Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-11-19

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All times shown according to UTC.

Time Nick Message
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10:05 jonalv moin
10:05 zarah saluton jonalv
10:09 egonw jonalv: still thinking about the DBMolecule/INChI problem
10:09 egonw but I have no solution yet
10:09 jonalv egonw: have you tried to run the code on your machine?
10:09 egonw no, still getting compile errors
10:09 egonw and not too much time, with my talk tomorrow
10:10 jonalv egonw: compile errors?
10:10 egonw I think I have not updated yet
10:10 egonw so no worries
10:10 jonalv right
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10:11 * jonalv is trying to get the plugin tests for StructureDB to run.
10:11 jonalv IT sort of works when I run Bioclipse but not when I run the plugin tests
10:11 jonalv I don't understand it
11:35 CIA-57 bioclipse.structuredb: jonalv NWO * r72ac0de / plugins/net.bioclipse.structuredb/src/n​et/bioclipse/structuredb/Activator.java :
11:35 CIA-57 bioclipse.structuredb: fix potential NPE
11:35 CIA-57 bioclipse.structuredb: apharently the getServices method returns an array with content or null (instead of an empty array) - http://bit.ly/NED23
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14:30 CIA-57 bioclipse.structuredb: jonalv NWO * ra50ad76 / plugins/net.bioclipse.structuredb.plugi​ntests/src/net/bioclipse/structuredb/Ab​stractStructuredbManagerPluginTest.java : reordered test cases - http://bit.ly/LPeo1
14:30 CIA-57 bioclipse.structuredb: jonalv NWO * r31f1e38 / (2 files): New World Order changes - http://bit.ly/2Y6AgY
14:59 jonalv egonw, olass: ping
14:59 olass pong
14:59 jonalv I am experiencing some strane behavior when runnign a JSscript
15:00 olass ok?
15:00 jonalv once upon a time the progressmonitor would be penind as if instnatiated with IPogressMonitor.INKNOWN for number opf ticks
15:00 jonalv now it seems to restart for each new manager method call in the script
15:00 jonalv has something broken or has someone changed this behavior in purpose?
15:00 jonalv |on purpose
15:01 olass jonalv: no idea
15:02 jonalv mhm
15:02 olass but I suspect if anybody has changed that it is you
15:03 jonalv olass: yea that would be my guess as well only I don't understand why I would do that....
15:03 jonalv so it has probably broken then...
15:08 jonalv no it appears to be a difference between the console and runnign scripts from the editor
15:09 jonalv from the console it works as it should
15:09 jonalv this is baad..
15:13 egonw jonalv: what java version are you running?
15:13 egonw for me, the js editor is still broken
15:14 egonw edrin: I have not tried your patch yet...
15:14 jonalv egonw: java version "1.6.0_15"
15:14 egonw right
15:14 egonw I think that might be the cause
15:14 jonalv egonw: you asked...
15:15 egonw 1.6.0 comes with a rhino version itself
15:15 jonalv egonw: huh?
15:15 egonw putting *2* rhino libraries on the classpath
15:15 jonalv hm
15:15 jonalv that's bad
15:15 egonw that's why my js editor fails to compile
15:15 egonw jonalv: try running it with java5
15:15 jonalv egonw: but hold on. It works for me...
15:16 egonw then why do you tell us it doesn't?
15:16 jonalv egonw: read again
15:16 egonw [11/19/09 15:59] <jonalv> I am experiencing some strane behavior when runnign a JSscript
15:16 egonw ok, ok
15:16 egonw jonalv: what does strane mean?
15:16 jonalv egonw: strange behavior != not working
15:17 egonw ok, my mistake
15:17 egonw you pinged... so I thought something was wrong
15:17 jonalv egonw: it restarts the progressmonitor  over and over again
15:17 egonw if it's working...
15:17 egonw ah...
15:18 egonw you mean it is working *too much* :)
15:18 egonw seriously...
15:18 egonw what are you trying to aks me?
15:21 jonalv egonw: if I run a JavaScript script that contains multiple manager method calls which each runs as a job then the monitor for the entire script will restart once for each manager method call
15:21 jonalv egonw: is this intnetional?
15:21 jonalv that was the question. The asnwer should be "no"
15:22 jonalv it works as it should from the console but for some reason the editor and he console is not behaving similar. I though masak-- and edrin-- should have settled this by now but appharently it is still two very different approaches being run parallell here
15:24 egonw ah, it was a rethorical question
15:25 * egonw was unjustifiedly thinking about a possible cause...
15:25 jonalv egonw: well it became a rethoricla question when I realised it was only the editor and the console that missbehaved
15:25 egonw my bad
15:25 jonalv |and not the console
15:25 jonalv the console is behaving as it should but the editor is not
15:26 egonw yeah, i guess the parallels with the editor is not working, but the console does is merely pure luck
15:26 egonw with my editor
15:26 jonalv egonw: sry now I lost you
15:32 jonalv okey I am looking into this problem. It's not so nice... :(
15:35 jonalv egonw: what is merely pure luck?
15:36 egonw that we both find the editor not working, but no problems with the console
15:36 jonalv egonw: I am tempted to say that is becasue of the difference in code quality of those two projects....
15:38 egonw then you should be able to find the problem...
15:49 jonalv egonw: it's ugly. The editor uses a manager for running a JavaScript. That might seem like the way to do it but script running is a bit special I am afraid...
15:49 egonw I have no clue
15:49 jonalv no you wouldn't
15:49 * jonalv feels crap today
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16:36 edrin jonalv: the editor uses a bioclipse plugin to run the script (the execution plugin).
16:36 jonalv edrin: seems that it all goes thorugh js.runFile
16:36 edrin jonalv: yes
16:37 jonalv edrin: that is probably the reason but I am not quite sure why...
16:37 edrin jonalv: it pushs the script to this run method
16:38 edrin jonalv: actually the idea was that this execution plugin would also provide a manager methode to get a pipe to a console (like getJavaScriptConsolePipe)
16:38 edrin jonalv: or more simple explained:
16:39 edrin execution should provide the following manager methods:
16:39 jonalv edrin: it's difficult to do this with a vanilla manager. Since when we run a method on a standard manager we are already creatinga job but when we run a script we want to create a very special job
16:39 edrin io-pipe = ex.spawnNewConsoleIOPipe();
16:39 edrin result = ex.runScript(script);
16:40 jonalv edrin: yea I can see the uses of that
16:40 edrin jonalv: sorry, students now again, must go again
16:40 jonalv edrin: oki
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