Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-08-09

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All times shown according to UTC.

Time Nick Message
05:57 egonw joined #bioclipse
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08:03 edrin morning
08:05 edrin egonw: it is incredible how this Web Service environment could get such a large communitiy. it is incredible how such a shit technology could get that far
08:07 edrin yesterday i realized this once again - when i  tried to use axis1 rpc/encoded webservices with yet any other Java Web Service library (Apache CXF or Axis2)
08:08 edrin using the DynamicClientFactory of CXF - it would be so cool, especially for scripting:
08:08 edrin http://cwiki.apache.org/CXF​20DOC/dynamic-clients.html
08:51 jonalv joined #bioclipse
09:04 CIA-7 bioclipse: jonalv * r3670 /trunk/plugins/net.bioclipse.statistics/jars​/org.eclipse.nebula.widgets.grid_1.0.0.jar: New nightly build of Nebula grid widget jar with a bugfix for SWT.VIRTUAL
09:05 CIA-7 bioclipse: jonalv * r3671 /trunk/plugins/net.bioclipse.statistics/s​rc/net/bioclipse/editors/GridEditor.java: Modified the GridEditor to use SWT.VIRTUAL to lazy load matrix rows as needed.
09:40 masak @tell olas I emailed basedb-devel and they replied immediately. seems I shouldn't use a BASE2 plug-in after all. instead I will need to interact with their API, possibly through experimental webservices functionality of theirs. I'm now investigating this further
09:40 lambdabot2 Consider it noted.
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10:05 jonalv hi olas
10:05 olas hijonalv
10:05 lambdabot2 olas: You have 1 new message. '/msg lambdabot2 @messages' to read it.
10:05 olas /msg lambdabot2 @messages
10:05 olas nope, that didn't work
10:06 masak hm, try just @messages
10:06 olas Have a really bad irc client
10:06 olas @messages
10:06 lambdabot2 masak said 25m 32s ago: I emailed basedb-devel and they replied immediately. seems I shouldn't use a BASE2 plug-in after all. instead I will need to interact with their API, possibly through
10:06 lambdabot2 experimental webservices functionality of theirs. I'm now investigating this further
10:06 olas masak: yes
10:06 masak ...and it involves Perl :)
10:06 olas that was what I thought
10:06 olas no
10:06 olas not perl!
10:07 masak mwhaha
10:07 jonalv olas, There was a bug in the Grid widget but the latest nightly build contained a bug fix and now our GridEditor supports lazy loading
10:07 olas Can't you just use their API?
10:07 masak olas: yes, probably
10:07 olas jonalv: great
10:07 masak but the one existing client is in Perl
10:07 masak so I will need to translate it to Java
10:07 olas I see
10:08 masak feels pretty good
10:08 olas If there is an API for java, why do they use Perl for the client?
10:08 masak beats me
10:08 jonalv masak, I guess you are the right person for that. Pugs developer and all...
10:09 masak jonalv: thx
10:10 * jonalv off hunting for food
10:10 * masak hunts along
10:26 * olas will bite his teeth deep in his prey
10:26 * Nielsout hunts at another place to get a better prey :p
10:47 edrin olas?
10:47 edrin ah gone again
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11:16 EskilA Hello
11:19 Nielsout hi EskilA
11:22 jonalv joined #bioclipse
11:25 edrin http://www.pubmedcentral.nih.gov/articlere​nder.fcgi?tool=pmcentrez&artid=1933145
11:25 edrin the "FUTURE PLANS" somehow reflects the problems with current web services in bioinformatics
11:25 lambdabot2 Title: Web Services at the European Bioinformatics Institute, http://tinyurl.com/2c6ejh
11:31 masak edrin: in what way?
12:04 edrin current bio web services are all using RPC/encoded in their wsdls. and there is only one - very old - very slow - somehow outdated - library: axis1. this means all the new libraries that are currently under development (cxf and axis2) will have problems or more likely wont support any existing bio webservice.
12:09 masak sounds bad
12:09 masak will the situation improve, do you think?
12:12 edrin at least they realized this now. in this article they claim: "After a careful evaluation of existing technologies, and taking into consideration our users feedback, we are planning for continuous improvement and re-engineering of implementation of future services. We have chosen JAX-WS (http://java.sun.com/webservices/jaxws/) as a basis for our future Web Services infrastructure."
12:13 edrin but this will take ages
12:13 masak yes
12:13 edrin ;)
12:13 masak at least they started down that road
12:53 sobu joined #bioclipse
12:58 edrin hello sobu
12:58 sobu hello edrin
13:01 jonalv @tell egonw I have started implemention of a new matrix editor using the Nebula Grid widget. It is supposed to do lazy loading of elements and so on. However I haven't managed to get the old editor which I think still have some more features to be the default editor. Please if you have time could you make the old editor the default editor?
13:01 lambdabot2 Consider it noted.
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13:41 CIA-7 bioclipse: biocoder * r3672 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Added fields for column and row headers
14:02 CIA-7 bioclipse: ospjuth * r3673 /trunk/playground/plugins/net.bioclipse.b​iomoby/src/net/bioclipse/biomoby/wizards/ (3 files): Added title image
14:02 CIA-7 bioclipse: ospjuth * r3674 /trunk/playground/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/views/MobyViewLabelProvider.java: Use new icons
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14:03 CIA-7 bioclipse: ospjuth * r3675 /trunk/playground/plugins/net.bioclipse.biomoby​/src/net/bioclipse/biomoby/views/MobyView.java: Added refresh and reload actions and fixed offline initialization errors
14:03 CIA-7 bioclipse: ospjuth * r3676 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/​views/MobyViewContentProvider.java: Do not cache ServiceTypes
14:04 CIA-7 bioclipse: ospjuth * r3677 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyViewServiceType.java: Better error messaging
14:04 CIA-7 bioclipse: ospjuth * r3678 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyViewContainer.java: Fixed children error reporting
14:05 CIA-7 bioclipse: ospjuth * r3679 /trunk/playground/plugins/net.bioc​lipse.biomoby/src/net/bioclipse/bi​omoby/model/MobyViewCentral.java: Use non-cached list of servicetypes
14:06 CIA-7 bioclipse: ospjuth * r3680 /trunk/playground/plugins/net.bioclipse.biomoby/s​rc/net/bioclipse/biomoby/BioclipseMobyModel.java: Do not update cache in job
14:06 CIA-7 bioclipse: ospjuth * r3681 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/acti​ons/ExecuteMobyServiceAction.java: Do not update cache in job
14:06 CIA-7 bioclipse: ospjuth * r3682 /trunk/playground/plugins/net.bioclipse.biomoby/sr​c/net/bioclipse/biomoby/UpdateCacheListener.java: Added listener for updateCache job. Not used currently.
14:07 CIA-7 bioclipse: ospjuth * r3683 /trunk/playground/plugins/net.bioclipse.biomob​y/src/net/bioclipse/actions/testBiomoby2.java: Standalone test to try complex service (failing at present)
14:08 CIA-7 bioclipse: ospjuth * r3684 /trunk/playground/plugins/net.​bioclipse.biomoby/plugin.xml: Removed SeahawkView as it is not working and use new action for Moby Service View.
14:09 CIA-7 bioclipse: ospjuth * r3685 /trunk/playground/plugins/n​et.bioclipse.biomoby/icons/ (6 files): Added new icons
14:14 EskilA left #bioclipse
14:23 CIA-7 bioclipse: ospjuth * r3686 /trunk/playground/plugins/net.bioclipse.biomoby​/src/net/bioclipse/biomoby/views/MobyView.java: Added run action for services
14:23 CIA-7 bioclipse: ospjuth * r3687 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyViewServiceType.java: Set description for children
14:25 edrin hello olas
14:26 CIA-7 bioclipse: ospjuth * r3688 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyPropertySource.java: Only show name and description in properties view
14:26 olas hello edrin
14:28 CIA-7 bioclipse: ospjuth * r3689 /trunk/playground/plugins/n​et.bioclipse.biomoby/icons/ (6 files): Added some more icons
14:29 CIA-7 bioclipse: ospjuth * r3690 /trunk/playground/plugins/net.b​ioclipse.biomoby/icons/wizard/ (. run_wiz.png): Added some more icons
14:30 CIA-7 bioclipse: ospjuth * r3691 /trunk/playground/plugins/net.bioclipse.biomoby/: Added svn:ignore
14:32 edrin olas: how are you progressing with the BioMoby?
14:33 edrin olas: btw. I found a really cool webservice thing for scripting. The bad is that this library does not support the old axis1 rpc encoded style...
14:33 olas Pretty good
14:33 olas I see
14:33 edrin anyway, (bio) web service people finally realized that axis is outdated
14:33 edrin http://www.pubmedcentral.nih.gov/articlere​nder.fcgi?tool=pmcentrez&artid=1933145
14:33 lambdabot2 Title: Web Services at the European Bioinformatics Institute, http://tinyurl.com/2c6ejh
14:34 olas In biomoby, I have succeeded with everything but the actual invokation of complex services
14:34 olas have emailed the list about it
14:34 olas Hope to get a working version online tomorrow (then I'm off for vaction for 2 weeks)
14:36 edrin this article shows that they realized and want to change all the ebi webservices to document/literal style. this style should be compatible with newer libs. i think it does not make sense to spend too much time on axis1 code in future. i.e. the developers of current active Java Web Service Libraries will not support rpc/encoded style (because it is a "bad" technology), I just had a chat with a developer of the apache cxf lib...
14:36 olas so what do you recommend to use?
14:37 edrin back in a minute...
14:37 olas ok
14:49 edrin olas: one thing i like very much (because it is somehow well documented) is xfire that has a new name now: cxf
14:49 edrin http://incubator.apache.org/cxf/
14:49 olas yes
14:50 edrin the thing i like very much there is the DynamicClientFactory:
14:50 edrin http://cwiki.apache.org/CXF​20DOC/dynamic-clients.html
14:50 edrin i found now at least one EBI webservice that should - in theory - be compatible with it as it is already document/literal. i will try tonight
14:51 edrin olas: as far as i understand it, the CXF DynamicClientFactor would be very cool in combination with scripting:
14:54 edrin DynamicClientFactory = Packages.org....DynamicClientFactory;
14:54 edrin Client = Packages.org....Client;
14:54 edrin dcf = DynamicClientFactory.newInstance();
14:54 edrin clt = dcf.createClient("http://the-webservice.wsdl");
14:54 edrin res = client.invoke("function-name", "some input blah");
14:54 edrin rhin.ShowMessage(res);
14:55 edrin that means the lib can generate the client stub against the service just at runtime dynamically. and i expect the rhino engine to take care of "casting" the objects somehow in the background anyway...
14:56 edrin wouldN#t this be great?
14:57 edrin writing a workflow engine (like taverna) that uses javascript somewhere behind the scene would be quite easy then...
14:58 edrin just some drag and drop "boxes" in a elipse view, some scripting application logic (in the background) and some import webservice by wsdl ...
14:59 edrin * import webservice by wsdl wizard
15:00 edrin anyway - i still doubt that workflows like taverna are more comfortable than actually a script.
15:00 edrin because if someone has the knowledge to use taverna, he would do the job much faster and much more flexible with a script.
15:01 olas I agree
15:04 edrin i think we should have a graphical view where you can define the application or execution logic of scripts. this would reduce the complexity of such scientific-analytic scripts (because you wont have a megascript then). on the other side each of the boxes represents a .js and the results of the scripts can than be defined by drag and drop to call yet another script
15:17 olas that sounds like a really great app
15:18 olas On the way to systems biology (integrative bioinformatics)
15:18 olas A meta language
15:18 olas btw, see http://wiki.bioclipse.net/in​dex.php?title=BioMoby_plugin
15:18 lambdabot2 Title: BioMoby plugin - BioclipseWiki
15:18 olas have to run to the train now
15:18 olas Let's continue this discussion later
15:18 olas CHeers!
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