Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-14

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All times shown according to UTC.

Time Nick Message
05:26 Gpox joined #bioclipse
06:11 malick joined #bioclipse
07:14 olas joined #bioclipse
07:15 olas hi
07:15 zarah hi olas
07:15 zarah olas: You have new messages. Write '@messages' to read them.
07:15 olas @msg
07:15 zarah olas: edrin said I will be available tomorrow but I can't tell you a certain time, i am sorry. I am currently very occupied with diagnostics stuff. But I started working on the source again and merged client and component in one lib to decrease redundancy of source
07:46 CIA-49 bioclipse: goglepox * r6587 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (17 files in 11 dirs): New JChemPaint editor with SWT rendering a work in progress
07:50 jonalv joined #bioclipse
07:53 jonalv moin
07:53 zarah hi jonalv
07:57 CIA-49 bioclipse: jonalv * r6588 /bioclipse2/trunk/plugins/net.bioclipse.ui/s​rc/net/bioclipse/ui/jobs/BioclipseJob.java: Make the try go over all the stuff since exception can be thrown at more places...
07:57 CIA-49 bioclipse: goglepox * r6589 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (30 files in 7 dirs): and the files
08:08 CIA-49 bioclipse: goglepox * r6590 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk.business/plugin.xml: Added extension for CDKAdapterFactory
08:39 thomas_ku joined #bioclipse
09:08 CIA-49 bioclipse: goglepox * r6591 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/src/net/bioclipse/cdk​/jchempaint/widgets/SWTRenderer.java: commented out System.out debug messages
09:41 CIA-49 bioclipse: jonalv * r6592 /bioclipse2/trunk/plugins/ (10 files in 6 dirs):
09:41 CIA-49 bioclipse: [core]
09:41 CIA-49 bioclipse: Created ICachedModel an interface for cached objects which must be possible to listen for changes on.
09:41 CIA-49 bioclipse: [core.tests]
09:41 CIA-49 bioclipse: added log4j.properties to get logging when running tests
10:56 maclean joined #bioclipse
11:38 olas hi maclean
11:38 olas maclean: saw your commit about image export from jmol
11:39 olas will you continue or shall I?
12:05 maclean joined #bioclipse
12:11 maclean Hi olas (I forgot to set away for lunch again, sorry)
12:11 maclean I can continue with it - it needs some polish.
12:12 maclean I'm also working on the equivalent JCP export.
12:21 malick joined #bioclipse
12:27 edrin joined #bioclipse
12:31 shk3 joined #bioclipse
12:41 olas maclean: nice
12:42 olas hi edrin
12:42 olas hi shk3
12:42 maclean The only problem is getting hold of the molecule that's being displayed (or, the JCP editor).
12:43 olas hmm
12:43 maclean It was easy with JMol.
12:43 olas getActiveEditor()
12:43 olas ?
12:43 maclean Oh.
12:43 olas mom
12:44 maclean I have lots to learn about these frameworks...
12:44 olas right
12:45 olas they are quite big
12:45 olas PlatformUI.getWorkbench().getActiveWorkbenc​hWindow().getActivePage().getActiveEditor()
12:45 olas that's the generic way to get the active editor
12:45 maclean Chain-tastic! thanks.
12:45 olas :-)
13:08 edrin ola?
13:09 olas yes
13:09 edrin do you have a minute?
13:09 olas sure!
13:09 edrin i will send you the component stuff now
13:09 olas great!
13:09 CIA-49 bioclipse: jonalv * r6593 /bioclipse2/trunk/plugins/ (8 files in 4 dirs): Reverted my last commit. Will not introduce changelistener on bioobjects. We seem to be able to make it anyway
13:10 edrin olas: do you have PSI installed?
13:10 olas yes
13:11 edrin ok
13:12 olas can you talk me through the setup of the jars and how to test the coffee machine sample?
13:12 olas I have ejabberd installed
13:12 olas psi running and connected to the server
13:12 jonalv http://www.comics.com//comics/getfu​zzy/archive/getfuzzy-20080814.html
13:12 zarah jonalv's link is also http://tinyurl.com/6grroz
13:17 olas edrin: waiting for the jar...
13:17 edrin email sent...
13:17 edrin i also sent a mail with a test account stuff... however it appears the jabber test server seems to be down...
13:17 edrin ayena.de
13:18 olas can you talk me through installing the jars?
13:18 edrin we can try your ejabberd directly
13:18 edrin yes
13:18 edrin olas: you will have to download the jso jar
13:19 olas link on wiki?
13:19 edrin https://jso.dev.java.net/
13:19 edrin yes
13:19 edrin https://jso.dev.java.net/bin/jso-full.jar
13:19 edrin back in a minute
13:20 olas ok
13:23 olas I have got your email
13:33 edrin olas: back#
14:32 CIA-49 bioclipse: shk3 * r6594 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (3 files in 3 dirs): solves a problem with adding peaks, new jcamp parser (fixed a bug in there)
14:45 CIA-49 bioclipse: shk3 * r6595 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (2 files in 2 dirs): hm, thought my fix would work without this change, but doesn't look like
14:58 edrin olas: I am back
14:58 edrin how did you solve the classpath issue
14:58 edrin ?
15:00 olas java -classpath "jso-full.jar:xws4j-alpha1_ola.jar" net.bioclipse.xws.component.Component new-cfg xws-component.cfg
15:00 olas (for the log :-))
15:00 edrin heh :=
15:00 edrin :)
15:00 edrin olas: maybe you could add this line to the xws wiki page#
15:01 edrin with the todo instructions
15:11 olas sure
15:11 olas will do that after this
15:16 olas edrin: we'll have to continue here
15:17 olas please explain what I need to edit
15:18 edrin i am back
15:18 edrin olas:
15:18 olas COMPONENT_JID should be ?
15:18 olas ok
15:18 olas please explain here
15:18 olas yes
15:19 olas yes
15:19 olas that's my account
15:19 olas what do you mean?
15:19 olas the jabber server and my component are on the same machine
15:19 olas isnät that as it should be?
15:19 olas is that wrong?
15:20 olas or good?
15:20 olas edrin: please explain
15:20 olas you are taking this in so small parts
15:20 edrin ah
15:20 olas it takes ages
15:20 edrin :)
15:20 edrin ok
15:20 olas what did you not get before?
15:20 edrin well. you will have to change ejabberd cfg then again
15:21 olas to what?
15:21 edrin ws1.bmc.uu.se must become xws.ws1.bmc.uu.se
15:21 olas ok
15:21 olas is that hardcoded?
15:21 edrin no
15:21 olas or can I use what I like?
15:21 edrin you can use what you like
15:22 olas ok
15:22 olas will do this
15:22 olas what is TEST_FUNCTION
15:22 olas and ADMINS?
15:23 olas and can I use coffee-machine-sample as FUNCTION_JARS?
15:23 olas edrin?
15:23 edrin yes
15:23 edrin yes
15:23 olas how do I test it with psi?
15:23 olas service discovery?
15:23 CIA-49 bioclipse: jonalv * r6596 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/domain/BioObject.java: Made resource in bioobject protected. Extending classes might want to set it for example...
15:24 edrin TEST_FUNCTION is optional. it is a hardcoded set of 4 functions to test async and sync function xep protocol stuff
15:24 olas olas (5:26:11 PM): what is TEST_FUNCTION olas (5:26:15 PM): and ADMINS?
15:24 edrin just let it be true for now
15:24 olas ADMINS is not a boolean
15:25 edrin ADMINS has no functionality yet. it will probably be used to identify users that may administrate the service via jabber
15:25 edrin you may set your own JID for ADMINS now
15:26 olas ok
15:26 edrin FUNCTION_JARS: this is the coffee-machine-example
15:26 edrin and
15:26 edrin the COMPONENT_JID is xws.ws1.bmc.uu.se or whatever u set in ejabberd config
15:26 edrin also set the correct port
15:27 edrin and secret of course
15:27 edrin PORT and KEY
15:28 edrin does it work?
15:29 olas I need to run the jar first
15:29 olas how?
15:29 olas oh
15:29 edrin from my edrin@jabber.org account i cannot discover the ws1.bmc.uu.se server... why?
15:30 olas try again
15:30 olas restarted it
15:30 edrin still not working. maybe add my JID edrin@jabber.org to your roster
15:31 olas added
15:31 olas theres a questionmark on you
15:31 edrin to starte the component... just add the parameters "run configfile.cfg"  instead of "new-cfg configfile"
15:31 olas will do
15:31 olas Remote server not found.
15:32 olas Remote server not found. A remote server or service specified as part or all of the JID of the intended recipient does not exist.
15:32 olas got that answer
15:32 edrin it seems that your server cannot connect to jabber.org
15:32 olas how resolve that?
15:32 edrin is the s2s component activated?
15:32 olas how can I tell?
15:32 olas cfg file says so
15:33 olas {5269, ejabberd_s2s_in, [    {shaper, s2s_shaper},    {max_stanza_size, 131072}   ]},
15:33 edrin :/
15:33 olas how can I tell if s2s is on?
15:33 edrin from another jabber account i cannot connect to your server, too
15:34 olas so?
15:34 olas how do I fix it?
15:34 edrin i cannot connect to your server directly too
15:34 edrin is your server firewalled?
15:34 olas it should have ports open
15:35 olas but sure there's a fw
15:35 edrin meaning i cannot create a edrin@ws1.bmc.uu.se account
15:35 olas how do I fix it?
15:35 edrin i cant tell you here and now
15:35 edrin i dont know what the problem is
15:36 olas haha
15:36 edrin but as you can connect to the server and i cannot there seems to be something blocking it
15:36 olas I can look up the XMPP service
15:37 edrin fine... but I cannot
15:37 olas brews new coffee
15:37 edrin you most likely can also browse ...
15:37 edrin yes you noticed already
15:37 olas hmm
15:37 olas how do I run it?
15:37 olas console gives me errer 400
15:37 edrin however you cannot execute the functions with PSI directly by db click... this is because PSI only supports DATA FORMS
15:38 olas ok
15:38 edrin in your PSI roster:
15:38 edrin rightclick your account and click XML console
15:38 edrin Enable the console
15:39 olas done
15:39 olas I get errors
15:40 edrin errors ?
15:40 edrin what errors
15:40 olas http://paste2.org/p/58821
15:41 edrin yes, sure... that's because you db clicked the service in PSI Disco browser and the component reports "I do not understand your command (DATA FORMS)"
15:41 edrin try this:
15:41 edrin on the different test functions
15:42 edrin <iq type='set'
15:42 edrin from='user@university.example.org'
15:42 edrin to='service.university.example.org'
15:42 edrin id='iq_127'>
15:42 edrin <command xmlns='http://jabber.org/protocol/commands'
15:42 zarah edrin's link is also http://tinyurl.com/6bmxzt
15:42 edrin node='get_proteinsequence'
15:42 edrin action='execute'>
15:42 edrin <iodata xmlns='urn:xmpp:tmp:io-data' type='input'>
15:42 edrin <in>
15:42 edrin </in>
15:42 edrin </iodata>
15:42 edrin </command>
15:42 edrin </iq>
15:42 olas please pastebin
15:42 edrin olas: what is the component's JID now?
15:43 olas and explain how to use the paste
15:43 olas xws.ws1.bmc.uu.se
15:43 edrin ok, second, have to adapt the stanza
15:44 edrin in the meanwhile maybe goto http://www.xmpp.org/extensions/xep-0244.html and take a look at section 4.3 example 6
15:44 zarah edrin's link is also http://tinyurl.com/69rrkt
15:44 olas must run off now unfortunately
15:44 olas please send me an email and explain in more detail
15:45 olas I will test and update the wiki
15:45 olas have to go :-(
15:45 edrin wait
15:45 olas 1 min max
15:45 edrin just this one command :)
15:45 olas will miss train
15:45 edrin http://paste2.org/p/58825
15:45 edrin go there
15:46 olas how use it?
15:46 edrin copy content. replace the get_proteinsequence with the function_name of your choice
15:46 olas how use it?
15:46 edrin and the goto PSI XMPP console click "XML Input" and paste there
15:47 edrin function name is case sesitive!!
15:47 edrin for example testFunction
15:48 olas WORKS
15:48 olas gotta run now
15:48 olas thx edrin
15:48 olas byew
15:48 olas left #bioclipse
15:48 edrin :) no prob
15:54 shk3 just updated bioclipse
15:54 shk3 in net.bc.cdk10.jchempaint,
15:55 shk3 import sun.text.CompactShortArray.Iterator; isn't found
15:55 shk3 any idea?
16:01 maclean Yes, we discussed this yesterday :)
16:01 maclean Delete it, it's an error.
16:02 maclean (this is why I need to write the irc logfile analysis program I was planning)
16:05 shk3 ah, thanks
16:05 shk3 shouldn't somebody commit this?
16:06 maclean definitely. I keep reverting the file, forgetting about the error! :)
16:07 shk3 i leave the commit to you
16:10 maclean Done.
16:10 CIA-49 bioclipse: gilleain * r6597 /bioclipse2/trunk/plugins/net.bioclipse.cdk1​0.jchempaint/src/net/bioclipse/cdk10/jchempa​int/outline/StructureContentProvider.java: Removed an errant import statement.
16:11 maclean @seen goglepox
16:11 zarah I have not seen goglepox
16:11 maclean oh.
16:12 maclean Well, robot, if you do see goglepox say that the SWTMosueEventRelay class should be renamed.
16:16 maclean Stefan : is your bug referring to the class CmlSpectrumFileDescriber?
16:16 maclean Because, if so, it's not surprising that it doesn't work.
16:18 maclean Oh, right sorry, just re-read the bug report.
16:42 shk3 how can I re-add a deleted folder to svn
16:42 shk3 ?
16:43 maclean revert?
16:43 shk3 but that will revert everything done since then?
16:44 maclean hmm.
16:44 maclean not sure.
16:48 CIA-49 bioclipse: shk3 * r6598 /bioclipse2/trunk/plugins/net.biocl​ipse.data.sampledata/data/spectra/ (15 files): added sample spectra
16:49 edrin left #bioclipse
16:52 CIA-49 bioclipse: shk3 * r6599 /bioclipse2/trunk/plugins/net.bioclip​se.data.sampledata/data/spectra/NIST/ (90 files in 4 dirs): added sample spectra
17:21 malick joined #bioclipse
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19:16 edrin joined #bioclipse
19:16 edrin hi
19:16 zarah hi edrin
19:16 edrin hi egonw
19:16 egonw hi edrin
19:16 zarah egonw: You have new messages. Write '@messages' to read them.
19:16 egonw @msg
19:16 zarah egonw: sneumann_ said that JSF can do REST, as in https://scales.dev.java.net/prettyUrl.html he mentioned that ages ago as JSF drawback ;-)
19:16 zarah egonw: sneumann said sneumann now has the MetHouse Biomart running (again) with not only litlist, but also xcms peaks at http://msbi.ipb-halle.de/MetHouse
19:18 edrin egonw: how are you?
19:18 egonw busy
19:18 egonw too busy
19:18 egonw :(
19:18 edrin hehe
20:19 egonw_ joined #bioclipse

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