ontology¶
A module adding additional functionality to owlready2.
If desirable some of these additions may be moved back into owlready2.
BlankNode
¶
Represents a blank node.
A blank node is a node that is not a literal and has no IRI. Resources represented by blank nodes are also called anonumous resources. Only the subject or object in an RDF triple can be a blank node.
Source code in ontopy/ontology.py
class BlankNode:
"""Represents a blank node.
A blank node is a node that is not a literal and has no IRI.
Resources represented by blank nodes are also called anonumous resources.
Only the subject or object in an RDF triple can be a blank node.
"""
def __init__(self, onto: Union[World, Ontology], storid: int):
"""Initiate a blank node.
Args:
onto: Ontology or World instance.
storid: The storage id of the blank node.
"""
if storid >= 0:
raise ValueError(
f"A BlankNode is supposed to have a negative storid: {storid}"
)
self.onto = onto
self.storid = storid
def __repr__(self):
return repr(f"_:b{-self.storid}")
def __hash__(self):
return hash((self.onto, self.storid))
def __eq__(self, other):
"""For now blank nodes always compare true against each other."""
return isinstance(other, BlankNode)
__init__(self, onto, storid)
special
¶
Initiate a blank node.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
onto |
Union[ontopy.ontology.World, ontopy.ontology.Ontology] |
Ontology or World instance. |
required |
storid |
int |
The storage id of the blank node. |
required |
Source code in ontopy/ontology.py
def __init__(self, onto: Union[World, Ontology], storid: int):
"""Initiate a blank node.
Args:
onto: Ontology or World instance.
storid: The storage id of the blank node.
"""
if storid >= 0:
raise ValueError(
f"A BlankNode is supposed to have a negative storid: {storid}"
)
self.onto = onto
self.storid = storid
Ontology (Ontology)
¶
A generic class extending owlready2.Ontology.
Source code in ontopy/ontology.py
class Ontology(owlready2.Ontology): # pylint: disable=too-many-public-methods
"""A generic class extending owlready2.Ontology."""
def __init__(self, *args, **kwargs):
# Properties controlling what annotations that are considered by
# get_by_label()
super().__init__(*args, **kwargs)
self._label_annotations = None
self.prefix = None
# Properties controlling what annotations that are considered by
# get_by_label()
label_annotations = property(
fget=lambda self: self._label_annotations,
doc="List of label annotation searched for by get_by_label().",
)
# Name of special unlabeled entities, like Thing, Nothing, etc...
_special_labels = None
# Some properties for customising dir() listing - useful in
# interactive sessions...
_dir_preflabel = isinteractive()
_dir_label = isinteractive()
_dir_name = False
_dir_imported = isinteractive()
dir_preflabel = property(
fget=lambda self: self._dir_preflabel,
fset=lambda self, v: setattr(self, "_dir_preflabel", bool(v)),
doc="Whether to include entity prefLabel in dir() listing.",
)
dir_label = property(
fget=lambda self: self._dir_label,
fset=lambda self, v: setattr(self, "_dir_label", bool(v)),
doc="Whether to include entity label in dir() listing.",
)
dir_name = property(
fget=lambda self: self._dir_name,
fset=lambda self, v: setattr(self, "_dir_name", bool(v)),
doc="Whether to include entity name in dir() listing.",
)
dir_imported = property(
fget=lambda self: self._dir_imported,
fset=lambda self, v: setattr(self, "_dir_imported", bool(v)),
doc="Whether to include imported ontologies in dir() listing.",
)
# Other settings
_colon_in_label = False
colon_in_label = property(
fget=lambda self: self._colon_in_label,
fset=lambda self, v: setattr(self, "_colon_in_label", bool(v)),
doc="Whether to accept colon in name-part of IRI. "
"If true, the name cannot be prefixed.",
)
def __dir__(self):
dirset = set(super().__dir__())
lst = list(self.get_entities(imported=self._dir_imported))
if self._dir_preflabel:
dirset.update(
_.prefLabel.first() for _ in lst if hasattr(_, "prefLabel")
)
if self._dir_label:
dirset.update(_.label.first() for _ in lst if hasattr(_, "label"))
if self._dir_name:
dirset.update(_.name for _ in lst if hasattr(_, "name"))
dirset.difference_update({None}) # get rid of possible None
return sorted(dirset)
def __getitem__(self, name):
item = super().__getitem__(name)
if not item:
item = self.get_by_label(name)
return item
def __getattr__(self, name):
attr = super().__getattr__(name)
if not attr:
attr = self.get_by_label(name)
return attr
def __contains__(self, other):
if self.world[other]:
return True
try:
self.get_by_label(other)
except NoSuchLabelError:
return False
return True
def __objclass__(self):
# Play nice with inspect...
pass
def __hash__(self):
"""Returns a hash based on base_iri.
This is done to keep Ontology hashable when defining __eq__.
"""
return hash(self.base_iri)
def __eq__(self, other):
"""Checks if this ontology is equal to `other`.
This function compares the result of
``set(self.get_unabbreviated_triples(label='_:b'))``,
i.e. blank nodes are not distinguished, but relations to blank
nodes are included.
"""
return set(self.get_unabbreviated_triples(blank="_:b")) == set(
other.get_unabbreviated_triples(blank="_:b")
)
def get_unabbreviated_triples(
self, subject=None, predicate=None, obj=None, blank=None
):
"""Returns all matching triples unabbreviated.
If `blank` is given, it will be used to represent blank nodes.
"""
# pylint: disable=invalid-name
return _get_unabbreviated_triples(
self, subject=subject, predicate=predicate, obj=obj, blank=blank
)
def get_by_label(
self,
label: str,
label_annotations: str = None,
prefix: str = None,
imported: bool = True,
colon_in_label: bool = None,
):
"""Returns entity with label annotation `label`.
Args:
label: label so serach for.
May be written as 'label' or 'prefix:label'.
get_by_label('prefix:label') ==
get_by_label('label', prefix='prefix').
label_annotations: a sequence of label annotation names to look up.
Defaults to the `label_annotations` property.
prefix: if provided, it should be the last component of
the base iri of an ontology (with trailing slash (/) or hash
(#) stripped off). The search for a matching label will be
limited to this namespace.
imported: Whether to also look for `label` in imported ontologies.
colon_in_label: Whether to accept colon (:) in a label or name-part
of IRI. Defaults to the `colon_in_label` property of `self`.
Setting this true cannot be combined with `prefix`.
If several entities have the same label, only the one which is
found first is returned.Use get_by_label_all() to get all matches.
Note, if different prefixes are provided in the label and via
the `prefix` argument a warning will be issued and the
`prefix` argument will take precedence.
A NoSuchLabelError is raised if `label` cannot be found.
"""
# pylint: disable=too-many-arguments,too-many-branches,invalid-name
if not isinstance(label, str):
raise TypeError(
f"Invalid label definition, must be a string: {label!r}"
)
if self._label_annotations is None:
for iri in DEFAULT_LABEL_ANNOTATIONS:
try:
self.add_label_annotation(iri)
except ValueError:
pass
if colon_in_label is None:
colon_in_label = self._colon_in_label
if colon_in_label:
if prefix:
raise ValueError(
"`prefix` cannot be combined with `colon_in_label`"
)
else:
splitlabel = label.split(":", 1)
if len(splitlabel) == 2 and not splitlabel[1].startswith("//"):
label = splitlabel[1]
if prefix and prefix != splitlabel[0]:
warnings.warn(
f"Prefix given both as argument ({prefix}) "
f"and in label ({splitlabel[0]}). "
"Prefix given in argument takes presendence "
)
if not prefix:
prefix = splitlabel[0]
if prefix:
entitylist = self.get_by_label_all(
label,
label_annotations=label_annotations,
prefix=prefix,
)
if len(entitylist) > 0:
return entitylist[0]
raise NoSuchLabelError(
f"No label annotations matches {label!r} with prefix "
f"{prefix!r}"
)
# Label is a full IRI
entity = self.world[label]
if entity:
return entity
# First entity with matching label annotation
annotation_ids = (
(self._abbreviate(ann, False) for ann in label_annotations)
if label_annotations
else (ann.storid for ann in self.label_annotations)
)
get_triples = (
self.world._get_data_triples_spod_spod
if imported
else self._get_data_triples_spod_spod
)
for annotation_id in annotation_ids:
for s, _, _, _ in get_triples(None, annotation_id, label, None):
return self.world[self._unabbreviate(s)]
# Special labels
if self._special_labels and label in self._special_labels:
return self._special_labels[label]
# Check if label is a name under base_iri
entity = self.world[self.base_iri + label]
if entity:
return entity
# Check if label is a name in any namespace
for namespace in self._namespaces.keys():
entity = self.world[namespace + label]
if entity:
return entity
raise NoSuchLabelError(f"No label annotations matches '{label}'")
def get_by_label_all(self, label, label_annotations=None, prefix=None):
"""Like get_by_label(), but returns a list with all matching labels.
Returns an empty list if no matches could be found.
Note
----
The current implementation also supports "*" as a wildcard
matching any number of characters. This may change in the future.
"""
if not isinstance(label, str):
raise TypeError(
f"Invalid label definition, " f"must be a string: {label!r}"
)
if " " in label:
raise ValueError(
f"Invalid label definition, {label!r} contains spaces."
)
if label_annotations is None:
annotations = (_.name for _ in self.label_annotations)
else:
annotations = (
_.name if hasattr(_, "storid") else _ for _ in label_annotations
)
entity = self.world.search(**{next(annotations): label})
for key in annotations:
entity.extend(self.world.search(**{key: label}))
if self._special_labels and label in self._special_labels:
entity.append(self._special_labels[label])
entity_accessed_directly = self.world[self.base_iri + label]
if entity_accessed_directly and entity_accessed_directly not in entity:
entity.append(entity_accessed_directly)
if prefix:
return [_ for _ in entity if _.namespace.ontology.prefix == prefix]
return entity
def add_label_annotation(self, iri):
"""Adds label annotation used by get_by_label().
May be provided either as an IRI or as its owlready2 representation.
"""
if self._label_annotations is None:
self._label_annotations = []
label_annotation = iri if hasattr(iri, "storid") else self.world[iri]
if label_annotation is None:
warnings.warn(f"adding new IRI to ontology: {iri}")
name = iri.rsplit("/")[-1].rsplit("#")[-1]
bases = (owlready2.AnnotationProperty,)
with self:
label_annotation = types.new_class(name, bases)
if label_annotation not in self._label_annotations:
self._label_annotations.append(label_annotation)
def remove_label_annotation(self, iri):
"""Removes label annotation used by get_by_label().
May be provided either as an IRI or as its owlready2 representation.
"""
label_annotation = iri if hasattr(iri, "storid") else self.world[iri]
if not label_annotation:
raise ValueError(f"IRI not in ontology: {iri}")
self._label_annotations.remove(label_annotation)
def set_common_prefix(
self,
iri_base: str = "http://emmo.info/emmo",
prefix: str = "emmo",
) -> None:
"""Set a common prefix for all imported ontologies
with the same first part of the base_iri.
Args:
iri_base: The start of the base_iri to look for. Defaults to
the emmo base_iri http://emmo.info/emmo
prefix: the desired prefix. Defaults to emmo.
"""
if self.base_iri.startswith(iri_base):
self.prefix = prefix
for onto in self.imported_ontologies:
onto.set_common_prefix(iri_base=iri_base, prefix=prefix)
def load( # pylint: disable=too-many-arguments,arguments-renamed
self,
only_local=False,
filename=None,
format=None, # pylint: disable=redefined-builtin
reload=None,
reload_if_newer=False,
url_from_catalog=None,
catalog_file="catalog-v001.xml",
emmo_based=True,
prefix=None,
prefix_emmo=None,
**kwargs,
):
"""Load the ontology.
Parameters
----------
only_local: bool
Whether to only read local files. This requires that you
have appended the path to the ontology to owlready2.onto_path.
filename: str
Path to file to load the ontology from. Defaults to `base_iri`
provided to get_ontology().
format: str
Format of `filename`. Default is inferred from `filename`
extension.
reload: bool
Whether to reload the ontology if it is already loaded.
reload_if_newer: bool
Whether to reload the ontology if the source has changed since
last time it was loaded.
url_from_catalog: bool | None
Whether to use catalog file to resolve the location of `base_iri`.
If None, the catalog file is used if it exists in the same
directory as `filename`.
catalog_file: str
Name of Protègè catalog file in the same folder as the
ontology. This option is used together with `only_local` and
defaults to "catalog-v001.xml".
emmo_based: bool
Whether this is an EMMO-based ontology or not, default `True`.
prefix: defaults to self.get_namespace.name if
prefix_emmo: bool, default None. If emmo_based is True it
defaults to True and sets the prefix of all imported ontologies
with base_iri starting with 'http://emmo.info/emmo' to emmo
kwargs:
Additional keyword arguments are passed on to
owlready2.Ontology.load().
"""
# TODO: make sure that `only_local` argument is respected...
if self.loaded:
return self
self._load(
only_local=only_local,
filename=filename,
format=format,
reload=reload,
reload_if_newer=reload_if_newer,
url_from_catalog=url_from_catalog,
catalog_file=catalog_file,
**kwargs,
)
# Enable optimised search by get_by_label()
if self._special_labels is None and emmo_based:
for iri in DEFAULT_LABEL_ANNOTATIONS:
self.add_label_annotation(iri)
top = self.world["http://www.w3.org/2002/07/owl#topObjectProperty"]
self._special_labels = {
"Thing": owlready2.Thing,
"Nothing": owlready2.Nothing,
"topObjectProperty": top,
"owl:Thing": owlready2.Thing,
"owl:Nothing": owlready2.Nothing,
"owl:topObjectProperty": top,
}
# set prefix if another prefix is desired
# if we do this, shouldn't we make the name of all
# entities of the given ontology to the same?
if prefix:
self.prefix = prefix
else:
self.prefix = self.name
if emmo_based and prefix_emmo is None:
prefix_emmo = True
if prefix_emmo:
self.set_common_prefix()
return self
def _load( # pylint: disable=too-many-arguments,too-many-locals,too-many-branches,too-many-statements
self,
only_local=False,
filename=None,
format=None, # pylint: disable=redefined-builtin
reload=None,
reload_if_newer=False,
url_from_catalog=None,
catalog_file="catalog-v001.xml",
**kwargs,
):
"""Help function for load()."""
web_protocol = "http://", "https://", "ftp://"
url = str(filename) if filename else self.base_iri.rstrip("/#")
if url.startswith(web_protocol):
baseurl = os.path.dirname(url)
catalogurl = baseurl + "/" + catalog_file
else:
if url.startswith("file://"):
url = url[7:]
url = os.path.normpath(os.path.abspath(url))
baseurl = os.path.dirname(url)
catalogurl = os.path.join(baseurl, catalog_file)
def getmtime(path):
if os.path.exists(path):
return os.path.getmtime(path)
return 0.0
# Resolve url from catalog file
iris = {}
dirs = set()
if url_from_catalog or url_from_catalog is None:
not_reload = not reload and (
not reload_if_newer
or getmtime(catalogurl)
> self.world._cached_catalogs[catalogurl][0]
)
# get iris from catalog already in cached catalogs
if catalogurl in self.world._cached_catalogs and not_reload:
_, iris, dirs = self.world._cached_catalogs[catalogurl]
# do not update cached_catalogs if url already in _iri_mappings
# and reload not forced
elif url in self.world._iri_mappings and not_reload:
pass
# update iris from current catalogurl
else:
try:
iris, dirs = read_catalog(
uri=catalogurl,
recursive=False,
return_paths=True,
catalog_file=catalog_file,
)
except ReadCatalogError:
if url_from_catalog is not None:
raise
self.world._cached_catalogs[catalogurl] = (0.0, {}, set())
else:
self.world._cached_catalogs[catalogurl] = (
getmtime(catalogurl),
iris,
dirs,
)
self.world._iri_mappings.update(iris)
resolved_url = self.world._iri_mappings.get(url, url)
# Append paths from catalog file to onto_path
for path in sorted(dirs, reverse=True):
if path not in owlready2.onto_path:
owlready2.onto_path.append(path)
# Use catalog file to update IRIs of imported ontologies
# in internal store and try to load again...
if self.world._iri_mappings:
for abbrev_iri in self.world._get_obj_triples_sp_o(
self.storid, owlready2.owl_imports
):
iri = self._unabbreviate(abbrev_iri)
if iri in self.world._iri_mappings:
self._del_obj_triple_spo(
self.storid, owlready2.owl_imports, abbrev_iri
)
self._add_obj_triple_spo(
self.storid,
owlready2.owl_imports,
self._abbreviate(self.world._iri_mappings[iri]),
)
# Load ontology
try:
self.loaded = False
fmt = format if format else guess_format(resolved_url, fmap=FMAP)
if fmt and fmt not in OWLREADY2_FORMATS:
# Convert filename to rdfxml before passing it to owlready2
graph = rdflib.Graph()
try:
graph.parse(resolved_url, format=fmt)
except URLError as err:
raise EMMOntoPyException(
"URL error", err, resolved_url
) from err
with tempfile.NamedTemporaryFile() as handle:
graph.serialize(destination=handle, format="xml")
handle.seek(0)
return super().load(
only_local=True,
fileobj=handle,
reload=reload,
reload_if_newer=reload_if_newer,
format="rdfxml",
**kwargs,
)
elif resolved_url.startswith(web_protocol):
return super().load(
only_local=only_local,
reload=reload,
reload_if_newer=reload_if_newer,
**kwargs,
)
else:
with open(resolved_url, "rb") as handle:
return super().load(
only_local=only_local,
fileobj=handle,
reload=reload,
reload_if_newer=reload_if_newer,
**kwargs,
)
except owlready2.OwlReadyOntologyParsingError:
# Owlready2 is not able to parse the ontology - most
# likely because imported ontologies must be resolved
# using the catalog file.
# Reraise if we don't want to read from the catalog file
if not url_from_catalog and url_from_catalog is not None:
raise
warnings.warn(
"Recovering from Owlready2 parsing error... might be deprecated"
)
# Copy the ontology into a local folder and try again
with tempfile.TemporaryDirectory() as handle:
output = os.path.join(handle, os.path.basename(resolved_url))
convert_imported(
input_ontology=resolved_url,
output_ontology=output,
input_format=fmt,
output_format="xml",
url_from_catalog=url_from_catalog,
catalog_file=catalog_file,
)
self.loaded = False
with open(output, "rb") as handle:
try:
return super().load(
only_local=True,
fileobj=handle,
reload=reload,
reload_if_newer=reload_if_newer,
format="rdfxml",
**kwargs,
)
except HTTPError as exc: # Add url to HTTPError message
raise HTTPError(
url=exc.url,
code=exc.code,
msg=f"{exc.url}: {exc.msg}",
hdrs=exc.hdrs,
fp=exc.fp,
).with_traceback(exc.__traceback__)
except HTTPError as exc: # Add url to HTTPError message
raise HTTPError(
url=exc.url,
code=exc.code,
msg=f"{exc.url}: {exc.msg}",
hdrs=exc.hdrs,
fp=exc.fp,
).with_traceback(exc.__traceback__)
def save(
self,
filename=None,
format=None,
dir=".",
mkdir=False,
overwrite=False,
recursive=False,
squash=False,
write_catalog_file=False,
append_catalog=False,
catalog_file="catalog-v001.xml",
):
"""Writes the ontology to file.
Parameters
----------
filename: None | str | Path
Name of file to write to. If None, it defaults to the name
of the ontology with `format` as file extension.
format: str
Output format. The default is to infer it from `filename`.
dir: str | Path
If `filename` is a relative path, it is a relative path to `dir`.
mkdir: bool
Whether to create output directory if it does not exists.
owerwrite: bool
If true and `filename` exists, remove the existing file before
saving. The default is to append to an existing ontology.
recursive: bool
Whether to save imported ontologies recursively. This is
commonly combined with `filename=None`, `dir` and `mkdir`.
squash: bool
If true, rdflib will be used to save the current ontology
together with all its sub-ontologies into `filename`.
It make no sense to combine this with `recursive`.
write_catalog_file: bool
Whether to also write a catalog file to disk.
append_catalog: bool
Whether to append to an existing catalog file.
catalog_file: str | Path
Name of catalog file. If not an absolute path, it is prepended
to `dir`.
"""
# pylint: disable=redefined-builtin,too-many-arguments
# pylint: disable=too-many-statements,too-many-branches
# pylint: disable=too-many-locals,arguments-renamed
if not _validate_installed_version(
package="rdflib", min_version="6.0.0"
) and format == FMAP.get("ttl", ""):
from rdflib import ( # pylint: disable=import-outside-toplevel
__version__ as __rdflib_version__,
)
warnings.warn(
IncompatibleVersion(
"To correctly convert to Turtle format, rdflib must be "
"version 6.0.0 or greater, however, the detected rdflib "
"version used by your Python interpreter is "
f"{__rdflib_version__!r}. For more information see the "
"'Known issues' section of the README."
)
)
revmap = {value: key for key, value in FMAP.items()}
if filename is None:
if format:
fmt = revmap.get(format, format)
filename = f"{self.name}.{fmt}"
else:
raise TypeError("`filename` and `format` cannot both be None.")
filename = os.path.join(dir, filename)
dir = Path(filename).resolve().parent
if mkdir:
outdir = Path(filename).parent.resolve()
if not outdir.exists():
outdir.mkdir(parents=True)
if not format:
format = guess_format(filename, fmap=FMAP)
fmt = revmap.get(format, format)
if overwrite and filename and os.path.exists(filename):
os.remove(filename)
EMMO = rdflib.Namespace( # pylint:disable=invalid-name
"http://emmo.info/emmo#"
)
if recursive:
if squash:
raise ValueError(
"`recursive` and `squash` should not both be true"
)
base = self.base_iri.rstrip("#/")
for onto in self.imported_ontologies:
obase = onto.base_iri.rstrip("#/")
newdir = Path(dir) / os.path.relpath(obase, base)
onto.save(
filename=None,
format=format,
dir=newdir.resolve(),
mkdir=mkdir,
overwrite=overwrite,
recursive=recursive,
squash=squash,
write_catalog_file=write_catalog_file,
append_catalog=append_catalog,
catalog_file=catalog_file,
)
if squash:
from rdflib import ( # pylint:disable=import-outside-toplevel
URIRef,
RDF,
OWL,
)
graph = self.world.as_rdflib_graph()
graph.namespace_manager.bind("emmo", EMMO)
# Remove anonymous namespace and imports
graph.remove((URIRef("http://anonymous"), RDF.type, OWL.Ontology))
imports = list(graph.triples((None, OWL.imports, None)))
for triple in imports:
graph.remove(triple)
graph.serialize(destination=filename, format=format)
elif format in OWLREADY2_FORMATS:
super().save(file=filename, format=fmt)
else:
# The try-finally clause is needed for cleanup and because
# we have to provide delete=False to NamedTemporaryFile
# since Windows does not allow to reopen an already open
# file.
try:
with tempfile.NamedTemporaryFile(
suffix=".owl", delete=False
) as handle:
tmpfile = handle.name
super().save(tmpfile, format="rdfxml")
graph = rdflib.Graph()
graph.parse(tmpfile, format="xml")
graph.serialize(destination=filename, format=format)
finally:
os.remove(tmpfile)
if write_catalog_file:
mappings = {}
base = self.base_iri.rstrip("#/")
def append(onto):
obase = onto.base_iri.rstrip("#/")
newdir = Path(dir) / os.path.relpath(obase, base)
newpath = newdir.resolve() / f"{onto.name}.{fmt}"
relpath = os.path.relpath(newpath, dir)
mappings[onto.get_version(as_iri=True)] = str(relpath)
for imported in onto.imported_ontologies:
append(imported)
if recursive:
append(self)
write_catalog(
mappings,
output=catalog_file,
directory=dir,
append=append_catalog,
)
def get_imported_ontologies(self, recursive=False):
"""Return a list with imported ontologies.
If `recursive` is `True`, ontologies imported by imported ontologies
are also returned.
"""
def rec_imported(onto):
for ontology in onto.imported_ontologies:
if ontology not in imported:
imported.add(ontology)
rec_imported(ontology)
if recursive:
imported = set()
rec_imported(self)
return list(imported)
return self.imported_ontologies
def get_entities( # pylint: disable=too-many-arguments
self,
imported=True,
classes=True,
individuals=True,
object_properties=True,
data_properties=True,
annotation_properties=True,
):
"""Return a generator over (optionally) all classes, individuals,
object_properties, data_properties and annotation_properties.
If `imported` is `True`, entities in imported ontologies will also
be included.
"""
generator = []
if classes:
generator.append(self.classes(imported))
if individuals:
generator.append(self.individuals(imported))
if object_properties:
generator.append(self.object_properties(imported))
if data_properties:
generator.append(self.data_properties(imported))
if annotation_properties:
generator.append(self.annotation_properties(imported))
for entity in itertools.chain(*generator):
yield entity
def classes(self, imported=False):
"""Returns an generator over all classes.
If `imported` is `True`, will imported classes are also returned.
"""
if imported:
return self.world.classes()
return super().classes()
def individuals(self, imported=False):
"""Returns an generator over all individuals.
If `imported` is `True`, will imported individuals are also returned.
"""
if imported:
return self.world.individuals()
return super().individuals()
def object_properties(self, imported=False):
"""Returns an generator over all object properties.
If `imported` is true, will imported object properties are also
returned.
"""
if imported:
return self.world.object_properties()
return super().object_properties()
def data_properties(self, imported=False):
"""Returns an generator over all data properties.
If `imported` is true, will imported data properties are also
returned.
"""
if imported:
return self.world.data_properties()
return super().data_properties()
def annotation_properties(self, imported=False):
"""Returns a generator iterating over all annotation properties
defined in the current ontology.
If `imported` is true, annotation properties in imported ontologies
will also be included.
"""
if imported:
return self.world.annotation_properties()
return super().annotation_properties()
def get_root_classes(self, imported=False):
"""Returns a list or root classes."""
return [
cls
for cls in self.classes(imported=imported)
if not cls.ancestors().difference(set([cls, owlready2.Thing]))
]
def get_root_object_properties(self, imported=False):
"""Returns a list of root object properties."""
props = set(self.object_properties(imported=imported))
return [p for p in props if not props.intersection(p.is_a)]
def get_root_data_properties(self, imported=False):
"""Returns a list of root object properties."""
props = set(self.data_properties(imported=imported))
return [p for p in props if not props.intersection(p.is_a)]
def get_roots(self, imported=False):
"""Returns all class, object_property and data_property roots."""
roots = self.get_root_classes(imported=imported)
roots.extend(self.get_root_object_properties(imported=imported))
roots.extend(self.get_root_data_properties(imported=imported))
return roots
def sync_python_names(self, annotations=("prefLabel", "label", "altLabel")):
"""Update the `python_name` attribute of all properties.
The python_name attribute will be set to the first non-empty
annotation in the sequence of annotations in `annotations` for
the property.
"""
def update(gen):
for prop in gen:
for annotation in annotations:
if hasattr(prop, annotation) and getattr(prop, annotation):
prop.python_name = getattr(prop, annotation).first()
break
update(
self.get_entities(
classes=False,
individuals=False,
object_properties=False,
data_properties=False,
)
)
update(
self.get_entities(
classes=False, individuals=False, annotation_properties=False
)
)
def rename_entities(
self,
annotations=("prefLabel", "label", "altLabel"),
):
"""Set `name` of all entities to the first non-empty annotation in
`annotations`.
Warning, this method changes all IRIs in the ontology. However,
it may be useful to make the ontology more readable and to work
with it together with a triple store.
"""
for entity in self.get_entities():
for annotation in annotations:
if hasattr(entity, annotation):
name = getattr(entity, annotation).first()
if name:
entity.name = name
break
def sync_reasoner(
self, reasoner="FaCT++", include_imported=False, **kwargs
):
"""Update current ontology by running the given reasoner.
Supported values for `reasoner` are 'Pellet', 'HermiT' and 'FaCT++'.
If `include_imported` is true, the reasoner will also reason
over imported ontologies. Note that this may be **very** slow
with Pellet and HermiT.
Keyword arguments are passed to the underlying owlready2 function.
"""
if reasoner == "FaCT++":
sync = sync_reasoner_factpp
elif reasoner == "Pellet":
sync = owlready2.sync_reasoner_pellet
elif reasoner == "HermiT":
sync = owlready2.sync_reasoner_hermit
else:
raise ValueError(
f"unknown reasoner {reasoner!r}. Supported reasoners "
'are "Pellet", "HermiT" and "FaCT++".'
)
# For some reason we must visit all entities once before running
# the reasoner...
list(self.get_entities())
with self:
if include_imported:
sync(self.world, **kwargs)
else:
sync(self, **kwargs)
def sync_attributes( # pylint: disable=too-many-branches
self,
name_policy=None,
name_prefix="",
class_docstring="comment",
sync_imported=False,
):
"""This method is intended to be called after you have added new
classes (typically via Python) to make sure that attributes like
`label` and `comments` are defined.
If a class, object property, data property or annotation
property in the current ontology has no label, the name of
the corresponding Python class will be assigned as label.
If a class, object property, data property or annotation
property has no comment, it will be assigned the docstring of
the corresponding Python class.
`name_policy` specify wether and how the names in the ontology
should be updated. Valid values are:
None not changed
"uuid" `name_prefix` followed by a global unique id (UUID).
If the name is already valid accoridng to this standard
it will not be regenerated.
"sequential" `name_prefix` followed a sequantial number.
EMMO conventions imply ``name_policy=='uuid'``.
If `sync_imported` is true, all imported ontologies are also
updated.
The `class_docstring` argument specifies the annotation that
class docstrings are mapped to. Defaults to "comment".
"""
for cls in itertools.chain(
self.classes(),
self.object_properties(),
self.data_properties(),
self.annotation_properties(),
):
if not hasattr(cls, "prefLabel"):
# no prefLabel - create new annotation property..
with self:
# pylint: disable=invalid-name,missing-class-docstring
# pylint: disable=unused-variable
class prefLabel(owlready2.label):
pass
cls.prefLabel = [locstr(cls.__name__, lang="en")]
elif not cls.prefLabel:
cls.prefLabel.append(locstr(cls.__name__, lang="en"))
if class_docstring and hasattr(cls, "__doc__") and cls.__doc__:
getattr(cls, class_docstring).append(
locstr(inspect.cleandoc(cls.__doc__), lang="en")
)
for ind in self.individuals():
if not hasattr(ind, "prefLabel"):
# no prefLabel - create new annotation property..
with self:
# pylint: disable=invalid-name,missing-class-docstring
# pylint: disable=function-redefined
class prefLabel(owlready2.label):
iri = "http://www.w3.org/2004/02/skos/core#prefLabel"
ind.prefLabel = [locstr(ind.name, lang="en")]
elif not ind.prefLabel:
ind.prefLabel.append(locstr(ind.name, lang="en"))
chain = itertools.chain(
self.classes(),
self.individuals(),
self.object_properties(),
self.data_properties(),
self.annotation_properties(),
)
if name_policy == "uuid":
for obj in chain:
try:
# Passing the following means that the name is valid
# and need not be regenerated.
if not obj.name.startswith(name_prefix):
raise ValueError
uuid.UUID(obj.name.lstrip(name_prefix), version=5)
except ValueError:
obj.name = name_prefix + str(
uuid.uuid5(uuid.NAMESPACE_DNS, obj.name)
)
elif name_policy == "sequential":
for obj in chain:
counter = 0
while f"{self.base_iri}{name_prefix}{counter}" in self:
counter += 1
obj.name = f"{name_prefix}{counter}"
elif name_policy is not None:
raise TypeError(f"invalid name_policy: {name_policy!r}")
if sync_imported:
for onto in self.imported_ontologies:
onto.sync_attributes()
def get_relations(self):
"""Returns a generator for all relations."""
warnings.warn(
"Ontology.get_relations() is deprecated. Use "
"onto.object_properties() instead.",
DeprecationWarning,
)
return self.object_properties()
def get_annotations(self, entity):
"""Returns a dict with annotations for `entity`. Entity may be given
either as a ThingClass object or as a label."""
warnings.warn(
"Ontology.get_annotations(entity) is deprecated. Use "
"entity.get_annotations() instead.",
DeprecationWarning,
)
if isinstance(entity, str):
entity = self.get_by_label(entity)
res = {"comment": getattr(entity, "comment", "")}
for annotation in self.annotation_properties():
res[annotation.label.first()] = [
obj.strip('"')
for _, _, obj in self.get_triples(
entity.storid, annotation.storid, None
)
]
return res
def get_branch( # pylint: disable=too-many-arguments
self,
root,
leaves=(),
include_leaves=True,
strict_leaves=False,
exclude=None,
sort=False,
):
"""Returns a set with all direct and indirect subclasses of `root`.
Any subclass found in the sequence `leaves` will be included in
the returned list, but its subclasses will not. The elements
of `leaves` may be ThingClass objects or labels.
Subclasses of any subclass found in the sequence `leaves` will
be excluded from the returned list, where the elements of `leaves`
may be ThingClass objects or labels.
If `include_leaves` is true, the leaves are included in the returned
list, otherwise they are not.
If `strict_leaves` is true, any descendant of a leaf will be excluded
in the returned set.
If given, `exclude` may be a sequence of classes, including
their subclasses, to exclude from the output.
If `sort` is True, a list sorted according to depth and label
will be returned instead of a set.
"""
def _branch(root, leaves):
if root not in leaves:
branch = {
root,
}
for cls in root.subclasses():
# Defining a branch is actually quite tricky. Consider
# the case:
#
# L isA R
# A isA L
# A isA R
#
# where R is the root, L is a leaf and A is a direct
# child of both. Logically, since A is a child of the
# leaf we want to skip A. But a strait forward imple-
# mentation will see that A is a child of the root and
# include it. Requireing that the R should be a strict
# parent of A solves this.
if root in cls.get_parents(strict=True):
branch.update(_branch(cls, leaves))
else:
branch = (
{
root,
}
if include_leaves
else set()
)
return branch
if isinstance(root, str):
root = self.get_by_label(root)
leaves = set(
self.get_by_label(leaf) if isinstance(leaf, str) else leaf
for leaf in leaves
)
leaves.discard(root)
if exclude:
exclude = set(
self.get_by_label(e) if isinstance(e, str) else e
for e in exclude
)
leaves.update(exclude)
branch = _branch(root, leaves)
# Exclude all descendants of any leaf
if strict_leaves:
descendants = root.descendants()
for leaf in leaves:
if leaf in descendants:
branch.difference_update(
leaf.descendants(include_self=False)
)
if exclude:
branch.difference_update(exclude)
# Sort according to depth, then by label
if sort:
branch = sorted(
sorted(branch, key=asstring),
key=lambda x: len(x.mro()),
)
return branch
def is_individual(self, entity):
"""Returns true if entity is an individual."""
if isinstance(entity, str):
entity = self.get_by_label(entity)
return isinstance(entity, owlready2.Thing)
# FIXME - deprecate this method as soon the ThingClass property
# `defined_class` works correct in Owlready2
def is_defined(self, entity):
"""Returns true if the entity is a defined class.
Deprecated, use the `is_defined` property of the classes
(ThingClass subclasses) instead.
"""
warnings.warn(
"This method is deprecated. Use the `is_defined` property of "
"the classes instad.",
DeprecationWarning,
stacklevel=2,
)
if isinstance(entity, str):
entity = self.get_by_label(entity)
return hasattr(entity, "equivalent_to") and bool(entity.equivalent_to)
def get_version(self, as_iri=False) -> str:
"""Returns the version number of the ontology as inferred from the
owl:versionIRI tag or, if owl:versionIRI is not found, from
owl:versionINFO.
If `as_iri` is True, the full versionIRI is returned.
"""
version_iri_storid = self.world._abbreviate(
"http://www.w3.org/2002/07/owl#versionIRI"
)
tokens = self.get_triples(s=self.storid, p=version_iri_storid)
if (not tokens) and (as_iri is True):
raise TypeError(
"No owl:versionIRI "
f"in Ontology {self.base_iri!r}. "
"Search for owl:versionInfo with as_iri=False"
)
if tokens:
_, _, obj = tokens[0]
version_iri = self.world._unabbreviate(obj)
if as_iri:
return version_iri
return infer_version(self.base_iri, version_iri)
version_info_storid = self.world._abbreviate(
"http://www.w3.org/2002/07/owl#versionInfo"
)
tokens = self.get_triples(s=self.storid, p=version_info_storid)
if not tokens:
raise TypeError(
"No versionIRI or versionInfo " f"in Ontology {self.base_iri!r}"
)
_, _, version_info = tokens[0]
return version_info.strip('"').strip("'")
def set_version(self, version=None, version_iri=None):
"""Assign version to ontology by asigning owl:versionIRI.
If `version` but not `version_iri` is provided, the version
IRI will be the combination of `base_iri` and `version`.
"""
_version_iri = "http://www.w3.org/2002/07/owl#versionIRI"
version_iri_storid = self.world._abbreviate(_version_iri)
if self._has_obj_triple_spo( # pylint: disable=unexpected-keyword-arg
# For some reason _has_obj_triples_spo exists in both
# owlready2.namespace.Namespace (with arguments subject/predicate)
# and in owlready2.triplelite._GraphManager (with arguments s/p)
# owlready2.Ontology inherits from Namespace directly
# and pylint checks that.
# It actually accesses the one in triplelite.
# subject=self.storid, predicate=version_iri_storid
s=self.storid,
p=version_iri_storid,
):
self._del_obj_triple_spo(s=self.storid, p=version_iri_storid)
if not version_iri:
if not version:
raise TypeError(
"Either `version` or `version_iri` must be provided"
)
head, tail = self.base_iri.rstrip("#/").rsplit("/", 1)
version_iri = "/".join([head, version, tail])
self._add_obj_triple_spo(
s=self.storid,
p=self.world._abbreviate(_version_iri),
o=self.world._abbreviate(version_iri),
)
def get_graph(self, **kwargs):
"""Returns a new graph object. See emmo.graph.OntoGraph.
Note that this method requires the Python graphviz package.
"""
# pylint: disable=import-outside-toplevel,cyclic-import
from ontopy.graph import OntoGraph
return OntoGraph(self, **kwargs)
@staticmethod
def common_ancestors(cls1, cls2):
"""Return a list of common ancestors for `cls1` and `cls2`."""
return set(cls1.ancestors()).intersection(cls2.ancestors())
def number_of_generations(self, descendant, ancestor):
"""Return shortest distance from ancestor to descendant"""
if ancestor not in descendant.ancestors():
raise ValueError("Descendant is not a descendant of ancestor")
return self._number_of_generations(descendant, ancestor, 0)
def _number_of_generations(self, descendant, ancestor, counter):
"""Recursive help function to number_of_generations(), return
distance between a ancestor-descendant pair (counter+1)."""
if descendant.name == ancestor.name:
return counter
try:
return min(
self._number_of_generations(parent, ancestor, counter + 1)
for parent in descendant.get_parents()
if ancestor in parent.ancestors()
)
except ValueError:
return counter
def closest_common_ancestors(self, cls1, cls2):
"""Returns a list with closest_common_ancestor for cls1 and cls2"""
distances = {}
for ancestor in self.common_ancestors(cls1, cls2):
distances[ancestor] = self.number_of_generations(
cls1, ancestor
) + self.number_of_generations(cls2, ancestor)
return [
ancestor
for ancestor, distance in distances.items()
if distance == min(distances.values())
]
@staticmethod
def closest_common_ancestor(*classes):
"""Returns closest_common_ancestor for the given classes."""
mros = [cls.mro() for cls in classes]
track = defaultdict(int)
while mros:
for mro in mros:
cur = mro.pop(0)
track[cur] += 1
if track[cur] == len(classes):
return cur
if len(mro) == 0:
mros.remove(mro)
raise EMMOntoPyException(
"A closest common ancestor should always exist !"
)
def get_ancestors(
self,
classes: "Union[List, ThingClass]",
closest: bool = False,
generations: int = None,
strict: bool = True,
) -> set:
"""Return ancestors of all classes in `classes`.
Args:
classes: class(es) for which ancestors should be returned.
generations: Include this number of generations, default is all.
closest: If True, return all ancestors up to and including the
closest common ancestor. Return all if False.
strict: If True returns only real ancestors, i.e. `classes` are
are not included in the returned set.
Returns:
Set of ancestors to `classes`.
"""
if not isinstance(classes, Iterable):
classes = [classes]
ancestors = set()
if not classes:
return ancestors
def addancestors(entity, counter, subject):
if counter > 0:
for parent in entity.get_parents(strict=True):
subject.add(parent)
addancestors(parent, counter - 1, subject)
if closest:
if generations is not None:
raise ValueError(
"Only one of `generations` or `closest` may be specified."
)
closest_ancestor = self.closest_common_ancestor(*classes)
for cls in classes:
ancestors.update(
anc
for anc in cls.ancestors()
if closest_ancestor in anc.ancestors()
)
elif isinstance(generations, int):
for entity in classes:
addancestors(entity, generations, ancestors)
else:
ancestors.update(*(cls.ancestors() for cls in classes))
if strict:
return ancestors.difference(classes)
return ancestors
def get_descendants(
self,
classes: "Union[List, ThingClass]",
generations: int = None,
common: bool = False,
) -> set:
"""Return descendants/subclasses of all classes in `classes`.
Args:
classes: class(es) for which descendants are desired.
common: whether to only return descendants common to all classes.
generations: Include this number of generations, default is all.
Returns:
A set of descendants for given number of generations.
If 'common'=True, the common descendants are returned
within the specified number of generations.
'generations' defaults to all.
"""
if not isinstance(classes, Iterable):
classes = [classes]
descendants = {name: [] for name in classes}
def _children_recursively(num, newentity, parent, descendants):
"""Helper function to get all children up to generation."""
for child in self.get_children_of(newentity):
descendants[parent].append(child)
if num < generations:
_children_recursively(num + 1, child, parent, descendants)
if generations == 0:
return set()
if not generations:
for entity in classes:
descendants[entity] = entity.descendants()
# only include proper descendants
descendants[entity].remove(entity)
else:
for entity in classes:
_children_recursively(1, entity, entity, descendants)
results = descendants.values()
if common is True:
return set.intersection(*map(set, results))
return set(flatten(results))
def get_wu_palmer_measure(self, cls1, cls2):
"""Return Wu-Palmer measure for semantic similarity.
Returns Wu-Palmer measure for semantic similarity between
two concepts.
Wu, Palmer; ACL 94: Proceedings of the 32nd annual meeting on
Association for Computational Linguistics, June 1994.
"""
cca = self.closest_common_ancestor(cls1, cls2)
ccadepth = self.number_of_generations(cca, self.Thing)
generations1 = self.number_of_generations(cls1, cca)
generations2 = self.number_of_generations(cls2, cca)
return 2 * ccadepth / (generations1 + generations2 + 2 * ccadepth)
def new_entity(
self, name: str, parent: Union[ThingClass, Iterable]
) -> ThingClass:
"""Create and return new entity
Makes a new entity in the ontology with given parent(s).
Return the new entity.
Throws exception if name consists of more than one word.
"""
if " " in name:
raise LabelDefinitionError(
f"Error in label name definition '{name}': "
f"Label consists of more than one word."
)
parents = tuple(parent) if isinstance(parent, Iterable) else (parent,)
for thing in parents:
if not isinstance(thing, owlready2.ThingClass):
raise ThingClassDefinitionError(
f"Error in parent definition: "
f"'{thing}' is not an owlready2.ThingClass."
)
with self:
entity = types.new_class(name, parents)
return entity
colon_in_label
property
writable
¶
Whether to accept colon in name-part of IRI. If true, the name cannot be prefixed.
dir_imported
property
writable
¶
Whether to include imported ontologies in dir() listing.
dir_label
property
writable
¶
Whether to include entity label in dir() listing.
dir_name
property
writable
¶
Whether to include entity name in dir() listing.
dir_preflabel
property
writable
¶
Whether to include entity prefLabel in dir() listing.
label_annotations
property
readonly
¶
List of label annotation searched for by get_by_label().
add_label_annotation(self, iri)
¶
Adds label annotation used by get_by_label().
May be provided either as an IRI or as its owlready2 representation.
Source code in ontopy/ontology.py
def add_label_annotation(self, iri):
"""Adds label annotation used by get_by_label().
May be provided either as an IRI or as its owlready2 representation.
"""
if self._label_annotations is None:
self._label_annotations = []
label_annotation = iri if hasattr(iri, "storid") else self.world[iri]
if label_annotation is None:
warnings.warn(f"adding new IRI to ontology: {iri}")
name = iri.rsplit("/")[-1].rsplit("#")[-1]
bases = (owlready2.AnnotationProperty,)
with self:
label_annotation = types.new_class(name, bases)
if label_annotation not in self._label_annotations:
self._label_annotations.append(label_annotation)
annotation_properties(self, imported=False)
¶
Returns a generator iterating over all annotation properties defined in the current ontology.
If imported is true, annotation properties in imported ontologies
will also be included.
Source code in ontopy/ontology.py
def annotation_properties(self, imported=False):
"""Returns a generator iterating over all annotation properties
defined in the current ontology.
If `imported` is true, annotation properties in imported ontologies
will also be included.
"""
if imported:
return self.world.annotation_properties()
return super().annotation_properties()
classes(self, imported=False)
¶
Returns an generator over all classes.
If imported is True, will imported classes are also returned.
Source code in ontopy/ontology.py
def classes(self, imported=False):
"""Returns an generator over all classes.
If `imported` is `True`, will imported classes are also returned.
"""
if imported:
return self.world.classes()
return super().classes()
closest_common_ancestor(*classes)
staticmethod
¶
Returns closest_common_ancestor for the given classes.
Source code in ontopy/ontology.py
@staticmethod
def closest_common_ancestor(*classes):
"""Returns closest_common_ancestor for the given classes."""
mros = [cls.mro() for cls in classes]
track = defaultdict(int)
while mros:
for mro in mros:
cur = mro.pop(0)
track[cur] += 1
if track[cur] == len(classes):
return cur
if len(mro) == 0:
mros.remove(mro)
raise EMMOntoPyException(
"A closest common ancestor should always exist !"
)
closest_common_ancestors(self, cls1, cls2)
¶
Returns a list with closest_common_ancestor for cls1 and cls2
Source code in ontopy/ontology.py
def closest_common_ancestors(self, cls1, cls2):
"""Returns a list with closest_common_ancestor for cls1 and cls2"""
distances = {}
for ancestor in self.common_ancestors(cls1, cls2):
distances[ancestor] = self.number_of_generations(
cls1, ancestor
) + self.number_of_generations(cls2, ancestor)
return [
ancestor
for ancestor, distance in distances.items()
if distance == min(distances.values())
]
common_ancestors(cls1, cls2)
staticmethod
¶
Return a list of common ancestors for cls1 and cls2.
Source code in ontopy/ontology.py
@staticmethod
def common_ancestors(cls1, cls2):
"""Return a list of common ancestors for `cls1` and `cls2`."""
return set(cls1.ancestors()).intersection(cls2.ancestors())
data_properties(self, imported=False)
¶
Returns an generator over all data properties.
If imported is true, will imported data properties are also
returned.
Source code in ontopy/ontology.py
def data_properties(self, imported=False):
"""Returns an generator over all data properties.
If `imported` is true, will imported data properties are also
returned.
"""
if imported:
return self.world.data_properties()
return super().data_properties()
get_ancestors(self, classes, closest=False, generations=None, strict=True)
¶
Return ancestors of all classes in classes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
classes |
Union[List, ThingClass] |
class(es) for which ancestors should be returned. |
required |
generations |
int |
Include this number of generations, default is all. |
None |
closest |
bool |
If True, return all ancestors up to and including the closest common ancestor. Return all if False. |
False |
strict |
bool |
If True returns only real ancestors, i.e. |
True |
Returns:
| Type | Description |
|---|---|
set |
Set of ancestors to |
Source code in ontopy/ontology.py
def get_ancestors(
self,
classes: "Union[List, ThingClass]",
closest: bool = False,
generations: int = None,
strict: bool = True,
) -> set:
"""Return ancestors of all classes in `classes`.
Args:
classes: class(es) for which ancestors should be returned.
generations: Include this number of generations, default is all.
closest: If True, return all ancestors up to and including the
closest common ancestor. Return all if False.
strict: If True returns only real ancestors, i.e. `classes` are
are not included in the returned set.
Returns:
Set of ancestors to `classes`.
"""
if not isinstance(classes, Iterable):
classes = [classes]
ancestors = set()
if not classes:
return ancestors
def addancestors(entity, counter, subject):
if counter > 0:
for parent in entity.get_parents(strict=True):
subject.add(parent)
addancestors(parent, counter - 1, subject)
if closest:
if generations is not None:
raise ValueError(
"Only one of `generations` or `closest` may be specified."
)
closest_ancestor = self.closest_common_ancestor(*classes)
for cls in classes:
ancestors.update(
anc
for anc in cls.ancestors()
if closest_ancestor in anc.ancestors()
)
elif isinstance(generations, int):
for entity in classes:
addancestors(entity, generations, ancestors)
else:
ancestors.update(*(cls.ancestors() for cls in classes))
if strict:
return ancestors.difference(classes)
return ancestors
get_annotations(self, entity)
¶
Returns a dict with annotations for entity. Entity may be given
either as a ThingClass object or as a label.
Source code in ontopy/ontology.py
def get_annotations(self, entity):
"""Returns a dict with annotations for `entity`. Entity may be given
either as a ThingClass object or as a label."""
warnings.warn(
"Ontology.get_annotations(entity) is deprecated. Use "
"entity.get_annotations() instead.",
DeprecationWarning,
)
if isinstance(entity, str):
entity = self.get_by_label(entity)
res = {"comment": getattr(entity, "comment", "")}
for annotation in self.annotation_properties():
res[annotation.label.first()] = [
obj.strip('"')
for _, _, obj in self.get_triples(
entity.storid, annotation.storid, None
)
]
return res
get_branch(self, root, leaves=(), include_leaves=True, strict_leaves=False, exclude=None, sort=False)
¶
Returns a set with all direct and indirect subclasses of root.
Any subclass found in the sequence leaves will be included in
the returned list, but its subclasses will not. The elements
of leaves may be ThingClass objects or labels.
Subclasses of any subclass found in the sequence leaves will
be excluded from the returned list, where the elements of leaves
may be ThingClass objects or labels.
If include_leaves is true, the leaves are included in the returned
list, otherwise they are not.
If strict_leaves is true, any descendant of a leaf will be excluded
in the returned set.
If given, exclude may be a sequence of classes, including
their subclasses, to exclude from the output.
If sort is True, a list sorted according to depth and label
will be returned instead of a set.
Source code in ontopy/ontology.py
def get_branch( # pylint: disable=too-many-arguments
self,
root,
leaves=(),
include_leaves=True,
strict_leaves=False,
exclude=None,
sort=False,
):
"""Returns a set with all direct and indirect subclasses of `root`.
Any subclass found in the sequence `leaves` will be included in
the returned list, but its subclasses will not. The elements
of `leaves` may be ThingClass objects or labels.
Subclasses of any subclass found in the sequence `leaves` will
be excluded from the returned list, where the elements of `leaves`
may be ThingClass objects or labels.
If `include_leaves` is true, the leaves are included in the returned
list, otherwise they are not.
If `strict_leaves` is true, any descendant of a leaf will be excluded
in the returned set.
If given, `exclude` may be a sequence of classes, including
their subclasses, to exclude from the output.
If `sort` is True, a list sorted according to depth and label
will be returned instead of a set.
"""
def _branch(root, leaves):
if root not in leaves:
branch = {
root,
}
for cls in root.subclasses():
# Defining a branch is actually quite tricky. Consider
# the case:
#
# L isA R
# A isA L
# A isA R
#
# where R is the root, L is a leaf and A is a direct
# child of both. Logically, since A is a child of the
# leaf we want to skip A. But a strait forward imple-
# mentation will see that A is a child of the root and
# include it. Requireing that the R should be a strict
# parent of A solves this.
if root in cls.get_parents(strict=True):
branch.update(_branch(cls, leaves))
else:
branch = (
{
root,
}
if include_leaves
else set()
)
return branch
if isinstance(root, str):
root = self.get_by_label(root)
leaves = set(
self.get_by_label(leaf) if isinstance(leaf, str) else leaf
for leaf in leaves
)
leaves.discard(root)
if exclude:
exclude = set(
self.get_by_label(e) if isinstance(e, str) else e
for e in exclude
)
leaves.update(exclude)
branch = _branch(root, leaves)
# Exclude all descendants of any leaf
if strict_leaves:
descendants = root.descendants()
for leaf in leaves:
if leaf in descendants:
branch.difference_update(
leaf.descendants(include_self=False)
)
if exclude:
branch.difference_update(exclude)
# Sort according to depth, then by label
if sort:
branch = sorted(
sorted(branch, key=asstring),
key=lambda x: len(x.mro()),
)
return branch
get_by_label(self, label, label_annotations=None, prefix=None, imported=True, colon_in_label=None)
¶
Returns entity with label annotation label.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
label |
str |
label so serach for. May be written as 'label' or 'prefix:label'. get_by_label('prefix:label') == get_by_label('label', prefix='prefix'). |
required |
label_annotations |
str |
a sequence of label annotation names to look up.
Defaults to the |
None |
prefix |
str |
if provided, it should be the last component of the base iri of an ontology (with trailing slash (/) or hash (#) stripped off). The search for a matching label will be limited to this namespace. |
None |
imported |
bool |
Whether to also look for |
True |
colon_in_label |
bool |
Whether to accept colon (:) in a label or name-part
of IRI. Defaults to the |
None |
If several entities have the same label, only the one which is found first is returned.Use get_by_label_all() to get all matches.
Note, if different prefixes are provided in the label and via
the prefix argument a warning will be issued and the
prefix argument will take precedence.
A NoSuchLabelError is raised if label cannot be found.
Source code in ontopy/ontology.py
def get_by_label(
self,
label: str,
label_annotations: str = None,
prefix: str = None,
imported: bool = True,
colon_in_label: bool = None,
):
"""Returns entity with label annotation `label`.
Args:
label: label so serach for.
May be written as 'label' or 'prefix:label'.
get_by_label('prefix:label') ==
get_by_label('label', prefix='prefix').
label_annotations: a sequence of label annotation names to look up.
Defaults to the `label_annotations` property.
prefix: if provided, it should be the last component of
the base iri of an ontology (with trailing slash (/) or hash
(#) stripped off). The search for a matching label will be
limited to this namespace.
imported: Whether to also look for `label` in imported ontologies.
colon_in_label: Whether to accept colon (:) in a label or name-part
of IRI. Defaults to the `colon_in_label` property of `self`.
Setting this true cannot be combined with `prefix`.
If several entities have the same label, only the one which is
found first is returned.Use get_by_label_all() to get all matches.
Note, if different prefixes are provided in the label and via
the `prefix` argument a warning will be issued and the
`prefix` argument will take precedence.
A NoSuchLabelError is raised if `label` cannot be found.
"""
# pylint: disable=too-many-arguments,too-many-branches,invalid-name
if not isinstance(label, str):
raise TypeError(
f"Invalid label definition, must be a string: {label!r}"
)
if self._label_annotations is None:
for iri in DEFAULT_LABEL_ANNOTATIONS:
try:
self.add_label_annotation(iri)
except ValueError:
pass
if colon_in_label is None:
colon_in_label = self._colon_in_label
if colon_in_label:
if prefix:
raise ValueError(
"`prefix` cannot be combined with `colon_in_label`"
)
else:
splitlabel = label.split(":", 1)
if len(splitlabel) == 2 and not splitlabel[1].startswith("//"):
label = splitlabel[1]
if prefix and prefix != splitlabel[0]:
warnings.warn(
f"Prefix given both as argument ({prefix}) "
f"and in label ({splitlabel[0]}). "
"Prefix given in argument takes presendence "
)
if not prefix:
prefix = splitlabel[0]
if prefix:
entitylist = self.get_by_label_all(
label,
label_annotations=label_annotations,
prefix=prefix,
)
if len(entitylist) > 0:
return entitylist[0]
raise NoSuchLabelError(
f"No label annotations matches {label!r} with prefix "
f"{prefix!r}"
)
# Label is a full IRI
entity = self.world[label]
if entity:
return entity
# First entity with matching label annotation
annotation_ids = (
(self._abbreviate(ann, False) for ann in label_annotations)
if label_annotations
else (ann.storid for ann in self.label_annotations)
)
get_triples = (
self.world._get_data_triples_spod_spod
if imported
else self._get_data_triples_spod_spod
)
for annotation_id in annotation_ids:
for s, _, _, _ in get_triples(None, annotation_id, label, None):
return self.world[self._unabbreviate(s)]
# Special labels
if self._special_labels and label in self._special_labels:
return self._special_labels[label]
# Check if label is a name under base_iri
entity = self.world[self.base_iri + label]
if entity:
return entity
# Check if label is a name in any namespace
for namespace in self._namespaces.keys():
entity = self.world[namespace + label]
if entity:
return entity
raise NoSuchLabelError(f"No label annotations matches '{label}'")
get_by_label_all(self, label, label_annotations=None, prefix=None)
¶
Like get_by_label(), but returns a list with all matching labels.
Returns an empty list if no matches could be found.
Note¶
The current implementation also supports "*" as a wildcard matching any number of characters. This may change in the future.
Source code in ontopy/ontology.py
def get_by_label_all(self, label, label_annotations=None, prefix=None):
"""Like get_by_label(), but returns a list with all matching labels.
Returns an empty list if no matches could be found.
Note
----
The current implementation also supports "*" as a wildcard
matching any number of characters. This may change in the future.
"""
if not isinstance(label, str):
raise TypeError(
f"Invalid label definition, " f"must be a string: {label!r}"
)
if " " in label:
raise ValueError(
f"Invalid label definition, {label!r} contains spaces."
)
if label_annotations is None:
annotations = (_.name for _ in self.label_annotations)
else:
annotations = (
_.name if hasattr(_, "storid") else _ for _ in label_annotations
)
entity = self.world.search(**{next(annotations): label})
for key in annotations:
entity.extend(self.world.search(**{key: label}))
if self._special_labels and label in self._special_labels:
entity.append(self._special_labels[label])
entity_accessed_directly = self.world[self.base_iri + label]
if entity_accessed_directly and entity_accessed_directly not in entity:
entity.append(entity_accessed_directly)
if prefix:
return [_ for _ in entity if _.namespace.ontology.prefix == prefix]
return entity
get_descendants(self, classes, generations=None, common=False)
¶
Return descendants/subclasses of all classes in classes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
classes |
Union[List, ThingClass] |
class(es) for which descendants are desired. |
required |
common |
bool |
whether to only return descendants common to all classes. |
False |
generations |
int |
Include this number of generations, default is all. |
None |
Returns:
| Type | Description |
|---|---|
set |
A set of descendants for given number of generations. If 'common'=True, the common descendants are returned within the specified number of generations. 'generations' defaults to all. |
Source code in ontopy/ontology.py
def get_descendants(
self,
classes: "Union[List, ThingClass]",
generations: int = None,
common: bool = False,
) -> set:
"""Return descendants/subclasses of all classes in `classes`.
Args:
classes: class(es) for which descendants are desired.
common: whether to only return descendants common to all classes.
generations: Include this number of generations, default is all.
Returns:
A set of descendants for given number of generations.
If 'common'=True, the common descendants are returned
within the specified number of generations.
'generations' defaults to all.
"""
if not isinstance(classes, Iterable):
classes = [classes]
descendants = {name: [] for name in classes}
def _children_recursively(num, newentity, parent, descendants):
"""Helper function to get all children up to generation."""
for child in self.get_children_of(newentity):
descendants[parent].append(child)
if num < generations:
_children_recursively(num + 1, child, parent, descendants)
if generations == 0:
return set()
if not generations:
for entity in classes:
descendants[entity] = entity.descendants()
# only include proper descendants
descendants[entity].remove(entity)
else:
for entity in classes:
_children_recursively(1, entity, entity, descendants)
results = descendants.values()
if common is True:
return set.intersection(*map(set, results))
return set(flatten(results))
get_entities(self, imported=True, classes=True, individuals=True, object_properties=True, data_properties=True, annotation_properties=True)
¶
Return a generator over (optionally) all classes, individuals, object_properties, data_properties and annotation_properties.
If imported is True, entities in imported ontologies will also
be included.
Source code in ontopy/ontology.py
def get_entities( # pylint: disable=too-many-arguments
self,
imported=True,
classes=True,
individuals=True,
object_properties=True,
data_properties=True,
annotation_properties=True,
):
"""Return a generator over (optionally) all classes, individuals,
object_properties, data_properties and annotation_properties.
If `imported` is `True`, entities in imported ontologies will also
be included.
"""
generator = []
if classes:
generator.append(self.classes(imported))
if individuals:
generator.append(self.individuals(imported))
if object_properties:
generator.append(self.object_properties(imported))
if data_properties:
generator.append(self.data_properties(imported))
if annotation_properties:
generator.append(self.annotation_properties(imported))
for entity in itertools.chain(*generator):
yield entity
get_graph(self, **kwargs)
¶
Returns a new graph object. See emmo.graph.OntoGraph.
Note that this method requires the Python graphviz package.
Source code in ontopy/ontology.py
def get_graph(self, **kwargs):
"""Returns a new graph object. See emmo.graph.OntoGraph.
Note that this method requires the Python graphviz package.
"""
# pylint: disable=import-outside-toplevel,cyclic-import
from ontopy.graph import OntoGraph
return OntoGraph(self, **kwargs)
get_imported_ontologies(self, recursive=False)
¶
Return a list with imported ontologies.
If recursive is True, ontologies imported by imported ontologies
are also returned.
Source code in ontopy/ontology.py
def get_imported_ontologies(self, recursive=False):
"""Return a list with imported ontologies.
If `recursive` is `True`, ontologies imported by imported ontologies
are also returned.
"""
def rec_imported(onto):
for ontology in onto.imported_ontologies:
if ontology not in imported:
imported.add(ontology)
rec_imported(ontology)
if recursive:
imported = set()
rec_imported(self)
return list(imported)
return self.imported_ontologies
get_relations(self)
¶
Returns a generator for all relations.
Source code in ontopy/ontology.py
def get_relations(self):
"""Returns a generator for all relations."""
warnings.warn(
"Ontology.get_relations() is deprecated. Use "
"onto.object_properties() instead.",
DeprecationWarning,
)
return self.object_properties()
get_root_classes(self, imported=False)
¶
Returns a list or root classes.
Source code in ontopy/ontology.py
def get_root_classes(self, imported=False):
"""Returns a list or root classes."""
return [
cls
for cls in self.classes(imported=imported)
if not cls.ancestors().difference(set([cls, owlready2.Thing]))
]
get_root_data_properties(self, imported=False)
¶
Returns a list of root object properties.
Source code in ontopy/ontology.py
def get_root_data_properties(self, imported=False):
"""Returns a list of root object properties."""
props = set(self.data_properties(imported=imported))
return [p for p in props if not props.intersection(p.is_a)]
get_root_object_properties(self, imported=False)
¶
Returns a list of root object properties.
Source code in ontopy/ontology.py
def get_root_object_properties(self, imported=False):
"""Returns a list of root object properties."""
props = set(self.object_properties(imported=imported))
return [p for p in props if not props.intersection(p.is_a)]
get_roots(self, imported=False)
¶
Returns all class, object_property and data_property roots.
Source code in ontopy/ontology.py
def get_roots(self, imported=False):
"""Returns all class, object_property and data_property roots."""
roots = self.get_root_classes(imported=imported)
roots.extend(self.get_root_object_properties(imported=imported))
roots.extend(self.get_root_data_properties(imported=imported))
return roots
get_unabbreviated_triples(self, subject=None, predicate=None, obj=None, blank=None)
¶
Returns all matching triples unabbreviated.
If blank is given, it will be used to represent blank nodes.
Source code in ontopy/ontology.py
def get_unabbreviated_triples(
self, subject=None, predicate=None, obj=None, blank=None
):
"""Returns all matching triples unabbreviated.
If `blank` is given, it will be used to represent blank nodes.
"""
# pylint: disable=invalid-name
return _get_unabbreviated_triples(
self, subject=subject, predicate=predicate, obj=obj, blank=blank
)
get_version(self, as_iri=False)
¶
Returns the version number of the ontology as inferred from the owl:versionIRI tag or, if owl:versionIRI is not found, from owl:versionINFO.
If as_iri is True, the full versionIRI is returned.
Source code in ontopy/ontology.py
def get_version(self, as_iri=False) -> str:
"""Returns the version number of the ontology as inferred from the
owl:versionIRI tag or, if owl:versionIRI is not found, from
owl:versionINFO.
If `as_iri` is True, the full versionIRI is returned.
"""
version_iri_storid = self.world._abbreviate(
"http://www.w3.org/2002/07/owl#versionIRI"
)
tokens = self.get_triples(s=self.storid, p=version_iri_storid)
if (not tokens) and (as_iri is True):
raise TypeError(
"No owl:versionIRI "
f"in Ontology {self.base_iri!r}. "
"Search for owl:versionInfo with as_iri=False"
)
if tokens:
_, _, obj = tokens[0]
version_iri = self.world._unabbreviate(obj)
if as_iri:
return version_iri
return infer_version(self.base_iri, version_iri)
version_info_storid = self.world._abbreviate(
"http://www.w3.org/2002/07/owl#versionInfo"
)
tokens = self.get_triples(s=self.storid, p=version_info_storid)
if not tokens:
raise TypeError(
"No versionIRI or versionInfo " f"in Ontology {self.base_iri!r}"
)
_, _, version_info = tokens[0]
return version_info.strip('"').strip("'")
get_wu_palmer_measure(self, cls1, cls2)
¶
Return Wu-Palmer measure for semantic similarity.
Returns Wu-Palmer measure for semantic similarity between two concepts. Wu, Palmer; ACL 94: Proceedings of the 32nd annual meeting on Association for Computational Linguistics, June 1994.
Source code in ontopy/ontology.py
def get_wu_palmer_measure(self, cls1, cls2):
"""Return Wu-Palmer measure for semantic similarity.
Returns Wu-Palmer measure for semantic similarity between
two concepts.
Wu, Palmer; ACL 94: Proceedings of the 32nd annual meeting on
Association for Computational Linguistics, June 1994.
"""
cca = self.closest_common_ancestor(cls1, cls2)
ccadepth = self.number_of_generations(cca, self.Thing)
generations1 = self.number_of_generations(cls1, cca)
generations2 = self.number_of_generations(cls2, cca)
return 2 * ccadepth / (generations1 + generations2 + 2 * ccadepth)
individuals(self, imported=False)
¶
Returns an generator over all individuals.
If imported is True, will imported individuals are also returned.
Source code in ontopy/ontology.py
def individuals(self, imported=False):
"""Returns an generator over all individuals.
If `imported` is `True`, will imported individuals are also returned.
"""
if imported:
return self.world.individuals()
return super().individuals()
is_defined(self, entity)
¶
Returns true if the entity is a defined class.
Deprecated, use the is_defined property of the classes
(ThingClass subclasses) instead.
Source code in ontopy/ontology.py
def is_defined(self, entity):
"""Returns true if the entity is a defined class.
Deprecated, use the `is_defined` property of the classes
(ThingClass subclasses) instead.
"""
warnings.warn(
"This method is deprecated. Use the `is_defined` property of "
"the classes instad.",
DeprecationWarning,
stacklevel=2,
)
if isinstance(entity, str):
entity = self.get_by_label(entity)
return hasattr(entity, "equivalent_to") and bool(entity.equivalent_to)
is_individual(self, entity)
¶
Returns true if entity is an individual.
Source code in ontopy/ontology.py
def is_individual(self, entity):
"""Returns true if entity is an individual."""
if isinstance(entity, str):
entity = self.get_by_label(entity)
return isinstance(entity, owlready2.Thing)
load(self, only_local=False, filename=None, format=None, reload=None, reload_if_newer=False, url_from_catalog=None, catalog_file='catalog-v001.xml', emmo_based=True, prefix=None, prefix_emmo=None, **kwargs)
¶
Load the ontology.
Parameters¶
bool
Whether to only read local files. This requires that you have appended the path to the ontology to owlready2.onto_path.
str
Path to file to load the ontology from. Defaults to base_iri
provided to get_ontology().
str
Format of filename. Default is inferred from filename
extension.
bool
Whether to reload the ontology if it is already loaded.
bool
Whether to reload the ontology if the source has changed since last time it was loaded.
bool | None
Whether to use catalog file to resolve the location of base_iri.
If None, the catalog file is used if it exists in the same
directory as filename.
str
Name of Protègè catalog file in the same folder as the
ontology. This option is used together with only_local and
defaults to "catalog-v001.xml".
bool
Whether this is an EMMO-based ontology or not, default True.
prefix: defaults to self.get_namespace.name if
bool, default None. If emmo_based is True it
defaults to True and sets the prefix of all imported ontologies with base_iri starting with 'http://emmo.info/emmo' to emmo
Kwargs
Additional keyword arguments are passed on to owlready2.Ontology.load().
Source code in ontopy/ontology.py
def load( # pylint: disable=too-many-arguments,arguments-renamed
self,
only_local=False,
filename=None,
format=None, # pylint: disable=redefined-builtin
reload=None,
reload_if_newer=False,
url_from_catalog=None,
catalog_file="catalog-v001.xml",
emmo_based=True,
prefix=None,
prefix_emmo=None,
**kwargs,
):
"""Load the ontology.
Parameters
----------
only_local: bool
Whether to only read local files. This requires that you
have appended the path to the ontology to owlready2.onto_path.
filename: str
Path to file to load the ontology from. Defaults to `base_iri`
provided to get_ontology().
format: str
Format of `filename`. Default is inferred from `filename`
extension.
reload: bool
Whether to reload the ontology if it is already loaded.
reload_if_newer: bool
Whether to reload the ontology if the source has changed since
last time it was loaded.
url_from_catalog: bool | None
Whether to use catalog file to resolve the location of `base_iri`.
If None, the catalog file is used if it exists in the same
directory as `filename`.
catalog_file: str
Name of Protègè catalog file in the same folder as the
ontology. This option is used together with `only_local` and
defaults to "catalog-v001.xml".
emmo_based: bool
Whether this is an EMMO-based ontology or not, default `True`.
prefix: defaults to self.get_namespace.name if
prefix_emmo: bool, default None. If emmo_based is True it
defaults to True and sets the prefix of all imported ontologies
with base_iri starting with 'http://emmo.info/emmo' to emmo
kwargs:
Additional keyword arguments are passed on to
owlready2.Ontology.load().
"""
# TODO: make sure that `only_local` argument is respected...
if self.loaded:
return self
self._load(
only_local=only_local,
filename=filename,
format=format,
reload=reload,
reload_if_newer=reload_if_newer,
url_from_catalog=url_from_catalog,
catalog_file=catalog_file,
**kwargs,
)
# Enable optimised search by get_by_label()
if self._special_labels is None and emmo_based:
for iri in DEFAULT_LABEL_ANNOTATIONS:
self.add_label_annotation(iri)
top = self.world["http://www.w3.org/2002/07/owl#topObjectProperty"]
self._special_labels = {
"Thing": owlready2.Thing,
"Nothing": owlready2.Nothing,
"topObjectProperty": top,
"owl:Thing": owlready2.Thing,
"owl:Nothing": owlready2.Nothing,
"owl:topObjectProperty": top,
}
# set prefix if another prefix is desired
# if we do this, shouldn't we make the name of all
# entities of the given ontology to the same?
if prefix:
self.prefix = prefix
else:
self.prefix = self.name
if emmo_based and prefix_emmo is None:
prefix_emmo = True
if prefix_emmo:
self.set_common_prefix()
return self
new_entity(self, name, parent)
¶
Create and return new entity
Makes a new entity in the ontology with given parent(s). Return the new entity.
Throws exception if name consists of more than one word.
Source code in ontopy/ontology.py
def new_entity(
self, name: str, parent: Union[ThingClass, Iterable]
) -> ThingClass:
"""Create and return new entity
Makes a new entity in the ontology with given parent(s).
Return the new entity.
Throws exception if name consists of more than one word.
"""
if " " in name:
raise LabelDefinitionError(
f"Error in label name definition '{name}': "
f"Label consists of more than one word."
)
parents = tuple(parent) if isinstance(parent, Iterable) else (parent,)
for thing in parents:
if not isinstance(thing, owlready2.ThingClass):
raise ThingClassDefinitionError(
f"Error in parent definition: "
f"'{thing}' is not an owlready2.ThingClass."
)
with self:
entity = types.new_class(name, parents)
return entity
number_of_generations(self, descendant, ancestor)
¶
Return shortest distance from ancestor to descendant
Source code in ontopy/ontology.py
def number_of_generations(self, descendant, ancestor):
"""Return shortest distance from ancestor to descendant"""
if ancestor not in descendant.ancestors():
raise ValueError("Descendant is not a descendant of ancestor")
return self._number_of_generations(descendant, ancestor, 0)
object_properties(self, imported=False)
¶
Returns an generator over all object properties.
If imported is true, will imported object properties are also
returned.
Source code in ontopy/ontology.py
def object_properties(self, imported=False):
"""Returns an generator over all object properties.
If `imported` is true, will imported object properties are also
returned.
"""
if imported:
return self.world.object_properties()
return super().object_properties()
remove_label_annotation(self, iri)
¶
Removes label annotation used by get_by_label().
May be provided either as an IRI or as its owlready2 representation.
Source code in ontopy/ontology.py
def remove_label_annotation(self, iri):
"""Removes label annotation used by get_by_label().
May be provided either as an IRI or as its owlready2 representation.
"""
label_annotation = iri if hasattr(iri, "storid") else self.world[iri]
if not label_annotation:
raise ValueError(f"IRI not in ontology: {iri}")
self._label_annotations.remove(label_annotation)
rename_entities(self, annotations=('prefLabel', 'label', 'altLabel'))
¶
Set name of all entities to the first non-empty annotation in
annotations.
Warning, this method changes all IRIs in the ontology. However, it may be useful to make the ontology more readable and to work with it together with a triple store.
Source code in ontopy/ontology.py
def rename_entities(
self,
annotations=("prefLabel", "label", "altLabel"),
):
"""Set `name` of all entities to the first non-empty annotation in
`annotations`.
Warning, this method changes all IRIs in the ontology. However,
it may be useful to make the ontology more readable and to work
with it together with a triple store.
"""
for entity in self.get_entities():
for annotation in annotations:
if hasattr(entity, annotation):
name = getattr(entity, annotation).first()
if name:
entity.name = name
break
save(self, filename=None, format=None, dir='.', mkdir=False, overwrite=False, recursive=False, squash=False, write_catalog_file=False, append_catalog=False, catalog_file='catalog-v001.xml')
¶
Writes the ontology to file.
Parameters¶
None | str | Path
Name of file to write to. If None, it defaults to the name
of the ontology with format as file extension.
str
Output format. The default is to infer it from filename.
str | Path
If filename is a relative path, it is a relative path to dir.
bool
Whether to create output directory if it does not exists.
bool
If true and filename exists, remove the existing file before
saving. The default is to append to an existing ontology.
bool
Whether to save imported ontologies recursively. This is
commonly combined with filename=None, dir and mkdir.
bool
If true, rdflib will be used to save the current ontology
together with all its sub-ontologies into filename.
It make no sense to combine this with recursive.
bool
Whether to also write a catalog file to disk.
bool
Whether to append to an existing catalog file.
str | Path
Name of catalog file. If not an absolute path, it is prepended
to dir.
Source code in ontopy/ontology.py
def save(
self,
filename=None,
format=None,
dir=".",
mkdir=False,
overwrite=False,
recursive=False,
squash=False,
write_catalog_file=False,
append_catalog=False,
catalog_file="catalog-v001.xml",
):
"""Writes the ontology to file.
Parameters
----------
filename: None | str | Path
Name of file to write to. If None, it defaults to the name
of the ontology with `format` as file extension.
format: str
Output format. The default is to infer it from `filename`.
dir: str | Path
If `filename` is a relative path, it is a relative path to `dir`.
mkdir: bool
Whether to create output directory if it does not exists.
owerwrite: bool
If true and `filename` exists, remove the existing file before
saving. The default is to append to an existing ontology.
recursive: bool
Whether to save imported ontologies recursively. This is
commonly combined with `filename=None`, `dir` and `mkdir`.
squash: bool
If true, rdflib will be used to save the current ontology
together with all its sub-ontologies into `filename`.
It make no sense to combine this with `recursive`.
write_catalog_file: bool
Whether to also write a catalog file to disk.
append_catalog: bool
Whether to append to an existing catalog file.
catalog_file: str | Path
Name of catalog file. If not an absolute path, it is prepended
to `dir`.
"""
# pylint: disable=redefined-builtin,too-many-arguments
# pylint: disable=too-many-statements,too-many-branches
# pylint: disable=too-many-locals,arguments-renamed
if not _validate_installed_version(
package="rdflib", min_version="6.0.0"
) and format == FMAP.get("ttl", ""):
from rdflib import ( # pylint: disable=import-outside-toplevel
__version__ as __rdflib_version__,
)
warnings.warn(
IncompatibleVersion(
"To correctly convert to Turtle format, rdflib must be "
"version 6.0.0 or greater, however, the detected rdflib "
"version used by your Python interpreter is "
f"{__rdflib_version__!r}. For more information see the "
"'Known issues' section of the README."
)
)
revmap = {value: key for key, value in FMAP.items()}
if filename is None:
if format:
fmt = revmap.get(format, format)
filename = f"{self.name}.{fmt}"
else:
raise TypeError("`filename` and `format` cannot both be None.")
filename = os.path.join(dir, filename)
dir = Path(filename).resolve().parent
if mkdir:
outdir = Path(filename).parent.resolve()
if not outdir.exists():
outdir.mkdir(parents=True)
if not format:
format = guess_format(filename, fmap=FMAP)
fmt = revmap.get(format, format)
if overwrite and filename and os.path.exists(filename):
os.remove(filename)
EMMO = rdflib.Namespace( # pylint:disable=invalid-name
"http://emmo.info/emmo#"
)
if recursive:
if squash:
raise ValueError(
"`recursive` and `squash` should not both be true"
)
base = self.base_iri.rstrip("#/")
for onto in self.imported_ontologies:
obase = onto.base_iri.rstrip("#/")
newdir = Path(dir) / os.path.relpath(obase, base)
onto.save(
filename=None,
format=format,
dir=newdir.resolve(),
mkdir=mkdir,
overwrite=overwrite,
recursive=recursive,
squash=squash,
write_catalog_file=write_catalog_file,
append_catalog=append_catalog,
catalog_file=catalog_file,
)
if squash:
from rdflib import ( # pylint:disable=import-outside-toplevel
URIRef,
RDF,
OWL,
)
graph = self.world.as_rdflib_graph()
graph.namespace_manager.bind("emmo", EMMO)
# Remove anonymous namespace and imports
graph.remove((URIRef("http://anonymous"), RDF.type, OWL.Ontology))
imports = list(graph.triples((None, OWL.imports, None)))
for triple in imports:
graph.remove(triple)
graph.serialize(destination=filename, format=format)
elif format in OWLREADY2_FORMATS:
super().save(file=filename, format=fmt)
else:
# The try-finally clause is needed for cleanup and because
# we have to provide delete=False to NamedTemporaryFile
# since Windows does not allow to reopen an already open
# file.
try:
with tempfile.NamedTemporaryFile(
suffix=".owl", delete=False
) as handle:
tmpfile = handle.name
super().save(tmpfile, format="rdfxml")
graph = rdflib.Graph()
graph.parse(tmpfile, format="xml")
graph.serialize(destination=filename, format=format)
finally:
os.remove(tmpfile)
if write_catalog_file:
mappings = {}
base = self.base_iri.rstrip("#/")
def append(onto):
obase = onto.base_iri.rstrip("#/")
newdir = Path(dir) / os.path.relpath(obase, base)
newpath = newdir.resolve() / f"{onto.name}.{fmt}"
relpath = os.path.relpath(newpath, dir)
mappings[onto.get_version(as_iri=True)] = str(relpath)
for imported in onto.imported_ontologies:
append(imported)
if recursive:
append(self)
write_catalog(
mappings,
output=catalog_file,
directory=dir,
append=append_catalog,
)
set_common_prefix(self, iri_base='http://emmo.info/emmo', prefix='emmo')
¶
Set a common prefix for all imported ontologies with the same first part of the base_iri.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
iri_base |
str |
The start of the base_iri to look for. Defaults to the emmo base_iri http://emmo.info/emmo |
'http://emmo.info/emmo' |
prefix |
str |
the desired prefix. Defaults to emmo. |
'emmo' |
Source code in ontopy/ontology.py
def set_common_prefix(
self,
iri_base: str = "http://emmo.info/emmo",
prefix: str = "emmo",
) -> None:
"""Set a common prefix for all imported ontologies
with the same first part of the base_iri.
Args:
iri_base: The start of the base_iri to look for. Defaults to
the emmo base_iri http://emmo.info/emmo
prefix: the desired prefix. Defaults to emmo.
"""
if self.base_iri.startswith(iri_base):
self.prefix = prefix
for onto in self.imported_ontologies:
onto.set_common_prefix(iri_base=iri_base, prefix=prefix)
set_version(self, version=None, version_iri=None)
¶
Assign version to ontology by asigning owl:versionIRI.
If version but not version_iri is provided, the version
IRI will be the combination of base_iri and version.
Source code in ontopy/ontology.py
def set_version(self, version=None, version_iri=None):
"""Assign version to ontology by asigning owl:versionIRI.
If `version` but not `version_iri` is provided, the version
IRI will be the combination of `base_iri` and `version`.
"""
_version_iri = "http://www.w3.org/2002/07/owl#versionIRI"
version_iri_storid = self.world._abbreviate(_version_iri)
if self._has_obj_triple_spo( # pylint: disable=unexpected-keyword-arg
# For some reason _has_obj_triples_spo exists in both
# owlready2.namespace.Namespace (with arguments subject/predicate)
# and in owlready2.triplelite._GraphManager (with arguments s/p)
# owlready2.Ontology inherits from Namespace directly
# and pylint checks that.
# It actually accesses the one in triplelite.
# subject=self.storid, predicate=version_iri_storid
s=self.storid,
p=version_iri_storid,
):
self._del_obj_triple_spo(s=self.storid, p=version_iri_storid)
if not version_iri:
if not version:
raise TypeError(
"Either `version` or `version_iri` must be provided"
)
head, tail = self.base_iri.rstrip("#/").rsplit("/", 1)
version_iri = "/".join([head, version, tail])
self._add_obj_triple_spo(
s=self.storid,
p=self.world._abbreviate(_version_iri),
o=self.world._abbreviate(version_iri),
)
sync_attributes(self, name_policy=None, name_prefix='', class_docstring='comment', sync_imported=False)
¶
This method is intended to be called after you have added new
classes (typically via Python) to make sure that attributes like
label and comments are defined.
If a class, object property, data property or annotation property in the current ontology has no label, the name of the corresponding Python class will be assigned as label.
If a class, object property, data property or annotation property has no comment, it will be assigned the docstring of the corresponding Python class.
name_policy specify wether and how the names in the ontology
should be updated. Valid values are:
None not changed
"uuid" name_prefix followed by a global unique id (UUID).
If the name is already valid accoridng to this standard
it will not be regenerated.
"sequential" name_prefix followed a sequantial number.
EMMO conventions imply name_policy=='uuid'.
If sync_imported is true, all imported ontologies are also
updated.
The class_docstring argument specifies the annotation that
class docstrings are mapped to. Defaults to "comment".
Source code in ontopy/ontology.py
def sync_attributes( # pylint: disable=too-many-branches
self,
name_policy=None,
name_prefix="",
class_docstring="comment",
sync_imported=False,
):
"""This method is intended to be called after you have added new
classes (typically via Python) to make sure that attributes like
`label` and `comments` are defined.
If a class, object property, data property or annotation
property in the current ontology has no label, the name of
the corresponding Python class will be assigned as label.
If a class, object property, data property or annotation
property has no comment, it will be assigned the docstring of
the corresponding Python class.
`name_policy` specify wether and how the names in the ontology
should be updated. Valid values are:
None not changed
"uuid" `name_prefix` followed by a global unique id (UUID).
If the name is already valid accoridng to this standard
it will not be regenerated.
"sequential" `name_prefix` followed a sequantial number.
EMMO conventions imply ``name_policy=='uuid'``.
If `sync_imported` is true, all imported ontologies are also
updated.
The `class_docstring` argument specifies the annotation that
class docstrings are mapped to. Defaults to "comment".
"""
for cls in itertools.chain(
self.classes(),
self.object_properties(),
self.data_properties(),
self.annotation_properties(),
):
if not hasattr(cls, "prefLabel"):
# no prefLabel - create new annotation property..
with self:
# pylint: disable=invalid-name,missing-class-docstring
# pylint: disable=unused-variable
class prefLabel(owlready2.label):
pass
cls.prefLabel = [locstr(cls.__name__, lang="en")]
elif not cls.prefLabel:
cls.prefLabel.append(locstr(cls.__name__, lang="en"))
if class_docstring and hasattr(cls, "__doc__") and cls.__doc__:
getattr(cls, class_docstring).append(
locstr(inspect.cleandoc(cls.__doc__), lang="en")
)
for ind in self.individuals():
if not hasattr(ind, "prefLabel"):
# no prefLabel - create new annotation property..
with self:
# pylint: disable=invalid-name,missing-class-docstring
# pylint: disable=function-redefined
class prefLabel(owlready2.label):
iri = "http://www.w3.org/2004/02/skos/core#prefLabel"
ind.prefLabel = [locstr(ind.name, lang="en")]
elif not ind.prefLabel:
ind.prefLabel.append(locstr(ind.name, lang="en"))
chain = itertools.chain(
self.classes(),
self.individuals(),
self.object_properties(),
self.data_properties(),
self.annotation_properties(),
)
if name_policy == "uuid":
for obj in chain:
try:
# Passing the following means that the name is valid
# and need not be regenerated.
if not obj.name.startswith(name_prefix):
raise ValueError
uuid.UUID(obj.name.lstrip(name_prefix), version=5)
except ValueError:
obj.name = name_prefix + str(
uuid.uuid5(uuid.NAMESPACE_DNS, obj.name)
)
elif name_policy == "sequential":
for obj in chain:
counter = 0
while f"{self.base_iri}{name_prefix}{counter}" in self:
counter += 1
obj.name = f"{name_prefix}{counter}"
elif name_policy is not None:
raise TypeError(f"invalid name_policy: {name_policy!r}")
if sync_imported:
for onto in self.imported_ontologies:
onto.sync_attributes()
sync_python_names(self, annotations=('prefLabel', 'label', 'altLabel'))
¶
Update the python_name attribute of all properties.
The python_name attribute will be set to the first non-empty
annotation in the sequence of annotations in annotations for
the property.
Source code in ontopy/ontology.py
def sync_python_names(self, annotations=("prefLabel", "label", "altLabel")):
"""Update the `python_name` attribute of all properties.
The python_name attribute will be set to the first non-empty
annotation in the sequence of annotations in `annotations` for
the property.
"""
def update(gen):
for prop in gen:
for annotation in annotations:
if hasattr(prop, annotation) and getattr(prop, annotation):
prop.python_name = getattr(prop, annotation).first()
break
update(
self.get_entities(
classes=False,
individuals=False,
object_properties=False,
data_properties=False,
)
)
update(
self.get_entities(
classes=False, individuals=False, annotation_properties=False
)
)
sync_reasoner(self, reasoner='FaCT++', include_imported=False, **kwargs)
¶
Update current ontology by running the given reasoner.
Supported values for reasoner are 'Pellet', 'HermiT' and 'FaCT++'.
If include_imported is true, the reasoner will also reason
over imported ontologies. Note that this may be very slow
with Pellet and HermiT.
Keyword arguments are passed to the underlying owlready2 function.
Source code in ontopy/ontology.py
def sync_reasoner(
self, reasoner="FaCT++", include_imported=False, **kwargs
):
"""Update current ontology by running the given reasoner.
Supported values for `reasoner` are 'Pellet', 'HermiT' and 'FaCT++'.
If `include_imported` is true, the reasoner will also reason
over imported ontologies. Note that this may be **very** slow
with Pellet and HermiT.
Keyword arguments are passed to the underlying owlready2 function.
"""
if reasoner == "FaCT++":
sync = sync_reasoner_factpp
elif reasoner == "Pellet":
sync = owlready2.sync_reasoner_pellet
elif reasoner == "HermiT":
sync = owlready2.sync_reasoner_hermit
else:
raise ValueError(
f"unknown reasoner {reasoner!r}. Supported reasoners "
'are "Pellet", "HermiT" and "FaCT++".'
)
# For some reason we must visit all entities once before running
# the reasoner...
list(self.get_entities())
with self:
if include_imported:
sync(self.world, **kwargs)
else:
sync(self, **kwargs)
World (World)
¶
A subclass of owlready2.World.
Source code in ontopy/ontology.py
class World(owlready2.World):
"""A subclass of owlready2.World."""
def __init__(self, *args, **kwargs):
# Caches stored in the world
self._cached_catalogs = {} # maps url to (mtime, iris, dirs)
self._iri_mappings = {} # all iri mappings loaded so far
super().__init__(*args, **kwargs)
def get_ontology(self, base_iri="emmo-inferred"):
"""Returns a new Ontology from `base_iri`.
The `base_iri` argument may be one of:
- valid URL (possible excluding final .owl or .ttl)
- file name (possible excluding final .owl or .ttl)
- "emmo": load latest version of asserted EMMO
- "emmo-inferred": load latest version of inferred EMMO
(default)
- "emmo-development": load latest inferred development version
of EMMO. Until first stable release emmo-inferred and
emmo-development will be the same.
"""
base_iri = base_iri.as_uri() if isinstance(base_iri, Path) else base_iri
if base_iri == "emmo":
base_iri = (
"http://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl"
)
elif base_iri == "emmo-inferred":
base_iri = (
"https://emmo-repo.github.io/versions/1.0.0-beta4/"
"emmo-inferred.ttl"
)
elif base_iri == "emmo-development":
base_iri = (
"https://emmo-repo.github.io/versions/1.0.0-beta4/"
"emmo-inferred.ttl"
)
if base_iri in self.ontologies:
onto = self.ontologies[base_iri]
elif base_iri + "#" in self.ontologies:
onto = self.ontologies[base_iri + "#"]
elif base_iri + "/" in self.ontologies:
onto = self.ontologies[base_iri + "/"]
else:
if os.path.exists(base_iri):
iri = os.path.abspath(base_iri)
elif os.path.exists(base_iri + ".ttl"):
iri = os.path.abspath(base_iri + ".ttl")
elif os.path.exists(base_iri + ".owl"):
iri = os.path.abspath(base_iri + ".owl")
else:
iri = base_iri
if iri[-1] not in "/#":
iri += "#"
onto = Ontology(self, iri)
return onto
def get_unabbreviated_triples(
self, subject=None, predicate=None, obj=None, blank=None
):
# pylint: disable=invalid-name
"""Returns all triples unabbreviated.
If any of the `subject`, `predicate` or `obj` arguments are given,
only matching triples will be returned.
If `blank` is given, it will be used to represent blank nodes.
"""
return _get_unabbreviated_triples(
self, subject=subject, predicate=predicate, obj=obj, blank=blank
)
get_ontology(self, base_iri='emmo-inferred')
¶
Returns a new Ontology from base_iri.
The base_iri argument may be one of:
- valid URL (possible excluding final .owl or .ttl)
- file name (possible excluding final .owl or .ttl)
- "emmo": load latest version of asserted EMMO
- "emmo-inferred": load latest version of inferred EMMO
(default)
- "emmo-development": load latest inferred development version
of EMMO. Until first stable release emmo-inferred and
emmo-development will be the same.
Source code in ontopy/ontology.py
def get_ontology(self, base_iri="emmo-inferred"):
"""Returns a new Ontology from `base_iri`.
The `base_iri` argument may be one of:
- valid URL (possible excluding final .owl or .ttl)
- file name (possible excluding final .owl or .ttl)
- "emmo": load latest version of asserted EMMO
- "emmo-inferred": load latest version of inferred EMMO
(default)
- "emmo-development": load latest inferred development version
of EMMO. Until first stable release emmo-inferred and
emmo-development will be the same.
"""
base_iri = base_iri.as_uri() if isinstance(base_iri, Path) else base_iri
if base_iri == "emmo":
base_iri = (
"http://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl"
)
elif base_iri == "emmo-inferred":
base_iri = (
"https://emmo-repo.github.io/versions/1.0.0-beta4/"
"emmo-inferred.ttl"
)
elif base_iri == "emmo-development":
base_iri = (
"https://emmo-repo.github.io/versions/1.0.0-beta4/"
"emmo-inferred.ttl"
)
if base_iri in self.ontologies:
onto = self.ontologies[base_iri]
elif base_iri + "#" in self.ontologies:
onto = self.ontologies[base_iri + "#"]
elif base_iri + "/" in self.ontologies:
onto = self.ontologies[base_iri + "/"]
else:
if os.path.exists(base_iri):
iri = os.path.abspath(base_iri)
elif os.path.exists(base_iri + ".ttl"):
iri = os.path.abspath(base_iri + ".ttl")
elif os.path.exists(base_iri + ".owl"):
iri = os.path.abspath(base_iri + ".owl")
else:
iri = base_iri
if iri[-1] not in "/#":
iri += "#"
onto = Ontology(self, iri)
return onto
get_unabbreviated_triples(self, subject=None, predicate=None, obj=None, blank=None)
¶
Returns all triples unabbreviated.
If any of the subject, predicate or obj arguments are given,
only matching triples will be returned.
If blank is given, it will be used to represent blank nodes.
Source code in ontopy/ontology.py
def get_unabbreviated_triples(
self, subject=None, predicate=None, obj=None, blank=None
):
# pylint: disable=invalid-name
"""Returns all triples unabbreviated.
If any of the `subject`, `predicate` or `obj` arguments are given,
only matching triples will be returned.
If `blank` is given, it will be used to represent blank nodes.
"""
return _get_unabbreviated_triples(
self, subject=subject, predicate=predicate, obj=obj, blank=blank
)
flatten(items)
¶
Yield items from any nested iterable.
Source code in ontopy/ontology.py
def flatten(items):
"""Yield items from any nested iterable."""
for item in items:
if isinstance(item, Iterable) and not isinstance(item, (str, bytes)):
for sub_item in flatten(item):
yield sub_item
else:
yield item
get_ontology(*args, **kwargs)
¶
Returns a new Ontology from base_iri.
This is a convenient function for calling World.get_ontology().
Source code in ontopy/ontology.py
def get_ontology(*args, **kwargs):
"""Returns a new Ontology from `base_iri`.
This is a convenient function for calling World.get_ontology()."""
return World().get_ontology(*args, **kwargs)