OEWG 20110830: Difference between revisions

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*** Added bug report for this: [http://sourceforge.net/tracker/?func=detail&aid=3384594&group_id=36855&atid=418257 Checks run "on text commit" don't show warning messages]
*** Added bug report for this: [http://sourceforge.net/tracker/?func=detail&aid=3384594&group_id=36855&atid=418257 Checks run "on text commit" don't show warning messages]
**** This is not generally an issue, because the Redundant Name Check was in fact the ONLY verification check that was set to run "On text commit" but not "During text edit".
**** This is not generally an issue, because the Redundant Name Check was in fact the ONLY verification check that was set to run "On text commit" but not "During text edit".
** I fixed this by making this check run "On text edit", and now you see a warning (in the Text Editor titlebar) if you give a term a name that another (non-obsolete) term has.
** I fixed this by making this check run "On text edit", and now you see a warning (in the Text Editor titlebar) if you give a term a name that another (non-obsolete) term has. (Like before, this is not a fatal error; it's a warning.)
** This is not a fatal error; it's a warning.
** Future feature request: [http://sourceforge.net/tracker/?func=detail&atid=418260&aid=3397656&group_id=36855 Enable users to configure checks as warnings or errors]
** Future feature request: [http://sourceforge.net/tracker/?func=detail&atid=418260&aid=3397656&group_id=36855 Enable users to configure checks as warnings or errors]
*** Note that this could be a way to mitigate this problem: [http://sourceforge.net/tracker/index.php?func=detail&aid=3213853&group_id=36855&atid=418257 fatal errors in ontologies that aren't yours preventing you from saving edits you've made to your ontology after loading multiple ontologies].
*** Note that this could be a way to mitigate this problem: [http://sourceforge.net/tracker/index.php?func=detail&aid=3213853&group_id=36855&atid=418257 fatal errors in ontologies that aren't yours preventing you from saving edits you've made to your ontology after loading multiple ontologies].


* [http://sourceforge.net/tracker/?func=detail&aid=3388601&group_id=36855&atid=418257 obo2obo no longer prints status messages to stdout]
* [http://sourceforge.net/tracker/?func=detail&aid=3388601&group_id=36855&atid=418257 obo2obo no longer prints status messages to stdout]
* [ http://sourceforge.net/tracker/?func=detail&aid=3394041&group_id=36855&atid=418257 Quick fix for repeated words etc. adds to wrong file]
* [http://sourceforge.net/tracker/?func=detail&aid=3394041&group_id=36855&atid=418257 Quick fix for repeated words etc. adds to wrong file]
** The quick fixes were adding to files in oboedit_config instead of oboedit_config/dict (so Jane and other users had to add the fixes by hand)
** The quick fixes were adding to files in oboedit_config instead of oboedit_config/dict (so Jane and other users had to add the fixes by hand)



Revision as of 18:21, 24 August 2011

OBO-Edit Working Group Meeting: Tuesday, August 30, 2011, 8:30am PDT

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Minutes:
Attendees:

Bug and Feature Trackers

Fixed since last meeting

Discussion Items

  • New file browser had bug in b17--Heiko quickly fixed it and we released b18 the next day.
  • Did anyone (other than Midori) get a chance to test obo2obo to make sure my fix for [ geneontology-Bugs-3316815 ] (filtered save doesn't save dangling parents) didn't break anything in obo2obo?
    • Midori found one issue in obo2obo but it turned out to be old and unimportant
    • Fixed problem where obo2obo recently stopped printing status messages to stdout.
    • The obo2obo tests I tried yielded the same output for OE 2.0 and 2.1-b18.
  • Next meeting: we will skip Tuesday, September 6 and meet next on September 20.
  • With a new academic year starting, should we revisit the meeting day/time or just keep it as it is?

Currently working on

  • Working towards making an official 2.1 release
    • Trying to get JUnit tests working again (for OBO and OBO-Edit) and make sure that current OE behavior is no worse than the behavior of 2.0.
  • Is_a closure broken
    • Terry wrote, "I just used beta14 to do is_a closure on cell.edit.obo with GO and PR. Overall it worked but there were two issues. 1) Non is_a relationships for previously MIREOTED terms were added, leading to a dangling parents error. For example, "regulates" relationships were added to many GO terms that were already in CL. 2nd, all typedefs disappeared."
    • Midori commented, "I can confirm that I get the same thing (or at least something similar) happening with 'regulates' relationships: is_a closure saves some terms that would only be there if it followed at least one 'regulates' link. Curiously, it didn't include all 'regulates' links; the term I used for testing had a regulates link itself that apparently wasn't followed. Specifically, I tested using a nonsense xp in SO, with the GO term 'regulation of polysaccharide metabolic process' in an intersection_of tag. The saved file contained all the is_a ancestors I expected, plus the is_a ancestors of 'polysaccharide metabolic process' -- but it didn't have 'polysaccharide metabolic process' itself. I'm getting typedefs saved if they match the filter, and not if they don't (all are saved if I tick 'always save properties' - that seems to be working fine).


Next bugs to work on

  • Fixing JUnit tests for OBO and OBO-Edit
  • Fixing any bugs that the JUnit tests reveal

Discussion

Links

Back to OEWG meeting agenda and minutes list