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 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)