Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-15

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All times shown according to UTC.

Time Nick Message
05:05 masak joined #bioclipse
06:27 CIA-28 bioclipse: carl_masak * r8265 /bot/trunk/zarah.pl: [zarah] expanded greeting repertoire
06:33 masak zarah: restart
06:33 zarah joined #bioclipse
07:18 masak @tell edrin I'm about to scrap the old js console and replace it fully with the new one, but I'd like to be sure that I'm not leaving any users behind. the new console is being developed in a branch, and currently supports manager calls, history and tab completion, just like the old one. it should also work well on Windows.
07:18 zarah Consider it noted.
07:20 masak @tell edrin what concerns me a bit is that so far, I've only received "it doesn't work" reports from you. jonalv has confirmed that it works on his Windows installation, and I'm very anxious to make any further adjustments that might be needed for the new console to work under Win32. please tell me if there is anything more I can do.
07:20 zarah Consider it noted.
08:01 Gpox joined #bioclipse
08:36 edrin1 joined #bioclipse
08:56 olass joined #bioclipse
08:58 masak @tell edrin1 I'm about to scrap the old js console and replace it fully with the new one, but I'd like to be sure that I'm not leaving any users behind. the new console is being developed in a branch, and currently supports manager calls, history and tab completion, just like the old one. it should also work well on Windows.
08:58 zarah Consider it noted.
08:58 masak @tell edrin1 what concerns me a bit is that so far, I've only received "it doesn't work" reports from you. jonalv has confirmed that it works on his Windows installation, and I'm very anxious to make any further adjustments that might be needed for the new console to work under Win32. please tell me if there is anything more I can do.
08:58 zarah Consider it noted.
08:59 jonalv joined #bioclipse
08:59 jonalv hi
08:59 zarah oh hai jonalv
08:59 jonalv OH HAI zarah :)
09:05 edrin joined #bioclipse
09:05 CIA-28 bioclipse: goglepox * r8266 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): [jonalv-branch] First step, using different structuredb instances for jsconsole and gui accomplished
09:05 edrin hi
09:05 edrin hi olass
09:05 zarah ni hao edrin
09:05 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
09:05 edrin @msg
09:06 zarah edrin: 1 h 47 m 42 s ago, masak said I'm about to scrap the old js console and replace it fully with the new one, but I'd like to be sure that I'm not leaving any users behind. the new console is being developed in a branch, and currently supports manager calls, history and tab completion, just like the old one. it should also work well on Windows.
09:06 zarah edrin: 1 h 45 m 25 s ago, masak said what concerns me a bit is that so far, I've only received "it doesn't work" reports from you. jonalv has confirmed that it works on his Windows installation, and I'm very anxious to make any further adjustments that might be needed for the new console to work under Win32. please tell me if there is anything more I can do.
09:06 CIA-28 bioclipse: goglepox * r8267 /bioclipse2/trunk/plugins/ (7 files in 5 dirs): It works! Further testing is needed but then there will come a blog post!
09:06 CIA-28 bioclipse: goglepox * r8268 /bioclipse2/trunk/plugins/net.b​ioclipse.core/META-INF/spring/ (context-osgi.xml context.xml): [jonalv-branch] two xml files. (Subversion is putting up a fight today...):
09:06 olass hi edrin
09:06 olass we are in a meeting now
09:06 olass will be back in 30 mins or so
09:06 edrin ok
09:06 CIA-28 bioclipse: goglepox * r8269 /bioclipse2/trunk/plugins/net.bioclipse.scri​pting/src/net/bioclipse/scripting/business/ (. IJSJobCreatorAdvice.java JSJobCreatorAdvice.java): [jonalv-branch] a few files. (Subversion is putting up a fight today...):
09:07 CIA-28 bioclipse: goglepox * r8270 /bioclipse2/trunk/plugins/net.bio​clipse.scripting/META-INF/spring/ (. context-osgi.xml context.xml): [jonalv-branch] a few xml files. (Subversion is really putting up a fight today...):
09:07 CIA-28 bioclipse: goglepox * r8271 /bioclipse2/trunk/plugins/net.b​ioclipse.core/META-INF/spring/ (context-osgi.xml context.xml): hopefully fixed strange things I did the day me and SVN had a little fight...
09:07 CIA-28 bioclipse: goglepox * r8272 /bioclipse2/trunk/plugins/net.bioclipse​.core/META-INF/spring/context-osgi.xml: fixed typo.
09:08 CIA-28 bioclipse: goglepox * r8273 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/SubStructureIterator.java: removed code used during devlopment
09:08 CIA-28 bioclipse: goglepox * r8274 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: adapted tab completion to work on the new manager objects
09:09 CIA-28 bioclipse: goglepox * r8275 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
09:09 CIA-28 bioclipse: [JsConsoleView] refined the search for methods to also recurse
09:09 CIA-28 bioclipse: through parent interfaces
09:09 CIA-28 bioclipse: goglepox * r8276 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: fixed interface inheritance problem in man command
09:10 CIA-28 bioclipse: goglepox * r8277 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): made graphical progressmonitor for addStructuresFromSDF when running it from js console
09:10 CIA-28 bioclipse: goglepox * r8278 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (2 files in 2 dirs): made graphical progressmonitor for deleteWithMolecules when running it from js console (couldn't test it though):
09:11 CIA-28 bioclipse: goglepox * r8279 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): Changed cdk business plugin to support new progressmonitors during javascript console running
09:11 CIA-28 bioclipse: goglepox * r8280 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): changed order of paramaters and added TODO comment for what I should pick up and work with tomorrow
09:12 CIA-28 bioclipse: goglepox * r8281 /bioclipse2/trunk/plugins/net.bioclipse.scri​pting/src/net/bioclipse/scripting/business/ (BioclipseUIJob.java JSJobCreatorAdvice.java): fixed (I hope) JSJobCreatorAdvice resolves bug #235
09:12 zarah bug #235 | http://tinyurl.com/8n86z9
09:12 CIA-28 bioclipse: goglepox * r8282 /bioclipse2/trunk/plugins/net.bioclip​se.scripting/src/net/bioclipse/script​ing/business/JSJobCreatorAdvice.java: Added code to run BioclipseUIJob from JSJobCreatorAdvice
09:12 CIA-28 bioclipse: goglepox * r8283 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added createSDFFileIndex(IFile, BioclipseUIJob)
09:13 CIA-28 bioclipse: goglepox * r8284 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Uses new UIjob runner for managers
09:13 CIA-28 bioclipse: goglepox * r8285 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Added monitor canceled check in createSDFFileIndex
09:14 CIA-28 bioclipse: goglepox * r8286 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added uiJob to numbersOfEntriesInSDF
09:15 CIA-28 bioclipse: goglepox * r8287 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): getting BioclipseUIJob to work. Moleculestable example is now working. (Hope I haven't broken the other cases too much...)
09:15 CIA-28 bioclipse: goglepox * r8288 /bioclipse2/trunk/plugins/net.bioclipse.structur​edb/src/net/bioclipse/structuredb/Database.java: removed job creation from gui code. (didn't know it was there...)
09:15 CIA-28 bioclipse: goglepox * r8289 /bioclipse2/trunk/plugins/net.bioclipse.struct​uredb/src/net/bioclipse/structuredb/business/ (IStructuredbManager.java StructuredbManager.java): removed unneeded method
09:16 CIA-28 bioclipse: goglepox * r8290 /bioclipse2/trunk/plugins/net.bioclipse.ui/s​rc/net/bioclipse/ui/jobs/BioclipseJob.java: indentation
09:16 CIA-28 bioclipse: goglepox * r8291 /bioclipse2/trunk/plugins/net.bioclip​se.structuredb/META-INF/MANIFEST.MF: added dep to ne.bc.ui
09:16 CIA-28 bioclipse: goglepox * r8292 /bioclipse2/trunk/plugins/net.biocl​ipse.ui/src/net/bioclipse/ui/jobs/ (BioclipseJob.java CreateJobAdvice.java): Rewrote CreateJobadvice to work for gui (that is, no more waiting for it to finish)
09:17 CIA-28 bioclipse: goglepox * r8293 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/jobs/CreateJobAdvice.java: cleaned up a bit and made the solution a bit more backwards compatible
09:17 CIA-28 bioclipse: goglepox * r8294 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: added cancelability to numberOfentriesInSDF
09:18 CIA-28 bioclipse: goglepox * r8295 /bioclipse2/trunk/plugins/net.bioclip​se.scripting/src/net/bioclipse/script​ing/business/JSJobCreatorAdvice.java: Fixed the advice creating jobs from JavaScript methods
09:22 shk3 joined #bioclipse
09:42 edrin masak: see this: http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=244
09:42 zarah edrin's link is also http://tinyurl.com/axjm5g
09:53 edrin olass: when your meeting is over can you test the code i put in svn and tell me if i works for you as it is? if it is not then i must find the bug, and this wont be easy
09:55 CIA-28 bioclipse: shk3 * r8296 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (3 files in 2 dirs): activated the help->welcome menu item
09:56 jonalv joined #bioclipse
09:57 edrin jonalv:  http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=244
09:57 zarah edrin's link is also http://tinyurl.com/axjm5g
09:59 jonalv edrin: okey, I think we should concentrate on the new js-console instead actually
10:00 jonalv oh this was the new js-console
10:00 edrin jonalv: yes, the version in trunk
10:01 edrin it is exactly the same problem i have myself i guess
10:01 jonalv edrin: yea I think masak is gonna merge today or tomorrow. I wonder if there are similar problems in the branch
10:01 masak I haven't fixed anything of that sort in the branch.
10:01 masak but thing should work, both in trunk and in the branch.
10:02 jonalv edrin: as for the fact that you don't get the managers I don't know why that is but it's probably not related to the consoles
10:02 edrin masak: i think this is not the problem of the console, it is the platform
10:02 edrin yes
10:02 masak edrin: logging configuration problems are usually a sign that you missed a step in the setting up of bc2
10:03 edrin masak: logging problems?
10:03 edrin why logging problems?
10:03 masak edrin: it sayd log4j in your stacktrace in the bug ticket you indicated.
10:03 masak that's logging.
10:04 edrin the logging problems from yesterday magically disappeared today :/ ... btw.
10:04 masak edrin: that's what I'm saying. logging sucks, in a very unpredictable way.
10:04 masak we don't like it, but apparently we need the logging.
10:04 jonalv things magicliy disaapering is not something that makes me feel good...
10:04 edrin masak: http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=244 <- where is there a logging problem?
10:04 zarah edrin's link is also http://tinyurl.com/axjm5g
10:05 masak edrin: just below the big words "ERROR LOG:"
10:05 edrin these i wrote
10:05 masak uh, maybe I'm wrong.
10:06 masak seems that the error is not in log4j.
10:06 edrin log4j.configuration = file:/C:/Dokumente und Einstellungen/edrin/eclipse-workspace/​net.bioclipse.logger/log4j.properties
10:06 edrin bioclipse.defaultLogDir = C:\Dokumente und Einstellungen\edrin
10:06 edrin this just means logging is ok and strated
10:06 masak aye, I see that now.
10:06 masak was confused by the words "ERROR LOG:" which I took to mean that log4j was part of the error.
10:06 edrin net.bioclipse.scripting.ui.business.Js​ConsoleManagerFactory.setInitializatio​nData(JsConsoleManagerFactory.java:35)
10:06 edrin this is the prob
10:06 masak and it still is?
10:07 edrin exactly same prob for my own plugin
10:07 edrin yes
10:07 masak same line and everything?
10:07 masak I'll go check what it is.
10:07 edrin no, it looks different just because i catched exceptions
10:07 masak installJsTools does the manager binding magic.
10:07 olass this could be missing plugins from what I think
10:07 edrin not the same line
10:07 masak edrin: which line?
10:08 edrin .setInitializationData always this command
10:08 edrin all lines
10:08 olass I have experienced this too
10:08 edrin .setInitializationData on *all* manager faisl
10:08 olass when I have a faulty setup
10:08 edrin olass: is the project hivpred in svn working for you
10:09 masak yes, I think a faulty setup is behind edrin's problems.
10:09 edrin olass: yes, maybe it is a faulty setup...
10:09 olass not cchecked today
10:09 olass edrin: I am sure it is
10:09 olass it has every sign of it at least
10:09 egonw joined #bioclipse
10:09 edrin olass: can you try it? i uploaded to to svn xws/
10:09 olass will do today
10:09 edrin hivpred it is
10:09 olass yes
10:10 edrin just checkout and run... it is ready to use...
10:10 olass but I think you sort of threw away the point of my plugin when you replaced with a new binding
10:10 edrin just enter valide testaccount
10:10 olass my plugin uses EMF
10:10 olass but could be useful to find teh problem maybe
10:10 olass will try it
10:10 edrin olass: yes, but i think this is not the problem... i just fear there is a threading problem in xws
10:10 olass hmm, ok...
10:11 olass yes, my EMF based USED to work..
10:11 olass and still works when run in Bioclipse
10:11 olass did you fix anything in xws?
10:11 edrin no
10:11 olass so, what do you want me to do?
10:11 olass run the new?
10:11 olass and then?
10:12 olass report what?
10:12 olass traces/stanzas?
10:12 edrin yes, checout the thing: xws4j-hivpred-client/
10:12 olass ok
10:12 * olass is doing this now
10:12 edrin change the settings in your .java file in it and insert valid test@ws1.bmc.uu.se password again
10:13 edrin and then run it
10:13 edrin and tell me if it works
10:16 olass yes, runs
10:16 olass edrin: it runs fine
10:16 edrin very strange then
10:17 olass what do you mean?
10:17 edrin olass: can you also replace the xws4j.jar in the server with the one in this project at some occasion ?
10:17 olass what did this prove?
10:17 olass ok
10:17 edrin i was wondering... there is basically no difference between the code you are running now and the code you were runnning ysersterday
10:18 edrin olass: btw. it seems the xml schemata of hivpred are now working withou the output object validation, too
10:18 olass running works with old jar as well
10:18 masak edrin: a minor thing described in your bug is about the character `. I've seen it used in other contexts to surround commands, and that's why I used it to surround `help <manager>`. but if it bothers you, I can change it to ordinary single quotes.
10:18 olass 01.12 instead of 14
10:18 edrin olass: ok?
10:18 olass I donät mind
10:19 olass do as you like
10:19 edrin olass: strange?
10:19 * masak thinks of donuts
10:19 edrin masak: up to you :)
10:19 olass edrin: well, you do something completely different than I
10:19 edrin olass: do i ?
10:19 olass you create a dinding
10:19 olass binding
10:19 olass using iofactory
10:19 olass I don't
10:19 olass I use my lib
10:19 edrin yes
10:20 olass my EMMF binding lib
10:20 olass could you run my code yesterday?
10:20 edrin the problem is, it looked like the thread in xws4j responsible for processing the incoming stanzas was halted...i did not get how this can be...
10:21 olass I looked in that
10:21 masak edrin: if it's up to me, then I still think my reason for putting that kind of quotes there holds. but I don't want to use something that looks directly wrong to a large group of people.
10:21 olass it never reachd onResult() or onError() etc
10:21 edrin olass: can you pastbin the output of the working example you were just running?
10:21 CIA-28 bioclipse: jonalv * r8297 /bioclipse2/trunk/plugins/net.​bioclipse.biojava/src/README: added empty src folder to biojava, Eclipse needs a src folder and git doesn't seem to support empty folders. (git--)
10:21 olass sure
10:21 edrin olass: and then compare with this: http://paste2.org/p/129752
10:21 edrin (yours from yesterday
10:21 edrin )
10:21 masak jonalv: that's right, git doesn't support empty folders.
10:21 olass http://paste2.org/p/130265
10:22 masak jonalv: http://kerneltrap.org/maila​rchive/git/2007/7/17/251902
10:22 zarah masak's link is also http://tinyurl.com/65ss2l
10:22 edrin olass: you see: XWS4J: xmpp: CommandProcessor.processAdHocCommand()
10:22 edrin this one did never appear in the thing you run yesterday
10:22 olass never reached in my client
10:23 edrin meanding the processing thread was halted
10:23 olass how come?
10:23 edrin or pasued
10:23 edrin paused
10:23 edrin no clue
10:23 olass did the same thing happen to you running it?
10:23 edrin i really dont know
10:23 edrin no, never
10:23 olass so my client worked with you?
10:23 olass or did you not test my client?
10:24 edrin i could not test your client because i did not have the remaining files
10:24 olass ?
10:24 edrin just the java
10:24 olass they are in svn, right?
10:24 edrin are they?
10:24 edrin oh
10:24 edrin hm
10:24 edrin wasnt aware
10:24 olass I think I had only deps to things in svn
10:24 olass at least 98% sure
10:24 edrin was quit tired yesterday, too
10:25 edrin so maybe i missed it :/
10:25 olass only needed 3 plugins
10:25 edrin anyway... how can this be? how could this freeze the
10:25 olass se.uu....hivpred.model and net.bc.xws4j from svn
10:25 edrin how could your code have influence on the processing thread of xws?
10:25 olass and org.apache.log4j from eclipse WS
10:26 olass edrin: please run my code
10:26 olass and debug it
10:26 edrin tonight maybe
10:26 olass it's too hard for me to debug xws4j
10:26 olass you wrote it
10:26 olass and I don't really know how it works
10:26 edrin can you write me in an email what files to checkout to run your code?
10:26 edrin olass: i know
10:26 olass did I not write that?
10:26 olass mom
10:26 zarah my son!
10:27 olass ;-)
10:27 edrin olass: ah, you mean the bc plugin?
10:27 edrin could not run it because i cant use any managers in bioclipse :)
10:27 olass I wrote: You need to add the projects net.bioclipse.xws4j AND se.uu.farmbio.hivpred.model to the classpath.
10:27 edrin ok
10:28 olass edrin: we need you to get the managers up and running
10:28 edrin i will trey tonight
10:28 olass can you please do a new workspace checkout following the wiki?
10:28 edrin how to setup bc correctly, to date i always just click set target platform...
10:28 edrin ok
10:29 olass http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
10:29 zarah olass's link is also http://tinyurl.com/58kmzp
10:29 olass just to be sure this is not the problem...
10:31 edrin ok
10:31 olass edrin: do you not think at all that this can be because my Schema is incorrect?
10:31 edrin olass: no
10:31 olass and that this is causing the problem?
10:32 olass ok
10:32 olass (besides, it works when run inside Bioclipse)
10:32 edrin olass: so far i mainly fear that there is a platform issue with xws4j on mac... multithreading is done differently on windows and unix
10:33 edrin olass: oh... it always works from within bc!?
10:33 olass when run from console in bc2 via the manager, yes
10:33 edrin can you run it differently in bc2, too?
10:34 edrin and it does not run when you run it from where?
10:34 olass my PluginJunitTests testing the HivpredManager (that uses the XWSManager) used to work but now fails with an EMF exception
10:34 olass edrin: it works from BC old console here
10:34 olass it does not work when run from my client (that I sent you)
10:34 olass neither does it work from a JUnit test
10:35 edrin the client you run from where?
10:35 edrin from whose main() =
10:35 edrin ?
10:35 olass client is just java
10:35 olass with a main
10:35 olass that I sent you
10:36 edrin TestPredictionServiceWS1.java does not contain a main()
10:36 egonw edrin: what replaces XMLConverter.w3cElementToString()
10:36 egonw in the latest XWS4J?
10:36 edrin egonw: i moved this file to
10:36 jonalv egonw: Can I test run net.bioclipse.rdf, or perhaps just get it to compile as first step... :)
10:36 olass well it is a JUnit test
10:36 olass same same
10:37 olass but different
10:37 egonw jonalv: it doesn't compile?
10:37 jonalv egonw: nope
10:37 edrin egonw: i mean, i moved this function to net/bioclipse/xws/JavaDOMTools.jav
10:38 jonalv egonw: I don't have org.eclipse.zest.core, org.eclipse.zest.layouts
10:38 edrin olass: does JUnit have issues with multithread applications?
10:38 edrin olass: can you try one thing and run your client with a main and not from JUnit ?
10:39 olass did that before
10:39 olass but ok
10:41 edrin olass: http://today.java.net/pub/a/today/​2003/08/06/multithreadedTests.html section Problems with JUnit and Multithreaded Tests... could this be the problem?
10:41 zarah edrin's link is also http://tinyurl.com/yfgss8
10:41 edrin although invokeSync() should block for the thing to finish?
10:43 olass mom
10:43 zarah mom, I'm home!
10:44 egonw edrin: what replaces XMLConverter.w3cElementToString()
10:46 olass edrin: blocks in the same position
10:47 olass I will send you this file as well
10:47 olass now with a main
10:47 olass if you like
10:49 olass edrin: still this: http://paste2.org/p/130281
10:51 edrin egonw: : sorry: here net/bioclipse/xws/JavaDOMTools.java
10:51 egonw edrin: tack!
10:51 edrin egonw: i moved the function to this file
10:51 olass edrin: IT WORKED NOW
10:51 edrin olass: huh?
10:51 olass what is going on here....
10:51 olass mom
10:51 zarah dad!
10:52 egonw zarah--
10:52 edrin olass: what timeout did you set?
10:52 egonw (for being not being funny, and obstructing common IRC practices)
10:52 olass 40000
10:53 olass masak: I must agree with rgonw on that :-)
10:53 edrin olass: ok, sometimes it works, sometimes not?
10:53 olass no
10:53 olass this is different
10:53 olass I copied to another eclipse project
10:53 masak olass: I know. I'll remove the feature. :)
10:53 edrin hm...
10:53 olass hmmm
10:53 olass testing old again
10:54 masak olass: but it _is_ very funny. zarah is just expressing what I think every time I see 'mom' on the channel.
10:54 edrin masak: please can you also remove the "hi" when saying hi the first time in the channel
10:54 masak edrin: no, that's a feature.
10:54 edrin hm ok
10:54 masak edrin: if you don't want a reply, say "greetings" or something else.
10:55 jonalv I want zarah to say hi. it confirms that everything is working
10:55 masak exactly.
10:55 masak hi
10:55 zarah saluton masak
10:55 masak :)
10:55 jonalv I also sometimes use:
10:55 jonalv zarah: ping
10:55 zarah jonalv: pong
10:55 masak zarah: you're a smart girl.
10:55 zarah masak: If I'm smart, why wasn't _I_ invited, too? Am I a second-class citizen? Over.
10:55 jonalv just to see that I am online and evryhting is up and running
10:55 masak zarah: because you don't eat lunch.
10:55 zarah masak: please rephrase or stop trying to be witty :)
10:56 masak zarah: :)
10:56 zarah masak: please rephrase or stop trying to be witty :)
10:56 masak :/
10:56 edrin how do i spell the .se "hey" ?
10:56 edrin hey
10:56 masak edrin: 'hej'.
10:56 edrin hei?
10:56 edrin hej
10:56 edrin ok
10:56 masak edrin: no, 'hei' is norweigan
10:56 masak s/ig/gi/
10:56 olass ok edrin: I have a observation
10:56 olass you will not like this
10:56 edrin isn't norweigan and .se almost the same country ?
10:57 edrin ;)
10:57 olass I will write and pastebin the text
10:57 edrin olass:  ok
10:57 olass wait 2 mins
10:57 masak edrin: not since 1905.
10:57 edrin ok
10:57 egonw what ahppened then?
10:57 masak edrin: it was their choice to leave us. and they celebrate it every anniversary with a big national holiday.
10:58 masak they are so happy!
10:58 edrin k
10:58 masak waving flags and blowing trumpets...
10:58 masak real national spirit there, just from not being Swedish anymore.
10:58 masak lunch &
10:59 olass 1) Run from a JUNIT test, fails.
10:59 olass 2) run from main in same project as junit test: fails
10:59 olass 3) Run from main in another project: works
10:59 olass 4) run step 2 again (main from junit test project) works
10:59 olass 5) Run from a JUNIT test, fails.
10:59 olass 6) run step 2 again (main from junit test project): fails
10:59 olass must go for lunch now
10:59 olass be back later
10:59 jonalv what features will be in Bioclipse 2/beta?
11:00 jonalv lunch it is then!
11:00 edrin olass: so sometimes it works, sometimes not?
11:18 CIA-28 bioclipse: egonw * r8298 /bioclipse2/trunk/features/ (5 files in 2 dirs): Factored out a XML feature: people can now also richly edit PubChem XML documents, without pulling in all sorts of CML and CDK deps
11:24 gilleain joined #bioclipse
11:54 CIA-28 bioclipse: shk3 * r8299 /bioclipse2/trunk/plugins/net.bio​clipse.spectrum.test/.classpath: bug #178
11:55 zarah bug #178 | http://tinyurl.com/7r28q2
12:01 gilleain Is there really a computer in uppmax (uppsala?) called 'Isis' with 800 cores?
12:06 egonw well, not for bioclipse development, at least
12:08 CIA-28 bioclipse: shk3 * r8300 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): bug #195
12:08 zarah bug #195 | http://tinyurl.com/9qde73
12:22 CIA-28 bioclipse: egonw * r8301 /bioclipse2/trunk/plugins/net.bi​oclipse.cml/schema24/schema.xsd: Updated to most recent CML Schema, to match the current CMLXOM library
12:23 CIA-28 bioclipse: egonw * r8302 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Renamed plugin to use convention: x.y.test tests x.y
12:27 CIA-28 bioclipse: egonw * r8303 /bioclipse2/trunk/plugins/ (23 files in 12 dirs): Renamed folder to match plugin name change
12:30 olass edrin: around?
12:44 edrin olass: yes
12:44 olass your comments on my 1) to 6)?
12:44 olass a junit problem?
12:45 edrin really strange
12:46 edrin i dont know what to conclude here
12:46 egonw ummm.... my JCP editor seems broken
12:47 edrin olass: running junit from another project?
12:47 edrin is it really junit?
12:47 edrin the problem?
12:47 olass < olass> 1) Run from a JUNIT test, fails.
12:47 olass [12:04] < olass> 2) run from main in same project as junit test: fails
12:47 olass [12:04] < olass> 3) Run from main in another project: works
12:47 olass [12:04] < olass> 4) run step 2 again (main from junit test project) works
12:47 olass [12:04] < olass> 5) Run from a JUNIT test, fails.
12:48 olass [12:04] < olass> 6) run step 2 again (main from junit test project): fails
12:48 olass [12:04] < olass> must go for lunch now
12:48 olass you see?
12:48 edrin if you run main from the other project (like in step 3) several times, does it sometimes fail?
12:48 olass no
12:48 edrin currently it seems to fail sometimes, and sometimes it works?
12:48 olass strictly depending on what you ran before
12:48 olass edrin: no
12:48 edrin very strange
12:48 olass it is reproducible
12:48 olass 1-6 above
12:49 olass hmm
12:49 edrin but in the meantime the instance of xws4j client (and xws4j .jar itself) should be gone, right?
12:49 olass could it be a listener problem? Like some listeners are not disposed etc?
12:49 olass gone?
12:49 edrin disposed...
12:50 edrin i thought if you run a main, a complete new instance of everything should be spawned...
12:51 olass so is a junit test AFAIK
12:51 edrin thus, how can a junit call before influence a completely new run afterfwards
12:51 olass is in same project, it does affect it
12:51 olass in anotehr project, it doesn't
12:51 olass can this be an eclipse thing?
12:51 edrin maybe i dont know
12:51 edrin egonw: do you have an idea?
12:53 olass hmm
12:53 edrin http://www.junit.org/node/54
12:53 olass I have another thing
12:53 olass how come it works from Bioclipse but not from a JUnit plugin test?
12:53 olass I get an NPE when serializing
12:54 olass service works fine there
12:54 olass but not the conversion back from DOM to EMF
12:54 olass the same thing works from Bioclipse
12:54 edrin and what produces the NPE?
12:54 olass hmm
12:54 edrin oh, so xws4j is not the only thing causing trouble in the project?
12:55 edrin the problem with NPE is independent from xws?
12:56 olass edrin: I think so
12:56 olass will try your JavaDOMtools now
12:56 olass but still
12:57 edrin ok
12:57 olass it DOES work in Bioclipse
12:57 olass but not in a JuniPluginTest
12:57 olass and I use your Element from the service
12:57 edrin maybe the plugin is broken?
12:57 olass so....
12:58 edrin olass: btw. the Element from the service: w3c dom Element's toString() does not work, it will not return a string representation of the element but always nothing
12:58 egonw ha, my bug list is back in order...
12:58 egonw nothing to do...
12:58 olass egonw: sure :-)
12:58 edrin egonw: ola has a bug problem
12:58 egonw hehehehe
12:58 olass CDKManager?
12:58 olass (just a hint)
12:58 edrin back in 5 min
12:58 olass k
12:59 egonw CDKManager is currently borken, pending a fix by jonathan
12:59 egonw olass: can we talk XWS?
12:59 olass want to test this first
12:59 olass 30 mins
12:59 * egonw thinks olass' problems have to do with XML Schema stuff...
12:59 olass not this
12:59 olass that is another thing...
12:59 egonw ack
12:59 olass need to resolve that too
13:00 olass 29 mins ok?
13:00 egonw yes
13:01 olass in xml, does it matter if I use ' or " ?
13:02 olass egonw?
13:02 olass masak?
13:02 olass is ther ea difference?
13:02 masak olass: no difference.
13:02 olass thx
13:02 masak olass: you use either one based on convenience.
13:03 masak (say, if you need single quotes inside the string value, you surround it with double quotes, and vice versa)
13:03 edrin regarding the xws problem, my main fear is that there is a bug in the multithreading of xws4j. there are various (2 min.) threads, one for processing incoming stanzas (incoming socket) and one for sending stuff out.
13:04 masak (ah -- 'min.' is an abbrev for 'at least', not for 'minutes')
13:04 edrin olass: in yuor examples it seems that the thread responsible for processing incoming stuff seems to freeze because the response of the service is not processed in your test case...
13:05 edrin olass: one question: if you set a timeout of 40 seconds, does it really sleep these 40 seconds and then reports timeout or does it say timeout immediately after stratr?
13:06 CIA-28 bioclipse: carl_masak * r8304 /bot/trunk/zarah.pl: [zarah] no longer says anything on "mom" lines
13:06 masak it was fun while it lasted. :)
13:06 egonw mom
13:06 zarah grandpa!
13:06 masak zarah: reboot, dear
13:06 masak egonw: congrats, you got the last one.
13:06 egonw yeah :)
13:06 zarah joined #bioclipse
13:11 CIA-28 bioclipse: jonalv * r8305 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Reintroduced stuff neeeded for recording to the cdk manager. I turned on recording for the cdk manager in my job branch... fixes bug #248
13:11 zarah bug #248 | http://tinyurl.com/9oph4p
13:18 maclean joined #bioclipse
13:18 egonw edrin: ping
13:25 olass joined #bioclipse
13:25 olass hi
13:25 zarah hello olass, you fantastic person you
13:26 olass zarah: ?
13:26 zarah olass: yes?
13:26 olass zarah: are you trying to impress me?
13:26 zarah olass: are you making fun of me?
13:26 olass lol
13:26 masak *lol*
13:27 olass edrin: I managed to convert my unit testing plugins now
13:27 olass *PHEW*
13:28 CIA-28 bioclipse: ospjuth * r8306 /bioclipse2/trunk/plugins/s​e.uu.farmbio.hivpred.model/ (2 files in 2 dirs): Use JavaDOMtools for XML conversion. Requires dep to xws4j.
13:29 CIA-28 bioclipse: ospjuth * r8307 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Use new XML conversion DOM to EMF. Now also works in JUnit plugin tests.
13:30 CIA-28 bioclipse: ospjuth * r8308 /bioclipse2/trunk/plugins/se.uu.farmb​io.hivpred.model/src/org/hivdrc/hivpr​ed/conversion/EMFDOMConversion.java: Express API without EMF EObject.
13:32 masak @start egonw-..
13:32 zarah masak: There is no task planned by the name 'egonw-..'.
13:32 masak @plan old bc2
13:32 zarah masak: bc2/console-egonw-single-line-refactor: 2 h planned, 4 h 2 m elapsed
13:32 zarah masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 37 m elapsed
13:32 zarah masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 10 m elapsed
13:32 zarah masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed
13:32 zarah masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed
13:32 masak @start console-egonw..
13:32 zarah masak: Starting task 'bc2/console-egonw-single-line-refactor'.
13:34 edrin egonw: yes?
13:35 edrin olass: what means "convert"? you mean it works now?
13:35 edrin test
13:35 olass edrin: I think my classpath must have been broken
13:35 olass I cleaned, updated classpathy, restarted eclipse etc
13:35 olass and now It actually works
13:35 olass I also fixed my EMF conversions
13:35 olass so getting there!
13:35 edrin !
13:35 edrin good
13:36 olass really a Classpath/eclipse flinge
13:36 olass will talk to egonw now about the schema difference and how to resolve
13:36 edrin i hope that xws client will now work without problems
13:36 edrin ok
13:36 olass probably I can just rewrite my schema in some clever way
13:36 edrin olass:
13:36 olass egonw: ping
13:36 edrin yesterday i tried the autogenerated
13:36 edrin binding
13:36 olass yes?
13:37 edrin and it seemed to do the parsing correct now
13:37 edrin see the client project for hivpred
13:38 olass hmm
13:38 olass you mean schema parsing into binding?
13:38 edrin 104 try {
13:38 edrin 105 HIVPredOutputDocument  output_doc = ioFactory.getHIVPredOutputDocument(result);
13:38 edrin 106 //XmlObject output_doc = ioFactory.getOutputObject(result);
13:38 edrin 107 System.out.println("Result from prediction: " + output_doc);
13:38 edrin 108 } catch (Exception e) {
13:38 edrin 109 System.out.println(e.getMessage());
13:38 edrin 110 }
13:38 edrin yes
13:38 olass oh
13:38 olass will try from console now
13:38 olass to generate binding
13:38 olass and use it
13:38 edrin ok
13:40 edrin olass: if everything is working for you now, could you maybe also try to set the FunctionInformation to true to make it an async service function again and test with it?
13:40 olass sure
13:40 olass hmm
13:40 olass my script does not run...
13:41 edrin why not?
13:41 edrin the xws failed again?
13:41 egonw edrin: ping
13:41 edrin egonw: yes?
13:41 egonw edrin: did something change in XWS how functions are defined?
13:41 egonw it no longer sees my functions, while the component shows up
13:41 egonw but don't see any error in the component log either...
13:42 olass edrin: an API suggestion
13:42 olass var iof=xmpp.getIoFactory(func);//Try to load generated binding
13:42 edrin egonw: the component log should print the functions it loads now to the log
13:42 olass should return null if not found, not throw exception
13:42 olass IMO
13:42 edrin var iof=xmpp.getIoFactory(func); // throws an exception if not there
13:42 olass what do you think?
13:43 olass I hate try/catch in small scripts
13:43 edrin true
13:43 edrin can do this, write me an email :)
13:43 olass currently, JSconsole dies if exception is thrown and halts execution
13:43 olass is that as it should be?
13:43 olass masak?
13:43 masak oh hai
13:43 zarah oh hai masak
13:44 olass masak: should an exception halt script execution?
13:44 masak olass: ideally, JsConsoleView should never die, no.
13:44 olass not die
13:44 olass just halt execution of current script
13:44 egonw edrin: ah, ok... spotted: XWS4J: Error, cloud not load
13:44 egonw ...
13:44 edrin egonw: are you using current xws4j.jar ? the current version should print what jar it loads and wha functions are in it... ola requested this. if you do not see the name of
13:44 edrin ah
13:44 edrin ok
13:44 edrin was a good idea, i think it helps alot
13:44 olass egonw: get the latest xws4j jar in the net.sf.xws4j/jar folder
13:45 edrin olass: had a similar error
13:45 egonw olass: I got the last...
13:45 olass ok
13:45 egonw that's why it is not working now :)
13:45 olass I got things working now
13:45 olass (after MUCH MUCH problems)
13:46 * olass will now go over to masak IRL
13:48 egonw edrin: has the bla.cfg format changed?
13:49 egonw ok, progress
13:49 olass edrin: we agreed on the following:
13:50 olass it is OK if you throw an exception in your getIoFactory(func) if there is a way to check that it exists first
13:50 olass so an xmpp.existsIoFactory(func)
13:50 olass you should NOT be required to try catch, there should be a way around it
13:50 olass will file you a bug for this
13:51 olass (or even write it myself)
13:56 olass done
14:00 CIA-28 bioclipse: ospjuth * r8309 /bioclipse2/trunk/plugins/net.bioclipse.​xws4j/src/net/bioclipse/xws4j/business/ (IXwsManager.java XwsManager.java): Added function boolean existsIoFactory().
14:11 CIA-28 bioclipse: carl_masak * r8310 /bioclipse2/branches/masak-new-console/plugins/​net.bioclipse.scripting.ui/src/net/bioclipse/sc​ripting/ui/views/NewScriptingConsoleView.java:
14:11 CIA-28 bioclipse: [NewScriptingConsoleView] added dnd support
14:11 CIA-28 bioclipse: Copied the drag'n'drop from the old scripting console.
14:12 olass edrin: around?
14:12 edrin yes
14:13 olass binding fails for me from console
14:13 edrin what does it say?
14:13 olass mom
14:13 olass zarah++
14:13 masak dad!
14:13 olass java.lang.NoSuchMethodException: org.hivdrc.hivpred.impl.HIVPredInputTypeIm​pl.<init>(org.apache.xmlbeans.SchemaType)
14:14 edrin strange
14:14 olass yes
14:14 edrin but the project i did was working for you, too?
14:14 olass how can I tell if my service output validates?
14:15 olass edrin: I think so, yes
14:15 olass yes it did
14:15 olass (tested again)
14:17 edrin olass: HIVPredOutputDocument  output_doc = ioFactory.getHIVPredOutputDocument(result); this seemed to work in the client
14:18 edrin but the exactly same thing does not in console?
14:18 edrin hm...
14:18 olass hmm
14:18 olass getting errors preparing the input now
14:18 olass testing what it REALLY is that fails...
14:19 jonalv building Bioclipse in Windows on parallells is so sloooooooow. :(
14:19 olass i.addNewHIVPredInput()
14:19 olass fails
14:19 olass coffee now
14:19 olass brb
14:19 edrin olass: it 'could' be that you need a bioclipse restart if you generated a binding. i am not 100% sure here but in fact it loads the new binding to the classpath. dunno what happens if there was already an old one in the classpath
14:21 egonw js> service.discoverSync()
14:21 egonw Can't find method net.bioclipse.xws.client.ad​hoc.Service.discoverSync().
14:22 egonw edrin: what's that about?
14:22 egonw http://gist.github.com/22185
14:23 edrin egonw: does it fail in net.bioclipse.rhino, too?
14:24 egonw mom, will test
14:24 edrin and please do service = service.discoverSync();
14:24 edrin :)
14:24 edrin or not
14:24 edrin it's not a must
14:24 edrin not sure though
14:25 egonw where is .rhino?
14:25 edrin egonw: in xws/trunk right now
14:25 edrin egonw: ah!
14:26 edrin service.discoverSync(); -> you forgot the timeout ;)
14:26 egonw ok, mom
14:26 edrin service.discoverSync(20000);
14:26 CIA-28 bioclipse: carl_masak * r8311 /bioclipse2/branches/masak-new-console/plugins/​net.bioclipse.scripting.ui/src/net/bioclipse/sc​ripting/ui/views/NewScriptingConsoleView.java:
14:26 CIA-28 bioclipse: [NewScriptingConsoleView] added context menus
14:26 CIA-28 bioclipse: added one context menu for the input field, and one for the output text
14:26 CIA-28 bioclipse: widget.
14:28 olass edrin: will restart BC and test again
14:29 edrin ok
14:31 * jonalv can report that the new javascript console works fine in Windows XP
14:31 edrin good to hear :)
14:32 egonw ok, the CDK service works fine with the new XWS too
14:32 egonw at least the calculateMass
14:32 egonw I have updated the Gist: http://gist.github.com/22185
14:33 edrin cool :)
14:33 edrin "cdk.xxx.xxx.uu.se" ?
14:33 maclean hmmm. it seeeems. to work. I suspect witchcraft.
14:34 olass edrin: it is the inputDoc.addNewHIVPredInput() that throws exception
14:34 olass org.mozilla.javascript.WrappedException: Wrapped java.lang.ClassCastException: org.apache.xmlbeans.impl.va​lues.XmlComplexContentImpl
14:35 egonw olass: can I change that value to the real location?
14:35 olass which in the sorce (generated binding) us:
14:35 olass target = (org.hivdrc.hivpred.HIVPredInputType)get_​store().add_element_user(HIVPREDINPUT$0);
14:35 edrin does it? but it worked in the hivpred client in xws/
14:36 olass egonw: yes, cdk.ws1.bmc.uu.se
14:36 olass it is an official address now
14:36 olass (if that was your question)
14:37 egonw changed
14:38 olass egonw: can I create gists?
14:38 olass and how in that case?
14:39 olass egonw: I'd like us to have a schema so that we easily can send IBioObjects (like IMolecule and ISequence) to an XMPP service
14:39 shk3 egonw?
14:39 olass egonw?
14:40 shk3 hi olass
14:40 shk3 perhaps you can answer my question as well
14:41 shk3 I updated bioclipse
14:41 shk3 and get an error in plugin.xml of net.bc.cml
14:41 shk3 <extension
14:41 shk3 point="org.eclipse.wst.xml.​core.catalogContributions">
14:41 shk3 <catalogContribution>
14:41 shk3 <uri name="http://www.xml-cml.org/schema" uri="schema24/schema.xsd"/>
14:41 shk3 </catalogContribution>
14:41 shk3 </extension>
14:41 shk3 was added by egonw
14:41 shk3 my eclipse says unknown extension point
14:41 olass no, I'll let egonw answer that
14:42 olass but my guess is that you have not updated your Eclipse with WST packages
14:42 olass using online update
14:42 olass my proposal (in the long run) is to add these to the target platform
14:42 olass egonw: correct me if I'm wrong
14:44 olass egonw: also check http://gist.github.com/47421
14:46 shk3 is wst the same as web tools platform?
14:46 olass yes
14:46 olass wst is part of that I think
14:47 egonw yes, missing plugin
14:48 egonw shk3: please check the plugins deps, and indeed install WTP
14:48 egonw shk3: but I see the problem...
14:48 egonw shk3: is nb.cml doing anything for speclipse?
14:49 egonw that is... does speclipse depend on nb.cml?
14:50 egonw bug noted...
14:50 egonw me will introduce net.bioclipse.xml
14:50 egonw to solve the dep...
14:51 shk3 don't think speclipse uses xml
14:51 shk3 xml=cml
14:51 egonw oh, OK...
14:51 shk3 it uses cml-xom
14:52 shk3 but that's another plugin, right?
14:52 egonw right
14:52 egonw the org.cml-xml.xom plugin has the library
14:54 CIA-28 bioclipse: carl_masak * r8312 /bioclipse2/trunk/plugins/net.bioclipse.sc​ripting.ui/src/net/bioclipse/scripting/ui/ (2 files in 2 dirs): [net.bioclipse.scripting.ui] made the JsConsoleManager print its output to the NewScriptingConsoleView
14:55 CIA-28 bioclipse: carl_masak * r8313 /bioclipse2/trunk/ (4 files in 3 dirs):
14:55 CIA-28 bioclipse: removed all traces of ConsoleEchoer
14:55 CIA-28 bioclipse: this is one more step towards making the R mode unusable. will fix when the
14:55 CIA-28 bioclipse: need arises -- the plan is to have a dedicated scripting console for R
14:56 CIA-28 bioclipse: carl_masak * r8314 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java: [net.bioclipse.scripting.ui] set the background color of the output field to white
14:56 CIA-28 bioclipse: carl_masak * r8315 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java: [NewScriptingConsoleView] copied history from old console
14:56 CIA-28 bioclipse: carl_masak * r8316 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java: [NewScriptingConsoleView] added class JavaDoc
14:57 CIA-28 bioclipse: carl_masak * r8317 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java:
14:57 CIA-28 bioclipse: [NewScriptingConsoleView] implemented general tab completion
14:57 CIA-28 bioclipse: still needs to be hooked up in NewJsConsoleView to work for js
14:57 CIA-28 bioclipse: carl_masak * r8318 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (NewJsConsoleView.java NewScriptingConsoleView.java):
14:57 CIA-28 bioclipse: [NewJsConsoleView] implemented js-style tab completion
14:57 CIA-28 bioclipse: this also required an extra method currentCommand() in NewScriptingConsoleView
14:58 CIA-28 bioclipse: carl_masak * r8319 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java:
14:58 CIA-28 bioclipse: [NewScriptingConsoleView] added dnd support
14:58 CIA-28 bioclipse: Copied the drag'n'drop from the old scripting console.
14:58 CIA-28 bioclipse: carl_masak * r8320 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java:
14:58 CIA-28 bioclipse: [NewScriptingConsoleView] added context menus
14:58 CIA-28 bioclipse: added one context menu for the input field, and one for the output text
14:58 CIA-28 bioclipse: widget.
14:58 egonw he, no source info on the original commit??
15:00 edrin egonw: just a question, do the js command to invoke your service work from the editor of net.bioclipse.rhino ?
15:01 egonw have not tried that yet
15:01 edrin ok
15:01 maclean masak : d'n'd paths are wrong way round on windows...
15:01 masak maclean: oki. please file a bug ticket. I'm in the middle of something.
15:01 shk3 where can I get this fucking wspbla from?
15:02 maclean masak : oki-doki.
15:02 shk3 web tools (WTP) update site doesn't seem to contain it
15:02 egonw isn't it part of the Ganymedes update site?
15:03 shk3 where exactly?
15:03 egonw Help -> Available bla...
15:04 shk3 aha, looks like it's in uncategorized
15:04 shk3 I meant "where on the update site"
15:06 egonw shk3: that edit field up in the Avail tab is actually a filter...
15:06 shk3 says it's already there
15:06 egonw I think, search for WST XML Core
15:10 olass @tell edrin: Please test my script(http://gist.github.com/47421) on masak++ new console and in yours
15:10 zarah Consider it noted.
15:12 shk3 for some reason it now works without any wst stuff
15:15 jonalv egonw: ping
15:15 egonw pong
15:15 jonalv masaks last commit removed the echo functionality on the console
15:16 jonalv cdk.debug is using that
15:16 jonalv is there some easy way to change that?
15:16 egonw edrin: ping
15:16 jonalv it seems cdk.debug is in the chemoinfoartics feature...
15:17 egonw wait for masak to add that functionality again?
15:17 egonw file a bug report against masak?
15:17 jonalv egonw: no it is gone as in it will not come back
15:17 masak egonw: that class was obsolete.
15:17 egonw ah, then file a bug against masak
15:17 masak aye.
15:18 egonw @tell masak to reply explaining how to fix the cdk.debug code...
15:18 zarah Consider it noted.
15:18 masak @clear
15:18 zarah masak: Messages cleared.
15:18 masak egonw: I'm here.
15:18 egonw edrin: ping
15:18 jonalv egonw: I wondered a little if you might have some smart idea since you wrote the manager code...
15:18 masak egonw: js.print() will work well.
15:19 masak egonw: or js.say(), depending on whether you want a final newline.
15:19 jonalv okey guys I will take it
15:19 jonalv |fix it
15:19 egonw tack
15:19 olass js.scream() ?
15:19 egonw oh, yes :)
15:19 egonw nice one...
15:19 olass with capital letters
15:19 jonalv in cdk.debuf. the other places will hve to be fixed by someone else...
15:19 jonalv they are not as importnat..
15:19 egonw hahaha :)
15:20 egonw olass: ping
15:20 olass pong
15:20 egonw olass: what does this mean to you?
15:20 olass not much
15:20 egonw XWS4J: [Stanza] received : <iq from='cdk.ws1.bmc.uu.se' id='JSO-0.12.5-6' to='egonw@ws1.bmc.uu.se/home' type='error' xml:lang='en'><error code='404' type='cancel'><item-not-found xmlns='urn:ietf:params:xml:ns:xmpp-stanzas'/><text xmlns='urn:ietf:params:xml:ns​:xmpp-stanzas'/></error></iq>
15:20 olass hmm
15:20 olass error
15:20 olass but in my experience, service might be down
15:21 olass check with PSI that it is up
15:21 olass I have complained about this to edrin, that error messages if function/service is unavailable is hard to find out
15:21 olass invalid reply
15:21 olass 404
15:22 olass jonalv: I have many red crosses now in trunk!
15:22 olass ServiceManager etc
15:22 jonalv olass: complain with masak but yea I ahve wuite a few too
15:22 olass are you wiping them out?
15:22 jonalv olass: the most important ones
15:23 egonw masak: the idea of branches is, that you get thinks working before you merge :)
15:23 jonalv aouch
15:23 masak egonw: OIC
15:23 olass :-)
15:23 masak consider yourself collateral damage to this great new merge... :)
15:23 olass yup
15:24 * egonw is still struggling to get a XMPP cloud service going that eat CML :(
15:25 olass eat==consume
15:25 maclean CML-eating clouds, eh? Sounds dangerous.
15:26 CIA-28 bioclipse: carl_masak * r8321 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java:
15:26 CIA-28 bioclipse: [NewScriptingConsoleView] made new console independent
15:26 CIA-28 bioclipse: there was a KeyAction that wasn't copied over from the old class. copied that.
15:26 masak people, I'm sorry about the red crosses. I didn't have all the plugins checked out.
15:26 CIA-28 bioclipse: carl_masak * r8322 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (JsConsoleView.java ScriptingConsoleView.java): [net.bioclipse.scripting.ui] deleted old consoles
15:27 CIA-28 bioclipse: carl_masak * r8323 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (6 files in 3 dirs): [net.bioclipse.scripting.ui] renamed the new consoles into non-new names
15:27 masak ...and we've landed.
15:27 masak let the testing commence.
15:27 egonw crash landed?
15:27 masak (and the bug reporting)
15:27 masak egonw: that remains to be seen.
15:28 egonw normally one tests an airplane before one flies it, and tries to land it again...
15:28 masak egonw: I know some things are not as good as before yet, but all of them are minor issues.
15:28 * egonw saw "the aviator" the other day
15:28 masak haven't seen that.
15:28 egonw masak: curiouos what it looks like...
15:28 CIA-28 bioclipse: ospjuth * r8324 /bioclipse2/trunk/plugins/net.bioclipse.services/ (4 files in 4 dirs): Changed console.ECHO to JSManager.print.
15:29 masak egonw: then have a look!
15:29 * egonw , meanwhile, is happy to note that his XMPP cloud functions boot when I pass it the full CML XML Schema
15:29 maclean tab-complete seems to be broke.
15:29 masak maclean: works here...
15:29 * egonw and realizes that will be some nice binding stress case :)
15:30 egonw maclean: hahaha
15:30 maclean masak : weird. works now.
15:30 egonw brokeTAB-COMPLETE ?
15:30 masak maclean: phew.
15:30 masak the tab complete got case-insensitive a few days ago, btw.
15:30 egonw ha, proof that morphogenetic fields do not go at the speed of light
15:30 maclean Suggestions : brokeN, brokeD, brokeISH.
15:31 masak b0rked
15:33 maclean I prefer brokeish. Also masak++ for all the work.
15:33 maclean Also, also. Can there be a "cdk.toSMILES" method?
15:34 egonw maclean: please file a bug report
15:34 masak maclean: the functionality is there. you can call a method on a molecule to do that.
15:35 maclean 'kay.
15:35 olass gotta catch the train now
15:35 olass see you later today
15:35 olass bye
15:36 maclean so: cdk.loadMolecule("/path/to/molecule").SMILES works.
15:37 maclean heh. cdk.numberOfEntriesInSDF is great.
15:41 masak wow, people are actually using our manager methods. cool.
15:41 maclean hooray! :
15:41 maclean m = cdk.fromSMILES("c1ccc1")
15:42 maclean mm = cdk.generate2dCoordinates(m)
15:42 maclean jcp.setModel(mm)
15:42 egonw :)
15:42 maclean => A square!
15:42 * egonw is glad to see you like the JChemPaint scripting langauge :)
15:42 maclean (an anti-aromatic square, too :)
15:43 egonw hahahaha
15:44 CIA-28 bioclipse: jonalv * r8325 /bioclipse2/trunk/plugins/net.bioclipse.cdk.debug/ (2 files in 2 dirs): s/CONSOLE.echo/JsConsoleManager().print/
15:45 CIA-28 bioclipse: jonalv * r8326 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.debug/src/net/bioclipse/cdkd​ebug/business/CDKDebugManager.java: Fixed whitespaces according to my preferences. The file had no empty rows and was strangely indented (also including tabs) Some automagic scripting attempts must have wrecked havoc at some point.
15:46 maclean jcp.setModel(cdk.generate2dCoordinates(c​dk.fromSMILES("c1ccccc1-c1ccccc1")))...
15:46 maclean is a quite easy way to get a picture of a smiles.
15:46 egonw which brings me to...
15:47 egonw can we define JS functions?
15:47 maclean aliases?
15:47 egonw function depict(smiles) {
15:47 maclean ahh.
15:47 egonw jcp.set...fromSMILES(smiles);
15:47 egonw }
15:47 egonw let's say, it's not a one liner
15:48 maclean that would be useful
15:49 jonalv @pz
15:49 zarah jonalv: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
15:49 edrin i am here now
15:49 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
15:49 egonw @pz TPSA
15:49 egonw (miltestone)
15:49 egonw @pelezilla TPSA
15:49 egonw zarah: ?
15:49 * egonw is going to catch a bus
15:49 egonw hopefully the right one
15:49 zarah [250] TPSA cloud service fails           http://tinyurl.com/96rr3x
15:49 zarah Entire list at http://tinyurl.com/84fmtq
15:49 zarah [250] TPSA cloud service fails           http://tinyurl.com/96rr3x
15:49 zarah Entire list at http://tinyurl.com/84fmtq
15:49 zarah egonw: yes?
15:50 egonw zarah: are you ill too?
15:50 edrin @msg
15:50 zarah egonw: that was not so easy for a little bot to understand
15:50 zarah edrin: 40 m 5 s ago, olass said Please test my script(http://gist.github.com/47421) on masak++ new console and in yours
15:50 egonw edrin: please test this one too:
15:50 egonw http://gist.github.com/47449
15:51 egonw that one might fail becuase the past XML has a <?xml> header?
15:51 edrin could be
15:51 edrin is lilely
15:51 edrin likly
15:51 edrin likely
15:51 egonw ok, will test tonite
15:52 egonw edrin: I have the FunctionDef() now return the full CML speca
15:52 egonw don't try IoSchemata stuff on it :)
15:52 egonw bye all!
15:52 edrin it's too big?
15:52 edrin :)
15:52 edrin ok
16:11 CIA-28 bioclipse: carl_masak * r8327 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
16:11 CIA-28 bioclipse: [JsConsoleView] added help method lister from the past
16:11 CIA-28 bioclipse: This commit got lost somewhere in the hustle and bustle of merging. Adding it
16:11 CIA-28 bioclipse: back now.
16:16 CIA-28 bioclipse: carl_masak * r8328 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
16:16 CIA-28 bioclipse: [JsConsoleView] added help method lister from the past
16:16 CIA-28 bioclipse: This commit got lost somewhere in the hustle and bustle of merging. Adding it
16:16 CIA-28 bioclipse: back now.
16:41 CIA-28 bioclipse: shk3 * r8329 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (3 files in 2 dirs): removed usage of extension point="org.eclipse.ui.popupMenus"
16:58 CIA-28 bioclipse: shk3 * r8330 /bioclipse2/trunk/plugins/net.bioclipse.bibtex/ (4 files in 4 dirs): removed usage of extension point="org.eclipse.ui.popupMenus"
17:01 CIA-28 bioclipse: egonw * r8331 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (2 files in 2 dirs): Cleaned up code: use the CMLDOM convertor directly, without the CMLWriter
17:23 CIA-28 bioclipse: shk3 * r8332 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (2 files in 2 dirs): removed usage of extension point="org.eclipse.ui.popupMenus"
17:33 CIA-28 bioclipse: shk3 * r8333 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (3 files in 2 dirs): removed usage of extension point="org.eclipse.ui.popupMenus"
17:38 gilleain joined #bioclipse
17:44 CIA-28 bioclipse: shk3 * r8334 /bioclipse2/trunk/plugins/net.​bioclipse.specmol/plugin.xml: removed usage of extension point="org.eclipse.ui.popupMenus"
18:20 egonw joined #bioclipse
18:21 egonw @tell masak why does autocomplete no longer work for all managers?
18:21 zarah Consider it noted.
18:21 egonw @tell masak can I request echoing of the command to the output windows?
18:21 zarah Consider it noted.
18:21 egonw @tell masak that the new console looks not bad at all :)
18:21 zarah Consider it noted.
18:23 edrin left #bioclipse
18:23 egonw @tell masak that Egon was stupid enough to not notice that his bioclipse.product was reset, and no longer had the XMPP manager :)
18:23 zarah Consider it noted.
18:29 shk3 joined #bioclipse
18:48 gilleain egonw : are you still having troubles with unit-tests on clone methods?
18:49 gilleain as I am finding that some cdk classes are not implementing things like clone, equals, etc properly :(
18:50 gilleain Probably hashCode is a problem somewhere, too.
18:54 gilleain I have only just learnt this week how to clone properly in java. Only took 10 years...
18:55 egonw :)
18:55 egonw yes, this is still a problem
18:55 egonw there is no defined use of equals() and hashCode()...
18:55 egonw so that would require discussion on the NL
18:56 gilleain Turns out, what I thought I knew about copy constructors is wrong.
18:56 gilleain ML?
18:56 egonw Mailing List
18:56 gilleain Well, equals and hashCode are essential for storing custom objects in Collections.
18:58 gilleain I think there could usefully be a wiki page on "How to code things properly". Chem/bioinformatics has lots of mutable hierarchies which can cause problems.
18:59 egonw yes, the services eats CML, spits CML :)
19:01 egonw defining when an IChemObject is 'equal' is they key here...
19:01 egonw not trivial...
19:01 gilleain Perhaps, but it should be possible for subclasses.
19:02 gilleain I know there are the o.o.cdk.tools.diff classes.
19:02 egonw yes, but they are different
19:02 egonw (hahaha)
19:03 gilleain hmmm.
19:03 egonw f.invokeSync(cdk.fromSMILES("CO").CML, 5000).getTextContent()
19:04 egonw 23.something
19:04 egonw yeah :)
19:12 gilleain gaaahhhhhhh. "java.lang.String.valueOf"!!!
19:15 egonw ok, enough for today
19:15 egonw for me at least
19:15 egonw will blog about the results tomorrow
19:15 gilleain okay, cool.
19:16 egonw @tell edrin that my CML services work now, and that a 500 on invalid CML is a good thing...
19:16 zarah Consider it noted.
19:16 egonw @tell olass that my services are up and running now
19:16 zarah Consider it noted.
19:16 egonw bye!
19:16 gilleain bye
21:01 edrin1 joined #bioclipse

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