Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-03

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All times shown according to UTC.

Time Nick Message
05:02 Gpox joined #bioclipse
06:23 sneumann__ joined #bioclipse
07:53 egonw joined #bioclipse
08:12 olass joined #bioclipse
08:12 olass moin
08:12 zarah ni hao olass
08:16 olass egonw: ping
08:17 egonw pong, I guess
08:17 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:17 egonw @msg
08:17 zarah egonw: 1 d 17 h 20 m 1 s ago, masak said thanks. :)
08:17 zarah egonw: 10 h 29 m 13 s ago, sneumann__ said where to get the dependencies for BC SDK, especially GMF runtime, I only find GMF experimental SDK
08:17 olass egonw: I checked out cdk-jchempaint but I cannot find org.openscience.cdk.renderer.IGenerator in it...
08:17 olass GMF runtime???
08:18 olass we have a dep to that?
08:18 egonw @tell sneumann ... please file a bug report, I look at it shortly... I don't think there really should be a dep on GMF for the SDK ...
08:18 zarah Consider it noted.
08:18 egonw olass: did you take master?
08:18 olass yes
08:18 egonw because you should not :)
08:19 olass oh
08:19 egonw take the 13-this-is-for-bioclipse branch
08:19 egonw or so...
08:19 olass ok
08:19 olass 13-bioclipse2.1.x
08:20 egonw right
08:20 olass we are in 2.2 now :)
08:20 egonw quite so
08:20 egonw I'll rename later...
08:20 egonw today I'll release CDK 1.3.2
08:21 olass thx for the help
08:25 egonw lots of traffic from bioclipse.net to my homepage :)
08:30 olass your homepage?
08:30 olass what is the URL?
08:30 egonw good point
08:30 egonw my blog really
08:30 olass ah
08:30 egonw my homepage is at: http://egonw.github.com/
08:31 olass nice
08:31 annzi joined #bioclipse
08:36 egonw hi annzi
08:37 annzi hi egonw
08:48 egonw olass: what was that page again at uu.se to register publications?
08:48 olass diva
08:48 olass mom
08:48 olass http://uu.diva-portal.org/smash/search.jsf
08:48 zarah olass's link is also http://tinyurl.com/yfeeh6l
08:48 egonw tack!
08:49 olass ingen orsak
09:09 jonalv joined #bioclipse
09:12 sneumann__ joined #bioclipse
09:15 sneumann__ moin!
09:15 zarah hi sneumann__
09:16 s_wolf hi egonw
09:16 egonw hi s_wolf
09:16 s_wolf now i am back
09:17 egonw s_wolf: I'm setting up template code for metfrag
09:17 egonw we also need a source plugin for metfrag
09:17 egonw with the metfrag lib
09:17 s_wolf cool thank you....but i can't work on it next week because i am on holidays
09:17 s_wolf ok
09:18 egonw np
09:18 egonw we'll continue when you're back then, ok?
09:18 s_wolf ok of course :)
09:19 sneumann I couldn't resist, that's why I was lookig for the BC SDK
09:19 zarah sneumann: You have new messages. Write '/msg zarah @messages' to read them.
09:19 sneumann @messages
09:19 zarah sneumann: 1 h 1 m 30 s ago, egonw said ... please file a bug report, I look at it shortly... I don't think there really should be a dep on GMF for the SDK ...
09:19 egonw sneumann: right
09:19 sneumann done ;-)
09:20 egonw ack
09:20 sneumann So I need either SDK or the template to continue
09:20 sneumann At least I got a working BC workspace in eclipse
09:20 egonw ah, cool
09:20 egonw I will commit the template shortly
09:21 sneumann so I don't need the SDK now ?
09:21 egonw no
09:23 egonw my workspace was unclean once more...
09:23 egonw cleaning, refreshing, etc to remove all those red crosses
09:23 egonw also, lot's of missing plugins, due to merges with 2.2.x :)
09:28 jonalv o/
09:33 CIA-71 bioclipse.metabolomics: Egon Willighagen master * ra58c313 / (32 files in 11 dirs): Added a template for the MetFrag plugin - http://bit.ly/c34fIj
09:33 egonw sneumann: there you go
09:33 egonw sneumann: there is a metfrag.product
09:33 egonw which has the metfrag feature
09:33 egonw and will boot a small Bioclipse instance with the MetFrag manager
09:34 egonw well, I hope...
09:34 egonw let me try :)
09:34 egonw sneumann: the next step, is to add a source plugin into the bioclipse.metabolomics/externals
09:34 egonw folder...
09:34 egonw with the source of the MetFrag lib...
09:35 egonw I prefer the source, as that is easier to debug...
09:36 CIA-71 bioclipse.metabolomics: Egon Willighagen master * ra90170d / features/net.bioclipse.metf​rag_feature/metfrag.product : Fixed versioned dependencies - http://bit.ly/dulSK1
09:36 egonw ok, that should make it run
09:37 s_wolf so the source is the metfrag jar with all the source code in it?
09:37 egonw yes, something like that
09:38 egonw that jar would be a good starting indeed
09:38 * sneumann has ordered 4GB to speed up BC development
09:38 s_wolf :)
09:38 egonw sneumann: try the 2.6.32 kernel
09:38 egonw with 4GB runs 10 eclipses :)
09:38 egonw due to the shared mem patch
09:39 sneumann I might. I think I gave you a PPA URL ?!
09:39 egonw no recent core dumps anymore
09:39 egonw with the 2.6.32.5 deb
09:39 sneumann Or I backport lucid's kernel ?
09:39 egonw I used the ppa
09:40 CIA-71 bioclipse.metabolomics: Egon Willighagen master * r4103d89 / features/net.bioclipse.metfrag_feature/feature.xml : Now includes the proper MetFrag plugin - http://bit.ly/drRdjl
09:42 egonw http://kernel.ubuntu.com/~ke​rnel-ppa/mainline/v2.6.32.5/
09:42 zarah egonw's link is also http://tinyurl.com/yateeqw
09:42 egonw but there is even:
09:42 egonw http://kernel.ubuntu.com/~ke​rnel-ppa/mainline/v2.6.32.7/
09:42 zarah egonw's link is also http://tinyurl.com/yheglnl
09:50 sneumann ack, where do I reference the metfrag.jar ? metfrag.business ?
09:51 egonw net.bioclipse.metfrag
09:51 egonw should depend on the new plugin in externals/
09:52 egonw so, the metfrag should go in a separate plugin
09:52 egonw that's much easier to debug
09:52 egonw particularly, if it is a source plugin
09:59 sneumann ack.
09:59 sneumann Maybe I want to have metfrag as sth like
09:59 sneumann Running manager methods as jobs which return partial results
10:00 egonw yes, yes...
10:00 egonw jonalv: do you hear that!
10:00 sneumann or should I start slowly :-)
10:00 egonw no, please don't
10:00 egonw I have not used IPartialReturner
10:00 egonw or whatever that thing is called, but it's there for a reason...
10:00 * jonalv heard that
10:00 egonw olass, jonalv, Gpox:
10:01 * jonalv tries to remember where we had a use case..
10:01 egonw now, next thing is we need to be able to hook that up to a mol table !
10:01 jonalv some example code
10:01 egonw and dynamically fill an opened mol table
10:01 egonw olass, Gpox: listening in, I hope?
10:01 jonalv I think shk3 did some dynamic updates but I don't know for what
10:01 olass egonw: pong
10:02 olass egonw: what is the question?
10:02 egonw [02/03/10 11:01] <egonw> now, next thing is we need to be able to hook that up to a mol table !
10:02 olass how to use IPartialreturner?
10:02 egonw [02/03/10 11:01] <egonw> and dynamically fill an opened mol table
10:02 egonw so, formulating that as question:
10:02 olass never filled a moltable
10:03 egonw how do we hook up IPartialReturner with the mol table
10:03 olass ask Gpox and jonalv
10:03 * olass has never filled a moltable
10:03 jonalv olass: I think you can go back to whatever you were doing :)
10:03 * olass does so
10:03 * olass continues to sip his coffee
10:04 jonalv egonw: Yea this is something that we need to hook into the moltable. Gpox are you there? :)
10:04 jonalv olass: lol :) (So you are not on the phone?)
10:04 sneumann I need an import for IMolecule, which needs some project on the buildpath of org.bc.metfrag. org.bc.cdk.business ?
10:05 Gpox yes, that is something I have to look in to
10:05 Gpox what if the result set is very large?
10:06 jonalv we have discussed this mechanism for presenting result of StructureDB searches too
10:06 egonw Gpox: would that be a problem?
10:06 egonw I'd love to use this for PubChem search too!
10:06 jonalv Gpox: maybe a tempfile?
10:07 jonalv egonw, Gpox: Is there a bug report for this?
10:07 egonw no, not yet
10:07 Gpox egonw: you run out of memory
10:10 jonalv Gpox: so we need a temp file in the background...
10:10 egonw it would be kind of special resource anyway...
10:10 egonw so, dumping what comes in to a temp file might very well work
10:18 egonw sneumann: you got a github account?
10:18 egonw I need to give you write access
10:20 sneumann not yet
10:26 CIA-71 bioclipse.core: jonalv master * r26aa708 / plugins/net.bioclipse.ui.business/src/ne​t/bioclipse/ui/business/IUIManager.java : clarified some method summaries in @PublishedMe... - http://bit.ly/c4EGOm
10:26 CIA-71 bioclipse.core: jonalv master * r8be6bbc / plugins/net.bioclipse.doc/​parse-file-for-annotations : Merge branch 'master' of github.com:olas/bioclipse.core - http://bit.ly/av6DSt
10:27 sneumann egonw: sneumann worked ;-)
10:27 olass hmm, I think I forgot to merge 2.2 into master and tag..
10:27 olass egonw: can I do it now?
10:28 egonw which of the two?
10:28 olass merge 2.2.x into master
10:28 olass stand in master and say "git merge 2.2.x"
10:28 olass correct?
10:28 egonw stand in master -> git checkout master
10:28 egonw yes
10:29 olass and about the tag.. how did I tag on a certain commit?
10:29 egonw sneumann: added
10:30 olass egonw: should I do a "git pull origin master" before the merge or after?
10:31 olass I am not up to date.
10:31 egonw or:
10:31 egonw git fetch origin
10:31 egonw git status
10:31 egonw git pull
10:31 egonw that's the pattern I follow
10:32 egonw then I get to see with 'git status' I am indeed in the proper branch, and that I have no local commits no upstream
10:32 olass should I tag 2.2.0 in branch 2.2.x and/or master?
10:32 olass both?
10:32 egonw so to not cause one of those ugly merge commits just because I messed up
10:32 egonw only 2.2.x
10:33 olass "git tag -m 2.2.0" does not work.. what is missing?
10:34 olass do I need -a?
10:34 egonw drop the -m
10:34 olass right
10:34 egonw or add a message :)
10:36 CIA-71 bioclipse.core: jonalv master * rf367bdb / plugins/net.bioclipse.usermanager/src/net/bio​clipse/usermanager/business/IUserManager.java : fixed methodSummaries in @PublishedMethods - http://bit.ly/bMa19K
10:40 olass so, merged
10:40 olass hope it went well
10:46 CIA-71 bioclipse.cheminformatics: jonalv 2.2.x * r6a328da / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/ICDKManager.java : fixed spelling errors in @PublishedMethod notes - http://bit.ly/beKPuo
10:46 CIA-71 bioclipse.cheminformatics: jonalv 2.2.x * rf589a7d / plugins/net.bioclipse.cdk.jchempai​nt/src/net/bioclipse/cdk/jchempain​t/business/IJChemPaintManager.java :
10:46 CIA-71 bioclipse.cheminformatics: Rewrote strange methodSummarys (@PublishedMethods)
10:46 CIA-71 bioclipse.cheminformatics: Strange being spelling errors and in some cases just plain strange... - http://bit.ly/bCoEQW
10:46 CIA-71 bioclipse.balloon: Ola Spjuth master * r2158213 / (8 files in 8 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/8nkUIR
10:46 CIA-71 bioclipse.cheminformatics: jonalv 2.2.x * r21dbe8f / plugins/net.bioclipse.cdk.jchempaint/src​/net/bioclipse/cdk/jchempaint/business/I​JChemPaintGlobalPropertiesManager.java : rewrote more methodSummaries to match the others - http://bit.ly/drypoR
10:46 CIA-71 bioclipse.balloon: Ola Spjuth master * r746f16d / (8 files in 8 dirs): Set version to 2.2.0.RC3. - http://bit.ly/4wN6mg
10:46 CIA-71 bioclipse.cheminformatics: jonalv 2.2.x * r9587f12 / plugins/net.bioclipse.jmol/src/net/bio​clipse/jmol/business/IJmolManager.java : fixed spelling error - http://bit.ly/bbYHyi
10:46 CIA-71 bioclipse.balloon: Ola Spjuth master * r7f82609 / (8 files in 8 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/boPbAu
10:47 CIA-71 bioclipse.core: jonalv master * r8d164d8 / plugins/net.bioclipse.webservices/src/net/bioclip​se/webservices/business/IWebservicesManager.java : Layout, (80 cols and stuff) - http://bit.ly/coRuiO
10:47 CIA-71 bioclipse.core: jonalv master * r087e8a2 / plugins/net.bioclipse.webservices/src/net/bioclip​se/webservices/business/IWebservicesManager.java : fixed some methods summaries - http://bit.ly/bnnnzZ
10:47 CIA-71 bioclipse.core: jonalv master * r45233be / (30 files in 27 dirs): Merge branch 'master' of github.com:olas/bioclipse.core - http://bit.ly/9no0Hr
10:48 olass jonalv: you never do pull before push?
10:48 jonalv olass: I do pull before push
10:48 olass so why the merge commits?
10:48 * olass is just curious
10:48 jonalv olass: because to avoid them I ahve to do pull before commit
10:48 jonalv or rebase
10:48 olass and you don't like that?
10:48 jonalv But I don't trust the pull -rebase option
10:49 jonalv maybe I should?
10:49 * olass has no idea
10:49 jonalv I have heard it is dangerous...
10:50 CIA-71 bioclipse.ds: Ola Spjuth master * rd46cafa / (9 files in 9 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/6TC1CY
10:50 CIA-71 bioclipse.ds: Ola Spjuth master * re697e74 / (2 files in 2 dirs): Set feature deps to 2.2.0.RC2. - http://bit.ly/6A0Hz8
10:50 CIA-71 bioclipse.ds: Ola Spjuth master * r11cfe7e / (9 files in 9 dirs): set version to 2.2.0.RC3. - http://bit.ly/6mC7Oi
10:50 CIA-71 bioclipse.ds: Ola Spjuth master * r2a771ec / (9 files in 9 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/bfvMfY
10:53 CIA-71 bioclipse.cheminformatics: jonalv master * r6a328da / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/ICDKManager.java : fixed spelling errors in @PublishedMethod notes - http://bit.ly/beKPuo
10:53 CIA-71 bioclipse.cheminformatics: jonalv master * rf589a7d / plugins/net.bioclipse.cdk.jchempai​nt/src/net/bioclipse/cdk/jchempain​t/business/IJChemPaintManager.java :
10:53 CIA-71 bioclipse.cheminformatics: Rewrote strange methodSummarys (@PublishedMethods)
10:53 CIA-71 bioclipse.cheminformatics: Strange being spelling errors and in some cases just plain strange... - http://bit.ly/bCoEQW
10:53 CIA-71 bioclipse.cheminformatics: jonalv master * r21dbe8f / plugins/net.bioclipse.cdk.jchempaint/src​/net/bioclipse/cdk/jchempaint/business/I​JChemPaintGlobalPropertiesManager.java : rewrote more methodSummaries to match the others - http://bit.ly/drypoR
10:53 CIA-71 bioclipse.cheminformatics: jonalv master * r9587f12 / plugins/net.bioclipse.jmol/src/net/bio​clipse/jmol/business/IJmolManager.java : fixed spelling error - http://bit.ly/bbYHyi
10:53 CIA-71 bioclipse.cheminformatics: Egon Willighagen master * r858d7c8 / (4 files in 3 dirs): Merge remote branch 'origin/2.2.x' - http://bit.ly/bqpWGB
10:53 CIA-71 bioclipse.qsar: Ola Spjuth 2.2.x * r32a21f4 / features/net.bioclipse.qsa​r.xmpp_feature/feature.xml : Added more explicit feature deps. - http://bit.ly/a8U0b1
11:04 masak joined #bioclipse
11:10 sneumann Ack, I now have an metfragManager
11:10 sneumann that has a method calculateMetfragScore()
11:10 egonw cool :)
11:10 egonw sneumann++
11:10 sneumann which currently runs a pre-canned query against kegg,
11:10 sneumann so I only need to actually *run* this method.
11:10 sneumann js.cosole ?
11:10 egonw yes
11:11 sneumann metfrag.calculateMetFragScore()
11:11 sneumann org.mozilla.javascript.EcmaError: ReferenceError: "metfrag" is not defined.
11:12 egonw using the metfrag.product?
11:12 egonw if so, check the console for error messages...
11:12 sneumann missing from metfrag.product ? It doesn't show in the console where I get Bioclipse manager: ws added to JavaScript environment.
11:13 egonw right
11:13 egonw check the console for messages about missing plugins
11:13 sneumann none
11:13 egonw a manager not loading, is often a missing dependency
11:13 egonw can you commit?
11:14 sneumann no, eager to manage myself ;-)
11:14 egonw well, won't complain about that :)
11:15 egonw what about putting the console output on a pastebin?
11:17 sneumann http://pastebin.com/m2e363070
11:19 sneumann OK, how to commit ?
11:19 sneumann git gommit -a and the git push ?
11:19 sneumann git commit -a and the git push ?
11:21 CIA-71 bioclipse.statistics: Ola Spjuth master * r3fa7335 / (2 files in 2 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/5cHVTT
11:21 CIA-71 bioclipse.statistics: Egon Willighagen master * r6583943 / (5 files): Added a Statistics Feature - http://bit.ly/82l4gR
11:21 CIA-71 bioclipse.statistics: Egon Willighagen master * re383d41 / features/net.bioclipse.stat​istics_feature/feature.xml : Bumped version to 2.2.0.RC2 - http://bit.ly/6uLTgW
11:21 CIA-71 bioclipse.statistics: Ola Spjuth master * r4204a47 / (3 files in 3 dirs): set version to 2.2.0.RC3. - http://bit.ly/8gm6g8
11:21 CIA-71 bioclipse.statistics: Ola Spjuth master * r4cd7769 / (3 files in 3 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/bOQgu3
11:21 egonw sneumann: was afk, back now
11:22 egonw checking the pastebin
11:22 egonw sneumann: ok... here's the deal
11:22 egonw you see line 14?
11:22 sneumann !MESSAGE Bundle net.bioclipse.metfrag_1.0.0.qualifier [32] was not resolved.
11:22 egonw that's my fault... that dep is false
11:22 sneumann JavaSE-1.6
11:22 egonw that's 12 in the pastebin I have
11:22 egonw yes, that one :)
11:23 egonw let me fix that
11:23 egonw sneumann: that said...
11:23 egonw Java 1.6 will be required for 2.4
11:24 olass egonw: that is not decided yet but hopefully true
11:24 sneumann and then I do what ? git rebase or git fetch  or git pull ?
11:24 olass if weget JRE bundling to work
11:24 CIA-71 bioclipse.metabolomics: Egon Willighagen master * rca0be81 / plugins/net.bioclipse.metfrag/META-INF/MANIFEST.MF : Removed hard-coded dep on Java1.6 - http://bit.ly/aU6XBo
11:24 egonw olass: ack
11:24 egonw sneumann:
11:24 egonw git stash
11:24 egonw git pull
11:24 egonw git stash apply
11:25 egonw assuming you have not commited anything yet, have you?
11:25 egonw if you did:
11:25 egonw git stash
11:25 egonw git rebase origin/master
11:25 egonw umm...
11:25 egonw no, from the start
11:25 egonw git stash
11:25 egonw git fetch origin
11:25 egonw git rebase origin/master
11:25 egonw git stash apply
11:25 sneumann too late ...
11:25 egonw :)
11:26 egonw well, you can still do the: git rebase origin/master
11:26 egonw after the fetch
11:31 sneumann INFO - Bioclipse manager: metfrag added to JavaScript environment.
11:31 egonw sneumann++
11:31 sneumann DEBUG - org.mozilla.javascript.EcmaError: TypeError: Cannot find function calculateMetFragScore in object net.bioclipse.metfrag.business.MetfragManager@45e4d960.
11:31 sneumann sneumann--
11:32 egonw sneumann: did you add it API to the IMetFragManager too?
11:32 egonw and marked it with @PublishedMethod ?
11:32 sneumann nope
11:32 egonw annotated, that is
11:33 sneumann checking wiki
11:38 egonw sneumann: http://wiki.bioclipse.net/index.p​hp?title=How_to_make_a_manager_2
11:38 zarah egonw's link is also http://tinyurl.com/ouun2r
11:39 sneumann PublishedMethod cannot be resolved to a type
11:39 sneumann nedd to import what ?
11:40 sneumann http://pastebin.com/m5ba88fba
11:40 egonw net.bioclipse.core
11:40 sneumann got it
11:41 egonw but why in the metware manager?
11:41 egonw typo, I guess :)
11:41 egonw s/IMetwareManager/IMetFragManager/
11:42 * egonw is dumping 1.1GB of chembl activities into the SPARQL end point
11:42 egonw annzi: ping
11:42 egonw annzi: I think I got the indexing tables properly set up now
11:44 Gpox olass: What is the resone? http://github.com/olas/bioclipse.core/commi​t/a40acf708dfdff85d449f476bc83d38a35691ea9
11:44 zarah Gpox's link is also http://tinyurl.com/yd6dabr
11:46 * egonw is making lunch
11:54 sneumann > metfrag.calculateMetfragScore()
11:54 sneumann Can't find method $Proxy126.calculateMetfragScore().
11:55 egonw jonalv: ping
11:55 egonw sneumann: please show jonalv the code
11:56 egonw the proxy figures out on the fly what method to use in the MetFragManager implementation
11:56 egonw but not sure what the pattern is when using IReturner
11:56 sneumann Should I try to remove it ?
11:57 egonw I suggest looking for an example in one of the other existing managers
12:00 egonw sneumann: have a look at ICDKManager.calculateSMILES(IMolecule)
12:00 sneumann java.lang.NoClassDefFoundError: de/ipbhalle/metfrag/main/MetFlowConvenience
12:00 sneumann How to bundle the org.metware
12:00 sneumann into the product ?
12:00 egonw put it as plugin in the metfrag_feature
12:01 sneumann closing in ...
12:02 egonw well done :)
12:04 * egonw is happy that we can now bootstrap a working manager within one day :)
12:07 sneumann Caused by: java.lang.NoClassDefFoundError: de/ipbhalle/metfrag/main/MetFlowConvenience
12:07 sneumann which is in org.metware
12:07 sneumann and metfrag.jar is part of the binary build
12:07 sneumann and supposedly exported. Hm.
12:07 egonw @google site:pele.farmbio.uu.se classpath horror
12:07 zarah egonw: No hits.
12:08 egonw @google site:uu.se classpath horror
12:08 zarah egonw: No hits.
12:08 sneumann but not in Bundle-ClassPath of org.metware
12:09 egonw @google site:bioclipse.net classpath horror
12:09 zarah egonw: http://wiki.bioclipse.net/index​.php%3Ftitle%3DClasspath_Horror
12:09 egonw ah :)
12:17 sneumann Caused by: java.lang.UnsupportedClassVersionError: Bad version number in .class file
12:17 sneumann just one more 1.5 setting ...
12:17 egonw :)
12:39 jonalv egonw: ping
12:39 egonw pong
12:40 jonalv egonw: seems you merged my changes into 2.2.x
12:40 egonw yes, intentionally
12:40 jonalv I thought we were working on master now
12:40 egonw it's a bug fix, not?
12:40 jonalv okey, why?
12:40 jonalv egonw: hm yea I guess... :)
12:40 jonalv egonw: will you merge it into master too?
12:40 egonw already done
12:41 egonw git++
12:41 jonalv roger
12:41 egonw @seen roger
12:41 zarah I have not seen roger
12:41 jonalv zarah: seen me?
12:41 zarah I have not seen me
12:41 jonalv hahaha
12:48 sneumann closing in:
12:48 sneumann Caused by: java.lang.NoClassDefFoundError: org/openscience/cdk/interfaces/IChemObject
12:48 egonw depend on:
12:48 sneumann so the metfrag.jar in org.metware needs cdk stuff
12:48 egonw org.openscience.cdk.interfaces
12:49 sneumann for org.metware
12:49 egonw these are in bioclipse.cheminformatics/externals
12:49 sneumann orr n.bc.metfrag ?
12:49 egonw sorry?
12:49 sneumann which plugin needs org.openscience.cdk.interfaces as dependency ?
12:50 sneumann org.metware where metfrag.jar is ?
12:50 egonw ah...
12:50 egonw what is the full stacktrace for the NCDFE ?
12:50 sneumann http://pastebin.com/m49c6e279
12:51 sneumann at net.bioclipse.metfrag.business.MetfragManager.​calculateMetFragScore(MetfragManager.java:81)
12:51 egonw net.bioclipse.metfrag needs to depend on org.openscience.cdk.interfaces
12:52 sneumann hm, already does ?!
12:52 sneumann ah, but not imported ...
12:58 sneumann hm, n.bc.metfrag has MANIFEST.MF
12:58 sneumann Require-Bundle: org.eclipse.ui, ...  org.openscience.cdk.interfaces,
12:58 sneumann looks alright
12:59 egonw please pastebin the full MANIFEST
13:02 sneumann http://pastebin.com/m54e25943
13:08 egonw remove those import-package lines
13:08 egonw leave only org.apache.log4j
13:08 egonw Require-Bundle: section looks fine
13:09 egonw sneumann: I think this is what is going on:
13:09 egonw the metfrag.jar requires a different version of IChemObject
13:09 egonw because it was compiled against a different version of the CDK
13:09 egonw that's what I suspect
13:09 sneumann Yup.
13:09 egonw this is solved by putting the MetFrag code in net.bioclipse.metfrag/src/ instead
13:10 egonw I have had a lot of trouble with these kind of things
13:10 egonw which is why I use src/ plugins now as much as possible
13:10 egonw oh...
13:10 egonw and please put that source code in a new source plugin:
13:10 egonw de.ipbhalle.metfrag
13:10 sneumann already in the works...
13:40 egonw annzi: http://pele.farmbio.uu.se/chembl/sn​orql/?query=SELECT+DISTINCT+%3Fg+%3​Fproperty+%3FhasValue%0D%0AWHERE+{%0D%0A++GRAPH+%3Fg+{+<http://pele.farmbio.uu.se/ch​embl/%3FactivityId%3D107445>+%3Fproperty+%3FhasValue+}%0D%0A}%0​D%0AORDER+BY+%3Fproperty+%3FhasValue
13:40 zarah egonw's link is also http://tinyurl.com/yhlbqgl
13:44 * sneumann is in dependency hell.
13:44 sneumann How to find plugin for Atom / AtomCaintainer etc.
13:44 egonw annzi: http://pele.farmbio.uu.se/chembl/snorql/?​query=SELECT+DISTINCT+%3Fact%0D%0AWHERE+{%0D%0A++%3Fact+a+chembl:Act​ivity+.%0D%0A}%0D%0ALIMIT+5
13:44 zarah egonw's link is also http://tinyurl.com/yf2b4jt
13:44 sneumann I thought that is in o.o.cdk.data
13:44 egonw sneumann: yes
13:44 sneumann Require-Bundle: org.openscience.cdk.data,
13:45 egonw yeah, sounds good to me
13:50 annzi egonw: does this mean that the sparql endpoint works again?
13:50 egonw annzi: yes, it's back online
13:50 egonw but I am still populating it
13:51 egonw that takes some time, see my tweets
13:51 annzi will I be able to make it local, like snapshot?
13:52 egonw [02/03/10 14:51] <egonw> the activities (2.4M) are in
13:52 egonw [02/03/10 14:51] <egonw> assays are being inserted
13:52 egonw [02/03/10 14:51] <egonw> but molecules, targets and docs still have to be done
13:52 egonw [02/03/10 14:51] <egonw> done == started
13:53 annzi didn't know that you tweet, but I found ypu
14:00 sneumann import org.openscience.cdk.formula.MolecularFormula; is not accessible due to access restrictions
14:00 sneumann that seems a difference between cdk1.2 and 1.3 ?
14:01 egonw git log cdk-1.2.x..master -- src/main/org/openscience/cdk/​formula/MolecularFormula.java
14:01 egonw nothing shows up
14:04 sneumann Is there a successor to Render2DModel ?
14:04 * sneumann is porting metfrag to cdk-1.3.x
14:04 egonw yes
14:05 egonw org.openscience.cdk.render*
14:05 sneumann any "Porting" documents about those ?
14:06 egonw well.... no, not really
14:06 egonw but you can remove certain metfrag code from the Build Path
14:07 egonw and then file me a bug report to fix it
15:18 egonw http://barryhardy.blogs.com/cheminfost​ream/2010/02/bursary-award-application​s-echeminfo-oxford-2010-workshops.html
15:18 zarah egonw's link is also http://tinyurl.com/yfcck8d
15:38 egonw joined #bioclipse
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17:36 sneumann joined #bioclipse
18:40 sneumann hi egonw,
18:40 egonw hi
18:40 zarah saluton egonw
18:40 sneumann I am down to ~18 problems in porting to cdk-1.3
18:40 * egonw is only briefly back at keyboard
18:40 egonw :)
18:41 egonw good
18:41 sneumann leaving mostly access restrictions
18:41 sneumann where I am unsure whether that is due to them being BC plugins
18:41 sneumann of whether something changed on the way to 1.3.x
18:41 egonw if you commit, I can fix them
18:41 egonw or at least look at them
18:41 sneumann how do I commit ?
18:42 sneumann git push ?
18:42 egonw as one of the last steps
18:42 egonw first, git add
18:42 sneumann of d.i.m.metfrag
18:42 sneumann after discoupling from svn, that is.
18:42 egonw to make sure all files you want the have in the commit are marked
18:42 egonw 'staged' is the proper term
18:42 egonw git diff --cached
18:43 egonw allows you to check all changes that are staged
18:43 egonw once you are happy about those, you can commit
18:43 egonw if you just want all changed in the commit, simply do:
18:43 egonw git add .
18:43 egonw then, you make the commit with:
18:43 egonw git commit -m "Your message"
18:43 egonw which will make everything that was staged a single commit
18:43 sneumann how do I eclipse-bioclipse/de.ipbhalle.metfrag$ git ignore bin
18:44 egonw all commits you have locally, you can then push with: git push
18:44 egonw ah...
18:44 egonw make a .gitignore file
18:44 egonw and add that file to the repos
18:44 egonw ok, got to read Harry P. to my son now...
18:44 egonw bbl
18:45 egonw check: http://help.github.com/
18:45 egonw for many good tutorials
18:46 egonw note the right-hand side 'Everyday git'
19:04 sneumann So, I tried to put metfrag to http://github.com/sneumann/de.ipbhalle.msbi
19:04 zarah sneumann's link is also http://tinyurl.com/ya9mxv8
19:13 egonw indeed
19:13 egonw seems to have worked
19:14 sneumann :-)
19:14 egonw interesting package names
19:15 sneumann which is why I didn't want them in "official" repositories yet
19:15 egonw ah, no... that was positive :)
19:15 egonw I see eutils stuff for pubchem
19:15 egonw that's really interesting...
19:15 egonw and code for chemspider...
19:15 egonw I can see that used for other plugins too :)
19:16 egonw ok, /me is forking
19:16 egonw done
19:16 egonw http://github.com/egonw/de.ipbhalle.msbi
19:16 zarah egonw's link is also http://tinyurl.com/yf8xugb
19:16 egonw I will put some commits there...
19:16 egonw just so that you can merge them in via the website...
19:18 sneumann ?
19:19 egonw I'll explain in some minutes...
19:19 egonw I'll rebase to downstairs
19:19 egonw which will require a bump of network connectivity...
19:19 egonw brb
19:23 egonw_ joined #bioclipse
19:23 egonw_ Bioclipse 2.2.0 is already downloaded 800+ times :)
19:24 egonw 200 linux, 100 os/x, 500 windows
19:24 egonw (bit more on each category)
19:25 egonw sneumann: the git clone connection is ridiculously slow right now
19:25 egonw at about 10% is my download capacity
19:45 sneumann hm, maybe I just pushed the n.bc.metfrag stuff into your repo ?
19:46 sneumann but git status still says # Your branch is ahead of 'origin/master' by 6 commits.
19:46 egonw git push origin master
19:47 egonw it's back now
19:47 sneumann git push origin master
19:47 sneumann fatal: remote error:
19:47 sneumann You can't push to git://github.com/egonw/bioclipse.metabolomics.git
19:47 sneumann Use git@github.com:egonw/bioclipse.metabolomics.git
19:48 egonw yes
19:48 egonw edit .git/config
19:48 egonw and change the url
19:49 egonw in the appropraite [remote] section
19:51 sneumann yes, worked
19:51 egonw good :)
19:51 egonw mom, need to reboot konversation
19:51 egonw bug in qt 4.6 :)
19:52 egonw joined #bioclipse
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20:46 sneumann_ joined #bioclipse
22:45 sneumann_ switching to BC ...
22:45 sneumann_ log4j:ERROR A "org.apache.log4j.RollingFileAppender" object is not assignable to a "org.apache.log4j.Appender" variable.
22:45 sneumann_ log4j:ERROR The class "org.apache.log4j.Appender" was loaded by
22:45 sneumann_ log4j:ERROR [org.eclipse.osgi.internal.ba​seadaptor.DefaultClassLoader@136fb9fd] whereas object of type
22:45 sneumann_ log4j:ERROR "org.apache.log4j.RollingFileAppender" was loaded by [org.eclipse.osgi.internal.ba​seadaptor.DefaultClassLoader@7d6fdcc1].
22:45 sneumann_ log4j:ERROR Could not instantiate appender named "file".
22:46 sneumann_ log4j:ERROR A "org.apache.log4j.ConsoleAppender" object is not assignable to a "org.apache.log4j.Appender" variable.
22:46 sneumann_ log4j:ERROR The class "org.apache.log4j.Appender" was loaded by
22:46 sneumann_ log4j:ERROR [org.eclipse.osgi.internal.ba​seadaptor.DefaultClassLoader@136fb9fd] whereas object of type
22:46 sneumann_ log4j:ERROR "org.apache.log4j.ConsoleAppender" was loaded by [org.eclipse.osgi.internal.ba​seadaptor.DefaultClassLoader@7d6fdcc1].
22:46 sneumann_ log4j:ERROR Could not instantiate appender named "stdout".
22:46 sneumann_ log4j:WARN No appenders could be found for logger (org.apache.axis.configuration.En​gineConfigurationFactoryFinder).
22:46 sneumann_ log4j:WARN Please initialize the log4j system properly.
22:47 sneumann_ someone else has that as well
22:47 sneumann_ http://dev.eclipse.org/newslists/news.e​clipse.technology.equinox/msg05959.html
22:47 zarah sneumann_'s link is also http://tinyurl.com/yau7vqx
22:48 sneumann_ egonw: is that something where I need net.bioclipse.logger ?
22:51 egonw the net.bioclipse.metfrag has an Import-Package for org.apache.log4j
22:51 egonw that's the Bioclipse way
22:52 egonw perhaps add that to de.ipbhalle.metfrag too
22:59 sneumann_ logging works,
22:59 sneumann_ still fighting java.lang.ClassCastException: org.apache.axis.attachments.AttachmentsImpl
23:00 egonw making progress here too
23:00 egonw rebasing last branch
23:01 sneumann_ I'll hand that off to Sebastian tomorrow.
23:01 sneumann_ Also will be asking here how to get a moltable into MetFrag
23:01 sneumann_ good night,
23:01 sneumann_ Steffeb
23:01 egonw nighty night
23:01 * olass is going to bed too
23:02 olass bye

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