def main():
olr = auth.get_path('ontology-local-repo')
ori = OntResIri('http://purl.obolibrary.org/obo/doid.owl')
orp = OntResPath(olr / 'ttl/external/doid.owl')
ort = ori
g = ori.graph
query = """
SELECT DISTINCT ?s ?o ?l
WHERE {
?s a owl:Class .
?s rdfs:subClassOf* <http://purl.obolibrary.org/obo/DOID_4> .
?s rdfs:subClassOf ?o .
?s rdfs:label ?l .
}"""
res = list(g.query(query))
filt = [r for r in res if not isinstance(r[1], rdflib.BNode)]
spath = 'ttl/generated/doidslim.ttl'
go = OntGraph(path=olr / spath)
# TODO prov record like the one we have for chebi
go.bind('DOID', 'http://purl.obolibrary.org/obo/DOID_')
s = rdflib.URIRef('http://ontology.neuinfo.org/NIF/' + spath)
go.populate_from_triples(
((s, p, o) for p, o in
((rdf.type, owl.Ontology),
(rdfs.label, rdflib.Literal("NIF DOID slim")),)))
ds = rdflib.URIRef('http://purl.obolibrary.org/obo/DOID_4')
go.add((ds, rdf.type, owl.Class))
go.add((ds, rdfs.label, rdflib.Literal('disease')))
go.populate_from_triples(
(t for s, o, l in filt for t in
((s, rdf.type, owl.Class),
(s, rdfs.subClassOf, o),
(s, rdfs.label, l))))
go.write()
def sneechReviewGraph(self,
source_graph,
namespaces,
sneech_file=None,
path_out=None):
# TODO cache
(already, cannot, maybe, sneeches,
maybe_sneeches) = self.preSneech(source_graph, namespaces)
# TODO not entirely sure about the best place to put this ...
self.reView(source_graph, maybe_sneeches) # FIXME dump and commit
review_graph = OntGraph(path=path_out)
oq.OntCuries.populate(review_graph)
review_graph.bind('snchn', str(snchn)) # FIXME -> curies probably
review_graph.bind('sncho', str(sncho)) # FIXME -> curies probably
review_graph.bind('h', str(sghashes)) # FIXME -> curies probably
if sneech_file:
sneech_file.populate(review_graph)
gen = self.triples_review(already, cannot, maybe, sneeches,
sneech_file)
[review_graph.add(t) for t in gen]
# TODO hasReport -> maybe_sneeches report / reView
# TODO snchn predicate ordering
return review_graph, maybe_sneeches
def npokb():
index_graph = OntGraph(path=auth.get_path('ontology-local-repo') /
'ttl/generated/neurons/npokb-index.ttl')
if index_graph.path.exists():
index_graph.parse()
# testing
index_graph.bind('npokb', npokb)
#[index_graph.add((npokb[str(i)], rdf.type, owl.Class)) for i in range(1, 11)]
#[index_graph.add((npokb[str(i)], ilxtr.hasTemporaryId, TEMP[str(i)])) for i in range(1, 11)]
ios = []
for eff in ('common-usage-types', 'huang-2017', 'markram-2015',
'allen-cell-types'):
path = auth.get_path(
'ontology-local-repo') / f'ttl/generated/neurons/{eff}.ttl'
input_graph = OntGraph(path=path)
input_graph.parse()
output_graph = input_graph.mapTempToIndex(index_graph, npokb, TEMP)
ios.append((input_graph, output_graph))
input_graph, output_graph = ios[0]
a, r, c = output_graph.subjectsChanged(input_graph)
index_graph.write()
# [o.write() for i, o, in ios] # when ready
#from sparcur.paths import Path
#Path(index_graph.path).xopen()
breakpoint()
def graph(self):
g = OntGraph()
OntCuries.populate(g)
self.populate(g)
g.bind('local', self.context)
g.bind('apinatomy', readable) # FIXME populate from store
g.bind('elements', elements)
return g
def build_instances(self, instances, dids):
folder = Path(self.config.out_graph_path()).parent
# WOW do I need to implement the new/better way of
# managing writing collections of neurons to graphs
neuron_uri = next(NeuronACT.out_graph[:rdf.type:owl.Ontology])
name = 'allen-cell-instances.ttl'
base, _ = neuron_uri.rsplit('/', 1)
uri = rdflib.URIRef(base + '/' + name)
metadata = ((uri, rdf.type, owl.Ontology),)
instance_graph = OntGraph(path=folder / name)
instance_graph.bind('AIBSSPEC', AIBSSPEC)
instance_graph.bind('npokb', npokb)
[instance_graph.add(t) for t in metadata]
[instance_graph.add(t) for t in instances]
[instance_graph.add(t) for t in allDifferent(None, distinctMembers(*dids))]
instance_graph.write()
def npokb_mapping():
index_graph = OntGraph(path=auth.get_path('ontology-local-repo') /
'ttl/generated/neurons/npokb-index.ttl')
if index_graph.path.exists():
index_graph.parse()
# testing
index_graph.bind('npokb', npokb)
#[index_graph.add((npokb[str(i)], rdf.type, owl.Class)) for i in range(1, 11)]
#[index_graph.add((npokb[str(i)], ilxtr.hasTemporaryId, TEMP[str(i)])) for i in range(1, 11)]
ios = []
for eff in (
'common-usage-types',
'huang-2017',
'markram-2015',
'allen-cell-types',
):
# FIXME if the index id is already being used it is still added as a temp id incorrectly
path = auth.get_path(
'ontology-local-repo') / f'ttl/generated/neurons/{eff}.ttl'
org = OntResGit(
path, ref='HEAD'
) # HEAD is default but just for clarity set it explicitly here
prev_graph = org.graph
input_graph = OntGraph(path=path)
input_graph.parse()
mapped_graph = input_graph.mapStableIdentifiers(
prev_graph, ilxtr.origLabel)
output_graph = mapped_graph.mapTempToIndex(index_graph, npokb, TEMP)
ios.append((mapped_graph, output_graph))
mapped_graph, output_graph = ios[0]
a, r, c = output_graph.subjectsChanged(mapped_graph)
index_graph.write()
[o.write() for i, o, in ios] # when ready
#from sparcur.paths import Path
#Path(index_graph.path).xopen()
breakpoint()
def fixns(g):
ns = rdflib.Namespace(dict(g.namespace_manager)[''])
nsb = ns + 'pCL_'
nsu = ns + 'UBERON_'
nsc = ns + 'CL_'
ng = OntGraph()
ng.namespace_manager.populate_from(g)
ng.bind('ilxtr', ilxtr)
ng.bind('CL', CL)
ng.bind('pCL', pCL)
ng.bind('UBERON', UBERON)
ng.bind('NCBITaxon', NCBITaxon)
ng.bind('HGNC', HGNC)
ng.bind('LOC', LOC)
ng.populate_from_triples(
(rdflib.URIRef(str(e.replace(nsb, pCL))) if e.startswith(nsb) else
(rdflib.URIRef(str(e.replace(nsu, UBERON))) if e.startswith(nsu) else
(rdflib.URIRef(str(e.replace(nsc, CL))) if e.startswith(nsc) else e))
for e in t) for t in g)
return ng
