OEWG 20090120

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OBO-Edit Working Group, Tuesday January 20th, 2008 9.30 a.m. PST

Agenda/Chair: Jeniffer
Minutes: Karen C

Attendees: Karen C, Midori, Jen, Harold, DavidOS, Amina, Chris

Meeting Agenda

not posted

Action items carried over

Deadline for testing: January 31st Editors dedicate more time - other members pick a component every week.

Report testing progress the following on Tuesday Jan 20th
Jen: All sections I signed up for
Melissa: Ontology Tree Editor
KarenC: Graph Editor w/ graphics
DavidOS: xps and related topics
Amina testing and bugs -
- Filters and Renderers section.
- Cross products tab in Text Editor
- Manual and auto-commit
- Graphviz viewer save image gif format

Discussion items



For US residents, this was a short week due to the Monday holiday, Martin Luther King day. KarenC also took Friday off. DavidOS didn't get the MLK holiday but was sick most of the week. Thus, neither of these two did any testing during the past week. Melissa was absent so did not report on her progress.


Midori reported that she had tested, on an OSX platform, all of the metadata items, most of which were working, and made appropriate comments on the web.

Dbxref bug

Amina asked if Midori had had a chance to test the fix to the dbxref bug that was made in beta-53. Midori did that during the meeting and reported that it now worked but was unpleasantly slow.

Graph Editor

Jen asked what it meant when a link in the Graph Editor was indicated with a thick, light blue line. Both David and Karen answered that this is how a link is displayed when it is selected.

Import Terms

Jane had asked if there was a problem with the Import Terms function. Amina reports that it works for her, but that there is no documentation as to usage or expected behavior, so she will add this documentation.


Jen reported that making cross products isn't as hard as might be expected and that this project is going quite well. However, it terms of relative priority compared with testing OE2 to make the release date, Chris felt that it is not urgent that all the cross-products be ready to go live immediately once OE2 is allowed to be used for editing GO.

GraphViz saving image files

Last week we discussed the fact that GraphViz was producing corrupted files when Jen attempted to save images in .gif format. It turns out that this is a Mac OSX specific problem. Saving .gif format works just fine in either Windows or Linux OS's. This appears to be related to OSX and gif files and has nothing to do with OBO-Edit. Two options were mentioned. We could either eliminate the option to save gifs, or we could just document the fact that saving .gif filess does not work in OSX, that one should save the .png format instead. We decided just to mark the gif option in the save dialogue as 'except Mac OS X'. Jen made this fix immediately.


Jen requested that Amina look at some of the OBO-Merge bugs. Amina and Jen will do this together later in the week.

Idea of having Benchmarks

Midori commented that she is starting to think that there may be a difference between running OE2 on a Mac with a PowerPC chip than a Mac with an Intel chip, specfically that OE2 may be slower on a PowerPC chip than an Intel chip, other things on the machine being equal, or at least comparable. Chris suggested that it might be a good idea to have benchmarks posted on the web so that people can compare. Jen mentioned that OBO-Edit has always been faster on Windows than Mac OS X, and that this may be to do with Intel chips or with the JVMs.

Beta-53 available

Due to both the MLK holiday and a day visiting Stanford to work with David Hill and Tanya, Amina had a short week. She spent most of her time fixing the slow searching issue that had been reported by numerous people for beta-52. Multiple meeting attendees indicated during the meeting that the search in beta-53 is now speedy again, at least as fast as beta-52, if not faster.

Proposed Release Schedule

Amina has set a target release date of March 1st, several weeks before the next GO meeting. Thus it is very important that we all achieve the current testing deadline of January 31st, so that we know what the problems are and can give Amina enough time to fix them and then do final testing.

Jen suggested the idea of releasing the software but not announcing it until after a 2-3 week period where some additional people, not in the working group, can test and comment on functionality. Karen and Midori were both hesitant to call it a "release" until we're really sure it should be. Karen felt that having some additional people test and comment on usability, functionality, etc. once we get to a version we think is a really good idea, but would just rather do that before we call it an official release. We did not discuss the proposal further or come to a conclusion.

Possible "new" features for OE2

Features from OE1 not in OE2

Amina spent a day at Stanford with Tanya and David Hill watching them edit and getting feedback from them. David Hill has only recently begun to use OE2 and he commented that there were some features in OE1 which don't seem to be in OE2:

  • The OE1 Tree Editor icon bar (at the bottom of the panel) contained right and left arrows which let you select the next or previous term when a group of terms were highlighted. No one at the meeting was aware of anything comparable present in OE2
  • hotkeys - don't seem to work as well in OE2
  • switching between 2 (or more) Tree Editor panels in terms of global versus local selection. In OE1, one panel iss termed the primary selector, which means that it responds to selections made in the Search (or other) panel such that the term selected in the Search results becomes selected in that Tree Editor panel (referred to as global selection). Any additional Tree Editors panels can not be the primary selector and do not respond to terms selected in the Search panel (referred to as local selection). In OE2, the Tree Editor panel controls are different such that control of whether a given tree Editor panel follows Global or Local selection is made for each panel. This can be done independently, such that all panels follow global selection or all follow local selection, as desired. For those preferring to only allow one global selection Tree Editor panel, with all others automatically becoming local selection, there is an option in the Configs that can be selected.
  • panel scroll lock - In OE1, locking a panel was allowed independent of whether it was in global or local selection mode. The OE2 behavior is not the same.

For each of these, we will have to decide whether the existing OE2 behaviour is sufficient, or whether the OE1 behaviour needs to be duplicated in OE2, and also whether a given item is critical for release or not.

Other suggestions

Viewing log files from config tab

Harold commented that it would be reallly helpful if there was a way, perhaps a button, to access the log files from the config tab. Amina asked him to submit a SF item with the suggestion. Harold did comment that he didn't feel this was required for the initial release.

Do undocked panels always need to be on top?

Harold commented that he sometimes finds it annoying that undocked GraphViz panels are always on top of the main window. He can of course drag them to the side, but he felt this is more difficult on a small screen. Jen commented that she thought the historical reason for this is so that small popup windows don't get lost behind the main window waiting for input, such that it appears that OBO-Edit has stalled when if fact it just requires input from a window.

Action Items

Test, test, test


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