Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-01

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All times shown according to UTC.

Time Nick Message
05:26 Gpox joined #bioclipse
07:15 olas joined #bioclipse
07:17 olas @tell egonw your 5 mins are up, coffee!!
07:17 zarah Consider it noted.
07:18 olas @msg
07:18 zarah olas: You have no new messages.
07:18 egonw joined #bioclipse
07:18 egonw moin
07:18 zarah hi egonw
07:18 zarah egonw: You have new messages. Write '@messages' to read them.
07:19 * egonw hopes it says: 'coffee is ready'
07:19 egonw @messages
07:19 zarah egonw: olas said your 5 mins are up, coffee!!
07:19 egonw yes!
07:32 jonalv joined #bioclipse
07:33 jonalv hi
07:33 zarah hi jonalv
07:33 zarah jonalv: You have new messages. Write '@messages' to read them.
07:34 jonalv zarah: tell me
07:34 zarah jonalv: masak said http://nice.sourceforge.net/visitor.html -- jag brukar glömma bort hur Visitor fungerar mellan varven, men den här sidan både förklarade det bra och förklarade hur man kan göra det bättre i ett mer flexibelt språk än Java
07:39 jonalv Gpox: It seems your commit to r7118 did strange things with net.bioclipse-feature for me. Am I the only onw having problems?
07:48 olas jonalv: if you are an onw, then you are probably the only onw I know, so... probably yes.
07:49 jonalv could you check?
07:49 olas what is the problem?
07:49 olas I have problems currently
07:50 jonalv net.bioclipse_feature lacks a projct file I think
07:50 olas so will take a while to settle those
07:50 olas Gpox: can you look at it?
07:50 jonalv but I wanted a second opinion...
07:51 jonalv ...it might  be something else...
07:51 rojasm joined #bioclipse
07:53 egonw hi rojasm!
07:55 rojasm hi egonw
08:01 Gpox jonalv: the plugin and the directory had different names if you delete it and import it again it should work
08:02 jonalv Gpox: oki, thanks
08:04 egonw Gpox: need to do some admin stuff for my new position...
08:04 egonw Gpox: let's reschedule for 11:00? is that OK?
08:05 Gpox sure
08:49 shk3 joined #bioclipse
08:56 egonw shk3: hi
09:10 olas egonw: you joining for lunch at Sven Dufva?
09:10 egonw olas: no, got sandwitches
09:10 olas we leave 11.45
09:10 olas ok
09:10 egonw and lots of thing to do...
09:11 egonw when did I join Bioclipse development?
09:11 egonw mmm... browsing SF archives...
09:13 shk3 hi egonw
09:14 shk3 you got sandwitches?
09:14 shk3 is that a witch from the sand?
09:14 jonalv shk3: oh be nice >)
09:14 egonw :)
09:15 egonw fair... you live in the UK now... you may complain about such things now :)
09:16 egonw though: http://en.wikipedia.org/wiki/Sandwitch
09:16 egonw also many hits on Google
09:17 egonw I am amongst a large group if bad writers :)
09:17 egonw olas: ping
09:17 egonw olas: when did I join Bioclipse?
09:17 egonw SF does not seem informative regarding this
09:18 egonw I'll say 2005
09:18 egonw SF project was created that year, 10-14
09:18 egonw ah... party in two weeks ! :)
09:22 olas party?
09:22 olas where's the party?
09:22 egonw yeah, third birthday of Bioclipse
09:22 egonw here?
09:22 olas why not?
09:26 jonalv yey party, and in Uppsala too :)
09:26 jonalv egonw++
09:28 shk3 we should have a bioclipse workshop soon and combine this with a party
09:29 olas shk3: that will be in may approx
09:29 olas we can have a party then too
09:36 shk3 yeah, more parties
09:47 malick joined #bioclipse
09:50 edrin joined #bioclipse
09:51 edrin hi
09:51 zarah hi edrin
10:06 gilleain joined #bioclipse
10:08 egonw hi gilleain
10:09 gilleain hi - saw your comment.
10:09 egonw yeah, I'm now reading your blogs about JCP and commenting on it...
10:10 gilleain I guess the problem is that I don't know enough about the Medea plugin yet.
10:10 gilleain What it can do, what it is meant to do, and so on.
10:10 egonw right
10:10 egonw rojasm: might you please send some documentation to gilleain?
10:11 gilleain I mean, I've read through the code - but that's not always the best way to understand things :)
10:36 * gilleain would like to thank google for sending me messages on my gmail account about my own comments on my google blog...
10:50 thomasku joined #bioclipse
11:06 Gpox egonw: I am back from lunch
11:06 egonw ok
11:06 jonalv Gpox: would real life ping olas for me?
11:06 jonalv |would you
11:07 olas jonalv: pong
11:07 jonalv olas: time for skyope call? I will head to CLaes and call you if you have time...
11:08 olas 5 mins
11:09 * jonalv heads over to Clas with his computer then
11:09 jonalv brb
11:10 egonw Gpox: 3 minutes
11:32 Goran joined #bioclipse
11:34 edrin hi olas, available?
11:50 edrin olas, egonw: i sent a mail to you
11:55 egonw Gpox: http://gilleain.blogspot.com/
11:55 egonw edrin: thanx!
11:57 edrin if you have bc1 installed you can immediately play around
12:32 charlgren joined #bioclipse
12:36 gilleain joined #bioclipse
13:06 CIA-30 bioclipse: goglepox * r7128 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Now redraws when the input changes.
13:06 edrin egonw: did you look into the pdf?
13:07 egonw no, later this week
13:07 egonw still so many things to do :(
13:39 jonalv joined #bioclipse
13:40 jonalv charlgren: jdbc:mysql://bob.cpi.medsci.uu.se/brunn
13:40 jonalv hi all
13:40 zarah hi jonalv
14:05 gilleain joined #bioclipse
14:13 Goran left #bioclipse
14:15 CIA-30 bioclipse: shk3 * r7129 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum/src/net/bioclipse/spectrum/ (2 files in 2 dirs): the spectrum editor is now updated if a peak picking is done
14:30 CIA-30 bioclipse: shk3 * r7130 /bioclipse2/trunk/features/net.biocl​ipse.speclipse-feature/feature.xml: this seems to resolve logging problems
14:32 CIA-30 bioclipse: shk3 * r7131 /bioclipse2/trunk/plugins/net.bioclipse.​spectrum/src/net/bioclipse/spectrum/acti​on/contribution/PeakPickingAction.java: the spectrum editor is now updated if a peak picking is done
14:39 egonw edrin: did you send that PDF to ws-xmpp too?
14:52 edrin egonw: not yet
14:56 edrin egonw: it's just a sample at the moment... best would be to write an initial plugin for bc2 that brings xws client lib functionality
14:57 edrin i could port the half finished bc1 xws plugin. this does: 1) offers a button to connect/disconnect the default client to the server 2) offers a page in options to set your xmpp account data for default account 3) offers a way to get the default client from other plugins...
14:58 egonw edrin: it would be good to show that io-data is not dead... but alive and kciking
14:58 edrin and then port the scripts to bc2
14:58 edrin yes
14:58 egonw edrin: yes, that would be great anyway
14:58 egonw I'll read the PDF tonite, I hope...
14:58 egonw got to go now
14:58 egonw cu later!
15:32 edrin olas ?
15:33 olas hi edrin
15:33 edrin hello
15:33 zarah hi edrin
15:34 olas great docu edrin
15:34 olas zarah: oj shut up
15:34 zarah olas: :)
15:34 edrin did the sample scripts in the pdf explain the stuff well?
15:34 olas have been in meetings all day
15:34 edrin sure
15:34 olas will you be online now?
15:34 olas or leave soon?
15:34 edrin no
15:34 edrin i am available
15:35 olas ok, will read now then and get back to you in 10 mins
15:35 edrin ok
15:35 olas will ping you after reading
15:35 edrin ok
15:36 olas ok
15:36 olas ok
15:36 zarah ok
15:37 olas zarah: dz
15:37 zarah you're welcome, olas :)
15:50 olas edrin: ping
15:50 olas Read the doc, it is VERY good
15:51 olas would love to be able to run it in Bc2 though
15:51 olas I was just wondering how hard it will be to reproduce in java
15:51 olas probably very easy, right?
15:52 olas First: Some comments on the text
15:52 olas 1) The article lacks a title
15:52 olas 2) the following:
15:52 olas Prepare an ISimpleProcessListener – this listener will show the result or errors. The  user does have to take care of remote process deletion as it will be deleted  automatically:
15:53 olas should probably have a NOT included
15:53 olas like
15:53 olas Prepare an ISimpleProcessListener – this listener will show the result or errors. The  user does NOT have to take care of remote process deletion as it will be deleted  automatically:
15:53 edrin it's very easy in yes
15:53 olas 3) What is "delayed" mode?
15:53 olas async?
15:54 olas I'd love to get all the scripts and not having to copy/paste from pdf
15:54 edrin I added "not"
15:55 edrin delayed mode means functions that do not finish immediately
15:55 olas define immediately
15:55 olas async?
15:55 edrin yes
15:55 edrin async
15:56 olas why call the delayed services and not async services?
15:56 olas is there a difference?
15:56 edrin however async can be confusing as i used async in the api, too (for listener based or blocking api calls)
15:56 olas I see
15:56 olas maybe define "delayed" in the text?
15:56 edrin invokeAsync() and invokeSync() for example...
15:56 edrin ok
15:57 olas anyway, that was a small point
15:57 olas I'll try this out today
15:57 edrin :)
15:57 olas and will report any problems
15:57 olas can I connect to your server?
15:57 edrin great
15:57 olas ayena.de?
15:58 olas and invoke the coffee-machine?
15:58 olas or do I need my own service?
15:58 edrin if you run bc1 you should have it showing the bioclipse/eclipse debug info in a console window. the lib will print stuff to it
15:58 olas jup
15:58 olas will probably translate to java
15:58 olas that's easier for me
15:58 edrin the services of ayena.de are not available because i am not at home right now ;)
15:59 olas ok
15:59 olas will use our here then, just need to start it up
15:59 edrin yes, it is very easy to run in java, too.
15:59 olas I'd like to create a simple view that discovers services
15:59 edrin the execution pipe thing is clear to you, right?
15:59 olas we have that for BioMoby
15:59 olas pretty clear
15:59 olas however
16:00 olas I have one request which is important
16:00 olas I'd like to write a junit test for my service
16:00 olas which means I need to call it NOT via network
16:00 edrin olas: yes. that would be great. i tried hard to make the service discovery possible
16:00 olas and I'm stuck at one point
16:00 olas could you help me?
16:01 olas I will send you a mail explaining the problem
16:01 edrin ok, i can try ;)
16:02 edrin best would be if we could run the lib in bc2... then we could invite interested people and give a "tutorial IRC lesson"
16:02 olas yes
16:02 olas I will talk to masak about this
16:03 olas @tell masak Ping me, I want to discuss getting XWS running in javascript in BC2.
16:03 zarah Consider it noted.
16:03 olas brb
16:03 edrin i wanted to port the xws unfinished plugin from bc1. it would 1) export all xws client functionality to rest of bc2 and 2) maintain the setup (in bc options) and connection (connect/disconnect button) of user's default account
16:04 edrin in addition to that it could export the xws functionality not only to other plugins but also to a manager
16:05 edrin like xws4j.getDefaultClient() ...
16:05 olas indeed it should
16:06 olas I want this to be scriptable
16:06 olas so we need convenience calls in the manager
16:06 olas like
16:06 olas xws.discover("my.ws.jid")
16:07 olas xws.run("my.fctn", "my.server", molecule1)
16:07 olas bla bla
16:07 olas something along those lines :-)
16:07 olas (well, maybe not exactly like that but anyway)
16:07 edrin one second
16:07 edrin back in 5 min
16:07 olas will get some food
16:07 olas be back in 10 :-)
16:08 olas will work late tonight so will continue with XWS
16:19 edrin ok, I am back
16:30 edrin olas: new bc2 plugins do just have to be eclipse plugins, right?
16:32 olas yes
16:32 olas that's correct
16:36 edrin ok, how to proceed
16:37 edrin should we first write a "simple" demo service that is offered/used via xws and the client is a plugin for bc 1/2 ?
16:39 olas bc2 imo
16:39 olas yes, sounds good
16:39 olas I have a question
16:39 edrin ok
16:39 edrin ?
16:40 olas In my junit, I need to call the run (ProcessStatus, input)
16:40 olas how can I create a ProcessStatus?
16:40 olas oh
16:40 olas the new file, is it buiöt with java 1.5?
16:40 olas else I cannot use it :-(
16:41 * olas just remembered that it was the problem
16:41 olas else, can you guide me through the process of compiling it myself?
16:41 edrin ok
16:41 olas is it 1.5?
16:42 edrin the source should work in 1.5 at least i used the default settings in eclipse
16:42 olas what should I check out?
16:42 edrin just xws4j
16:42 olas doing that now
16:43 olas does it include jso-jar?
16:43 edrin no
16:43 olas ok
16:43 edrin at least it's not in svn
16:43 olas ok
16:44 edrin but it is in my local project in /jars
16:44 olas I will start plugin net.bioclipse.xws in BC2 if that's OK with you
16:44 olas need to test and might as well set it up anyway
16:44 olas with a manager etc
16:45 olas or do you want to do it?
16:45 edrin i just strated a plugin ;)
16:45 edrin but you can add a manager later
16:45 olas where?
16:46 edrin i am currently just clicking together the bc2 plugin in the wizard
16:46 olas great
16:46 olas commit to bioclipse2/trunk/plugins as net.bioclipse.xws
16:47 edrin then i will add functionality to setup a "general default" xmpp account and buttons to connect
16:47 edrin yes
16:47 olas excellent
16:48 edrin the manager should maybe just return the "default client"
16:48 olas ok
16:49 edrin currently looking at class ProcessManager (of component) it is a very complex class at it offers the "interface" to everything...
16:49 edrin it is not very easy to just spawn an instance of it
16:49 olas edrin: String.isEmpty() is java 1.6 :-(
16:49 edrin oh?
16:49 edrin didn't know
16:50 olas me neither
16:50 olas but now I do
16:50 olas Should I update this?
16:50 edrin where is it?
16:50 olas many places...
16:50 edrin how many errors?
16:50 olas just looking into xws4j
16:51 olas 11 it seems
16:51 olas fixing
16:51 edrin i can do this later tonight
16:51 olas need it now in order to test
16:51 olas so fixing
16:52 edrin is it only isEmpty() =
16:52 olas no idea
16:52 olas starting there
16:54 edrin olas: when setting my projects compiler compliance level to 5.0 it compiles without problems
16:55 olas strange
16:55 olas it is definitely a 1.6 feature
16:57 olas http://java.sun.com/javase/6/d​ocs/api/java/lang/String.html
16:57 olas http://java.sun.com/j2se/1.5.0/​docs/api/java/lang/String.html
16:57 edrin yes
16:57 edrin are there other problems, too?
16:57 edrin bc2 is 1.5 or 1.6 ?
16:58 olas 1.5
16:58 olas all bc is 1.5
16:58 olas and no end in sight :-(
16:58 edrin ok...
17:00 olas ok, please review and test my commit, r7132
17:00 olas our CIA bot does not seem to be working
17:00 edrin this I cannot because I am not home
17:00 olas anyways, after 11 isEmpty() it compiles fine
17:00 edrin can you tell me the files you changed?
17:00 edrin ah
17:01 edrin isEmpty() was the only problem?
17:01 olas yup
17:01 edrin you just replaced it with (string == "") ?
17:01 olas yes
17:02 olas http://paste2.org/p/80817
17:02 edrin the it should be fine
17:02 edrin *then
17:04 olas ok, built and exported jar
17:05 edrin fine :)
17:05 edrin did you set default class to Component.java ? it's not a must be but makes things more easy i guess
17:06 olas yes
17:06 olas hmm
17:09 edrin ok, i will now leave and do some sports...
17:09 edrin what means hmm ?
17:09 olas help
17:09 olas I need help setting up a Process
17:09 olas and a ProcessStatus
17:10 olas so I can call an IFunction from a JUnit test
17:10 olas how do I do that?
17:11 edrin hm... :)
17:11 olas you get my problem?
17:11 edrin yes
17:13 olas any solution at hand?
17:14 edrin that's difficult. you would need a "simulated" ProcessStatus
17:14 edrin because the ProcessStatus usually passed to this function contains various links to objects ...
17:15 edrin that only exist if the whole component thing is running
17:18 edrin that would require some work if fear
17:19 olas it is important to be able to write tests for services
17:19 olas so I am afraid I must request that quite strongly
17:19 edrin i will think about how to solve this problems
17:19 olas great
17:19 edrin but I must leave now, cu tonight or later
17:19 edrin left #bioclipse
17:39 CIA-30 bioclipse: ospjuth * r7133 /xws/trunk/xws4j/ (8 files in 7 dirs): Updated =="" to "".equals(String) according to masak++ suggestion to get rid of checking for null. Also added jso-full.jar for convenience.
19:05 ChanServ joined #bioclipse
20:22 edrin joined #bioclipse
20:49 CIA-30 bioclipse: edrin_t * r7134 /xws/trunk/xws4j/src/net/bioclipse/xws/cli​ent/listeners/SimpleProcessListener.java:
20:53 CIA-30 bioclipse: edrin_t * r7135 /xws/trunk/xws4j/jso-full.jar: please do not store it here
20:56 CIA-30 bioclipse: edrin_t * r7136 /xws/trunk/xws4j/ (7 files in 4 dirs):

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