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Parse error using .obo URLs #302

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kimrutherford opened this issue May 27, 2020 · 18 comments
Open

Parse error using .obo URLs #302

kimrutherford opened this issue May 27, 2020 · 18 comments

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@kimrutherford
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Hi.

We're seeing a problem with .obo URLs using the 2020-04-06 release.

Command lines this work fine:

owltools http://purl.obolibrary.org/obo/cl.owl --ancestors neuron

But changing to a .obo purl results in a parse error. Here's an example:

owltools http://purl.obolibrary.org/obo/cl.obo --ancestors neuron

Here is the full output from the command:
errors.txt

@jseager7 noticed this in the error output and suggested that perhaps the 304 redirect isn't being followed:

Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@35835fa
    Stack trace:
LINENO: 1 - Could not find tag separator ':' in line.
LINE: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60)

The pattern seems the same with other ontologies. @jseager7 first noticed the problem with: http://purl.obolibrary.org/obo/phipo/phipo-simple.obo

Please let us know if you need any other details.

Thanks.
@kimrutherford kimrutherford mentioned this issue May 27, 2020
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@matentzn
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I noticed that as well! High priority, because it happens for robot as well! @balhoff @jamesaoverton

robot -vvv merge -i http://purl.obolibrary.org/obo/cl.obo -o test.obo

@balhoff
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balhoff commented May 27, 2020

@matentzn so must be related to OWL API version?

@matentzn
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But that has not been updated for so long! No one noticed for such a long time?

@balhoff
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balhoff commented May 27, 2020

By the way your command should be: robot -vvv merge -I http://purl.obolibrary.org/obo/cl.obo -o test.obo

(does show the problem)

@matentzn
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Oh yeah sorry.

@matentzn
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@ignazio1977 did we know about this? Is this a problem with how the obo purls are redirected?

@balhoff
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balhoff commented May 27, 2020 •
edited

owltools is on OWL API 4.5.6. I tested rolling back to 4.5.1 and it works again.

Update—4.5.4 also errors. For some reason I can't compile owltools with 4.5.2.

@balhoff
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balhoff commented May 27, 2020

owltools has been using this OWL API version for about 18 months: ad67869#diff-852a5f234948b0c35064c26937d12558

Not sure how no one noticed this!

balhoff added a commit that referenced this issue May 27, 2020
@balhoff
Roll back to OWL API 4.5.1. See #302.
cdacc6b
@ignazio1977
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@matentzn Nothing I'm aware of but the OBO parser manages imports and URL loading differently from the other parsers, and more so in those fairly ancient releases.

@matentzn
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Thanks, @ignazio1977, do you know if anyone has changed the OBO parser between 4.5.1 and 4.5.6?

@ignazio1977
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Most likely me :-) I'll replicate and see if it can be fixed.

@matentzn
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Thanks a ton! :)

@ignazio1977
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Failure can be replicated on the latest version 4 but not on version 5 and 6. So this seems tied to the changes in handling HTTP connections, if I remember correctly we changed http libraries in version 5.

@matentzn
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Thanks a lot @ignazio1977! Do you think the churn is too high to fix this for the 4.X versions of OWL API as well? I have started to migrate some tools to 5 and 6, but it may take a while for other toolkits like this here owltools to catch up..

@ignazio1977
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Can't tell just yet.

@ignazio1977
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Adapting the obo parser to behave like the other parsers seems to have been effective. owlcs/owlapi@7919ca9

@matentzn
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Wow that is a serious change :) THANKS a lot! If you remember to: ping us when the change is live. Thank you again!

@ignazio1977
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Fix included in OWLAPI 4.5.17

balhoff added a commit that referenced this issue Jul 9, 2020
@balhoff
Update to OWL-API 4.5.17. Should address #302.
b44a727
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@kimrutherford @balhoff @ignazio1977 @matentzn