Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-21

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Time Nick Message
05:34 egonw joined #bioclipse
05:47 sneumann_ joined #bioclipse
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07:00 egonw joined #bioclipse
07:15 edrin joined #bioclipse
07:16 egonw hi edrin
07:25 edrin hi egonw
07:50 jonalv joined #bioclipse
07:51 jonalv oh hai
07:51 zarah ni hao jonalv
07:53 olass joined #bioclipse
07:54 egonw hi olass
07:54 olass hi
07:54 zarah ni hao olass
07:54 olass egonw: replying to your email as we speak
07:54 egonw tack
07:54 olass sent
07:55 olass egonw: bug 1427 contains some git refactoring that I think should be undertaken
07:55 egonw ok, please assign to me
07:56 olass yup
07:56 olass just filed it :)
07:56 edrin uhm, do you maybe have access on the following two articles' pdfs ?
07:56 edrin http://www.cell.com/developmental-c​ell/abstract/S1534-5807(09)00254-8
07:56 zarah edrin's link is also http://tinyurl.com/mk5yw9
07:56 edrin http://www.cell.com/developmental-c​ell/abstract/S1534-5807(09)00255-X
07:56 zarah edrin's link is also http://tinyurl.com/kktbds
07:56 olass egonw: let me know if you disagree
07:57 edrin olass: can you access them and mail them maybe :)?
07:57 olass edrin: sure
07:57 edrin thanks :)
07:59 olass edrin: sent
07:59 olass edrin: any news about xmpp?
07:59 edrin olass: thank you
07:59 edrin no, not yet
08:02 egonw can I remind everyone this is a open and logged channel?
08:02 egonw I know at least a few persons you check the logs of this channel for keeping up with discussions here
08:02 egonw which is good
08:02 egonw it might also be indexed by google, not sure about that, though
08:03 rojasm joined #bioclipse
08:11 shk3 joined #bioclipse
08:11 rojasm hi all
08:11 zarah ni hao rojasm
08:12 rojasm someone knows how can I read file line by line using javascript?
08:12 rojasm is there some example in bioclipse2 already
08:39 jonalv rojasm: any particular file?
08:42 egonw http://www.wired.com/images_blogs/b​eyond_the_beyond/2009/07/020709.jpg
08:42 zarah egonw's link is also http://tinyurl.com/ntk68j
08:44 egonw btw, you can prefix any line with [off] to make it not show up in the logs...
08:44 egonw http://colabti.org/IrcLoggerHelp.html
08:44 zarah egonw's link is also http://tinyurl.com/nexuvn
08:53 masak joined #bioclipse
08:54 egonw hi masak
08:54 masak egonw: oh hai
08:54 egonw masak: how much work would a groovy script console be...
08:54 egonw roughly estimated?
08:54 masak egonw: not much. an hour, perhaps.
08:54 egonw really...
08:54 egonw ok, how do I start?
08:55 masak egonw: dig up the old one. extract the part that talks to Groovy. use that in a brand new one, subclassed from ScriptingConsoleView
08:56 egonw ok
08:56 * egonw is setting up a new plugin...
08:56 masak the revision of the old one is noted in an XML file in the scripting.ui plugin.
09:01 jonalv egonw: around?
09:01 egonw yes
09:01 jonalv if I do "cdk.loadMolecule("/Sample Data/2D structures/0037.cml").getName();" I get null
09:01 jonalv I don\t like null
09:01 jonalv I hate null
09:01 jonalv + this breaks StrucutreDB
09:02 egonw :)
09:02 egonw ok, file a bug report, plese
09:02 egonw +a
09:02 jonalv egonw: Do you have a very good reason for keeping it this way?
09:02 jonalv otherwise I will change it...
09:02 egonw I don't think I did ICDKMolecule.getName()
09:02 egonw jonalv: yes, please do
09:02 egonw check the CML file, if there is anything namelike...
09:03 jonalv egonw: I am pretty sure it already does that
09:03 egonw and if so, still file a bug report against me for extracting the anem
09:03 jonalv I am just gonna add code that puts in the molecular formula if nothing else is in the name
09:03 jonalv can that work?
09:03 olass yes, but please use property cdk:title if that exists
09:04 jonalv |Does that sounds okey?
09:04 egonw I though that was the current behaviour already...
09:04 jonalv olass: how do I do that?
09:04 * jonalv thought so too...
09:04 olass read the property cdk:title from the AC
09:05 olass if exists, this is the title read by CDK
09:05 olass for exampåle in an MDL molfile or SDFile
09:05 olass probbaly cml as well, if converted from legacy format
09:05 olass egonw: right?
09:06 egonw yes, sounds good
09:06 jonalv atomContainer.getProperty( "cdk:title" );?
09:06 jonalv but that returns an Object...
09:07 jonalv egonw: help...
09:07 egonw atomContainer.getProperty(CDKConstants.TITLE):
09:07 egonw the returned object is a String
09:08 jonalv egonw: so you usually just casdt it?
09:09 jonalv egonw: and I guess that method returns null if there is no such proerty?
09:09 jonalv egonw: yes, javadoc says so actually... :)
09:12 egonw yes, and yes
09:19 CIA-52 bioclipse.structuredb: jonalv master * rba79117 / (3 files in 3 dirs): made it possible to drop single files on StructureDB instances - http://bit.ly/aXuX9
09:23 masak my branch is now publicly available: http://github.com/masak/bioclip​se.bioinformatics/tree/biojava
09:23 zarah masak's link is also http://tinyurl.com/nxdwd8
09:50 CIA-52 bioclipse.cheminformatics: jonalv master * r7736746 / (2 files in 2 dirs): No need to declare methods as throwing Bioclipse Exception in the interface. It is caught and handled by AOP during the method call. - http://bit.ly/1Peth
09:50 CIA-52 bioclipse.cheminformatics: jonalv master * r61e1881 / plugins/net.bioclipse.cdk.business/src/n​et/bioclipse/cdk/domain/CDKMolecule.java : make the CdkMolecule.getName return something instead of null - http://bit.ly/135dr0
10:11 egonw lunch time
10:52 egonw joined #bioclipse
10:57 shk3 hi egonw
11:00 egonw hi shk3
11:01 egonw rojasm:
11:01 egonw org.springframework.bundle.spring.aop
11:01 egonw net.sf.cglib
11:01 egonw org.springframework.osgi.aopalliance.osgi
11:02 shk3 egown: how do I make patches per module for cdk?
11:04 egonw the patches are split up by module
11:05 shk3 going for lunch
11:05 shk3 will be back
11:05 shk3 sorry
11:05 egonw and the module content you can find in build/*.javafiles
11:07 jonalv the Ritter sport machine over at Bikupan is totally broken. Don't go putting any money in it becasue you will quite some time to get them out again... :(
11:11 egonw phew...
11:11 egonw thanx foo I am in Leiden now
11:12 egonw jonalv: ping
11:12 egonw jonalv: we got a SpringProxy not found error...
11:12 egonw in the medea plugin
11:12 jonalv egonw: never heard of that
11:12 rojasm aused by: java.lang.NoClassDefFoundError: org/springframework/aop/SpringProxy
11:13 egonw while it does depend on the three plugins I gave above...
11:15 jonalv I thought that class would be in the org.springframework.bundle.spring.aop bundle
11:16 egonw yeah... think so too
11:18 egonw ah...
11:18 egonw I think we solved it
11:18 egonw we were adding the deps to the wrong plugin...
11:18 jonalv aha
11:19 jonalv been there done that :)
11:52 masak CIA-52: Come back! :/
11:57 shk3 hi egonw
11:57 shk3 sorry for interrupion
11:57 shk3 you said
11:57 shk3 Please split up patches according to the module they are in
11:57 shk3 my question was how to do that?
11:57 shk3 or do I need to do it manually?
11:58 egonw [07/21/09 13:05] <egonw> and the module content you can find in build/*.javafiles
12:00 shk3 so I need to do gi format-patch list-changed-filens-in-module for each module?
12:02 shk3 hm, no such option
12:02 shk3 sorry, I don't understand this
12:02 shk3 I know the .javafiles files
12:03 shk3 but how do I make the actual patch for only some of the changed files?
12:03 egonw masak: what was that command again to iteratively stage stuff?
12:03 egonw shk3: I think: git add -i
12:04 egonw so, what you can do is:
12:04 egonw git reset HEAD^1
12:04 egonw to undo the most recent patch
12:05 egonw and then interactively (-i) add the bits one by one... splitting up things into two or more patches, one patch for each cdk module (render, renderextra, control, controlbasic, etc)
12:05 shk3 ok
12:06 shk3 do you really men HEAD^1 ?
12:06 shk3 or is ^1 a typo?
12:07 masak shk3: no, that should be right.
12:07 masak ^1 means 'one step before' or 'parent'.
12:07 shk3 ah
12:08 masak http://www.kernel.org/pub/softwar​e/scm/git/docs/git-rev-parse.html
12:08 zarah masak's link is also http://tinyurl.com/5e9cex
12:11 CIA-65 joined #bioclipse
12:11 egonw CIA-65: welcome back!
12:17 shk3 egonw: all my changes were in teh same module
12:17 shk3 I am confused
12:17 shk3 what am I supposed to do?
12:19 egonw when did you sent the patch again?
12:20 egonw Jul 19, right?
12:21 shk3 17th
12:21 shk3 friday
12:21 egonw indeed
12:22 egonw I see classes from the module: controlbasic and controlawt
12:23 shk3 mom
12:24 shk3 ah, looked into the wrong checkout
12:32 egonw olass: I get compile errors in bioclipse.qsar due to a commit by jonalv
12:32 egonw minor ones... loadMolecule no longer throws a BioclipseException
12:32 egonw so it complains about those being catches
12:32 egonw so it complains about those being catched
12:33 olass I have not rebased lately
12:33 jonalv olass: oops, sry I don't have bioclipse.qsar checked out so I didn't spot that...
12:33 olass or rather, not pulled
12:33 olass or rather, not pulled core
12:33 olass so not my fault
12:34 jonalv or rather pulled cheminformatics in this case... :)
12:34 jonalv well, egonw you applied my patches... :)
12:34 olass lol
12:34 egonw yeah, my fault
12:34 egonw it is
12:34 egonw I allowed you to change the API
12:34 masak o_O
12:35 egonw did not anticipate removing exceptions being thrown giving compile errors...
12:35 egonw should have tried it in my workspace first
12:35 jonalv actually this change should be made all over at very many places...
12:35 olass _._-.____@_
12:35 * masak sorely tempted to decrease egonw's karma
12:35 jonalv for simialr methods
12:35 egonw yes, spotting in bioclipse.reaction problems too
12:35 egonw masak: why?
12:36 egonw the right thing was still to fix the API
12:36 olass true
12:36 egonw I'm just a bit slow with informing downstream
12:36 olass well, it was not applied in 2.0.x, right?
12:36 egonw no
12:36 shk3 egonw: sorry, I doublechecheck, but for me, all classes are in controlbasic
12:36 olass we cannot guranatee for all forkers that API is stable in master
12:36 olass right?
12:36 shk3 this is in the latest jchempaint-primary checkout
12:36 shk3 I edited
12:37 shk3 SwingMouseEventRelay AddAtomModule.java AddBondDragModule
12:37 egonw 10-unsorted ?
12:37 egonw check the emails...
12:37 egonw 10-unsorted is the branch to use
12:37 shk3 all are in controlbasic for me
12:37 shk3 10-unsorted, yes
12:38 shk3 I did a fresh checkout to verify
12:38 egonw /**
12:38 egonw * @cdk.module controlawt
12:38 egonw */
12:38 egonw public class SwingMouseEventRelay implements MouseMotionListener,
12:39 shk3 /**
12:39 shk3 * @cdk.module controlbasic
12:39 shk3 */
12:39 shk3 public class SwingMouseEventRelay implements MouseMotionListener,
12:39 shk3 MouseListener, MouseWheelListener {
12:39 shk3 that is what I have got
12:40 shk3 git log gives me your commit form 16th as last commit
12:40 egonw http://pele.farmbio.uu.se/cgi-bin/gitweb.cgi?p=​jchempaint-primary.git;a=blob;f=src/main/org/op​enscience/cdk/controller/SwingMouseEventRelay.j​ava;h=defc7a8ddedd87e145d9aece5ec4426f10b1fa5c;​hb=25e3e7d31f7a6913388971874606e2bad3fd254e
12:40 zarah egonw's link is also http://tinyurl.com/l4vhuz
12:40 egonw shk3: you can always check with the repos website to see if you really are up to date
12:41 shk3 git pull says Already up-to-date
12:41 shk3 what else can I do?
12:41 egonw shk3: you can always check with the repos website to see if you really are up to date
12:41 egonw shk3: check that the hashes match
12:42 egonw you can also run a git diff against upstream
12:42 egonw git fetch
12:42 egonw git diff yourCurrentBranch..origin/10-unsorted
12:43 egonw or just the log:
12:43 egonw git log yourCurrentBranch..origin/10-unsorted
12:43 shk3 i don't understand the web interface
12:43 shk3 if I click on history,
12:43 shk3 the last commit is from may
12:43 egonw URL?
12:44 shk3 ah need to switch branch
12:44 shk3 hm
12:45 shk3 your commit was in 11-controlawt
12:45 shk3 shouldn't I use that then?
12:45 egonw see my email about the order of patches
12:45 egonw numbering is not indicating the order, just when I started them
12:46 shk3 ok
12:46 egonw use 10-unsorted
12:46 shk3 but how do I get your changes then into my local repository?
12:46 shk3 I am apparently missing
12:46 shk3 3 days ago  Egon Willighagen  Setting up the controlawt module.  11-controlawt
12:47 shk3 ok
12:47 shk3 git pull does not fetch it
12:47 shk3 what to do then?
12:47 egonw git fetch
12:47 shk3 does not do anything
12:47 egonw git checkout -b local-10-unsorted origin/unsorted
12:47 egonw (or something like that... see: git branch -r)
12:48 shk3 that what I did
12:48 shk3 I did
12:48 shk3 git checkout -b latest origin/10-unsorted
12:48 shk3 anyway, I will make that split patch
12:49 masak olass: sequence alignment editor now runs on top of the Biojava manager. \o/
12:49 * masak pushes
12:49 jonalv \o/
12:49 masak jonalv++
12:49 jonalv masak++
12:49 masak "karma cycle detected"
12:49 egonw zarah: they are cheating
12:49 zarah egonw: please rephrase or stop trying to be witty :)
12:49 egonw ha :)
12:49 masak "you will be exTERminated"
12:49 jonalv Automatic merge failed; fix conflicts and then commit the result. :(
12:50 masak yes, I got there first.
12:50 masak now plz fix. ktxhbai.
12:50 jonalv masak: of course, you cheat
12:50 masak mohaha.
12:50 masak I AM THE SWORDMASTER!
13:05 edrin egonw, olass: no news from the bmc
13:06 edrin hm, is this a good sign or a Bad sign?
13:07 masak why does it have to be a sign at all?
13:07 masak maybe it's just an anomaly.
13:09 jonalv masak: everything is a sign
13:19 masak jonalv: that's what the new age weirdos say, too.
13:19 masak and the religious nuts.
13:20 masak and people who are just plain out of their minds.
13:20 jonalv masak: thanks
13:20 jonalv :)
13:20 masak no offense. :P
13:20 masak just saying not everything is a sign.
13:21 jonalv <Blue Obelisk mail list> I will be there </Blue Obelisk mail list>
13:21 jonalv <AOL>Me too</AOL>
13:21 jonalv :)
13:22 masak using email like it's 1992.
13:25 jonalv egonw, masak: How about setting up CIA commit log for masaks bioclipse.bioinformatics?
13:25 CIA-65 bioclipse.medea: Miguel Rojas Cherto master * rd2e421c / (2 files in 2 dirs): block that a ICDKReactionScheme can be saved only in cml format - http://bit.ly/lL3kb
13:25 CIA-65 bioclipse.medea: Miguel Rojas Cherto master * r5aa031d / plugins/net.bioclipse.reaction/src/net/biocl​ipse/reaction/business/ReactionManager.java : removing some stuff - http://bit.ly/3Tr9S
13:25 CIA-65 bioclipse.medea: Miguel Rojas Cherto master * ra4a6d99 / (3 files in 3 dirs): added reactions examples - http://bit.ly/VFuWk
13:25 masak jonalv: Date:   Tue Jul 21 20:05:31 2009 +0800
13:26 masak jonalv: your clock is set to the wrong time zone.
13:27 jonalv masak: $ date
13:27 jonalv Tue Jul 21 15:26:50 CEST 2009
13:27 jonalv
13:27 jonalv masak: seems about right to me...
13:27 masak and if you do 'git log'?
13:28 jonalv masak: 'git log' does nt o show curerent time now does it?
13:28 masak jonalv: no, but the date/time of your commit.
13:28 jonalv masak: they look about right yea
13:28 masak ok.
13:28 masak I'm getting +0800 here on your commits.
13:29 jonalv +0200 here...
13:29 masak :/
13:29 masak maybe it's because github is situated in the US or something...
13:29 jonalv masak: maybe
13:30 egonw weird
13:31 egonw there supposed to be 6 hours behind, not ahead
13:31 CIA-65 bioclipse.medea: Egon Willighagen master * r6690ed5 / plugins/net.bioclipse.reaction/src/net/bioclipse​/reaction/editparts/RAbstractObjectEditPart.java : CDKManager.loadMolecule no longer throws Exceptions - http://bit.ly/M99rr
13:33 masak aye, strange indeed.
13:44 CIA-65 bioclipse.qsar: Ola Spjuth master * r91beae0 / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/QsarManager.java : Removed import of inchi in QSARManager since not used. - http://bit.ly/WkOEo
13:49 CIA-65 bioclipse.statistics: Ola Spjuth master * r988d7ca / .gitignore : Added a .gitignore to filter out bin/ - http://bit.ly/BZAFq
13:49 CIA-65 bioclipse.statistics: Ola Spjuth master * r7e1ae76 / (4 files in 3 dirs): Updated MatrixResource and Jama implementation to support a RESPONSE variable of type String. - http://bit.ly/CGTyJ
14:15 edrin http://www.youtube.com/watch?​v=at_f98qOGY0&amp;feature=fvw
14:15 zarah edrin's link is also http://tinyurl.com/mrvt9s
14:28 egonw guys...
14:28 egonw how does on delete all vars in a javsscript console session?
14:29 egonw btw, it would be useful that people cannot overwrite manager variables...
14:29 egonw like in:
14:29 egonw ui = "Yes, now the manager can not be accessed anymore!";
14:39 edrin egonw: that is exactly the reason why I always say it is essential to have the possibility of multiple JS contexts and not do everything in one "never ending" context;
14:40 egonw well, I would be fine with some equivalent for the R rm(ls())
14:40 edrin egonw:  btw. this was the reason why I insisted on running javascript scripts myself in a context from the jseditor and not with the global js environment context the jsconsole is connected to, thanks that now one beside me realizes this (or maybe others did but did not tell me)
14:42 edrin egonw: when you discuss the js environment design in Uppsala one day, can you remember this problem and mention it there?
14:42 olass edrin, you know we understand what you mean, but you are just not understanding our point here it seems
14:43 olass since you keep bringing it up
14:43 olass there are two ways of doing things
14:43 olass both with pros and cons
14:43 egonw edrin: I don't have a problem with a monolithic JS env
14:43 egonw I just asked how I could delete existing vars
14:45 jonalv olass: is there a wiki page listein all bioclipse rpos?
14:46 olass no
14:46 olass you have to guess :)
14:46 jonalv I c
14:46 mgerlich joined #bioclipse
14:47 jonalv hi mgerlich
14:47 mgerlich hi
14:47 zarah ni hao mgerlich
14:48 edrin olass: I have to apologize this was not a personal thing
14:49 olass edrin: no offense taken :)
14:49 olass but seriously
14:49 olass we should work on this
14:49 olass to find a better solution than the current one
14:49 edrin yes
14:49 olass but that will have to wait until after summer
14:50 edrin olass: I suggest an API like  .spawnNewJsContext()
14:51 edrin that returns a new context, with all managers in, for those that need a new one.
14:52 edrin this way one could spawn different parallel consoles (if someone wants to do this) or run a js script in its own context, for example from the editor
14:59 CIA-65 bioclipse.medea: Miguel Rojas Cherto master * r917f335 / (5 files in 3 dirs): Implemented method to convert ICDKREactionScheme to ISpectrum - http://bit.ly/29pmc
15:09 CIA-65 bioclipse.medea: Miguel Rojas Cherto master * ra6b1ee2 / plugins/net.bioclipse.data.medea​/data/Javascripts/prediction.js : adapted to return ICDKReactionScheme - http://bit.ly/b1ao3
15:30 olass masak: http://wiki.bioclipse.net/index.php?title​=Contributing_a_data_plugin_to_Bioclipse
15:30 zarah olass's link is also http://tinyurl.com/dhzfvm
15:30 masak olass: dz
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