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Added function new_entitiy to ontology #207

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Sep 7, 2021
Merged

Added function new_entitiy to ontology #207

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9da48e5
Added function new_entitiy to ontology
francescalb Sep 3, 2021
4051131
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francescalb Sep 3, 2021
01d4b18
Docstring according to pep8
francescalb Sep 7, 2021
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10 changes: 10 additions & 0 deletions emmo/ontology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import warnings
import uuid
import tempfile
import types
from collections import defaultdict

import rdflib
Expand Down Expand Up @@ -1014,3 +1015,12 @@ def get_wu_palmer_measure(self, cls1, cls2):
n1 = self.number_of_generations(cls1, cca)
n2 = self.number_of_generations(cls2, cca)
return 2 * ccadepth / (n1 + n2 + 2 * ccadepth)

def new_entity(self, name, parent):
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'''
Makes a new entity in the ontology with given parent.
Return the new entity
'''
with self:
e = types.new_class(name, (parent, ))
return e
15 changes: 7 additions & 8 deletions emmo/tests/test_basic.py
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Expand Up @@ -20,27 +20,27 @@
onto.imported_ontologies.append(emmo)
onto.base_iri = 'http://emmo.info/examples/test#'

with onto:
# Add entity directly
onto.new_entity('Hydrogen', emmo.Atom)

class Hydrogen(emmo.Atom):
pass
with onto:

# Add entity using python classes
class Oxygen(emmo.Atom):
pass

class H2O(emmo.Molecule):
"""Water molecule."""
emmo.hasSpatialDirectPart.exactly(2, Hydrogen)
emmo.hasSpatialDirectPart.exactly(2, onto.Hydrogen)
emmo.hasSpatialDirectPart.exactly(1, Oxygen)

# Create some
H1 = Hydrogen()
H2 = Hydrogen()
H1 = onto.Hydrogen()
H2 = onto.Hydrogen()
O = Oxygen() # noqa: E741
w = H2O()
w.hasSpatialDirectPart = [H1, H2, O]


onto.sync_attributes(name_policy='sequential', name_prefix='myonto_')
assert onto.base_iri + 'myonto_0' in onto
assert onto.base_iri + 'myonto_6' in onto
Expand All @@ -49,7 +49,6 @@ class H2O(emmo.Molecule):
assert w.name.startswith('onto_')
assert len(w.name) == 5 + 36


# Remove all traces of onto such that they do not mess up other tests
# when running pytest
for e in itertools.chain(onto.classes(), onto.individuals()):
Expand Down