Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-29

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All times shown according to UTC.

Time Nick Message
05:15 thomas_ku joined #bioclipse
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07:44 jonalv moin
07:44 zarah hi jonalv
08:03 masak hi jonalv
08:11 egonw joined #bioclipse
08:11 edrin joined #bioclipse
08:14 CIA-49 bioclipse: ospjuth * r6294 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.business.test/ (2 files in 2 dirs): Some test editing for the Jumbo bug.
08:16 CIA-49 bioclipse: jonalv * r6295 /bot/trunk/zarah.pl: [zarah] answers ehlo!
08:16 zarah joined #bioclipse
08:18 olas joined #bioclipse
08:18 olas hi all
08:18 zarah hi olas
08:27 edrin hi olas
08:27 olas hi edrin
08:32 CIA-49 bioclipse: ospjuth * r6296 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/views/Java2DRendererView.java: Replaced the getAdapter with the one from cdk10. Still not working, but a start. Needs some work by egonw, see bug 2027732.
08:33 CIA-49 bioclipse: ospjuth * r6297 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKChemObject.java ChemObjectPropertySource.java): Copied CDKChemObject as they are needed by cdk as well.
08:33 CIA-49 bioclipse: ospjuth * r6298 /bioclipse2/trunk/plugins/net.bioclips​e.qsar/src/net/bioclipse/qsar/builder/ (QSARBuilderREF.java QSARNatureREF.java): Removed obsolete classes.
08:34 CIA-49 bioclipse: ospjuth * r6299 /bioclipse2/trunk/plugins/net.bi​oclipse.scripting.ui/plugin.xml: Scripting.ui now contributes JSConsole via a perspectiveContribution.
08:35 CIA-49 bioclipse: ospjuth * r6300 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Removed commons.logging. This might be a mistake, but at least solves race problem on startup.
08:41 olas masak: are all bugs on SF group 2.0-alpha assigned to you still valid or could some be closed?
08:42 masak olas: hold on, will check
08:47 masak olas: there. I redirected one to you for closing. the js editor one is half complete. also, I'd like to check the prio 9 bug and see if I can do something about it.
08:48 olas what is it about?
08:59 masak it's about `structuredb.delete( db, l )` not working in the js console
09:06 shk3 joined #bioclipse
09:06 CIA-49 bioclipse: ospjuth * r6301 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (26 files in 5 dirs): Updated copyright and license.
09:09 CIA-49 bioclipse: carl_masak * r6302 /bioclipse2/trunk/plugins/ (5 files in 3 dirs):
09:09 CIA-49 bioclipse: [net.bioclipse.structuredb]
09:09 CIA-49 bioclipse: [net.bioclipse.structuredb.tests]
09:09 CIA-49 bioclipse: * renamed the two methods delete(db, label) and
09:09 CIA-49 bioclipse:  delete(db, structure) into deleteLabel and
09:09 CIA-49 bioclipse:  deleteStructure, respectively. seems to be
09:09 CIA-49 bioclipse:  interference from js with the name 'delete'
09:15 masak fixed it :)
09:17 olas masak++
09:20 CIA-49 bioclipse: ospjuth * r6303 /bioclipse2/trunk/plugins/net.bioc​lipse.jmol/src/net/bioclipse/jmol/ (adapter/cdk/CdkJmolAdapter.java views/JmolComposite.java): Updated copyright.
09:24 olas masak: jag lägger till lite copyright innan du ersätter... ok?
09:24 masak oki
09:30 masak I have a new philosophy. it's bit harsh, but it's good to keep in mind
09:30 CIA-49 bioclipse: carl_masak * r6304 /bioclipse2/trunk/plugins/net.bioclipse.​cdk10.jchempaint/src/net/bioclipse/cdk10​/jchempaint/outline/JCPOutlinePage.java:
09:30 CIA-49 bioclipse: [JCPOutlinePage]
09:30 CIA-49 bioclipse: * removed unused imports
09:30 CIA-49 bioclipse: * replaced block of commented-out code with
09:30 CIA-49 bioclipse:  comment on where to find fresh code
09:30 masak don't comment out code.
09:30 CIA-49 bioclipse: ospjuth * r6305 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (31 files in 9 dirs): Updated copyright and license on files missing this information. People might want to add themselves in contributors section, that is manual work.
09:32 CIA-49 bioclipse: ospjuth * r6306 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (3 files in 2 dirs): Added missing copyright statements.
09:32 CIA-49 bioclipse: ospjuth * r6307 /bioclipse2/trunk/plugins/net​.bioclipse.usermanager.tests/ (4 files in 3 dirs): Added missing copyright statements.
09:35 CIA-49 bioclipse: carl_masak * r6308 /bioclipse2/trunk/plugins/net.bioclips​e.biojava.business/src/net/bioclipse/b​iojava/business/BiojavaManager.java:
09:35 CIA-49 bioclipse: [BiojavaManager]
09:35 CIA-49 bioclipse: * better comments and javadoc
09:35 CIA-49 bioclipse: * whitespace
09:35 masak olas: let me know when you're done
09:39 olas true
09:39 olas will do so
09:40 olas masak: you never add license to your classes?
09:41 masak olas: no, I've never gotten into the habit
09:41 masak sorry :/
09:41 olas ok
09:41 olas will add a standard one
09:41 olas it's an eclipse preference
09:41 olas btw
09:41 masak yes, I know
09:42 olas hence: it's not a habit, it's a preference you have not set
09:42 olas jonalv: you're pretty bad at this as well
09:43 * masak sets preference
09:43 masak I know I looked at it when I sent out the style files
09:44 * olas is adding a lot of license/copyright statements
09:44 CIA-49 bioclipse: ospjuth * r6309 /bioclipse2/trunk/plugins/ (29 files in 15 dirs): Added missing license and copyright statements.
09:44 masak olas: if you ask me, the "Contributors" part of the License comment is not very valuable
09:45 CIA-49 bioclipse: ospjuth * r6310 /bioclipse2/trunk/features​/net.bioclipse.sampledata/ (.project feature.xml): Replaced ID.
09:45 olas in what respect?
09:45 olas if you are a contributor, you have copyright
09:45 olas at least partial
09:46 olas which means people should consult you with issues regarding licensing
09:46 masak it's information that needs constant updating
09:46 olas I know
09:46 masak and not very useful
09:46 olas what do you propose as alternative?
09:46 masak yes, nothing
09:46 olas so just write: Copyright Bioclispe contributors and others?
09:47 masak yes. the rights belong to the project, and that includes all contributors
10:10 shk3 sorry, but this isn't quite right. "the project" ist not a legal entity and can therefore not own rights.
10:10 shk3 plus the so-called moral right cannot be transferred anyway.
10:10 shk3 So in our case the people working on a separable piece are joint owners.
10:40 egonw joined #bioclipse
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10:57 CIA-49 bioclipse: ospjuth * r6311 /bioclipse2/trunk/features/net.bioc​lipse.sampledata/build.properties: Added missing license and copyright statements.
10:58 CIA-49 bioclipse: ospjuth * r6312 /bioclipse2/trunk/plugins/net.bioclipse.r/ (5 files in 2 dirs): Added missing license and copyright statements.
11:03 CIA-49 bioclipse: ospjuth * r6313 /bioclipse2/trunk/plugins/ (52 files in 10 dirs): Added missing license and copyright statements.
11:07 CIA-49 bioclipse: ospjuth * r6314 /bioclipse2/trunk/plugins/ (58 files in 15 dirs): Added missing license and copyright statements.
11:11 CIA-49 bioclipse: ospjuth * r6315 /bioclipse2/trunk/plugins/ (53 files in 28 dirs): Added missing license and copyright statements.
11:19 CIA-49 bioclipse: jonalv * r6316 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Introduced create job advice on cdk manager methods. This needs to be tested! :)
11:40 olas jonalv: how to test?
11:40 jonalv olas: I need hwlp... :(
11:40 jonalv I am stuck...
11:40 olas oh no
11:40 * olas is on his way
11:40 jonalv freaking dependenioces are killing me
11:41 CIA-49 bioclipse: ospjuth * r6317 /bioclipse2/trunk/plugins/net.bioclipse.analysis/ (3 files in 3 dirs): Added missing license and copyright statements.
11:42 masak olas: could you have a look at this before I commit?
11:42 masak http://paste2.org/p/53202
11:42 zarah masak's link is also http://tinyurl.com/6mlmd6
11:42 masak zarah: you're shortening links sometimes even though they are short already
11:42 zarah masak: I did not understand that
11:45 masak zarah: restart, please
11:45 CIA-49 bioclipse: carl_masak * r6318 /bot/trunk/zarah.pl: [zarah] increased lower URL shortening length limit
11:45 zarah joined #bioclipse
11:46 masak http://paste2.org/p/53202
11:46 masak zarah++
11:54 masak olas: how does it look? do you want a paste with a list of the files affected?
12:03 masak major commit coming
12:04 masak I'd recommend that everyone update after this one.
12:09 * olas will update after this one
12:09 olas just tell me when
12:10 olas jonalv: about the install on linux
12:10 olas did you postpone that?
12:10 jonalv don't know :)
12:10 CIA-49 bioclipse: carl_masak * r6319 /bioclipse2/trunk/plugins/ (167 files in 45 dirs): added copyright statements to Java files in our own plugins
12:11 masak there you go.
12:11 olas danke
12:11 olas but
12:11 olas there will be more, right?
12:11 masak a little, yes :)
12:11 jonalv masak++ //looks like a cool thing
12:11 masak maybe in half an hour
12:11 olas masak++
12:11 masak dz
12:11 masak it was fun to write
12:11 * olas wishes he was as wise in the ways of science as masak
12:12 masak science!
12:12 olas "A duck!"
12:13 olas masak: are you good with XSLT?
12:13 masak olas: frankly, yes :)
12:13 olas I have an open bug from bc1
12:13 olas nice
12:13 * olas is coming over again
12:13 masak heh
12:23 olas masak: http://www.linuxdevices.com​/articles/AT4973246138.html
12:23 zarah olas's link is also http://tinyurl.com/5zylyc
12:23 CIA-49 bioclipse: jonalv * r6320 /bioclipse2/trunk/plugins/net.bioclipse​.scripting/src/net/bioclipse/scripting/ (JsThread.java ScriptingThread.java): Created base class ScriptingThread to be used for "scripting worker" threads
12:23 masak olas: looks relevant
12:23 olas hmm
12:23 olas on second thoughts, maybe not
12:25 olas masak: have you worked with docbook xsl?
12:25 olas http://www.xml.com/lpt/a/1265
12:25 malic1 joined #bioclipse
12:25 masak olas: no
12:25 olas looks interesting
12:26 masak it looks like normal XSL :)
12:29 CIA-49 bioclipse: jonalv * r6321 /bioclipse2/trunk/plugins/ (14 files in 7 dirs): Moved create job advice from core into ui. Hopefully this will work better. (Although it wouldn't suprise me if it will end up in some scripting plugin finally...)
12:30 shk3 hi all
12:30 zarah hi shk3
12:30 shk3 some questions
12:30 shk3 anybody has a minute?
12:31 olas fire off
12:32 shk3 ok, i am trying to do the create coordinates stuff
12:32 shk3 this should be in the context menu, right?
12:33 shk3 so i need a menu item for all molecule files.
12:33 shk3 Is there a definition for this?
12:33 shk3 in net.bc.cdk10.ui there is a molecule content
12:34 shk3 but this is only for sdf and cml?
12:34 shk3 the editors are directly called via file extensions?
12:34 shk3 so how to define the visibility of the menu item?
12:35 CIA-49 bioclipse: jonalv * r6322 /bioclipse2/trunk/plugins/net.bioclipse​.core/src/net/bioclipse/core/business/ (CreateJobAdvice.java ICreateJobAdvice.java): hm here comes hte CreateJobAdvice and it's interface. It's strange that they didn't join my last commit... :)
12:37 masak olas: those on #eclipse thought that this might be a starting point for finding out more about the XSLT stuff
12:37 masak http://wiki.eclipse.org/Platform-releng-faq
12:37 zarah masak's link is also http://tinyurl.com/29q8v2
12:44 shk3 olas: what do you think?
12:46 masak olas: looks good? http://paste2.org/p/53214
12:46 olas mom
12:47 masak I really like to work this way!
12:47 masak \o/
12:47 olas :-)
12:47 olas looks good
12:47 olas but you are the master
12:47 masak committing, then
12:47 masak I'm no master
12:47 masak I just try stuff
12:47 olas right
12:48 olas but you have more exp than I regarding this
12:48 masak exhibitionism?
12:48 olas that too
12:48 olas also experience
12:48 masak anyhoo, here comes a commit
12:48 olas could be exponentialism as well
12:49 masak exports
12:49 olas expertise
12:49 masak expressionism
12:49 olas expansion
12:50 olas expectations (I like that one!)
12:50 masak explanations
12:50 * olas is waiting for the commit
12:50 masak it's on its way
12:51 masak committing 166 files takes a while
12:51 olas masak: I know I'm bothering you a lot today
12:51 olas sorry about that (I know you are not feeling too well)
12:52 masak as long as the tasks are fun...
12:52 olas :-)
12:52 masak olas: I'm in a bit of pain, that's all
12:52 masak no worries
12:52 olas you want painkillers? (got some in my bag)
12:52 olas (I think)
12:52 masak olas: hm, drugs... interesting suggestion
12:52 masak I'll think about it
12:53 olas just ask
12:53 masak "just say yes" :)
12:53 olas we are in drug design, we should use as many as possible
12:53 olas (right?)
12:53 masak true
12:53 masak "eating our own dogfood"
12:53 olas zarah: should we use as many drugs as possible?
12:53 zarah olas: excuse me?
12:53 masak haha
12:53 olas oh, sorry
12:54 masak zarah: drugs, for or against?
12:54 zarah masak: please rephrase or stop trying to be witty :)
12:54 masak oki
12:54 olas zarah: could you please speed up SF?
12:54 zarah olas: I'm just a bot, you expect me to understand that?
12:54 CIA-49 bioclipse: carl_masak * r6323 /bioclipse2/trunk/plugins/ (166 files in 59 dirs): updated copyright notes on Java files
12:54 olas understand, yes. Fix, no
12:54 masak there we go
12:54 olas great
12:54 * olas is updating
13:02 CIA-49 bioclipse: carl_masak * r6324 /bot/trunk/zarah.pl: [zarah] "no you are the cute one"
13:02 masak zarah: update
13:02 zarah joined #bioclipse
13:03 masak zarah++
13:03 masak @dz
13:03 zarah you're welcome, masak :)
13:03 masak @dz
13:03 zarah you're welcome, masak :)
13:03 masak @dz
13:03 zarah no, YOU'RE the cute one! :)
13:03 masak zarah: no, you're the cute one!
13:03 zarah masak: no, YOU'RE the cute one! :)
13:03 zarah masak: please rephrase or stop trying to be witty :)
13:03 masak oops
13:03 olas shk3: sorry
13:03 olas was lost in space for a while
13:03 olas your questions are important
13:05 masak @restart
13:06 zarah joined #bioclipse
13:06 CIA-49 bioclipse: carl_masak * r6325 /bot/trunk/zarah.pl: [zarah] now does not get confused by cuteness messages
13:06 masak zarah: no, you're the cute one!
13:06 zarah masak: no, YOU'RE the cute one!
13:06 masak :)
13:34 masak zarah: no, YOU'RE the cute one!
13:34 zarah masak: no, YOU'RE the cute one!
13:34 masak zarah: no, YOU'RE the cute one!
13:34 zarah masak: no, YOU'RE the cute one! :)
13:34 masak zarah: no, YOU'RE the cute one! :)
13:34 zarah masak: no, YOU'RE the cute one! :)
13:34 masak :)
13:34 jonalv @dz
13:34 zarah no, YOU'RE the cute one! :)
13:35 jonalv no, YOU'RE the cute one!
13:35 zarah jonalv: no, YOU'RE the cute one!
13:35 olas zarah: shut up
13:35 zarah olas: eh... wha'?
13:35 jonalv no, YOU'RE the cute one!
13:35 zarah jonalv: no, YOU'RE the cute one! :)
13:35 olas zarah: that means: STOP IT!
13:35 zarah olas: I did not understand that
13:35 masak :)
13:35 masak zarah: no, YOU'RE the cute one! :)
13:35 zarah masak: no, YOU'RE the cute one! :)
13:35 olas zarah: you are the stupid one
13:35 zarah olas: no, YOU'RE the stupid one! :)
13:36 olas god damn it
13:36 masak hahaha
13:36 jonalv zarah++
13:36 masak zarah++
13:36 olas masak-- for implementing such a feature
13:36 masak :D :D :D
13:36 jonalv masak++
13:36 jonalv this made my day :)
13:36 masak mine too
13:37 masak Perl++
13:37 * olas doesn't like zarah anymore
13:37 * olas doesn't like Perl either anymore
13:37 olas :-(
13:37 masak zarah: you're the Perly one!
13:37 zarah masak: no, YOU'RE the Perly one! :)
13:37 olas actually really funny
13:40 olas jonalv: structuredb does not compile
13:40 olas neither does quickimage
13:41 olas hmm
13:41 CIA-49 bioclipse: carl_masak * r6326 /bot/trunk/zarah.pl: [zarah] more varied "cute one" message
13:41 olas @restart
13:42 jonalv olas: structuredb doesn't have my priority this week
13:42 olas good
13:42 masak @restart
13:42 zarah joined #bioclipse
13:43 jonalv no, YOU'RE the cute one!
13:43 zarah jonalv: no, YOU are the cute one! :)
13:43 jonalv no, YOU'RE the cute one!
13:43 zarah jonalv: no, YOU are the cute one!
13:43 olas varied?
13:43 masak no, YOU are the cute one!
13:43 zarah masak: no, YOU are the cute one!
13:43 jonalv no, YOU'RE the cute one!
13:43 zarah jonalv: no, YOU'RE the cute one!
13:43 masak well, slightly varied
13:43 olas (very slightly)
13:44 olas shk3: around?
13:45 shk3 yes
13:45 olas http://wiki.bioclipse.net/index.php​?title=How_to_add_menus_and_actions
13:45 zarah olas's link is also http://tinyurl.com/55gl83
13:45 shk3 i know that
13:45 olas did you read that?
13:45 olas ok
13:45 shk3 but i am unsure about the file types right now
13:46 olas what is missing?
13:46 olas ok
13:46 olas we should define contentTypes
13:46 olas I am not sure about this either
13:46 olas we need to figure it out
13:46 olas I will attack it too
13:47 shk3 the is no molecule content type right now?
13:47 olas no
13:47 olas and should not be
13:47 olas (IMO)
13:47 olas perhaps a CDKMoleculeType
13:47 olas I am not sure about that
13:47 shk3 me neither
13:48 olas or even MDLMolfileCOntentType
13:48 shk3 I try the actions on mol files first
13:48 olas great
13:48 olas I will try to open Jmol if cml file with 3D and JCP if cml file with 2D
13:49 CIA-49 bioclipse: carl_masak * r6327 /bot/trunk/zarah.pl: [zarah] now tires of "cute one" exchanges after some time
13:50 zarah joined #bioclipse
13:53 CIA-49 bioclipse: goglepox * r6328 /bioclipse2/trunk/plugins/net.bioc​lipse.core/src/net/bioclipse/core/ (3 files in 2 dirs): Fixed exception complaining that .project does not exist for project Virutal
13:56 olas shk3: is there a root object in all cml files?
13:56 olas like <molecule>
13:56 olas molecule cml files that is
14:05 shk3 not sure right now
14:05 shk3 often there is <cml>
14:05 shk3 but starting with <molecule> should be all right as well
14:12 jonalv olas: There are many TODO in the cdk manager and there are many methods that doesn\t do anything with the monitors... :(
14:13 jonalv olas: And 0 methods supports cancel...
14:21 CIA-49 bioclipse: carl_masak * r6329 /bot/trunk/zarah.pl: [zarah] added @message
14:22 zarah joined #bioclipse
14:28 CIA-49 bioclipse: ospjuth * r6330 /bioclipse2/trunk/plugins/net.​bioclipse.cdk10.ui/plugin.xml: Commented out SDFile navigator content. In fact, cdk10.ui should not be used at all as it has no used functionality for now.
14:37 CIA-49 bioclipse: carl_masak * r6331 /bot/trunk/zarah.pl: [zarah] now greets meklund whenever he enters a channel
14:38 zarah joined #bioclipse
14:55 CIA-49 bioclipse: jonalv * r6332 /bioclipse2/trunk/plugins/ (4 files in 2 dirs):
14:55 CIA-49 bioclipse: Moved ConsoleProgressmonitor over to ui.jobs
14:55 CIA-49 bioclipse: For the moment consoleprogressmonitor is used a bit eager. We need to think through how and where we want to have it if at all.
15:25 CIA-49 bioclipse: carl_masak * r6333 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (Activator.java ApplicationWorkbenchAdvisor.java):
15:25 CIA-49 bioclipse: [Activator]
15:25 CIA-49 bioclipse: [ApplicationWorkbenchAdvisor]
15:25 CIA-49 bioclipse: * tidied up indentation, line length and idioms
15:34 CIA-49 bioclipse: carl_masak * r6334 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java):
15:34 CIA-49 bioclipse: [ICDKManager]
15:34 CIA-49 bioclipse: [CDKManager]
15:34 CIA-49 bioclipse: * fromString -> fromCml
15:43 CIA-49 bioclipse: carl_masak * r6335 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
15:43 CIA-49 bioclipse: [ScriptingConsoleView] fixed a bug which made the final quote
15:43 CIA-49 bioclipse: ('"') not appear when dragging-and-dropping a file into the
15:43 CIA-49 bioclipse: console
15:56 CIA-49 bioclipse: jonalv * r6336 /bioclipse2/trunk/plugins/net.biocl​ipse.ui/src/net/bioclipse/ui/jobs/ (3 files): Removed consoleprogressmonitor. It was more problems than it was worth.
16:07 shk3 one more question
16:07 shk3 anybody willing to answer?
16:08 shk3 jonalv, masak?
16:08 jonalv oh
16:08 jonalv sure if I know the answer :)
16:09 shk3 ok, I want to write this generate2d action
16:09 shk3 problem:
16:09 shk3 how is parsing done?
16:10 shk3 I just get the selection
16:10 shk3 so I have to look if it is mol, cml...
16:10 shk3 and do the parsing?
16:10 jonalv You should really ask olas about that. I don'r know the policy...
16:10 shk3 ok, will do that tomorrow
16:10 jonalv he left though... :(
16:11 shk3 no problem
16:11 shk3 will leave myself
16:11 shk3 soon
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