Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-04

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All times shown according to UTC.

Time Nick Message
05:54 thomas_ku joined #bioclipse
06:25 Gpox joined #bioclipse
08:17 egonw joined #bioclipse
08:22 edrin joined #bioclipse
08:22 edrin morning
08:58 egonw hi edrin
09:00 edrin hi egonw
09:02 egonw http://embraceregistry.net/
09:02 egonw anyone can register WDSLs there...
09:02 egonw and if you upload some test code, it will regularly check if the service is still up and running and behaving as expected
09:03 jonalv joined #bioclipse
09:03 jonalv hi
09:03 zarah hi jonalv
09:05 stain egonw: nice
09:05 egonw stain: we briefly talked about integration with the Taverna2 annotation stuff Tom talked about last year at the EBI T2 devel meeting
09:06 egonw my catch: http://friendfeed.com/e/09618715-7c​c6-4db0-996e-4fde282945dc/Talk-star​ted-about-the-EMBRACE-webservice/
09:06 zarah egonw's link is also http://tinyurl.com/5oqb4t
09:06 stain egonw: yeah, that will be part of the BioCatalogue work
09:06 egonw ah ok :)
09:06 stain it's not exactly what Tom talked about, but taken a step further, perhaps
09:07 egonw biocatalogue could use opening up
09:07 stain Taverna will pick up service annotations so that you can both query to find new services from Taverna, but also you should be able to click on a service in a workflow to get more info about it
09:07 egonw looks interesting, but being a closed project so far...
09:08 egonw we can use, nor contribute :(
09:08 stain they are doing a prototype for this (or next?) month
09:08 egonw stain: we need annotation for Bioclipse
09:08 stain it's not really closed.. but perhaps they have not showed where the door is
09:08 stain I'll let them know in our meeting in 1 hour
09:08 egonw right
09:08 egonw yes, please do
09:08 stain ok, so do you say you have a developer ready to contribute..? :)
09:09 egonw check my presentation of yesterday
09:09 stain how many hours a week..? ;)
09:09 egonw not sure
09:09 egonw but we are going to build a GUI for bioclipse
09:09 egonw to browse, discover services
09:09 stain I thought BioClipse was a gui
09:09 stain stupid me
09:09 egonw so will have man power
09:09 egonw ah, sorry...
09:09 egonw read "GUI element"
09:10 egonw but we are going to build a GUI element (a SWT View to be precise) for bioclipse
09:10 * jonalv thinks of Bioclipse as something more than a GUI...
09:10 egonw yeah, Bioclipse is a window to the cloud
09:10 jonalv yea
09:10 jonalv >(
09:10 jonalv aouch
09:10 egonw anyway...
09:10 stain cloud computing visualizer component registry entity
09:10 egonw yeah, now you're talking
09:10 * jonalv needs to get used to this keyboard... :)
09:10 stain so what exactly are you building..?
09:10 egonw ok, coffee time here...
09:11 egonw check my presentation
09:11 egonw and wishlist
09:11 egonw in my blog
09:11 jonalv afk
09:11 stain I don't know what is your presentation :-(
09:11 egonw chem-bla-ics.blogspot.com
09:11 egonw last blog post
09:11 egonw can't miss it
09:11 egonw it's on slideshare
09:11 stain cheers
09:11 egonw skip that chats about what a webservice is
09:12 egonw in bioclipse we'll mix SOAP, XWS, local, Taverna, ... whatever else X-service...
09:12 egonw into one central 'service list'
09:12 egonw to browse this we need the annotation
09:12 stain I see the cloud
09:12 egonw good :)
09:12 edrin cool
09:12 edrin cool
09:12 egonw cool
09:12 zarah cool
09:12 stain cool
09:12 egonw hahahah
09:13 edrin hehe
09:13 stain all 5+4!
09:13 egonw zarah: funny as always :)
09:13 zarah egonw: you've just exceeded my capabilities :/
09:13 egonw ok, going for coffee now
09:14 stain can't you use BioCatalogue / Embrace as that service registry?
09:14 stain I'm not sure about embrace, but at least biocatalogue will have API-access to both register and query the registry
09:16 egonw stain: yes, that's the idea!
09:16 egonw we'd much rather use something than reinvent the wheel...
09:17 egonw that's why we are so disappointed with the lack of openess of biocatalogue
09:17 egonw and why I am so happy with this embraceregister.net talk and website
09:17 egonw btw, a comment here was the annotation with literature...
09:17 egonw link a WSDL to a publication describing it...
09:18 egonw it was even suggested to set up some best practice that the service itself actually reports it...
09:18 egonw edrin: that would be something we can suggest for io-data too...
09:19 edrin yes
09:19 edrin i think xeps often have such a section
09:19 edrin we should set it to todo list when modifying/updateing it. there are some "spelling errors" in the xep, anyway
09:20 edrin egonw: do you have bc2 installed? can you checkout newest xws4j bc2 plugin?
09:20 stain it seems the embraceregistry is missing something essential such as having URLs?
09:21 egonw edrin: will try
09:21 egonw asked about that...
09:21 stain can't trust these europeans!
09:21 egonw it's a front, as it is still running on a staging machine...
09:21 stain hehe
09:21 stain it's running here
09:21 stain http://prints.cs.man.ac.uk:8081/bling
09:21 egonw http://prints.cs.man.ac.uk:8081/
09:21 zarah stain's link is also http://tinyurl.com/6ld4ym
09:21 zarah egonw's link is also http://tinyurl.com/58dsa3
09:21 egonw ah, right :)
09:21 stain it's probably two rooms next to me!
09:22 stain this is how it is.. we go to some international chat room and figure out what's going on next door
09:22 egonw you're in the myexperiment.org room?
09:22 egonw then it would be next door indeed :)
09:22 stain hihi
09:22 stain it's very confusingly called the ESNW lab, something about eScience North West
09:23 stain we're not allowed to do regular science
09:23 stain ok, I'll really let them know that more openness is needed
09:23 edrin egonw: can you try the following script
09:23 edrin xws.connect();
09:23 edrin f = xws.getFunction("cdk.ws1.bmc.uu.se", "  YOUR FUNCTION ");
09:23 edrin ios = f.getIoSchemataSync(90000);
09:23 edrin iof = xws.getIoFactory(ios);
09:23 edrin and then tab browse the iof and also take a look in the xws subfolder in bioclipse2. it should contain the full binding...
09:23 egonw yes, that would be very much appreciated
09:24 egonw edrin: ok, hang on
09:24 edrin egonw: of course you should checkout xws4j plugin first
09:25 egonw yes, yes :)
09:36 egonw added on of Rajarshi's services to embraceregistry: http://prints.cs.man.ac.uk:808​1/service/lipinskis-rule-five
09:36 zarah egonw's link is also http://tinyurl.com/5v8fmz
10:03 egonw stain: if you're still here...
10:03 egonw there is discussion among the EMBRACE people, including your neighbor next door...
10:03 egonw that they too like more openness
10:06 jonalv zarah: tell gilleain I think we are still not using java 6 for Bioclipse (unless something have changed during the last week) so please don't commit Java 6 specific code
10:06 zarah Consider it noted.
10:06 stain egonw: yeah
10:06 stain in the meeting now :)
10:06 egonw ah, ic
10:06 egonw was hoping for that...
10:07 stain yeah :)
10:07 stain Biocatalogue is a bit furhter down.. in 1.5 h I guess
10:07 egonw if you got news about opening up the project, or not... I could relay that message to the EMBRACE workshop
10:07 egonw ah ok
10:07 CIA-52 bioclipse: jonalv * r7533 /bioclipse2/trunk/plugins/net.biocl​ipse.compute/src/net/bioclipse/comp​ute/business/ComputeManager.java: Removed Java 6 specific annotation
10:09 stain egonw: all right, I'll let you know :)
10:09 stain relay by Internet Relay Chat
10:09 egonw Steve Pettifer \
10:10 egonw I thikn that's the name of the guy who should be next door
10:10 stain he's on our UI team as well
10:10 stain ;)
10:18 jonalv edrin: I just updated my Bioclipse checkout... Does net.bioclipse.xws4j really require Eclipse 3.4.1?
10:21 edrin no
10:21 edrin does it?
10:21 edrin why?
10:23 egonw the deps say so
10:23 egonw MANIFEST.MF
10:23 jonalv yea
10:32 CIA-52 bioclipse: jonalv * r7534 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (3 files in 3 dirs): [structuredb] s/smiles/SMILES/
10:37 gilleain joined #bioclipse
10:41 gilleain hi
10:41 zarah hi gilleain
10:41 zarah gilleain: You have new messages. Write '@messages' to read them.
10:41 gilleain @messages
10:41 zarah gilleain: 35 m 42 s ago, jonalv said I think we are still not using java 6 for Bioclipse (unless something have changed during the last week) so please don't commit Java 6 specific code
10:42 gilleain hmm. didn't think that i did.
10:44 egonw edrin: ok, finally got around to running the xws4j plugin
10:44 egonw well..
10:44 egonw sort fo...
10:44 egonw it does not boot...
10:45 edrin oh?
10:45 egonw sorry...
10:45 egonw wrong feature
10:45 edrin :)
10:45 egonw had the bioclipse_feature_patch :)
10:45 edrin i'll be for lunch now
10:46 gilleain jonalv: surely @Override is Java5, not Java6?
10:47 egonw there was something about it...
10:50 gilleain Ah, it exists in 5, but is used in different place to 6. Right.
10:50 gilleain "With java 6 @Override can also be used if your method implements a method in a base interface."
10:51 egonw ah, ok
10:51 egonw good explanation
10:54 egonw edrin:
10:54 egonw Caused by: net.bioclipse.xws4j.exceptions.Xws4jException: Could not create default client: the plug-in has set invalide account data in preferences.
10:54 egonw at net.bioclipse.xws4j.DefaultClientCurator.get​DefaultClient(DefaultClientCurator.java:76)
10:54 egonw at net.bioclipse.xws4j.business.XwsMa​nager.connect(XwsManager.java:64)
10:54 egonw ... 60 more
10:54 egonw edrin: (for when you're back from lunch)
10:56 stain egonw: ok, discussing it heatedly now :)
10:56 egonw :)
10:56 jonalv gilleain: exactly
10:57 gilleain I blame eclipse : I don't hold with this new-fangled annotation stuff :)
10:57 gilleain Well, actually, I should blame myself for not setting the project to be java5.
10:57 stain we agree about opening up, but the current focus is to get the first internal pilot out, and they'll update the web pages. We'll need to just say publicly how ready we are
10:58 egonw I would really like to see specifications... impl can come later
10:58 stain that's exactly what they've worked on
10:58 jonalv gilleain: I think you can set the entire workspace to be java 5
10:58 egonw but I cannot give input when I do no see the scope and functionality
10:59 gilleain jonalv: oh, no doubt. I hadn't done that either, though.
10:59 stain egonw: like what's it goint to do when, or more like UML diagrams, or what..?
10:59 egonw nah, no UML please
10:59 stain they'll send the report they just did to the friends mailing list
10:59 egonw but what is the anticipated functionality, like:
10:59 egonw REST interface
10:59 egonw query by: tag, services, category
11:00 egonw which ontologies are planned to be used
11:00 egonw what license people will be able to use for contributions
11:00 egonw REST interface, or SOAP, or whatever... just say what is intended to be used...
11:01 egonw demo code online would be nice, and the webpage could indicate with whom to get in contact
11:01 egonw to do some testing or so...
11:01 egonw see if ideas work well from, in my case, Bioclipse...
11:01 egonw I'm happy with half broken prototypes
11:01 egonw "release soon, release often"
11:01 egonw that really is true
11:02 egonw but a no info on the currently anticipated design is a plain killer
11:02 stain <jits> we've been working on the feature list, roadmap and so on... just that its yet to go out
11:02 egonw compare it to Taverns2
11:02 egonw while not finished yet, people can start play with the code...
11:02 egonw look at it
11:02 egonw comment on it
11:03 stain exactly
11:03 egonw contribute to it
11:03 stain I think they were a bit too "We want it to work first" attitude
11:03 egonw the latter is eventually what matters to the source of the project
11:04 stain could you contact "Jiten Bhagat" <jits@cs.man.ac.uk> ..? He's one of the main developers and he's very happy to get these kind of comments
11:05 stain I guess you could just paste him the last page of your lines ;)
11:05 egonw ok, will do
11:05 stain also perhaps you could mention what you said about contributing
11:05 egonw yes, that should get his attention :)
11:11 jonalv joined #bioclipse
11:24 edrin egonw:
11:24 edrin Caused by: net.bioclipse.xws4j.exceptions.Xws4jException: Could not create default client: the plug-in has set invalide account data in preferences.
11:25 edrin did you set account data in XMPP preference page?
11:25 edrin :)
11:30 egonw edrin: ah, no, I did not
11:30 egonw that was not in your messages I read :)
11:30 egonw we'll have lunch in about 20 minutes or so
11:30 egonw now booting BC2 again
11:32 egonw ok, better error message would be helpful :)
11:32 egonw you got an account on pelezilla?
11:32 egonw oh...
11:32 egonw lunch is now
11:33 egonw ok, bbl
11:33 egonw stain: I emailed Jiten
11:33 stain nice
11:34 egonw syed haider also got email from the project leader with the same message
11:34 egonw he also said something about the data from ebrace registry
11:34 egonw ok, gone now
12:21 gilleain joined #bioclipse
12:51 charlgren joined #bioclipse
13:01 egonw edrin: ping
13:10 edrin egonw: im here
13:11 edrin egonw: you don't like "Could not create default client: the plug-in has set invalide account data in preferences." as error message? well, i agree that it should be visible in console...
13:12 egonw ok, made good progree
13:12 egonw ess...
13:12 egonw but how do I actually invoke the function
13:12 egonw ?
13:12 egonw invokeSync()
13:12 egonw what input does that take
13:12 egonw it does not like the smiDoc I created
13:13 egonw miDoc = iof.createSmilesDocument()
13:13 egonw smiDoc = iof.createSmilesDocument()
13:13 egonw smiDoc.setSmiles("CCC")
13:13 egonw which creates good input
13:13 egonw but how to invoke the function?
13:13 egonw > f.invokeSync(smiDoc)
13:13 egonw Can't find method
13:14 edrin egonw: try f.invokeSync(smiDoc.toString(), 90000);
13:14 egonw ok
13:14 jonalv joined #bioclipse
13:15 jonalv zarah: ping
13:15 zarah jonalv: pong
13:15 egonw cool
13:15 egonw the output was not good though
13:15 egonw the service did calculate a mass
13:15 egonw but it does not look good in the console:
13:15 egonw js> f.invokeSync(smiDoc.toString(), 900000)
13:15 egonw [mass: null]
13:15 edrin yes, sure
13:15 egonw ah, ok :)
13:15 edrin because it is w3c dom element
13:16 edrin do this:
13:16 edrin r = f.invokeSync(smiDoc.toString(), 900000)
13:16 egonw result =
13:16 egonw done that :)
13:16 egonw result.toString()
13:16 egonw give the above output
13:16 egonw so, on the console
13:16 egonw what's that XMLConvertor thingy equivalent?
13:16 edrin output = iof.getSmiDoc(r);
13:17 edrin nono
13:17 edrin well
13:17 egonw getOutputObject()
13:17 edrin yesyes i mean
13:17 egonw that works :)
13:17 edrin yes
13:17 edrin BUT!
13:17 egonw > iof.getOutputObject(result)
13:17 egonw <mass xmlns="urn:xmpp:tmp:io-data​">36.032207690364004</mass>
13:18 egonw cool !
13:18 edrin sadfully, although the getOutputObject() is instanceof SmiDoc, console tab javascript  does not return correct functions (reflection problem)
13:19 egonw ah, ok
13:19 egonw but all this makes me pretty happy :)
13:19 edrin thus i added specific function that return null if XmlObject of r is not instanceof the defined XmlObject derivative but if it is it returns the correct XmlObject derivative
13:20 edrin egonw: try tabbing the function similar tho this in your iof: iof.getSmilesDocument( r );
13:21 edrin egonw: in any case you may take a look in the auto-generated IoFactory.java file in your xws subfolder in the bioclipse file navigator ... :)
13:23 egonw nice :)
13:23 edrin egonw: the files in this folder are the binding (BatchBinder console app would create exactly the same files!)... you could also use the generated binding in your java new project
13:27 jonalv zarah: ping
13:27 zarah jonalv: pong
14:47 egonw @msg edrin http://chem-bla-ics.blogspot.com/2008​/11/next-generation-asynchronous.html
14:47 zarah egonw's link is also http://tinyurl.com/54wz53
14:47 zarah egonw: You have no new messages.
14:47 egonw @tell edrin http://chem-bla-ics.blogspot.com/2008​/11/next-generation-asynchronous.html
14:47 zarah egonw's link is also http://tinyurl.com/54wz53
14:47 zarah Consider it noted.
16:28 edrin @tell egonw I read it sounds great
16:28 zarah Consider it noted.
16:28 zarah edrin: You have new messages. Write '@messages' to read them.
16:28 edrin @messages
16:28 zarah edrin: 1 h 40 m 49 s ago, egonw said http://chem-bla-ics.blogspot.com/2008​/11/next-generation-asynchronous.html
16:28 edrin left #bioclipse
18:45 egonw joined #bioclipse

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