Skip to content

Commit

Permalink
validate input parameters, refactor axioms dict
Browse files Browse the repository at this point in the history
  • Loading branch information
@muddymudskipper
muddymudskipper committed Jun 26, 2024
1 parent 7dfcff7 commit def966d
Show file tree
Hide file tree
Showing 2 changed files with 46 additions and 54 deletions.
98 changes: 45 additions & 53 deletions cmem_plugin_robotreason/plugin_robotreason.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ def convert_iri_to_filename(value: str) -> str:
),
PluginParameter(
param_type=StringParameterType(),
name="result_iri",
name="result_graph_iri",
label="Result graph IRI",
description="The IRI of the output graph for the reasoning result. "
"WARNING: existing graph will be overwritten!",
Expand Down Expand Up @@ -216,7 +216,7 @@ def __init__( # noqa: PLR0913
self,
data_graph_iri: str = "",
ontology_graph_iri: str = "",
result_iri: str = "",
result_graph_iri: str = "",
reasoner: str = "elk",
class_assertion: bool = False,
data_property_characteristic: bool = False,
Expand All @@ -234,51 +234,49 @@ def __init__( # noqa: PLR0913
sub_object_property: bool = False,
) -> None:
"""Init"""
self.axioms_dict = {
"SubClass": sub_class,
"EquivalentClass": equivalent_class,
"DisjointClasses": disjoint_classes,
"DataPropertyCharacteristic": data_property_characteristic,
"EquivalentDataProperties": equivalent_data_properties,
"SubDataProperty": sub_data_property,
"ClassAssertion": class_assertion,
"PropertyAssertion": property_assertion,
"EquivalentObjectProperty": equivalent_object_property,
"InverseObjectProperties": inverse_object_properties,
"ObjectPropertyCharacteristic": object_property_characteristic,
"SubObjectProperty": sub_object_property,
"ObjectPropertyRange": object_property_range,
"ObjectPropertyDomain": object_property_domain,
}

errors = ""
iris = [
(data_graph_iri, "Data graph IRI"),
(ontology_graph_iri, "Ontology graph IRI"),
(result_graph_iri, "Result graph IRI"),
]
not_iri = sorted([i[1] for i in iris if not validators.url(i[0])], key=lambda n: n[1])
if not_iri:
errors += f"Invalid IRI for parameters: {', '.join(not_iri)}. "
if result_graph_iri == data_graph_iri:
errors += "Result graph IRI cannot be the same as the data graph IRI. "
if result_graph_iri == ontology_graph_iri:
errors += "Result graph IRI cannot be the same as the ontology graph IRI. "
not_bool = sorted([k for k, v in self.axioms_dict.items() if not isinstance(v, bool)])
if not_bool:
errors += f"Invalid value for parameters: {', '.join(not_bool)}. "
if True not in self.axioms_dict.values():
errors += "No axiom generator selected. "
if errors:
raise ValueError(errors[:-1])

self.data_graph_iri = data_graph_iri
self.ontology_graph_iri = ontology_graph_iri
self.result_iri = result_iri
self.result_graph_iri = result_graph_iri
self.reasoner = reasoner
self.temp = f"robot_{uuid4().hex}"
self.sub_class = sub_class
self.equivalent_class = equivalent_class
self.disjoint_classes = disjoint_classes
self.data_property_characteristic = data_property_characteristic
self.equivalent_data_properties = equivalent_data_properties
self.sub_data_property = sub_data_property
self.class_assertion = class_assertion
self.property_assertion = property_assertion
self.equivalent_object_property = equivalent_object_property
self.inverse_object_properties = inverse_object_properties
self.object_property_characteristic = object_property_characteristic
self.sub_object_property = sub_object_property
self.object_property_range = object_property_range
self.object_property_domain = object_property_domain

if result_iri == data_graph_iri:
raise ValueError("Result graph IRI cannot be the same as the data graph IRI.")
if result_iri == ontology_graph_iri:
raise ValueError("Result graph IRI cannot be the same as the ontology graph IRI.")
if not validators.url(result_iri):
raise ValueError("Result graph IRI is invalid.")

self.axioms_dict = {
"sub_class": "SubClass",
"equivalent_class": "EquivalentClass",
"disjoint_classes": "DisjointClasses",
"data_property_characteristic": "DataPropertyCharacteristic",
"equivalent_data_properties": "EquivalentDataProperties",
"sub_data_property": "SubDataProperty",
"class_assertion": "ClassAssertion",
"property_assertion": "PropertyAssertion",
"equivalent_object_property": "EquivalentObjectProperty",
"inverse_object_properties": "InverseObjectProperties",
"object_property_characteristic": "ObjectPropertyCharacteristic",
"sub_object_property": "SubObjectProperty",
"object_property_range": "ObjectPropertyRange",
"object_property_domain": "ObjectPropertyDomain",
}
if True not in [self.__dict__[k] for k in self.axioms_dict]:
raise ValueError("No axiom generator selected.")

def create_xml_catalog_file(self, graphs: dict) -> None:
"""Create XML catalog file"""
Expand Down Expand Up @@ -323,30 +321,24 @@ def get_graphs_tree(self) -> dict:
graphs[iri] = convert_iri_to_filename(iri)
return graphs

def set_axioms(self) -> str:
"""Set asserted axioms"""
axioms = " ".join(v for k, v in self.axioms_dict.items() if self.__dict__[k])
if not axioms:
raise ValueError("No axioms selected.")
return axioms

def reason(self, graphs: dict) -> None:
"""Reason"""
axioms = " ".join(k for k, v in self.axioms_dict.items() if v)
data_location = f"{self.temp}/{graphs[self.data_graph_iri]}"
utctime = str(datetime.fromtimestamp(int(time()), tz=UTC))[:-6].replace(" ", "T") + "Z"
cmd = (
f'java -XX:MaxRAMPercentage=15 -jar {ROBOT} merge --input "{data_location}" '
"--collapse-import-closure false "
f"reason --reasoner {self.reasoner} "
f'--axiom-generators "{self.set_axioms()}" '
f'--axiom-generators "{axioms}" '
f"--include-indirect true "
f"--exclude-duplicate-axioms true "
f"--exclude-owl-thing true "
f"--exclude-tautologies all "
f"--exclude-external-entities "
f"reduce --reasoner {self.reasoner} "
f'unmerge --input "{data_location}" '
f'annotate --ontology-iri "{self.result_iri}" '
f'annotate --ontology-iri "{self.result_graph_iri}" '
f"--remove-annotations "
f'--language-annotation rdfs:label "Eccenca Reasoning Result {utctime}" en '
f"--language-annotation rdfs:comment "
Expand All @@ -371,7 +363,7 @@ def reason(self, graphs: dict) -> None:
def send_result(self) -> None:
"""Send result"""
post_streamed(
self.result_iri,
self.result_graph_iri,
str(Path(self.temp) / "result.ttl"),
replace=True,
content_type="text/turtle",
Expand Down
2 changes: 1 addition & 1 deletion tests/test_robotreason.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def test_reasoner(reasoner: str, err_list: list) -> list:
RobotReasonPlugin(
data_graph_iri=DATA_GRAPH_IRI,
ontology_graph_iri=ONTOLOGY_GRAPH_IRI,
result_iri=RESULT_GRAPH_IRI,
result_graph_iri=RESULT_GRAPH_IRI,
reasoner=reasoner,
sub_class=False,
class_assertion=True,
Expand Down

0 comments on commit def966d

Please sign in to comment.