Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-09-25

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All times shown according to UTC.

Time Nick Message
05:09 rojasm joined #bioclipse
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07:17 CIA-30 bioclipse: edrin_t * r7087 /xws/trunk/xws4j/src/net/bioclips​e/xws/client/adhoc/Function.java: now ISimpleListener is compatible with js
07:17 CIA-30 bioclipse: edrin_t * r7088 /xws/trunk/xws4j/src/net/bioclips​e/xws/client/adhoc/Process.java: now ISimpleListener is compatible with js
07:18 CIA-30 bioclipse: edrin_t * r7089 /xws/trunk/xws4j/src/net/bioclipse/xws/cli​ent/listeners/ISimpleProcessListener.java: now ISimpleListener is compatible with js
07:19 CIA-30 bioclipse: edrin_t * r7090 /xws/trunk/xws4j/src/net/bioclipse/xws/c​lient/listeners/SimpleProcListener.java: now ISimpleListener is compatible with js
08:34 edrin joined #bioclipse
08:35 edrin hi
08:35 zarah hi edrin
08:49 shk3 joined #bioclipse
08:55 shk3 does anybody know what the figures in this smiles mean:
08:55 shk3 [4C]1CC[19C]CC1
08:55 shk3 should be a simple ring
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10:07 masak joined #bioclipse
10:37 edrin hm
10:37 edrin where are all the Uppsala people?
10:45 shk3 perhaps still at euroqsar?
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14:20 olas joined #bioclipse
14:20 olas hi
14:20 zarah hi olas
14:20 olas @msg
14:20 zarah olas: You have no new messages.
14:21 olas edrin: We are all at EuroQSAR 2008
14:21 olas will be back on monday
14:21 edrin hi olas
14:21 edrin ok
14:21 olas anything I can help with?
14:22 * olas is on a boring lecture
14:22 olas glad we have wireless
14:22 edrin no, not really :)
14:22 olas busy with work?
14:23 olas curing people :-) ?
14:23 edrin somehow...
14:23 edrin no, not curing people
14:23 olas saw some commits on XWS
14:23 edrin i have spare time for research the whole october
14:23 olas what remains for you toi do with the library?
14:23 edrin cam back from a conference yesterday
14:23 olas ah
14:24 olas any new features I should be aware of? :-)
14:24 edrin library is ready for usage... maybe we should discuss some API related things (to make the API more convenient for users)
14:24 olas yes
14:25 olas next week?
14:25 olas must go offline very soon
14:25 edrin i added a simplified async remote process listener. in this case the user does not have to take care of deleting remote processes, thus the complexity i described in my email to you is not important for the user
14:25 edrin ok
14:26 olas I will try to make use of it and give you feedback in the following weeks
14:26 olas will go for 5 weeks of holiday entire november
14:27 edrin the user just handles onResult() and onError() in his simple listener...
14:27 edrin ok
14:27 olas sounds good
14:27 olas will you be online next week?
14:27 edrin i would suggest i give a irc lecture based on the java script test scripts i wrote to ppl that are interested in this stuff
14:28 edrin yes
14:28 olas sounds good
14:28 olas could you maybe organize an online IRS lecture for people?
14:28 olas and advertize it on bioclipse-devel?
14:29 olas gotta go now
14:29 edrin yes, that's I will do
14:29 olas ttl
14:29 edrin bye
14:29 olas bye
14:29 olas left #bioclipse
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15:17 CIA-30 bioclipse: shk3 * r7091 /bioclipse2/trunk/plugins/​net.bioclipse.webservices/ (6 files in 4 dirs): most of the functions of the web services plugin are now active
15:17 jonalv joined #bioclipse
15:17 shk3 hi jonalv
15:18 shk3 you just missed my commit:
15:18 shk3 r7091 /bioclipse2/trunk/plugins/​net.bioclipse.webservices/ (6 files in 4 dirs): most of the functions of the web services plugin are now active
15:19 shk3 the rhino scripting should become a net.bioclipse.scripting.contribution in bc2, right?
15:34 jonalv shk3: there is a js manager already I think
15:35 jonalv shk3: I saw that commit in my mail inbox yea. Got me a bit worried. I think we have plans on Bioclipsetwoifying that... :)
15:36 jonalv Is that what you hvae done or is what now is runnign just the functionality from Bioclipse 1?
15:39 shk3 i just ported bc1 stuff
15:39 shk3 what means Bioclipsetwoifying?
15:39 shk3 right now, the new from wsdbfetch wizard works
15:40 shk3 was like 10 minutes to do
15:40 shk3 so worth doing, I think
15:40 jonalv okey I ahven't started to look at it.
15:40 jonalv _absolutely_ worth doing
15:41 jonalv I just wonder if it integrates with Bioclipse2 or if it is "in a bubble" so to speak...
15:41 shk3 no, looks all fine
15:41 shk3 just the WebservicesTools class doesn't integrate
15:41 shk3 but that's what is a manager now,
15:41 shk3 I think
15:42 shk3 so i would convert this as well
15:42 jonalv okey
15:42 jonalv sounds great
15:42 shk3 there is an extension point org.eclipse.ui.actionSets used in the plugin xml
15:42 shk3 seems to be menu stuff
15:42 jonalv I am going to rebuild the Services view sometime in the future so I might start messing around with those things by then...
15:43 shk3 do you know what the effect of this should be?
15:43 shk3 ie what should I see in bioclipse?
15:43 jonalv Uhm how do you mean?
15:43 jonalv You know the Services voiew in bc2 right?
15:43 edrin you ported the web service plugin to bc2?
15:44 shk3 well, there is this in the plugin.xml:
15:44 shk3 <extension
15:44 shk3 point="org.eclipse.ui.actionSets">
15:44 shk3 <actionSet
15:44 shk3 label="Web Services Action Set"
15:44 shk3 visible="true"
15:44 shk3 id="net.bioclipse.WSactionSet">
15:44 shk3 <menu
15:44 shk3 label="Web services"
15:44 shk3 id="webServices"
15:44 shk3 path="additions">
15:45 shk3 <groupmarker name="group1"/>
15:45 shk3 </menu>
15:45 shk3 </actionSet>
15:45 shk3 </extension>
15:45 shk3 where can I see if this works?
15:45 shk3 or what should it do?
15:45 shk3 edrin: yes
15:45 shk3 did you write it?
15:45 edrin yes
15:46 edrin i did the Web Service and WSDbfetch wizard
15:46 shk3 aha
15:46 shk3 it works fine in bc2
15:46 edrin and the rhino plugin but it's not depending on each other i think
15:46 edrin oh, cool :)
15:46 shk3 no
15:46 shk3 just net.bioclipse.rhino.scripting extension point is used,
15:47 shk3 but this will become a net.bioclipse.scripting.contribution
15:47 shk3 I think
15:47 edrin ok
15:47 shk3 can you tell me what this actionSets is about?
15:47 * edrin already tries to remember
15:47 jonalv I don't even know what his code does. Ola has given me instructions to rework the Services view in bc2 soon so I will have to read up on your code. :)
15:48 shk3 good luck
15:48 jonalv *what _this_ code does
15:48 edrin i think
15:49 edrin this is somehow associated with a menu
15:49 edrin maybe it adds the service to some dropdown menu
15:49 edrin or to the "new" wizard
15:50 edrin yes
15:50 edrin something like this...
15:50 edrin i dont have it here, thus i cant tell you
15:50 * jonalv is leaving soon
15:51 edrin jonalv: the scripting engine...
15:51 jonalv edrin: yes...? :)
15:51 edrin who wrote the code for running scripts in bc2?
15:52 edrin js scripts
15:52 jonalv I would say masak and me but mostly masak
15:52 shk3 olas and jonalv i think
15:52 shk3 ah, masak
15:52 edrin ok
15:52 shk3 masak++
15:52 jonalv I might be able to anser questions though...
15:52 jonalv :)
15:52 edrin ok
15:53 jonalv I was heavily involved in the threading part...
15:53 jonalv what do you wonder?
15:53 edrin using API from new plugins will work with this extension thing right?
15:53 edrin err manager
15:53 edrin ok
15:53 jonalv yea
15:54 edrin is there a rhino. helper thing already ?
15:54 jonalv yea there is a manager with the short names js
15:54 edrin ah
15:54 edrin what functionality does it support so far?
15:54 jonalv I think the interface should be IJSManager
15:54 jonalv hang on
15:57 jonalv http://bioclipse.svn.sourceforge.net/viewvc/b​ioclipse/bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scripting/u​i/business/IJsConsoleManager.java?view=markup
15:59 jonalv that interface needs javadoc btw...
15:59 jonalv Well I am on my way out here. One last question? :)
16:00 edrin yes
16:00 edrin not only one
16:00 edrin 1. why is this called IJsConsoleManager? wont it be used in non-console js scripts as well?
16:01 edrin 2. this interface is to be used bye other plugins to push their manager to rhino "runtime" ?
16:01 jonalv 1. good question. I think it's mostly historical reasons. I think I have asked masak the same thing but I don't really remember the answer.
16:02 edrin 3. where is the code of the "js" (rhino) manager located?
16:02 jonalv 2. This is used to write things on the js console but as for pushing their manager to rhino that is done through an extenstion point
16:03 jonalv 3. The manager implementation for that interface is in the same package in the same plugin
16:03 jonalv was that sufficient answers?
16:04 jonalv edrin: use @ask masak about the first one. I think he ahd a reason...
16:05 edrin can you give me a link to the js manager code?
16:06 jonalv http://bioclipse.svn.sourceforge.net/viewvc/b​ioclipse/bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scripting/u​i/business/JsConsoleManager.java?view=markup
16:07 edrin ok, so if my plugin should export certain functionality as a manager i have to use this interface here...
16:07 edrin public void executeFile( IFile file )
16:07 edrin how can a file be executed?
16:08 jonalv uhm this seems to be the code that runs js scripts from files
16:09 edrin public void executeFile( IFile file, final IProgressMonitor monitor )  under what circumsatnces this monitor thing will be passed in a script?
16:09 edrin ah
16:09 edrin you should rename this to executeScript() then
16:09 jonalv If you are making a plugin with a manager you only have to implement the interface called IBioclipseManager
16:10 edrin oh? what is the difference between IBioclipseManager and IJsConsoleManager
16:10 edrin ?
16:10 jonalv This is a special manager that handles javascript console related things. Like printing things to the javasciprt console
16:11 edrin i dont understand
16:11 jonalv IJSConsoleMAnager defines the methods that the js manager has. If you want another example you could have a look at IStructuredbManager. That one I hvae written. Or ICDKManager which I ahve been higly involved in
16:12 edrin ok, can you give me a link?
16:12 jonalv don't you have eclipse running and bioclipse checked out? :)
16:12 edrin ok
16:12 edrin hm
16:13 edrin hm
16:13 jonalv http://bioclipse.svn.sourceforge.net/viewvc/b​ioclipse/bioclipse2/trunk/plugins/net.bioclip​se.structuredb/src/net/bioclipse/structuredb/​business/IStructuredbManager.java?view=markup
16:13 jonalv and the implementation:
16:13 edrin why is there an interface for IStructuredbManager and ICDKManage ?
16:14 edrin ah
16:14 jonalv http://bioclipse.svn.sourceforge.net/viewvc/b​ioclipse/bioclipse2/trunk/plugins/net.bioclip​se.structuredb/src/net/bioclipse/structuredb/​business/StructuredbManager.java?view=markup
16:14 edrin this interface thing is only because of @PublishedMethod ?
16:14 jonalv edrin: both yea and no. The interface is for all AOP stuff
16:15 edrin is it required?
16:15 jonalv is what required?
16:15 edrin cant this info be exctracted from the class that implements it?
16:15 edrin i guess this interface will never be used by any other plugin to implement it
16:16 jonalv There is some magic going on with proxies here. And proxies work better if there is an interface
16:17 edrin ok, but in theory "from java code view" this interfaces make no sense... (except that we need it for this publishmethod thing)
16:17 jonalv Spring builds and object that implements the Interface and does AOP stuff before calling the actual method in the "implementation class
16:17 jonalv Examples of this is wrapping the entire call in an Eclispe job
16:18 edrin hm
16:18 jonalv so if you annotate a method with @job Spring will wrap the call in an eclipse job
16:18 jonalv it's a bit magic but _very_ powerful
16:18 edrin ah
16:18 edrin yes
16:18 edrin nice
16:18 edrin but on the other hand
16:18 jonalv also we need the interface I jsut realised
16:18 edrin what does the call return then?
16:19 jonalv becuase publishing objects to the osgi container is done by interfaces
16:19 jonalv edrin: that depends :)
16:19 edrin these functions can be void only then
16:20 jonalv nope, but if they are not void then they are not run asynchronisly :)
16:20 edrin because the script will be finished when job finished
16:20 jonalv yea there are a few different cases here...
16:20 edrin meaning spring first checks for @job and then if it is void ?
16:20 jonalv I don't remember it all now. It's been a few weeks since we did this and I have to leave soon :)
16:21 edrin ok
16:21 edrin one last thing
16:21 edrin i would like to add some functionalities to the js
16:21 jonalv I can look into this and point you to the relevant code. I think masak knows this better thoguh...
16:21 jonalv edrin: okey which one? :)
16:21 edrin or to some "tool" thing if you do not want code in js
16:22 edrin do you want a new manager or should i extend the code in JsConsoleManager ? (I guess the JsConsoleManager is available in all scripts, anyway...)
16:23 jonalv I think that depends on what functionality you are adding :)
16:23 edrin on the other hand console only manager (code) should become a "console" manager ?
16:24 jonalv well this is the console manager. hence the name... :)
16:24 edrin but so far the code in JsConsoleManager rather looks like JsManager code ;)
16:24 jonalv yea I know it's confusing but the print code is definitly console code...
16:25 jonalv but what is it hat you want to add?
16:25 * jonalv is curious and needs to get going...
16:25 edrin functionalities to: 1. add a lib to bc runtime at runtime
16:26 edrin 2. job specific stuff, if it is not there...
16:26 edrin err
16:26 edrin monitor specific stuff
16:26 edrin for example to a way check if the job was canceled
16:26 edrin a way to
16:27 CIA-30 bioclipse: shk3 * r7092 /bioclipse2/trunk/plugins/​net.bioclipse.webservices/ (6 files in 3 dirs): added a manager
16:27 edrin 3. maybe other thing
16:27 edrin s
16:27 jonalv ah I read a bit of your own code examples. We are doing a javascript a bit differently in Bioclispe 2... But not too differently I hope
16:28 edrin no, it is not too different
16:28 jonalv edrin: You really should talk to masak about this. He has been our javascript guy in this. I am know what he has done but I am not the one who has done it so I don't fully know the best way to do things...
16:28 edrin but from within a script i think it is important to check if the script was canceled from outside
16:29 edrin ok
16:29 edrin will he return today?
16:29 jonalv absolutly and this is rather complex since we have methods in other managers that also takes monitors...
16:30 jonalv probably not to #bioclipse but maybe to some other channel zarah frequently visits...
16:30 edrin what does public String eval( String command ) do?
16:30 jonalv he said something about only being in #Bioclispe when working but being available using @tell at other times :)
16:30 edrin ok
16:30 jonalv evaluates a js commando I would say...
16:31 edrin what does this mean?
16:31 jonalv well gtg, use zarah :)
16:31 jonalv zarah: edrin should use you :)
16:31 zarah jonalv: are you talking to *me*?
16:31 jonalv zarah: yes.. :)
16:31 zarah jonalv: I see.
16:31 edrin ok
16:31 edrin cu jonalv have a nice evening
16:31 jonalv cu
16:32 CIA-30 bioclipse: shk3 * r7093 /bioclipse2/trunk/plugins/net.bioc​lipse.webservices/META-INF/spring/ (. context-osgi.xml context.xml): added a manager
16:34 edrin shk3: are you know working in uppsala, too?
16:36 shk3 no, cambridge
16:36 edrin ok
16:36 shk3 could somebody try running the werbservices plugin?
16:36 shk3 for some reason, the scripting stuff
16:36 edrin currently not at home, sorry :)
16:37 shk3 fails when starting up
16:37 shk3 I suppose an obvious bug, but can't find it right now
16:46 edrin me must go
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