"""
http://ontology.neuinfo.org/trees/query/swanr:hasPart1/SWAN:1/ttl/generated/swanson.ttl?restriction=true&depth=40&direction=OUTGOING
human cns gray matter regions
http://ontology.neuinfo.org/trees/query/swanr:hasPart3/SWAN:1/ttl/generated/swanson.ttl?restriction=true&depth=40&direction=OUTGOING
surface features, handy to have around
http://ontology.neuinfo.org/trees/query/swanr:hasPart5/SWAN:629/ttl/generated/swanson.ttl?restriction=true&depth=40&direction=OUTGOING
"""
sgraph = rdflib.Graph().parse(
(Neuron.local_base / 'ttl/generated/swanson.ttl').as_posix(), format='ttl')
# restriction.parse(sgraph) # FIXME this breaks with weird error message
OntCuries({**graphBase.prefixes, **PREFIXES})
rests = [r for r in restriction.parse(graph=sgraph) if r.p == swanr.hasPart3]
#restriction = Restriction2(rdfs.subClassOf)
class LocalGraphService(ontquery.services.BasicService):
def __init__(self, graph):
self.graph = graph
super().__init__()
def query(self,
curie=None,
iri=None,
label=None,
term=None,
search=None,
**kwargs
def main():
for filename in ('mbaslim', 'hbaslim', 'paxinos-rat-labels',
'waxholm-rat-labels'):
filepath = gitf / 'NIF-Ontology/ttl/generated/parcellation' / (
filename + '.ttl')
dir_ = filepath.parent.as_posix()
print(dir_)
file_commit = subprocess.check_output(
[
'git', 'log', '-n', '1', '--pretty=format:%H', '--',
filepath.name
],
cwd=dir_,
stderr=subprocess.DEVNULL).decode().rstrip()
graph = rdflib.Graph().parse(filepath.as_posix(), format='ttl')
g = makeGraph('', graph=graph)
annos = defaultdict(set)
anno_trips = defaultdict(set)
for triple, predicate_objects in annotation.parse(graph=graph):
for a_p, a_o in predicate_objects:
annos[a_p, a_o].add(triple)
anno_trips[triple].add((a_p, a_o))
anno_trips = {k: v for k, v in anno_trips.items()}
for lifted_triple in restriction.parse(graph=graph):
graph.add(lifted_triple)
out_header = 'label|abbrev|curie|superPart curie\n'
out = []
editions_header = 'edition|label|abbrev|curie\n'
editions = []
for s in graph.subjects(rdf.type, owl.Class):
rdfsLabel = next(graph.objects(s, rdfs.label))
try:
prefLabel = next(graph.objects(s, skos.prefLabel))
except StopIteration:
print(tc.red('WARNING:'),
f'skipping {s} {rdfsLabel} since it has no prefLabel')
continue
syns = sorted(
graph.objects(s, NIFRID.synonym)
) # TODO are there cases where we need to recaptulate what we are doing for for abbrevs?
abbrevs = sorted(graph.objects(
s, NIFRID.abbrev)) # FIXME paxinos has more than one
try:
if annos:
if len(abbrevs) > 1:
print(tc.blue('INFO:'), g.qname(s),
repr(prefLabel.value), 'has multiple abbrevs',
[a.value for a in abbrevs])
# prefer latest
current_edition = ''
for a in abbrevs:
for a_p, edition in anno_trips[s, NIFRID.abbrev, a]:
if a_p == ilxtr.literalUsedBy:
if current_edition < edition:
current_edition = edition
abbrev = a
else:
abbrev = abbrevs[0]
except IndexError:
abbrev = ''
try:
superPart = next(graph.objects(s, ilxtr.labelPartOf))
except StopIteration:
superPart = ''
out.append(
f'{prefLabel}|{abbrev}|{g.qname(s)}|{g.qname(superPart)}')
if annos:
#asdf = {'ed':{'label':,'abbrev':,'curie':}}
asdf = defaultdict(dict)
triple = s, skos.prefLabel, prefLabel
eds = anno_trips[triple]
for a_p, a_o in eds:
asdf[a_o]['curie'] = g.qname(s)
asdf[a_o]['label'] = prefLabel
for syn in graph.objects(s, NIFRID.synonym):
triple = s, NIFRID.synonym, syn
eds = anno_trips[triple]
for a_p, a_o in eds:
asdf[a_o]['curie'] = g.qname(s)
if 'label' in asdf[a_o]:
print(
tc.red('WARNING:'),
f'{a_o} already has a label "{asdf[a_o]["label"]}" for "{syn}"'
)
asdf[a_o]['label'] = syn
for abbrev in graph.objects(s, NIFRID.abbrev):
triple = s, NIFRID.abbrev, abbrev
eds = anno_trips[triple]
#print('aaaaaaaaaaa', g.qname(s), )
for a_p, a_o in eds:
asdf[a_o]['curie'] = g.qname(s)
if 'abbrev' in asdf[a_o]:
print(
tc.red('WARNING:'),
f'{a_o} already has a abbrev "{asdf[a_o]["abbrev"]}" for "{abbrev}"'
)
asdf[a_o]['abbrev'] = abbrev
#print(asdf)
for ed, kwargs in sorted(asdf.items()):
if 'abbrev' not in kwargs:
print('Skipping', ed, 'for\n', kwargs)
continue
editions.append('{ed}|{label}|{abbrev}|{curie}'.format(
ed=g.qname(ed), **kwargs))
with open('/tmp/' + filename + f'-{file_commit[:8]}.psv', 'wt') as f:
f.write(out_header + '\n'.join(sorted(out, key=labelkey)))
if editions:
with open('/tmp/' + filename + f'-editions-{file_commit[:8]}.psv',
'wt') as f:
f.write(editions_header +
'\n'.join(sorted(editions, key=edkey)))