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/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/ontology.py:283: in __init__
cls(self).parse_from(_handle) # type: ignore
/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/parsers/obo.py:26: in parse_from
self.process_imports(
/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/parsers/base.py:70: in process_imports
return dict(pool.map(lambda i: (i, process(i)), imports))
/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py:364: in map
return self._map_async(func, iterable, mapstar, chunksize).get()
/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py:771: in get
raise self._value
/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py:125: in worker
result = (True, func(*args, **kwds))
/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py:48: in mapstar
return list(map(*args))
/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/parsers/base.py:70: in <lambda>
return dict(pool.map(lambda i: (i, process(i)), imports))
/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/parsers/base.py:49: in process_import
return Ontology(url, max(import_depth - 1, -1), timeout)
/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/ontology.py:283: in __init__
cls(self).parse_from(_handle) # type: ignore
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self = <pronto.parsers.rdfxml.RdfXMLParser object at 0x7f8f390bb490>
handle = <BufferedReader>, threads = None
def parse_from(self, handle, threads=None):
# Load the XML document into an XML Element tree
tree: etree.ElementTree = etree.parse(handle)
# Load metadata from the `owl:Ontology` element
owl_ontology = tree.find(_NS["owl"]["Ontology"])
if owl_ontology is None:
> raise ValueError("could not find `owl:Ontology` element")
E ValueError: could not find `owl:Ontology` element
/Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pronto/parsers/rdfxml.py:89: ValueError
the imported ontology can be loaded fine into pronto directly
Ideally:
it should be possible to specify a dict for rewiring imports
there would a reader for the catalog format that would make this dict
It should also be possible to map an ontology import to a /dev/null empty ontology. It's not atypical for an edit version of an ontology to import a local ontology in functional syntax (e.g. go-edit.obo does this for GCIs)
The text was updated successfully, but these errors were encountered:
…urce and CLI, to determine how deep in import hierarchy to traverse (#249)
* Adding tests for import behavior.
Adding import_depth to OntologyResource and CLI,
to determine how deep in import hierarchy to traverse
* black
* Skipping pronto import test; awaiting althonos/pronto#186
It is common practice to include a catalog-v001.xml file that determines how imports should be resolved,
e.g:
https://github.com/INCATools/ontology-access-kit/blob/20e82c06b53e414454f50ca9d9f82468b5867f9d/tests/input/catalog-v001.xml
example input:
https://github.com/INCATools/ontology-access-kit/blob/20e82c06b53e414454f50ca9d9f82468b5867f9d/tests/input/test_import_root.obo
When running locally, the import would resolve to:
https://github.com/INCATools/ontology-access-kit/blob/20e82c06b53e414454f50ca9d9f82468b5867f9d/tests/input/test_imported_ontology.owl
gives a stack trace:
the imported ontology can be loaded fine into pronto directly
Ideally:
It should also be possible to map an ontology import to a /dev/null empty ontology. It's not atypical for an edit version of an ontology to import a local ontology in functional syntax (e.g. go-edit.obo does this for GCIs)
The text was updated successfully, but these errors were encountered: