Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-21

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All times shown according to UTC.

Time Nick Message
05:22 egonw joined #bioclipse
05:50 rojasm joined #bioclipse
05:54 rojasm moin
05:54 zarah oh hai rojasm
06:00 egonw hi rojasm
06:09 rojasm joined #bioclipse
06:13 * egonw will now cycle to work
06:13 egonw bbl
06:15 rojasm don't you have today holidays?
07:04 egonw joined #bioclipse
07:18 olass joined #bioclipse
07:19 olass egonw: http://sv.wikipedia.org/wiki/Vaxholm
07:19 zarah olass's link is also http://tinyurl.com/qoyyhj
07:20 egonw tack
07:36 egonw olass: do you want to see Miguel's reaction stuff in action?
07:43 CIA-40 bioclipse: egonw * r10652 /bioclipse2/trunk/features/net.bio​clipse.medea_feature/feature.xml: Added missing GEF feature as included feature (fixes opening the reaction editor)
07:50 olass egonw: ok
08:15 shk3 joined #bioclipse
08:58 egonw shk3: the medea feature is now fully working for, including reaction stuff
08:59 shk3 great
09:00 CIA-40 bioclipse: egonw * r10653 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Removed core_patch feature (which it should not depend on in any case)
09:00 CIA-40 bioclipse: egonw * r10654 /bioclipse2/trunk/features/net.bioc​lipse.chemrdf_feature/feature.xml: The ZEST feature should be included instead of depended on
10:19 CIA-40 bioclipse: shk3 * r10655 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (12 files in 3 dirs): separated the validation and execution in manager
10:21 CIA-40 bioclipse: shk3 * r10656 /bioclipse2/trunk/_playground_/net.bio​clipse.medea.case/src/net/bioclipse/pl​ugins/extensions/WCCMedeaJudge.java: IJudge interface changed, adopted medea judge.
10:36 CIA-40 bioclipse: egonw * r10657 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated namespace of JCPGlobalProperertiesManager which was changed some time ago from jcpprop to jcpglobal (fixes #1091)
10:36 zarah bug #1091 | http://tinyurl.com/olmf7v
10:36 CIA-40 bioclipse: egonw * r10658 /bioclipse2/trunk/plugins/net.biocli​pse.chemoinformatics/cheatsheets/Gen​eralChemoinformaticsCheatSheet.xml: Fixed introduction to list all features mentioned in this cheat sheet (fixes #1063)
10:36 zarah bug #1063 | http://tinyurl.com/oavman
10:37 CIA-40 bioclipse: egonw * r10659 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Removed autogenerated files: .settings folders
10:37 CIA-40 bioclipse: egonw * r10660 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): (log message trimmed)
10:37 CIA-40 bioclipse: Added the optional @PublishedMethod(doi="") (implements #1080)
10:37 CIA-40 bioclipse: Output shows as (try 'man spectrum.calculateSimilarityWCC'):
10:37 CIA-40 bioclipse: Further information (DOI):
10:37 CIA-40 bioclipse: [SOME-DOI]
10:37 CIA-40 bioclipse: In anticipation of the 'doi' complement of 'man' (viz.
10:37 CIA-40 bioclipse: 'doi spectrum.calculateSimilarityWCC' which will open a HTML browser in Bioclipse
11:19 CIA-40 bioclipse: shk3 * r10661 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (4 files in 3 dirs): Removed ReactMolDrawingComposite, which was just an unnecessary wrapper round JChemPaintEditorWidget.
11:40 jonalv joined #bioclipse
11:42 maclean joined #bioclipse
11:42 egonw olass: where is the XMPP cheat sheet?
11:42 egonw in xws4j?
11:42 egonw nvm
11:42 olass yes
11:42 egonw found it
11:42 egonw hi jonalv, maclean
11:43 maclean hi
11:43 zarah hi maclean
11:43 egonw jonalv: I heard you'll join for a beer this afternoon?
11:43 jonalv egonw: yea I might, depends on masak and when and where you are having a beer
11:43 egonw not too late
11:44 egonw say, 16:00 or so ?
11:44 * jonalv probably should eat something before that...
11:44 olass no later
11:44 olass no, later
11:44 olass 1800?
11:44 olass 18 is much better
11:44 jonalv I think 16:00 is ?very? early
11:45 olass well it is not an evening out, just a beer at bmc
11:45 olass I will go to gym 17-18
11:45 jonalv but still
11:45 egonw ok, will consult home
11:45 olass so beer at 18 sounds fine with me
11:46 olass I will put beer in the fridge
11:46 olass (I have some at bmc)
11:46 olass jonalv, egonw: sounds good?
11:46 olass martin is on
11:47 * jonalv thiks the later the better but please not before 18
11:57 egonw yesm 18:00 here at BMC.
11:57 egonw excetllent
12:12 egonw how can I have some code open a HTML browser to show a URL?
12:14 maclean for the doi stuff?
12:14 maclean I just updated, and 'man spectrum.wcc..." doesn't seem to print it. do I have to wait for the 'doi spectrum.wcc'?
12:15 egonw no, that man command should do it
12:16 maclean hmmm.
12:16 egonw @tell masak, can you please review commit 10660 and let me know if you have further comments?
12:16 zarah Consider it noted.
12:16 egonw maclean: you have commit 10660 ?
12:17 maclean 10661
12:17 maclean so, yes
12:18 egonw OK, found some code which should open a browser...
12:18 maclean http://www.eclipse.org/articles/Arti​cle-SWT-browser-widget/browser.html
12:18 zarah maclean's link is also http://tinyurl.com/oethaq
12:23 maclean gah! how does the cambridge uni library not have books published by the cambridge uni press?
12:23 maclean godverdammen.
12:23 egonw very weird
12:28 maclean perhaps it is a way to make you buy their books....
12:28 egonw yes, not unlikely nowadays
12:29 olass maclean: eclipse comes with an internal web browser
12:29 olass but if you like, we'd be happy if you set up the mozilla eclipse plugin in Bioclipse
12:30 * maclean has no opinion one way or the other, I just linked to a likely-looking hit from google
12:30 maclean :)
12:31 maclean oh, and olass : how would I use the ds plugins?
12:31 maclean (if at all)
12:31 olass well.. they are not 100% working yet
12:31 maclean ah.
12:31 olass but the idea is
12:31 olass have the TestsView open
12:31 maclean ok
12:31 olass open a mol in JCP
12:32 olass click the "run" button in testsView local toolbar
12:32 olass any hits from the tests should appear and click it to highlight in JCP
12:32 maclean hmmm. ok. something happened
12:32 maclean oooh.
12:33 maclean I get 'amino' under sample simple smarts, which (when clicked) highlights a benzene ring.
12:33 maclean hmmm.
12:33 olass maclean: that is 6 aromatic hits
12:34 maclean ok
12:34 olass could be something wrong
12:34 olass but you get the point
12:34 maclean I do, I do. Looks good.
12:34 olass open proerties view and look at/edit the smarts
12:34 olass hmm, maybe that is not working yet...
12:34 olass bah
12:35 maclean well the properties view whos matching atoms
12:35 maclean s/whos/shows/
12:37 egonw OK
12:38 egonw doi manager.method
12:38 egonw about works
12:40 shk3 can somebody help me with new world order stuff?
12:41 egonw what's the problem?
12:41 CIA-40 bioclipse: egonw * r10662 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (2 files in 2 dirs): Added new JS command: 'doi manager.method' which uses the @PublishedMethod doi field to open a web browser (if any)
12:42 shk3 two problems:
12:43 jonalv egonw: that sounds intresting, you will have to explain sometime I am grabbing some food now... :)
12:43 shk3 in seneca, if I call executeJob(SenecaJobSpecification sjs) on console, i get a progress monitor
12:43 shk3 if I call it from java, I do not get it
12:43 shk3 wrong way round, I think.
12:43 shk3 don't really understand why
12:44 shk3 and createSenecaJob(IContainer parent, String jobTitle) still gives me
12:44 shk3 wrong number of arguments
12:45 egonw is the involved code in the repository?
12:45 egonw or something local?
12:45 shk3 in repository
12:45 shk3 seneca manager
12:46 shk3 if you try the new seneca job wizard, you get the create job problem
12:46 shk3 if you try example2 or hko1, you get the progress monitor problem
12:48 egonw OK, I'll have a look at it
12:48 maclean oh, and egonw : sorry to mention it, but I get a 'restricted access exception' on the browser stuff you just added. I put in a supress warnings, but...
12:49 maclean the code works though - very nice,  egonw++
12:50 shk3 thanks a lot
12:50 olass http://bioclipse.blogspot.com/2009/​05/bioclipse-20-beta5-released.html
12:50 zarah olass's link is also http://tinyurl.com/qbfync
12:51 egonw maclean: yes, ack on the suppress
12:51 egonw it runs even without the suppres warning...
12:51 egonw not sure how to fix this cleanly
12:52 egonw and no clue yet why I should not use that code
12:52 egonw eclipse can be pretty uninformative
12:52 maclean true
12:53 maclean there's probably a configmanagerfactoryadapter that you should be using.
12:53 maclean :)
12:53 maclean oh, and olass++ for beta5!
12:53 olass :)
12:53 olass that belongs to us all
12:54 olass all++
13:12 CIA-40 bioclipse: egonw * r10663 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/business/ISpectrumManager.java: Pointed to paper with full details on the method using the new PublishedMethod DOI field (closes #1082)
13:25 CIA-40 bioclipse: carl_masak * r10664 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
13:25 CIA-40 bioclipse: [JsConsoleView] reviewed egonw++'s additions
13:25 CIA-40 bioclipse: This resolves #1097.
13:26 egonw oh no...
13:26 egonw white space changes mixed with possible code changes
13:27 egonw @tell masak please don't mix whitespace clean up with code changes... I have no clue what functionality changes you now made...
13:27 zarah Consider it noted.
13:28 egonw it seems he have been fixing his own code
13:28 egonw but only for my copy
13:28 egonw not for the original
13:28 egonw @tell masak please apply the parts[] changes you made in commit 10664 to the code for man and help too
13:28 zarah Consider it noted.
13:54 CIA-40 bioclipse: egonw * r10665 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: Any way to get the workbench works: removes warning
14:01 CIA-40 bioclipse: shk3 * r10666 /bioclipse2/trunk/plugins/net.bioclipse.spectrum​/src/spok/parser/JcampToCMLSpectrumMapper.java: hz is converted to ppm during reading
14:08 shk3 I am going doing the speclipse beta5 release
14:08 shk3 shall I include seneca?
14:09 shk3 the problem is, we won't have something ready for the release or release candidate
14:09 egonw I would not do it
14:09 shk3 thin so as well
14:09 egonw here at uppsala we'll have an experimental update site...
14:09 egonw with experimental features
14:09 shk3 so I make a seneca feature
14:09 egonw for the daring few who want to try bleeding edge stuff
14:10 egonw I suggest two updates sites:
14:10 egonw one with speclipse
14:10 egonw a second with medea and seneca
14:12 CIA-40 bioclipse: shk3 * r10667 /bioclipse2/trunk/ (8 files in 8 dirs): preparing speclipse beta 5
14:13 egonw maclean: the problem with jcp is that the Nightly script is assuming git :(
14:13 maclean hah! "Step 1: assume git. Step 2: ..."
14:13 egonw yeah, I need an older version of Nightly
14:23 CIA-40 bioclipse: shk3 * r10668 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/: added .settings to svn ignore
14:35 shk3 if I try to install via software update (no matter what), I get errors
14:36 shk3 balloon and chemoinformtics reqire net.bc.core.pathc (2.0.0.b20090520)
14:36 shk3 is that my fault?
14:36 shk3 did you try installing/updating?
14:39 shk3 can/did anybody try this?
14:43 egonw mmm...
14:43 egonw ola and I noted a dep on the core.patch feature in a feature
14:43 egonw maybe there are more
14:43 egonw checking...
14:43 egonw http://chem-bla-ics.blogspot.com/2009/05/​bioclipse-beta5-really-last-one-now.html
14:43 zarah egonw's link is also http://tinyurl.com/q596fr
14:44 maclean joined #bioclipse
14:44 egonw spreading the word
15:01 shk3 it really looks like the download already has that problem
15:01 shk3 without any update
15:02 rojasm joined #bioclipse
15:02 shk3 so looks like wrong dependencies in featuers
15:03 egonw net.bioclipse.balloon_feature/feature.xml:      <import feature="net.bioclipse.core.patch" version="2.0.0.B20090520" match="greaterOrEqual"/>
15:03 egonw net.bioclipse.chemoinforma​tics_feature/feature.xml:      <import feature="net.bioclipse.core.patch" version="2.0.0.B20090520" match="greaterOrEqual"/>
15:07 shk3 and this core.patch is not existing, it seems
15:08 rojasm1 joined #bioclipse
15:08 egonw no
15:09 egonw it should not have been mentioned in those two features
15:09 egonw I need to check how they sneaked in
15:09 egonw just spoken with ola
15:09 egonw and this blocks using the update site for any feature
15:09 egonw so any update site is useles with beta5
15:09 egonw and it is about weekend here...
15:10 egonw (we switched todays day off with tomorrow)
15:10 egonw he won't be able to fix this before monday
15:11 egonw I'm fixing the features now, though
15:12 egonw but that won't help unfortunately
15:15 shk3 ok
15:16 egonw now debugging how and when that line got into those features
15:20 egonw it sneaked in with commit 9701
15:20 egonw that was before beta4
15:20 egonw (but after beta3)
15:21 egonw so, the update site should have failed for beta4 already
15:21 CIA-40 bioclipse: egonw * r10669 /bioclipse2/trunk/features/ (2 files in 2 dirs): Removed erronous importing of the core patch features, making update sites of the current beta5 impossible
15:21 egonw but apparently no one ever noticed that before :(
15:22 maclean well shk3++ for noticing then! :) (and egonw++ for fixing it..)
15:23 * maclean is now in a good mood
15:23 egonw maclean++
15:23 egonw good moods are good for productivity
15:23 maclean indeed they are.
15:23 maclean now - another diagram!
15:30 shk3 hm, i think i tried installing speclipse in beta4 as well
15:30 shk3 pretty sure i did, actually
15:31 egonw maybe that had that specific core patch
15:33 CIA-40 bioclipse: egonw * r10670 /bioclipse2/trunk/tabless.xml: 4 space indentation (fixes #1038)
15:34 zarah bug #1038 | http://tinyurl.com/qmxfk5
15:35 maclean no, i remember on chris' machine there were update problems, I think that was with the download...
15:38 egonw stupid thing is...
15:38 egonw many earlier betas had an update site from the start
15:38 egonw but at some beta is was decided to ship with the cheminfo feature on SF itself
15:38 egonw so far, Ola always asked us to test the update site...
15:38 egonw :(
15:42 edrin joined #bioclipse
15:42 edrin hi
15:42 zarah hi edrin
15:42 edrin oh
15:43 edrin obviously this is not a holiday in SWeden
15:45 egonw oh, it is
15:45 egonw several of us, however, switch today with tomorrow
15:45 edrin oh ok
15:45 CIA-40 bioclipse: miguelrojasch * r10671 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/src/net/bioclipse/rea​ction/editor/ReactionEditor.java: Synchronization with the Outline viewer. The Outline incorporates a global viewer of the reaction.
15:46 edrin i had to do plattenschaufeln since for the whole day
15:47 egonw rojasm1: you impress me with your knowledge how to get things done in eclipse/rcp !
15:49 rojasm1 :) don't believe that. Only taking examples in Google
15:49 rojasm1 Google is the maestro
15:59 egonw beer time
15:59 egonw bye!
15:59 edrin ciao
16:05 rojasm1 I try to figure out how a class can communicate with the properties panel. I see that for molecules we have to use the CDKMoleculePropertySource and this is request by the CDKMolecule.getAdapter(). Could somenone tell where class for example in JCP is given to the adapter the properties information?
16:07 rojasm1 shk3: stefan do you know maybe?
16:07 shk3 mom
16:08 shk3 sorry, never used that
16:08 shk3 no idea
16:09 rojasm1 mmm. So is egonw maybe wo knows.
16:10 maclean and sadly he has left :(
16:10 shk3 yes
16:10 shk3 or google
16:10 rojasm1 thanks anyway
16:11 rojasm1 I will try to find it
16:14 rojasm1 I think I miss the class. I should look for ChemObjectProperySource
16:32 edrin ehm
16:32 edrin could someone remove the old bc extensions from the update site?
16:32 maclean rojasm : Ctrl-Shift-T is helpful here :)
16:33 edrin olass: ping
16:33 maclean net.bioclipse.cdk.domain.ChemObjectPropertySource in the net.bioclipse.cdk.business plugin
16:35 shk3 edrin: having update problems?
16:35 rojasm1 thanks maclean
16:35 shk3 the update site needs to be changed for that
16:36 maclean n/p
16:36 shk3 which can't be done before monday
16:36 shk3 I was tolk
16:36 edrin shk3: i think the bc update site is too old for current bc2 beta
16:36 shk3 sorry for that
16:36 maclean edrin : I think ola is having an end-of-week beer....
16:36 rojasm1 other question!  is not the same JCP viewer to show a molecule that this used in reactionEditor?
16:36 edrin ok
16:36 shk3 well, the problem is there is a dependency which should not be there
16:36 edrin thanks for the info
16:36 shk3 so this core.patch is outdated
16:37 shk3 but it should not be required
16:37 shk3 but the configuration askes for current version of it.
16:37 edrin shk3: can anyone remove the current extensions that report error when you try to install them?
16:37 shk3 no
16:37 shk3 only uppsala can
16:37 shk3 sorry
16:37 shk3 rojasm: yes
16:38 rojasm1 when I try to open a reaction with the JCP editor/viewer it shows only the reactants
16:38 shk3 ah
16:38 shk3 mom
16:38 shk3 you mean the "normal" jcp
16:38 shk3 not the one in reaction editor
16:38 shk3 ?
16:38 rojasm1 the normal JCP to open molecules
16:38 shk3 yes
16:38 shk3 no, this is for mols only
16:38 shk3 no reactions
16:39 shk3 it might pick the first molecule in the reaction to display by accident
16:39 rojasm1 ups! but the JCP editor of reactionEditor is not the same
16:39 shk3 but it is not intended for reactions
16:39 shk3 no
16:39 shk3 it is not
16:39 rojasm1 ok
16:39 shk3 it is a renderer only
16:39 shk3 but the rendering components in both is the same
16:39 shk3 jcp could render reactions
16:39 shk3 but jcp in bioclipse is not loading them
16:40 shk3 file handling etc. is not aimed for reactions
16:41 shk3 net.bc.reactions is our reaction editor right now
16:41 rojasm1 ok!
16:42 rojasm1 the problem is when you want to modify some of the reactants or products
16:43 rojasm1 the JCP in reactionEditor is only a viewer, isn't it?
16:43 rojasm1 but not problem
16:48 maclean yes, it's just a viewer.
16:50 maclean I wonder if you could click on a molecule in the reaction viewer, and have it open in a new JCP editor?
16:51 shk3 might be nice
16:51 rojasm1 it is what I am triyng now
16:51 maclean oh, ok.
16:51 shk3 great
16:51 maclean great
16:51 rojasm1 load firs Load molecule dialog
16:51 maclean er, what?
16:52 shk3 pardon?
16:52 maclean "load first"?
16:52 rojasm1 sorry. Yes. double-click -> pop up a dialog asking if you want to load a molecule
16:53 maclean or through the right-click popup menu?
16:54 rojasm1 yes. But I don't remember how to introduce the popup menu in the box
16:55 shk3 sounds like a gef issue
16:55 shk3 no idea about that really
16:55 rojasm1 but good point checking
16:58 CIA-40 bioclipse: miguelrojasch * r10672 /bioclipse2/trunk/plugins/net.bioclipse.re​action/src/net/bioclipse/reaction/dialog/ (. LoadMoleculeDialog.java): Dialog to load a Molecule
17:07 rojasm1 sorry again question! is there some class as example which make the action to open a new panel the "normal" JCP
17:12 shk3 I would think jcp right now works on files always
17:12 shk3 which would mean it can't really be used for what you thought about
17:13 shk3 it would need to be modified to work on an object
17:13 rojasm1 mmm. Ok!
17:13 shk3 mom
17:14 rojasm1 specmol can do it. But you are right only from File
17:15 shk3 yes
17:15 shk3 specmol is using t temp file
17:16 shk3 just had a look at jcpeditor, it expects a fileeditorinput
17:16 rojasm1 the trick is to store in a temp file
17:16 rojasm1 yes
17:16 shk3 not too nice, but works
18:33 rojasm1 does someone know how I can convert a org.openscience.cdk.Molecule to net.bioclipse.core.domain.IMolecule or net.bioclipse.core.domain.ICDKMolecule
18:53 * rojasm1 discovered getAdapter() method
19:03 sneumann_ joined #bioclipse
19:20 CIA-40 bioclipse: miguelrojasch * r10673 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKReaction.java CDKReactionPropertySource.java): Create a new class to handle the viewer reaction properties
19:21 CIA-40 bioclipse: miguelrojasch * r10674 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKReactionPropertySource.java: Removed some unnecessary imports
19:33 CIA-40 bioclipse: miguelrojasch * r10675 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (3 files in 3 dirs): Adapted AbstractObjectEditPart to the CDKReactionPropertySource
20:16 CIA-40 bioclipse: miguelrojasch * r10676 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (2 files in 2 dirs): Added double-click to the reactant/product boxes. The action opens the JCP editor in a new Panel to be able to modify the structure. Still is necessary to synchronize the change produced by JCP with ReactionEditor
20:56 CIA-40 bioclipse: miguelrojasch * r10677 /bioclipse2/trunk/plugins/net.bioclipse​.reaction/src/net/bioclipse/reaction/ed​itparts/MyAbstractObjectEditPart.java: When a box is empty is created a IAtomContainer to be able to open JCP
20:58 CIA-40 bioclipse: miguelrojasch * r10678 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/src/net/bioclipse/rea​ction/editor/ReactionEditor.java: uncomment drag&drop functionalities
21:02 sneumann__ joined #bioclipse

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