owltools Parse error using .obo URLs

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.

May 27 '20 12:05 kimrutherford

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

May 27 '20 15:05 matentzn

@matentzn so must be related to OWL API version?

May 27 '20 15:05 balhoff

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

May 27 '20 15:05 matentzn

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)

May 27 '20 15:05 balhoff

Oh yeah sorry.

May 27 '20 15:05 matentzn

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

May 27 '20 15:05 matentzn

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.

May 27 '20 15:05 balhoff

owltools has been using this OWL API version for about 18 months: https://github.com/owlcollab/owltools/commit/ad678691f43d1cdb1c445a294f77ac9f6ed3fc26#diff-852a5f234948b0c35064c26937d12558

Not sure how no one noticed this!

May 27 '20 16:05 balhoff

@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.

May 27 '20 20:05 ignazio1977

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

May 27 '20 20:05 matentzn

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

May 27 '20 20:05 ignazio1977

Thanks a ton! :)

May 27 '20 21:05 matentzn

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.

May 27 '20 22:05 ignazio1977

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..

May 28 '20 06:05 matentzn

Can't tell just yet.

May 28 '20 19:05 ignazio1977

Adapting the obo parser to behave like the other parsers seems to have been effective. https://github.com/owlcs/owlapi/commit/7919ca9b865b703cf0ac9c70efbba10968b1206a

May 28 '20 22:05 ignazio1977

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

May 29 '20 07:05 matentzn

Fix included in OWLAPI 4.5.17

Jul 05 '20 08:07 ignazio1977