def test_part_of(self):
eeeee = self.OntTerm('UBERON:0008933',
label='primary somatosensory cortex')
g = OntGraph()
[g.add(t) for t in eeeee.triples_simple]
g.debug()
po = [t for t in eeeee.triples_simple if partOf in t]
assert po, 'sadness'
def triples(self):
crossref_doi_pred = rdflib.term.URIRef('http://prismstandard.org/namespaces/basic/2.1/doi')
for blob in self.data['identifier_metadata']:
id = blob['id']
if not isinstance(id, idlib.Stream):
id = idlib.Auto(id)
if not hasattr(id, 'asUri'):
breakpoint()
s = id.asUri(rdflib.URIRef)
if 'source' in blob:
source = blob['source'] # FIXME we need to wrap this in our normalized representation
if source == 'Crossref': # FIXME CrossrefConvertor etc. OR put it in idlib as a an alternate ttl
pos = (
(rdf.type, owl.NamedIndividual),
(rdf.type, TEMP[blob['type']]),
(dc.publisher, blob['publisher']),
#(dc.type, blob['type']), # FIXME semantify
(dc.title, blob['title']),
(dc.date, self.published_online(blob)), # FIXME .... dangerzone
)
g = OntGraph()
doi = idlib.Doi(id) if not isinstance(id, idlib.Doi) else id # FIXME idlib streams need to recognize their own type in __new__
data = doi.ttl()
if data is None: # blackfynn has some bad settings on their doi records ...
return
try:
g.parse(data=data, format='ttl') # FIXME network bad
except BaseException as e:
loge.exception(e)
_tr = [s for s, p, o in g if p == crossref_doi_pred]
if _tr:
_their_record_s = _tr[0]
yield s, owl.sameAs, _their_record_s
yield from g
else:
g.debug()
log.critical('No crossref doi section in graph!')
else:
msg = f'dont know what to do with {source}'
log.error(msg)
#raise NotImplementedError(msg)
return
else:
msg = f'dont know what to do with {blob} for {id.identifier}'
log.error(msg)
#raise NotImplementedError(msg)
return
for p, oraw in pos:
if oraw is not None:
o = rdflib.Literal(oraw) if not isinstance(oraw, rdflib.URIRef) else oraw
yield s, p, o
def methods_mapping():
from pyontutils.namespaces import TEMP, ilxtr, tech
from nifstd_tools import methods as m
import rdflib
# TODO add this to ibnode tests
_before = OntResGit(methods,
ref='8c30706cbc7ccc7443685a34dec026e8afbbedd1')
after = OntResGit(
methods,
ref='860c88a574d17e0d427c1101fa1947b730b613a9') # renaming commit
before = OntResGit(after.path, ref=after.ref + '~1')
assert before.graph.identity() == _before.graph.identity()
bg = before.graph
ag = after.graph
_, local = next(ag[:ilxtr.indexNamespace:])
local = rdflib.Namespace(str(local))
T0 = TEMP['0']
l0 = local['0']
b = OntGraph().populate_from_triples(bg.subjectGraph(T0))
a = OntGraph().populate_from_triples(ag.subjectGraph(l0))
b.debug()
a.debug()
it = b.subjectIdentity(T0)
il = a.subjectIdentity(l0)
assert it == il
assert it in (il, )
assert il in (it, ) # (it,) ni il # SIGH
assert it in {il: None}
assert il in {it: None}
r = b.subjectsRenamed(a)
renamed = before.graph.subjectsRenamed(after.graph)
assert (len(renamed) - 1 == max([
int(v.rsplit('/', 1)[-1]) for v in renamed.values()
if v != ilxtr.Something
]))
(OntGraph(
namespace_manager=after.graph.namespace_manager).populate_from_triples(
before.graph.subjectsRenamedTriples(after.graph)).debug())
return renamed
index_graph = OntGraph(path=olr / 'ttl/generated/index-methods.ttl')
# FIXME either use or record for posterity the commits where these
# transformations were run rather than pointing to the branch name
with org.repo.getRef('methods'):
input_graph = org.graph
output_graph = input_graph.mapTempToIndex(index_graph, TEMP, m.local)
a, r, c = output_graph.subjectsChanged(input_graph)
index_graph.write()
def test_new_index(self):
rp = temp_path / 'sneechenator'
wrangler = snch.SneechWrangler(rp)
path_index = wrangler.new_index('uri.interlex.org')
assert path_index.exists(), 'wat'
g = OntGraph(path=path_index).parse()
try:
next(g[:rdf.type:snch.snchn.IndexGraph])
except StopIteration:
assert False, g.debug()
def debug(self):
g = OntGraph()
self.populate(g)
log.debug('printing graph')
g.debug()
