Gene Ontology

Thanks for sending your oboedit_config. When I put it in place of my oboedit_config and tried creating a new term and editing its name, it all worked fine.

I see from your log file that you're also running phenoscape. I'm wondering if it's somehow interfering with OBO-Edit. (It's writing its output to OBO-Edit's log file, so maybe it's mucking with OBO-Edit in some other way as well?)

Notice all the phenoscape messages followed by some messages from OBO-Edit indicating trouble:

[12-01-30 15:41:48] phenoscape.oboedit.synch.MissingXrefSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:41:48] phenoscape.oboedit.synch.ConflictingDataSynchComponentRefreshing view in ConflictingData component^M
[12-01-30 15:41:48] phenoscape.oboedit.synch.ConflictingDataSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:41:48] phenoscape.oboedit.synch.MissingTermsSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:41:48] org.oboedit.controller.SessionManager>>> SessionManager doApply:Add new child to synostosis^M
[12-01-30 15:42:03] phenoscape.oboedit.synch.MissingXrefSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:42:03] phenoscape.oboedit.synch.ConflictingDataSynchComponentRefreshing view in ConflictingData component^M
[12-01-30 15:42:03] phenoscape.oboedit.synch.ConflictingDataSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:42:03] phenoscape.oboedit.synch.MissingTermsSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:43:27] obo.datamodel.impl.DefaultOperationModelgot warning [Operation Warning] Could not change namespace of unrecognized term ZFA:0005614 from Assigned namespace "zebrafish_anatomy" to ZFA:0005614^M
[12-01-30 15:43:27] obo.datamodel.impl.DefaultOperationModelgot warning [Operation Warning] no term for ID ZFA:0005614 from Changed name of ZFA:0005614 from "ZFA:0005614" to "entopterygoid-metapterygoid joint"^M
[12-01-30 15:43:27] obo.datamodel.impl.DefaultOperationModelgot warning [Operation Warning] Could not apply definition change to non definable object ZFA:0005614 from Set definition of ZFA:0005614 to "Synostosis formed between  the entopterygoid and  metapterygoid."^M
[12-01-30 15:43:27] obo.datamodel.impl.DefaultOperationModelgot warning [Operation Warning] Could not add dbxref to non-existant object ZFA:0005614 from Added definition dbxref ZFIN:ZDB-PUB-961014-192 to ZFA:0005614^M
[12-01-30 15:43:27] org.oboedit.controller.SessionManagerSessionManager.doApply [Assigned namespace "zebrafish_anatomy" to ZFA:0005614, Changed name of ZFA:0005614 from "ZFA:0005614" to "entopterygoid-metapterygoid joint", Set definition of ZFA:0005614 to "Synostosis formed between  the entopterygoid and  \
metapterygoid.", Added definition dbxref ZFIN:ZDB-PUB-961014-192 to ZFA:0005614] (warnings: [Operation Warning] Couldn't apply macro history item
  Could not change namespace of unrecognized term ZFA:0005614
  no term for ID ZFA:0005614
  Could not apply definition change to non definable object ZFA:0005614
  Could not add dbxref to non-existant object ZFA:0005614)^M
[12-01-30 15:43:27] phenoscape.oboedit.synch.MissingXrefSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:43:27] phenoscape.oboedit.synch.ConflictingDataSynchComponentRefreshing view in ConflictingData component^M
[12-01-30 15:43:27] phenoscape.oboedit.synch.ConflictingDataSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:43:27] phenoscape.oboedit.synch.MissingTermsSynchComponentGetting master namespace: null using: null^M
[12-01-30 15:43:27] org.oboedit.controller.SessionManager>>> SessionManager doApply:Text edit^M
[12-01-30 15:43:45] Uncaught event dispatch exception^M
java.lang.NullPointerException^M
        at org.obo.datamodel.impl.DefaultOperationModel.reverse(DefaultOperationModel.java:1964)^M
        at org.obo.datamodel.impl.DefaultOperationModel.reverse(DefaultOperationModel.java:2428)^M
        at org.obo.datamodel.impl.DefaultOperationModel.reverse(DefaultOperationModel.java:1852)^M
        at org.obo.datamodel.impl.DefaultOperationModel.reverse(DefaultOperationModel.java:2422)^M
        at org.oboedit.controller.SessionManager.reverse(SessionManager.java:520)^M
        at org.oboedit.controller.SessionManager.undo(SessionManager.java:540)^M
        at org.oboedit.gui.menu.EditMenu$3$1.actionPerformed(EditMenu.java:92)^M
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)^M
        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)^M
        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)^M
        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)^M
        at javax.swing.AbstractButton.doClick(Unknown Source)^M
        at javax.swing.AbstractButton.doClick(Unknown Source)^M
        at org.bbop.swing.AbstractDynamicMenuItem.processComponent(AbstractDynamicMenuItem.java:119)^M
        at org.bbop.swing.AbstractDynamicMenuItem.processComponent(AbstractDynamicMenuItem.java:125)^M
        at org.bbop.swing.AbstractDynamicMenuItem.processKeyBinding(AbstractDynamicMenuItem.java:107)^M
        at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(Unknown Source)^M
[rest of the stack is all javax and java]

Maybe try quitting Phenoscape, removing your ~/oboedit_config again, and launching OE without Phenoscape running, and see if that fixes it?

OE users, is there anyone else on Windows who can test Autocommit? (I know some of you on Macs have already tested it and found it to work fine, right?)

By the way, I didn't see any screenshot attached to your message; only the oboedit_config.zip.

	Nomi


On Jan 30, 2012, at 4:30 PM, Ceri Van Slyke wrote:

> Hi Nomi,
> 
> I think I am using OE 2.1.
> Most noticiable when creating new term like in the screen shot.  I created new term, put in a term name wrote a def. and made a def dbxref and navigated away using the OTE.  looked up and saw there was the <new term> label instead of the term I had just made.
> 
> Sending a zip file because windows doesn't do TAR without adding software.
> 
> Ceri
> 
> 
> 
> I will change back to the autocommit and
> At 04:06 PM 1/30/2012, you wrote:
>> Hi Ceri,
>> 
>> I'm sorry you're having trouble with autocommit. (Is anyone else? It works for me when I test it.)
>> 
>> Let me make sure I understand the scenario. So you do some edits, and select another term (to make autocommit save your changes) and then come back to the term you change, and it's reverted to what it had before and your changes are gone? Does this now happen reliably when you start up OE? (You're using 2.1.1-b4, right?)
>> 
>> In order to help me figure out what's going on, can you start up OE, edit a term, select another term, return to the original one and verify that your changes have vanished, and then quit OE, tar up your oboedit_config directory and send it to me?
>>        cd ~
>>        tar cf ceri-oboedit-config.tar oboedit_config
>>        gzip ceri-oboedit-config.tar
>> (Mail me and attach ~/ceri-oboedit-config.tar.gz)
>> 
>> Thanks,
>>        Nomi
>> 
>> 
>> On Jan 30, 2012, at 12:37 PM, SourceForge.net wrote:
>> 
>> > Bugs item #3481747, was opened at 2012-01-30 12:34
>> > Message generated for change (Settings changed) made by ceri_van_slyke
>> > You can respond by visiting:
>> > https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3481747&group_id=36855
>> >
>> > Please note that this message will contain a full copy of the comment thread,
>> > including the initial issue submission, for this request,
>> > not just the latest update.
>> > Category: None
>> > Group: None
>> > Status: Open
>> > Resolution: None
>> >> Priority: 7
>> > Private: No
>> > Submitted By: Ceri (ceri_van_slyke)
>> > Assigned to: Nobody/Anonymous (nobody)
>> > Summary: Autocommit text edits not working again
>> >
>> > Initial Comment:
>> > It worked the day I blew away the perspectives but it isn't working again today.  I can't reconfigure OE every single time I edit.  So there has to be a better fix.
>> >
>> > Have the configuration set to auto commit text edits.
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Comment By: Ceri (ceri_van_slyke)
>> > Date: 2012-01-30 12:36
>> >
>> > Message:
>> > This is preventing adding new terms to our ontology.
>> >
>> > ----------------------------------------------------------------------
>> >
>> > You can respond by visiting:
>> > https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3481747&group_id=36855
> <oboedit_config.zip>*******************************************
> Ceri E. Van Slyke, Ph.D.
> ZFIN Scientific Curator
> http://zfin.org
> Zebrafish Information Network
> 5291 University of Oregon
> Eugene, OR  97403-5291
> 
> Phone:  (541) 346-2116
> *******************************************

(I already told Paola and Becky this, but others might find it useful as well.)

Another way to get around the unique-launch problem is that you can launch multiple versions of OE at the same time if you launch from the command line instead of by double-clicking on the app. To launch OBO-Edit from the command line, just cd to the directory where you installed it, and type ./oe-command-line. For example:
	cd /Applications/OBO-Edit-2.1.1-b4
	./oe-command-line

An advantage to using the command-line version is that you can have it open an ontology file as it launches by specifying it on the command line:
	./oe-command-line /users/nomi/ontology-files/gene_ontology_edit.obo


Another thing I wanted to mention about the unique-launch problem is that I think it's only an issue on Macs.

	Nomi


On Jan 28, 2012, at 9:34 PM, Nomi Harris wrote:

> Release 2.1.1-b5 has a temporary workaround for an issue that was bothering some of you (and that may be an issue for some of you at the ontology editing workshop):
> [ geneontology-Bugs-3481225 ] Can't launch two (recent) OBO-Edits at the same time
> 
> Some users like to to have two different versions of OBO-Edit running
> at the same time--for example, stable release 2.1.0 and new beta
> 2.1.1-b4. Starting with version 2.1-b19, this became impossible--if
> you have one OBO-Edit running, you can't launch another (post-2.1-b19)
> OBO-Edit.
> It turns out this is due to the installer fix (added in 2.1-b19) that
> lets the installer detect whether you have a 64-bit machine, and, if
> so, lets you set a higher memory setting (which is otherwise limited
> to 1860M). Setting the OBO-Edit memory allocation higher is useful for
> the many users who do have 64-bit-capable computers, because they can
> then load bigger ontologies (and even run the reasoner on them)
> without running out of memory.
> 
> The temporary workaround in 2.1.1-b5 is that I commented out that 64-bit
> Java stuff from the installer, so you can run 2.1.1-b5 (which is otherwise basically
> the same as 2.1.1-b4) at the same time as 2.1.0. However, you will not be
> able to set your memory allocation higher than 1860M when you install
> 2.1.1-b5, so if that is a problem for you, then just stick with
> 2.1.1-b4 for now until we figure out a better way to fix the
> unique-launch problem without breaking the 64-bit-capable install.
> 
> You can download 2.1.1-b5 from http://www.oboedit.org/test_release/2.1.1-b5
> 
> If you are looking for the latest release that is 64-bit capable, use http://www.oboedit.org/test_release/2.1.1-b4
> 
> 
> 2.1.1-b4 has a number of useful new features and bug fixes that have been added since 2.1.0 was released in December:
> 
> New features:
> - Chris and Heiko got OBO<->OWL conversion working inside OBO-Edit, so you can load and/or save in OWL format.
> 
> - [ geneontology-Feature Requests-1604638 ] quick save
> After your first Save As, you can do a quick Save (command-S) to save the ontology again with the same save parameters.
> (A message window briefly appears letting you know the quick save worked.)
> 
> - [ geneontology-Feature Requests-3375766 ] Automatic detection of changed files/reload option
> A new background thread checks whether the file you're looking at has changed on disk since you last loaded or saved it.
> If it changes, a popup advises you to save your work (if you've made changes) and reload.
> 
> - [ geneontology-Feature Requests-3469108 ] Titlebar should show last saved-as filename
> 
> - [ geneontology-Feature Requests-3476913 ] Warn about possible stale config files when launching new version
> Whenever you upgrade to a new version of OBO-Edit, there is the risk that
> out-of-date binary files in your ~/oboedit_config (mostly in
> oboedit_config/perspectives) will cause bad behavior of various unexpected
> sorts (for example, sometimes it makes Autocommit in the Text Editor not
> work). Now a warning message about it pops up the first time you run a new
> OBO-Edit release (and it offers to rename oboedit_config/perspectives for
> you.)
> 
> 
> Changes:
> - When you save your configuration in the Configuration Manager, you now get a
> popup message reminding you that you may need to quit and restart OE for your
> changes to take effect.  (If people find this annouying, I can take it out.)
> New feature:
> 
> - I made the configuration option "Confirm on exit" say "Confirm on exit, even                                                                                                                                                                                                                                     
> if there are no changes to be saved", and I made it default to false instead of true.
> 
> - Fixed the evil twin Cross Product Editor problems:
> [ geneontology-Bugs-3471901] can't delete cross products
> [ geneontology-Bugs-3303595] deleting genus relationship in cross product tab
> In an earlier version of OE, the genus would mysteriously disappear
> when you committed. Chris and Amina fixed this by caching the value of
> the genus field in AutocompleteBox and restoring it when it
> disappeared. However, this had the unwanted side effect of making it
> impossible to delete the genus by erasing the genus field--it would
> simply reappear, like a zombie returned from the dead, when you committed.
> Now you should be able to save OR delete your genus.
> 
> - OWL Adapter: Fixed issue where file browser strips off .owl extension if you select an
> existing .owl file. (Can't fix problem in file browser itself, which is
> native, but the OWL adapter now restores the .owl suffix after you select the file.)
> 
>

You can also open multiple copies on the command line without changing
directories, using "open -n -a/Applications/OBO-Edit2/OBO-Edit.app",
substituting the path to OE on your computer, and then using file>open in
OE. I can't remember exactly who taught me this, but it was several people
on this list.

Ramona

On 1/29/12 3:43 PM, "Nomi Harris" <nlharris@...> wrote:

>(I already told Paola and Becky this, but others might find it useful as
>well.)
>
>Another way to get around the unique-launch problem is that you can
>launch multiple versions of OE at the same time if you launch from the
>command line instead of by double-clicking on the app. To launch OBO-Edit
>from the command line, just cd to the directory where you installed it,
>and type ./oe-command-line. For example:
>    cd /Applications/OBO-Edit-2.1.1-b4
>    ./oe-command-line
>
>An advantage to using the command-line version is that you can have it
>open an ontology file as it launches by specifying it on the command line:
>    ./oe-command-line /users/nomi/ontology-files/gene_ontology_edit.obo
>
>
>Another thing I wanted to mention about the unique-launch problem is that
>I think it's only an issue on Macs.
>
>    Nomi
>
>
>On Jan 28, 2012, at 9:34 PM, Nomi Harris wrote:
>
>> Release 2.1.1-b5 has a temporary workaround for an issue that was
>>bothering some of you (and that may be an issue for some of you at the
>>ontology editing workshop):
>> [ geneontology-Bugs-3481225 ] Can't launch two (recent) OBO-Edits at
>>the same time
>> 
>> Some users like to to have two different versions of OBO-Edit running
>> at the same time--for example, stable release 2.1.0 and new beta
>> 2.1.1-b4. Starting with version 2.1-b19, this became impossible--if
>> you have one OBO-Edit running, you can't launch another (post-2.1-b19)
>> OBO-Edit.
>> It turns out this is due to the installer fix (added in 2.1-b19) that
>> lets the installer detect whether you have a 64-bit machine, and, if
>> so, lets you set a higher memory setting (which is otherwise limited
>> to 1860M). Setting the OBO-Edit memory allocation higher is useful for
>> the many users who do have 64-bit-capable computers, because they can
>> then load bigger ontologies (and even run the reasoner on them)
>> without running out of memory.
>> 
>> The temporary workaround in 2.1.1-b5 is that I commented out that 64-bit
>> Java stuff from the installer, so you can run 2.1.1-b5 (which is
>>otherwise basically
>> the same as 2.1.1-b4) at the same time as 2.1.0. However, you will not
>>be
>> able to set your memory allocation higher than 1860M when you install
>> 2.1.1-b5, so if that is a problem for you, then just stick with
>> 2.1.1-b4 for now until we figure out a better way to fix the
>> unique-launch problem without breaking the 64-bit-capable install.
>> 
>> You can download 2.1.1-b5 from
>>http://www.oboedit.org/test_release/2.1.1-b5
>> 
>> If you are looking for the latest release that is 64-bit capable, use
>>http://www.oboedit.org/test_release/2.1.1-b4
>> 
>> 
>> 2.1.1-b4 has a number of useful new features and bug fixes that have
>>been added since 2.1.0 was released in December:
>> 
>> New features:
>> - Chris and Heiko got OBO<->OWL conversion working inside OBO-Edit, so
>>you can load and/or save in OWL format.
>> 
>> - [ geneontology-Feature Requests-1604638 ] quick save
>> After your first Save As, you can do a quick Save (command-S) to save
>>the ontology again with the same save parameters.
>> (A message window briefly appears letting you know the quick save
>>worked.)
>> 
>> - [ geneontology-Feature Requests-3375766 ] Automatic detection of
>>changed files/reload option
>> A new background thread checks whether the file you're looking at has
>>changed on disk since you last loaded or saved it.
>> If it changes, a popup advises you to save your work (if you've made
>>changes) and reload.
>> 
>> - [ geneontology-Feature Requests-3469108 ] Titlebar should show last
>>saved-as filename
>> 
>> - [ geneontology-Feature Requests-3476913 ] Warn about possible stale
>>config files when launching new version
>> Whenever you upgrade to a new version of OBO-Edit, there is the risk
>>that
>> out-of-date binary files in your ~/oboedit_config (mostly in
>> oboedit_config/perspectives) will cause bad behavior of various
>>unexpected
>> sorts (for example, sometimes it makes Autocommit in the Text Editor not
>> work). Now a warning message about it pops up the first time you run a
>>new
>> OBO-Edit release (and it offers to rename oboedit_config/perspectives
>>for
>> you.)
>> 
>> 
>> Changes:
>> - When you save your configuration in the Configuration Manager, you
>>now get a
>> popup message reminding you that you may need to quit and restart OE
>>for your
>> changes to take effect.  (If people find this annouying, I can take it
>>out.)
>> New feature:
>> 
>> - I made the configuration option "Confirm on exit" say "Confirm on
>>exit, even       
>>                 
>>                 
>>                 
>> if there are no changes to be saved", and I made it default to false
>>instead of true.
>> 
>> - Fixed the evil twin Cross Product Editor problems:
>> [ geneontology-Bugs-3471901] can't delete cross products
>> [ geneontology-Bugs-3303595] deleting genus relationship in cross
>>product tab
>> In an earlier version of OE, the genus would mysteriously disappear
>> when you committed. Chris and Amina fixed this by caching the value of
>> the genus field in AutocompleteBox and restoring it when it
>> disappeared. However, this had the unwanted side effect of making it
>> impossible to delete the genus by erasing the genus field--it would
>> simply reappear, like a zombie returned from the dead, when you
>>committed.
>> Now you should be able to save OR delete your genus.
>> 
>> - OWL Adapter: Fixed issue where file browser strips off .owl extension
>>if you select an
>> existing .owl file. (Can't fix problem in file browser itself, which is
>> native, but the OWL adapter now restores the .owl suffix after you
>>select the file.)
>> 
>> 
>
>
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True--I didn't suggest that because I would have expected that to fail the way double-clicking on the app fails to launch a second instance, but it works. Thanks for the tip!
	Nomi

On Jan 29, 2012, at 2:39 PM, Walls, Ramona wrote:

> You can also open multiple copies on the command line without changing
> directories, using "open -n -a/Applications/OBO-Edit2/OBO-Edit.app",
> substituting the path to OE on your computer, and then using file>open in
> OE. I can't remember exactly who taught me this, but it was several people
> on this list.
> 
> Ramona
> 
> On 1/29/12 3:43 PM, "Nomi Harris" <nlharris@...> wrote:
> 
>> (I already told Paola and Becky this, but others might find it useful as
>> well.)
>> 
>> Another way to get around the unique-launch problem is that you can
>> launch multiple versions of OE at the same time if you launch from the
>> command line instead of by double-clicking on the app. To launch OBO-Edit
>> from the command line, just cd to the directory where you installed it,
>> and type ./oe-command-line. For example:
>>   cd /Applications/OBO-Edit-2.1.1-b4
>>   ./oe-command-line
>> 
>> An advantage to using the command-line version is that you can have it
>> open an ontology file as it launches by specifying it on the command line:
>>   ./oe-command-line /users/nomi/ontology-files/gene_ontology_edit.obo
>> 
>> 
>> Another thing I wanted to mention about the unique-launch problem is that
>> I think it's only an issue on Macs.
>> 
>>   Nomi
>> 
>> 
>> On Jan 28, 2012, at 9:34 PM, Nomi Harris wrote:
>> 
>>> Release 2.1.1-b5 has a temporary workaround for an issue that was
>>> bothering some of you (and that may be an issue for some of you at the
>>> ontology editing workshop):
>>> [ geneontology-Bugs-3481225 ] Can't launch two (recent) OBO-Edits at
>>> the same time
>>> 
>>> Some users like to to have two different versions of OBO-Edit running
>>> at the same time--for example, stable release 2.1.0 and new beta
>>> 2.1.1-b4. Starting with version 2.1-b19, this became impossible--if
>>> you have one OBO-Edit running, you can't launch another (post-2.1-b19)
>>> OBO-Edit.
>>> It turns out this is due to the installer fix (added in 2.1-b19) that
>>> lets the installer detect whether you have a 64-bit machine, and, if
>>> so, lets you set a higher memory setting (which is otherwise limited
>>> to 1860M). Setting the OBO-Edit memory allocation higher is useful for
>>> the many users who do have 64-bit-capable computers, because they can
>>> then load bigger ontologies (and even run the reasoner on them)
>>> without running out of memory.
>>> 
>>> The temporary workaround in 2.1.1-b5 is that I commented out that 64-bit
>>> Java stuff from the installer, so you can run 2.1.1-b5 (which is
>>> otherwise basically
>>> the same as 2.1.1-b4) at the same time as 2.1.0. However, you will not
>>> be
>>> able to set your memory allocation higher than 1860M when you install
>>> 2.1.1-b5, so if that is a problem for you, then just stick with
>>> 2.1.1-b4 for now until we figure out a better way to fix the
>>> unique-launch problem without breaking the 64-bit-capable install.
>>> 
>>> You can download 2.1.1-b5 from
>>> http://www.oboedit.org/test_release/2.1.1-b5
>>> 
>>> If you are looking for the latest release that is 64-bit capable, use
>>> http://www.oboedit.org/test_release/2.1.1-b4
>>> 
>>> 
>>> 2.1.1-b4 has a number of useful new features and bug fixes that have
>>> been added since 2.1.0 was released in December:
>>> 
>>> New features:
>>> - Chris and Heiko got OBO<->OWL conversion working inside OBO-Edit, so
>>> you can load and/or save in OWL format.
>>> 
>>> - [ geneontology-Feature Requests-1604638 ] quick save
>>> After your first Save As, you can do a quick Save (command-S) to save
>>> the ontology again with the same save parameters.
>>> (A message window briefly appears letting you know the quick save
>>> worked.)
>>> 
>>> - [ geneontology-Feature Requests-3375766 ] Automatic detection of
>>> changed files/reload option
>>> A new background thread checks whether the file you're looking at has
>>> changed on disk since you last loaded or saved it.
>>> If it changes, a popup advises you to save your work (if you've made
>>> changes) and reload.
>>> 
>>> - [ geneontology-Feature Requests-3469108 ] Titlebar should show last
>>> saved-as filename
>>> 
>>> - [ geneontology-Feature Requests-3476913 ] Warn about possible stale
>>> config files when launching new version
>>> Whenever you upgrade to a new version of OBO-Edit, there is the risk
>>> that
>>> out-of-date binary files in your ~/oboedit_config (mostly in
>>> oboedit_config/perspectives) will cause bad behavior of various
>>> unexpected
>>> sorts (for example, sometimes it makes Autocommit in the Text Editor not
>>> work). Now a warning message about it pops up the first time you run a
>>> new
>>> OBO-Edit release (and it offers to rename oboedit_config/perspectives
>>> for
>>> you.)
>>> 
>>> 
>>> Changes:
>>> - When you save your configuration in the Configuration Manager, you
>>> now get a
>>> popup message reminding you that you may need to quit and restart OE
>>> for your
>>> changes to take effect.  (If people find this annouying, I can take it
>>> out.)
>>> New feature:
>>> 
>>> - I made the configuration option "Confirm on exit" say "Confirm on
>>> exit, even       
>>> 
>>> 
>>> 
>>> if there are no changes to be saved", and I made it default to false
>>> instead of true.
>>> 
>>> - Fixed the evil twin Cross Product Editor problems:
>>> [ geneontology-Bugs-3471901] can't delete cross products
>>> [ geneontology-Bugs-3303595] deleting genus relationship in cross
>>> product tab
>>> In an earlier version of OE, the genus would mysteriously disappear
>>> when you committed. Chris and Amina fixed this by caching the value of
>>> the genus field in AutocompleteBox and restoring it when it
>>> disappeared. However, this had the unwanted side effect of making it
>>> impossible to delete the genus by erasing the genus field--it would
>>> simply reappear, like a zombie returned from the dead, when you
>>> committed.
>>> Now you should be able to save OR delete your genus.
>>> 
>>> - OWL Adapter: Fixed issue where file browser strips off .owl extension
>>> if you select an
>>> existing .owl file. (Can't fix problem in file browser itself, which is
>>> native, but the OWL adapter now restores the .owl suffix after you
>>> select the file.)

Hi folks,

I'll have to miss today's meeting -- away from work this afternoon to help 
set up for the next beer festival.

Midori

On Mon, 16 Jan 2012, Nomi Harris wrote:

> We will meet tomorrow, January 17. The meeting agenda is at http://wiki.geneontology.org/index.php/OEWG_20120117
> Feel free to add to it.
>
> Conference call numbers:
> US: 1 866 953 9688
> UK: 0808 238 6001
> pin: 801561
>
> WebEx link (in case we need it): https://geneontology.webex.com/geneontology/j.php?ED=150627732&UID=480077942&PW=NMjgwYmQ3MTA4&RT=MiM0
> Password: Oboedit2
>
> 	Nomi

Apologies I missed the meeting this morning. Bill had a work event at 7:30 am that he had to attend so I was going the kid dropoffs this morning.

-Karen

On Jan 16, 2012, at 10:31 AM, Nomi Harris wrote:

> We will meet tomorrow, January 17. The meeting agenda is at http://wiki.geneontology.org/index.php/OEWG_20120117
> Feel free to add to it.
> 
> Conference call numbers:
> US: 1 866 953 9688
> UK: 0808 238 6001
> pin: 801561
> 
> WebEx link (in case we need it): https://geneontology.webex.com/geneontology/j.php?ED=150627732&UID=480077942&PW=NMjgwYmQ3MTA4&RT=MiM0 
> Password: Oboedit2
> 
> 	Nomi
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2_______________________________________________
> Geneontology-oboedit-working-group mailing list
> Geneontology-oboedit-working-group@...
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group

Hi Nomi,
I'd go with the simpler option, i.e. call the next release 2.2. I think 
it would be easier and quicker to implement for you, and less confusing 
than the other two options for us users.
Paola

On 1/17/12 3:33 AM, Nomi Harris wrote:
> I'm trying to figure out the best naming scheme for future OBO-Edit releases.
>
> The code that deals with version numbers was set up to accommodate two digits separated by a ., with an optional beta or rc number at the end, e.g., 2.0-b19 or 2.1-rc4. It was not set up to deal with three-part version numbers like 2.1.1 or 2.1.1-b1.
>
> The (many) beta releases before 2.1(.0) were called, e.g., 2.1-b19, which the installer software called 2.1.19. This means it would be potentially confusing to call the next release 2.1.1.
>
> There are a few options:
> - I could call the next release 2.2. In a way, that seems too drastic a version number bump, given that it was several years and many beta releases between official release 2.0 and 2.1. (However, there are a few new features in this upcoming release that will be fairly visible.)
> - I could call it 2.101 (where the previous release could be thought of as 2.100).
> - I could go ahead and call it 2.1.1 (and the first beta of that would be 2.1.1-b1), and (as I am currently trying to do) fix the code that the installer uses to figure out the version number and make it capable with dealing with the extra piece.
>
> Any thoughts?
>
> 	Nomi
>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
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-- 
Dr Paola Roncaglia
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492600
f: +44 1223 494468

No particular preference ... I'll go along with whatever you think is the 
best balance between Easy Now and Future-Proof.

cheers,
m

On Mon, 16 Jan 2012, Nomi Harris wrote:

> I'm trying to figure out the best naming scheme for future OBO-Edit releases.
>
> The code that deals with version numbers was set up to accommodate two digits separated by a ., with an optional beta or rc number at the end, e.g., 2.0-b19 or 2.1-rc4. It was not set up to deal with three-part version numbers like 2.1.1 or 2.1.1-b1.
>
> The (many) beta releases before 2.1(.0) were called, e.g., 2.1-b19, which the installer software called 2.1.19. This means it would be potentially confusing to call the next release 2.1.1.
>
> There are a few options:
> - I could call the next release 2.2. In a way, that seems too drastic a version number bump, given that it was several years and many beta releases between official release 2.0 and 2.1. (However, there are a few new features in this upcoming release that will be fairly visible.)
> - I could call it 2.101 (where the previous release could be thought of as 2.100).
> - I could go ahead and call it 2.1.1 (and the first beta of that would be 2.1.1-b1), and (as I am currently trying to do) fix the code that the installer uses to figure out the version number and make it capable with dealing with the extra piece.
>
> Any thoughts?
>
> 	Nomi
>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Geneontology-oboedit-working-group mailing list
> Geneontology-oboedit-working-group@...
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group
>

Hmmm. I could have sworn that I have deleted cross products in 2.0. 
Anyways, the trash can didn't appear to be working either. Both the 
genus and differentium were still there. I did have auto-commit on.

David

On 1/10/12 12:17 PM, Nomi Harris wrote:
> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
>
> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
>
> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
>
> 	Nomi
>
> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>
>> Bugs item #3471901, was opened at 2012-01-10 07:48
>> Message generated for change (Tracker Item Submitted) made by ukemi
>> You can respond by visiting:
>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>
>> Please note that this message will contain a full copy of the comment thread,
>> including the initial issue submission, for this request,
>> not just the latest update.
>> Category: OBO-Edit
>> Group: Mac OS X
>> Status: Open
>> Resolution: None
>> Priority: 5
>> Private: No
>> Submitted By: David Hill (ukemi)
>> Assigned to: Nobody/Anonymous (nobody)
>> Summary: can't delete cross products
>>
>> Initial Comment:
>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
>>
>> ----------------------------------------------------------------------
>>
>> You can respond by visiting:
>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855

On Jan 10, 2012, at 9:30 AM, David Hill wrote:

> Hmmm. I could have sworn that I have deleted cross products in 2.0.

Not in the Text Editor. You can do it in the Parent Editor.

> Anyways, the trash can didn't appear to be working either. Both the genus and differentium were still there. I did have auto-commit on.

Huh. I just tested in 2.1 and the differentium trash can worked for me. Has anyone else had problems with it? David, which ontology were you editing, and which term? Did you try to add a new cross product and then delete the differentium, or were you adding a new differentium and then deleting it? What happened when you clicked the differentium trash can--nothing? Was this true consistently or just for some terms?

	Nomi

> 
> David
> 
> On 1/10/12 12:17 PM, Nomi Harris wrote:
>> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
>> 
>> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
>> 
>> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
>> 
>> 	Nomi
>> 
>> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>> 
>>> Bugs item #3471901, was opened at 2012-01-10 07:48
>>> Message generated for change (Tracker Item Submitted) made by ukemi
>>> You can respond by visiting:
>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>> 
>>> Please note that this message will contain a full copy of the comment thread,
>>> including the initial issue submission, for this request,
>>> not just the latest update.
>>> Category: OBO-Edit
>>> Group: Mac OS X
>>> Status: Open
>>> Resolution: None
>>> Priority: 5
>>> Private: No
>>> Submitted By: David Hill (ukemi)
>>> Assigned to: Nobody/Anonymous (nobody)
>>> Summary: can't delete cross products
>>> 
>>> Initial Comment:
>>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
>>> 
>>> ----------------------------------------------------------------------
>>> 
>>> You can respond by visiting:
>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855

On Jan 10, 2012, at 1:33 PM, Tanya Berardini wrote:

> Hi,
> 
> > Hmmm. I could have sworn that I have deleted cross products in 2.0.
> 
> Not in the Text Editor. You can do it in the Parent Editor.
> 
> I confirm that I used to be able to delete cross products in 2.0 in the Text Editor.  First, trash the differentium, then highlight and delete the genus, then click on Commit.  XP gone. 

Hmm, I was under the impression that this did not work reliably (which is why there was a request to add the Genus trash can). Didn't the genus tend to come back if you tried to delete it like that?

	Nomi

> The same procedure doesn't work in 2.1 anymore but the Parent Editor deletion does.
> 
>  
> 
> > Anyways, the trash can didn't appear to be working either. Both the genus and differentium were still there. I did have auto-commit on.
> 
> Huh. I just tested in 2.1 and the differentium trash can worked for me. Has anyone else had problems with it? David, which ontology were you editing, and which term? Did you try to add a new cross product and then delete the differentium, or were you adding a new differentium and then deleting it? What happened when you clicked the differentium trash can--nothing? Was this true consistently or just for some terms?
> 
> I was able to trash the differentium of an existing term (cellular process involved in reproduction) in the current GO using the Text Editor.
> 
> Tanya
> 
>  
> 
>        Nomi
> 
> >
> > David
> >
> > On 1/10/12 12:17 PM, Nomi Harris wrote:
> >> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
> >>
> >> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
> >>
> >> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
> >>
> >>      Nomi
> >>
> >> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
> >>
> >>> Bugs item #3471901, was opened at 2012-01-10 07:48
> >>> Message generated for change (Tracker Item Submitted) made by ukemi
> >>> You can respond by visiting:
> >>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
> >>>
> >>> Please note that this message will contain a full copy of the comment thread,
> >>> including the initial issue submission, for this request,
> >>> not just the latest update.
> >>> Category: OBO-Edit
> >>> Group: Mac OS X
> >>> Status: Open
> >>> Resolution: None
> >>> Priority: 5
> >>> Private: No
> >>> Submitted By: David Hill (ukemi)
> >>> Assigned to: Nobody/Anonymous (nobody)
> >>> Summary: can't delete cross products
> >>>
> >>> Initial Comment:
> >>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
> >>>
> >>> ----------------------------------------------------------------------
> >>>
> >>> You can respond by visiting:
> >>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
> 
> 
> ------------------------------------------------------------------------------
> Write once. Port to many.
> Get the SDK and tools to simplify cross-platform app development. Create
> new or port existing apps to sell to consumers worldwide. Explore the
> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
> http://p.sf.net/sfu/intel-appdev
> _______________________________________________
> Geneontology-oboedit-working-group mailing list
> Geneontology-oboedit-working-group@...
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group
>

Hi,

>
> > Hmmm. I could have sworn that I have deleted cross products in 2.0.
>>
>> Not in the Text Editor. You can do it in the Parent Editor.
>>
>
> I confirm that I used to be able to delete cross products in 2.0 in the
> Text Editor.  First, trash the differentium, then highlight and delete the
> genus, then click on Commit.  XP gone.
>
>
> Hmm, I was under the impression that this did not work reliably (which is
> why there was a request to add the Genus trash can). Didn't the genus tend
> to come back if you tried to delete it like that?
>

Not in my experience (and I've removed a lot of xps this way) but others
may had a different result.

T



>
> Nomi
>
>  The same procedure doesn't work in 2.1 anymore but the Parent Editor
> deletion does.
>
>
>
>>
>> > Anyways, the trash can didn't appear to be working either. Both the
>> genus and differentium were still there. I did have auto-commit on.
>>
>> Huh. I just tested in 2.1 and the differentium trash can worked for me.
>> Has anyone else had problems with it? David, which ontology were you
>> editing, and which term? Did you try to add a new cross product and then
>> delete the differentium, or were you adding a new differentium and then
>> deleting it? What happened when you clicked the differentium trash
>> can--nothing? Was this true consistently or just for some terms?
>>
>
> I was able to trash the differentium of an existing term (cellular process
> involved in reproduction) in the current GO using the Text Editor.
>
> Tanya
>
>
>
>>
>>        Nomi
>>
>> >
>> > David
>> >
>> > On 1/10/12 12:17 PM, Nomi Harris wrote:
>> >> How is this any different from OE 2.0? There has never been a way to
>> delete the genus of a cross product. I implemented a genus trash can in a
>> beta version of 2.1, but unfortunately it only worked with Autocommit off,
>> so I was not able to include it in the 2.1.0 release. I hope to get that
>> working soon.
>> >>
>> >> Please clarify if there is any new issue with cross products other
>> than the fact that there's still no way to delete the genus (you can delete
>> the differentia with the differentia trash can).
>> >>
>> >> Also note that, as always, you can use the Parent Editor to delete
>> unwanted cross products.
>> >>
>> >>      Nomi
>> >>
>> >> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>> >>
>> >>> Bugs item #3471901, was opened at 2012-01-10 07:48
>> >>> Message generated for change (Tracker Item Submitted) made by ukemi
>> >>> You can respond by visiting:
>> >>>
>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>> >>>
>> >>> Please note that this message will contain a full copy of the comment
>> thread,
>> >>> including the initial issue submission, for this request,
>> >>> not just the latest update.
>> >>> Category: OBO-Edit
>> >>> Group: Mac OS X
>> >>> Status: Open
>> >>> Resolution: None
>> >>> Priority: 5
>> >>> Private: No
>> >>> Submitted By: David Hill (ukemi)
>> >>> Assigned to: Nobody/Anonymous (nobody)
>> >>> Summary: can't delete cross products
>> >>>
>> >>> Initial Comment:
>> >>> I cannot delete cross products in OE21. I am trying to clarify some
>> definitions for Val that would result in the cross-products being
>> incorrect, but can't seem to delete them from the terms.
>> >>>
>> >>> ----------------------------------------------------------------------
>> >>>
>> >>> You can respond by visiting:
>> >>>
>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Write once. Port to many.
>> Get the SDK and tools to simplify cross-platform app development. Create
>> new or port existing apps to sell to consumers worldwide. Explore the
>> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
>> http://p.sf.net/sfu/intel-appdev
>> _______________________________________________
>> Geneontology-oboedit-working-group mailing list
>> Geneontology-oboedit-working-group@...
>>
>> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group
>>
>
>
>

Hi,

> Hmmm. I could have sworn that I have deleted cross products in 2.0.
>
> Not in the Text Editor. You can do it in the Parent Editor.
>

I confirm that I used to be able to delete cross products in 2.0 in the
Text Editor.  First, trash the differentium, then highlight and delete the
genus, then click on Commit.  XP gone.  The same procedure doesn't work in
2.1 anymore but the Parent Editor deletion does.



>
> > Anyways, the trash can didn't appear to be working either. Both the
> genus and differentium were still there. I did have auto-commit on.
>
> Huh. I just tested in 2.1 and the differentium trash can worked for me.
> Has anyone else had problems with it? David, which ontology were you
> editing, and which term? Did you try to add a new cross product and then
> delete the differentium, or were you adding a new differentium and then
> deleting it? What happened when you clicked the differentium trash
> can--nothing? Was this true consistently or just for some terms?
>

I was able to trash the differentium of an existing term (cellular process
involved in reproduction) in the current GO using the Text Editor.

Tanya



>
>        Nomi
>
> >
> > David
> >
> > On 1/10/12 12:17 PM, Nomi Harris wrote:
> >> How is this any different from OE 2.0? There has never been a way to
> delete the genus of a cross product. I implemented a genus trash can in a
> beta version of 2.1, but unfortunately it only worked with Autocommit off,
> so I was not able to include it in the 2.1.0 release. I hope to get that
> working soon.
> >>
> >> Please clarify if there is any new issue with cross products other than
> the fact that there's still no way to delete the genus (you can delete the
> differentia with the differentia trash can).
> >>
> >> Also note that, as always, you can use the Parent Editor to delete
> unwanted cross products.
> >>
> >>      Nomi
> >>
> >> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
> >>
> >>> Bugs item #3471901, was opened at 2012-01-10 07:48
> >>> Message generated for change (Tracker Item Submitted) made by ukemi
> >>> You can respond by visiting:
> >>>
> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
> >>>
> >>> Please note that this message will contain a full copy of the comment
> thread,
> >>> including the initial issue submission, for this request,
> >>> not just the latest update.
> >>> Category: OBO-Edit
> >>> Group: Mac OS X
> >>> Status: Open
> >>> Resolution: None
> >>> Priority: 5
> >>> Private: No
> >>> Submitted By: David Hill (ukemi)
> >>> Assigned to: Nobody/Anonymous (nobody)
> >>> Summary: can't delete cross products
> >>>
> >>> Initial Comment:
> >>> I cannot delete cross products in OE21. I am trying to clarify some
> definitions for Val that would result in the cross-products being
> incorrect, but can't seem to delete them from the terms.
> >>>
> >>> ----------------------------------------------------------------------
> >>>
> >>> You can respond by visiting:
> >>>
> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>
>
>
> ------------------------------------------------------------------------------
> Write once. Port to many.
> Get the SDK and tools to simplify cross-platform app development. Create
> new or port existing apps to sell to consumers worldwide. Explore the
> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
> http://p.sf.net/sfu/intel-appdev
> _______________________________________________
> Geneontology-oboedit-working-group mailing list
> Geneontology-oboedit-working-group@...
>
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group
>

I was not able to delete the genus by deleting it in the text editor in any of the 2.1 betas. I usually work with autocommit on, but I think  I have tried it using the commit button as well, without success.

Ramona

From: Tanya Berardini <tberardi@...>>
Date: Tue, 10 Jan 2012 13:51:29 -0800
To: Nomi Harris <nlharris@...>>
Cc: OBO-Edit Working Group <geneontology-oboedit-working-group@...>>, David Hill <dph@...>>
Subject: Re: [OBO-Edit Working Group] [ geneontology-Bugs-3471901 ] can't delete cross products

Hi,

> Hmmm. I could have sworn that I have deleted cross products in 2.0.

Not in the Text Editor. You can do it in the Parent Editor.

I confirm that I used to be able to delete cross products in 2.0 in the Text Editor.  First, trash the differentium, then highlight and delete the genus, then click on Commit.  XP gone.

Hmm, I was under the impression that this did not work reliably (which is why there was a request to add the Genus trash can). Didn't the genus tend to come back if you tried to delete it like that?

Not in my experience (and I've removed a lot of xps this way) but others may had a different result.

T



Nomi

The same procedure doesn't work in 2.1 anymore but the Parent Editor deletion does.



> Anyways, the trash can didn't appear to be working either. Both the genus and differentium were still there. I did have auto-commit on.

Huh. I just tested in 2.1 and the differentium trash can worked for me. Has anyone else had problems with it? David, which ontology were you editing, and which term? Did you try to add a new cross product and then delete the differentium, or were you adding a new differentium and then deleting it? What happened when you clicked the differentium trash can--nothing? Was this true consistently or just for some terms?

I was able to trash the differentium of an existing term (cellular process involved in reproduction) in the current GO using the Text Editor.

Tanya



       Nomi

>
> David
>
> On 1/10/12 12:17 PM, Nomi Harris wrote:
>> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
>>
>> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
>>
>> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
>>
>>      Nomi
>>
>> On Jan 10, 2012, at 7:48 AM, SourceForge.net<http://SourceForge.net> wrote:
>>
>>> Bugs item #3471901, was opened at 2012-01-10 07<tel:2012-01-10%2007>:48
>>> Message generated for change (Tracker Item Submitted) made by ukemi
>>> You can respond by visiting:
>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>>
>>> Please note that this message will contain a full copy of the comment thread,
>>> including the initial issue submission, for this request,
>>> not just the latest update.
>>> Category: OBO-Edit
>>> Group: Mac OS X
>>> Status: Open
>>> Resolution: None
>>> Priority: 5
>>> Private: No
>>> Submitted By: David Hill (ukemi)
>>> Assigned to: Nobody/Anonymous (nobody)
>>> Summary: can't delete cross products
>>>
>>> Initial Comment:
>>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
>>>
>>> ----------------------------------------------------------------------
>>>
>>> You can respond by visiting:
>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855


------------------------------------------------------------------------------
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Get the SDK and tools to simplify cross-platform app development. Create
new or port existing apps to sell to consumers worldwide. Explore the
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http://p.sf.net/sfu/intel-appdev
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I just tried this (highlighting and deleting the genus) in a pre-2.1 version and, as I had remembered, the deleted genus comes back after I hit Commit. I'm not sure how/why this ever worked for you! Which version of OE were you using that was able to do this?

I'm clearly not the only person who had trouble deleting the genus; see this bug report: http://sourceforge.net/tracker/index.php?func=detail&aid=3303595&group_id=36855&atid=418257
"Karen reported that she can remove discriminating relationships from cross-products, but there's no trashcan icon for removing the intersection genus. Sometimes she wants to get rid of the whole cross product. She has tried clearing out all the fields and committing, but that doesn't (always?) work."

Maybe clearing the genus field and committing worked some of the time, but it was clearly problematic.

	Nomi

On Jan 10, 2012, at 1:51 PM, Tanya Berardini wrote:

> Hi,
>> 
>> > Hmmm. I could have sworn that I have deleted cross products in 2.0.
>> 
>> Not in the Text Editor. You can do it in the Parent Editor.
>> 
>> I confirm that I used to be able to delete cross products in 2.0 in the Text Editor.  First, trash the differentium, then highlight and delete the genus, then click on Commit.  XP gone. 
> 
> Hmm, I was under the impression that this did not work reliably (which is why there was a request to add the Genus trash can). Didn't the genus tend to come back if you tried to delete it like that?
> 
> Not in my experience (and I've removed a lot of xps this way) but others may had a different result.
> 
> T
>  
> 
> 	Nomi
> 
>> The same procedure doesn't work in 2.1 anymore but the Parent Editor deletion does.
>> 
>>  
>> 
>> > Anyways, the trash can didn't appear to be working either. Both the genus and differentium were still there. I did have auto-commit on.
>> 
>> Huh. I just tested in 2.1 and the differentium trash can worked for me. Has anyone else had problems with it? David, which ontology were you editing, and which term? Did you try to add a new cross product and then delete the differentium, or were you adding a new differentium and then deleting it? What happened when you clicked the differentium trash can--nothing? Was this true consistently or just for some terms?
>> 
>> I was able to trash the differentium of an existing term (cellular process involved in reproduction) in the current GO using the Text Editor.
>> 
>> Tanya
>> 
>>  
>> 
>>        Nomi
>> 
>> >
>> > David
>> >
>> > On 1/10/12 12:17 PM, Nomi Harris wrote:
>> >> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
>> >>
>> >> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
>> >>
>> >> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
>> >>
>> >>      Nomi
>> >>
>> >> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>> >>
>> >>> Bugs item #3471901, was opened at 2012-01-10 07:48
>> >>> Message generated for change (Tracker Item Submitted) made by ukemi
>> >>> You can respond by visiting:
>> >>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>> >>>
>> >>> Please note that this message will contain a full copy of the comment thread,
>> >>> including the initial issue submission, for this request,
>> >>> not just the latest update.
>> >>> Category: OBO-Edit
>> >>> Group: Mac OS X
>> >>> Status: Open
>> >>> Resolution: None
>> >>> Priority: 5
>> >>> Private: No
>> >>> Submitted By: David Hill (ukemi)
>> >>> Assigned to: Nobody/Anonymous (nobody)
>> >>> Summary: can't delete cross products
>> >>>
>> >>> Initial Comment:
>> >>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
>> >>>
>> >>> ----------------------------------------------------------------------
>> >>>
>> >>> You can respond by visiting:
>> >>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>

Hi Nomi,

Just cc'ing Tanya to see if I am having a senior moment, but I could 
have sworn that in 2.0 if we deleted both a genus and a differentium, 
tabbed out and then committed, the cross product went away.
>> Anyways, the trash can didn't appear to be working either. Both the genus and differentium were still there. I did have auto-commit on.
> Huh. I just tested in 2.1 and the differentium trash can worked for me. Has anyone else had problems with it? David, which ontology were you editing, and which term? Did you try to add a new cross product and then delete the differentium, or were you adding a new differentium and then deleting it? What happened when you clicked the differentium trash can--nothing? Was this true consistently or just for some terms?
It was a pre-existing term where the cross product was incorrect. When I 
clicked on the differentium trash can, it looked like it worked. If I 
then went to another term and came back, the differentium was not gone. 
The parent editor did work.
>
> 	Nomi
>
>> David
>>
>> On 1/10/12 12:17 PM, Nomi Harris wrote:
>>> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
>>>
>>> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
>>>
>>> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
>>>
>>> 	Nomi
>>>
>>> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>>>
>>>> Bugs item #3471901, was opened at 2012-01-10 07:48
>>>> Message generated for change (Tracker Item Submitted) made by ukemi
>>>> You can respond by visiting:
>>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>>>
>>>> Please note that this message will contain a full copy of the comment thread,
>>>> including the initial issue submission, for this request,
>>>> not just the latest update.
>>>> Category: OBO-Edit
>>>> Group: Mac OS X
>>>> Status: Open
>>>> Resolution: None
>>>> Priority: 5
>>>> Private: No
>>>> Submitted By: David Hill (ukemi)
>>>> Assigned to: Nobody/Anonymous (nobody)
>>>> Summary: can't delete cross products
>>>>
>>>> Initial Comment:
>>>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> You can respond by visiting:
>>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855

I'm going to Berkeley this afternoon - will have a chance to demo the
behavior in person!

Tanya


On Wed, Jan 11, 2012 at 4:57 AM, David Hill <dph@...> wrote:

> Hi Nomi,
>
> Just cc'ing Tanya to see if I am having a senior moment, but I could have
> sworn that in 2.0 if we deleted both a genus and a differentium, tabbed out
> and then committed, the cross product went away.
>
>  Anyways, the trash can didn't appear to be working either. Both the genus
>>> and differentium were still there. I did have auto-commit on.
>>>
>> Huh. I just tested in 2.1 and the differentium trash can worked for me.
>> Has anyone else had problems with it? David, which ontology were you
>> editing, and which term? Did you try to add a new cross product and then
>> delete the differentium, or were you adding a new differentium and then
>> deleting it? What happened when you clicked the differentium trash
>> can--nothing? Was this true consistently or just for some terms?
>>
> It was a pre-existing term where the cross product was incorrect. When I
> clicked on the differentium trash can, it looked like it worked. If I then
> went to another term and came back, the differentium was not gone. The
> parent editor did work.
>
>
>>        Nomi
>>
>>  David
>>>
>>> On 1/10/12 12:17 PM, Nomi Harris wrote:
>>>
>>>> How is this any different from OE 2.0? There has never been a way to
>>>> delete the genus of a cross product. I implemented a genus trash can in a
>>>> beta version of 2.1, but unfortunately it only worked with Autocommit off,
>>>> so I was not able to include it in the 2.1.0 release. I hope to get that
>>>> working soon.
>>>>
>>>> Please clarify if there is any new issue with cross products other than
>>>> the fact that there's still no way to delete the genus (you can delete the
>>>> differentia with the differentia trash can).
>>>>
>>>> Also note that, as always, you can use the Parent Editor to delete
>>>> unwanted cross products.
>>>>
>>>>        Nomi
>>>>
>>>> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>>>>
>>>>  Bugs item #3471901, was opened at 2012-01-10 07:48
>>>>> Message generated for change (Tracker Item Submitted) made by ukemi
>>>>> You can respond by visiting:
>>>>> https://sourceforge.net/**tracker/?func=detail&atid=**
>>>>> 418257&aid=3471901&group_id=**36855<https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855>
>>>>>
>>>>> Please note that this message will contain a full copy of the comment
>>>>> thread,
>>>>> including the initial issue submission, for this request,
>>>>> not just the latest update.
>>>>> Category: OBO-Edit
>>>>> Group: Mac OS X
>>>>> Status: Open
>>>>> Resolution: None
>>>>> Priority: 5
>>>>> Private: No
>>>>> Submitted By: David Hill (ukemi)
>>>>> Assigned to: Nobody/Anonymous (nobody)
>>>>> Summary: can't delete cross products
>>>>>
>>>>> Initial Comment:
>>>>> I cannot delete cross products in OE21. I am trying to clarify some
>>>>> definitions for Val that would result in the cross-products being
>>>>> incorrect, but can't seem to delete them from the terms.
>>>>>
>>>>> ------------------------------**------------------------------**
>>>>> ----------
>>>>>
>>>>> You can respond by visiting:
>>>>> https://sourceforge.net/**tracker/?func=detail&atid=**
>>>>> 418257&aid=3471901&group_id=**36855<https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855>
>>>>>
>>>>

Sorry--I wasn't testing 2.0, but one of the interim versions. You are right--in turns out that in 2.0, when you delete a genus, it is gone; by version 2.1-b7, the genus reappears. I think it must have something to do with other fixes that Amina made in the Text Editor around that time. I will do more investigation.
	Nomi

On Jan 11, 2012, at 4:57 AM, David Hill wrote:

> Hi Nomi,
> 
> Just cc'ing Tanya to see if I am having a senior moment, but I could have sworn that in 2.0 if we deleted both a genus and a differentium, tabbed out and then committed, the cross product went away.
>>> Anyways, the trash can didn't appear to be working either. Both the genus and differentium were still there. I did have auto-commit on.
>> Huh. I just tested in 2.1 and the differentium trash can worked for me. Has anyone else had problems with it? David, which ontology were you editing, and which term? Did you try to add a new cross product and then delete the differentium, or were you adding a new differentium and then deleting it? What happened when you clicked the differentium trash can--nothing? Was this true consistently or just for some terms?
> It was a pre-existing term where the cross product was incorrect. When I clicked on the differentium trash can, it looked like it worked. If I then went to another term and came back, the differentium was not gone. The parent editor did work.
>> 
>> 	Nomi
>> 
>>> David
>>> 
>>> On 1/10/12 12:17 PM, Nomi Harris wrote:
>>>> How is this any different from OE 2.0? There has never been a way to delete the genus of a cross product. I implemented a genus trash can in a beta version of 2.1, but unfortunately it only worked with Autocommit off, so I was not able to include it in the 2.1.0 release. I hope to get that working soon.
>>>> 
>>>> Please clarify if there is any new issue with cross products other than the fact that there's still no way to delete the genus (you can delete the differentia with the differentia trash can).
>>>> 
>>>> Also note that, as always, you can use the Parent Editor to delete unwanted cross products.
>>>> 
>>>> 	Nomi
>>>> 
>>>> On Jan 10, 2012, at 7:48 AM, SourceForge.net wrote:
>>>> 
>>>>> Bugs item #3471901, was opened at 2012-01-10 07:48
>>>>> Message generated for change (Tracker Item Submitted) made by ukemi
>>>>> You can respond by visiting:
>>>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855
>>>>> 
>>>>> Please note that this message will contain a full copy of the comment thread,
>>>>> including the initial issue submission, for this request,
>>>>> not just the latest update.
>>>>> Category: OBO-Edit
>>>>> Group: Mac OS X
>>>>> Status: Open
>>>>> Resolution: None
>>>>> Priority: 5
>>>>> Private: No
>>>>> Submitted By: David Hill (ukemi)
>>>>> Assigned to: Nobody/Anonymous (nobody)
>>>>> Summary: can't delete cross products
>>>>> 
>>>>> Initial Comment:
>>>>> I cannot delete cross products in OE21. I am trying to clarify some definitions for Val that would result in the cross-products being incorrect, but can't seem to delete them from the terms.
>>>>> 
>>>>> ----------------------------------------------------------------------
>>>>> 
>>>>> You can respond by visiting:
>>>>> https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3471901&group_id=36855