Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-02

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Time Nick Message
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07:40 jonalv Gpox:
07:40 jonalv Gpox: ping
07:40 Gpox pong
07:41 jonalv Gpox: I am trying the jchempaint editor in 2.4.0.RC1
07:41 jonalv I don't seem to be able to save
07:41 olass joined #bioclipse
07:41 jonalv on Ubuntu I got an error message on mac nothing happends
07:41 olass moin
07:41 zarah saluton olass
07:45 Gpox jonalv: bug report? is in only when you save as?
07:46 jonalv @pz 1975
07:46 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1975
07:46 jonalv Gpox: den
07:55 olass jonalv++ //I never thanked you for the release!
07:56 jonalv :)
07:56 olass good job!
07:56 * jonalv is oin bug hunt now. olass will you join me?
07:56 olass did you tag also?
07:56 * olass is already hunting
07:56 jonalv olass: yes I created tags
07:56 * olass will also be in tel conf for most of the day
07:56 jonalv they are in my forks
07:57 olass as it should be
07:57 olass pull reqs?
07:57 jonalv olass: right yea I should maybe send such
07:57 olass please push for core (if you have not done that)
07:57 olass or send patches
07:57 olass either or
07:58 jonalv but to be honest I think it's too much work sending pull requests to everyone
07:58 * jonalv is looking forwards to the bioclipse account on github
07:58 olass I agree
07:59 olass we'll set that up when I get back
07:59 olass jonalv: since I will leave for holiday, is it OK if I  assign some new bugs to you (instead of myself as before) so they don't get lost?
07:59 olass previously I kept many bugs for later
07:59 jonalv olass: hm hopw much work is it, do you think we could do it?
07:59 olass let's do it when I get back please
07:59 olass I want to be in on this
08:00 jonalv :)
08:00 jonalv olass: yea I guess I can take the bugs
08:00 olass for distribution I mean
08:00 jonalv I will try to get rid of them... :)
08:00 olass not that you should solve them all :)
08:00 olass hehe
08:22 Gpox grr
08:25 jonalv Gpox: huh?
08:25 olass lejon?
08:25 Gpox logger.setLevel(Level.INFO);
08:25 Gpox logger.setLevel(Level.INFO);
08:25 Gpox @pz 1975
08:25 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1975
08:26 Gpox it uses setLevel which caues the error but the logger isn't even used in anywhere in that class
08:59 Gpox jonalv: I can take bug 1977 if you are not working on it
08:59 jonalv @pz 1977
08:59 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1977
08:59 jonalv Gpox: please go ahead :)
09:00 Gpox allready see the error, new Shell()
09:00 jonalv okcool, Gpox++
09:29 CIA-69 bioclipse.ds: Ola Spjuth jcp-moltable-events * r35309a1 / plugins/net.bioclipse.ds.ui/src/net/​bioclipse/ds/ui/views/Eventview.java : Fixed events. - http://bit.ly/9imk0h
09:31 annzi joined #bioclipse
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09:39 egonw joined #bioclipse
09:39 egonw annzi: http://github.com/egonw/chembl.rdf
09:39 zarah egonw's link is also http://tinyurl.com/ygu5bqw
09:39 egonw moin all
09:39 zarah saluton egonw
09:45 masak public static void moin(String[] _) {}
09:56 CIA-69 bioclipse.moss: Egon Willighagen 1-mossProps * rcbceb48 / plugins/net.bioclipse.moss.business/src/net/bio​clipse/moss/business/props/MossProperties.java : Added template properties class. (+48 more commits...) - http://bit.ly/93pxPT
09:57 egonw jonalv: RC1 is not based on CDK 1.3.5
09:57 egonw or is it?
09:57 * egonw is confused...
09:57 jonalv egonw: beats me I just copied olass text... :)
09:58 jonalv egonw: will you test the Ubuntu version?
09:58 egonw jonalv-- (for not thinking for himself)
09:58 egonw jonalv: yes, I guess so
09:58 jonalv cool
09:59 * jonalv @ lunch
10:28 CIA-69 bioclipse.moss: annzi master * re3a7fe7 / plugins/net.bioclipse.moss.business/plugin.xml : removed duplicated line (+16 more commits...) - http://bit.ly/cHu6Tb
10:56 egonw all: do we have plugins, bundles, or whatever, for JFreeChart?
11:04 olass egonw: we have that in net.b.chart plugin I think
11:05 olass maybe we should refactor this out to a net.b.jfreechart plugin, with unpacked jars
11:05 olass Gpox: what do you suggest?
11:05 egonw yeah, annzi is using it too
11:05 olass and I am using it in HIVDRC plugins
11:05 egonw :)
11:06 olass on the other hand, the net.bc.chart can reexport the packages
11:06 olass but I guess it is nic eto have a proper plugin for jfreechart
11:06 egonw I rather see separate bundels, personally...
11:06 egonw indeed
11:08 Gpox http://www.springsource.com/repository/ap​p/library/version/detail?name=org.jfree.c​hart&version=1.0.9&searchType=lib​rariesByName&searchQuery=jfreechart
11:08 zarah Gpox's link is also http://tinyurl.com/2dtvlae
11:08 egonw no newer version?
11:08 egonw .chart uses .10
11:09 olass add to TP?
11:09 egonw anzzi has .13
11:09 Gpox probably
11:10 Gpox 1.0.13 latest version
11:10 egonw right
11:15 CIA-69 bioclipse.moss: Egon Willighagen master * r6ca7ac4 / plugins/net.bioclipse.moss.business/src/net/bioc​lipse/moss/business/chemblMoss/ui/Activator.java : Removed redundant file - http://bit.ly/9PkewG
11:15 CIA-69 bioclipse.moss: Egon Willighagen master * r3a1a4f2 / plugins/net.bioclipse.moss.business/src/ne​t/bioclipse/moss/business/MossManager.java : Fixed layout of copyright header - http://bit.ly/atsuOV
11:48 CIA-69 bioclipse.cheminformatics: Arvid Berg 2.4.x * r4c6cbd4 / (4 files):
11:48 CIA-69 bioclipse.cheminformatics: Changed handler to use shell from event.
11:48 CIA-69 bioclipse.cheminformatics: Also did some cleanup of the code to simplify the introduction of the shell parameter.
11:48 CIA-69 bioclipse.cheminformatics: Solves bug 1977 - http://bit.ly/9YmLFq
11:48 zarah bug #1977 | http://tinyurl.com/3anjq6y
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12:15 CIA-69 bioclipse.moss: Egon Willighagen master * rd951313 / plugins/net.bioclipse.moss.business/src/ne​t/bioclipse/moss/business/MossManager.java : Removed unused import - http://bit.ly/aD6J0G
12:15 CIA-69 bioclipse.moss: Egon Willighagen master * r9ca920c / plugins/net.bioclipse.moss.b​usiness/META-INF/MANIFEST.MF : Dependencies on Bioclipse functionality should use Bundle-Depends, not Import-Pacakge - http://bit.ly/dcQUmD
12:15 CIA-69 bioclipse.moss: Egon Willighagen master * r08249a4 / features/net.bioclipse.moss_feature/feature.xml : Added current ChEMBL dependency - http://bit.ly/cSnsPM
12:15 CIA-69 bioclipse.moss: Egon Willighagen master * r5e17e13 / features/net.bioclipse.moss_feature/moss.product : Updated the MoSS product definition - http://bit.ly/8XgJDu
12:31 egonw jonalv: bug report
12:31 egonw BioclipseExceptions do not get nicely displayed in the console
12:31 egonw but it dumps a javax.script.ScriptException instead
12:32 egonw javax.script.ScriptException: sun.org.mozilla.javascript.WrappedException:
12:32 egonw Wrapped java.lang.reflect.UndeclaredThrowableException (<Unknown source>#1) in
12:32 egonw <Unknown source> at line number 1
12:33 jonalv egonw: is that what's going on?
12:33 jonalv egonw: how can I reproduce easily?
12:42 jonalv egonw: do you have a minute?
12:42 jonalv I can't reproduce
12:43 egonw yes, in 5 minutes or so...
12:57 jonalv olass: regarding 1210
12:57 jonalv @pz 1210
12:57 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1210
12:57 jonalv olass: what is the problem?
12:58 egonw annzi: moss.createMoSSProperties(moss.cr​eateMoSSProperties().toString())
12:58 egonw roundtripping moss properties in JSON :)
13:06 CIA-69 bioclipse.moss: Egon Willighagen master * rba13b12 / (3 files in 2 dirs): Implemented roundtripping of moss properties in JSON (+6 more commits...) - http://bit.ly/bD2YvE
13:17 egonw jonalv: no, adding throws BioclipseException to the IMossManager interface does not help
13:17 jonalv as expected
13:18 egonw there *is* another diff
13:18 egonw fromSMILES has an alternative in the interface with a hook
13:18 jonalv mhm?
13:18 jonalv whic one is being run?
13:19 egonw no idea
13:19 CIA-69 bioclipse.moss: Egon Willighagen master * rd012a82 / plugins/net.bioclipse.moss.business/src/net​/bioclipse/moss/business/IMossManager.java : Methods throws an BioclipseException: added this info to the interface too now - http://bit.ly/a25yne
13:19 egonw how can I tell?
13:19 egonw olass: ping
13:19 jonalv egonw: debug? System.out.println, logger.Debug...
13:20 jonalv egonw: maybe it's time to add debug flag to the dispatcher?
13:20 egonw yes, interesting idea!
13:20 egonw jonalv++
13:20 jonalv olass: ping
13:21 egonw I was first
13:21 egonw olass: implemented bioclipse.isOnline()
13:21 jonalv egonw: actually no I don't thin so
13:21 egonw patch or direct commit?
13:21 egonw true, if you count that questions half an hour ago
13:21 egonw -s
13:21 egonw singluar
13:22 egonw > bioclipse.isOnline()
13:22 jonalv egonw: it's the same question I am waiting for an answer on...
13:22 egonw true
13:22 egonw @pz online
13:22 zarah [1398] Generate HTML from update sites   http://tinyurl.com/32vb3kz
13:22 zarah [1411] XML-feature is not operational    http://tinyurl.com/nlswk5
13:22 zarah [343] Task list in Bioclipse for sett... http://tinyurl.com/3ydypjq
13:22 zarah [319] Server for automatic builds wit... http://tinyurl.com/37r8ho2
13:22 zarah Entire list at http://tinyurl.com/3x3k7cb
13:22 egonw @pz isOnline
13:22 zarah egonw: I couldn't find anything on 'isOnline' in the database.
13:25 egonw olass: please let me know if I can commit the bioclipse.isOnline() functionality
13:33 samuell joined #bioclipse
13:36 jonalv egonw, Gpox: Who wrote "snapshoot" for Jchempaint?
13:36 olass egonw: please do
13:36 olass jonalv: pong
13:37 jonalv olass: please explain what your oroblem is with the updates site dialog
13:37 olass I don't see the apply /restore to default buttons until I resize the dialog
13:38 olass jonalv: ping me if you'd like a screenshot
13:38 jonalv olass: hm that is strange
13:38 Gpox jonalv: I did
13:38 jonalv olass: I can confirm that behavior
13:39 jonalv Gpox: was it not possible to use png? jpg is very ugly...
13:42 jonalv olass: why is it? It is only on mac, on Windows it looks good and also on Ubuntu
13:43 CIA-69 bioclipse.core: Egon Willighagen 2.4.x * ra1eb48b / (2 files): Implemented bioclipse.isOnline() - http://bit.ly/9nSQI1
13:49 samuell left #bioclipse
13:50 Gpox jonalv: fixed
13:50 jonalv Gpox: fixed what?
13:51 Gpox png
13:51 jonalv ah sweet
13:53 egonw olass: and did you see I rebased that qsar patch?
13:54 olass no, but thanks
13:54 olass in the bug?
13:54 egonw Gpox: why not use the IFile file for defining a better image.png file name?
13:55 egonw olass: yeah, in the same report
13:55 egonw Gpox: oh... you are
13:55 egonw Gpox: nvm :)
13:55 egonw stupid diffs only showing a small snippet
13:56 CIA-69 bioclipse.cheminformatics: Arvid Berg 2.4.x * r5f965e5 / plugins/net.bioclipse.cdk.jchempaint/src/net/biocl​ipse/cdk/jchempaint/handlers/SnapshotHandler.java : Change snapshot to use png and method from widget to retrive the image - http://bit.ly/bnSCyx
13:57 olass egonw++
14:11 CIA-69 bioclipse.core: jonalv 2.4.x * ra88e371 / plugins/net.bioclipse.ui/src/net/bioclips​e/ui/prefs/UpdateSitesPreferencePage.java : call pack() on parent too, fixes bug: #1210 - http://bit.ly/9O3kZN
14:11 zarah bug #1210 | http://tinyurl.com/yg2supz
14:13 olass egonw: what was the bug number again for teh rebased qsar commit?
14:13 egonw @pz isValid
14:13 zarah [1537] Implement isValidDescriptorDef... http://tinyurl.com/2ufvn9a
14:13 zarah Entire list at http://tinyurl.com/3abc7hs
14:13 egonw zarah++
14:15 egonw Gpox: ping
14:15 Gpox pong
14:16 egonw Gpox: can everyone now move to the new-target-platform ?
14:16 Gpox I don't see why not
14:17 egonw olass: can I propse to replace target.platform with the new one then?
14:17 olass +1
14:17 egonw Gpox: can you make it so?
14:17 egonw slyrus: please take note of this
14:17 egonw and everyone else who has a bioclipse2.4 workspace
14:18 CIA-69 bioclipse.cheminformatics: Arvid Berg 2.4.x * rd86e9bd / plugins/net.bioclipse.cdk.jchempain​t/src/net/bioclipse/cdk/jchempaint/​widgets/JChemPaintEditorWidget.java :
14:18 CIA-69 bioclipse.cheminformatics: Only update dirty flag on undo/redo
14:18 CIA-69 bioclipse.cheminformatics: Not when adding or removing actions from the undo stack.
14:18 CIA-69 bioclipse.cheminformatics: solves bug 1979 - http://bit.ly/aknW8J
14:18 zarah bug #1979 | http://tinyurl.com/385u8r7
14:22 CIA-69 bioclipse.core: Arvid Berg 2.4.x * r2e87679 / (2 files): Replaced target-platform.target with new-target-platform.target - http://bit.ly/cNJTxh
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14:23 jonalv google make it so
14:23 zarah jonalv: http://en.wikiquote.org/wiki/Jean-Luc_Picard
14:23 jonalv sweet zarah++
14:23 jonalv google++
14:24 egonw (J-L)++
14:24 samuell left #bioclipse
14:28 CIA-69 bioclipse.chembl: Egon Willighagen master * r7b55e93 / (5 files): Added a ChEMBL feature - http://bit.ly/9ALcAs
14:28 CIA-69 bioclipse.chembl: Egon Willighagen master * r0bbb4c4 / (2 files in 2 dirs): Updated the version numbers to something relating to the 2.4.0 series - http://bit.ly/bLja2N
14:30 CIA-69 bioclipse.chembl: Egon Willighagen master * r5f1916e / (5 files): Added a feature for Annzi's ChEMBL-MoSS mashup - http://bit.ly/d7qMa9
14:36 olass egonw: qsar patch does not apply to 2.4.x branch
14:36 egonw que?
14:36 egonw mmm
14:36 egonw it did here...
14:36 egonw mom
14:41 egonw mmm... seems I rebased on the wrong branch
14:42 egonw sorry about that
14:43 jonalv egonw: did you figure anyhting out about that exception handling?
14:43 egonw jonalv: nope
14:44 jonalv egonw: can I reproduce the problem?
14:44 egonw yes, with the updated bioclipse.moss repos
14:48 egonw olass: please try the new patch
14:48 olass will do
14:50 jonalv egonw: which branch in moss?
14:50 egonw master, /me thinks
14:51 CIA-69 bioclipse.qsar: Egon Willighagen 2.4.x * r1424697 / (3 files in 2 dirs): Added implementation of isValidDescriptor(); assumes RDF/XML. Implements #1537. - http://bit.ly/calTTV
14:52 egonw good :)
14:53 olass thanks
14:56 jonalv egonw: right, and then what do I do?
15:01 egonw moss.createMoTAB("{'foo':1}")
15:01 egonw note the TAB
15:19 edrin joined #bioclipse
15:21 edrin hello
15:21 zarah hi edrin
15:21 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
15:21 egonw hi edrin
15:21 edrin hi egon
15:38 CIA-69 bioclipse.chembl: Egon Willighagen master * r5fafa12 / (22 files in 9 dirs): Moved the chEMBL-MoSS mashup code into a separate plugin - http://bit.ly/b9BlmI
15:41 CIA-69 bioclipse.moss: Egon Willighagen master * rfe902cd / (14 files in 5 dirs): Removed ChEMBL depending code, which is now available as separate plugin in the bioclipse.chembl repository - http://bit.ly/b4YHad
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