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Replace EX by NS because I guess EX stands for example #97

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merged 1 commit into from
Jan 21, 2025
Merged

Replace EX by NS because I guess EX stands for example #97

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30 changes: 15 additions & 15 deletions pyiron_ontology/parser.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,46 +48,46 @@ def get_inputs_and_outputs(node):

def get_triples(
data,
EX,
NS,
hasSourceFunction=None,
hasUnits=None,
inheritsPropertiesFrom=None,
update_query=True,
):
if hasSourceFunction is None:
hasSourceFunction = EX.hasSourceFunction
hasSourceFunction = NS.hasSourceFunction
if hasUnits is None:
hasUnits = EX.hasUnits
hasUnits = NS.hasUnits
if inheritsPropertiesFrom is None:
inheritsPropertiesFrom = EX.inheritsPropertiesFrom
inheritsPropertiesFrom = NS.inheritsPropertiesFrom
graph = Graph()
# Triple already exists
label_def_triple = (EX[data["label"]], hasSourceFunction, EX[data["function"]])
label_def_triple = (NS[data["label"]], hasSourceFunction, NS[data["function"]])
if len(list(graph.triples(label_def_triple))) > 0:
return graph
graph.add(label_def_triple)
for io_ in ["inputs", "outputs"]:
for key, d in data[io_].items():
full_key = data["label"] + f".{io_}." + key
label = EX[full_key]
label = NS[full_key]
graph.add((label, RDFS.label, Literal(full_key)))
if d.get("uri", None) is not None:
graph.add((label, RDF.type, d["uri"]))
if d.get("value", NOT_DATA) is not NOT_DATA:
graph.add((label, RDF.value, Literal(d["value"])))
graph.add((label, EX[io_[:-1] + "Of"], EX[data["label"]]))
graph.add((label, NS[io_[:-1] + "Of"], NS[data["label"]]))
if d.get("units", None) is not None:
graph.add((label, hasUnits, EX[d["units"]]))
graph.add((label, hasUnits, NS[d["units"]]))
if d.get("connection", None) is not None:
graph.add((label, inheritsPropertiesFrom, EX[d["connection"]]))
for t in _get_triples_from_restrictions(d, EX):
graph.add(_parse_triple(t, EX, label=label, data=data))
graph.add((label, inheritsPropertiesFrom, NS[d["connection"]]))
for t in _get_triples_from_restrictions(d, NS):
graph.add(_parse_triple(t, NS, label=label, data=data))
if update_query:
inherit_properties(graph, EX)
inherit_properties(graph, NS)
return graph


def _get_triples_from_restrictions(data, EX):
def _get_triples_from_restrictions(data, NS):
triples = []
if data.get("restrictions", None) is not None:
triples = restriction_to_triple(data["restrictions"])
Expand All @@ -114,7 +114,7 @@ def restriction_to_triple(restrictions):
return triples


def _parse_triple(triples, EX, label=None, data=None):
def _parse_triple(triples, NS, label=None, data=None):
if len(triples) == 2:
subj, pred, obj = label, triples[0], triples[1]
elif len(triples) == 3:
Expand All @@ -124,7 +124,7 @@ def _parse_triple(triples, EX, label=None, data=None):
if obj.startswith("inputs.") or obj.startswith("outputs."):
obj = data["label"] + "." + obj
if not isinstance(obj, URIRef):
obj = EX[obj]
obj = NS[obj]
return subj, pred, obj


Expand Down
36 changes: 18 additions & 18 deletions tests/unit/test_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
from rdflib import Namespace


EX = Namespace("http://example.org/")
NS = Namespace("http://example.org/")


@Workflow.wrap.as_function_node("speed")
Expand All @@ -22,22 +22,22 @@ def calculate_speed(
) -> u(
float,
units="meter/second",
triples=((EX.isOutputOf, "inputs.time"), (EX.subject, EX.predicate, EX.object)),
triples=((NS.isOutputOf, "inputs.time"), (NS.subject, NS.predicate, NS.object)),
):
return distance / time


@Workflow.wrap.as_function_node("result")
def add(a: float, b: float) -> u(float, triples=(EX.HasOperation, EX.Addition)):
def add(a: float, b: float) -> u(float, triples=(NS.HasOperation, NS.Addition)):
return a + b


@Workflow.wrap.as_function_node("result")
def multiply(a: float, b: float) -> u(
float,
triples=(
(EX.HasOperation, EX.Multiplication),
(EX.inheritsPropertiesFrom, "inputs.a"),
(NS.HasOperation, NS.Multiplication),
(NS.inheritsPropertiesFrom, "inputs.a"),
),
):
return a * b
Expand All @@ -48,8 +48,8 @@ def correct_analysis(
a: u(
float,
restrictions=(
(OWL.onProperty, EX.HasOperation),
(OWL.someValuesFrom, EX.Addition),
(OWL.onProperty, NS.HasOperation),
(OWL.someValuesFrom, NS.Addition),
),
)
) -> float:
Expand All @@ -61,8 +61,8 @@ def wrong_analysis(
a: u(
float,
restrictions=(
(OWL.onProperty, EX.HasOperation),
(OWL.someValuesFrom, EX.Division),
(OWL.onProperty, NS.HasOperation),
(OWL.someValuesFrom, NS.Division),
),
)
) -> float:
Expand All @@ -84,34 +84,34 @@ def test_parser(self):
def test_triples(self):
speed = calculate_speed()
data = get_inputs_and_outputs(speed)
graph = get_triples(data, EX)
graph = get_triples(data, NS)
self.assertGreater(
len(list(graph.triples((None, EX.hasUnits, EX["meter/second"])))), 0
len(list(graph.triples((None, NS.hasUnits, NS["meter/second"])))), 0
)
self.assertEqual(
len(
list(
graph.triples(
(None, EX.isOutputOf, EX["calculate_speed.inputs.time"])
(None, NS.isOutputOf, NS["calculate_speed.inputs.time"])
)
)
),
1,
)
self.assertEqual(
len(list(graph.triples((EX.subject, EX.predicate, EX.object)))), 1
len(list(graph.triples((NS.subject, NS.predicate, NS.object)))), 1
)

def test_correct_analysis(self):
def get_graph(wf):
graph = Graph()
graph.add((EX.HasOperation, RDF.type, RDF.Property))
graph.add((EX.Addition, RDF.type, OWL.Class))
graph.add((EX.Multiplication, RDF.type, OWL.Class))
graph.add((NS.HasOperation, RDF.type, RDF.Property))
graph.add((NS.Addition, RDF.type, OWL.Class))
graph.add((NS.Multiplication, RDF.type, OWL.Class))
for value in wf.children.values():
data = get_inputs_and_outputs(value)
graph += get_triples(data, EX)
inherit_properties(graph, EX)
graph += get_triples(data, NS)
inherit_properties(graph, NS)
DeductiveClosure(OWLRL_Semantics).expand(graph)
return graph

Expand Down
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