Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-23

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All times shown according to UTC.

Time Nick Message
04:19 sneumann_ joined #bioclipse
05:29 egonw joined #bioclipse
06:15 Gpox joined #bioclipse
06:21 Gpoks joined #bioclipse
06:26 CIA-54 bioclipse: egonw * r11465 /bioclipse2/trunk/plugins/net.biocli​pse.pubchem/src/net/bioclipse/pubche​m/wizards/NewFromPubChemWizard.java:
06:26 CIA-54 bioclipse: Updated NewFromPubChemWizard to current BC2 standards.
06:26 CIA-54 bioclipse: * put search results in a subfolder
06:26 CIA-54 bioclipse: * better monitor use
06:26 CIA-54 bioclipse: * support cancel
06:27 CIA-54 bioclipse: egonw * r11466 /bioclipse2/trunk/plugins/net.biocli​pse.pubchem/src/net/bioclipse/pubche​m/wizards/NewFromPubChemWizard.java: Don't let exceptions disappear: use LogUtils.handleException() instead
06:28 CIA-54 bioclipse: egonw * r11467 /bioclipse2/trunk/plugins/net.bioclips​e.pubchem/src/net/bioclipse/pubchem/wi​zards/NewFromPubChemWizardPage.java: Removed debug output to STDOUT
06:45 CIA-54 bioclipse: egonw * r11468 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java: Added equivalent revealAndSelect for IFolder
06:53 CIA-54 bioclipse: egonw * r11469 /bioclipse2/trunk/plugins/net.bioclipse.pubchem/ (2 files in 2 dirs): Reader to reveal and select, but got an NPE, see bug #1352
06:53 zarah bug #1352 | http://tinyurl.com/lmsumv
07:54 egonw Gpox: do you remember the name of that desktop sharing software we used with Christoph two months ago?
08:00 CIA-54 bioclipse: egonw * r11470 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/business/IJChemPaintManager.java: Fixed params field of @PublishedMethod: only repeat the API, no explanation
08:19 CIA-54 bioclipse: egonw * r11471 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/business/IJChemPaintManager.java:
08:19 CIA-54 bioclipse: Cleaned up the @PublishedMethod summary fields.
08:19 CIA-54 bioclipse: * consistency: all capital first charecters and periods at end of summary.
08:19 CIA-54 bioclipse: * removed duplication of words (fixes #1351)
08:19 zarah bug #1351 | http://tinyurl.com/nmctfl
08:20 egonw I wonder where olass is...
08:20 egonw he better show up if he wants a RC3 today...
08:29 masak joined #bioclipse
08:50 Gpox egonw: http://www.teamviewer.com
08:50 egonw Gpox: thanx!
08:50 egonw sneumann_: got that?
08:55 CIA-54 bioclipse: goglepox * r11472 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/business/JChemPaintManager.java: Added refresh on removing of explicit hydrogens
09:08 egonw Gpox: tack... bug closed
09:13 sneumann_ egonw: yup
09:21 CIA-54 bioclipse: goglepox * r11473 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint.view/src/net/bioclipse/cdk/jc​hempaint/view/CenterMoleculeHandler.java: Class is not used and do nothing, removed
09:22 CIA-54 bioclipse: goglepox * r11474 /bioclipse2/trunk/plugins/ (12 files in 9 dirs):
09:22 CIA-54 bioclipse: Added copyright/license statement
09:22 CIA-54 bioclipse: see bug #1333
09:22 zarah bug #1333 | http://tinyurl.com/nz9aff
09:41 shk3 joined #bioclipse
10:00 olass joined #bioclipse
10:00 olass moin
10:00 zarah hello olass, you fantastic person you
10:00 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
10:00 olass @msg
10:00 zarah olass: 11 m 49 s ago, masak said jag bedriver undervisning mellan 10 och 15 på torsdag. kanske ses efter 15?
10:01 olass masak: låter bra
10:01 masak godt.
10:24 CIA-54 bioclipse: ospjuth * r11475 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml: Removed duplicated net.bioclipse.cheminformatics newwizard category.
10:25 CIA-54 bioclipse: ospjuth * r11476 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.sdfeditor/html/newwizard.html: Renamed reference to new cheminformatics newwizard category.
10:33 olass egonw: ping
10:33 olass egonw: could you help me draw something that demonstrates the show/hide implicit hydrogens functionality
10:33 egonw pong
10:34 egonw toluene?
10:34 olass can you try it please?
10:34 egonw yes, mom
10:34 egonw meanwhile
10:34 egonw can you please check bioclipse.product
10:34 egonw ?
10:34 olass sure
10:34 egonw the cdk feature should not be there, correct?
10:34 egonw I might have accidentally commited that
10:34 olass no
10:34 olass please remove it
10:35 olass onlu core, balloon, cheminfo features in product
10:35 egonw will do
10:35 egonw you mean
10:35 egonw only core_feature in bioclipse.product
10:35 olass no
10:35 egonw and balloon & cheminfo in core_feature
10:35 egonw (was not finished yet)
10:35 olass ah
10:35 olass platform feature
10:35 olass sry
10:35 egonw right
10:35 egonw good
10:36 egonw ok, just making sure I make the right commit :)
10:36 olass no worries
10:36 olass I check this in teh release process
10:36 olass does show/hide implicit H work for you on toluene?
10:36 egonw show/not-show implicit works for me
10:37 olass ok
10:37 egonw implicit hydrogens for toluene only show up when ...
10:37 olass yes it does
10:37 egonw when you have also on:
10:37 egonw show End Carbons
10:37 olass no menu for that
10:37 egonw preference page
10:38 olass ok
10:38 egonw (where it should be, I think)
10:38 egonw not sure who requested show implicit hydrogens in menu
10:38 egonw I personally don't like it there so much...
10:40 olass I did
10:40 olass thought it was a nice feature
10:41 olass but now that inchi is solved...
10:41 CIA-54 bioclipse: egonw * r11477 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.render/src/org/openscien​ce/cdk/renderer/RenderingParameters.java: Showing aromaticity rings should be the default, since we can now properly draw them (upstream in jchempaint-primary as commit 14619, fixes #504).
10:41 zarah bug #504 | http://tinyurl.com/lmxttl
10:43 egonw OK, /me has nothing to commit for RC3
10:43 egonw unless... 1352 gets fixed
10:46 olass good
10:48 CIA-54 bioclipse: ospjuth * r11478 /bioclipse2/trunk/plugins/net.​bioclipse.pubchem/plugin.xml: New GetPubChemWizard is not a NewProjectWizard.
10:49 * egonw is now directing efforts to a MetWare plugin for BC2(.1)
10:51 olass egonw: do not forget the descriptor ontology project
10:51 olass but lets talk about that on thursday
10:51 egonw yes, let's do that
10:51 olass @tell Gpox: new P1 bugs for you available
10:51 zarah Consider it noted.
10:51 * olass is off for lunmch in the sun
10:59 CIA-54 bioclipse: shk3 * r11479 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.ui/src/net/bioclipse/cdk/ui/ha​ndlers/Create2dHandlerWithReset.java: handles cancel in file dialog
11:03 shk3 olass: verapamil.mol should be attached to bug 1061
11:03 shk3 but I can't find it
11:03 shk3 can you attach or send me the file?
11:38 CIA-54 bioclipse: goglepox * r11480 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
11:38 CIA-54 bioclipse: Undo/redo now fires structureChanged events
11:38 CIA-54 bioclipse: Solves bug #1323
11:38 zarah bug #1323 | http://tinyurl.com/krv3ho
12:04 shk3 olass: back?
12:09 masak @tell olass "The syntax of FASTA Deflines used by the NCBI BLAST server depends on the database from which each sequence was obtained." http://rcc.uga.edu/applications/bioin​formatics/ncbiblast2210/formatdb.html
12:09 zarah masak's link is also http://tinyurl.com/m6v5o2
12:09 zarah Consider it noted.
12:39 olass shk3: yes
12:39 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
12:40 olass @msg
12:40 zarah olass: 30 m 49 s ago, masak said "The syntax of FASTA Deflines used by the NCBI BLAST server depends on the database from which each sequence was obtained." http://rcc.uga.edu/applications/bioin​formatics/ncbiblast2210/formatdb.html
12:40 egonw [06/23/09 13:03] <shk3> olass: verapamil.mol should be attached to bug 1061
12:40 egonw [06/23/09 13:03] <shk3> but I can't find it
12:40 egonw [06/23/09 13:03] <shk3> can you attach or send me the file?
12:40 olass hmm
12:40 olass @pz verapamil.mol
12:41 zarah [1339] Generate2D with CDK fails for ... http://tinyurl.com/msea97
12:41 zarah Entire list at http://tinyurl.com/lrrhs2
12:41 olass strange
12:41 olass will attach to bug 1339
12:42 olass shk3: done
12:42 shk3 thanks
12:55 CIA-54 bioclipse: ospjuth * r11481 /bioclipse2/trunk/features/net.bioclip​se.platform_feature/bioclipse.product: Removed cdk feature from product.
13:19 olass egonw, shk3: no blockers?
13:19 olass then RC3
13:19 egonw only the pubchem revealAndSelect thingy
13:19 shk3 don't see any
13:19 egonw but hardly a blocker
13:19 shk3 for/from me
13:20 CIA-54 bioclipse: goglepox * r11482 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java:
13:20 CIA-54 bioclipse: Checks all WorkbenchWindows
13:20 CIA-54 bioclipse: see bug #1352
13:20 egonw from my perspective: good to go
13:20 zarah bug #1352 | http://tinyurl.com/lmsumv
13:20 egonw Gpox: ah, right on time
13:20 CIA-54 bioclipse: goglepox * r11483 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (2 files):
13:20 CIA-54 bioclipse: Commented out adding of ResourceChangeListener as it breaks other functionality
13:20 CIA-54 bioclipse: see bug #1206
13:20 zarah bug #1206 | http://tinyurl.com/llw6vr
13:21 egonw olass: if I have 5 minutes, I can check the revealAndSelect for PubChem...
13:21 olass sure
13:21 olass Gpox tried a fix there
13:21 olass but could not test it
13:29 CIA-54 bioclipse: ospjuth * r11484 /bioclipse2/trunk/ (43 files in 43 dirs): Set version to 2.0.0.RC3
13:30 egonw that fix by Gpox is not working for me
13:30 egonw invalid thread access
13:31 egonw I'll try wrapping it...
13:31 egonw trying to recover how that was done again...
13:32 CIA-54 bioclipse: ospjuth * r11485 /bioclipse2/trunk/ (2 files in 2 dirs): Updated update sites for RC3.
13:33 CIA-54 bioclipse: ospjuth * r11486 /bioclipse2/trunk/plugins/ (12 files in 12 dirs): Set version to 2.0.0.RC3
13:34 CIA-54 bioclipse: ospjuth * r11487 /bioclipse2/trunk/features/ (17 files in 16 dirs): Set version to 2.0.0.RC3
13:38 egonw ok, that's a long 5 minutes...
13:38 egonw but almost done, I think
13:39 egonw OK, seems to work
13:41 egonw ... commiting is slow
13:41 CIA-54 bioclipse: egonw * r11488 /bioclipse2/trunk/plugins/net.biocli​pse.pubchem/src/net/bioclipse/pubche​m/wizards/NewFromPubChemWizard.java: Enabled reveal of results folder (fixes #1349)
13:41 zarah bug #1349 | http://tinyurl.com/m5pq48
13:44 olass great
13:47 olass egonw: what does the following mean?
13:47 olass Buildfile: /Users/ola/Workspaces/bioclipse2_1/ne​t.bioclipse.doc.developers/build.xml
13:47 olass runPerl:
13:47 olass [exec] Cannot open file '-q' at /System/Library/Perl/Extras/5.8.8/XML/XPath.pm line 53.
13:47 olass [exec] Execution of xpath failed; please check your xpath installation.
13:47 olass did it owrk?
13:47 olass [exec] Result: 255
13:47 olass work?
13:48 olass BUILD SUCCESSFUL
13:48 olass Total time: 20 seconds
13:48 olass or fail?
13:48 olass egonw: if it failed, please run doc devel and commit latest version
13:48 olass so I can get it from svn
13:50 olass egonw: ping
13:50 CIA-54 bioclipse: ospjuth * r11489 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Commented out generators view. Solves 1254.
13:50 egonw please install 'xpath'
13:51 olass I did
13:51 egonw where?
13:51 olass BUILD SUCCESSFUL seems to indicate it worked anyway
13:51 egonw ok, that's something you can file a bug about
13:51 egonw the error is not picked up by Ant
13:51 olass egonw: you looked at it here, don't you remember?
13:51 olass (xpath)
13:52 egonw don't remember the outcome
13:52 olass with no solution found
13:52 olass you gave up ;)
13:52 egonw stupid OS/X
13:52 olass hah
13:52 egonw masak: at BMC?
13:52 olass egonw: masak looked too
13:52 egonw why can't those guys write a decent OS?
13:52 olass why can't you write a decent perl script?
13:52 egonw no, the Perl script is fine
13:52 olass ..sure..
13:52 egonw it now nicely reports that it does not find xpath
13:53 egonw ask masak
13:53 egonw he made me write proper Perl
13:53 * masak wakes up
13:53 olass masak: can you help?
13:53 masak did someboday say Perl?
13:53 olass egonw sort of mentioned it...
13:53 egonw olass: please try xpath from the command line
13:53 olass how?
13:53 olass xpath
13:54 egonw the reported error indicates that your xpath installation is broken
13:54 olass mbpro:~ ola$ xpath
13:54 olass Usage:
13:54 olass /usr/bin/xpath [filename] query
13:54 olass
13:54 olass If no filename is given, supply XML on STDIN.
13:54 olass mbpro:~ ola$
13:54 egonw not that the perl script is...
13:54 masak note that me checking egonw's Perl script is not a guarantee that it works...
13:54 olass masak: does your doc.devel plugin run without problems?
13:54 masak I don't know.
13:55 masak I'm not really in a position to check right now.
13:55 olass ok
13:55 egonw xpath -e "//plugin" plugin.xml
13:55 egonw in plugins/net.bioclipse.foo/
13:55 * olass does not have time now
13:55 olass should I omit doc.devel in RC3?
13:55 egonw olass: you have the wrong xpath
13:56 egonw the command line syntax of your executable is different
13:56 masak egonw: the usage above seems to indicate that that might not work with olass' xpath version.
13:56 masak egonw: yes, exactly.
13:57 olass egonw: could you improve the perl script or do I need to install Linux on my machine to run your scripts?
13:57 olass I do have xpath
13:57 olass not just your version
13:57 egonw yeah, will add some information to that error log, what xpath to install, and which version
13:57 olass thanks
13:57 olass or even better
13:57 olass support more xpath versions
13:58 olass so it works on OS X
13:58 * olass will release as it is now
13:58 CIA-54 bioclipse: ospjuth * r11490 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Set version to 2.0.0.RC3
13:59 olass egonw: could you close 1352 if it now works?
14:00 olass egonw: I also would like to move 1240 to 2.1 if you don't mind?
14:01 egonw fine with me
15:01 CIA-54 bioclipse: shk3 * r11491 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (2 files in 2 dirs): MoleculeAnnealerAdapter takes a ChiefJustice instead of an IJudge
15:10 CIA-54 bioclipse: ospjuth * r11492 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (html/glance.html intro/firststeps.xml): Updated and fixed link to "Bioclipse at a glance". Solves 765.
15:14 CIA-54 bioclipse: ospjuth * r11493 /bioclipse2/trunk/plugins/​net.bioclipse.ui/toc.xml: Removed duplicated "Customizing the workbench" entry in help
15:25 CIA-54 bioclipse: ospjuth * r11494 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (15 files in 5 dirs):
15:25 CIA-54 bioclipse: Brushed up Bioclipse help system
15:25 CIA-54 bioclipse: * Entry and image for JSConsoleView
15:25 CIA-54 bioclipse: * Use correct stylesheet in many pages
15:25 CIA-54 bioclipse: * Spelling errors
15:25 olass egonw: ping
15:26 egonw pong
15:26 olass egonw: can you please take 5 minutes to add references to CDK publication in the cdk.ui plugin?
15:26 olass under html/maintopic.html
15:26 olass please update that page
15:26 olass it talks about the cml plugin too
15:26 olass which is wrong
15:27 olass and it should state the license of CDK, authors, and link to CDK website IMO
15:27 olass ok?
15:27 egonw who wrote that page?
15:30 egonw shk3: why did you not just copy the docs from the BC1 cdk plugin?
15:31 egonw shk3: can I fix the HTML by copying that content?
15:31 egonw OK, making it so
15:31 egonw shk3: if you object, please file a bug report later
15:32 shk3 mom
15:32 shk3 what are you talking about?
15:32 egonw cdk.ui/html
15:32 egonw which lists the wrong license
15:32 egonw talks about the CML plugin
15:33 CIA-54 bioclipse: ospjuth * r11495 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (doc/jcpPlugin.html toc.xml): Brushed up JCP help system.
15:33 shk3 hm, forgot to change that, it seems
15:33 shk3 wait a minute before you copy old help
15:33 egonw well, I'm fixing things now
15:33 CIA-54 bioclipse: egonw * r11496 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.ui/html/artistic.html: Removed incorrect license
15:34 shk3 the old help had lots of things not applicable
15:35 shk3 and did not have things which are in the new plugin
15:35 shk3 so copying the old one was not an option
15:40 egonw such as?
15:40 egonw I see nothing wrong with cdk_home.html
15:40 egonw or lgpl.html
15:40 CIA-54 bioclipse: ospjuth * r11497 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (7 files in 3 dirs): Brushed up SDF help system.
15:41 shk3 the file formats stuff is not part of cdk.ui
15:41 shk3 in bc2
15:41 shk3 is it?
15:41 shk3 the about cdk stuff would be ok
15:41 shk3 although
15:41 CIA-54 bioclipse: ospjuth * r11498 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk.smartsmatching/html/ (smartsmatchingview.html smartstheory.html): Brushed up SmartsMatching help system.
15:41 shk3 it could go in any net.bc.cdk.* plugin
15:50 shk3 oh, and the views.html is also outdated
15:51 egonw olass: commit pending
15:51 CIA-54 bioclipse: egonw * r11499 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (4 files in 2 dirs):
15:51 CIA-54 bioclipse: Fixed CDK plugin documentation.
15:51 CIA-54 bioclipse: * correct LGPL license
15:51 CIA-54 bioclipse: * added information from BC1 plugin, including literature and author list
15:51 CIA-54 bioclipse: * added information about the CDK manager
15:52 shk3 is net.bc.cdk.ui the right place for cdk manager info?
15:52 shk3 shouldn't that be in net.bc.cdk.business?
15:53 egonw not until we resolved how one plugin can contribute to the TOC of another plugin, I'd say no
15:54 egonw otherwise we get too many TOC top pages
15:54 shk3 hm
15:54 shk3 but that means the user may get help on plugins he does not have installed
15:54 shk3 confusing
15:54 egonw how so?
15:54 shk3 and why then use net.bc.cdk.ui plugin for cdk stuff?
15:54 egonw cdk.ui depends on cdk.business
15:54 shk3 ah, dependencies
15:54 shk3 ok
15:55 shk3 but he might have a plugin and not get the help
15:55 egonw remember that UI code is supposed to use the manager
15:55 shk3 if he has business and not ui
15:55 egonw true
15:55 shk3 (which is possible, if a use does scripting only)
15:55 egonw fortunately there is 'man cdk'
15:55 egonw and the help is actually to be used in a UI environment
15:55 egonw and not from the manager
15:58 shk3 btw, I am again observing virtual to disappear randomly
15:59 CIA-54 bioclipse: egonw * r11500 /bioclipse2/trunk/ (29 files in 11 dirs): Added an initial plugin for MetWare, which bears only a preference page to set some JDBC information for the SQL backend
16:01 egonw happens to all of us...
16:01 egonw but once there is content, it should be fine
16:19 CIA-54 bioclipse: egonw * r11501 /bioclipse2/trunk/plugins/net.bioclipse.metware/ (11 files in 5 dirs): Added infrastructure for the metware manager.
17:18 sneumann__ joined #bioclipse
19:01 sneumann joined #bioclipse

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