Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-03

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All times shown according to UTC.

Time Nick Message
07:21 Gpox joined #bioclipse
07:42 jonalv joined #bioclipse
07:45 jonalv hi
07:45 zarah hi jonalv
08:08 olas joined #bioclipse
08:14 jonalv olas: hi
08:22 masak joined #bioclipse
08:32 egonw joined #bioclipse
08:37 thomasku joined #bioclipse
08:44 egonw_ joined #bioclipse
09:01 shk3 joined #bioclipse
09:01 egonw I hope SF works better today...
09:02 egonw shk3: going to release CDK 1.0.4
09:02 egonw right now
09:02 egonw shk3: please let me know if you have to make patches to the non-jcp related classes in the cdk1.0.x branch
09:02 egonw which would mean I'd have to make a 1.0.5 release at some point
09:03 shk3 will do so
09:09 CIA-30 bioclipse: shk3 * r7140 /bioclipse2/trunk/features/net.biocl​ipse.speclipse-feature/feature.xml: problems with dependencies solved
09:09 CIA-30 bioclipse: shk3 * r7141 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/META-INF/MANIFEST.MF: problems with dependencies solved
09:11 gilleain joined #bioclipse
09:31 CIA-30 bioclipse: carl_masak * r7142 /bot/trunk/zarah.pl: [zarah] supports stubbed planning. also rearranged a few actions in the table
09:31 zarah joined #bioclipse
09:31 gilleain stubbed planning?
09:31 olas egonw: around?
09:32 olas if I have an AC with properties set
09:32 egonw yes, for another 15 minutes
09:32 egonw at UU?
09:32 olas and then do mol=new Molecule(AC)
09:32 olas do I loose the properties of the AC then?
09:32 egonw they get lost?
09:32 egonw no idea
09:32 olas they do get lost
09:32 olas is that desired?
09:32 * olas is at home
09:33 egonw not sure if that is intended...
09:33 olas I donät see the reason for the props to be lost...
09:33 olas should I file a bug?
09:34 olas or discuss on cdk-devel?
09:34 gilleain The copy constructor in AtomContainer does not copy all the fields.
09:34 egonw make it cdk-devel
09:34 olas ok
09:35 gilleain I guess there should be a call to super?
09:37 olas mail sent
09:39 egonw olas: will go home in some 5 minutes
09:40 olas ok
09:46 edrin joined #bioclipse
09:46 edrin hi
09:46 zarah hi edrin
09:47 olas hi edrin
09:47 olas work on XWS in BC2 after lunch?
09:48 gilleain Yes, in fact just the line : "super(container);" in the constructor that takes an IAtomContainer should work.
09:48 edrin sure
09:48 edrin i did already...
09:48 olas oh? have not seen the commit
09:48 edrin now commiting
09:48 CIA-30 bioclipse: edrin_t * r7143 /xws/trunk/xws4j/src/net/bioclipse/xws/component/ (8 files in 3 dirs): now supporting a mock ProcessStatus
09:49 zarah CIA-30: You have new messages. Write '@messages' to read them.
09:49 egonw gilleain: it then copies all props?
09:49 edrin but the plugin, in need some more minutes...
09:49 egonw @msg
09:49 zarah egonw: You have no new messages.
09:49 edrin it's almost complete
09:49 olas @msg
09:49 zarah olas: You have no new messages.
09:49 egonw oh CIA-30 has new messages
09:49 egonw hahahah
09:49 edrin but have a question: how is logging done in bc2?
09:49 olas very easy
09:49 olas mom
09:49 edrin maybe I should spawn a XWS console where i write XWS stuff to..
09:50 olas in the manifest, do not import the net.bc.logger plugin
09:50 edrin i think this would make sanese
09:50 olas yes
09:50 edrin ok
09:50 olas in the manifest, tab dependencies, import packages org.apache.log4j
09:50 olas then in your class, add:
09:50 gilleain egon: well, actually, no...
09:51 olas private static final Logger logger = Logger.getLogger(CDKManager.class);
09:51 olas replace CDKManager with class name
09:51 egonw ok, bye!
09:51 olas gilleain: please comment on cdk-devel
09:51 edrin ok
09:51 gilleain olas : ok.
10:14 edrin olas: how would eclipse default logger be used instead of bc logger? i currently do not have net.bc.logger checkout...
10:14 edrin and i guess net.bc.logger depends on other bc plugins, right?
10:21 olas edrin: did it not work as I explained?
10:21 gilleain Nope. logger is at the base of the dependencies.
10:22 olas edrin: please commit and I'll set up logging for you
10:26 edrin ok...
10:26 edrin olas: onlye a few more minutes...
10:28 olas hahaha
10:28 olas :-)
10:30 olas edrin: whenever you are ready
10:31 CIA-30 bioclipse: ospjuth * r7144 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/SDFWriter.java: Added SDFWriter to cdk.business.
10:32 CIA-30 bioclipse: ospjuth * r7145 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Implemented saveMolecules() that saves a list of IMolecules to CML or SDF. Also persists properties.
10:32 CIA-30 bioclipse: ospjuth * r7146 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Wrote tests for saving multiple molecules as SDF and CML with properties.
10:33 CIA-30 bioclipse: ospjuth * r7147 /bioclipse2/trunk/plugins/net.biocli​pse.cdk10.jchempaint/src/net/bioclip​se/cdk10/business/CDK10Manager.java: If already CDK10Molecule, just return it in create(IMolecule) method.
10:34 CIA-30 bioclipse: ospjuth * r7148 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/META-INF/MANIFEST.MF: A missing version update.
10:34 CIA-30 bioclipse: ospjuth * r7149 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/META-INF/MANIFEST.MF: A missing version update.
10:34 CIA-30 bioclipse: ospjuth * r7150 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: Removed J2SE requirement as does not work on my mac.
11:02 CIA-30 bioclipse: carl_masak * r7151 /bot/trunk/zarah.pl: [zarah] rewrote regex for plan, which was overly simplistic before
11:02 zarah joined #bioclipse
11:05 zarah joined #bioclipse
11:05 CIA-30 bioclipse: carl_masak * r7152 /bot/trunk/zarah.pl: [zarah] fixed small glitch in time reporting
11:05 zarah CIA-30: You have new messages. Write '@messages' to read them.
11:08 CIA-30 bioclipse: carl_masak * r7153 /bot/trunk/zarah.pl: [zarah] added full stop at the end of a reply
11:09 CIA-30 bioclipse: carl_masak * r7154 /bot/trunk/zarah.pl: [zarah] never reports new messages to CIA bots
11:29 olas edrin: is the commit on the way?
11:29 edrin almost :)
11:31 olas hahaha
11:31 olas edrin: commits don't need to be complete
11:31 olas commit often
11:31 edrin want to test if its working
11:32 edrin or: want to remove all errors at least
11:32 edrin to make it compile...
11:32 olas ok
11:32 edrin but its almost done...
11:32 edrin 10 minutes maximum
11:48 CIA-30 bioclipse: carl_masak * r7155 /bot/trunk/zarah.pl: [zarah] implemented planning data structure modification
11:48 masak zarah, reload
11:48 zarah joined #bioclipse
11:49 jonalv masak: hi there and welcome back to #Bioclipse :)
11:49 masak jonalv: hello.
11:50 masak thank yo
11:50 masak it's been a week full of Chinese studies
11:50 edrin I know kung-fu!
11:54 masak edrin: how nice, dear.
12:03 olas edrin (1:36:36 PM): 10 minutes maximum <- that was 30 mins ago
12:03 maclean joined #bioclipse
12:03 olas :-)
12:03 edrin seconds
12:03 olas wahaha
12:03 edrin i will test the plugin now
12:03 CIA-30 bioclipse: edrin_t * r7156 /xws/trunk/xws4j/src/net/bioclipse/xws/ (ILogPipe.java XwsLogger.java): added preliminary support for logger setup
12:04 edrin there is no errors right now
12:17 masak zarah: boo!
12:18 masak hm.
12:18 masak permanent scare...
12:18 CIA-30 bioclipse: shk3 * r7158 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (3 files in 3 dirs): better handling of combined peak and continuous spectra in jcamp
12:19 masak CIA-30: you missed r7157!
12:19 masak CIA-30--
12:23 maclean Revision 7157 was redacted for reasons of national security.
12:25 olas edrin (2:07:32 PM): seconds <- that was 23 minutes ago!
12:25 olas edrin: are we down to miliseconds now :-) ?
12:28 zarah joined #bioclipse
12:29 masak google bioclipse
12:29 zarah masak: http://www.bioclipse.net/
12:31 edrin ok, in theory the plugin should work fine now....
12:32 edrin but there is a problem initializing it somewhere...
12:32 CIA-30 bioclipse: edrin_t * r7159 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/: Initial import.
12:33 CIA-30 bioclipse: edrin_t * r7160 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (36 files in 15 dirs): Initial import.
12:33 edrin olas: maybe you can check it out and try?
12:33 thomasku joined #bioclipse
12:35 CIA-30 bioclipse: carl_masak * r7161 /bot/trunk/ (. zarah.pl): [zarah] decided to call a hash key "tasks" instead of "plans" for consistency
12:36 zarah joined #bioclipse
12:36 olas edrin: ok
12:40 edrin it says it cannot activate the plugin properly...
12:41 edrin and thus the button and preference page cannot be loaded...
12:43 olas checking out
12:44 edrin ah
12:44 edrin it might be associated with the .jars that i put in the subfolder
12:47 edrin or maybe not
12:49 olas edrin: we donät use the eclipse console in bioclipse2
12:49 olas we have our own
12:49 olas but you can of course use the console
12:49 olas I will add it
12:49 olas mom
12:49 edrin ok
12:50 jonalv huh are we adding yet another console now?
12:50 jonalv could someone motivate this?
12:50 olas for echoing the XML in/out from XMPP
12:50 olas that will only be used by developers
12:50 edrin no
12:50 olas users will hardly ever have it open
12:51 olas right?
12:51 edrin it's a general log
12:51 olas users don't care about logs
12:51 olas hence it will not be open by default
12:51 edrin i would suggest to have a console for xws stuff... so the user sees when he is online/offline and when functions complete...
12:51 jonalv masak: Do you have some thoughts about this?
12:51 edrin it is an option though...
12:52 masak jonalv: not really. what edrin says sounds good.
12:52 jonalv okey I am just a bit worried about console explosion
12:52 olas we REALLY don't want more views unless they are important
12:53 edrin info like "XWS Client connected" will be written there...
12:53 olas and we could echo to the JSConsole
12:53 olas that is really not enough for another view
12:53 olas ConsoleEchoer echoes to the JSConsole
12:53 edrin i think it will be very confusing to have this there
12:53 olas use this instead
12:53 olas else you will end up switching views all the time
12:53 olas one console is enough
12:54 jonalv edrin: I see your point but I am not sure I agree
12:54 olas why have two?
12:54 masak olas: it's pretty confusing to be echoing non-js stuff to the js console, as well
12:54 masak especially for a non-js user, who might not even have the console in view
12:54 jonalv well but we already are aren't we?
12:54 edrin that I think, too
12:54 masak jonalv: like what?
12:54 edrin i eat now, will be back in 20 minutes
12:55 masak @start eating
12:55 zarah masak: There is no task planned by the name 'eating'.
12:55 masak :)
12:55 jonalv hm perhaps nothing. I just thouht somene was using it sionce feature has been around for a while now...
12:55 olas edrin: stop
12:55 olas did you compile with 1.5?
12:55 masak jonalv: no, I've been sort of guarding against it
12:55 olas Bioclipse2 ONLY works with 1.5
12:56 masak jonalv: it's almost happened a few times
12:56 jonalv masak: but?
12:56 olas edrin?
12:56 masak jonalv: but, well, it didn't
12:56 masak you know
12:57 jonalv you stopped it?
12:57 masak a few of the times
12:57 masak mostly it was common sense that stopped it, though
12:57 jonalv oh okey so you think that we need yet another console?
12:58 masak jonalv: not personally, no. I just thought edrin's suggestion sounded sane
12:58 jonalv okey I will stay out of this one then...
12:59 masak @reload
12:59 zarah joined #bioclipse
12:59 CIA-30 bioclipse: carl_masak * r7162 /bot/trunk/zarah.pl: [zarah] no-argument @plan now outputs the tasks planned, along with times
13:01 olas should we have one console where we type things and get the results in another console?
13:01 olas does not make sanse to me
13:01 olas but if you like it that way...
13:01 olas personally I think it would be REALLY annoying
13:01 masak olas: I agree.
13:02 jonalv olas++
13:02 * jonalv cares again
13:03 masak :)
13:03 masak @reload, whatever
13:03 zarah joined #bioclipse
13:03 jonalv perhaps a switch to get the plugin in wordy mode where it echoes to the javascript console? (Then t won't always dirty that console)
13:04 jonalv I mean it can hardly be the idea that the main output is gonan be in the console?
13:04 olas main output of what? xmpp?
13:04 jonalv It should be connected to Eclipse gui / jobs and such
13:04 olas right
13:05 olas hence my oposition
13:08 olas edrin: I have fixed the plugin now. Also committed a feature that simplifies running things. Just add it to bioclipse.product and click "run" in the product editor.
13:08 olas r7166
13:08 olas CIA really buggy today
13:09 olas masak: or did you turn all CIA off?
13:09 masak olas: I have no control over CIA, no
13:09 masak olas: and I agree it's really buggy, not just today, but overall
13:10 olas edrin: nice, I can connect in Bioclispe now
13:10 olas but edrin, could you not use ECF, Eclipse Communication Framework for this?
13:10 olas it has support for XMPP
13:11 olas link coming up
13:11 olas http://www.eclipse.org/ecf/
13:11 masak google eclipse ecf
13:11 olas http://wiki.eclipse.org/ECF_Providers
13:11 zarah masak: http://www.eclipse.org/ecf/
13:12 masak google eclipse ecf providers
13:12 zarah masak: http://dev.eclipse.org/viewcvs/index.cgi/or​g.eclipse.ecf/providers/org.eclipse.ecf.pro​vider.r_osgi/%3Froot%3DTechnology_Project
13:12 masak oops, something else :)
13:12 olas shouldn't it be @google?
13:13 masak it is, as well
13:13 olas I don't like google, it's evil
13:13 olas oh
13:13 olas puh
13:13 masak it has been conjectured that if people start an utterance with 'google', they will not be inconvenienced by a search result :)
13:13 olas thought zarah would pick that up :-)
13:13 masak olas: no, just start of line
13:14 olas google is a good thing
13:14 zarah olas: http://www.youtube.com/watch%3Fv%3DxrOek4z32Vg
13:14 olas you see?
13:14 masak olas: aye. not very common, though
13:14 olas true
13:14 olas google can be a pain sometimes
13:14 zarah olas: http://www.gamespot.com/pages/unions/forums/show​_msgs.php%3Ftopic_id%3D24048809%26union_id%3D408
13:14 olas woops
13:14 masak now who *ever* says a thing like that? :)
13:15 jonalv google masak
13:15 maclean Wow. That's a fascinating story about a dog, right there.
13:15 zarah jonalv: http://masak-masak.blogspot.com/
13:16 jonalv zarah++
13:16 olas google olas
13:16 zarah olas: http://www.olasjobs.org/
13:16 olas ?
13:16 masak haha
13:16 olas nice!
13:16 masak "masak-masak is a cottage game played by young girls whereby they pretend to cook delicious dishes from imaginary ingredients and plastic utensils."
13:16 olas “OLAS is fast, friendly, and a click away!...” - Rose Prati
13:16 masak haha
13:16 edrin olas: I was away, can you update me?
13:17 jonalv google jonalv
13:17 zarah jonalv: https://www.ohloh.net/accounts/jonalv/messages
13:17 masak a hit!
13:17 masak cool
13:17 olas olas (3:12:35 PM): edrin: I have fixed the plugin now. Also committed a feature that simplifies running things. Just add it to bioclipse.product and click "run" in the product editor.
13:17 olas edrin: got it to connect
13:17 edrin olas: what was wrong with the plugin?
13:17 olas did you build xws4j with java 1.5?
13:17 edrin olas: no clue ;)
13:18 olas big problem was you didn't add the jars in the manifest
13:18 olas runtime tab
13:18 olas please update
13:18 olas I also added a feature
13:18 olas simplifies running
13:18 edrin ok, what feature?
13:18 edrin ok
13:18 olas look in bioclipse2/features
13:18 olas net.bioclipse.xws-feature
13:19 olas it just says that xws needs console, variables, and wxs plugins to run
13:19 edrin ok
13:19 edrin slowly...
13:19 edrin this is all too fast
13:19 olas ok
13:20 olas first: update plugin
13:20 edrin done
13:20 olas open manifest
13:20 olas see runtime tab
13:20 edrin currently checking out the feature thing
13:20 olas I added jso and xws jars there
13:20 olas do you see that?
13:21 olas edrin?
13:21 edrin ok
13:21 edrin found it
13:21 edrin why is this required?
13:21 CIA-30 bioclipse: carl_masak * r7163 /bot/trunk/zarah.pl: [zarah] minor tweaks to @plan reporting
13:21 olas that was the big thing
13:21 olas and I built xws4j with Java 1.5
13:22 edrin ah, because jar must not be in a jar ?
13:22 edrin ok, the current checked out version from today?
13:22 olas yes
13:22 olas updated
13:22 olas then built
13:22 edrin how can i switch eclipse to java 1.5 in general?
13:22 olas preferences
13:23 olas Java -> Compiler
13:23 edrin but it is set to 5.0 there
13:24 edrin ok, first i must get bc2 to run now...
13:25 zarah joined #bioclipse
13:25 olas I didnät say you built with 1.6, I built it with 1.5 just to be sure
13:25 olas manifest thingy was the key part
13:25 edrin ok. :)
13:26 edrin and I am still curious if everything in the plugin will work as I designed it...
13:26 zarah joined #bioclipse
13:28 zarah joined #bioclipse
13:28 olas I could log in
13:28 olas and it connected
13:28 olas rest I donät see how to use
13:28 olas if there is anything to see :-)
13:31 zarah joined #bioclipse
13:32 olas edrin: can you get it to run?
13:32 edrin bc2 is not running yet...
13:32 edrin but my plugin starts up at least
13:32 edrin thx for the fix :)
13:32 olas no prob
13:33 olas I want to make a manager to show the functionality
13:33 olas can I do that?
13:33 edrin i noticed bugs...
13:33 zarah joined #bioclipse
13:33 olas right
13:33 olas there are always bugs :-)
13:37 edrin olas id you write the manager it should in principle support only one function for now:
13:39 edrin if the manager is "xws" it should support a function "xws.getDefaultClient()" and this should wrap plugin's Activator.getDefaultClientC​urator().getDefaultClient()
13:40 edrin this will return the (default) Client
13:40 edrin with this the user can do everything from console...
13:43 CIA-30 bioclipse: ospjuth * r7164 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (4 files in 3 dirs): Fixed XWS plugin. Added jars to manifest and replaced xws jar with version compiled with Java 1.5.
13:44 CIA-30 bioclipse: ospjuth * r7165 /bioclipse2/trunk/features/n​et.bioclipse.xws4j-feature/: Initial import.
13:45 CIA-30 bioclipse: ospjuth * r7166 /bioclipse2/trunk/features/n​et.bioclipse.xws4j-feature/ (.project build.properties feature.xml): Feature to simplify installtion/running of XWS4J in Bioclipse2.
13:51 CIA-30 bioclipse: carl_masak * r7167 /bot/trunk/zarah.pl: [zarah] reports elapsed time since @tell message was sent
13:51 CIA-30 bioclipse: carl_masak * r7169 /bot/trunk/zarah.pl: [zarah] switched on telling the time
13:51 CIA-30 bioclipse: carl_masak * r7170 /bot/trunk/zarah.pl: [zarah] added "ago" in return expression of &nice_ago
13:52 masak CIA-30: oh, so _now_ you wake up?
13:52 CIA-30 bioclipse: shk3 * r7171 /bioclipse2/trunk/plugins/net.biocli​pse.specmol/src/net/bioclipse/specmo​l/outline/SpecmolOutlinePage.java: avoids an npe
13:54 olas edrin: ok, will do that
13:57 olas edrin: IMO it should be able to log in via JS as well
13:58 edrin olas: sure
13:58 CIA-30 bioclipse: edrin_t * r7172 /bioclipse2/trunk/plugins/net.biocli​pse.xws4j/src/net/bioclipse/xws4j/ac​tions/ToggleConnectionAction.java: bug fix, now disconnecting should work
13:58 edrin with the client returned by getDefaultClient()
13:58 edrin user can just do client.connect()
14:00 jonalv so you can have many clients?
14:00 * jonalv doesn't really know what you are doing but it soudns very intresting... :)
14:00 edrin jonalv sure you can
14:00 edrin but i would recommend to use the default one ;)
14:01 edrin there user has setup account data in preferences
14:01 jonalv okey so you can't change that from the manager?
14:02 edrin jonalv: I do not understand
14:03 jonalv there are things that can be changed in preferences?
14:03 jonalv Can those things be changed from the manager as well?
14:03 edrin well, one could also add a function to the manager that wraps ClientFactory stuff
14:03 jonalv hm, you and me are thinking upside down to eachother
14:04 jonalv I would have the preferences page wrap around the manager methods and not have the manager method wrap aroud what is done in the preferences page :)
14:06 olas I have now made a manager
14:07 edrin And I got bc2 environment running
14:07 olas and agree with jonalv
14:08 olas nice, I can get the client from JSConsole
14:08 edrin :)
14:08 edrin that was the plan
14:08 edrin and
14:08 edrin cool is
14:09 edrin the client is optimized for this ;)
14:09 jonalv edrin: in what way :)
14:09 edrin you will see
14:10 edrin cannot explain it here now
14:10 edrin the API is optimized to be used from a console ;)
14:10 olas hmm, I get a invalidthreadexpetion if not connected
14:10 olas ok, commit coming up
14:11 edrin olas: the feature thing, what do i do with it?
14:11 jonalv edrin do you have help texts for the methods too?
14:11 olas run it
14:11 edrin not yet
14:11 olas jonalv: I have not even committed the manager!
14:11 edrin jonalv not yet
14:11 * jonalv looks forward to olas demo of this
14:12 edrin olas: how do i run a feature?
14:12 olas jonalv: you have a jabber account?
14:12 olas else, get one
14:12 olas (you'll need it)
14:12 jonalv actually I don't know. is google chat?
14:12 edrin jonalv: yes it is
14:13 CIA-30 bioclipse: ospjuth * r7173 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (11 files in 5 dirs): Added XWSManager.
14:13 edrin olas: how do i run a feature?
14:13 olas ok, update
14:13 olas edrin: open bioclispe.product
14:13 olas switch to configuration tab
14:13 olas there you list features you'd like to run
14:13 olas then click run INSIDE the product editor
14:14 olas this is by far the simplest way to run features
14:14 edrin ok
14:14 olas if the features are complete, no need to edit run configuration
14:14 olas I almost always start Bioclipse this way when something has changed :-)
14:15 * jonalv is still running Bioclipse plugin by plugin...
14:15 olas that's your decision
14:15 jonalv is that bad?
14:16 masak jonalv: what does it mean, more exactly?
14:16 masak jonalv: if it means what I think it means, you're a hero
14:16 jonalv masak: then I don't think it means what you think it means
14:17 * jonalv might be a hero but not because of the way he starts Bioclipse... :)
14:17 jonalv although it might be herotic to run as many plugins as I do togheter...
14:18 olas edrin: all functionality should lie in the manager
14:18 olas the action should just call the manager methods
14:18 olas do you see why?
14:18 edrin yes
14:19 edrin hm...
14:19 edrin 04:19:28 Could not create default client: java.lang.NullPointerException
14:19 edrin what is this?
14:19 olas ?
14:19 olas debug
14:20 olas I see threading issues
14:20 olas the calls from the manager is run in the JSThread, right masak,jonalv?
14:21 masak olas: well, JSThread is a class, but yes
14:22 olas hmm
14:22 masak anything that goes through the js env is in its own thread
14:22 CIA-30 bioclipse: edrin_t * r7174 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/Activator.java: shows XwsConsole when connecting
14:22 olas it seems edrin's implementation requires it to be run in the SWT thread
14:22 olas edrin: why have you done it so?
14:22 masak no can do
14:22 edrin that was my plan
14:22 edrin well you can set any execution pipe if you want
14:23 olas it doesn't work now :-(
14:24 edrin strange, now I can connect
14:24 olas please update to 7175
14:24 edrin olas what does not work now?
14:24 olas and try to connect from JSConsole
14:24 olas type xws.connect()
14:24 olas you can tab-complete
14:24 masak ideally, managers shouldn't do GUI stuff
14:24 olas it's not gui stuff
14:24 masak but SWT?
14:24 olas that's why I donät see why it is done this way
14:25 edrin hm?
14:25 olas edrin: could you please change it?
14:25 edrin i dont really understand the problem
14:25 masak ok, ideally, managers shouldn't do SWT stuff :)
14:25 olas we don't want to run in UI thread
14:25 masak we can't run _in_ a UI thread
14:25 edrin ehm
14:25 masak we can defer to it asynchronally
14:25 olas xws.connect() says IllegalThreadAccess
14:25 masak but not run in it directly
14:26 olas you are trying to do SWT stuff in a non-UI thread
14:26 edrin yes
14:26 edrin well
14:26 masak olas: maybe we can fix the more general problem of the js env dying on naughty managers by inserting a try/catch block somewhere in the inclusion code.
14:26 edrin it writes the connection status to console
14:26 masak I have to think more about that
14:26 olas Color color_blue = PlatformUI.getWorkbench().getDispla​y().getSystemColor(SWT.COLOR_BLUE);
14:27 olas that is the UI call
14:27 edrin yes
14:27 masak edrin: that's most likely the wrong thing to do in a manager
14:27 edrin but you need to be aware of the connection status
14:27 olas Could you please change that?
14:27 masak managers don't do UI
14:27 masak we should have a big notice about this somewhere...
14:28 edrin olas: for example if you want to write a graphical discovery browser this will be a lot GUI thing
14:28 olas ok, edrin: line 109 in DefaultClientCurator
14:28 charlgren joined #bioclipse
14:28 olas you need to wrap that in the UI thread
14:28 masak edrin: yes... but that still doesn't belong in a business namespace
14:29 olas edrin: yes, but you will not CALL it from the wrong thread
14:29 olas listening is the way
14:29 edrin olas: what is a business namepsace?
14:29 olas xws
14:29 olas if in console, you type "xws." and then tab complete
14:29 olas xws is the namespace
14:29 olas methods in XWSManager appears under this namespace
14:30 olas hence xws.connect()
14:30 masak edrin: a business namespace is a bioclipse namespace containing the name "business". these are the ones containing managers
14:30 edrin olas: xws is listener based. but the thread where the listeners are run in must be defined. i defined the GUI thread because the listeners will be used to write GUI against it
14:30 olas and xws.getDefaultClient()
14:30 olas edrin: you can't do it that way
14:31 olas or at least, it must be accommodated to run in another thread
14:31 olas and when calling UI code, wrap in Display.getDefault.async(...)
14:31 olas you get my point?
14:31 edrin yes
14:32 edrin but i must play around first to see where the problem is
14:32 jonalv this seems to be quite complicated discussion to have over irc... :)
14:32 olas indeed
14:32 edrin give me a few minutes i must fix other stuff first
14:32 olas edrin: have you tried running xws.connect()?
14:32 masak generally, this isn't a problem, because managers don't do GUI stuff
14:32 olas right
14:33 olas and connect() does not do GUI stuff
14:33 olas GUI stuff can listen to it and act upon it
14:33 jonalv The basic idea is that managers should do work on daomain models and the gui should listen to changes on the domain objects and respod to them
14:33 masak that sounds more like it
14:33 masak aye
14:33 edrin but in general xws is designed to be used either in blocking mode (from console) or in listener based mode (from GUI)
14:34 jonalv edrin: once again we are upsdie down...
14:34 jonalv :)
14:34 edrin anyway
14:34 edrin I think i know a solution
14:34 jonalv I don't think it's a problem though it's just different
14:34 edrin but first let me fix some other stuff
14:36 * olas is implementing service discovery in the manager
14:36 jonalv woho it sounds so cool the stuff you guys are doing :)
14:36 olas masak: if I want to output a list of strings as a result of a manager call, should it be a List<String>
14:37 olas will that display good?
14:37 masak olas: probably not
14:37 masak at least not if you don't like [] and , all over the place
14:37 edrin olas: you may also just use the toString() of all the xws objects, they will return data already human readable formated.
14:38 masak I suggest you condense it down to one string and return
14:38 olas edrin: sounds nice
14:38 olas will do that
14:38 edrin olas: see the js script examples
14:40 CIA-30 bioclipse: edrin_t * r7176 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/XwsConsole.java: fixed a variable name bug
14:40 edrin ah, ok, one bug fixed... debug mode is now fully working.
14:41 olas nice
14:42 edrin maybe it is a little bit too much debug info, but I can change this later
14:43 olas COOL
14:43 olas service discovery works!
14:44 edrin :)
14:44 edrin yes
14:44 olas edrin: this is so nice!
14:44 olas ok, you want to test?
14:44 edrin it works without thread invalid problems
14:44 jonalv how can I test "this"? :)
14:44 edrin ?
14:44 olas edrin: have you fixed it?
14:45 edrin it works without thread invalid problems?
14:45 olas not really
14:45 edrin no
14:45 olas you need to connect via the toolbar button
14:45 edrin yes
14:45 olas commit pending
14:45 edrin olas i will fix this problem later
14:45 edrin currently fixing GUI stuff
14:46 olas ok
14:46 olas jonalv: you want to test?
14:46 olas update to r7177
14:46 olas run, open JSConsole
14:46 olas xws.listServices("xws.ayena.de")
14:46 jonalv olas: it's friday afternoon I just finnished my current task and you seem to be doing cool stuff.
14:47 jonalv yes I wanan test :)
14:47 olas yes, this IS cool stuff
14:47 CIA-30 bioclipse: edrin_t * r7178 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/src​/net/bioclipse/xws4j/actions/ActionPulldown.java: debug mod button is now synchronized with pref boolean
14:47 olas edrin: now connect does not work anymore...
14:48 edrin why not?
14:48 edrin what does it say?
14:48 olas teh cosen operation is currently unavailable
14:48 edrin reminds me of the problem i had
14:49 edrin this was solved by your manifest thing, no?
14:49 olas oh, I get exceptions on startup
14:49 olas edrin: that is not the way to show consoles on startup
14:49 edrin why not?
14:49 edrin left #bioclipse
14:50 olas too early
14:50 edrin joined #bioclipse
14:50 edrin ups
14:50 olas and not desirable
14:50 edrin wrong window
14:50 olas users should be able to choose to open it
14:50 edrin ok, where do I choose this?
14:50 olas you can make a perspectiveContribution
14:50 olas and say that it should be shown in a specific perspective
14:51 olas other than that, users can show view
14:51 olas you could create a menu option to show the view
14:51 olas but not like this, please
14:51 olas now I can't connect :-(
14:52 olas commenting out console.show() then it works again
14:52 edrin for me it was working
14:53 olas it'sa race
14:53 olas it MIGHT work
14:53 olas but will in some cases not
14:53 edrin ok
14:53 olas jonalv: did you get it to work?
14:53 edrin i will try it different then...
14:53 jonalv olas: I am working on it
14:54 jonalv I had to do some stufs on the way... :)
14:54 olas edrin: great
14:54 jonalv hm I got a XWS console now
14:54 olas jonalv: you need to comment out line 58 in Activator in xws plugin
14:54 jonalv Don't know where it came from...
14:54 edrin if you press the xws button it will be shown, ok?
14:54 olas ok
14:54 jonalv olas: seems rihgt thing won ther race for me this time :)
14:55 olas jonalv: you also need to set XWS preferences with your Jabber ID
14:55 olas and jabber.org as server
14:55 CIA-30 bioclipse: edrin_t * r7179 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/Activator.java: console.show() removed
14:55 jonalv uhm, perhaps...
14:55 olas then click the connect button
14:55 edrin server depends on your jabberID
14:55 edrin if you use google use this
14:55 olas then type xws.listServices("xws.ayena.de")
14:56 jonalv mom //many exceptions when showing jsconsole
14:56 olas let me know if it works
14:56 olas jonalv: please update
14:56 jonalv olas: what's my jabber id?
14:57 olas google account?
14:57 zarah olas: https://google.com/accounts/
14:57 olas edrin?
14:57 edrin yes?
14:57 olas whats jonalvs jabber id?
14:57 olas he usesd google chat
14:57 edrin ah
14:57 jonalv google google jabber accounts
14:57 zarah jonalv: http://www.google.com/support/talk/bin​/answer.py%3Fhl%3Den%26answer%3D24076
14:58 olas edrin: have you tested the command line service discovery?
14:58 jonalv nah no good hit
14:58 olas from JSConsole in bc2?
14:58 edrin olas: it is most likely his googlemail email
14:58 edrin olas: not yet, i was fixing other stuff
14:59 maclean http://www.google.com/support/talk/b​in/answer.py?hl=en&amp;answer=24076
14:59 maclean half way down.
14:59 maclean "If you're signing in with a Gmail or Google Mail username, enter your full email address"
14:59 jonalv maclean: dz
15:00 maclean .dz == tld for Algeria?
15:01 masak maclean: dz == "thank you" in Polish
15:01 maclean ohhh.
15:01 masak or a short form thereof
15:01 maclean tak.
15:02 jonalv maclean: that means roof in swedish :)
15:03 olas is there a pastebin for images?
15:04 maclean Well, I was speaking Danish (it appears) :)
15:06 olas http://bioclipse.net/dl/xws_service_listing.png
15:06 edrin hehe
15:06 masak olas: flickr
15:07 edrin i will pass this screenshot to the guy who is managing ayena.de
15:07 olas please do!
15:07 edrin hm
15:07 edrin he is offline...
15:07 olas it'll stay there
15:07 jonalv what was the server again?
15:07 olas see screenshot
15:08 olas xws.ayena.de
15:08 edrin ayena.de
15:08 edrin xws is the component name
15:08 jonalv is that what I should put in Preferencs?
15:08 edrin no
15:08 olas jabber.org
15:08 edrin no
15:08 olas no?
15:08 edrin jonalv: what is your JID/googlemain address?
15:09 olas maybe google accounts require a google server?
15:09 jonalv edrin: what's a JID?
15:09 edrin olas: sure it does
15:09 olas jonathan.alvarsson@gmail.com
15:09 olas right?
15:09 jonalv yea
15:09 edrin jonalv: your username is jonathan.alvarsson
15:09 edrin server is gmail.com
15:09 edrin port should be 5222
15:09 olas that was simple
15:10 jonalv where did that view go?
15:10 edrin what view ?
15:11 olas show view?
15:11 olas console
15:11 jonalv the new conosle...
15:11 olas is the name of it
15:11 olas does it appear when you connect?
15:11 jonalv hm Bioclipse locked down completly when I hit connect
15:12 olas for some time yes
15:12 olas 5 seks
15:12 jonalv no not 5 secs
15:12 jonalv that should not use the main thread btw
15:12 olas edrin: console does not show when I hit connect
15:12 olas jonalv: it should be annotated with @job I assume?
15:12 olas is it that simple?
15:12 jonalv where is that console?
15:13 olas show view -> general -> console
15:13 CIA-30 bioclipse: edrin_t * r7181 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/XwsConsole.java: renamed the window title to XMPP Web Services Console
15:13 jonalv olas: is it calling a manager method?
15:13 olas not yet
15:13 olas but if it did, would @job do the trick?
15:13 edrin jonalv: it should show up when you press the button
15:13 jonalv olas: that's the idea at least...
15:13 olas not for me it doesnt
15:13 edrin olas: i must check this first
15:14 jonalv not for me either. Perhaps I should update?
15:14 jonalv 05:12:04 Could not connect default client: net.bioclipse.xws.exceptions.XmppException: java.net.ConnectException: Operation timed out
15:14 edrin did you check out?
15:14 edrin jonalv: maybe you are firewalled?
15:15 edrin ah
15:15 edrin # Click Add.
15:15 edrin # Highlight your new account in the Accounts section, and then click Server Settings.
15:15 edrin # Enter the following information in the appropriate fields:
15:15 edrin * Server: talk.google.com
15:15 edrin * Port: 5223
15:15 edrin they are special...
15:15 edrin hm...
15:16 edrin not sure if this will work with the preference GUI then...
15:16 edrin maybe you can try out
15:16 CIA-30 bioclipse: ospjuth * r7182 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/Activator.java: getXWSmanager should return IXWSManager.
15:16 edrin because talk.google.com is the server and your JID is jonathan.alvarsson@gmail.com
15:17 edrin jonalv: usually your JID is the combination of user@server.com
15:17 edrin maybe I shoudl change this
15:18 CIA-30 bioclipse: ospjuth * r7183 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/sr​c/net/bioclipse/xws4j/business/IXWSManager.java: Annotated connect() with @job
15:18 edrin (xws4j alone would be compatible, though ;)
15:19 jonalv Could not create default client: org.jabberstudio.jso.JIDFormatException: domain is not a valid FQDN or IP address
15:20 CIA-30 bioclipse: ospjuth * r7184 /bioclipse2/trunk/plugins/net.biocli​pse.xws4j/src/net/bioclipse/xws4j/ac​tions/ToggleConnectionAction.java: Placed FIXME where run() method should be updated to use manager code when threading issue fixed.
15:20 edrin jonalv: maybe you should just download PSI from psi-im.org and create a jabber.org account
15:21 jonalv edrin: okey
15:25 olas how do I run a Job from within a non-GUI thread?
15:25 olas is that forbidden?
15:25 edrin do you think there should be a XMPP Web Services menu item ?
15:25 olas I donät know
15:25 olas if you have content to put there, yes
15:26 jonalv olas: why would that be forbidden?
15:26 CIA-30 bioclipse: carl_masak * r7185 /bot/trunk/zarah.pl: [zarah] now understands (things like this)++
15:26 jonalv (things like this)++
15:26 jonalv karma (things like this)
15:26 zarah (things like this) has a karma of 0
15:26 jonalv masak: nope
15:27 olas PlatformUI.getWorkbench().getProgr​essService().run(false,false,pr);
15:27 jonalv zarah--
15:27 olas that requires me to be in UI thread
15:27 masak karma things like this
15:27 zarah things like this has a karma of 0
15:27 olas karma olas
15:27 zarah olas has a karma of 25
15:27 olas :(
15:27 masak jonalv: did you reboot?
15:27 olas I remember...
15:27 masak olas: shut up
15:27 olas masak: you are evil
15:27 jonalv zarah: booh!
15:27 zarah jonalv: eh... wha'?
15:27 maclean ++++
15:27 olas masak: booh!
15:27 maclean karma ++
15:27 zarah ++ has a karma of 0
15:27 jonalv zarah: boo!
15:28 zarah joined #bioclipse
15:28 masak maclean: only words are counted in the short form
15:28 masak word++
15:28 masak karma word
15:28 zarah word has a karma of 1
15:28 masak (something longer)++
15:28 jonalv (things like this)++
15:28 masak karma something longer
15:28 zarah something longer has a karma of 1
15:28 maclean Curses. Next on my list was --++ and ++--
15:28 jonalv karma (things like this)
15:28 zarah (things like this) has a karma of 0
15:28 masak jonalv: chuck the parentheses
15:29 jonalv masak: I don't wanna
15:29 jonalv karma things like this
15:29 zarah things like this has a karma of 1
15:29 jonalv zarah++
15:29 masak jonalv: if you don't wanna, you'll have to do some extra programming
15:29 jonalv masak: I don't wanna
15:30 masak I thought so
15:30 jonalv ;)
15:30 jonalv it's 150% friday! :)
15:30 masak ouch -- Cmd-Q sits far too close to Cmd-Tab :(
15:30 jonalv heh
15:30 masak friday++
15:31 masak oh well, I guess it was time to reboot Firefox anyway...
15:32 jonalv xws.listServices("xws.ayena.de")
15:32 jonalv The request timed out.
15:32 jonalv :(
15:35 jonalv what could I be doing wrong?
15:35 edrin firewall?
15:35 edrin hm
15:35 edrin or are you connected?
15:36 jonalv 05:31:25 Default client connected.
15:36 edrin ok
15:36 edrin maybe ols switched off the service?
15:36 edrin jonalv: try this.
15:36 jonalv now I got invalid thread access instead...
15:36 edrin c = xws.getDefaultClient()
15:37 edrin x = c.getXmppItem("jabber.org");
15:37 edrin x = x.discover();
15:37 jonalv Can't find method net.bioclipse.xws.client.C​lient.getXmppItem(string)
15:37 edrin and then print x.toString() to console
15:37 olas no
15:37 olas service should be running
15:37 edrin ah
15:37 edrin jonalv: sorry
15:37 edrin x = c.getXmppItem("jabber.org", "");
15:38 jonalv x = c.getXmppItem("jabber.org", "");
15:38 jonalv Invalid thread access
15:38 edrin hm...
15:39 olas does it work from the JSConsole like my screenshot shows, jonalv?
15:39 jonalv olas: no
15:39 olas why not?
15:39 olas what error you get?
15:39 jonalv olas: that's the question...
15:39 jonalv first I got time out but now I get IllegalTrheadAccess
15:40 edrin strange
15:40 jonalv it's when it's writing to the conosle
15:40 olas I get erros now too
15:40 jonalv that must be done from the gui thread...
15:40 olas edrin: you have changed something
15:41 olas or?
15:41 olas Caused by: net.bioclipse.xws.exceptions.XwsException: The request timed out.
15:41 olas mom, will check the component
15:41 olas restarting component
15:42 edrin no, i did not change anything that should affect it
15:42 olas component says now:  net.bioclipse.xws.exceptions.XwsException: The request timed out. at net.bioclipse.xws.client.adhoc.Serv​ice.discoverSync(Service.java:157) at se.uu.farmbio.hivpred.tests.TestC​lient2.main(TestClient2.java:65)
15:43 olas well, it used to work
15:43 maclean there's pictural proof.
15:43 maclean I managed to log in as well, but not much further than that.
15:43 edrin olas: i changed the IFunction
15:44 olas maybe I need to rebuild my component?
15:44 edrin olas: yes, at least you must change run( ProcessStatus to run( IProcessStatus
15:44 olas he, I see jonalv connecting to my component
15:45 jonalv first time I get time out second thime I get Invalid thread access
15:46 olas I always get timed out
15:46 olas edirn: di you update the xws jar?
15:46 edrin no
15:46 edrin olas
15:46 edrin olas what timeout did you set?
15:47 edrin sometimes server 2 server communication is slow...
15:48 edrin 10 seconds might be not enough
15:48 edrin jabber.org has very high user rates, it might be the reason
15:49 olas edrin: I set no timeout
15:49 CIA-30 bioclipse: carl_masak * r7186 /bot/trunk/zarah.pl: [zarah] now recognizes the famous "smart girl" compliment
15:49 edrin yes, 10 seconds
15:50 edrin XmppItem x2 = x.discoverSync(10000);
15:50 olas ok, it works again
15:50 olas jonalv: test again
15:50 olas oh
15:50 olas please update first
15:50 olas I built a new jar
15:50 olas mom will commit
15:50 zarah joined #bioclipse
15:51 jonalv edrin: DefaultClientCurator row 107 should probably be wrapped over to the gui thread...
15:51 CIA-30 bioclipse: ospjuth * r7187 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (4 files in 3 dirs): New updated XWS jar.
15:51 olas ok, update and test again jonalv
15:51 edrin ok
15:51 olas I think it was my fault
15:51 jonalv roger
15:51 olas think I updated XWS
15:51 edrin what did you do?
15:51 olas rebuilt component and xws jar
15:52 edrin you updated the xws4j library?
15:52 olas now it works at least
15:52 olas yes
15:52 edrin what did you change?
15:52 olas did not change any
15:52 olas just rebuilöt
15:52 edrin ah
15:52 edrin ok
15:52 olas please verify that it works
15:52 olas I must run off VERY soon
15:52 olas but will leave the component on :-)
15:53 olas jonalv?
15:53 jonalv starting Bioclipse
15:53 jonalv connecting
15:53 jonalv yey
15:53 jonalv how do I call the services?
15:53 jonalv I don't?
15:53 edrin you can
15:54 edrin jonalv: try this
15:54 maclean yay also.
15:54 edrin s = c.getService(servicejid);
15:54 olas jonalv: have you seen my screenshot?
15:54 CIA-30 bioclipse: carl_masak * r7188 /bot/trunk/zarah.pl: [zarah] added a few forgotten whitespace markers to last commit
15:54 edrin f = s.getFunction(functionname);
15:54 zarah joined #bioclipse
15:55 olas can you list them?
15:55 edrin f.invokeSync(null, 30000);
15:55 olas jonalv?
15:55 jonalv olas: yea I get the same list now
15:55 olas GOOD
15:55 olas ok, I'm off for today
15:55 edrin olas: cu
15:55 olas have a nice weekend boys (and girl)
15:55 edrin will you be around at weekend?
15:56 CIA-30 bioclipse: edrin_t * r7189 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/src​/net/bioclipse/xws4j/actions/ActionPulldown.java: updated menu organization
15:56 olas left #bioclipse
15:56 edrin who is a girl here?
15:57 maclean Zarah?
15:57 edrin that's a bot but no girl
15:57 jonalv edrin: what is "functionname"?
15:57 edrin it's a bot with a girlish behaviour
15:57 jonalv a fembot perhaps?
15:58 edrin jonalv: is olas still running the component? then for example "testFunction"
16:00 masak edrin: the roadable to which the quote was first uttered wasn't a girl either, so I find it quite appropriate
16:00 maclean femputer : "Have you any idea how it feels to be a fembot living in a manbot's manputer's world?" bender : "what?"
16:01 jonalv f.invokeSync(null, 30000)
16:01 jonalv Invalid response.
16:01 * jonalv has no idea about what he is doing :)
16:02 jonalv maclean++
16:02 jonalv futurama++
16:02 maclean I also have no idea, but it seems like it is very clever.
16:02 edrin jonalv: you should activate the Debug Mode and then read the console log ;)
16:03 jonalv edrin: can't do that. Debug mode does not work
16:03 masak you're a smart girl, zarah.
16:03 zarah masak: I bet you tell that to all the girls. Over and out.
16:03 jonalv Illegal thread access
16:03 edrin hm
16:03 jonalv zarah: you are the smart one :)
16:03 zarah jonalv: no, YOU are the smart one! :)
16:03 masak :)
16:04 masak zarah: no, YOU are the smart one!
16:04 zarah masak: no, YOU'RE the smart one!
16:04 jonalv edrin++ //I think this looks very promising
16:04 edrin thanks
16:06 jonalv masak: can any method be annoted with published method and get help annotations in that way?
16:06 masak jonalv: I think so.
16:06 masak but currently, only methods in manager classes can be reached.
16:07 jonalv masak: why?
16:07 masak jonalv: because the others are not imported
16:07 maclean Oh, I was going to ask : what's the difference between @published and @recorded
16:07 maclean ?
16:07 maclean And should they always be used together?
16:08 masak in practice, yes :)
16:08 jonalv @published are things that have help text
16:08 jonalv @recorded are methods that should be recorded in some way
16:08 jonalv since recording isn't exactly working perfectly the answer is somewhat like " It dosn't matter too much right now"
16:08 maclean :)
16:09 jonalv However my plan was that some methods annotated as @recorded could leave another trail
16:09 jonalv recording sort of works though
16:09 jonalv has anyone tried it?
16:09 maclean Nope.
16:09 maclean (or, at least, not me:)
16:10 maclean How would I go about it?
16:10 jonalv I am thinking it's one of those things that I should just give up
16:10 jonalv "Kill your darlings..."
16:10 jonalv I learnt alot about AOP and annotations on it though...
16:10 masak aye
16:10 masak it's a beautiful idea, but it can't be done
16:11 masak not in Java 5, at least
16:11 jonalv it's just that _if_ it could work it would be SO cool...
16:11 maclean No, no - if Bioclipse commands could be recorded, and then exported to a script to be used in a Taverna workflow...
16:11 masak :)
16:11 jonalv maclean: exactly
16:11 masak oh my, we have a user base
16:11 maclean That would be the mutt's nuts.
16:11 jonalv it's sort of possible...
16:12 masak (mutt's nuts)++
16:12 maclean Also the bee's knees, and the cat's pajamas.
16:12 * jonalv smiles and nods
16:12 masak haha
16:12 jonalv (That means he didn't understand...)
16:12 masak jonalv: who?
16:12 edrin maclean: that actually was a plan
16:12 maclean Ah right, well here's wishing :)
16:13 jonalv who's mutt and what's up with his nuts?
16:13 masak jonalv: a mutt is a non-purebred dog. "nuts" is a euphemism for testicles. it's an expression approximately meaning "very good indeed"
16:14 jonalv okey
16:14 jonalv ...
16:14 maclean http://www.phrases.org.uk/m​eanings/the-bees-knees.html
16:14 masak jonalv: the origin of the expression, as well as that of "bee's knees" is likely based in its rhyming properties
16:15 maclean Anywaay. Back to what I was doing...
16:15 jonalv yea...
16:15 masak (very much Friday today)++
16:15 jonalv I think I am going home if noone has any special need of me...
16:15 masak who's noone?
16:15 jonalv home to eve online
16:16 jonalv masak: I thought you told me you didn't actively miss understand
16:16 maclean happy gaming!
16:16 masak jonalv: who's miss understand?
16:16 masak :P
16:16 masak ah, I kill me
16:16 masak anyway, I most certainly don't do her
16:16 jonalv masak: skit på dig!
16:17 masak no matter what you've heard
16:17 masak jonalv: re misunderstanding: I think I actually make a special exception for you, now that I think about it
16:19 jonalv well see you people! Have Fun!
16:19 masak happy Eve-ing!
16:39 edrin masak: how can I show the bc2 console?
16:39 masak edrin: no such thing as a bc2 console
16:39 masak do you mean the js console?
16:40 edrin yes
16:40 masak you show it like you show any other view
16:40 edrin what plugin do I need?
16:40 masak scripting.ui
16:41 edrin this I have
16:41 masak I think it's a dependency to get Bioclipse running at all
16:41 edrin ah found it
16:43 edr1n joined #bioclipse
16:44 CIA-30 bioclipse: goglepox * r7190 /bioclipse2/trunk/plugins/net.bioclipse.​biojava.ui/src/net/bioclipse/biojava/ui/​views/outline/AlignmentOutlinePage.java: Fixed horizontal scrollbar
17:16 CIA-30 bioclipse: edrin_t * r7191 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (5 files in 2 dirs):
17:31 CIA-30 bioclipse: edrin_t * r7192 /bioclipse2/trunk/plugins/net​.bioclipse.xws4j/plugin.xml: removed extension stuff not required
17:31 edr1n masak: I get strange characters in the jsconsole
17:31 masak edr1n: running windows?
17:31 edr1n masak: it seems the "new line"
17:31 edr1n yes
17:31 masak known problem
17:32 edr1n can you fix this?
17:32 masak sorry about that
17:32 masak edr1n: not directly, no
17:32 edr1n why not?
17:32 masak not running windows here
17:32 masak and far away from anyone who does
17:32 edr1n you must terminate your line differently
17:32 masak if you say so.
17:32 edr1n use another line termination character
17:33 edr1n \n
17:33 masak hokay.
17:33 edr1n something like this
17:33 masak as I said, if you have a fix, feel free to apply it.
17:33 edr1n where is the code line that does it?
17:33 masak I don't know.
17:33 masak if I did, I could fix it myself.
17:34 edr1n how does it work?
17:34 edr1n the console?
17:34 masak as far as I know, the characters that are appended are \n characters
17:34 masak edr1n: yes, ScriptingConsole
17:36 * edr1n must leave now
17:36 edr1n i will try later
17:36 edr1n cu
17:36 masak see ya

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