Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-07

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
04:59 thomas_ku joined #bioclipse
05:32 Gpox joined #bioclipse
06:58 egonw joined #bioclipse
07:15 malick joined #bioclipse
07:48 jonalv joined #bioclipse
08:02 jonalv egonw: Should we plan a little "Bioclipse2-managers" meeting?
08:03 egonw next week Tuesday?
08:06 jonalv oh I had a word with olas the other day and he thought that you would benefit from something earlier than that but perhaps you are busy? :)
08:08 jonalv but tuesdeay next week would have to be after lunch because theres a meeting at the Hospital at 10 which I am supposed to be at :)
08:15 edrin joined #bioclipse
08:15 edrin hi
08:15 zarah hi edrin
08:16 egonw jonalv: I'd like to be sure I have had the time to set up a manager myself first
08:16 egonw Fri I am not at UU
08:16 jonalv oh I just thought that you and me should sit down and do that sort of jump start you... :)
08:16 egonw I might have a working manager for cdk.debug by then, but adding some back up time
08:17 egonw oh, that one...
08:17 egonw yes, sorry...
08:17 egonw I was thinking about further discussing the proxy-proxy thingy
08:17 egonw that we can surely do today...
08:17 egonw 14:00 ?
08:18 jonalv I was planning on heading over to the Hospial after lunch...
08:19 egonw um, ok...
08:19 egonw 10:45 then?
08:19 jonalv okey :)
08:30 gilleain joined #bioclipse
08:32 edrin egonw: what is a prox-proxy thing?
08:33 gilleain I wondered that.
08:37 egonw very quick: we'll have one plugin for each CDK module, e.g. org.openscience.cdk.builder3d and org.openscience.cdk.interfaces.
08:37 egonw So, we can easily tune what functionality we offer and tune in detail how large the Bioclipse download is
08:38 egonw and to allow scripting to use all functionality from all those plugins using "cdk." we need to proxy things into the central 'proxy' that is the backend of the "cdk." obejct
08:38 egonw that's all
08:39 gilleain ahhh, so the cdk root proxies the cdk module proxies. understood.
08:39 edrin ok
08:40 jonalv joined #bioclipse
08:43 egonw jonalv: OK, make that 15 minutes later...
08:43 egonw 11:00 in my office ...
08:43 egonw hahaha... that sounds stupid...
08:44 egonw 11:00 in my room
08:46 edrin :)
08:46 edrin egonw: did you already try the xws plugin?
08:50 egonw edrin: close to it
08:51 egonw edrin: will start implementing CDK-based XWS services this week, if nothing comes in between
08:51 egonw olas showed me around yesterday
08:51 edrin great :)
09:22 egonw Gpox: could you please help me out with a Mylyn-SF issue here?
09:28 olas joined #bioclipse
09:28 olas hi
09:28 zarah hi olas
09:28 * olas is using macirssi for the first time
09:29 Gpox egonw: sure, what's the problem?
09:29 egonw it does not work
09:29 egonw hi olas
09:29 olas hi egonw
09:29 * olas is on an empty mac
09:29 egonw Gpox: that is, I don't get to see a list of bugs after a query
09:29 olas mac left for repair
09:29 egonw ETA?
09:29 olas no idea
09:29 olas hope just one day
09:29 olas can be more
09:31 CIA-30 bioclipse: carl_masak * r7241 /bot/trunk/zarah.pl: [zarah] now has @replan (and synonym @rename)
09:35 edrin hi olas
09:36 egonw Gpox: can you drop in in my room? To see what I do wrong?
09:36 olas hi edrin
09:36 olas edrin: cannot work today at all, no ocmputer :-(
09:36 olas was working on my server and trying to convert EMF objects to DOM elements
09:58 edrin i found at last code how to push xsd schema from a buffer into the thing...
10:11 egonw Gpox: did you manage to define multiple SF-based mylyn repositories?
10:11 egonw it seems to use the server URL as identifier :(
10:11 egonw which really, really sucks
10:12 egonw so, exit Mylyn
10:12 egonw (for now)
10:17 egonw joined #bioclipse
10:20 egonw quick question...
10:20 egonw BC2 is written for Eclipse 3.3 or 3.4?
10:20 egonw nevermind
10:20 egonw found it
10:21 olas 3.4
10:21 olas (just to be sure)
10:21 egonw :)
10:22 * egonw is hacking up net.bioclipse.cdk.debug
10:23 egonw wow... just booted Bioclipse from SVN...
10:23 egonw and I get the message there are new online updates :)
10:26 olas boot from SVN?
10:27 olas boot from within Eclipse?
10:27 egonw_ joined #bioclipse
11:03 egonw ha, this is quite fun!
11:05 gilleain what scripted cdk?
11:05 gilleain s/ /,/
11:05 egonw yes, in bioclipse
11:05 egonw js> mol = cdk.fromSmiles("CCC")
11:05 egonw net.bioclipse.cdk.domain.CDKMolecule@5b02a6
11:05 egonw js> mol2 = cdk.fromSmiles("CC[13C]")
11:05 egonw net.bioclipse.cdk.domain.CDKMolecule@ede59e
11:05 egonw js> cdkdebug.diff(mol, mol2)
11:05 egonw AtomContainerDiff{AtomDiff{H:3/0, AtomTypeDiff{IsotopeDiff{MN:NA/13}}},
11:05 egonw BondDiff{AtomDiff{H:3/0, AtomTypeDiff{IsotopeDiff{MN:NA/13}}}}}
11:06 gilleain :)
11:15 CIA-30 bioclipse: egonw * r7242 /bioclipse2/trunk/plugins/net.bioclipse.cdk.debug/ (18 files in 8 dirs): Copied example plugin template
11:15 CIA-30 bioclipse: egonw * r7243 /bioclipse2/trunk/plugins/net.bioclipse.cdk.debug/ (11 files in 5 dirs): First working implementation: no real functionality, just localized the example
11:16 gilleain what would be really fun would be things like (pseudocode):
11:16 CIA-30 bioclipse: egonw * r7244 /bioclipse2/trunk/plugins/net.bioclipse.cdk.debug/ (4 files in 3 dirs): Added cdkdebug.debug(ICDKMolecule) and cdkdebug.diff(ICDKMolecule, ICDKMolecule)
11:19 gilleain map(cdk.addHydrogens, moleculeList)
11:21 gilleain table.display(sort(cdk.calculateMass, moleculeList))?
11:23 olas joined #bioclipse
11:23 gilleain hmmm. or maybe table.sort(cdk.calculateMass)...
11:24 CIA-30 bioclipse: carl_masak * r7245 /bot/trunk/zarah.pl: [zarah] refactoring: abbreviated some expressions
11:25 egonw gilleain: if I only understood what that would be trying to acchieve ...
11:25 egonw olas: first Uppsala-based BC2 patches commited to SVN
11:25 olas egonw++
11:26 gilleain Well, lets say you have a table of molecules, which you want to sort in some way.
11:26 egonw ah, ok... that one I actually did understand...
11:26 egonw sorry for being imprecise :)
11:26 egonw but:
11:26 egonw [13:19] <gilleain> map(cdk.addHydrogens, moleculeList)
11:26 egonw ??
11:27 gilleain Well, javascript has a map function, right?
11:27 egonw olas: now working on the 150 new CDK plugins
11:27 egonw oh, no clue
11:27 olas 150+ I hope
11:27 egonw 151 was just commited
11:27 egonw now going to do the first 150
11:28 gilleain Well, instead of having functions like addHydrogens(MoleculeList), you just have addHydrogens(Molecule) and then map that function to every molecule in the list.
11:28 gilleain It's the same as a loop, but easier to write in one line.
11:29 egonw ah, interesting
11:29 egonw would have to ask our JS expert
11:29 gilleain python does it with list comprehensions like:
11:29 gilleain [cdk.addHydrogens(mol) for mol in moleculeList]
11:30 gilleain Anyway, I'll let you get on with the 10,000 new plugins.
11:30 egonw I wonder is JS support the J5 for (mol : moleculeList) { addHydrogens(mol) }
11:31 gilleain Whoah. What language is that?
11:32 egonw Java5:
11:32 egonw for (IMolecule mol : moleculeList) {
11:32 egonw StaticClass.addHydrogens(mol);
11:32 egonw {
11:32 egonw s/{/}/
11:32 gilleain ->lunch
11:32 egonw wondering if JS adopted this syntax too
11:36 * olas is setting up leopard!
11:37 Gpox egonw: use the same repository but change the 'group_id' and 'atid' in the query
11:37 egonw olas: why? don't you have to turn in this laptop again, when you get your repaired one back
11:38 olas can transfer all
11:38 olas mac is nice
11:38 egonw Gpox: yeah, but that would not solve the problem... I wanted to do this:
11:39 egonw - create a repository for CDK bugs for 'egonw'
11:39 egonw - create a repository for CDK bugs for group='cdk-1.2.x'
11:39 egonw might be able to do that on the query level...
11:39 egonw since that actually asks again for those two fields...
11:39 egonw let me try that...
11:39 olas egonw: did you update jmol to point to 11.6?
11:39 olas (or latest version I mean)
11:39 olas else, please do
11:40 egonw olas: mom
11:54 egonw Gpox: no, can't get that to work
11:55 egonw it always gets me all items
11:59 jonalv` joined #bioclipse
12:13 Gpox egonw: http://mozilla.queze.net/ the 'Links and Forms' plugin is what i use
12:14 Gpox egonw: this is what i use to get my own bugs 'set=custom&_status=1&_assigned_to=${uid}'
12:34 egonw !ENTRY org.eclipse.osgi 4 0 2008-10-07 14:34:30.186
12:34 egonw !MESSAGE
12:34 egonw !STACK 0
12:34 egonw java.lang.IllegalArgumentException: The System Bundle's start level can not be modified.
12:34 egonw at org.eclipse.osgi.framework.internal.​core.StartLevelManager.setBundleStar​tLevel(StartLevelManager.java:415)
12:34 egonw ???
12:35 egonw What's that exceptino about??
12:35 egonw I'm trying to run bioclipse with the Jmol plugin
12:45 gilleain Hmm, no idea, sorry.
12:46 gilleain Have you tried the usual project->clean and _set as target platform_ things?
12:46 gilleain oh, and PDE Tools->Update classpath, I suppose.
12:47 olas write bots using ECF? See: http://help.eclipse.org/ganymede/index.jsp?topi​c=/org.eclipse.ecf.doc/html/tutorials/bot.html
12:47 zarah olas's link is also http://tinyurl.com/3zl8ng
12:48 egonw can installing a Eclipse plugin require a new _set-as-target for Bioclipse?
12:48 olas no, don't think so
12:49 olas but not sure
12:50 egonw olas: cool link!
12:50 olas yes
12:51 olas for you bot-makers
12:51 olas (on your sparetime)
12:53 egonw olas: oh no...
12:53 egonw just imagine doing BIoclipse hacking from inside #bioclipse
12:54 egonw OK, stupid question
12:55 egonw where did my net.bioclipse.target.platform from my RunConfig dialog Plugin-Ins tab go?!?!?!
12:56 gilleain did it used to be there? I only know it in the target-platform.target
12:56 egonw ok, back with a running configuration
12:56 egonw no idea what was messed up, and what caused it...
12:57 egonw well, the wiki says in step 11...
12:57 egonw add the required plugins
12:57 egonw from that previous list
12:57 egonw and that includes the target.platform one too :)
12:58 egonw ok, running BC2 now with Jmol 11.6 RC18
13:01 edrin olas: regarding your question yesterday: why do you need access to getStatusMessage() and getStatus() of ProcessStatus ?
13:03 jonalv egonw: that problem seemed like the problem that usually is resolved by ressetting target paltform
13:05 egonw ack
13:05 egonw it's working now again, and issuing a 'git svn dcommit' :)
13:06 egonw olas: see commit:
13:06 olas edrin: I need to be able to get the resutls of the IFunction and verify them in my Junit test
13:06 CIA-30 bioclipse: egonw * r7246 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (3 files in 3 dirs): Upgraded to Jmol 11.6 RC18
13:20 jonalv wow for once things just worked
13:21 jonalv I have already built a new Brunn version and gotten it to run at test users computer
13:21 jonalv woho! :)
13:24 jonalv shk3: ping
13:25 egonw jonalv++
13:26 jonalv egonw: did you see revision #7238
13:26 jonalv ?
13:27 egonw jonalv: nope
13:27 egonw let me check
13:27 jonalv please do so
13:27 egonw ah, yes, I did see that
13:27 egonw git browsed "git log" which is tons faster than svn log
13:28 egonw yeah, I guess that one deserved an notificiation email to the list :)
13:28 egonw then again...
13:28 egonw everyone does read the commit messages, not?
13:28 jonalv oh okey I was looking at the commit mail whitch contains diffs and all... :)
13:28 egonw anyway... what did you want to say about that commit?
13:29 jonalv I am sort of suprised at the need of that helper method
13:29 jonalv And I don't liek it for some reason
13:29 jonalv I want more opinions
13:29 jonalv masak is also a bit sceptical
13:30 jonalv honestly I don't undestand when/where to use it...
13:30 gilleain what method, sorry?
13:30 egonw shk3: ping
13:31 jonalv LogUtils.handleException(Exception ex, Logger logger)
13:31 gilleain Ahhh. we talked about this.
13:31 jonalv okey?
13:31 jonalv please update me
13:31 gilleain There is a need for handling exceptions in bioclipse, yes?
13:31 jonalv uhm could you give me an example?
13:31 gilleain As in, all plugins will raise them at some point :)
13:32 gilleain And printing the exception to stdout tells the programmer something in eclipse, but not the user.
13:32 * jonalv is not sure we need a standard way to handle exceptions. After all exceptions should be used for exceptionable cases and thiose usually need different solutions in each case...
13:33 gilleain Well, informing the user is usually part of the solution, right?
13:33 jonalv so please: hit me whith an example
13:34 gilleain I think there's one in one of stefan's plugins.
13:34 gilleain mom.
13:35 jonalv I really don't like code like:
13:35 jonalv catch (Exception e) {
13:35 jonalv throw new RuntimeException(e.getMessage());
13:35 jonalv uhm sry
13:35 shk3 look at Create2dHandler
13:35 shk3 line 49/50
13:36 egonw I agree that that handling can be more gracious
13:36 egonw in particular, Bioclipse plugins should shield users from (CDK) internals...
13:36 shk3 if you rethrow here as runtimeException,
13:36 egonw in particular, Bioclipse plugins should spend some time on checking input
13:36 shk3 the only effect is a stactrace in console
13:37 shk3 nothing else
13:37 shk3 the user won't see this
13:37 jonalv but catching all Exceptions...
13:37 jonalv I don't know
13:37 shk3 and he will no clue why the actions doesn't do anything
13:37 shk3 bad, isn't it?
13:37 jonalv this feels wrong but I can't figure out why..
13:37 egonw gilleain: btw... I got some old presentation on bc_seneca for you
13:37 gilleain jonalv : I agree about catching all exceptions.
13:38 gilleain egonw: takk - where will you put it please?
13:38 egonw will email them
13:38 gilleain okey.
13:38 jonalv uhm
13:38 jonalv generate2dCoordinates thrwos Exception
13:38 jonalv who wrote this?
13:38 gilleain uhmmm.
13:39 jonalv I mean it's barey ok to catch exception but throwing exception?
13:39 gilleain It's bubbling up from the internals :)
13:39 gilleain There's a worrying tendancy of cdk to raise Exceptions.
13:40 gilleain Also, to declare classes as Serializable and Clonable for no reason.
13:41 jonalv Clonable is not worth the trouble...
13:41 egonw gilleain: see my above comments...
13:41 egonw CDK throws exceptions, but that does not mean that the Bioclipse2-CDK plugin has to
13:41 gilleain Agreed.
13:42 egonw gilleain: yes, CDK throws too many exceptions... bad design
13:42 jonalv there is also this "BioclipseException" thing that is troublesome...
13:42 egonw something that should be changed
13:42 egonw http://chem-bla-ics.blogspot.com/2008​/10/jmol-116-rc-18-in-bioclipse.html
13:42 zarah egonw's link is also http://tinyurl.com/3r3nbm
13:42 gilleain It's all the StructureDiagramGenerator's fault, in this case.
13:42 shk3 checking input is important
13:43 shk3 but there might still be problems
13:43 shk3 showing up later
13:44 egonw shk3: yeah, fine... the bioclipse plugin would catch those exceptions, and give a meaningful dialog to the user
13:44 gilleain There could even be an ErrorView?
13:44 egonw "Sorry, no idea what happened, but the CDK did not like your input."
13:45 shk3 this is what my method is supposed to do
13:45 shk3 if you would like to improve this, go ahead
13:45 shk3 I just wanted to make a start
13:45 egonw jonalv: so, what are the alternatives?
13:46 jonalv Well if this takes place in an Eclipse job there already is exception handling...
13:46 jonalv no loggin though...
13:46 jonalv hm..
13:47 jonalv This might be the way to go, just because I think it feels wrong doesn't mean it is. I wanted to rasie the discussion though
13:48 malick left #bioclipse
13:48 gilleain Huh. By the way. If you change the StructureDiagramGenerator methods so that they throw CDKException instead of just Exception, then it seems to complile...
13:48 gilleain (wrong channel, sorry :)
14:03 shk3 cdk should always throw cdkexception (or other more specific exceptions like ioexception etc.)
14:05 egonw http://torvalds-family.blogspot.com/ <- *the* Thorvalds
14:05 zarah egonw's link is also http://tinyurl.com/3vxyyl
14:07 jonalv lol
14:07 jonalv intresting idea :)
14:18 egonw WTF??
14:19 * jonalv is looking at cdkdebug
14:19 egonw Spring has just bought BioMed Central!
14:19 jonalv egonw: trouble?
14:19 gilleain springer?
14:19 egonw Springer has just bought BioMed Central!
14:19 egonw http://www.earlham.edu/~peters/fos/200​8/10/springer-buys-biomed-central.html
14:19 zarah egonw's link is also http://tinyurl.com/4qa2vg
14:27 egonw [java] Processing qsarcml...
14:27 egonw [java] Don't know which Eclipse project this jar maps to: jumbo-with-fix-by-jonalv.jar
14:28 egonw oh goodies... olas will be so pleased
14:28 jonalv egonw: huh?
14:28 egonw 62 CDK module plugins
14:28 gilleain Only?
14:28 gilleain Bah!
14:28 egonw yeah, I need to urge those lazy CDK developers to come up with more plugins
14:28 jonalv aouch I guess you will script up manager generation... :)
14:30 gilleain Generated plugins? hmmm.
14:32 CIA-30 bioclipse: jonalv * r7247 /bioclipse2/trunk/_playground_/net.bioclip​se.springBasedPrototypePlugin/src/net/bioc​lipse/springBasedPrototypePlugin/business/ (ExampleManager.java IExampleManager.java): Updated springBasedPrototypePlugin to publish the manager class and it's method.
14:32 jonalv egonw: I have updated the Spring example plugin now. sry... :)
14:33 jonalv it didn't publish any methods before...
14:33 egonw gilleain: yes, see cdk-eclipse
14:33 egonw jonalv: oh, but my cdkdebug methods are picked up nevertheless
14:33 jonalv cdk-eclipse?
14:33 jonalv egonw: yea but no help...
14:33 egonw yeah, autogenerated Eclipse plugins 4 CDK modules
14:34 egonw jonalv: help??
14:34 egonw who needs help?
14:34 jonalv don't we all? :)
14:35 egonw no, I'm the MotU
14:35 egonw hahaha
14:35 jonalv try: "help managerName" in the console
14:35 jonalv :)
14:35 egonw remind me of that next time I ask about Mylyn :)
14:35 egonw jonalv: ack... will check the updates
14:35 jonalv I thought that was MOTKU
14:35 egonw true
14:36 jonalv actually no tabcompleting either...
14:36 jonalv only tab completing on publisehd stuff on managers
14:36 jonalv they would have to many strange methods otherwise...
14:36 jonalv |too
14:37 jonalv for example try writing "help cdk"
14:37 jonalv the general help text isn't that great though...
14:38 jonalv "help cdk.calculateMass" though that's quite nice I think...
14:38 egonw yes, will update cdkdebug
14:42 * egonw wonders how he will publish his cdk150 branch for BC2...
14:43 egonw OK, let's see if Eclipse can deal with it
14:44 egonw refreshing workspace
14:57 jonalv egonw: has Eclipse died yet? :)
14:57 egonw nope. alive and kicking
15:06 egonw and it is working quite well...
15:06 egonw I leave in 4 minutes...
15:06 egonw if you want to see it, come now
15:09 jonalv I can't get to BMC in 4 minutes :)
15:11 egonw ah, right
15:11 egonw forgot about that :)
15:11 egonw OK, you'll see tomorrow
15:11 egonw bye all!
15:24 olas joined #bioclipse
15:24 olas hi
15:24 zarah hi olas
15:24 olas jonalv: did egonw finish setting up the new cdk plugins?
15:25 jonalv he was working on it
15:25 jonalv don't know how far he got exactly
15:25 olas ok
15:25 jonalv he said it was workign out quite well
16:02 malick joined #bioclipse
16:02 malick left #bioclipse
16:14 CIA-30 bioclipse: shk3 * r7248 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: the generate2d now handles split molecules
16:22 CIA-30 bioclipse: shk3 * r7249 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (.classpath lib/JCampParser.jar): updated jcamp library
16:40 olas shk3: id the net.bc.cdk10 plugin up to date?
16:40 olas id=is
16:49 olas shk3: it does not use externals that I know of...
16:58 shk3 my changes in cdk 1.0 got in there without me doing anything
16:59 shk3 not sure how it's done
16:59 shk3 but it seems to be done
16:59 shk3 so yes, it seems to be up to date (no guarantee, though)
18:10 olas shk3: ok, thx
18:10 olas wil have dinner now
18:10 olas bye all
18:29 edrin left #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary