_PROPS,
self.toc,
"objectproperties",
self.fids,
self.props_labeled,
)
d.render()
if (None, RDF.type, OWL.DatatypeProperty) in self.ont:
d = section_html(
"Datatype Properties",
self.ont,
self.back_onts,
self.ns,
OWL.DatatypeProperty,
PROP_PROPS,
self.toc,
"datatypeproperties",
self.fids,
self.props_labeled,
)
d.render()
if (None, RDF.type, OWL.AnnotationProperty) in self.ont:
d = section_html(
"Annotation Properties",
self.ont,
self.back_onts,
self.ns,
OWL.AnnotationProperty,
PROP_PROPS,
self.toc,
"annotationproperties",
self.fids,
self.props_labeled,
)
d.render()
if (None, RDF.type, OWL.FunctionalProperty) in self.ont:
d = section_html(
"Functional Properties",
self.ont,
self.back_onts,
self.ns,
OWL.FunctionalProperty,
PROP_PROPS,
self.toc,
"functionalproperties",
self.fids,
self.props_labeled,
)
d.render()
def _make_legend(self):
with self.content:
with div(id="legend"):
h2("Legend")
with table(_class="entity"):
if self.toc.get("classes") is not None:
with tr():
td(sup("c", _class="sup-c", title="OWL/RDFS Class"))
td("Classes")
if self.toc.get("properties") is not None:
with tr():
td(sup("p", _class="sup-p", title="RDF Property"))
td("Properties")
if self.toc.get("objectproperties") is not None:
with tr():
td(sup("op", _class="sup-op", title="OWL Object Property"))
td("Object Properties")
if self.toc.get("datatypeproperties") is not None:
with tr():
td(
sup(
"dp",
_class="sup-dp",
title="OWL Datatype Property",
)
)
td("Datatype Properties")
if self.toc.get("annotationproperties") is not None:
with tr():
td(
sup(
"ap",
_class="sup-ap",
title="OWL Annotation Property",
)
)
td("Annotation Properties")
if self.toc.get("functionalproperties") is not None:
with tr():
td(
sup(
"fp",
_class="sup-fp",
title="OWL Functional Property",
)
)
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("Named Individuals")
def _make_namespaces(self):
# only get namespaces used in ont
nses = {}
for n in chain(self.ont.subjects(), self.ont.predicates(), self.ont.objects()):
# a list of prefixes we don't like
excluded_namespaces = (
# "https://linked.data.gov.au/def/"
)
if not str(n).startswith(excluded_namespaces):
for prefix, ns in self.ont.namespaces():
if str(n).startswith(ns):
nses[prefix] = ns
# # deduplicate namespaces
# temp = []
# res = dict()
# for k, v in nses.items():
# if v not in temp:
# temp.append(v)
# res[k] = v
# nses = res
with self.content:
with div(id="namespaces"):
h2("Namespaces")
with dl():
if self.toc.get("namespaces") is None:
self.toc["namespaces"] = []
for prefix, ns in sorted(nses.items()):
p_ = prefix if prefix != "" else ":"
dt(p_, id=p_)
dd(code(ns))
self.toc["namespaces"].append(("#" + prefix, prefix))
def _make_toc(self):
with self.doc:
with div(id="toc"):
h3("Table of Contents")
with ul(_class="first"):
li(h4(a("Metadata", href="#metadata")))
if (
self.toc.get("classes") is not None
and len(self.toc["classes"]) > 0
):
with li():
h4(a("Classes", href="#classes"))
with ul(_class="second"):
for c in self.toc["classes"]:
li(a(c[1], href=c[0]))
if (
self.toc.get("properties") is not None
and len(self.toc["properties"]) > 0
):
with li():
h4(a("Properties", href="#properties"))
with ul(_class="second"):
for c in self.toc["properties"]:
li(a(c[1], href=c[0]))
if (
self.toc.get("objectproperties") is not None
and len(self.toc["objectproperties"]) > 0
):
with li():
h4(a("Object Properties", href="#objectproperties"))
with ul(_class="second"):
for c in self.toc["objectproperties"]:
li(a(c[1], href=c[0]))
if (
self.toc.get("datatypeproperties") is not None
and len(self.toc["datatypeproperties"]) > 0
):
with li():
h4(a("Datatype Properties", href="#datatypeproperties"))
with ul(_class="second"):
for c in self.toc["datatypeproperties"]:
li(a(c[1], href=c[0]))
if (
self.toc.get("annotationproperties") is not None
and len(self.toc["annotationproperties"]) > 0
):
with li():
h4(a("Annotation Properties", href="#annotationproperties"))
with ul(_class="second"):
for c in self.toc["annotationproperties"]:
li(a(c[1], href=c[0]))
if (
self.toc.get("functionalproperties") is not None
and len(self.toc["functionalproperties"]) > 0
):
with li():
h4(a("Functional Properties", href="#functionalproperties"))
with ul(_class="second"):
for c in self.toc["functionalproperties"]:
li(a(c[1], href=c[0]))
with li():
h4(a("Namespaces", href="#namespaces"))
with ul(_class="second"):
for n in self.toc["namespaces"]:
li(a(n[1], href="#" + n[1]))
li(h4(a("Legend", href="#legend")), ul(_class="second"))