Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-03

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All times shown according to UTC.

Time Nick Message
08:18 malick joined #bioclipse
08:30 Gpox joined #bioclipse
09:05 egonw joined #bioclipse
09:14 gilleain joined #bioclipse
09:20 edrin joined #bioclipse
09:21 egonw moin
09:21 zarah hi egonw
09:21 egonw live from the embrace meeting
09:22 edrin hi
09:22 zarah hi edrin
09:22 edrin hello egonw
09:22 egonw my presentation is in my blog
09:22 edrin and how is it ;)?
09:22 edrin ah
10:16 gilleain joined #bioclipse
10:54 thomasku joined #bioclipse
12:05 charlgren joined #bioclipse
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13:00 gilleain joined #bioclipse
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14:08 malick left #bioclipse
14:58 egonw edrin: got the async client working too now :)
14:58 edrin ah cool
14:58 edrin it's easy ?
14:58 egonw easy enough
14:58 egonw quite easy teally
14:58 edrin did you use the "simple listener"
14:59 egonw t=r
14:59 egonw yes
14:59 edrin good ok
14:59 gilleain I think I finally understand what this xmpp stuff is for.
15:00 gilleain It's like web-services, but without the http.
15:00 edrin good
15:00 egonw gilleain: yes
15:00 edrin exactly
15:00 egonw and without the soap too
15:00 gilleain So it's dirty?
15:00 gilleain :)
15:00 egonw it's so dirty, it sexy
15:01 gilleain I do think that some services don't make sense to do remotely - the simple ones.
15:02 gilleain I know it make sense to test with mol->smiles conversion, but...
15:02 gilleain anyway, I liked the presentation, egonw.
15:02 egonw gilleain: agreed...
15:03 gilleain It would be nice for remote services to publish (in a machine-readable form) what they are doing.
15:04 gilleain as a taverna workflow, maybe..
15:04 edrin but maybe there are others, too, gilleain, for example blasting and clustalw
15:04 gilleain true, blasting, clustering, tea-coffeing, etc.
15:05 gilleain sorry, I meant tcoffee.
15:06 egonw_ joined #bioclipse
15:07 * gilleain should be working on the gcc poster, not ircing.
15:31 egonw_ edrin: ping
15:31 edrin egonw: i am here
15:32 egonw run() now takes a IProcessStatus and Element
15:32 egonw but I rahter have IPS and a String
15:32 egonw or InputStream
15:32 egonw because I parse from that in the CDK
15:32 egonw is that possible
15:32 egonw ?
15:32 edrin hm
15:33 edrin sorry, i did not get the question
15:34 edrin egonw: what do you mean?
15:35 egonw is there an IFunction.run(IProcessStatus, String) ?
15:35 edrin no, why?
15:35 edrin do you want to get the Element as string ?
15:36 egonw because a String is the input for the CDK for my second service
15:36 edrin ah
15:36 egonw or does the library get an ELement anyway?
15:36 egonw if so, I'll just have to be happy with XMLConvertor.w3cElementToString()
15:37 edrin i know it's ugly but as long as you have no other function to get the String of an Element i can only offer the w3cElementToString() function. but this first transforms the Element in a JSO StreamElement again and then dumps it into a String
15:38 edrin Element.toString() does not work...
15:39 edrin but i fully agree that it is not really perfect to translate jso.StreamElement->dom.w3c.Elem​ent->jso.StreamElement->String
15:40 egonw ok, let's optimize later...
15:40 egonw it was just a thought...
15:40 edrin yeah
15:40 edrin no prob
16:32 egonw edrin: Element output = XMLConverter.getW3cElement(XMLConver​ter.getStreamElement(outputString));
16:32 egonw is that OK code?
16:35 edrin have to check
16:37 edrin egonw: there is a cleaner method in public static JavaDOMTools.string2Element(String element_string);
16:37 egonw ok, tack!
16:38 edrin this is code clean without jso or other things in
16:44 egonw yoohoo...
16:44 edrin :)
16:44 egonw I just send around CML, created 3D coordinates
16:55 edrin egonw:
16:55 egonw yes?
16:55 edrin question: does the BatchBinder work for your component
16:55 egonw commiting my code to CDK SVN
16:56 egonw BatchBinder?
16:56 egonw what's that?
16:57 edrin xws4j-binding: it's a console program (uses same code for generating IoFactories). It will create a binding for your service
16:57 egonw ah... have not tried that
16:57 edrin it will autogenerate all required java source classes to use the function
16:58 edrin you just have to import the java source (and xsb files) to your project and use it
17:00 edrin http://bioclipse.svn.sourceforge.net/vi​ewvc/bioclipse/xws/trunk/xws4j-binding/​src/net/bioclipse/xws/binding/BatchBind​er.java?revision=7463&view=markup
17:00 edrin this one
17:00 zarah edrin's link is also http://tinyurl.com/55fkrr
17:01 edrin Usage: java BatchBinder <clientJID> <pwd> <host> <port> <serviceJID> <functionName> <targetDirectory> <compileSrc> <classpathStr>
17:01 egonw nice
17:02 edrin Example: java BatchBinder user@server.example.com/home secret server.example.com 5222 xws.server.example.com testFunction c:/myBindingFiles true c:/xmlbeans/jsr173_1.0_api.jar;c:/xmlbeans/resolve​r.jar;c:/xmlbeans/xbean.jar;c:/xmlbeans/xbean_xpat​h.jar;c:/xmlbeans/xmlbeans-qname.jar;c:/xmlbeans/x​mlpublic.jar;c:/xws4j-binding-test.jar;c:/xws4j-te​st.jar;c:/Programme/Java/jre1.6.0_07/lib/rt.jar
17:02 edrin in linux use : and not ; to separate the paths
17:03 edrin it should work, altouh i will change it a little bit in future to make it rock...
17:04 edrin if <compileSrc> == false the <classpathstr> is not really important
17:09 edrin egonw: this client uses such autogenerated code to use the HIVpredict service of ola. athough i think there is a problem in the service itself...
17:09 edrin http://bioclipse.svn.sourceforge.net/v​iewvc/bioclipse/xws/trunk/xws4j-hivpre​d-client/src/hivpred/client/HIVPredCli​ent.java?revision=7523&amp;view=markup
17:09 zarah edrin's link is also http://tinyurl.com/6cmz9w
17:10 CIA-52 bioclipse: carl_masak * r7528 /bioclipse2/trunk/manager-apidocs/ (parse-file-for-annotations run-the-whole-thing):
17:10 CIA-52 bioclipse: [manager-apidocs] now recognizes @PublishedClass annotations and lists them
17:10 CIA-52 bioclipse: as YAML.
17:13 egonw edrin: try cdk1, with calculateMass
17:14 edrin egonw: cant do, i am in institute
17:14 egonw ah, ok
17:24 CIA-52 bioclipse: carl_masak * r7529 /bot/trunk/zarah.pl: [zarah] now greets meklund with "ni hao!" sometimes
17:24 zarah joined #bioclipse
17:48 * edrin goes
17:48 edrin left #bioclipse
17:55 * egonw too
19:27 edrin joined #bioclipse
19:31 CIA-52 bioclipse: edrin_t * r7530 /xws/trunk/xws4j/src/net/bioclipse/​xws/client/xmpp/ClientSession.java: test for IExecutionPipe != null when creating a client!
19:49 CIA-52 bioclipse: edrin_t * r7531 /xws/trunk/xws4j-binding/src/net/bioclipse​/xws/binding/tools/IoFactoryBuilder.java: optimized
22:07 CIA-52 bioclipse: edrin_t * r7532 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (7 files in 3 dirs):

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