def added(self):
data = super().added
# FIXME conditional lifts ...
if 'award_number' not in data['meta']:
am = self.lifters.award_manual
if am:
data['meta']['award_number'] = am
if 'modality' not in data['meta']:
m = self.lifters.modality
if m:
data['meta']['modality'] = m
if 'organ' not in data['meta']:
if 'award_number' in data['meta']:
an = data['meta']['award_number']
o = self.lifters.organ(an)
if o:
if o != 'othertargets':
o = OntId(o)
if o.prefix == 'FMA':
ot = OntTerm(o)
o = next(
OntTerm.query(label=ot.label,
prefix='UBERON')).OntTerm
data['meta']['organ'] = o
if 'organ' not in data['meta'] or data['meta'][
'organ'] == 'othertargets':
o = self.lifters.organ_term
if o:
if isinstance(o, str):
o = o,
out = tuple()
for _o in o:
_o = OntId(_o)
if _o.prefix == 'FMA':
ot = OntTerm(_o)
_o = next(
OntTerm.query(label=ot.label,
prefix='UBERON')).OntTerm
out += (_o, )
data['meta']['organ'] = out
return data
def _update_technique(self, cell):
# NOTE some rows won't update if the dataset no longer exists
value = cell.value
if value:
try:
term = next(OntTerm.query(label=value))
cell.value = term.asCellHyperlink()
except StopIteration:
log.info(f'no term for technique {value}')
def query(value, prefix):
for query_type in ('term', 'search'):
terms = [q.OntTerm for q in OntTerm.query(prefix=prefix, **{query_type:value})]
if terms:
#print('matching', terms[0], value)
#print('extra terms for', value, terms[1:])
return terms[0]
else:
continue
else:
log.warning(f'No ontology id found for {value}')
return value
def award_number(self, value):
_, s = self.c.award_number(value)
yield s, a, owl.NamedIndividual
yield s, a, TEMP.FundedResearchProject
return
o = self.integrator.organ(value)
if o:
if o != 'othertargets':
o = OntId(o)
if o.prefix == 'FMA':
ot = OntTerm(o)
o = next(OntTerm.query(label=ot.label, prefix='UBERON')).OntTerm
yield s, isAbout, o.u
def added(self):
data = super().added
if data['meta'] == {'techniques': []}:
breakpoint()
# FIXME conditional lifts ...
if 'award_number' not in data['meta']:
am = self.lifters.award_manual
if am:
data['meta']['award_number'] = am
if 'modality' not in data['meta']:
m = self.lifters.modality
if m:
data['meta']['modality'] = m
if False and 'organ' not in data['meta']:
# skip here, now attached directly to award
if 'award_number' in data['meta']:
an = data['meta']['award_number']
o = self.lifters.organ(an)
if o:
if o != 'othertargets':
o = OntId(o)
if o.prefix == 'FMA':
ot = OntTerm(o)
o = next(
OntTerm.query(label=ot.label, prefix='UBERON'))
data['meta']['organ'] = o
if 'organ' not in data['meta'] or data['meta'][
'organ'] == 'othertargets':
o = self.lifters.organ_term
if o:
if isinstance(o, str):
o = o,
out = tuple()
for _o in o:
_o = OntId(_o)
if _o.prefix == 'FMA':
ot = OntTerm(_o)
_o = next(
OntTerm.query(label=ot.label, prefix='UBERON'))
out += (_o, )
data['meta']['organ'] = out
if 'protocol_url_or_doi' not in data['meta']:
if self.lifters.protocol_uris:
data['meta']['protocol_url_or_doi'] = tuple(
self.lifters.protocol_uris)
else:
if not isinstance(data['meta']['protocol_url_or_doi'], tuple):
_test_path = deque(['meta', 'protocol_url_or_doi'])
if not [e for e in data['errors'] if e['path'] == _test_path]:
raise ext.ShouldNotHappenError('urg')
else:
data['meta']['protocol_url_or_doi'] += tuple(
self.lifters.protocol_uris)
data['meta']['protocol_url_or_doi'] = tuple(
sorted(set(data['meta']['protocol_url_or_doi']))) # ick
return data
def added(self):
data = super().added
if data['meta'] == {'techniques': []}:
breakpoint()
# FIXME conditional lifts ...
if 'award_number' not in data['meta']:
am = self.lifters.award_manual
if am:
data['meta']['award_number'] = am
if 'modality' not in data['meta']:
m = self.lifters.modality
if m:
data['meta']['modality'] = m
if False and 'organ' not in data['meta']:
# skip here, now attached directly to award
if 'award_number' in data['meta']:
an = data['meta']['award_number']
o = self.lifters.organ(an)
if o:
if o != 'othertargets':
o = OntId(o)
if o.prefix == 'FMA':
ot = OntTerm(o)
o = next(OntTerm.query(label=ot.label, prefix='UBERON'))
data['meta']['organ'] = o
if 'organ' not in data['meta'] or data['meta']['organ'] == 'othertargets':
o = self.lifters.organ_term
if o:
if isinstance(o, str):
o = o,
out = tuple()
for _o in o:
_o = OntId(_o)
if _o.prefix == 'FMA':
ot = OntTerm(_o)
_o = next(OntTerm.query(label=ot.label, prefix='UBERON'))
out += (_o,)
data['meta']['organ'] = out
if 'protocol_url_or_doi' not in data['meta']:
if self.lifters.protocol_uris:
data['meta']['protocol_url_or_doi'] = tuple(self.lifters.protocol_uris)
else:
if not isinstance(data['meta']['protocol_url_or_doi'], tuple):
_test_path = deque(['meta', 'protocol_url_or_doi'])
if not [e for e in data['errors']
if 'path' in e and e['path'] == _test_path]:
raise ext.ShouldNotHappenError('urg')
else:
data['meta']['protocol_url_or_doi'] += tuple(self.lifters.protocol_uris)
data['meta']['protocol_url_or_doi'] = tuple(sorted(set(data['meta']['protocol_url_or_doi']))) # ick
# FIXME this is a really bad way to do this :/ maybe stick the folder in data['prov'] ?
# and indeed, when we added PipelineStart this shifted and broke everything
local = (self
.previous_pipeline.pipelines[0]
.previous_pipeline.pipelines[0]
.previous_pipeline.pipelines[0]
.path)
remote = local.remote
if 'doi' not in data['meta']:
doi = remote.doi
if doi is not None:
try:
metadata = doi.metadata()
if metadata is not None:
data['meta']['doi'] = doi.identifier
except requests.exceptions.HTTPError:
data['meta']['doi'] = None
pass
else:
data['meta']['doi'] = None
if 'status' not in data:
data['status'] = {}
if 'status_on_platform' not in data['status']:
data['status']['status_on_platform'] = remote.bfobject.status
return data
