def _rowhack(self, ns, rdflib):
# can't overwrite pyontutils.sheets.Row like we do in other cases sigh
curie = self.curie().value
if not curie:
return
oid = OntId(curie)
s = oid.u
_lon = (lambda v: None if not v else rdflib.Literal(v))
lon = lambda c: _lon(c.value)
_blon = lambda v: _lon(True if v == 'TRUE' else False
) # sigh sheets datatypes
blon = lambda c: _blon(c.value)
_oon = (lambda v: None if not v else OntId(v).u)
oon = lambda c: _oon(c.value)
self.type().value
self.mistake().value
pos = (
(ns.ilxtr.curationInternal, blon(self.curation_internal())),
(ns.definition, lon(self.definition())),
(ns.editorNote, lon(self.notes())),
(ns.rdf.type, oon(self.rdf_type())),
(ns.replacedBy, oon(self.replacedby_())),
(ns.ilxtr.futureType, oon(self.future_type())),
)
for p, o in pos:
if o is not None:
yield s, p, o
def _process(self, contributor):
# get member if we can find them
he = dat.HasErrors(pipeline_stage=self.__class__.__name__ + '.data')
if 'name' in contributor and 'first_name' in contributor:
name = contributor['name']
if ';' in name:
msg = f'Bad symbol in name {name!r}'
he.addError(msg)
logd.error(msg)
fn = contributor['first_name']
ln = contributor['last_name']
if ' ' in fn:
fn, mn = fn.split(' ', 1)
contributor['middle_name'] = mn
contributor['first_name'] = fn
if ' ' in ln:
msg = f'Malformed last_name {ln!r}'
he.addError(msg)
logd.error(msg)
ln = ln.replace(' ', '-')
failover = f'{fn}-{ln}'
member = self.member(fn, ln)
if member is not None:
userid = OntId('https://api.blackfynn.io/users/' + member.id)
contributor['blackfynn_user_id'] = userid
else:
member = None
failover = 'no-orcid-no-name'
log.warning(f'No name!' + lj(contributor))
orcid = None
if 'contributor_orcid_id' in contributor:
orcid = contributor['contributor_orcid_id']
if type(orcid) == str and 'orcid.org' in orcid:
orcid = OrcidId(orcid) # FIXME reloading from json
if isinstance(orcid, OrcidId):
s = orcid
else: # it's not an orcid or its a bad orcid
orcid = None
if orcid is None:
if member is not None:
s = userid
else:
log.debug(lj(contributor))
s = OntId(self.dsid + '/contributors/' + failover)
contributor['id'] = s
he.embedErrors(contributor)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# PLEASE DO NOT PUT PMIDs as external ids!!!
# FIXME idlib PMID(thing) urg the regex state machine is so simple ;_;
if self.id.startswith('PMID:'):
log.warning('PMIDs should never be External IDs!')
self._c_term = fake
self.s = OntId(self.id).URIRef
return
self.s = OntId(self.id).URIRef
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 l(self, value):
if isinstance(value, idlib.Stream) and hasattr(value, '_id_class'):
if hasattr(value, 'asUri'): # FIXME
return value.asUri(rdflib.URIRef)
else:
return value.asType(rdflib.URIRef)
if isinstance(value, OntId):
return value.u
if isinstance(value, ProtcurExpression):
return value
if isinstance(value, Quantity):
return value
elif isinstance(value, str) and value.startswith('http'):
return OntId(value).u
elif isinstance(value, dict): # FIXME this is too late to convert?
# NOPE! This idiot put a type field in his json dicts!
if 'type' in value:
if value['type'] == 'quantity':
return self.pyru._Quant.fromJson(value)
elif value['type'] == 'range':
return self.pyru.Range.fromJson(value)
elif value['type'] == 'identifier':
return fromJson(value).asType(rdflib.URIRef)
raise ValueError(value)
else:
return rdflib.Literal(value)
def triples_protcur(self, protocol_subject):
ps = list(self._protcur(str(protocol_subject)))
anatomy = [(p,
OntId('UBERON:' +
str(p).split('UBERON:', 1)[-1].split(' ', 1)[0]))
for p in ps if p.astType == 'protc:input'
and '(protc:input (term UBERON' in str(p)]
#breakpoint()
dataset_subject = rdflib.URIRef(self.uri_api)
yield protocol_subject, TEMP.hasNumberOfProtcurAnnotations, rdflib.Literal(
len(ps))
done = set()
for anno, term in anatomy:
if term in done:
continue
done.add(term)
o = term.u
t = dataset_subject, TEMP.involvesAnatomicalRegion, o
sl = rdflib.URIRef(anno.shareLink)
av = (((ilxtr.annotationValue, rdflib.Literal(anno.value)), )
if anno.value != o else tuple())
notes = [(ilxtr.curatorNote, rdflib.Literal(n))
for n in anno.curatorNotes]
prov = [(ilxtr.hasAnnotation, sl)]
yield t
yield from cmb.annotation(t, *av, *notes, *prov)()
def organ_term(self, dataset_id):
row = self._lookup(dataset_id)
if row:
ot = row.organ_term if row.organ_term else None
if ot:
ts = tuple(OntId(t) for t in ot.split(' ') if t)
return ts
def normv(v):
if isinstance(v, str) and v.startswith('http'):
# needed for loading from json that has been serialized
# rather than from our internal representation
# probably better to centralized the reload ...
oid = OntId(v)
if oid.prefix in want_prefixes:
return OntTerm(v).tabular()
else:
return oid.iri
if isinstance(v, OntId):
if not isinstance(v, OntTerm):
v = OntTerm(v)
v = v.tabular()
if isinstance(v, list) or isinstance(v, tuple):
v = ','.join(
json.dumps(_, cls=JEncode) if isinstance(_, dict
) else normv(_)
for _ in v)
v = v.replace('\n', ' ').replace('\t', ' ')
elif any(isinstance(v, c) for c in (int, float, str)):
v = str(v)
v = v.replace('\n',
' ').replace('\t',
' ') # FIXME tests to catch this
elif isinstance(v, dict):
v = json.dumps(v, cls=JEncode)
return v
def l(self, value):
if isinstance(value, BlackfynnId):
# FIXME this has to come first due ordering and impl issues with
# bfpnids being streams but not supporting all sorts of stuff
return rdflib.URIRef(value.uri_api)
if isinstance(value, idlib.Stream) and hasattr(value, '_id_class'):
if hasattr(value, 'asUri'): # FIXME
return value.asUri(rdflib.URIRef)
else:
return value.asType(rdflib.URIRef)
if isinstance(value, OntId):
return value.u
if isinstance(value, ProtcurExpression):
return value
if isinstance(value, Quantity):
return value
elif isinstance(value, str) and value.startswith('http'):
return OntId(value).u
elif isinstance(value, dict): # FIXME this is too late to convert?
# NOPE! This idiot put a type field in his json dicts!
if 'type' in value:
if value['type'] == 'quantity':
return self.pyru._Quant.fromJson(value)
elif value['type'] == 'range':
return self.pyru.Range.fromJson(value)
elif value['type'] == 'identifier':
return fromJson(value).asType(rdflib.URIRef)
raise ValueError(value)
else:
return rdflib.Literal(value)
def organ_term(self, dataset_id):
row = self._lookup(dataset_id)
organ_term = self.byCol.header.index('organ_term')
if row:
ot = row[organ_term] if row[organ_term] else None
if ot:
ts = tuple(OntId(t) for t in ot.split(' ') if t and t.lower() != 'na')
return ts
def triples_objects_ordered(self):
for key, predicate in self.objects_ordered_succession.items():
if key in self.blob:
values = self.blob[key]
if values:
assert not isinstance(values, str), f'{values} in {key}'
objects = [OntId(self.context[v.replace(' ', '-')]).URIRef for v in values]
for s, o in zip(objects[:-1],objects[1:]):
yield s, predicate, o
for key in self.objects_ordered:
if key in self.blob:
values = self.blob[key]
if values:
assert not isinstance(values, str), f'{values} in {key}'
objects = [OntId(self.context[v.replace(' ', '-')]).URIRef for v in values]
yield from cmb.olist(*objects)(self.s, ordered[key]) # NOTE scigraph does not translate rdf lists
def mkval(cell):
hl = cell.hyperlink
if hl is not None:
oid = OntId(hl)
if oid.prefix == 'TEMP':
logd.warning(f'{cell.value} -> {oid!r}')
#return OntTerm(curie=f'lex:{quote(cell.value)}')
#else:
return oid.asTerm()
else:
logd.warning(f'unhandled technique {cell.value}')
return cell.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 organ_term(self, dataset_id):
row = self._lookup(dataset_id)
if row:
organ_term = row.organ_term()
otv = organ_term.value
ot = otv if otv else None
if ot:
try:
ts = tuple(
OntId(t) for t in ot.split(' ')
if t and t.lower() != 'na')
return ts
except OntId.BadCurieError:
log.error(ot)
def fromRdf(cls, uri, graph, context=None):
oid = OntId(uri)
id = oid.curie
blob = {'id': id}
for p, o in graph[uri]:
if p == rdf.type:
key = 'class'
value = 'External'
else:
if p == rdfs.label:
key = 'name'
else:
_, key = p.rsplit('/', 1)
if isinstance(o, rdflib.Literal):
value = o.toPython()
elif isinstance(o, rdflib.URIRef):
oid = OntId(o)
if oid.prefix == 'local':
value = oid.suffix
elif oid.prefix == 'apinatomy': # FIXME hrm?
value = oid.suffix
else:
value = oid.curie # FIXME external is tricky
log.warning(f'{oid!r}')
if key in cls.objects_multi:
if key in blob:
blob[key].append(value)
else:
blob[key] = [value]
else:
blob[key] = value
return cls(blob, context)
def triples_objects_multi(self):
for key in self.objects_multi:
if key in self.blob:
values = self.blob[key]
assert not isinstance(values, str), f'{values} in {key}'
for value in values:
if key == 'external':
try:
o = OntId(value).URIRef
yield o, readable.annotates, self.s
except OntId.UnknownPrefixError as e:
log.exception(e)
continue
elif key == 'inheritedExternal':
try:
o = OntId(value).URIRef
except OntId.UnknownPrefixError as e:
log.exception(e)
continue
else:
value = value.replace(' ', '-') # FIXME require no spaces in internal ids
o = self.context[value]
yield self.s, readable[key], o
def fromRdf(cls, uri, graph, context=None):
_, id = uri.rsplit('/', 1)
blob = {'id': id}
for p, o in graph[uri]:
if p == rdf.type:
if o != owl.NamedIndividual:
key = 'class'
_, value = o.rsplit('/', 1)
else:
continue # TODO s rdf:type apinatomy:External ??
else:
_, key = p.rsplit('/', 1)
if isinstance(o, rdflib.Literal):
value = o.toPython()
elif isinstance(o, rdflib.URIRef):
oid = OntId(o)
if oid.prefix == 'local':
value = oid.suffix
elif oid.prefix == 'apinatomy': # FIXME hrm?
value = oid.suffix
else:
value = oid.curie # FIXME external is tricky
log.warning(f'{oid!r}')
elif isinstance(o, rdflib.BNode):
raise NotImplementedError(f'a bit more complex ...')
else:
raise NotImplementedError(f'{o}')
if key in cls.objects_ordered: # ordered representation takes priority
raise NotImplementedError('TODO this is quite a bit more complex')
if key in blob:
blob[key].append(value)
else:
blob[key] = [value]
elif key in cls.objects_multi:
if key in blob:
blob[key].append(value)
else:
blob[key] = [value]
else:
blob[key] = value
return cls(blob, context)
def _psd(self, rec, dsi):
type = rec['type']
spec_id = rec['specimen_id']
if type == 'SampleDirs':
sid = self.primary_key(spec_id)
elif type == 'SubjectDirs':
sid = self.subject_id(spec_id)
else:
raise NotImplementedError(f'wat {type}')
for drp in rec['dirs']:
path_record = dsi[drp]
collection_id = path_record['remote_id']
#p = (self.data['prov']['export_project_path'] /
#self.data['meta']['folder_name'] /
#drp)
#cid = p.cache.cache.uri_api
cid = OntId(collection_id).u
yield sid, TEMP.hasFolderAboutIt, cid
def l(self, value):
if isinstance(value, OntId):
return value.u
if isinstance(value, Expr):
return value
if isinstance(value, Quantity):
return value
elif isinstance(value, str) and value.startswith('http'):
return OntId(value).u
elif isinstance(value, dict): # FIXME this is too late to convert?
# NOPE! This idiot put a type field in his json dicts!
if 'type' in value:
if value['type'] == 'quantity':
return Quantity.fromJson(value)
elif value['type'] == 'range':
return Range.fromJson(value)
raise ValueError(value)
else:
return rdflib.Literal(value)
def triples_gen(self):
rm = self._source
# FIXME there doesn't seem to be a section that tells me the name
# of top level model so I have to know its name beforhand
# the id is in the model, having the id in the resource map
# prevents issues if these things get sent decoupled
id = rm['id']
mid = id.replace(' ', '-')
links = rm[id]['links']
#linknodes = [n for n in rm[id]['nodes'] if n['class'] == 'Link'] # visible confusion
st = []
from_to = []
ot = None
yield from self.apinatbase()
for link in links:
if 'conveyingType' in link:
if link['conveyingType'] == 'ADVECTIVE':
p_is = TEMP.isAdvectivelyConnectedTo
p_from = TEMP.advectivelyConnectsFrom
p_to = TEMP.advectivelyConnectsTo
p_cmat = TEMP.advectivelyConnectsMaterial
diffusive = False
elif link['conveyingType'] == 'DIFFUSIVE':
p_is = TEMP.isDiffusivelyConnectedTo
p_from = TEMP.diffusivelyConnectsFrom
p_to = TEMP.diffusivelyConnectsTo
p_cmat = TEMP.diffusivelyConnectsMaterial
diffusive = True
else:
log.critical(f'unhandled conveying type {link}')
continue
source = link['source']
target = link['target']
ok = True
if len(from_to) == 2: # otherwise
st = []
from_to = []
for i, e in enumerate((source, target)):
ed = rm[e]
if 'external' not in ed:
if not i and from_to:
# TODO make sure the intermediate ids match
pass
else:
ok = False
break
else:
st.append(e)
from_to.append(OntId(ed['external'][0]))
conveying = link['conveyingLyph']
cd = rm[conveying]
if 'external' in cd:
old_ot = ot
ot = OntTerm(cd['external'][0])
yield ot.u, rdf.type, owl.Class
yield ot.u, TEMP.internalId, rdflib.Literal(conveying)
yield ot.u, rdfs.label, rdflib.Literal(ot.label)
yield from self.materialTriples(
ot.u, link, p_cmat) # FIXME locate this correctly
if ok:
u, d = from_to
if st[0] == source:
yield u, rdfs.label, rdflib.Literal(
OntTerm(u).label)
yield u, rdf.type, owl.Class
yield from cmb.restriction.serialize(
ot.u, p_from, u)
if st[1] == target:
yield d, rdfs.label, rdflib.Literal(
OntTerm(d).label)
yield d, rdf.type, owl.Class
yield from cmb.restriction.serialize(ot.u, p_to, d)
if old_ot is not None and old_ot != ot:
yield from cmb.restriction.serialize(
ot.u, p_from, old_ot.u)
if diffusive:
# we can try to hack this using named individuals
# but it is not going to do exactly what is desired
s_link = TEMP[f'ApiNATOMY/{mid}/{link["id"]}']
s_cd = TEMP[f'ApiNATOMY/{mid}/{cd["id"]}']
yield s_link, rdf.type, owl.NamedIndividual
yield s_link, rdf.type, TEMP.diffusiveLink # FIXME I'm not sure these go in the model ...
yield s_cd, rdf.type, owl.NamedIndividual
if 'external' in cd and cd['external']:
oid = OntId(cd['external'][0])
yield s_cd, rdf.type, oid.u
ot = oid.asTerm()
if ot.label:
yield oid.u, rdfs.label, ot.label
else:
yield s_cd, rdf.type, TEMP.conveyingLyph
for icd in cd['inCoalescences']:
dcd = rm[icd]
log.info(lj(dcd))
s_icd = TEMP[f'ApiNATOMY/{mid}/{dcd["id"]}']
yield s_cd, TEMP.partOfCoalescence, s_icd
yield s_icd, rdf.type, owl.NamedIndividual
yield s_icd, rdf.type, TEMP[
'ApiNATOMY/Coalescence']
if 'external' in dcd and dcd['external']:
oid = OntId(dcd['external'][0])
yield s_icd, rdf.type, oid.u
ot = oid.asTerm()
if ot.label:
yield oid.u, rdfs.label, ot.label
for lyphid in dcd['lyphs']:
ild = rm[lyphid]
log.info(lj(ild))
if 'external' in ild and ild['external']:
yield s_icd, TEMP.hasLyphWithMaterial, OntId(
ild['external'][0])
if not ok:
logd.info(f'{source} {target} issue')
continue
for inid, e in zip(st, from_to):
yield e.u, rdf.type, owl.Class
yield e.u, rdfs.label, rdflib.Literal(OntTerm(e).label)
yield e.u, TEMP.internalId, rdflib.Literal(inid)
f, t = from_to
yield from cmb.restriction.serialize(f.u, p_is, t.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 '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
def triples_external(self):
if 'externals' in self.blob:
for external in self.blob['external']:
yield self.s, rdf.type, OntId(external).URIRef
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 _process(self, contributor):
# get member if we can find them
he = dat.HasErrors(pipeline_stage=self.__class__.__name__ + '.data')
if 'contributor_name' in contributor and 'first_name' in contributor:
name = contributor['contributor_name']
if ';' in name:
msg = f'Bad symbol in name {name!r}'
he.addError(msg)
logd.error(msg)
fn = contributor['first_name']
ln = contributor['last_name']
if ' ' in fn:
fn, mn = fn.split(' ', 1)
mn, _mn = mn.rstrip('.'), mn
if mn != _mn:
he.addError(f'Middle initials don\'t need periods :) {name!r}',
logfunc=logd.error)
contributor['middle_name'] = mn
contributor['first_name'] = fn
if ' ' in ln:
msg = f'Malformed last_name {ln!r}'
he.addError(msg)
logd.error(msg)
ln = ln.replace(' ', '-')
failover = f'{fn}-{ln}'
member = self.member(fn, ln)
if member is not None:
userid = OntId('https://api.blackfynn.io/users/' + member.id)
contributor['blackfynn_user_id'] = userid
else:
member = None
failover = 'no-orcid-no-name'
log.warning(f'No name!' + lj(contributor))
orcid = None
if 'contributor_orcid_id' in contributor:
orcid = contributor['contributor_orcid_id']
if type(orcid) == str and 'orcid.org' in orcid:
orcid = idlib.Orcid(orcid) # FIXME reloading from json
if isinstance(orcid, idlib.Orcid):
s = orcid
else: # it's not an orcid or its a bad orcid
orcid = None
if orcid is None:
if member is not None:
s = userid
else:
log.debug(lj(contributor))
s = OntId(self.dsid + '/contributors/' + failover)
contributor['id'] = s
he.embedErrors(contributor)
# lifting + adding
if 'contributor_affiliation' in contributor:
ca = contributor['contributor_affiliation']
maybe_ror = self.lifters.affiliations(ca)
if maybe_ror is not None:
contributor['affiliation'] = maybe_ror