OEWG 20090505: Difference between revisions
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Agenda/Chair:Amina<br> | Agenda/Chair: Amina<br> | ||
Minutes:Harold<br> | Minutes: Harold/Amina<br> | ||
Attendees: | Attendees: AA, hjd, KarenC, Midori, DavidOS, cjm, Thomas Wachter | ||
==Action items carried over== | ==Action items carried over== | ||
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* Graph Editor Crashes <br> | * Graph Editor Crashes <br> | ||
https://sourceforge.net/tracker/?func=detail&aid=2747794&group_id=36855&atid=418257 <br> | https://sourceforge.net/tracker/?func=detail&aid=2747794&group_id=36855&atid=418257 <br> | ||
** Error message on OSX: [0x0-0xb7fb7f].com.install4j.7283-8148-3557-2000.8[46157] Invalid access of | ** Explanation of Error message on OSX: [0x0-0xb7fb7f].com.install4j.7283-8148-3557-2000.8[46157] Invalid access of | ||
stack red zone b0c95ffc eip=642afeb9 | stack red zone b0c95ffc eip=642afeb9 | ||
<p> | <p> | ||
Each block of memory allocated to an application comes with a leading and trailing "redzone" which is a special signature in memory just before and just after the memory allocated to the application. If the application were to overwrite outside this region, the redzone signature would be overwritten. Then later on the application crashes and you get this abend when the memory is returned, and the OS can inspect the redzones. | Each block of memory allocated to an application comes with a leading and trailing "redzone" which is a special signature in memory just before and just after the memory allocated to the application. If the application were to overwrite outside this region, the redzone signature would be overwritten. Then later on the application crashes and you get this abend when the memory is returned, and the OS can inspect the redzones. | ||
</p> | </p> | ||
Amina: David how much memory did you have allocated to the application?<br> | |||
David: over 1024Mb <br> | |||
Chris: something to do with # of links showing up in the graph editor. <br> | |||
Amina: too many links yes memory hog. <br> | |||
David: tries to put every link in even if they are redundant. Feature request to trim the graph on demand. <br> | |||
Amina: we could have some kind of warning when the graph is getting out of control suggesting it might result in a crash or just allow the graph editor by itself to crash - will look into it. <br> | |||
* Config Manager memory settings not in sync - DONE | * Config Manager memory settings not in sync - DONE | ||
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** Code reveals this currently does not do anything - I think its placeholder for future implementation. | ** Code reveals this currently does not do anything - I think its placeholder for future implementation. | ||
** AI Amina: UTF8 support | ** AI Amina: UTF8 support | ||
Midori: Yes UTF8 support is not that crucial for GO but other users might want it. <br> | |||
* Potential Parent Editor Improvements: show which links are asserted and which ones are implied | * Potential Parent Editor Improvements: show which links are asserted and which ones are implied | ||
** check boxes to promote or demote intersection links | ** Chris's idea: check boxes to promote or demote intersection links | ||
*Jen: update period words and repeated words files | *Jen: update period words and repeated words files | ||
| Line 41: | Line 49: | ||
:still broken - [https://sourceforge.net/tracker/?func=detail&aid=2785044&group_id=36855&atid=418257 SF 2785044] | :still broken - [https://sourceforge.net/tracker/?func=detail&aid=2785044&group_id=36855&atid=418257 SF 2785044] | ||
*Jen: visiting Colin's group | *Jen: visiting Colin's group | ||
- Jen hasn't visited Colin yet <br> | |||
Colin: Chebi has never worked well for him <br> | |||
David: last time he tried, it worked; but may be too large for the reasoner. <br> | |||
Chris: run reasoner with Chebi ? Yes. <br> | |||
==Discussion items== | ==Discussion items== | ||
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** Need contributions from the Working Group | ** Need contributions from the Working Group | ||
** Record Demos | ** Record Demos | ||
David has some more OBO-Edit specific material he can share for the resources/demo's sections. <br> | |||
* verification plugin - not seeing dictionary? - ID: 2784937 <br> | * verification plugin - not seeing dictionary? - ID: 2784937 <br> | ||
| Line 58: | Line 72: | ||
https://sourceforge.net/tracker/?func=detail&aid=2749070&group_id=36855&atid=418257 | https://sourceforge.net/tracker/?func=detail&aid=2749070&group_id=36855&atid=418257 | ||
David: the Graph Viewer does not refresh after switching the reasoner off and its confusing switching b/w reasoners. <br> | |||
Will try to break the Reasoner Manager and report next week.<br> | |||
* Multiple hi-res image display support | * Multiple hi-res image display support | ||
** flickrj api - upload images to a service like flickr through the OBO-Edit user interface or have wiki pages? | ** flickrj api - upload images to a service like flickr through the OBO-Edit user interface or have wiki pages? | ||
Chris: all the image data needs to be posted online. <br> | |||
* David Hill reported an issue last week with adding child terms to a parent. The children were added to root and not the parent term in the OTE while the graphviz viewer displayed the correct hierarchy. I could not replicate the problem. David will try to replicate the problem and get back to me. | * David Hill reported an issue last week with adding child terms to a parent. The children were added to root and not the parent term in the OTE while the graphviz viewer displayed the correct hierarchy. I could not replicate the problem. David will try to replicate the problem and get back to me. | ||
* Melissa: OE clunky on windozzze | * Melissa: OE clunky on windozzze | ||
Amina: Melissa will be visiting Berkeley soon - will work with her then | |||
* Thomas Wachter presented the Ontogen plugin. | |||
** Davis has hundreds of pdf's he would like to mine. | |||
Revision as of 15:28, 5 May 2009
OBO-Edit Working Group, Tuesday May 5th, 2009 9.30 a.m. PST
Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425
Agenda/Chair: Amina
Minutes: Harold/Amina
Attendees: AA, hjd, KarenC, Midori, DavidOS, cjm, Thomas Wachter
Action items carried over
- Amina
- Assert Implied Links Component
- - Reverse select term- link from OTE to AssertTable - useful when looking at a long list of asserted links
- - Bubble pop-up display for Explanation not sufficient to all levels of the explanation - clicking on the info icon opens the explanation in the Explanation Component. - DONE
- Graph Editor Crashes
https://sourceforge.net/tracker/?func=detail&aid=2747794&group_id=36855&atid=418257
- Explanation of Error message on OSX: [0x0-0xb7fb7f].com.install4j.7283-8148-3557-2000.8[46157] Invalid access of
stack red zone b0c95ffc eip=642afeb9
Each block of memory allocated to an application comes with a leading and trailing "redzone" which is a special signature in memory just before and just after the memory allocated to the application. If the application were to overwrite outside this region, the redzone signature would be overwritten. Then later on the application crashes and you get this abend when the memory is returned, and the OS can inspect the redzones.
Amina: David how much memory did you have allocated to the application?
David: over 1024Mb
Chris: something to do with # of links showing up in the graph editor.
Amina: too many links yes memory hog.
David: tries to put every link in even if they are redundant. Feature request to trim the graph on demand.
Amina: we could have some kind of warning when the graph is getting out of control suggesting it might result in a crash or just allow the graph editor by itself to crash - will look into it.
- Config Manager memory settings not in sync - DONE
- Configuration Manager -> Text Editing -> Allow extended characters options
- Code reveals this currently does not do anything - I think its placeholder for future implementation.
- AI Amina: UTF8 support
Midori: Yes UTF8 support is not that crucial for GO but other users might want it.
- Potential Parent Editor Improvements: show which links are asserted and which ones are implied
- Chris's idea: check boxes to promote or demote intersection links
- Jen: update period words and repeated words files
- Karen: file verification feature request
- item opened - SF 2784022
- Midori: check if the "on text commit" verification manager check is fixed
- still broken - SF 2785044
- Jen: visiting Colin's group
- Jen hasn't visited Colin yet
Colin: Chebi has never worked well for him
David: last time he tried, it worked; but may be too large for the reasoner.
Chris: run reasoner with Chebi ? Yes.
Discussion items
- Incremental Reasoning on/off demo postponed to next meeting - May 12th
- Teaching Resources/ Demos/ Cool Stuff section on the OBO-Edit website
- Need contributions from the Working Group
- Record Demos
David has some more OBO-Edit specific material he can share for the resources/demo's sections.
- verification plugin - not seeing dictionary? - ID: 2784937
http://sourceforge.net/tracker/?func=detail&aid=2784937&group_id=36855&atid=418257
- OBO-Edit2-rc still present - ID: 2785074
http://sourceforge.net/tracker/?func=detail&aid=2785074&group_id=36855&atid=418257
- reasoner active even in OFF mode
https://sourceforge.net/tracker/?func=detail&aid=2749070&group_id=36855&atid=418257
David: the Graph Viewer does not refresh after switching the reasoner off and its confusing switching b/w reasoners.
Will try to break the Reasoner Manager and report next week.
- Multiple hi-res image display support
- flickrj api - upload images to a service like flickr through the OBO-Edit user interface or have wiki pages?
Chris: all the image data needs to be posted online.
- David Hill reported an issue last week with adding child terms to a parent. The children were added to root and not the parent term in the OTE while the graphviz viewer displayed the correct hierarchy. I could not replicate the problem. David will try to replicate the problem and get back to me.
- Melissa: OE clunky on windozzze
Amina: Melissa will be visiting Berkeley soon - will work with her then
- Thomas Wachter presented the Ontogen plugin.
- Davis has hundreds of pdf's he would like to mine.
Action Items