Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-11-11

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All times shown according to UTC.

Time Nick Message
06:09 egonw_ joined #bioclipse
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07:51 olass moin
07:51 zarah privet olass
08:29 egonw_ moin
08:29 zarah oh hai egonw_
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10:51 jonalv oh hai
10:51 zarah ni hao jonalv
10:51 jonalv I forgot to sign in. ooops... :)
11:08 * samuell goes for lunch
12:27 jonalv joined #bioclipse
12:27 jonalv o/
12:31 edrin joined #bioclipse
12:32 edrin hi
12:32 zarah hello edrin, you fantastic person you
12:44 egonw jonalv++ (for joining http://blueobelisk.stackexchange.com)
12:44 zarah egonw's link is also http://tinyurl.com/ygkhvp6
12:45 jonalv egonw: yea, only problem is that I can't even vote for answers... Appharently I need something called 'reputation'. Too much bootstrapping for my taste I think... :(
12:48 egonw just leave two comments somewhere, and I'll get you reputation
12:50 egonw oh, and read this page: http://blueobelisk.stackexchange.com/questions/10/​how-can-we-bootstrap-critical-mass-for-this-forum
12:50 zarah egonw's link is also http://tinyurl.com/yep8z5d
12:55 masak joined #bioclipse
13:18 CIA-51 bioclipse.structuredb: jonalv master * r2d9039c / plugins/net.bioclipse.structuredb/src/net/bioc​lipse/structuredb/DBMoleculesEditorModel.java :
13:18 CIA-51 bioclipse.structuredb: Made StructureDB compile.
13:18 CIA-51 bioclipse.structuredb: Fixes bug: #1692 - http://bit.ly/2HQAgw
13:18 zarah bug #1692 | http://tinyurl.com/ydkdjd5
13:30 samuell How to print out to the console from a JS script?
13:33 masak samuell: by using the js manager.
13:33 masak js.print() and js.say()
13:33 samuell Ah...
13:33 samuell Thanks!
13:33 masak np.
13:51 egonw say() does the newline, right?
13:54 masak yes.
13:54 * egonw needs to make more use of that
13:54 masak it's a more pronouncible spelling of 'println' :)
13:54 egonw js.print() feels so natural
13:54 egonw like println()
13:55 masak trust me, js.say() feels natural after a while, too.
13:55 masak also, use Perl 5.10. it has &say :)
14:03 jonalv samuell: How do I change an image in this new mediawiki version?
14:04 samuell jonalv: Hmm... should be as normal... experienced problems?
14:04 samuell Link?
14:04 jonalv it looks different...
14:04 jonalv ah the upload option was only there if I was loged in.
14:05 jonalv I guess I was expecting to be asked to log in when trying to do it...
14:05 samuell Ok
14:08 jonalv samuell: it's not wroking
14:09 jonalv samuell: I uploaded a new verison of the image at: http://wiki.bioclipse.net/i​ndex.php?title=Structure_DB
14:09 zarah jonalv's link is also http://tinyurl.com/y8qk9o8
14:09 jonalv but it is still the same
14:09 samuell Oh, ok
14:10 samuell Could be something with file permissions, that has changed after our upgrade
14:10 jonalv I have tried a couple of times and the history looks right but the current refuses to hagne
14:11 samuell Ok, even after Ctrl + Shift + R?
14:11 samuell Then it is surely file permissions...
14:11 samuell I'll see if I can fix it
14:12 jonalv samuell: Ctrl + Shift + R>
14:12 jonalv samuell: what do you mean with Ctrl + Shift + R?
14:14 samuell (Deep refresh in firefox)
14:14 samuell (Might not be the same in your browser)
14:15 jonalv samuell: Ctrl + Shift + R does nothing for me...
14:16 samuell It is probably a different command... what it does is to empty the browser cache, but that can be done in the menus also I guess
14:17 samuell Otherwise trying to look at the picture itself only, and refreshing, would do the same trick: http://wiki.bioclipse.net/imag​es/StructuredbClassDiagram.png
14:17 zarah samuell's link is also http://tinyurl.com/5z5cvk
14:17 samuell Does that still show the old image?
14:19 jonalv samuell: no when I refresh it chanes to the new one
14:20 samuell Ok... then it was indeed a problem with the browser cache
14:20 samuell I use to have the same problem
14:20 samuell ...until I realize that I have to "deep-refresh" again
14:21 jonalv samuell: okey, thanks
14:21 jonalv firefox--
14:21 samuell jonalv: np!
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14:35 CIA-51 bioclipse.structuredb: jonalv master * r33cca81 / (classDiagram.class.violet classDiagram.png): Class diagram for new slim StructureDB - http://bit.ly/3TlkG6
14:35 egonw jonalv: is the wiki updated?
14:35 egonw or do I need to look up the png in git ?
14:35 jonalv egonw: I have struggled a while and placed the new png on the wiki
14:35 egonw :)
14:35 egonw jonalv++
14:35 egonw (for struggling but persisting)
14:49 jonalv egonw: do you know anythign about this stack trace: http://pastebin.com/mc119858
14:50 egonw can you verify the input?
14:50 egonw I think the molecule passed to the InChI library is not correct
14:51 jonalv it's cycloPropane created from the cyclopropane testdata used by StructurDB
14:51 jonalv is that file broken?
14:51 jonalv egonw: I think it has worked before...
14:52 jonalv egonw: http://github.com/jonalv/bioclipse.structure​db/blob/master/plugins/net.bioclipse.structu​redb.tests/tests/testData/cyclopropane.mol
14:52 zarah jonalv's link is also http://tinyurl.com/yhtdzmg
14:56 egonw looks OK
15:00 jonalv egonw: so what can the problem be then?
15:02 egonw no idea
15:02 egonw did you try a system out of the input as it goes to the inchi lib?
15:02 egonw the actual data model?
15:06 jonalv egonw: nope, I don't een know what I would expect at that stage...
15:07 egonw try to debug CDKMolecule at line 437
15:07 egonw and dump what ever is passed to the calculateInchi() method ...
15:07 egonw oh, wait...
15:07 egonw at org.openscience.cdk.inchi.InChIGeneratorFacto​ry.getInstance(InChIGeneratorFactory.java:96)
15:08 egonw it fails when the factory is instantiated...
15:08 egonw mmm... perhaps a platform thingy...
15:08 egonw did you move to 64 bit OS/X or so?
15:08 jonalv egonw: I am commiting and then you can test run as well. Since you seem to be on the problem anyways... :)
15:08 egonw perhaps ask on blueobelisk.stackexchange.com ? ;)
15:08 egonw my bet is a platform issue
15:09 jonalv egonw: I ahve already asked there... :)
15:09 CIA-51 bioclipse.structuredb: jonalv master * rb485cc1 / (11 files in 2 dirs):
15:09 CIA-51 bioclipse.structuredb: removed domain objects.
15:09 CIA-51 bioclipse.structuredb: Domain tests except InChI related once pass - http://bit.ly/3oxFc2
15:09 egonw ah, indeed :)
15:09 egonw jonalv++
15:09 egonw @karma jonalv
15:09 zarah jonalv has a karma of 175
15:11 jonalv egonw: if so then Inchi generation shouldn\t work at ll in Bioclipse. gonna try that..
15:12 egonw true
15:12 jonalv egonw: nope I get them inside Bioclispe
15:12 jonalv |Bioclipse
15:13 egonw exceptions or inchis?
15:14 jonalv egonw: inchis
15:14 jonalv sry I was trying to aviod having to spell that strane word
15:14 jonalv but I guess all lower case is a good solution...
15:22 egonw then I guess it is a classpath issue?
15:22 jonalv egonw: possible
15:23 jonalv egonw: I have no idea
15:23 jonalv egonw: but how could it be a classpath issue? When running JUnit tests everything is on the class path in Eclipse, right?
15:24 jonalv egonw: + a NullPointerException is a strange exception to get...
15:24 egonw not running as plugin unit test?
15:24 jonalv egonw: nope
15:24 jonalv egonw: not these
15:24 jonalv egonw: could that be the reason?
15:24 egonw dunno
15:25 jonalv hm... But when you run CDK tests you don't run em as plugin tests do you?
15:26 egonw I do
15:26 egonw I now always run as plugin tests
15:26 jonalv egonw: I don't mean Bioclispe ones but CDK ones
15:27 egonw ah, no, those are indeed not run as plugin tests :)
15:34 jonalv egonw: so it should be possible to get it working...
15:34 jonalv I am moving on with the rest right now
15:34 jonalv going to have to come back to that one later...
16:15 CIA-51 bioclipse.core: jonalv 2.2.x * rb72fe70 / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : fixed layot - http://bit.ly/3y8PBR
16:15 CIA-51 bioclipse.core: jonalv 2.2.x * rdc80843 / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : new attempt at layout - http://bit.ly/2XQ0Eo
16:15 CIA-51 bioclipse.core: Ola Spjuth 2.2.x * rb38102d / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : Move Textbox down in dialog. - http://bit.ly/370YXW
16:15 CIA-51 bioclipse.core: Carl Masak 2.2.x * raa23262 / plugins/net.bioclipse.scripting.ui/src/net/bi​oclipse/scripting/ui/views/JsConsoleView.java :
16:15 CIA-51 bioclipse.core: [JsConsoleView] now summarizes long lists on output
16:15 CIA-51 bioclipse.core: A 'long list' is any list of more than two elements. The summary looks like
16:15 CIA-51 bioclipse.core: "List<$T> of size $size". - http://bit.ly/qwcHx
16:54 CIA-51 bioclipse.structuredb: jonalv master * r1439d1c / (37 files in 9 dirs):
16:54 CIA-51 bioclipse.structuredb: Removed stuff until StructureDB compiles again.
16:54 CIA-51 bioclipse.structuredb: Next step will be to remove stuff until it runs again. (And probably add some stuff as well) - http://bit.ly/1wVcfB
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