def test_construct_simple_file(self):
of = oio.OboFile()
ids_names = [['123', 'test'], ['234', 'yee'], ['345', 'haw'],
['456', 'oio']]
terms = [oio.Term(id=i, name=n) for i, n in ids_names]
of.add(*terms)
str(of)
def _todo(utr):
# real output
glb = auth.get_path('git-local-base')
uberon_edit = aug.RepoPath(
glb) / 'NOFORK/uberon/src/ontology/uberon-edit.obo'
of = oio.OboFile(path=uberon_edit, strict=False)
utr.submit_to_obofile(of, 'UBERON', uberon_id_range)
of.write(overwrite=True, version=oio.OBO_VER_ROBOT)
def test_header_treat_xrefs(self):
of = oio.OboFile()
test_tag = 'treat-xrefs-as-is_a'
tags_values = [
[test_tag, 'TEMP:test1'],
[test_tag, 'TEMP:test2'],
]
tvpairs = [oio.TVPair(tag=t, value=v) for t, v in tags_values]
of.header.add(*tvpairs)
tv = of.asObo()
assert len(tv.split(test_tag)) > 2, tv
def test_robot(self):
of1 = oio.OboFile(data=obo_test_string)
obo1 = of1.asObo(stamp=False)
obor1 = of1.asObo(stamp=False, version=oio.OBO_VER_ROBOT)
of2 = oio.OboFile(data=obo1)
obo2 = of2.asObo(stamp=False)
# can't test against obor2 because obo1 reordered the trailing qualifiers
# and since there is seemingly no rational way to predict those, we simply
# preserve the ordering that we got
obor2 = of2.asObo(stamp=False, version=oio.OBO_VER_ROBOT)
of3 = oio.OboFile(data=obor1)
obo3 = of3.asObo(stamp=False)
obor3 = of3.asObo(stamp=False, version=oio.OBO_VER_ROBOT)
print(obo1)
print(obo2)
print(obor1)
print(obor2)
assert obo1 == obo2 == obo3 != obor1
assert obor1 == obor3
def test_robot_rt(self):
of = oio.OboFile(data=obo_test_string)
obor1 = of.asObo(stamp=False, version=oio.OBO_VER_ROBOT)
rtp = temp_path / 'robot-test.obo'
robot_path = temp_path / 'robot-test.test.obo'
of.write(rtp, stamp=False, version=oio.OBO_VER_ROBOT)
cmd = f'robot convert -vvv -i {rtp.as_posix()} -o {robot_path.as_posix()}'
wat = os.system(cmd)
if wat:
raise ValueError(wat)
datas = []
for path in (rtp, robot_path):
with open(path, 'rt') as f:
datas.append(f.read())
ours, rob = datas
assert ours == rob
def main():
#ori = OntResIri('https://alt.olympiangods.org/sparc/ontologies/community-terms.ttl')
ori = OntResIri(
'http://localhost:8515/sparc/ontologies/community-terms.ttl')
rdfl = oq.plugin.get('rdflib')(ori.graph, OntId)
OntTerm.query_init(rdfl)
utr = UpstreamTermRequests()
_todo(utr)
return
# test output
tof = oio.OboFile()
utr.submit_to_obofile(tof, 'FIXME', (0, float('inf')))
tof.write(path=aug.RepoPath('/tmp/uberon-new-terms.obo'), overwrite=True)
ori_uberon = OntResIri('http://purl.obolibrary.org/obo/uberon.owl')
ori_uberon_meta = ori_uberon.metadata() # doap:GitRepository
breakpoint()
return