ValueError: could not find a parser to parse 'http://purl.obolibrary.org/obo/doid/obo/ext.owl' when parsing human disease ontology
Zethson opened this issue · 2 comments
Zethson commented
When attempting to get the human disease ontology (https://www.ebi.ac.uk/ols/ontologies/doid)
ontology = Ontology("doid.owl")
I run into
Traceback (most recent call last):
File "/home/zeth/PycharmProjects/bionty/test.py", line 8, in <module>
ontology = Ontology("/home/zeth/Downloads/doid.owl")
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/rdfxml.py", line 95, in parse_from
self.process_imports(
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/base.py", line 70, in process_imports
return dict(pool.map(lambda i: (i, process(i)), imports))
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/base.py", line 70, in <lambda>
return dict(pool.map(lambda i: (i, process(i)), imports))
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/base.py", line 49, in process_import
return Ontology(url, max(import_depth - 1, -1), timeout)
File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/ontology.py", line 286, in __init__
raise ValueError(f"could not find a parser to parse {handle!r}")
ValueError: could not find a parser to parse 'http://purl.obolibrary.org/obo/doid/obo/ext.owl'
Zethson commented
The current obo file is still working though
Zethson commented
Solved upstream