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Simplified implementation of label_annotations.
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@jesper-friis
jesper-friis committed Aug 19, 2023
1 parent fb65d81 commit 09677a9
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Showing 3 changed files with 164 additions and 105 deletions.
234 changes: 143 additions & 91 deletions ontopy/ontology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@
)

if TYPE_CHECKING:
from typing import List
from typing import List, Sequence


# Default annotations to look up
Expand All @@ -76,18 +76,31 @@ def __init__(self, *args, **kwargs):
self._iri_mappings = {} # all iri mappings loaded so far
super().__init__(*args, **kwargs)

def get_ontology(self, base_iri="emmo-inferred"):
def get_ontology(
self,
base_iri: str = "emmo-inferred",
OntologyClass: "owlready2.Ontology" = None,
label_annotations: "Sequence" = None,
) -> "Ontology":
# pylint: disable=too-many-branches
"""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.
Arguments:
base_iri: The base IRI of the ontology. 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.
OntologyClass: If given and `base_iri` doesn't correspond
to an existing ontology, a new ontology is created of
this Ontology subclass.
label_annotations: Sequence of IRIs used for accessing
classes in the ontology. The default correspond to
skos:prefLabel, rdfs:label and skos:altLabel.
"""
base_iri = base_iri.as_uri() if isinstance(base_iri, Path) else base_iri

Expand Down Expand Up @@ -124,7 +137,14 @@ def get_ontology(self, base_iri="emmo-inferred"):

if iri[-1] not in "/#":
iri += "#"
onto = Ontology(self, iri)

if OntologyClass is None:
OntologyClass = Ontology

onto = OntologyClass(self, iri)

if label_annotations:
onto.label_annotations = list(label_annotations)

return onto

Expand All @@ -148,19 +168,10 @@ 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.label_annotations = DEFAULT_LABEL_ANNOTATIONS[:]
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

Expand Down Expand Up @@ -275,12 +286,13 @@ def get_unabbreviated_triples(

def set_default_label_annotations(self):
"""Sets the default label annotations."""
if self._label_annotations is None:
for iri in DEFAULT_LABEL_ANNOTATIONS:
try:
self.add_label_annotation(iri)
except ValueError:
pass
warnings.warn(
"Ontology.set_default_label_annotations() is deprecated. "
"Default label annotations are set by Ontology.__init__(). ",
DeprecationWarning,
stacklevel=2,
)
self.label_annotations = DEFAULT_LABEL_ANNOTATIONS[:]

def get_by_label(
self,
Expand Down Expand Up @@ -320,9 +332,12 @@ def get_by_label(
# 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}"
f"Invalid label definition, must be a string: '{label}'"
)

if label_annotations is None:
label_annotations = self.label_annotations

if colon_in_label is None:
colon_in_label = self._colon_in_label
if colon_in_label:
Expand Down Expand Up @@ -353,39 +368,28 @@ def get_by_label(
return entityset.pop()
if len(entityset) > 1:
raise AmbiguousLabelError(
f"Several entities have the same label {label!r} "
f"with prefix {prefix!r}."
f"Several entities have the same label '{label}' "
f"with prefix '{prefix}'."
)
raise NoSuchLabelError(
f"No label annotations matches for {label!r} "
f"with prefix {prefix!r}."
f"No label annotations matches for '{label}' "
f"with prefix '{prefix}'."
)

# Label is a full IRI
entity = self.world[label]
if entity:
return entity

# First entity with matching label annotation

if label_annotations:
annotation_ids = (
self._abbreviate(ann, False) for ann in label_annotations
)
elif self._label_annotations:
annotation_ids = (ann.storid for ann in self._label_annotations)
else:
annotation_ids = None

get_triples = (
self.world._get_data_triples_spod_spod
if imported
else self._get_data_triples_spod_spod
)
if annotation_ids:
for annotation_id in annotation_ids:
for s, _, _, _ in get_triples(None, annotation_id, label, None):
return self.world[self._unabbreviate(s)]

for storid in self._to_storids(label_annotations):
for s, _, _, _ in get_triples(None, storid, label, None):
return self.world[self._unabbreviate(s)]

# Special labels
if self._special_labels and label in self._special_labels:
Expand All @@ -396,10 +400,9 @@ def get_by_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:
# Check label is the name of an entity
for entity in self.get_entities(imported=imported):
if label == entity.name:
return entity

raise NoSuchLabelError(f"No label annotations matches '{label}'")
Expand All @@ -424,20 +427,28 @@ def get_by_label_all(self, label, label_annotations=None, prefix=None):
f"Invalid label definition, {label!r} contains spaces."
)

if label_annotations:
annotations = (
ann.name if hasattr(ann, "storid") else ann
for ann in label_annotations
)
elif self._label_annotations:
annotations = (ann.name for ann in self.label_annotations)
if label_annotations is None:
label_annotations = self.label_annotations

else:
annotations = None
entities = set()
if annotations:
for key in annotations:
entities.update(self.world.search(**{key: label}))
for storid in self._to_storids(label_annotations):
label_entity = self._unabbreviate(storid)
key = (
label_entity.name
if hasattr(label_entity, "name")
else label_entity
)
entities.update(self.world.search(**{key: label}))

# ALTERNATIVE IMPLEMENTATION THAT DOESN'T INVOLVE search().
# IT IS FASTER AND MIGHT AVOID SURPRICES. SHOULD WE ADD AN
# OPTION TO CHOOSE BETWEEN SEARCH() AND THIS IMPLEMENTATION?
# entities = set()
# for storid in self._to_storids(label_annotations):
# entities.update(
# self.world[self._unabbreviate(s)]
# for s, _, _, _ in get_triples(None, storid, label, None)
# )

if self._special_labels and label in self._special_labels:
entities.update(self._special_labels[label])
Expand All @@ -459,32 +470,71 @@ def get_by_label_all(self, label, label_annotations=None, prefix=None):
)
return entities

def add_label_annotation(self, iri):
"""Adds label annotation used by get_by_label().
def _to_storids(self, sequence, create_if_missing=False):
"""Return a list of storid's corresponding to the elements in the
sequence `sequence`.
The elements may be either be full IRIs (strings) or Owlready2
entities with an associated storid.
May be provided either as an IRI or as its owlready2 representation.
If `create_if_missing` is true, new Owlready2 entities will be
created for IRIs that not already are associated with an
entity. Otherwise such IRIs will be skipped in the returned
list.
"""
if not sequence:
return []
storids = []
for element in sequence:
if hasattr(element, "storid"):
storids.append(element.storid)
else:
storid = self.world._abbreviate(element, create_if_missing)
if storid:
storids.append(storid)
return storids

def _to_entities(self, sequence, create_if_missing=False):
"""Like _to_storids(), but return a list of entities corresponding
to the elements in `sequence`.
"""
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)
entities = []
for storid in self._to_storids(sequence, create_if_missing):
entity = self.world._get_by_storid(
storid,
# full_iri=self.world._unabbreviate(storid),
)
if entity:
entities.append(entity)
return entities

def remove_label_annotation(self, iri):
"""Removes label annotation used by get_by_label().
def add_label_annotation(self, iri):
"""Adds label annotation used by get_by_label()."""
warnings.warn(
"Ontology.add_label_annotations() is deprecated. "
"Direct modify the `label_annotations` attribute instead.",
DeprecationWarning,
stacklevel=2,
)
if hasattr(iri, "iri"):
iri = iri.iri
if iri not in self.label_annotations:
self.label_annotations.append(iri)

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 remove_label_annotation(self, iri):
"""Removes label annotation used by get_by_label()."""
warnings.warn(
"Ontology.add_label_annotations() is deprecated. "
"Direct modify the `label_annotations` attribute instead.",
DeprecationWarning,
stacklevel=2,
)
if hasattr(iri, "iri"):
iri = iri.iri
try:
self.label_annotations.remove(iri)
except ValueError:
pass

def set_common_prefix(
self,
Expand Down Expand Up @@ -571,8 +621,6 @@ def load( # pylint: disable=too-many-arguments,arguments-renamed

# 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,
Expand Down Expand Up @@ -1265,6 +1313,7 @@ def get_relations(self):
"Ontology.get_relations() is deprecated. Use "
"onto.object_properties() instead.",
DeprecationWarning,
stacklevel=2,
)
return self.object_properties()

Expand All @@ -1275,6 +1324,7 @@ def get_annotations(self, entity):
"Ontology.get_annotations(entity) is deprecated. Use "
"entity.get_annotations() instead.",
DeprecationWarning,
stacklevel=2,
)

if isinstance(entity, str):
Expand Down Expand Up @@ -1746,12 +1796,14 @@ def new_entity(

with self:
entity = types.new_class(name, parents)

# AREN'T WE LITTLE TOO SMART HERE?
# Set prefLabel to name if label_annotations is set
# and prefLabel is one of the annotations
if self.label_annotations and "prefLabel" in [
ann.name for ann in self.label_annotations
]:
preflabel = "http://www.w3.org/2004/02/skos/core#prefLabel"
if preflabel in self.label_annotations and self.world[preflabel]:
entity.prefLabel = english(name)

return entity

# Method that creates new ThingClass using new_entity
Expand Down
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