Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-06

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All times shown according to UTC.

Time Nick Message
06:08 edrin joined #bioclipse
06:10 edrin zarah: tell olas I did several modification to the xws plugin, pls checkout and try. you will have to setup the JID account in preferences again...
06:10 zarah Consider it noted.
06:48 egonw joined #bioclipse
06:54 edrin hi egonw
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07:03 egonw moin
07:03 zarah hi egonw
07:05 egonw ha zarah 307.4.5
07:46 edrin egonw: did you notice the cool xws4j plugin for bc2?
07:47 egonw I saw the commits
07:47 egonw you got a new PDF?
07:48 egonw or does it work the same way?
07:48 edrin no, pdf not adapted
07:48 edrin yet
07:50 edrin egonw: but in principle its the same...
07:51 edrin egonw: if you have the plugin installed... it is very easy to use it in the javascript console :)
07:51 edrin in the jsconsole just do
07:51 egonw no, don't have it yet
07:51 edrin xws.connect()
07:52 egonw I start this week with converting BC2 to the new CDK trunk eclipse plugins...
07:52 edrin x = xws.getXmppItem("jabber.org","")
07:52 egonw and have not updated my BC2 checkout completely yet
07:52 edrin x = x.discoverSync(30000)
07:52 edrin x.getItems()
07:52 edrin x.getFunctions()
07:54 edrin if the variable x = xws.getXmppItem("xws.ayena.de","")  and the item was discovered then the x.getFunctions() would return all the functions of the component
07:54 edrin and you could create a function...
07:54 edrin f = x.getFunction("delayedTestFunction");
07:55 edrin and invoke it (with null input): r = f.invokeSync(null, 20000)
07:55 edrin 20000 and 3000 are just timeout in ms
07:56 olas joined #bioclipse
07:57 olas moin
07:57 zarah hi olas
07:57 zarah olas: You have new messages. Write '@messages' to read them.
07:57 olas @msg
07:57 zarah olas: 1 h 47 m 23 s ago, edrin said I did several modification to the xws plugin, pls checkout and try. you will have to setup the JID account in preferences again...
07:59 edrin hi olas
07:59 edrin olas: I think it should work now without bug
07:59 edrin thread access problem
08:00 edrin and
08:00 edrin the xws manager now reflects the important functions of the default client itself
08:01 edrin olas: try this
08:01 edrin xws.connect()
08:01 edrin x = xws.getXmppItem("xws.ayena.de","")
08:01 edrin x = x.discoverSync(30000)
08:02 edrin x.getFunctions() // returns the functions of this service
08:02 edrin f = x.getFunction("delayedTestFunction")
08:02 edrin r = f.invokeSync(null, 30000)
08:18 olas edrin: nice
08:18 olas will try in 10 mins
08:32 * olas and egon are having a meeting about bioclipse/cdk planning
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11:37 olas left #bioclipse
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11:37 olas hi
11:37 zarah hi olas
11:38 olas zarah: any messages?
11:38 zarah olas: eh... wha'?
11:38 olas zarah: DO I HAVE messages
11:38 zarah olas: excuse me?
11:38 olas zarah: tell me
11:38 zarah olas: You have no new messages.
11:38 olas help
11:38 olas @help
11:38 zarah olas: avaliable commands are boo botsnack clear-messages google help hi karma messages plan restart seen slap start stop tell thanks unplan
11:39 olas zarah: unplan jonalv
11:39 zarah olas: You don't have a task named 'jonalv'.
11:39 olas zarah: stop jonalv
11:39 zarah olas: There's nothing to stop.
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12:00 egonw grpmh....
12:00 egonw git-svn is taking ages again.... :(
12:04 jonalv hi zarah
12:07 jonalv joined #bioclipse
12:09 jonalv hi
12:09 zarah hi jonalv
12:25 olas edrin: around?
12:25 gilleain joined #bioclipse
12:25 olas what is the status of xws4j now in bc2?
12:26 olas looking at it now :-)
12:33 olas edrin: nice, you've solved the threading problem
12:33 olas will try to use thye mocked processstatus now
12:41 olas @tell edrin I need to be able to getStatus() and getStatusMessage, getOutputIOData and alike in the IProcessStatus interface
12:41 zarah Consider it noted.
12:41 Usiu joined #bioclipse
12:41 Usiu Hi
12:41 Usiu Any bioinformatics here ?
12:41 gilleain Hello.
12:42 Usiu I would like to know where to get epsilon value for a protein that I am puryfing
12:42 olas depends
12:42 egonw Usiu: what kind of bioinformatics?
12:42 Usiu from lamber beer law
12:42 Usiu I cant find it in databases
12:42 gilleain Oh.
12:42 olas no idea
12:42 gilleain this isn't really the right channel for this question, I feel.
12:42 olas ask on #bioinformatics
12:42 Usiu I asked
12:42 Usiu but no one is there
12:42 egonw gilleain: well... it's information...
12:43 egonw isn't that what bioinfromatics is about?
12:43 olas write to their ML
12:43 egonw Usiu: I guess you'll have to make a standard :)
12:44 gilleain It is information, that is true. I sit corrected :)
12:44 olas Usiu: you at Umeå Univ, Swe?
12:44 gilleain Also, did you mean the "Beer-Lambert" law?
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12:51 Usiu egonw: Ok I found extinction coefficient calculator, but I am not sure if its correct for native protein
12:51 egonw he, where did everyone go??
12:51 egonw and why am I not using the same node as Ola???
12:51 egonw maybe my laptop is still stick in CUBIC settings :)
12:52 egonw stick -> stuck
12:54 gilleain As far as I can tell, loads of people got disconnected at once.
12:54 egonw no clue, sorry
12:54 olas egonw: I see you
12:54 egonw I'm a chemist, not a biologist
12:54 egonw olas: I just experienced a (IRC) network split
12:54 olas egonw: are you feeling ok?
12:54 olas or did you get a split personality?
12:54 egonw :)
12:54 egonw gilleain: no, it;s not that
12:55 * gilleain denies all knowledge of any degree in biochemistry or anything.
12:55 * olas too
12:55 egonw gilleain: links between nodes on the irc.freenode.net network got lost
12:55 olas egonw: did you lose part of your personality?
12:55 egonw at least between the DE and SE nodes :)
12:55 olas :-)
12:55 egonw I got personality??
12:55 olas you had
12:55 olas (some)
12:56 olas donät worry, it's gone now
12:57 gilleain oh. I don't know how all this irc stuff works; I just type the words into the box.
12:59 olas left #bioclipse
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13:00 olas edrin: about results from a XWS, they must be DOM elements?
13:00 olas I guess that's ok
13:00 olas just need to adapt :-)
13:00 edrin hi olas, sorry, very occupied today...
13:00 zarah edrin: You have new messages. Write '@messages' to read them.
13:00 olas as you said, an XML binding framework fits in nicely here
13:00 edrin i think it is best to have them dom Elements, is this not good?
13:00 olas edrin: no worries
13:01 olas regular Java classes would be easiest (like SOAP) but I guess that's missing the point, right?
13:02 jonalv joined #bioclipse
13:02 jonalv hi again
13:04 edrin back in a few minutes
13:06 edrin olas: i would like java classes, too. why missing point?
13:06 edrin olas: but indeed this is difficult
13:06 edrin i tried emf, but i could not understand its code nor the documentation
13:06 edrin anyway.
13:07 olas edrin: me and egonw will look at it
13:07 edrin in asy way i would prefere a dom Element input/output 2 object factory...
13:07 olas right
13:08 edrin like the IoDataFactory thing in the xep
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13:08 olas will talk to egonw about this, will get back to you later
13:11 olas egonw: coffee
13:13 egonw almost done
13:13 edrin olas: for the scripting console (creating an object at runtime) i would like something like this:
13:13 edrin // Discover the input and output XML Schemata - required only once!
13:13 edrin schemata = function.getIoSchemata();
13:13 edrin
13:13 edrin // Dynamically marshal an API for the input and output - required only once!
13:13 edrin inputOutputFactory = new IoFactory( schemata );
13:13 edrin
13:14 edrin // Create and set the input
13:14 edrin input1 = inputOutputFactory.createInputObject();
13:14 edrin input1.setFileName("doc-ID-011021");
13:14 edrin taken from the xep (Example 1)
13:15 edrin of course the factory should create a call in .jar if you discover a function with yet to be written xws discovery browser gui.
13:15 edrin emf docu is not very good
13:17 olas right
13:19 * jonalv has a bunch of plugin in his Bioclipse 2 workspace that doesn't compile again...
13:20 * jonalv likes compiling plugins
13:20 gilleain I too like plugins that compile.
13:21 jonalv shk3: In the webservices plugin WebServicesManager row 9: The import uk.ac.ebi.www.ws.services.urn.Dbf​etch.DbfetchServiceServiceLocator cannot be resolved
13:21 gilleain I think he's gone for snacks.
13:22 jonalv oh gilleain perhaps you know something about it? :)
13:22 edrin jonalv: i noticed the web service plugin to be corrupt
13:22 gilleain Not me.
13:22 gilleain I haven't tried that plugin yes.
13:22 jonalv gilleain: nmrshiftdb then perhaps?
13:23 gilleain ah, really?
13:23 gilleain hmmm...
13:23 jonalv cdk10.jchempaint also has compile error on my system...
13:25 gilleain when did you last update cdk10.jcp?
13:25 edrin it is corrupt, most likely because they changed the service again on server side ...
13:26 jonalv gilleain: a couple of minutes ago, less than an hour...
13:27 gilleain huh. my cdk10.jcp is at revision 7233 and it's fine.
13:27 gilleain also nmrshiftdb (just checked out).
13:28 masak joined #bioclipse
13:28 masak hi
13:28 zarah hi masak
13:28 masak hi zarah
13:28 gilleain maybe they both rely on some plugin which had a class added?
13:34 shk3 the class not found should be in the plugin itself
13:37 jonalv hm a bit fewer plugins not compiling now
13:37 jonalv only jchempaint actually
13:38 gilleain hmm. what does that one say?
13:38 masak jonalv++ # testing plugins
13:38 gilleain (non working plugins)--
13:38 gilleain :)
13:38 jonalv in net.bioclipse.ck10.jchempaint.action.CleanUpAction row 138
13:39 jonalv The constructor CleanUpEdit(HashMap) is undefined
13:40 jonalv and in FlipAction row 106 same package: The constructor FlipEdit(HashMap) is undefined
13:41 shk3 sorry
13:41 shk3 my fault
13:41 shk3 I was working on the 1.0 branch
13:42 shk3 but I thought bioclipse has an independent copy of the source code?
13:42 jonalv for cdk?
13:42 jonalv no...
13:42 gilleain Some kind of svn:external thing?
13:42 jonalv yup
13:44 shk3 commited a fix
13:44 * jonalv is updating...
13:44 CIA-30 bioclipse: shk3 * r7234 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jche​mpaint/src/net/bioclipse/cdk10/jchempaint/action/ (CleanupAction.java FlipAction.java): changes needes for changes in cdk 1.0
13:54 jonalv now everything compiles for me. yey shk3++ :)
13:54 jonalv uhm or hang on
13:56 * gilleain finds something to hang on to...
14:07 * masak hangs onto the desk
14:07 jonalv uhm guys you are in the UK right?
14:08 jonalv I just got a hung up phone call from +44 and I think that's UK. Do you know some cool search site where I can tap in the number and find out who called me? :)
14:13 egonw google?
14:13 zarah egonw: No hits.
14:13 egonw google cdk
14:13 zarah egonw: http://cdk.sourceforge.net/
14:13 egonw ha!
14:13 egonw zarah: you're brilliant!
14:13 zarah egonw: I'm just a bot, you expect me to understand that?
14:14 egonw ha, modesty :)
14:14 jonalv zarah: you are a brilliant girl
14:14 zarah jonalv: are you talking to *me*?
14:14 egonw google bioclipse
14:14 zarah egonw: http://www.bioclipse.net/
14:14 jonalv zarah: you are a clever girl
14:14 zarah jonalv: please rephrase or stop trying to be witty :)
14:14 egonw phew :)
14:15 olas zarah: smart girl
14:15 zarah olas: eh... wha'?
14:15 olas zarah: just kidding, you are the STUPID one
14:15 zarah olas: no, YOU'RE the STUPID one!
14:15 jonalv zarah: you are a smart girl
14:15 zarah jonalv: Isn't it time you married me?
14:15 jonalv ah I found it :)
14:16 olas zarah: marry jonalv
14:16 zarah olas: I'm just a bot, you expect me to understand that?
14:16 jonalv zarah: you are a smart girl
14:16 zarah jonalv: But we _can't_ go on meeting like this!
14:17 jonalv tortoiseSVN--
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14:20 jonalv zarah: google bioclipse brunn
14:20 zarah jonalv: http://wiki.bioclipse.net/i​ndex.php%3Ftitle%3DProjects
14:21 jonalv zarah: google brunn sourceforge
14:21 zarah jonalv: https://sourceforge.net/projects/brunn
14:21 jonalv zarah++ //handy :)
14:27 CIA-30 bioclipse: carl_masak * r7235 /bot/trunk/zarah.pl: [zarah] now consideres "yup" and "nope" synonyms of "yes" and "no"
14:37 CIA-30 bioclipse: carl_masak * r7236 /bot/trunk/zarah.pl: [zarah] now creates an empty plan immediately for anyone who says @plan
14:38 zarah joined #bioclipse
14:38 egonw @plan ?
14:38 zarah egonw: syntax: @plan <task name> <number>h
14:38 masak :)
14:38 masak egonw: it's a project time estimation system I'm working on
14:38 egonw @plan to go home for 16h ?
14:38 zarah egonw: Syntax: @plan <task name> <number>h
14:38 egonw @plan to go home for 16h
14:38 zarah egonw: Syntax: @plan <task name> <number>h
14:39 masak egonw: one-word tasks only
14:39 egonw @plan to-go-home-for 16h
14:39 zarah egonw: Planned task 'to-go-home-for' for 16 h.
14:39 masak now type @plan
14:39 egonw @plan
14:39 zarah egonw: to-go-home-for: 16 h planned
14:39 egonw @plan jonalv
14:39 zarah egonw: syntax: @plan <task name> <number>h
14:39 egonw @help
14:39 zarah egonw: avaliable commands are boo botsnack clear-messages google help hi karma messages plan restart seen slap start stop tell thanks unplan
14:39 * jonalv feels planned
14:40 egonw @unplan to-go-home-for
14:40 zarah egonw: Ok, task 'to-go-home-for' removed.
14:40 masak egonw: plans are tied to single persons. one cannot peek at someone else's plan
14:40 masak maybe I'll add that, I dunno
14:40 * egonw uses his own private tool instead: http://github.com/egonw/gtd/tree/master
14:40 masak wooh, nice
14:40 * masak likes GTD
14:41 masak and git
14:41 egonw yeah, accidental name mix up
14:41 egonw it's not supposed to be a ful GTD specific tool...
14:41 egonw though much inspired by it
14:41 egonw the official name is GitToDo
14:41 egonw working title
14:41 masak egonw: but the @plan feature has a slightly different goal than GTD. this is for estimating launch dates.
14:41 egonw will likely use an animal name in the future or so
14:42 masak egonw: Squirrel!
14:42 masak egonw: Emu!
14:42 egonw I plans things like gtd-publish-plan-on-web
14:42 masak egonw: Lichen!
14:42 egonw he... you have to call me names !
14:42 egonw ;)
14:42 masak :)
14:43 gilleain naming tools is very important.
14:43 gilleain "Blast" got it right.
14:43 edrin olas, egonw: you came up with an idea !?
14:43 zarah edrin: You have new messages. Write '@messages' to read them.
14:45 masak ah, @plan is person-tied, just like @messages. that's a good comparison.
14:45 masak egonw: and the idea is that it'll be possible to statistically assess a person's ability to estimate project time
14:46 masak or rather, the average quotient between planned time and actual time :)
14:46 egonw ah, that's useful...
14:46 masak http://www.joelonsoftware.​com/items/2007/10/26.html
14:46 zarah masak's link is also http://tinyurl.com/2hfouh
14:47 egonw then zarah can automatically apply that ratio when the next plan time is given :)
14:48 masak egonw: even better, read the article :)
14:53 zarah joined #bioclipse
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14:58 jonalv charlgren: http://www.vogella.de/articl​es/EclipseBIRT/article.html
14:58 zarah jonalv's link is also http://tinyurl.com/3qcnxp
15:00 charlgren thanks for the link
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15:15 olas edrin: no
15:15 olas looking into EMF and DOM
15:28 * egonw is going home now
15:29 * egonw got fresh check outs of Bioclipse2 (git and svn) so promises first UU-based BC2 commits on Wednesday latest
15:29 egonw hopefully with a bit of IO-DATA too...
15:39 masak egonw++
15:47 edrin egonw++
15:47 zarah edrin: You have new messages. Write '@messages' to read them.
15:47 edrin @messages
15:47 zarah edrin: 3 h 6 m 20 s ago, olas said I need to be able to getStatus() and getStatusMessage, getOutputIOData and alike in the IProcessStatus interface
15:48 edrin zarah: consider it noted.
15:48 zarah edrin: are you talking to *me*?
15:48 edrin olas: these functions are not intended to be used by the function
15:48 edrin do you really need them?
15:50 CIA-30 bioclipse: carl_masak * r7237 /bot/trunk/zarah.pl: [zarah] replied "hokay" to "consider it noted"
15:50 masak hm. s/replied/replies/
16:01 edrin masak: did my last mail help you with this \n bug ? where i mention that the string given to ScriptingConsoleView.printMessage() are still formated correct and the error is somewhere in processing behind?
16:02 masak edrin: it helped me in the sense that I learned what you said. I do think it's mysterious, though.
16:03 edrin masak: maybe the replacement of \n leads to the corruption because there is now no \n behind "\r\n" or similar control characters (control characters are up to several bytes in unicode) ...
16:04 masak unicode? why would that come into the picture in the Windows case?
16:20 edrin masak: you never know... that's the problem
16:20 edrin java String may contain *any* encoding...
16:20 masak that's not specific to Java...
16:27 gilleain Well, at some point the strings are getting passed to the gui, which is partly native in eclipse - am i right?
16:28 gilleain oh, he's gone. never mind...
16:36 gilleain left #bioclipse
16:38 CIA-30 bioclipse: shk3 * r7239 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/util/LogUtils.java: added comment
16:51 CIA-30 bioclipse: shk3 * r7240 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: corrected icon path
18:25 edrin left #bioclipse
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