def test_threading_detect(self):
frame_count = sum(1 for _ in fastobo.iter(MS, threads=0))
self.assertEqual(frame_count, MS_FRAMES)
with open(MS, 'rb') as f:
frame_count = sum(1 for _ in fastobo.iter(f, threads=0))
self.assertEqual(frame_count, MS_FRAMES)
def parse_from(self, handle, threads=None):
# Load the OBO document through an iterator using fastobo
doc = fastobo.iter(handle, ordered=True)
# Extract metadata from the OBO header and resolve imports
self.ont.metadata = self.extract_metadata(doc.header())
self.ont.imports.update(
self.process_imports(
self.ont.metadata.imports,
self.ont.import_depth,
os.path.dirname(self.ont.path or str()),
self.ont.timeout,
)
)
# Merge inheritance cache from imports
self.import_inheritance()
# Extract frames from the current document.
try:
with multiprocessing.pool.ThreadPool(threads) as pool:
pool.map(self.extract_entity, doc)
except SyntaxError as s:
location = self.ont.path, s.lineno, s.offset, s.text
raise SyntaxError(s.args[0], location) from None
# Update inheritance cache with symmetric of `subClassOf`
self.symmetrize_inheritance()
def load_ontology(self, path):
"""Load and parse ontologies - currently support OBO files only."""
if path is None:
path = self.DefaultOnotology
try:
with fsspec.open(path) as f:
obo = fastobo.iter(f)
terms = filter(
lambda stanza: type(stanza) is fastobo.term.TermFrame, obo)
names = [
tag.name for term in terms for tag in term
if type(tag) is fastobo.term.NameClause
]
self.ontology_data = names
except FileNotFoundError as e:
raise OntologyLoadFailure(
"Unable to find OBO ontology path") from e
except SyntaxError as e:
raise OntologyLoadFailure(
f"{path}:{e.lineno}:{e.offset} OBO syntax error, unable to read ontology"
) from e
except Exception as e:
raise OntologyLoadFailure(f"{path}:Error loading OBO file") from e
def parse_from(self, handle):
# Load the OBO document through an iterator using fastobo
doc = fastobo.iter(handle)
# Extract metadata from the OBO header and resolve imports
self.ont.metadata = self.extract_metadata(doc.header())
self.ont.imports.update(
self.process_imports(
self.ont.metadata.imports,
self.ont.import_depth,
os.path.dirname(self.ont.path or str()),
self.ont.timeout,
))
# Extract frames from the current document.
try:
for frame in doc:
if isinstance(frame, fastobo.term.TermFrame):
self.enrich_term(frame)
elif isinstance(frame, fastobo.typedef.TypedefFrame):
self.enrich_relationship(frame)
except SyntaxError as s:
location = self.ont.path, s.lineno, s.offset, s.text
raise SyntaxError(s.args[0], location) from None
