Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-19

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All times shown according to UTC.

Time Nick Message
05:38 masak joined #bioclipse
07:32 Gpox joined #bioclipse
07:47 CIA-55 bioclipse: egonw * r8907 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Added additional properties (fixes #515 and #519)
07:47 zarah bug #515 | http://tinyurl.com/colx6d
07:48 CIA-55 bioclipse: egonw * r8908 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Use a four digit precision
08:10 rojasm joined #bioclipse
08:55 rojasm joined #bioclipse
09:07 CIA-55 bioclipse: carl_masak * r8909 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/business/JsConsoleManager.java:
09:07 CIA-55 bioclipse: [JsConsoleManager] replaced a "\n" with NEWLINE
09:07 CIA-55 bioclipse: Also added a comment after "\r\n" about why it cannot be similarly replaced.
09:10 masak @pz comment
09:10 zarah [468] Writing generated 3d coordinate... http://tinyurl.com/bzv583
09:10 zarah [469] Save as dialog when saving gene... http://tinyurl.com/bwgkja
09:10 zarah [78] CR/LF problems on windows           http://tinyurl.com/6eznsa
09:10 zarah [1] There are people not using Bioclipse http://tinyurl.com/55k8wf
09:10 zarah [475] Decide if ActionHistoryView sho... http://tinyurl.com/amp4rs
09:10 zarah Entire list (29) at http://tinyurl.com/cxnzrs
09:15 shk3 joined #bioclipse
09:20 rojasm joined #bioclipse
09:24 jonalv joined #bioclipse
09:25 jonalv hi
09:27 sneumann morning
09:27 CIA-55 bioclipse: carl_masak * r8910 /bot/trunk/zarah.pl:
09:27 CIA-55 bioclipse: Revert "[zarah] now doesn't greet people back if they spoke recently"
09:27 CIA-55 bioclipse: This reverts commit 12a7cb7080ae67554ff638211b70998938028fd8. Turns out
09:27 CIA-55 bioclipse: the effect was that zarah didn't greet anyone, and people missed the
09:27 CIA-55 bioclipse: functionality.
09:27 zarah joined #bioclipse
09:35 jonalv masak:
09:35 masak yeeees?
09:35 masak what is it? :)
09:35 jonalv @pz 468
09:35 masak come on!
09:35 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=468
09:35 jonalv masak: can you comment?
09:36 jonalv see the long discussion...
09:37 masak I guess I could comment, but it seems that you are perfectly capable of generating red tape on your own here...
09:37 masak maybe you should elect a committee to investigate standards for assigning tickets.
09:38 masak so that this atrocity does not occur again, I mean.
09:39 * masak wishes Bugzilla were a bit more like RT
09:55 shk3 sorry for trouble
09:55 shk3 I fixed that
09:56 shk3 forgot to mark as fixed
09:57 masak shk3: if it wasn't clear, I wasn't entirely serious above.
09:57 masak I don't consider the incident an atrocity.
09:57 shk3 well, it still was confusing
09:57 masak indeed.
09:58 shk3 hm, it seems you have to reassign first
09:58 shk3 and then mark as fixed
09:58 * masak doesn't think so
09:58 shk3 well, I can't reassign now
10:00 shk3 ok, you got it again
10:00 shk3 please check if it works
10:01 shk3 btw, working on undo redo in jcp right now
10:01 shk3 it's a bit tricky, but getting there
10:02 shk3 hopefully I will send an email around noon explaining the concept
10:06 edrin joined #bioclipse
10:07 olass joined #bioclipse
10:08 olass moin
10:08 zarah ni hao olass
10:08 olass zarah: botsnack
10:08 zarah ;)
10:08 olass zarah: who is the smart one?
10:08 zarah olass: I'm just a bot, you expect me to understand that?
10:08 olass zarah: ok, not you at least
10:08 zarah olass: I'm just a bot, you expect me to understand that?
10:12 masak zarah: don't mind him. he's just making fun of you.
10:12 zarah masak: please rephrase or stop trying to be witty :)
10:23 olass zarah: you are the dumb one
10:23 zarah olass: no, YOU are the dumb one! :)
10:23 olass zarah: no
10:23 zarah olass: I see.
10:26 jonalv @pz
10:26 zarah jonalv: Pelezilla is at http://bugs.bioclipse.net
10:26 egonw joined #bioclipse
10:26 jonalv bugs.bioclipse.net
10:26 jonalv bioclipse.net
10:27 masak net
10:27 * masak
10:33 jonalv @pz proofreading
10:33 zarah jonalv: Zarro boogs found.
10:33 jonalv @pz proof reading
10:33 zarah jonalv: I couldn't find anything on 'proof reading' in the database.
10:33 jonalv zarah: you suck!
10:33 zarah jonalv: I did not understand that
10:34 jonalv :)
10:34 masak @pz proofread
10:34 zarah [403] Proofread and extend documentat... http://tinyurl.com/b3sdg5
10:34 zarah Entire list at http://tinyurl.com/dmogv2
10:42 jonalv @pz wel;vome site
10:42 zarah [273] Validate CML actions shows ever... http://tinyurl.com/cfvur5
10:42 zarah [292] Update Welcome and Help            http://tinyurl.com/cnd7ky
10:42 zarah [25] Delete button does nothing in Bi... http://tinyurl.com/at93pw
10:42 zarah [45] Bioclipse system icons              http://tinyurl.com/bxxc9k
10:42 zarah [24] Simplify sampledata installation    http://tinyurl.com/5z6fej
10:42 zarah Entire list (13) at http://tinyurl.com/bvl7w6
10:42 jonalv @pz welcome page
10:42 zarah [24] Simplify sampledata installation    http://tinyurl.com/5z6fej
10:42 zarah [412] Links to help do not open navig... http://tinyurl.com/bers8k
10:42 zarah Entire list at http://tinyurl.com/djj3ly
10:43 olass joined #bioclipse
10:44 olass egonw: lunch
10:44 jonalv hi olass
10:44 egonw OK
10:44 olass hi jonalv
10:47 CIA-55 bioclipse: carl_masak * r8911 /bot/trunk/zarah.pl: [zarah] now says "you're welcome" when @thank-ed
11:52 CIA-55 bioclipse: goglepox * r8912 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml: Removed matching strategy fixes bug #524
11:52 zarah bug #524 | http://tinyurl.com/aos8qc
11:53 CIA-55 bioclipse: goglepox * r8913 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Changes due to selectin now contains CDKChemObjects
11:53 CIA-55 bioclipse: goglepox * r8914 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/editor/SWTMouseEventRelay.java: Changed to not react on Ctrl-click from macBooks bug #445
11:53 zarah bug #445 | http://tinyurl.com/bddfwo
12:05 masak :q
12:06 masak (oops, mistype)
12:19 jonalv jolt++
12:20 masak karma jolt
12:20 zarah jolt has a karma of 1
12:20 masak karma big_hairy_monkies
12:20 zarah big_hairy_monkies has a karma of 0
12:20 masak big_hairy_monkies--
12:21 jonalv when_fluffy_bunnies_attack++
12:21 masak http://www.bushorchimp.com/
12:21 jonalv @gg when fluffy bunnies atack magic
12:21 zarah jonalv: http://www.wizards.com/magic/magazine​/Article.aspx%3Fx%3Dmtgcom/arcana/696
12:24 masak jonalv: http://harpers.org/archive/2009/01/0082319
12:24 zarah masak's link is also http://tinyurl.com/72u35p
12:26 CIA-55 bioclipse: carl_masak * r8915 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] manager methods are now only found once
12:26 jonalv carl_masak++
12:26 masak karma carl_masak
12:26 zarah carl_masak has a karma of 1
12:26 masak poor guy. :)
12:34 masak jonalv:
12:34 masak @pz 534
12:34 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=534
12:35 egonw Gpox: ping
12:36 Gpox egonw: pong
12:36 egonw Gpox: what folder should I be using instead of /Virtual?
12:36 egonw I only see /Virtual
12:38 Gpox there is only virtual
12:39 egonw oh, OK
12:40 egonw excellent
12:40 egonw that makes things easier :)
12:43 CIA-55 bioclipse: goglepox * r8916 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Changed alignement direction for hydrogens
12:46 jonalv Gpox++
12:53 jonalv Why do I want N to be green? Where have I pickud such bad ideas?
12:56 jonalv edrin, olass: Is the new JS-editor in the net.bioclipse_feature?
12:57 egonw jonalv: N should be blue
12:57 egonw Cl should be green
12:57 olass jonalv: yes
13:00 jonalv olass: hm why don't I have it then? :/
13:01 olass jonalv: ask zarah and you get a suitable answer
13:01 olass zarah: why haven't jonalv updated?
13:01 zarah olass: you've just exceeded my capabilities :/
13:01 CIA-55 bioclipse: goglepox * r8917 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Uses SWT.COLOR_LIST_SELECTION for selection color in JCP
13:01 olass jonalv: you see?
13:02 jonalv olass: you lost me...
13:02 olass :-)
13:02 olass git rebase-merge-update-index-hash-blob-ish
13:03 * olass uses svn
13:03 egonw [14:02:54] <olass> git rebase-merge-update-index-hash-blob-ish
13:03 egonw <- you've given yourself away now
13:03 olass ?
13:03 egonw you sneaky bastard... just been using git all the time already!
13:03 olass mohaha
13:03 egonw making us believe you were still with svn...
13:03 * olass read a tutorial on the plane
13:04 olass git from the bottom up
13:04 olass nic earticle btw
13:04 egonw nice pictures?
13:04 olass grmpf
13:04 olass yes
13:04 olass Me CAN read too
13:04 egonw nothing as nice as a good diagram
13:04 * olass
13:04 egonw particularly for rebase
13:05 egonw :)
13:05 * olass thinks of freebase when seeing rebase
13:05 egonw using freebase?
13:05 egonw I have not made up my mind about it...
13:06 jonalv olass++ //can read, (too)
13:06 jonalv ;)
13:07 olass *murmel*
13:07 masak olass++
13:07 olass @thank masak and jonalv
13:07 zarah masak: olass says thank you
13:07 masak :)
13:07 olass zarah: and jonalv?
13:07 zarah olass: that was not so easy for a little bot to understand
13:08 jonalv zarah: I think you forgot me.. :(
13:08 zarah jonalv: please rephrase or stop trying to be witty :)
13:09 masak zarah: slap jonalv
13:09 * zarah smashes a lamp on jonalv's head
13:09 masak :D
13:09 olass zarah: easy sister
13:09 zarah olass: please rephrase or stop trying to be witty :)
13:09 jonalv @thank zarah
13:09 zarah zarah: jonalv says thank you
13:09 egonw zarah: please be careful with the furniture
13:09 zarah egonw: eh... wha'?
13:09 egonw zarah: you beast
13:09 zarah egonw: excuse me?
13:09 egonw that's better
13:09 masak zarah: reboot now!
13:10 olass *phew*
13:10 olass she was getting mad
13:10 zarah joined #bioclipse
13:10 olass zarah: better now?
13:10 zarah olass: that was not so easy for a little bot to understand
13:10 olass :-(
13:10 masak zarah: thank you
13:10 zarah masak: no, YOU'RE the cute one! :)
13:10 masak :)
13:10 masak @thank you
13:10 zarah masak: no, YOU'RE the cute one! :)
13:10 masak hm.
13:10 jonalv olass: I have updated now. I still don't have the js-editor. What am I doing wrong?
13:11 olass using git?
13:11 jonalv olass: what does that have to do with anything?
13:11 masak olass: oh, be nice. :)
13:11 jonalv olass: don't go blaming the messanger now
13:11 olass ok ok, I'll look at it
13:12 egonw jonalv: you can check the SVN repos via the SF website
13:12 jonalv egonw: yes?
13:12 olass this is what feature.xml says for net.bc_feature
13:12 egonw than you can check if it is your fault, or git-svn or svn repos
13:12 olass <plugin
13:12 olass id="net.bioclipse.jseditor"
13:12 olass download-size="0"
13:12 olass install-size="0"
13:12 olass version="0.0.0"
13:12 olass unpack="false"/>
13:12 olass so it IS there
13:13 olass please check any error messages when starting
13:13 olass so to see if you have a dependency problem
13:13 jonalv hm oki doing that
13:14 olass adding extra deps
13:14 olass just in case
13:14 olass but should run without them
13:14 CIA-55 bioclipse: ospjuth * r8918 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Added 2 deps for jseditor console.
13:14 jonalv no errors
13:14 olass strange
13:14 olass binaty version?
13:15 jonalv sry?
13:15 olass are you running binary version or from Eclipse?
13:15 jonalv what do you mean? binary version? Ah yea I am running from head
13:15 jonalv from within Eclipse
13:15 egonw jonalv, masak: is it OK to have a manager method return int[]?
13:15 masak hm...
13:15 egonw should I be using List<Integer> maybe?
13:16 olass are you running a binary build downloaded from SF or running a just-in-time compiled version from clicking the "run" button in Eclipse?
13:16 olass checked out from SVN?
13:16 jonalv olass: the second
13:16 olass or GIT?
13:16 jonalv git :)
13:16 masak egonw: I'd do List<Integer> unless there was a good reason to do otherwise.
13:16 olass jonalv: what is the first?
13:16 olass SVN?
13:16 egonw masak: OK, was not sure JS would be happy about that...
13:16 olass GIT was mentioned second
13:16 jonalv olass: a binary build from SF
13:16 masak egonw: I haven't tried, so I don't really know.
13:17 olass no JS editor?
13:17 olass :-(
13:17 olass :-(
13:17 egonw jonalv: one for you... I have a method search(String query) and a matching search(String query, IProgressMonitor monitor)... that fine?
13:17 olass in win or mac?
13:17 jonalv olass: mac
13:17 jonalv egonw: seems fine. What manager?
13:17 egonw PubChemManager
13:18 egonw IPubChemManager
13:18 olass tested a freshly downloaded binary beta2 from SF and I get JSEditor here
13:18 olass jonalv: so you are wrong :-)
13:19 jonalv egonw: oh never heard of that one. Have you made it according to the cdk manager receipe or?
13:19 egonw gist recipe
13:19 jonalv olass: yea I got it in the beta 2 release too but not when I a running from trunk from within Eclipse
13:19 olass jonalv: come here and see for yourself
13:19 olass good
13:20 jonalv olass: come here and see for yourself
13:55 jonalv olass, egonw, shk3 DO we still need the outdated folder?
13:55 jonalv ...or perhaps someone else knows something?
13:59 shk3 which folder are you talking about?
14:02 egonw jonalv: yes
14:02 egonw jonalv: AFAIK, not everything has been replaced yet
14:02 egonw e.g. the reaction plugins
14:04 jonalv egonw: okey, I am looking forward to the day when we don't need that one...
14:04 shk3 ah, you talk about svn
14:06 shk3 did anybody get my email about undo/redo from about 2h ago
14:06 shk3 ?
14:06 shk3 looks like this doesn't get through
14:07 shk3 sent to to bc-devel and cdk-jcp
14:07 jonalv shk3: no I don't think I have gotten anything..
14:08 shk3 hm
14:08 shk3 will resend it
14:09 egonw shk3: about the old class?
14:09 egonw just replied to that one
14:09 shk3 no, about the new classes
14:09 shk3 at least the one to cdk-jcp now arrived
14:09 egonw I had not received those yet, AFAIK
14:09 egonw just the ones that arrived 0min ago
14:10 shk3 resent the other one 1 min ago
14:10 shk3 lets wait
14:13 shk3 got it via bc-devel as well now
14:13 shk3 and right now, the one sent 12:03 arrived as well
14:20 masak egonw: re r8908, what's the reason for rounding?
14:20 egonw because it makes no sense to be more precise
14:21 egonw not in chemistry
14:21 egonw and makes it less readable
14:22 masak if it has to do with readability when outputting, dividing is not a foolproof way to make sure that you get a readable result.
14:23 egonw patches always welcome
14:24 masak egonw: sure, but I need to understand the domain first.
14:24 masak specifically, where this number is used.
14:25 masak I believe this is the Java way to round things: http://java.sun.com/j2se/1.5.0/doc​s/api/java/text/NumberFormat.html
14:25 zarah masak's link is also http://tinyurl.com/zv5jf
14:25 julio joined #bioclipse
14:25 julio left #bioclipse
14:27 egonw gilleain++ (for the cleanup() patch)
14:27 jonalv egonw: why does it say EXPERIMENTAL after jchempaint in pelezilla?
14:27 egonw because it was rather EXPERIMENTAL...
14:27 jonalv egonw: isn't jchempaint in the bheta release?
14:28 egonw I guess we can start consider removing it now...
14:28 egonw maybe call it beta or so ;)
14:28 jonalv egonw: oki...
14:28 jonalv or just jchempaint?
14:28 egonw oh, wait... that's a good idea :)
14:29 jonalv good :)
14:30 egonw jonalv: done
14:50 egonw http://www.ozonehouse.com/mark/periodic/
14:50 zarah egonw's link is also http://tinyurl.com/cgmm4w
14:50 egonw "Periodic Table of the Operators"
14:50 egonw the Noble Metaops :)
14:51 masak egonw: I contacted the guy a month or so ago, and he updated it.
14:51 masak he's been dropping by on #perl6 now and then to ask questions.
14:52 masak Larry Wall changed a few operators around due to some discussions that arose because of his work.
14:52 egonw good :)
14:52 egonw nothing as nice as symmetry
14:52 masak that's not the first thing that comes to mind when thinking of the Perl 6 operators, though :)
14:53 * egonw is heading home now
14:53 egonw bbl
15:32 * jonalv never reaches the js-editor. He just keeps finding more jchempaint bugs...
15:33 masak jonalv++
15:45 egonw joined #bioclipse
15:48 CIA-55 bioclipse: egonw * r8919 /bioclipse2/trunk/plugins/net.bioclipse.pubchem/ (15 files in 7 dirs): Copied the PubChem plugin from BC1
15:49 CIA-55 bioclipse: egonw * r8920 /bioclipse2/trunk/plugins/net.bioclipse.pubchem/sr​c/net/bioclipse/wizards/NewFromPubChemWizard.java: Added missing copyright/license header
15:49 CIA-55 bioclipse: egonw * r8921 /bioclipse2/trunk/plugins/net.bioclipse.pubchem/ (10 files in 6 dirs):
15:49 CIA-55 bioclipse: Cleanup:
15:49 CIA-55 bioclipse: * proper package names
15:49 CIA-55 bioclipse: * missing copyright notices (extract from svn logs in bioclipse/)
15:50 CIA-55 bioclipse: egonw * r8922 /bioclipse2/trunk/plugins/net.bioclipse.pubchem/ (11 files in 6 dirs):
15:50 CIA-55 bioclipse: Added manager:
15:50 CIA-55 bioclipse: * working loadCompound
15:50 CIA-55 bioclipse: * template search
15:50 CIA-55 bioclipse: Wizard is not working yet, and needs to be rewritten to use the above, once the search code has been transfered.
16:15 jonalv @tell edrin You have a new bug with number 551 in pelezilla :)
16:15 zarah Consider it noted.
16:15 edrin @pz 551
16:15 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=551
16:15 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
16:15 edrin @msg
16:15 zarah edrin: 20 s ago, jonalv said You have a new bug with number 551 in pelezilla :)
16:16 edrin jonalv: I dont understand this bug, what did you do?
16:16 jonalv edrin: good question. Nothing |I think...
16:17 edrin when did the error occur ?
16:17 jonalv but I don't understand it either...
16:17 edrin did you run a scipt?
16:17 jonalv I just imported it. I haven't had it imported in my workspace before.
16:18 edrin oh
16:18 edrin jonalv: can you rebuild your workspace?
16:18 jonalv edrin: it didn't help...
16:19 jonalv edrin: do you have any idea?
16:19 edrin was ther scripting plugin changed in the meantime? is it up to date on your eclipse checkout? The method enterContext() is undefined for the type ContextFactory <- this is solely rhino API,
16:20 jonalv everything should be up to date here...
16:21 edrin Context cx = ContextFactory.getGlobal().enterContext(); <- this is rhino API only
16:21 jonalv okey but what could have gone wrong?
16:22 edrin most likely it is a workspace problem, the only other case could be, in my opinion, that the rhino js.jar was changed or not properly exported in net.bioclipse.scripting
16:23 jonalv hm seems I have a js.jar too much...
16:23 edrin too much?
16:23 jonalv it has grabbed the js.jar from my Eclipse installation
16:23 jonalv is that the wrong version?
16:23 edrin ah ok
16:23 edrin most likely
16:24 jonalv We need to add a min version to that dep then. I will do that
16:24 edrin it should use the one of net.bioclipse.scripting
16:24 edrin ok
16:24 edrin thanks
16:25 jonalv edrin: you wouldn't happend to remember the version?
16:25 jonalv I can't find the jar... :/
16:26 edrin Rhino 1.7R1 is the most recent qualified release. <- this one
16:27 jonalv I can't specify that version
16:27 jonalv I can specify 1.7.0
16:28 jonalv let's see if that works
16:29 jonalv gah there is no version information exported
16:29 edrin oh :/
16:30 edrin unfortunately the API of 1.7 changed a bit compared to 1.6
16:30 jonalv maybe a hard dep to that plugin can enforce it?
16:30 jonalv best would be to add version information but that would mean that I really need to know the _exact_ version in the scripting plugin
16:32 jonalv okey a hard dep net.bioclipse.jseditor -> net.bioclispe.scripting did the trick
16:32 jonalv anyone have anything against that? olass? masak? edrin?
16:33 edrin hm...
16:34 edrin jonalv: why is rhino in eclipse imports
16:34 jonalv edrin: what do you mean? Eclispe imoirts?
16:34 edrin yes?
16:34 * masak does not have anything against that
16:34 edrin yes!
16:34 jonalv edrin: you lost me...
16:36 edrin jonalv: if there is no other way to make it running for you we can change it. i do not like it so much as the editor would fully work in eclipse itself this way, too.
16:37 jonalv edrin: okey, then it would be better to just import a js but it is very important to have the version numbering correct in that case
16:37 edrin jonalv: i think rhino should not be part of the eclipse packages
16:37 edrin jonalv: yes, i know
16:38 jonalv edrin: rhino is a part of net.bioclispe.scripting doesn't that make sence?
16:38 edrin jonalv: we have to expect a conflict if another bc plugin exports an old version of rhino, but is rhino really as part of eclipse?
16:39 jonalv edrin: I found a rhino jar in my Eclipse yes
16:39 edrin very strange
16:39 jonalv Most things end up there...
16:39 edrin did you install this monkey thing?
16:40 edrin these packages should not end up in bc?
16:40 edrin hm
16:40 jonalv enforcing versions by making sure that no jar with another version number is around is probably not the best way...
16:40 jonalv edrin: what monkey thing?
16:41 edrin jonalv: could it be that the "required plugins" in the run dialog were not calculated properly when you run your bc instance and it imported some strange eclipse plugin beside net.bioclipse.scripting?
16:41 jonalv edrin: yea that is exactly what happend
16:41 jonalv since there was no version on the javascript import
16:41 jonalv so it just took one, which should be okey
16:41 edrin jonalv: there are some rhino based plugins around for eclipse IDE with scripting support
16:42 jonalv but we need the latest version of js
16:42 jonalv so we need an import with a specified version
16:42 edrin jonalv: ok, then uncheck the wrong one, these packages should not end up in the bc standalone app anyway, correct?
16:42 jonalv question is just: how do we find out what version the js.jar in net.bioclispe.scripting is. It does not say anything about that...
16:43 jonalv edrin: I can't just uncheck it. That's not the way to do things
16:43 edrin jonalv: i think there is no way to do this
16:43 jonalv imports that are version critical should specify versions
16:43 edrin sorry :/
16:44 jonalv rhino seems like a more and more terribly bad run project in that case
16:44 jonalv it works for every other project why can't the prople writing rhino do it right?
16:45 jonalv edrin: We can do this in one of two ways
16:45 jonalv 1. have a direct dep to net.bioclispe.scripting
16:45 edrin jonalv: one way would be to 1) not re-export js.jar from net.bioclipse.scripting + 2) add a js.jar to .jseditor plugin. this would result in not too much space i guess...
16:45 jonalv 2. have a versioned import of a js.jar into the editor plugin
16:45 jonalv choose one
16:46 jonalv okey that's a thiord alternative but olass will not like that one...
16:46 jonalv masak: can you comment on this?
16:46 edrin i know ;)
16:47 edrin but it's not too worse in my opinion
16:47 edrin js.jar is not too big
16:47 masak I haven't been following the discussion, but instinctively I don't think we should have several js.jar files.
16:47 masak or even several ways to call js.
16:47 jonalv me neither
16:48 edrin it is 739 kb
16:48 masak the rogue js setup solution in the js editor is a temporary solution in my eyes
16:48 masak I'll try and refactor it so that it uses the js env.
16:49 edrin masak: why is that necessary ?
16:50 edrin masak: right now the jseditor is running standalone, it's not good to increase dependencies, especially when they are not required
16:50 masak edrin: I disagree.
16:50 masak it all has to do with the unified way Bioclipse treats js and managers.
16:50 edrin the jsconsole must run the rhino context alway in another way, anyway
16:51 masak edrin: I just don't like code duplication, and I see no need to have it here.
16:51 jonalv edrin: you may not be increasing deps but you are doing the same thing in many places in slightly different ways. That is in my oppinion worse.
16:51 masak edrin: why in another way?
16:52 edrin jonalv, masak: but that's what I say, js must be run from the jsc differently, comparing to jse. it is not a code duplication
16:52 masak I think it is.
16:52 edrin no
16:52 masak I haven't seen anything to prove the contrary.
16:52 edrin i can explain if you want
16:53 jonalv edrin: just because it's a little bit different doesn't mean that it is not doing about 90% similar stuff
16:53 edrin ok
16:53 edrin no
16:53 edrin ok on: jonalv: currently the editor would even run in solely
16:53 jonalv edrin: no
16:53 jonalv currently if you tried to run the editor solely you would end up with the same problem that I ahve
16:54 jonalv and that is if you ahve my setupo. Yopu might bnot ahve a js.jar at all
16:54 edrin jonalv: the thing that is 90% doing the same stuff is maybe 5 lines of code, but similar to creating a swt button i would not call this a code duplication
16:55 jonalv the problem is that the js.jar does not seem to contain any versioning information as far as I can see. If that is so then the rhino people need to add one or we can just make one up but that won't help you run your plugin in Eclispe without Bioclispe...
16:55 edrin creating the rhino context instance is really not much code, but in fact it is completely different using the context for the editor script, and for the jsconsole
16:56 jonalv edrin: I think we are talking about getting all the managers and starting up all the managers plugins... That is not just 5 rows of code I think... but I might be wrong...
16:56 masak edrin: how so?
16:56 edrin jonalv: context: this means it is used really in two way...
16:57 edrin the system of managers is quite well defined
16:57 edrin i can even use them without depending on the interfaces ;)
16:57 masak edrin: look. you're creating code duplication in the Bioclipse code base, and then you defend it without any substantial arguments.
16:58 masak I think that's not acceptable.
16:58 edrin what did I defined? there is a code duplication if to get the managers, that's true
16:59 masak yes, and we've worked hard not do duplicate that bit.
16:59 masak the whole rest of the Bioclipse GUI + console works with only one copy of that code.
16:59 masak and now the js editor works with a second copy.
17:00 masak what if we need to change the manager loading code slightly?
17:00 edrin but it is used by the jsconsole only, isn't it?
17:00 masak then the copies diverge, or we're lucky and remember to change it in both places.
17:00 masak edrin: no, the js env is used by all of bioclipse.
17:00 edrin masak: what is all of bioclipse?
17:01 masak edrin: it's the entire program.
17:01 masak all parts of it. not just the js console.
17:01 edrin like pressing a button?
17:02 masak sometimes.
17:02 edrin but I agree, maybe to have exactly this code at two location is suboptimal
17:02 masak I think so.
17:02 masak I'll try and refactor it in a day or so.
17:02 edrin hm, but on the other hand all this is eclipse standard extension points
17:03 edrin isn't it?
17:03 masak yes, but with spring and managers intertwined.
17:03 edrin what?
17:04 masak maybe we're talking across purposes.
17:04 masak what did you refer to by 'all this'?
17:05 edrin the way how the manager objects are defined in eclipse memory
17:06 edrin look, the problem I fear here is that all the API defined by bioclipse moves far away from eclipse API...
17:07 edrin like the bioclipse is creating or defining more and more API, and finally the eclipse part gets less then 10% or so...
17:08 edrin like wraping everything through bioclipse inables the possibility to port stuff to eclipse
17:09 edrin hm
17:09 edrin maybe i did not formulate this correctly
17:09 edrin in the right way
17:09 edrin ok
17:09 edrin jonalv: do you understand what I mean?
17:10 jonalv edrin: yes
17:11 masak edrin: I understand what you mean.
17:11 edrin do you agree?
17:11 jonalv edrin: you are the only one intrested in running Bioclipse without Bioclipse so to say I think
17:11 zarah jonalv: oh, shut up :)
17:11 edrin heh ;)
17:11 edrin jonalv: I know what you mean
17:11 masak 哈哈哈
17:12 jonalv edrin: you are the only one intrested in running Bioclipse without Bioclipse so to say I think
17:12 zarah jonalv: no, YOU are the only one! :)
17:12 jonalv *lol*
17:12 masak zarah: no, YOU shut up!
17:12 zarah masak: :)
17:12 edrin but in my believe biclipse should extend eclipse with API useful for bio/informaticians, and not replace or recreate eclipse
17:13 jonalv edrin: then please get the rhino people to add a version number to their jar file
17:13 jonalv edrin: that is what is the problem here
17:14 edrin masak has a point here, too. getting the managers as I do it is not 100% optimal, but maybe we can find a way to get the with API standard calls, too?
17:15 masak what API?
17:15 masak rhino's?
17:15 edrin jonalv: yes, they should add it
17:15 edrin jonalv: can you live, and maybe convince ola, to live with 700kb extra space for now?
17:16 edrin masak: no, the way of collecting managers from the API
17:16 masak it's not about the extra space.
17:16 masak it's about the duplicated code.
17:16 masak edrin: what about the way of collecting managers from the API?
17:16 * masak feels a bit like Eliza
17:18 * jonalv thinks we should proibably just create a new plugin. call it org.mozilla.rhino or something and just package the rhino jar there...
17:18 jonalv seems like the least evil...
17:18 edrin it's a question about the future longlivety of code, if bc dies (it does not) all the plugins that depend on it die too
17:18 edrin jonalv:  thats a good idea
17:19 edrin jonalv: that's exactly what I mean
17:19 masak edrin: I'm not sure I need to like a reasoning step that assumes bc will not survive.
17:20 edrin creating many small plugin, each with minimum dependencies, or at least limited complexity. this way it is much more clear what to do if there is a problem
17:21 edrin if you have one mega plugin that does everything, and a nuke hits it, the centralized system dies...
17:21 masak bc2 depends much on a unified scripting environment.
17:21 edrin if you have many independent cells
17:21 edrin each might constinue to live for itself
17:22 edrin increased survival
17:22 masak edrin: we're not developming individual plugins. we're developing a system of plugins.
17:22 masak I believe in decoupling too, but...
17:23 masak ...there are times when making things work together is nicer.
17:23 jonalv http://www.springsource.com/repository/app/b​undle/version/detail?name=com.springsource.o​rg.mozilla.javascript&amp;version=1.7.0.R1
17:23 zarah jonalv's link is also http://tinyurl.com/d3s4vt
17:23 edrin anyway, that's a more complex discussion and i must go, my clock said: fungal cells must be removed...
17:23 jonalv could we just use that one? :)
17:23 edrin ok
17:23 edrin well, what version is it?
17:24 edrin ah 1.7
17:24 edrin sorry
17:24 edrin have to
17:24 edrin go
17:24 edrin really
17:24 edrin my exp/cells
17:24 jonalv edrin: oki
17:26 jonalv @tell edrin I will use it...
17:26 zarah Consider it noted.
17:26 edrin ok
17:26 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
17:26 edrin protocl
17:49 CIA-55 bioclipse: jonalv * r8923 /bioclipse2/trunk/ (7 files in 7 dirs): switched to bundled version of rhino (1.7.0RC1) which resides in the target platform.
17:54 zarah joined #bioclipse
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17:55 maclean shk3: about selections not showing
17:56 shk3 yes
17:56 maclean update
17:56 maclean but yes, sorry I did break it
17:57 shk3 no problem
17:57 shk3 just wanted to make sure it's known
17:57 maclean ok
17:57 maclean by the way, in that update you might notice we changed how selections work
17:57 maclean (slightly)
17:57 jonalv oh for your information: After you update you need to set target platform due to my last commit
17:58 maclean shk3 : for details on the change, see the whiteboard behind you :)
17:58 maclean jonalv : oh hai prolific bug reporter! :)
17:58 jonalv :)
17:59 jonalv yup I was gonna move on to the js-editor but I couldn't get it to run untill after that commit :)
17:59 maclean I now have 4 times the bugs I had yesterday...
17:59 jonalv woho :)
17:59 shk3 in jcp or bioclipse?
17:59 maclean no just bioclpse
18:00 maclean but developing in both simultaneosly is a pain
18:00 jonalv tomorrow I will look at the js-editor :)
18:00 jonalv now I think it's time to head home
18:00 maclean bye
18:00 jonalv it's about 11 hours since I arrived here...
18:01 maclean !!
18:01 jonalv it's been a craxy day...
18:01 shk3 craxy?
18:01 jonalv |crazy
18:01 shk3 ah, crazy
18:01 jonalv I had an exam that started 11 hours ago...
18:02 maclean 8am?
18:02 jonalv and I sort of couldn't stop reporting bugs there for a while... :)
18:02 jonalv yup
18:02 maclean :(
18:02 jonalv and then I really wanted to solve the rhino trouble a litle bit
18:02 shk3 I am leaving as well
18:03 jonalv btw: can someone confirm that rhino is workling after my commit?
18:03 jonalv or nvm, it's not like I am gonna fix it now if it's not working... :)
18:04 maclean I'll try
19:42 egonw joined #bioclipse
19:42 egonw moin
19:42 zarah privet egonw
19:50 edrin left #bioclipse
20:13 maclean joined #bioclipse
21:58 CIA-55 bioclipse: egonw * r8924 /bioclipse2/trunk/cdk-externals​/trunk/org.openscience.cdk.io/ (3 files in 3 dirs): Updated to CDK 1.1.5.20090219, commit 14207: fixes reading of 2D and 3D coordinates from PubChem XML files
22:50 CIA-55 bioclipse: egonw * r8925 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Support reading PubChem Compound XML files too now
22:58 CIA-55 bioclipse: egonw * r8926 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Cleaned up code: removed unimportant IChemFile field (it was there only for the convention constructor, but the IChemFile is actually overwritten when being used, so no worries in setting it null)
23:16 CIA-55 bioclipse: egonw * r8927 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Show content-type in CDKMolecule props view
23:17 CIA-55 bioclipse: egonw * r8928 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Use the human readable name, not some cryptic internal representation

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