Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-07

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All times shown according to UTC.

Time Nick Message
10:52 egonw joined #bioclipse
10:59 edrin joined #bioclipse
10:59 edrin hi
10:59 zarah hello edrin, you fantastic person you
11:04 edrin egonw: around?
11:11 edrin joined #bioclipse
11:14 edrin egonw: around?
11:25 egonw joined #bioclipse
11:29 edrin hi egonw
11:29 edrin egonw: available?
11:53 egonw joined #bioclipse
12:12 egonw joined #bioclipse
12:13 egonw hi edrin
12:13 egonw yes, got your email
12:29 egonw joined #bioclipse
14:28 egonw @tell edrin the new XMPP services are up and running... now testing them with custom clients to verify they work properly after the refactoring
14:28 zarah Consider it noted.
14:28 egonw zarah: that took you long to think about
14:28 zarah egonw: I'm just a bot, you expect me to understand that?
14:52 egonw @tell edrin all services are up, running and tested
14:52 zarah Consider it noted.
16:41 edrin joined #bioclipse
16:42 edrin hi again
16:42 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
16:42 edrin @msg
16:42 zarah edrin: 2 h 13 m 42 s ago, egonw said the new XMPP services are up and running... now testing them with custom clients to verify they work properly after the refactoring
16:42 zarah edrin: 1 h 49 m 31 s ago, egonw said all services are up, running and tested
16:43 edrin very cool
16:44 edrin when hivpred and bioschemata are up again ws1 will look quite crowded...
16:51 egonw :)
16:51 egonw indeed
16:51 egonw are you testing the services?
16:51 egonw I see activity :)
16:51 edrin egonw: i tried to create bindings:
16:52 edrin got an error because the node of RDF service (service function name) containe spaces...
16:52 egonw make sure not to try for those services which do CML in or out
16:52 egonw edrin: ah... :(
16:52 egonw was wondering about that...
16:52 edrin that's a problem for my .java file generator ;)
16:52 egonw :)
16:53 edrin although i dont know if spaces in node names are legal in xmpp
16:53 egonw ok, have the .java file generator remove spaces?
16:53 egonw I did not get errors
16:53 egonw did not mine for warnings
16:53 edrin package se.uu.bmc.ws1.rdf.bridge to rdf.openmolecules.net;
16:53 edrin "bridge to rdf"
16:53 edrin yes
16:53 edrin have to look into it
16:54 edrin bur i am not 100% sure if spaces are allowed as nodes in xmpp
16:54 edrin anyway, it seems to work
16:55 edrin pls do not change now...
16:55 edrin i will try to fix the binding creator
16:55 edrin ...
16:55 egonw OK
17:23 egonw almost going for dinner
17:29 CIA-55 bioclipse: edrin_t * r8654 /xws/trunk/xws4j-binding/src/net/bioclip​se/xws/binding/tools/Function2Name.java: fixed a bug, now removes spaces from package name
17:30 egonw bbl
17:30 edrin ok
17:31 egonw quicky
17:31 egonw we are moving to LaTeX now, right?
17:31 edrin do you think we should do this?
17:31 egonw yes
17:31 edrin I cant use this in the lab
17:31 egonw I find it a pain to edit a larger document like this in GDoc
17:32 egonw in particular the refs I really like to start cleaning up
17:32 edrin yes
17:32 edrin i can do this
17:32 egonw that's is so much easier in BibTex
17:32 egonw yes, that was the deal... I know...
17:32 edrin i could compile everything together in an MS Office Doc
17:33 egonw the BMCBioInfo latex stylesheet is really good
17:33 egonw anyway... going to eat now :)
17:33 edrin ok, these QSAR stuff seems to use CML ;)
17:33 edrin ok, cu
17:34 egonw yes
17:35 egonw ok, really gone now :)
17:35 edrin zarah tell egonw would it be possible to use a slimmed down CML "derived" schema for these functions that would succeed to create bindings?
17:35 zarah Consider it noted.
17:49 CIA-55 bioclipse: edrin_t * r8655 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (5 files in 3 dirs): updated to current xws4j-binding
18:11 edrin scripting console is not working for me
18:13 edrin @pz
18:13 zarah edrin: Pelezilla is at http://bugs.bioclipse.net
18:23 shk3 joined #bioclipse
18:26 edrin hm....
18:26 edrin shk3 if you type the following command in your bc2 javascript console, does it work for you?
18:26 edrin f = xmpp.getFunction("rdf.ws1.bmc.uu.se","Bridge to RDF.OpenMolecules.net");
18:27 shk3 need to start bioclipse
18:31 edrin there seems to be a bug
18:31 edrin > f = xmpp.getFunction("rdf.ws1.bmc.uu.se","Bridge to RDF.OpenMolecules.");
18:31 edrin Function: rdf.ws1.bmc.uu.se (Bridge to RDF.OpenMolecules.)
18:31 edrin this line works:
18:31 edrin f = xmpp.getFunction("rdf.ws1.bmc.uu.se","Bridge to RDF.OpenMolecules.");
18:31 edrin this line does not:
18:31 edrin f = xmpp.getFunction("rdf.ws1.bmc.uu.se","Bridge to RDF.OpenMolecules.net");
18:32 edrin probably because the line is too long ("net")
18:34 shk3 Could not create default client: the plug-in has set invalide account data in
18:34 shk3 preferences.
18:34 shk3 that's what I get
18:34 edrin ok
18:34 edrin so this is windows specific again i guess
18:35 edrin shk3: I was talking about this line: f = xmpp.getFunction("rdf.ws1.bmc.uu.se","Bridge to RDF.OpenMolecules.net");
18:35 shk3 I am on Linux
18:35 shk3 yes, that's what I entered
18:35 edrin or this f = xmpp.getFunction("rdf.ws1.bmc.uu.se","looooo​oooooooooooooooooooooooooooooooooooooong");
18:35 edrin ok
18:36 shk3 same answer
18:36 edrin ok
18:36 edrin i get this:
18:36 edrin java.lang.StringIndexOutOfBoundsException: String index out of range: -1
18:36 edrin at java.lang.String.substring(Unknown Source)
18:36 edrin at net.bioclipse.scripting.ui.views.Scr​iptingConsoleView.splitIntoSeveralLi​nes(ScriptingConsoleView.java:406)
18:38 edrin shk3: are you using cml?
18:40 shk3 using cml?
18:40 shk3 in this command?
18:41 edrin no, in general, for your projects
18:42 edrin shk3: btw. if you want to use the xws4j plugin you will have to set a user account in preferences
18:42 shk3 yes
18:42 edrin you can register one for example for ws1.bmc.uu.se
18:43 edrin shk3: my binding lib always fails to create a binding for cml :/
18:43 edrin too complex i feart
18:44 shk3 binding?
18:44 shk3 sorry, I have to leave
18:48 CIA-55 bioclipse: edrin_t * r8656 /bioclipse2/trunk/plugins/ (net.bioclipse.jseditor/ net.bioclipse.rhino/): renamed to a more appropriate name
18:50 CIA-55 bioclipse: edrin_t * r8657 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/ (.project META-INF/MANIFEST.MF): updated for renaming
19:17 CIA-55 bioclipse: edrin_t * r8658 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/ (34 files in 10 dirs): renaming packages
19:54 egonw again?
19:54 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
19:55 egonw edrin: file a bug report about those long lines...
19:55 egonw masak and jonalv were working on wrapping...
19:55 egonw clearly something goes wrong
19:55 egonw @msg
19:55 zarah egonw: 2 h 19 m 56 s ago, edrin said would it be possible to use a slimmed down CML "derived" schema for these functions that would succeed to create bindings?
19:56 egonw edrin: yes, but not next week... a lot of manual work, and no clue how much smaller it would be in the end...
19:56 egonw moreover, I really do not want too...
19:56 egonw it basically says that the default, real world schema is too large...
19:57 * egonw is going offline for today...
19:58 egonw will be back tomorrow
21:32 CIA-55 bioclipse: edrin_t * r8659 /bioclipse2/trunk/plugins/net.bioc​lipse.jseditor/src/net/bioclipse/ (21 files in 5 dirs): updated file stuff like license and dec
23:02 CIA-55 bioclipse: edrin_t * r8660 /bioclipse2/trunk/plugins/net.bioclipse.js​editor/src/net/bioclipse/jseditor/editors/ (5 files): fixed bujg
23:02 CIA-55 bioclipse: edrin_t * r8661 /bioclipse2/trunk/plugins/net.biocli​pse.xws4j/src/net/bioclipse/xws4j/ac​tions/ToggleConnectionAction.java: fixed light bulb bug...
23:03 CIA-55 bioclipse: edrin_t * r8662 /bioclipse2/trunk/plugins/net.bioclips​e.jseditor/src/net/bioclipse/jseditor/ (Activator.java actions/RunRhinoScriptAsJobAction.java): updated Plugin ID

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