def main():
dandi_terms_path = aug.LocalPath.cwd()
g = OntGraph()
_ = [
populateFromJsonLd(g, path_yaml(p))
for p in dandi_terms_path.rglob('*.yaml')
]
g.write('dandi-raw.ttl')
remove = [(s, p, o) for p in (schema.domainIncludes, schema.rangeIncludes,
rdfs.subClassOf, rdf.type)
for s, o in g[:p:]]
add = [(s, p, (g.namespace_manager.expand(o.toPython()) if isinstance(
o, rdflib.Literal) else o)) for s, p, o in remove]
_ = [g.remove(t) for t in remove]
_ = [g.add(t) for t in add]
# TODO ontology metadata header section
g.write('dandi.ttl')
def inner(local_filepath, remote=False):
if noneMembers(local_filepath, *bigleaves) or dobig:
ext = os.path.splitext(local_filepath)[-1]
if ext == '.ttl':
infmt = 'turtle'
else:
log.info((ext, local_filepath))
infmt = None
if remote:
resp = requests.get(
local_filepath
) # TODO nonblocking pull these out, fetch, run inner again until done
raw = resp.text.encode()
else:
try:
with open(local_filepath, 'rb') as f:
raw = f.read()
except FileNotFoundError as e:
if local_filepath.startswith('file://'):
log.info(
f'local_imports has already been run, skipping {local_filepath}'
)
return
#raise ValueError('local_imports has already been run') from e
else:
log.exception(
e
) # TODO raise a warning if the file cannot be matched
# seems like good practice to have any imported ontology under
# version control so all imports are guaranteed to have good
# provenance and not split the prior informaiton between the
# scigraph config and the repository, the repository remains
# the source of truth, load.yaml files can then pick a subset
# of the properly tracked files to load as they see fit, but
# not add to them (at least in pyontutils land)
raw = b''
if oo in raw: # we only care if there are imports or an ontology iri
scratch = OntGraph()
if infmt == 'turtle':
data, rest = raw.split(b'###', 1)
elif infmt == None: # assume xml
xml_tree = etree.parse(BytesIO(raw))
xml_root = xml_tree.getroot()
xml_ontology = xml_tree.xpath(
"/*[local-name()='RDF']/*[local-name()='Ontology']")
xml_root.clear()
xml_root.append(xml_ontology[0])
data = etree.tostring(xml_root)
scratch.parse(data=data, format=infmt)
for s in scratch.subjects(rdf.type, owl.Ontology):
triples.add((s, owl.sameAs, rdflib.URIRef(local_filepath)))
# somehow this breaks computing the chain
#for p in (rdfs.comment, skos.definition, definition, dc.title, rdfs.label):
#for o in scratch[s:p]:
#triples.add((s, p, o))
for s, o in sorted(scratch.subject_objects(p)):
if revert:
raise NotImplementedError('TODO')
nlfp = o.replace(remote_base, local_base)
triples.add((s, p, o))
if 'http://' in local_filepath or 'external' in local_filepath: # FIXME what to do about https used inconsistently :/
if 'external' in local_filepath:
imported_iri = rdflib.URIRef(
local_filepath.replace(
local_base, remote_base)) # inefficient
else:
imported_iri = rdflib.URIRef(local_filepath)
if s != imported_iri:
imported_iri_vs_ontology_iri[
imported_iri] = s # kept for the record
triples.add((imported_iri, p,
s)) # bridge imported != ontology iri
if local_base in nlfp and 'file://' not in o: # FIXME file:// should not be slipping through here...
scratch.add((s, p, rdflib.URIRef('file://' + nlfp)))
scratch.remove((s, p, o))
if nlfp not in done:
done.append(nlfp)
if local_base in nlfp and 'external' not in nlfp: # skip externals TODO
inner(nlfp)
elif readonly: # read external imports
if 'external' in nlfp:
inner(nlfp)
else:
inner(nlfp, remote=True)
if not readonly:
_orp = CustomTurtleSerializer.roundtrip_prefixes # FIXME awful hack :/
CustomTurtleSerializer.roundtrip_prefixes = True
ttl = scratch.serialize(format='nifttl', encoding='utf-8')
CustomTurtleSerializer.roundtrip_prefixes = _orp
ndata, comment = ttl.split(b'###', 1)
out = ndata + b'###' + rest
with open(local_filepath, 'wb') as f:
f.write(out)
