Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-28

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Time Nick Message
05:04 egonw joined #bioclipse
06:30 Gpox joined #bioclipse
07:12 olass joined #bioclipse
07:22 egonw olass: my number one blocker is almost fixed
07:22 egonw NewJavaScriptWizard is implemented
07:22 egonw finally
07:22 olass sounds good
07:23 CIA-40 bioclipse: egonw * r10794 /bioclipse2/trunk/plugins/net.bioclips​e.jseditor/src/net/bioclipse/jseditor/ (4 files in 2 dirs):
07:23 CIA-40 bioclipse: Fixed saving of StringInput backed JavaScript files, forcing a doSaveAs() when StringInput.
07:23 CIA-40 bioclipse: * factored out StringInput and StringStorage
07:23 CIA-40 bioclipse: * JsEditor detects these and then triggers a doSaveAs()
07:23 egonw actually got to fix wiki.eclipse.org :)
07:23 olass :)
07:23 egonw which is cool
07:23 egonw Gpox: ping
07:23 egonw the new NewMoleculeWizard is half done
07:23 egonw but need Gpox's help here
07:23 Gpox egonw: pong
07:23 egonw as there are some interaction issues
07:23 egonw ah good...
07:23 egonw Gpox: filed a few bug reports...
07:24 egonw here's the story
07:24 egonw I had this bug on my list about creating a new JavaScript and open a fresh new JChemPaint editor
07:24 egonw which will trigger a saveAs() when trying to be saved
07:24 egonw because without IFile backend to start with...
07:25 egonw finally worked out the right buttons to push to make this happen in Eclipse
07:25 egonw and it works lovely for the JavaScriptEditor
07:25 egonw now...
07:25 egonw the JChemPaint editor also sort of works...
07:25 egonw the new wizards creates a new in memory resource too...
07:25 egonw and opens this in the CMLEditor (which is a JChemPaintEditor)
07:25 egonw but
07:25 egonw then
07:26 egonw @pz 1127
07:26 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1127
07:26 egonw doSave() throws a NPE
07:26 egonw which needs fixing
07:26 egonw not filed yet...
07:26 egonw but the doSave should check if the IEditorInput is actually the used anynomous internal class StringInput
07:27 egonw the commit I just did, factors it out into a separate class...
07:27 egonw but cannot reuse that for cdk.jchempaint
07:27 egonw nor does net.bioclipse.jseditor depend on nb.core or so...
07:27 egonw so maybe cdk.jchempaint needs to duplicate these classes...
07:27 egonw anyway...
07:28 egonw the JChemPaintEditor doSave() should check for this StringInput and then doSaveAs()
07:28 egonw that was issue two
07:28 egonw the third one is
07:28 egonw @pz 1128
07:28 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1128
07:28 egonw when I open the StringInput in the CMLEditor
07:28 egonw the screen goes grey
07:28 Gpox it would if widget.getMolecule() did not return null for some reason
07:28 egonw instead of the common white
07:28 egonw right...
07:29 egonw so I think the instantiation of the editor caused by the following code must be checked:
07:29 egonw page.openEditor(input, "net.bioclipse.cdk.ui.editors.jchempaint.cml");
07:29 egonw that's how I open the editor...
07:29 egonw and that is not setting the model correctly
07:30 egonw Gpox: can you have a look at those issues?
07:30 egonw if not, we disable this NewMoleculeWizard and use the old IFile-back solution for 2.0
07:30 egonw olass: your comment on that appreciated...
07:31 egonw I don't think it is much work, but always hard to estimate...
07:31 olass egonw: will look at it
07:31 egonw olass: depending on how much you would like this feature in, please let Gpox know if he should spend time on it
07:31 egonw olass: ack, thanx
07:31 olass maybe easy for Gpox, for me it would take some time to get into...
07:31 egonw oh, and please also let me know your experience with the NewJavaScriptWizard
07:32 olass yes, will try it
07:32 egonw (in the Other category right now)
07:32 egonw bbl
07:32 egonw back to packing
07:32 olass egonw++
07:53 jonalv joined #bioclipse
07:53 edrin joined #bioclipse
07:53 edrin hi
07:53 zarah oh hai edrin
08:08 shk3 joined #bioclipse
08:10 maclean joined #bioclipse
08:10 CIA-40 bioclipse: goglepox * r10795 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 3 dirs): Changed how property positions are stored when parsing SDFile
08:11 jonalv shk3: regarding bug: 1111. How do I reproduce?
08:11 CIA-40 bioclipse: goglepox * r10796 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (7 files in 5 dirs): Added property calculator
08:11 shk3 mom
08:11 jonalv shk3: oh hai btw :)
08:12 CIA-40 bioclipse: goglepox * r10797 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/META-INF/spring/content.xml: Removed newline character fixing molTable manager startup
08:12 egonw Gpox++
08:12 egonw forgot to ask about that...
08:12 egonw but that was giving trouble here too :)
08:12 shk3 try calculating tanimoto of a number of molecules, e. g. all in sample/2d
08:13 maclean ah, just getting that error message, too "could not get molTable manager"..I will update.
08:13 jonalv shk3: is there a script suffering from this problem or do I do somethign from the ui?
08:14 shk3 ui
08:14 shk3 I think it's only ui
08:14 shk3 select all files in sample/2d, right click, choose tanimotot
08:14 jonalv shk3: oki yea that actually makes sense (when I actually think about it)
08:14 shk3 this creates an sdf, which opens
08:14 shk3 but is empty
08:14 shk3 if you close it
08:15 shk3 and open again,
08:15 shk3 it's fine
08:16 jonalv shk3: yea I get a file not found exception. Is that it?
08:18 shk3 hm
08:18 shk3 is there a file in virtual?
08:18 shk3 an sdf?
08:18 jonalv shk3: yea there is now but not at the time it tried to open it...
08:19 shk3 right
08:19 shk3 when I try it, the file is there but still empty
08:19 shk3 but this is the same problem, I think
08:19 jonalv shk3: how do you know that it is empty?
08:20 jonalv shk3: seems we can't trust the molecules editor right now...
08:20 shk3 the sdf editor opens, but show no entries
08:20 shk3 I don't think its the editor
08:21 shk3 i think it file creation running in background
08:22 jonalv shk3: the editor does not open any sdf files at all for the moment...
08:22 shk3 oops
08:23 shk3 had that yesterday evening, but gpox seems to have fixed it
08:24 shk3 right, sdf editor still broken
08:25 shk3 but you see the problem of that bug?
08:25 jonalv shk3: yes I see your point and it's a valid one
08:25 jonalv I guess something with sheduling rules might help
08:26 jonalv shk3: does the open command run as a job?
08:26 shk3 don't know
08:28 masak joined #bioclipse
08:39 shk3 jonalv: could you have a look at 1099 and why the create isn't working?
08:40 jonalv shk3: trying to get some order on the moleculestable opening...
08:40 jonalv @pz 1099
08:40 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1099
08:40 shk3 sure
08:48 CIA-40 bioclipse: jonalv * r10798 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/IMoleculeTableManager.java: methods that are to be run as jobs may only return void or BioclipseJobs in their interface declaration
08:49 jonalv okey sdf editorn works again. back 1111
09:01 de__maas joined #bioclipse
09:02 egonw hi de__maas
09:02 egonw olass: de__maas asked about the lack of an update site with our cool PubChem stuff for beta5
09:03 olass egonw: ack
09:03 egonw olass: next time, we should do update sites again... so that people can actually test what they did in earlier versions...
09:03 olass egonw: ack
09:03 jonalv shk3: ping
09:03 CIA-40 bioclipse: jonalv * r10799 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java: Made sure methods that are tun as jobs uses any ISHedulingRules in their arguments as scheduling rules for their job. My hopes where that this would fix bug: 1111 but not. It should be a step on the way though.
09:03 de__maas Hi all
09:04 zarah bug #1111 | http://tinyurl.com/obe5ak
09:04 zarah saluton de__maas
09:04 shk3 jonalv: pong
09:04 CIA-40 bioclipse: egonw * r10800 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/src/net/bioclipse/core/test​s/coverage/AbstractCoverageTest.java:
09:04 CIA-40 bioclipse: Fixed coverage testing: getManagerInterface() was returning the proper
09:04 CIA-40 bioclipse: interfaces directly, and getInterfaces() now returned IBioclipseManager which
09:04 CIA-40 bioclipse: does not have anything testable, causing no errors to be found (fixes #1078)
09:04 jonalv shk3: The job should now use the IFile as a sheduling rule. Seems like the code that comes after does not however....
09:05 zarah bug #1078 | http://tinyurl.com/qp5my5
09:05 de__maas I can't find the qsar feature in the beta 5, is this correct?
09:06 shk3 seems like you are making progress
09:06 olass de__maas: correct
09:06 jonalv shk3: maybe you could pop up the dialog in a BioclipseUIJob for that method call? That would ensure that that code is run after the file is created. Or we could create the file in the main thread and not in a job. Or we  could figure out how to get the code that reads the file to actually wait. I am not sure how to do that though...
09:06 olass it is only experimental
09:06 jonalv anyone know?
09:07 de__maas olass: in that case you can't install the tutorials
09:07 olass de__maas: unfortunately I have not updated the qsar feature yet
09:07 olass de__maas: good point
09:07 * olass really would like to fix the beta5 update to be 100% correct
09:08 olass de__maas: We are aiming for Bioclipse 2.0 RC1 on monday/tuesday next week
09:08 olass very much work for this
09:08 de__maas olass: that's really cool
09:08 olass yes, thanks
09:08 olass it is a bold statement
09:09 olass but hopefully we'll make it
09:09 de__maas olass: btw, is there a space were one can leave their wishlist?
09:09 shk3 jonalv: using a bioclipseuijob sounds good
09:09 olass very welcome in any fora
09:09 olass best: bugs.bioclipse.net
09:09 jonalv shk3: you could run the code using a ISchedulingrule as well
09:09 shk3 but I would need to find out how to do that
09:09 jonalv shk3: that is using the IFIle as sheduling rule
09:09 olass bioclipse-devel mailing list is another good option
09:09 shk3 not sure about what ISchedulingrule is
09:10 olass suggestions here are alsow welcome
09:10 jonalv shk3: normally reading shouldn't need this but in this case we are waiting for the file to acutally be created so I guess that's a bit special...
09:10 de__maas olass: OK, but I guess there's enough to do right now
09:10 shk3 ok, sounds reasonable
09:10 olass de__maas: no, we really appreciate input
09:10 olass as early as possible please ;
09:11 olass we tend to get a bit home-blind ;)
09:11 * olass liked that translation
09:11 de__maas olass: well i like the sdfile editor very much. It would be very cool if you could order and/or filter on a column so one good get an initial feeling on the data in there.
09:12 olass indeed, that is a non-trivial problem
09:12 olass since we support large files
09:12 olass it would require reading all before doing a sort
09:12 olass we used to have sorting
09:12 olass but no solution for this yet unfortunately
09:12 olass there is a bug for it
09:13 olass but will not make 2.0
09:13 de__maas olass: well I prefer having the large file support. it's doing better then any I seen so far!
09:13 olass thanks!
09:13 olass Gpox++ has been doing a great job
09:13 olass but we want sorting too, we just haven't solved how it should be implemented
09:14 de__maas olass: filtering can be done via script so may be I should not be that lazy
09:14 olass lol
09:14 olass filtering should be easier
09:14 olass you mean filter by property values for example?
09:14 olass will file that as a bug for post 2.0
09:15 olass I have an ongoing project for filtering called molfiler (in lack of better name)
09:15 de__maas olass: yes, for instance if you have cluster numbers in a sdfile you can review a cluster.
09:15 olass but no time to work on that for now :(
09:15 olass de__maas: sounds logical
09:16 jonalv shk3: I think a BioclipseUIJob is the best way to go
09:17 shk3 ok
09:17 shk3 will try that later
09:17 shk3 thanks
09:18 shk3 could you have a look at 1099, why the create doesn't work?
09:18 shk3 its probably easy for you
09:20 jonalv shk3: oki
09:20 shk3 thanks
09:20 CIA-40 bioclipse: ospjuth * r10801 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (16 files in 4 dirs): New icons and actions for DSView. Also betetr error reporting but still not good.
09:22 jonalv shk3: where do I find this new seneca job file wizard?
09:22 jonalv shk3: do I need more features than chmoeinfoamrtics ans sencea?
09:23 shk3 sorry
09:24 shk3 we found that running seneca via features doesn't work
09:24 shk3 but since i can't run features at all, I can't really debug it
09:24 shk3 I will think about this
09:24 shk3 and come back to you
09:24 shk3 mom
09:24 shk3 spectrum is also needed.
09:25 shk3 speclipse_feature
09:25 shk3 can you try with that?
09:26 * maclean tried running seneca as a feature, as I can run features, and it indeed did not work
09:26 shk3 right, so we need to fix this
09:27 egonw joined #bioclipse
09:28 egonw olass: http://www2.computer.org/portal/web​/csdl/doi/10.1109/eScience.2008.26
09:28 zarah egonw's link is also http://tinyurl.com/ogvl2m
09:28 egonw eclipse based drug screening grid computing stuff
09:28 egonw recently registerd on SF, but no source code yet
09:28 egonw though seemingly available from another source
09:29 olass interesting
09:29 olass do you have the pdf?
09:29 egonw nope
09:29 olass maybe we can contact them?
09:29 egonw Ola Enquist pointed me to this
09:29 egonw yes, was thinking about that too
09:30 olass oh, it's vincent breton
09:30 olass cool
09:30 egonw who is he?
09:30 olass he is involved in embrace
09:31 egonw http://anakin.kisti.re.kr/trac/Dr​ugScreenerG/browser/trunk?rev=475
09:31 zarah egonw's link is also http://tinyurl.com/r2cnyj
09:31 egonw there's the source
09:31 olass met him a few times
09:31 olass would be cool to run their plugins in bioclipse
09:32 olass I can send vincent an email
09:32 olass since I already met him
09:32 edrin i have access to the pdf
09:33 olass edrin: coudl you email it?
09:33 edrin sure
09:33 olass ;)
09:33 edrin egonw: you too?
09:33 olass egonw: I'll write something up straight away
09:33 egonw no
09:33 egonw please forward
09:33 olass I'll CC of course
09:34 olass oh, you were talking to edrin
09:34 egonw yes :)
09:34 egonw edrin: please send a copy of the PDF
09:34 edrin sent two two
09:34 edrin to two
09:36 egonw btw, the SF project: http://sourceforge.net/projects/drugscreener-g/
09:36 zarah egonw's link is also http://tinyurl.com/o375ve
09:37 maclean does anyone know if it matters if you get the same plugin twice, through dependencies on two sub-features?
09:37 egonw not if the version is the same
09:37 maclean Hmmm.
09:38 egonw with the right set of deps
09:38 egonw without proper versioning
09:38 egonw and two plugin versions of the same plugin
09:38 egonw then you can get trouble
09:38 maclean right, I only understood 'trouble' at the end of all that...
09:38 egonw :)
09:39 maclean as that's what the seneca feature seems to have :(
09:39 jonalv shk3, maclean: That is intresting because I am running from features now and I ahve the create new structure elucidatin job wizard there. What exaclty is it that does not work when running from features?
09:40 maclean oh!
09:40 shk3 nice to hear
09:40 maclean jonalv : it's not loading the seneca plugin
09:41 * jonalv @lunch
09:42 egonw olass: that PDF actually evens mentions "Bioclipse Plugins" :)
09:42 egonw though does not cite the Bioclipse paper
09:42 maclean great, so it works only on jonalv's machine...
09:43 olass egonw: that's too bad
09:43 egonw indeed... it's a 2008 publication
09:43 egonw well, just a proceedings...
09:43 olass hmm
09:43 olass maybe not so active then
09:44 olass I'll write and ask the state of it and if they have any future plans
09:49 maclean I seem to remember that using the 'compute' button in the feature.xml editor was not recommended, not?
09:55 egonw well, eclipse has never been excellent with figuring out dependencies...
09:55 maclean egonw, olass : what is the difference between included features and dependent features? And can you have both?
09:55 egonw yes you can
09:55 maclean It now seems to work for me if you have the same features included/depended like this
09:55 egonw an included is better if the feature it depends on would be on a different update site
09:55 egonw by 'including' it, you will have it on the same update site
09:56 egonw so
09:56 maclean hmmm.
09:56 olass included = will be packaged together with it
09:56 egonw I have the .wst as 'included' feature for the XML feature
09:56 olass dependent = required but not packed
09:56 egonw and .zest for the 'ChemRDF feature'
09:56 egonw so that people do not have to install those features from the eclipse update site separately
09:56 maclean so I shouldn't include the cheminformatics feature in the seneca feature
09:56 egonw no, that would not be needed
09:57 maclean well, you say that...
09:57 egonw :)
09:57 egonw it should not matter anyway, for running from inside eclipse
09:57 maclean I'm just trying with only the speclispe feature included
09:57 maclean apparently it does.
09:58 maclean well, there's a correlation, in that it didn't work before I made it include, and it now works after I did.
09:59 maclean Right. So it works for me now with only the speclipse feature included.
10:03 egonw and when does it not work?
10:04 maclean well, it did not work before I included the features it depended on.
10:04 egonw ah, sure
10:04 maclean It might work now, even without those, due to some weird eclipse voodoo magic.
10:05 maclean But if it works for jonathan without the inclusions, then it's probably fine.
10:27 rojasm joined #bioclipse
10:30 CIA-40 bioclipse: miguelrojasch * r10802 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/src/net/bioclipse/rea​ction/editor/ReactionEditor.java: Parsing from CML the cdk:reactionProperty dictRef using the reactPlug:x/y property. It defines the position of the boxes in the network reaction.
10:38 sneumann hi olass
10:38 sneumann shk3 asked me a while ago if I could provide a Mass Spectrometry Data plugin
10:38 sneumann which reads mzML (or others reading mzData, for that matter)
10:39 sneumann I once did a plugin (back in eclipse-3.1 days) using EMF generated editors.
10:39 sneumann I can do that again, targeting BC2 environment.
10:40 sneumann Basically, what I did back then was New -> Plugin-Project and New -> EMF Model (from XSD) -> Generate -> Voila.
10:40 sneumann ( I also tweaked some settings and experimented with Teneo as Backend for the EMF/mzData stuff,
10:41 sneumann but that's probably not needed today.)
10:41 sneumann So question is:
10:41 sneumann How would you recommend starting a BC2 compliant Plugin that provides an EMF.Editor for certain mzML files ?
10:42 sneumann Start from scratch, start from the plugin template in BC2 SVN
10:42 sneumann or start from another Plugin ?
10:44 shk3 hm, no manager stuff needed, I think
10:44 shk3 so starting from scratch might be easiest
10:44 sneumann Glad to hear
10:45 sneumann would you be able to javascript
10:45 sneumann mzml.open("somefile.mzml") ?
10:47 jonalv sneumann: not without a manager
10:47 sneumann olass would probably have an idea how to get a manager
10:48 sneumann into a generated EMF Editor plugin.
10:49 * olass is back from lunch
10:49 * olass is backlogging
10:50 olass sneumann: the QSAR plugin is done in a similar way
10:50 olass I generate the model in a separate plugin
10:51 olass and then add a new plugin that has a manager
10:51 olass and that manager makes use of the generated model
10:51 olass so
10:51 olass a plugin with a Bioclipse2 manager is needed
10:51 sneumann OK
10:52 olass sneumann: manager is only needed if you want to access things from the JSConsole
10:52 sneumann So I do the standard bc2.mzML, bc2.mzML.edit and mzML.Editor plugins
10:52 olass yes
10:52 olass and add a second plugin that just provides functionality for scripting
10:52 sneumann and peek at e.g. QSAR whether it is an eclipse or equinox or whatever Plugin
10:52 olass QSAR is a good thing to look at
10:53 olass since it has the same architecture
10:53 sneumann and ask someone ;-) to add a manager thingy
10:53 sneumann who might be the one who asked for the plugins in first place ;-)
10:53 olass jonalv++ is good to ask about these things
10:53 sneumann and then we wrap all those plugins in a feature
10:53 olass sneumann: exactly
10:53 * olass is looking forward to seing it in action
10:53 sneumann I thought about shk3, but whoever has least hassle with it
10:54 olass shk3 can help too
10:54 jonalv shk3: regarding 1099. I can not confirm your trouble. I get a whole other trouble. Gonna reassign to you with description of my troubles...
10:54 egonw otherwise, I'll add the manager thingy
10:54 egonw that's a piece of cake for me now
10:54 olass egonw++
10:54 olass we are all slowly getting up to speed with the latest manager architcture
10:55 egonw jonalv: is that speclipse feature stuff?
10:55 egonw jonalv: if so, please cc me on that
10:55 jonalv egonw: yes, oki
10:55 * olass is exploring jobs in newest manager order
10:55 egonw as I did earlier work on some speclipse feature stuff too
10:55 egonw in relation to the medea feature
10:55 * egonw is writing a LaTeX template for his Bioclipse-RDF paper
10:56 egonw for which I want to have a draft next week
10:57 olass sounds good
11:03 CIA-40 bioclipse: ospjuth * r10803 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java: Added job.setUser( true ); since manager calls are user-initiated jobs and this should always be explicitly stated.
11:06 CIA-40 bioclipse: shk3 * r10804 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (domain/SenecaJobSpecification.java editor/JudgePage.java): fixes a bug with judges getting lost when running
11:07 CIA-40 bioclipse: ospjuth * r10805 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java: Changed to job.setUser( false ); since this gives desired behaviour (no dialogs by default).
11:18 jonalv olass: regarding
11:18 jonalv @pz 1115
11:18 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1115
11:18 olass yes
11:18 jonalv olass: which method call are we talking about?
11:18 olass I found a name param for the job when returning a BioclipseJob
11:19 olass so setting that
11:20 jonalv olass: you can use the one taking a BioclipseJobUpdateHook. It takes a job name in the constructor
11:20 olass yes, that is the one I am using
11:20 olass now
11:20 olass but have problems
11:20 jonalv olass: okey good
11:20 CIA-40 bioclipse: goglepox * r10806 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Added adapting to MoleculesEditor
11:20 olass looking into that now
11:20 jonalv olass: okey not good
11:20 jonalv olass: okey good
11:20 olass just started
11:20 jonalv olass: so I close the bug then?
11:21 CIA-40 bioclipse: goglepox * r10807 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java: Lets getPropertyFor handle properties that stored on the atomcontainer
11:21 olass does it work?
11:21 jonalv olass: you tell me...
11:21 olass if you have not verified that it works, don't close it
11:21 CIA-40 bioclipse: goglepox * r10808 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Hack to let the content provider use getPropertyFor(...) on SDFIndexEditorModel
11:21 olass asign to me for verification if you like
11:22 CIA-40 bioclipse: goglepox * r10809 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (3 files in 3 dirs):
11:22 CIA-40 bioclipse: Added command and menu item to generate property for number of atoms in molecule.
11:22 CIA-40 bioclipse: Fixes bug #813
11:22 CIA-40 bioclipse: The new property column dose not show up automatically, the user has to go in to the headers tab and add it to the visible coulumns
11:22 zarah bug #813 | http://tinyurl.com/r4u3b9
11:22 olass Gpox++ //I see progress for moltable props
11:22 olass Gpox: Is it possible for me to test?
11:23 Gpox the 'NumberOfAtomsCalculator' is working the menu option is hardcoded though
11:23 * olass will try soon
11:24 CIA-40 bioclipse: shk3 * r10810 /bioclipse2/trunk/plugins/net.biocl​ipse.seneca/src/net/bioclipse/senec​a/wizard/NewSenecaJobWizard.java: new seneca job creation now works
11:24 jonalv shk3: w00t
11:25 shk3 see the bug on pele
11:25 jonalv shk3: ah
11:25 jonalv shk3: will look into that later
11:26 shk3 thanks
11:47 CIA-40 bioclipse: jonalv * r10811 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/jobs/BioclipseJob.java: Better description of problem in Exception. Fixes bug: #1131
11:47 zarah bug #1131 | http://tinyurl.com/qyxuvs
12:19 CIA-40 bioclipse: jonalv * r10812 /bioclipse2/trunk/plugins/net.bioclipse.​core/src/net/bioclipse/managers/business​/AbstractManagerMethodDispatcher.java: added a lot of debug output and a warning. Made sure that BioclipseUIJobs are run even though the the original method could not be run as jobs because it returned something. This fixes bug: #1129
12:19 zarah bug #1129 | http://tinyurl.com/q4h37r
12:34 maclean In java, you are allowed to have nested types with interfaces, like List<List<Object>>?
12:35 stain yes
12:35 maclean but do you have to declare like List<List<Object>> llo = new ArrayList<List<Object>>();?
12:35 stain correct again :)
12:35 maclean ahh. right.
12:36 maclean you learn something every day :)
12:36 stain it can become a bit tedious with those nested things..
12:36 stain particularly when you have these <? extends Crap>
12:36 stain when it takes mroe than 50% of the line length I tend to just go for a @Override instead
12:37 edrin did you know that you can create and use new ArrayList() java objects from javascript via rhino, too?
12:37 maclean totally. there's a graph library that requires all that : Graph<? extends Node, ? extends Edge>...
12:38 maclean edrin : no, but sounds useful.
12:38 stain it can become silly.. but it's so that you can't just pretend a List<String> is a List<Object> - because then you could do list.add(new Object()) and confuse those who do String s = stringList.get(0)
12:38 maclean oh, I see the benefits for for loops.
12:39 maclean writing for (IAtom atom : molecule.atoms()) is great.
12:40 maclean but nothing in java will beat nested generator expressions like [x ** 2 for x in [2 * y for y in range(10)]]
12:45 CIA-40 bioclipse: ospjuth * r10813 /bioclipse2/trunk/plugins/net.bioclips​e.ds.smarts/src/net/bioclipse/ds/smart​s/model/impl/SmartsMatchingTest.java: Rewrote debugging of smarts matching to be more compact.
12:46 edrin egonw: question: how do you discuss chemical 2d structure stuff with someone else on a remote site? is there some shared chempaint thing via networks?
12:47 CIA-40 bioclipse: ospjuth * r10814 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (5 files in 4 dirs): Better presentation of Errors in TestsView. Now tests and hits show up next to each other.
12:47 egonw not that I am aware of
12:47 egonw but
12:47 egonw but an interesting idea
12:47 egonw workaround, is to just share a file
12:48 edrin yep
12:48 maclean or phone them up, and describe it? :)
12:48 edrin but you can paint in real time then ;)
12:48 egonw nah
12:48 edrin with the other one
12:48 egonw that's too easy
12:48 egonw webcam?
12:49 edrin remote desktop ?
12:49 edrin webcam on your paper
12:49 edrin /screen
12:49 egonw yes, share desktop is a good option
12:50 olass egonw: I'm sure you can twitter the smiles from a blog that you wire over connotea via RDF/OWL
12:51 olass :)
12:51 egonw nah
12:51 egonw too easy
12:51 olass hmm
12:51 * olass will think up of a harder solution
12:51 CIA-40 bioclipse: goglepox * r10815 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Added error message when trying to open jcp with no input.
12:52 olass you could draw it on a napkin, scan it, use some image analysis software, submit it to pubchem, and send the link
12:52 egonw OSRA!
12:52 olass ?
12:53 egonw "some image analysis software" -> OSRA
12:53 olass never heard of it
12:59 maclean you could make the molecule into a canonical signature. that's turning out to be quite difficult :/
12:59 * maclean goes back to doing that thing he just said
13:03 edrin so a smiles is a textual representation of the graphical thing on your screen?
13:04 edrin in the editor of bioclipse for example?
13:06 maclean well, really a smiles is a representation of a molecule, and the diagram is another representation
13:06 maclean there should be a one-to-one correspondence between the smiles, and the diagram...
13:07 edrin ok
13:07 maclean but I'm being a bit pedantic, really.
13:07 edrin but is there a way to serialize the thing in your diagram into textual representation  and reserialize , i.e. from diagram to xml to diagram ?
13:08 maclean C1CCCCC1 and a hexagon are the 'same' as cyclohexane.
13:08 maclean diagram -> smiles, yes. smiles -> diagram, perhaps.
13:08 edrin diagram in the editor to xml ?
13:08 CIA-40 bioclipse: ospjuth * r10816 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): Require all errors to have name and detailed message and implemented this for all tests.
13:09 maclean cml, yes.
13:09 edrin i.e. for sharing and editing a diagram in realtime
13:09 maclean well, strictly, the diagram would have to be exported to SVG (an xml)
13:09 * egonw sees edrin using XMPP for sharing CML for a shared editing tool using JChemPaint inside Bioclipse
13:10 maclean which is possible in the rendering architecture...see the new tutorial page on visitors for hints! :)
13:10 edrin yes, thats what i thought
13:10 edrin just wondering if this is easy to implement
13:10 maclean probably best done with a full-blown SVG library, like batik.
13:11 edrin (and if this would have users.)
13:11 maclean easy? perhaps.
13:11 edrin passing around at realtime is easy with xmpp
13:11 maclean it's just another output toolkit, like AWT/SWT.
13:11 edrin it's not like counterstrike but for our stuff good enough
13:12 maclean but how would synchronisation work? would there not be a danger of half-diagrams?
13:13 maclean Like, if I highlight an atom, that should change the SVG document (for the highlight element), but then I move my mouse, and the element is unhighlighted.
13:13 maclean in the meantime, the full representation has to be sent over the channel...
13:14 maclean Bit like how X works, I suppose.
13:14 edrin yes, maybe
13:26 CIA-40 bioclipse: jonalv * r10817 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/src/net/bioclipse/managers/tests/ (3 files): added test for situation causing bug: 1133
13:26 zarah bug #1133 | http://tinyurl.com/qubtrp
13:27 CIA-40 bioclipse: jonalv * r10818 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/jobs/BioclipseJob.java:
13:27 CIA-40 bioclipse: Set the return value on a BioclipsJob when calling completeReturn using a
13:27 CIA-40 bioclipse: BioclispeHook. When doing a partialReturn we do not want to set it because the
13:27 CIA-40 bioclipse: sum of all partial returns might be more than what can be kept in memory at the
13:27 CIA-40 bioclipse: same time. Fixes bug: 1133
13:27 zarah bug #1133 | http://tinyurl.com/qubtrp
13:32 jonalv shk3: around_
13:32 jonalv ?
13:32 maclean no, he's gone out to get some fresh air.
13:33 maclean there is construction going on outside, so the windows have to be closed. it is quite hot.
13:33 jonalv maclean: I can totally sympatise. It's hot here as well but I can at least open the window...
13:35 jonalv Can anyone here explain to me how to run a Seneca job?
13:36 shk3 either open it in the editor
13:36 shk3 and press the green arrow in the toolbar
13:36 shk3 or use seneca manager on console
13:36 maclean it = '.sjs file'
13:36 jonalv shk3: do I have to set it up somehow?
13:37 shk3 yes, if you are not using the examples
13:37 jonalv shk3: I just want to reproduce you bug...
13:38 shk3 so install the seneca examples
13:38 shk3 open seneca/hko1
13:38 shk3 directory
13:38 jonalv where are the seneca examples? :)
13:38 shk3 double click the hko1.sjs
13:38 shk3 and press the green arrow in toolbar
13:39 shk3 File -> New -> Data
13:39 shk3 Seneca Sample Data Project
13:39 jonalv I nly have new sample data and speclipse sample data there.. :(
13:40 shk3 mom
13:40 shk3 sorry
13:40 shk3 check out net.bc.data.seneca and include it in the feature
13:41 shk3 I am committing this
13:41 jonalv okey I will wait for your commit then
13:42 shk3 you still need to check out the sample data
13:43 CIA-40 bioclipse: shk3 * r10819 /bioclipse2/trunk/features/net.bio​clipse.seneca_feature/feature.xml: feature includes sample data
13:43 jonalv shk3: I use git and check out everything. I think I should have it imported into eclispe as well...
13:43 shk3 ok
13:43 shk3 then it should work now
13:44 jonalv but it did not work so better check aagain... :0
13:45 jonalv hm this time I don't think seneca started at all
13:46 jonalv ah stupid me
13:46 maclean what?
13:46 jonalv okey now
13:47 jonalv I reverted changes to mny product and then it's not so strange that seneca diddn't sart... :)
13:47 jonalv shk3: okey so trying example1 then?
13:48 shk3 please try hko1
13:49 shk3 here: http://pastebin.com/m6943ee6d you find a script running it
13:49 jonalv hm it's runnign in gui thread..
13:49 shk3 it should run with a progressmonitor, I think
13:50 jonalv I think my new logger warning that I added today might point to the problem: WARN - seneca.executeJob is not void or returning a BioclipseJob. But implementation takes a progress monitor.  Can not run as Job. Running in same thread.
13:51 shk3 that's what I call a good message
13:51 maclean indeed. jonalv++
13:52 shk3 So I must return the result via a BioclipseJob?
13:52 egonw jonalv: sounds like an excellent unit test!
13:52 jonalv shk3: Do you know what to do now?
13:52 jonalv egonw: patches welcome :)
13:52 shk3 well, I know what to find out to know how to do it
13:52 egonw yes, yes
13:52 jonalv shk3: yes
13:53 shk3 did you try the js?
13:53 shk3 this shows a progress monitor
13:53 CIA-40 bioclipse: egonw * r10820 /bioclipse2/trunk/ (6 files in 4 dirs): Updated the source files using Pellet explicitly to state that it is license AGPL v3
13:53 jonalv shk3: can't both run as job and wait for result...
13:53 shk3 will this be solved as well?
13:53 shk3 right
13:53 shk3 no problem
13:53 jonalv shk3: nope not yet. How do I test that?
13:54 shk3 here: http://pastebin.com/m6943ee6d you find a script running it
13:54 shk3 the hko1 job
13:55 jonalv shk3: may I suggest that the seneca sample data should install to "Seneca Sample Data" folder as default?
13:56 shk3 sure you may
13:56 shk3 will do that
13:58 shk3 the inchimanager.generate seems to be an example of what I need to do.
13:58 shk3 is this correct?
13:59 jonalv shk3: I would think so yes
13:59 shk3 ok, I will try
13:59 jonalv shk3: there are a few alteratives...
13:59 jonalv You can return a job. Better mgiht be to use a BioclipseUIJob to update things afterwards...
14:00 jonalv it sort of depends on what you want to do with the result...
14:00 jonalv you want to pop up a dialog right? I would probably suggest doing that with a BioclipseUIjob
14:01 jonalv you write the code for displaying the dialog in the uiJob and it will be run when the calcualtion is done. And the ui thread is frr to do other things in the mean time...
14:01 shk3 no popup
14:01 shk3 in ui action, the result will be saved to an sdf, which will be opened
14:01 shk3 on console, just the list should be returned
14:02 shk3 that was my idea at least
14:02 shk3 but the saving in the ui action will be done afterwards, so I thought
14:02 jonalv ah hm but if the list is very big maybe it's bvetter to always return a ref to a file instead?
14:02 shk3 the execute method would only return the result
14:02 shk3 hm, could do that
14:02 shk3 right now, lists aren't too big
14:02 jonalv shk3: or will the list of molecules never be too big to fit in memory?
14:03 shk3 it's limited to 20 entries, actually
14:04 jonalv shk3: ah in that case I doubt there would be a problem
14:05 jonalv I would still go with a BioclipseUIJob for opening the editor...
14:07 shk3 is there an example I can use?
14:07 shk3 sorry, this is a bit confusing for me
14:07 shk3 with all theses jobs
14:08 jonalv shk3: olass is working on an example. shk3 yes it is complicated and very new so all the corner casea re not founbd yet I am afraid...
14:08 shk3 no problem
14:10 shk3 perhaps we wait a few days till examples exist?
14:11 Gpox joined #bioclipse
14:11 CIA-40 bioclipse: ospjuth * r10821 /bioclipse2/trunk/plugins/ (8 files in 6 dirs): Added monitor to runTest to support cancellation of jobs.
14:13 Gpoks joined #bioclipse
14:13 jonalv shk3: Yes I am looking for a good simple example to put on the wiki. For the moment I have none... :/
14:14 Gpoks left #bioclipse
14:14 maclean does it have to be a real example?
14:14 jonalv @pz 1135
14:14 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1135
14:14 maclean Or can it be close enough to realistic?...
14:14 shk3 you could use running a seneca job...
14:15 jonalv shk3: I guess so...
14:15 jonalv shk3: I was hoping to find something in a core manager like ui though...
14:16 shk3 sure
14:16 shk3 don't feel pressed
14:17 jonalv shk3: I would like to find something simple. I hardly underatns what it is Seneca does you know...
14:19 shk3 sure
14:19 shk3 really, don't feel pressed ;-)
14:26 shk3 egonw: trying to do git pull gives me "
14:26 shk3 You asked me to pull without telling me which branch you
14:26 shk3 want to merge with
14:26 shk3 ..."
14:27 shk3 does that tell you anything? what do I need to do?
14:27 shk3 sorry, lost with git again
14:27 egonw this means that git does not understand which branch you want to see updated...
14:27 egonw it can mean that there is no 'origin' for you current branch
14:28 egonw if you work in a branch instead of master, and you want to pull changes from another branch...
14:28 egonw then
14:28 egonw you also need to say which branch you want to pull from...
14:28 egonw it's the git equivalent
14:28 egonw "can you please go to that shop?"
14:28 egonw (now you figure out which shop I am talking about)
14:29 egonw what shop?
14:29 shk3 git pull origin cdk-1.2.x seems to work
14:29 egonw good
14:30 maclean "Come to the CDK shop! For all your hose code and atom typing needs."
14:31 egonw (and we too got the stuff that allows you to design your home made drugs too...)
14:31 egonw you have to address a wide audience after all
14:34 maclean :)
14:47 shk3 I am always getting some errors
14:47 shk3 can you give me the commands to check out the 1.2.x branch?
14:49 egonw https://apps.sourceforge.net/mediaw​iki/cdk/index.php?title=Development​_with_Git#How_do_I_checkout_CDK_1.2.1.3F
14:49 egonw like that
14:49 egonw replace 1.2.1 with 1.2.x
14:49 egonw and give your local branch a name you like
14:51 shk3 if I do this and do git pull afterwards,
14:53 shk3 mom
14:53 shk3 using exaclty this command with 1.2.x gives me
14:53 shk3 fatal: git checkout: updating paths is incompatible with switching branches/forcing
14:53 shk3 Did you intend to checkout 'cdk-1.2.x' which can not be resolved as commit?
14:53 egonw shk3: do 'git branch -r'
14:54 egonw you might have to make that
14:54 egonw origin/cdk-1.2.x
14:54 egonw or remote/cdk-1.2.x
14:54 egonw branch -r
14:54 egonw gives the remote branches
14:54 shk3 ok
14:54 shk3 but
14:54 shk3 git pulll afterwards
14:54 shk3 gives the mentioned error
14:54 shk3 using
14:54 shk3 git pull origin cdk-1.2.x
14:54 shk3 gives merge conflicts
14:55 shk3 it seems of cdk-1.2.x and master
14:55 shk3 but I don't want to merge
14:56 egonw try: git fetch
14:57 shk3 doing git pull then gives
14:57 shk3 You are in the middle of a conflicted merge.
14:57 shk3 i will restart with the checkout mom
14:57 egonw there should be an abort option
14:57 egonw shk3: please read: http://www.kernel.org/pub/softw​are/scm/git/docs/git-pull.html
14:59 CIA-40 bioclipse: jonalv * r10822 /bioclipse2/trunk/plugins/net.bioclips​e.jsexecution/src/net/bioclipse/jsexec​ution/execution/ScriptExecution.java: Fix for ugly reflection code. getNameSpace has changed name into getManagerName
14:59 shk3 I don't understand it
14:59 shk3 sorry
15:00 shk3 I have done pull
15:00 shk3 doing git checkout -b cdk-1.2.x-copy cdk-1.2.x
15:00 shk3 gives me this "updating paths is incompatible" no matter what I do
15:03 shk3 ah, looks like it worked
15:17 maclean oh! save failed in jcp "Invocation target exception".. :(
16:11 de__maas left #bioclipse
16:28 jonalv (threading problems)--
16:28 maclean warning : cannot increment 'threading problems' on the gui!
16:28 maclean er...but seriously, they do suck, yes.
16:40 * jonalv gives up now, cya
16:40 maclean cya
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19:34 sneumann_ joined #bioclipse

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