Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Produce more informative errors messages when owlapi fails to parse manchester #347

Open
ramonawalls opened this issue Aug 26, 2021 · 2 comments
Assignees

Comments

@ramonawalls
Copy link

I have a pattern with 7 variables and an input file with 242 rows. When I try to run the file through dosdp-tools generate, I get an error message

An unchecked error was produced.
org.semanticweb.owlapi.manchestersyntax.renderer.ParserException: Encountered 'age category' at line 1 column 76. Expected one of:
	Class name
	(
	{
	Self

However, I know for sure 'age category' is a class. If I take the first 25 rows of the same file and run the tool, it works fine, so the age category label is not the problem. I am wondering if it could be throwing a strange error because the file is so large it times out. Even with only 25 rows, it takes several minutes to process.

@ramonawalls
Copy link
Author

Nevermind. Of course I stared at this for three days and found the problem right after submitting this ticket. It turns out that one of the rows much lower down had the variable ID and variable name switch. Fixing that solved the problem.

Perhaps the error message could be updated, though. "Encountered 'age category' at line 1 column 76." suggests that the problem was in the first row, when in fact it was in a much later row.

@dosumis
Copy link

dosumis commented Aug 26, 2021

The error message comes from the Manchester syntax parser and indicates an unknown OWL entity: the error is at line 1 column 76 of an OWL class expression - presumably your templated EquivalentTo statement. It may be possible to wrap the error message to indicate this context and to indicate the line in the table being processed that causes the problem.

  • @balhoff - do you think this would be straightforward to implement?
  • If so - @hkir-dev would you be able to look in to fixing?
  • @ramonawalls - could you post the broken example somewhere?

@cmungall cmungall changed the title Size limit on pattern files? Produce more informative errors messages when owlapi fails to parse manchester Nov 2, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

4 participants