althonos / althonos/pronto

.obo SyntaxErorrs

Aperta
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Lingua principale
Python
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267
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Descrizione

What is the best way to force pronto to continue in the face of messy/real data?

```
>>> cl = Ontology("http://purl.obolibrary.org/obo/uberon.obo")
Traceback (most recent call last):
File "", line 1, in
File "/home/plastic/anaconda3/envs/uberon/lib/python3.8/site-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/home/plastic/anaconda3/envs/uberon/lib/python3.8/site-packages/pronto/parsers/obo.py", line 45, in parse_from
raise SyntaxError(s.args[0], location) from None
File "http://purl.obolibrary.org/obo/uberon.obo", line 199316
def: "A free, modified neural spine of a preural or a ural vertebra that is placed between the last developed neural spine of a preural centrum and the dorsal axis (= anterior margin of first uroneural) of the caudal skeleton . An epural commonly supports one or more dorsal procurrent rays. An epural is an unpaired median perichondrally ossified bone." [TAO:Arratia and Schultze_1992]␊
^
SyntaxError: expected QuotedString

>>> cl = Ontology("http://purl.obolibrary.org/obo/cl.obo")
Traceback (most recent call last):
File "", line 1, in
File "/home/plastic/anaconda3/envs/uberon/lib/python3.8/site-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/home/plastic/anaconda3/envs/uberon/lib/python3.8/site-packages/pronto/parsers/obo.py", line 45, in parse_from
raise SyntaxError(s.args[0], location) from None
File "http://purl.obolibrary.org/obo/cl.obo", line 163708
creation_date: 202z-09-29T15:45:36Z␊
^
SyntaxError: expected Iso8601Year

>>> cl = Ontology("http://purl.obolibrary.org/obo/basic.obo")
Traceback (most recent call last):
File "", line 1, in
File "/home/plastic/anaconda3/envs/uberon/lib/python3.8/site-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/home/plastic/anaconda3/envs/uberon/lib/python3.8/site-packages/pronto/parsers/rdfxml.py", line 89, in parse_from
raise ValueError("could not find `owl:Ontology` element")
ValueError: could not find `owl:Ontology` element

```

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