def test_equivalent_to_union_of_complement(self):
Restriction = cmb.Restriction(None)
combinator = cmb.ObjectCombinator.full_combinator(
cmb.Class,
cmb.Pair(owl.complementOf, Restriction(ilxtr.property,
ilxtr.value)))
print(combinator)
gen = combinator(ilxtr.subject)
self._doit(gen)
combinator = cmb.unionOf(combinator)
print(combinator)
gen = combinator(ilxtr.subject, owl.equivalentClass)
self._doit(gen)
def test_predicate(self):
pc = cmb.PredicateCombinator(ilxtr.predicate)
objects1 = ilxtr.object1, ilxtr.object2
gen = pc(ilxtr.subject, *objects1)
self._doit(gen)
Restriction = cmb.Restriction(None)
objects2 = (cmb.unionOf(Restriction(ilxtr.property, ilxtr.value1)),
cmb.intersectionOf(
Restriction(ilxtr.property, ilxtr.value2)))
gen = pc(ilxtr.subject, *objects2)
self._doit(gen)
gen = pc(ilxtr.subject, *objects1, *objects2)
self._doit(gen)
def test_equivalent_to_union_of(self):
Restriction = cmb.Restriction(None)
#combinator = cmb.ObjectCombinator.full_combinator( # broken but don't need ..
#cmb.Class,
#cmb.unionOf(Restriction(ilxtr.property, ilxtr.value)))
combinator = cmb.unionOf(Restriction(ilxtr.property, ilxtr.value))
#ec = cmb.List({owl.Restriction, rf})
#combinator = ec(rf(ilxtr.a, ilxtr.b))
#combinator = ec(cmb.restriction(ilxtr.a, ilxtr.b))
print(combinator)
pos1 = combinator(ilxtr.subject, owl.equivalentClass)
pos2 = combinator(ilxtr.subject)
pos3 = combinator(ilxtr.subject, ilxtr.thisCanOverwrite)
self._doit(pos1)
self._doit(pos2)
self._doit(pos3)
def nodes(self):
a = rdf.type
for id, style_type, style_width, label, desc, url in super().nodes():
s = None
if desc == 'legend':
continue
if url:
if url.startswith('exact'):
s = workflow[url]
yield s, a, workflow.exact
elif url.startswith('RRIDscibot'):
s = workflow[url]
yield s, a, workflow.tagScibot
elif any(
url.startswith(prefix)
for prefix in ('release', 'resolver')):
s = wf[url]
else:
s = TEMP[url]
else:
if label == 'RRID:':
s = workflow['RRID']
elif label.startswith('RRIDCUR:'):
s = RRIDCUR[label.split(':')[-1]]
self.different_tags.add(s)
elif ' + ' in label:
suffixes = label.split(' + ') # FIXME
s = BNode()
# union of is the right way to go here I think, because union
# implies that both must be present, not either or ...
yield from unionOf(*(workflow[sfx] for sfx in suffixes))(s)
#self.node_name_lookup[id] = s
#self.types[s] = wf.tag
#continue # can't yield the type this node
elif label in ('DOI', 'PMID'):
s = wf[label]
yield s, a, wf.tag
else:
s = TEMP[label]
if s is None: # FIXME if this happens this late we don't get the error message
raise ValueError(f'unhandled node {id} {lable}')
else:
self.node_name_lookup[id] = s
#yield s, rdf.type, owl.Class
if isinstance(s, BNode):
#yield s, a, owl.NamedIndividual # FIXME apparently this doesn't serializer properly ...
yield s, a, wf.tag
elif style_type == 'dashed':
yield s, a, workflow.state
elif (style_type, style_width) == ('line', '1.0'):
pass
elif (style_type, style_width) == ('line', '2.0'):
pass
elif (style_type, style_width) == ('dashed_dotted', '2.0'):
#yield s, wf.isAttachedTo, wf.pageNote
self.insert_object(id, wf.pageNoteInstance)
yield wf.pageNoteInstance, wf.hasTag, s
if s not in self.types:
yield s, a, wf.tagCurator
elif (style_type, style_width) == ('dotted', '2.0'):
# yield s, wf.isAttachedTo, wf.pageNote
self.insert_object(id, wf.pageNoteInstance)
yield wf.pageNoteInstance, wf.hasTag, s
if s not in self.types:
yield s, a, wf.tagScibot
else:
msg = f'{id} {label} has unhandled type {style_type} {style_width}'
raise ValueError(msg)
oc(OntTerm('SO:0000234', label='mRNA'),
OntId('CHEBI:33697')), # FIXME not right ...
(ilxtr.mRNA, owl.equivalentClass, OntTerm('SO:0000234',
label='mRNA')), # FIXME role?
(OntTerm('GO:0005575', label='cellular_component'), rdfs.subClassOf,
ilxtr.physiologicalSystem),
# FIXME owl:sameAs is NOT for generic iris >_<
#oc(ilxtr.physiologicalSystem, ilxtr.materialEntity),
# FIXME what about things that were synthesized entirely?
# how about... constrainedBy _information_ derived from some organism?
# a protein is indeed constrained by that information regardless of
# whether it was synthesized or not...
#oc(OntTerm('NCBITaxon:1'), ilxtr.materialEntity), # needed to accomodate deadness?
oc(ilxtr.physiologicalSystem, ilxtr.materialEntity),
oc_(ilxtr.physiologicalSystem,
unionOf(OntTerm('NCBITaxon:1'), restN(partOf,
OntTerm('NCBITaxon:1')))),
#oec(ilxtr.materialEntity, # FIXME in vitro...
#restN(partOf, OntTerm('NCBITaxon:1'))
#)),
oc(OntTerm('NCBITaxon:1'),
ilxtr.physiologicalSystem), # needed to accomodate deadness?
#oc_(ilxtr.physiologicalSystemDisjointWithOrganism,
#oec(ilxtr.physiologicalSystem)
#),
#(ilxtr.physiologicalSystemDisjointWithOrganism, owl.disjointWith, OntTerm('NCBITaxon:1')),
oc(ilxtr.viralParticle, ilxtr.physiologicalSystem),
oc(ilxtr.AAVretro, ilxtr.viralParticle),
oc(OntTerm('UBERON:0000465'), ilxtr.materialEntity),
oc(OntTerm('UBERON:0000955'), OntTerm('UBERON:0000465')),
oc(OntTerm('UBERON:0007798'), OntTerm('UBERON:0000465')),