| Time |
S |
Nick |
Message |
| 08:18 |
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malick joined #bioclipse |
| 08:30 |
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Gpox joined #bioclipse |
| 09:05 |
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egonw joined #bioclipse |
| 09:14 |
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gilleain joined #bioclipse |
| 09:20 |
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edrin joined #bioclipse |
| 09:21 |
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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 |
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gilleain joined #bioclipse |
| 10:54 |
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thomasku joined #bioclipse |
| 12:05 |
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charlgren joined #bioclipse |
| 12:53 |
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egonw joined #bioclipse |
| 13:00 |
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gilleain joined #bioclipse |
| 13:00 |
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gilleain joined #bioclipse |
| 14:08 |
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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 |
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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.Element->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(XMLConverter.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.sourcefor[…]=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/resolver.jar;c:/xmlbeans/xbean.jar;c:/xmlbeans/xbean_xpath.jar;c:/xmlbeans/xmlbeans-qname.jar;c:/xmlbeans/xmlpublic.jar;c:/xws4j-binding-test.jar;c:/xws4j-test.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.sourcefor[…]=7523&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 |
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zarah joined #bioclipse |
| 17:48 |
|
* edrin |
goes |
| 17:48 |
|
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edrin left #bioclipse |
| 17:55 |
|
* egonw |
too |
| 19:27 |
|
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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): |
