Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-30

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All times shown according to UTC.

Time Nick Message
05:34 rojasm joined #bioclipse
06:04 Gpox joined #bioclipse
06:57 olas joined #bioclipse
06:57 olas hi all
06:57 zarah hi olas
07:27 jonalv joined #bioclipse
07:27 jonalv moin
07:27 zarah hi jonalv
07:27 olas moin jonalv
07:45 CIA-49 bioclipse: goglepox * r6337 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java:
07:45 CIA-49 bioclipse: Editor will only switch to JCPEditor if the selected molecule contains 2D-coordinates
07:45 CIA-49 bioclipse: and outputs a log message if it doesn't. Bug 2020723
07:47 olas goglepox: could it show an inputbox saying Molecule does not have 2D coordinates"?
07:49 CIA-49 bioclipse: jonalv * r6338 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/domain/tests/TestCDKMolecule.java: Updated tests to call fromCml instead of from String
08:04 thomas_ku joined #bioclipse
08:08 CIA-49 bioclipse: jonalv * r6339 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: [CDKManager] organized imports
08:17 shk3 joined #bioclipse
08:17 edrin joined #bioclipse
08:17 edrin hi
08:17 zarah hi edrin
08:21 olas hi edrin
08:22 egonw joined #bioclipse
08:22 jonalv hi edrin
08:23 shk3 hi olas
08:25 olas egonw: how do I scan an XML string for x2 or x3?
08:25 olas do you have any code snippet I can look at?
08:25 olas I assume I want to use SAX... right?
08:28 shk3 olas: worked on the generate2d yesterday
08:28 shk3 question: how to do parsing?
08:28 shk3 I just get the selection
08:28 shk3 do I need to parse that and take care of all the formats?
08:28 edrin ola, egon: http://news.yahoo.com/s/nf/20080729/bs_nf/61031
08:28 zarah edrin's link is also http://tinyurl.com/5rkv34
08:29 edrin seen this?
08:29 olas no
08:29 olas shk3: please explain more
08:29 olas a FIle?
08:29 olas i CDKMOlecule?
08:29 olas what is the selection?
08:30 olas and where?
08:30 olas (and how)
08:30 olas edrin: not bad
08:30 olas edrin: you have any connections in Karlsruhe?
08:30 shk3 well, I thought I do this via a handler and a manager
08:31 edrin olas: no, why?
08:31 shk3 the manager gets a file
08:31 egonw olas: no, no SAX
08:31 shk3 (or the handler has it, the same situation)
08:31 egonw that would require parsing the whole document
08:31 edrin olas: in science?
08:31 egonw but quick and dirty is just a text parser
08:31 egonw BufferedReader or so
08:31 shk3 I need a cdk molecule for coordinate generation
08:31 egonw and scan for x2=\".*\"
08:32 shk3 in bc1, the parsedresource could be used
08:32 shk3 but the system changed
08:32 shk3 so I am not sure what to do now
08:32 * olas has many conv at the same time now
08:32 olas egonw: what is fastest?
08:32 edrin olas: yep
08:32 olas edrin: no reason, just asking
08:33 egonw edrin: anything particular in that link I should pay attention too?
08:33 shk3 sorry
08:33 olas shk3: if the selection is a File, you need to parse it yourself
08:33 egonw olas: fastest is BufferedReader
08:33 egonw and good enough for now
08:34 olas faster than any XML parsing?
08:34 egonw considering it was already determined to be a CML file
08:34 egonw yes
08:34 shk3 hm, but then quite a few components do parsing
08:34 olas ok
08:34 edrin egonw: not really, just some research institutes are involved; cloud computing is very similar to what taverna does, and obvioulsy other xmpp companies are now working in this direction
08:34 shk3 e. g. the jcp editor parsed molecules as well
08:34 olas shk3: use the manager calls
08:34 shk3 ah, which manager?
08:34 olas CDKManager :-)
08:34 olas that's what it's for
08:35 edrin egonw: http://www.process-one.net/en/blogs/ar​ticle/at_the_heart_of_cloud_computing/
08:35 zarah edrin's link is also http://tinyurl.com/675mj9
08:35 olas in cdk.business
08:35 olas that has convenience calls for parsing
08:35 edrin olas: are you going to Karlsruhe?
08:35 shk3 ah, that's what I was looking for
08:35 shk3 thanks
08:35 olas shk3: all functionality should be wired via managers
08:35 olas great
08:36 olas egonw: how many chars do I need to scan?
08:36 olas 50?
08:36 olas 100?
08:36 olas until first x2/x3?
08:39 olas egonw?
08:39 egonw olas: no idea
08:39 egonw make it 2kB
08:40 egonw then your save
08:40 egonw that should still be fast enough for the purposes
08:40 egonw otherwise something wrong with Java
08:40 egonw oh wait, isn't that what everyone is saying? Java is slow? ;)
08:43 shk3 olas: shall I put the coordinates generation into the CDKManager?
08:43 shk3 or make a new one?
08:45 egonw 2D coord generation should be a method in the CDKManager
08:45 egonw so that it can be used from the console too
08:45 CIA-49 bioclipse: jonalv * r6340 /bioclipse2/trunk/plugins/net.bioclipse.data.​sampledata/src/net/bioclipse/data/sampledata/ (CopyTools.java wizards/NewSampleDataProjectWizard.java): Ensured files are closed when installing sampledata. Sampledata can now be installed in Linux. fixes: 2012433
08:48 olas jonalv++
08:48 olas great
08:48 olas shk3: egonw is right
08:48 olas shk3: please also test from console
08:49 olas this is a good opportunity to learn that too
08:49 olas ask here if you need assistance
08:49 shk3 yes, thought so, just wanted to make sure
08:49 shk3 btw, I found there is an IMolecule in bioclipse
08:49 shk3 what is that for?
08:49 * olas is working hard on the contentdescriber thingy
08:50 olas shk3: the super interface for a mloecule
08:50 shk3 e. g. calculateMass in cdkmanager takes such an IMolecule
08:50 olas we can have multiple instances
08:50 olas CDKMolecule implements IMolecule
08:50 shk3 ok
08:50 olas we say that all molecule implementations must be able to return SMILES and CML
08:50 olas other than that, implementors are free
08:50 shk3 ok, but for coordinate generation i need a cdk molecule
08:51 shk3 how should a handle this?
08:51 shk3 what should the manager method take?
08:51 olas there is a create(Imolecule mol) in CDKManager
08:51 olas check if instanceof CDKMolecule
08:51 olas if so, use it
08:51 olas else chekc if instanceof IMOlecule
08:52 shk3 ah, that goes via cml
08:52 olas if so, use CDKManager.create(Imolecule)
08:52 olas yes
08:52 egonw shk3: only if !instanceof CDKMolecule
08:52 shk3 hm, lots of parsin/conversions
08:52 olas heavier operation
08:52 olas you think so?
08:52 jonalv I think it's ok if the cdk managers methods only works with cdk molecules...
08:52 egonw olas: you talking to me?
08:52 olas egonw: nom shk3
08:52 olas nom=no
08:53 olas jonalv: I think they should be general
08:53 shk3 i can do it like in calculatemass, no problem
08:53 olas but that is my opinion
08:53 jonalv olas: I guess that's even better
08:53 shk3 just the cml writing of the other class as well as cml reading of cdk must fit together then
08:54 shk3 which is tricky sometimes (think about stereo chemistry etc.)
08:58 olas shk3: that's why we're happy to have you with us :-)
08:58 CIA-49 bioclipse: goglepox * r6341 /bioclipse2/trunk/plugins/net.bioclipse.core/ (icons/virtual.gif plugin.xml):
08:58 CIA-49 bioclipse: Decorates Virtual resources with a 'V'
08:58 CIA-49 bioclipse: bug 2026608
08:58 egonw shk3: that applies to any library conversion
08:59 egonw shk3: btw, that Indian student started who will look at stereoisomer enumeration
08:59 egonw that will boost stereochemistry in the CDK, I hope
08:59 egonw got to leave now
08:59 egonw bbl
08:59 egonw bye
09:01 olas bye egonw
09:10 CIA-49 bioclipse: jonalv * r6342 /bioclipse2/trunk/plugins/net.bioclipse.data.samp​ledata/src/net/bioclipse/data/sampledata/wizards/ (3 files): renamed getChecked to isChecked
09:10 olas shk3: I successfully created a describer
09:11 olas it distinguishes CML files with 2D and 3D coordinates
09:11 olas via a parameter in plugin.xml
09:11 olas will write a wiki page about this
09:12 olas the question is: where are cml content types located?
09:12 olas we have a CML plugin, but cdk does not depend on that
09:12 olas and I don't think this should be duplicated
09:13 olas and core does not seem to be the place either as it has no notion of cml at all
09:13 olas jonalv: comments on this?
09:13 olas I can put it in CDK for now
09:13 olas as cml plugin is not part of alpha
09:13 * olas will do that
09:17 jonalv olas: Honestly I am a bit confused to as why the CML plugin isn't a part of the cdk plugin. doesn't it use cdk for everything?
09:20 olas CML is much wider than molecules and cdk
09:20 olas it is used for e.g. spectra
09:20 olas and cdk cannot read that
09:21 jonalv okey then I understand
09:21 * jonalv doesn't know enough chemoinformatics :)
09:21 olas you are well on the way
09:22 olas it was like that for me a few years ago
09:22 olas well, not a few
09:22 olas 1 or 2
09:23 jonalv okey :)
09:24 shk3 olas: great you managed it
09:25 shk3 not sure what I did wrong
09:25 shk3 so we need describers to distinguish the following cml sub-types:
09:25 shk3 - singel molecule (jcp editor)
09:25 shk3 - multimolecule (sdf editor)
09:25 olas shk3: I thought I'd do one and you do the rest :-)
09:25 olas shk3: yes
09:26 shk3 - single spectrum (spectrum editor)
09:26 olas shk3: how do we distinguish between single mol and multi mol?
09:26 shk3 - spectrum and molecule (specmol editor to be ported from bc1)
09:26 shk3 - the rest (xml editor)
09:26 olas count <molecule> elements?
09:26 shk3 the describer should be able to do that, shouldn't it?
09:26 olas yes, but how
09:27 olas count # <molecule>
09:27 shk3 count molecule children of root element?
09:27 olas ?
09:27 olas ok
09:27 olas sounds good
09:27 shk3 think so
09:27 olas I will implement single and multi mol
09:27 olas and also 2D/3D
09:27 shk3 ok, i am working on spectrum stuff anyway
09:27 olas (needed for JCP or Jmol)
09:27 shk3 but might take some more time
09:27 olas did you finish the create2D?
09:27 shk3 working on this
09:28 olas good
09:28 shk3 came across another problem:
09:28 shk3 ICDKMolecule has getAtomContainer
09:28 shk3 returning IAtomContainer
09:28 olas what is prob with this?
09:28 shk3 the structurediagramgenerator needs an IMolecule
09:28 olas create one from the IAC
09:28 shk3 (not sure why)
09:28 shk3 can I do so?
09:29 shk3 ah, yes
09:29 shk3 that's the easy way
09:29 olas :-)
09:30 jonalv olas: I feel ready to start some testing. Maybe we should test builds?
09:30 shk3 can the manger methods only throw BioclipseExceptions?
09:30 jonalv shk3: no they can through anything
09:31 jonalv and BioclipseException is something that some people think we should get rid of...
09:31 shk3 ok
09:35 jonalv olas: about the jmol view. What does it listen to? I can seem to get it to show anything...
09:48 CIA-49 bioclipse: ospjuth * r6343 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs): Added contentTypes for PDB, MDLMolfile, CML in bioclipse.ui plugin (for now) as they need to be visible to many plugins. Also added a custom describer for distinguishing between CML files with 2D and 3D coordinates.
09:49 CIA-49 bioclipse: ospjuth * r6344 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol/plugin.xml: Only open CML files in Jmol that have 3D coordinates.
09:49 CIA-49 bioclipse: ospjuth * r6345 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/plugin.xml: Only open CML files in JCP that have 2D coordinates.
09:49 olas aaah
09:51 shk3 congratulations
09:51 olas olas ++?
09:52 olas ok, will write up the wiki page now
09:52 olas actually, will have lunch first
10:11 shk3 one more question
10:11 shk3 olas still available?
10:16 shk3 jonalv?
10:17 jonalv shk3?
10:17 shk3 a question?
10:17 jonalv don't ask to ask just ask :)
10:17 shk3 I generate the coordinates and need to write back to the file in the right format.
10:17 shk3 how to do this best?
10:17 shk3 i. e. the conversion?
10:17 jonalv if someone knows the answer they will answer :)
10:17 shk3 how do I get the format from the selection
10:18 jonalv right, it sounds like a manager method somewhere... Don't know if this feature exists...
10:19 shk3 there is saveMolecule in CDKManager, but this only takes a CDKMolecule and has void return type
10:19 shk3 no proper javadoc comment
10:19 shk3 so I don't know what this is doing
10:19 jonalv and it's implementation is empty if I am not mistaking...
10:19 shk3 yes
10:19 jonalv I have seen that method too :)
10:19 shk3 hmmm
10:19 jonalv don't know anything about it...
10:19 shk3 not of much use
10:20 jonalv seems like a work in progress...
10:20 shk3 it should take the molecule, an IFile and a format type or so
10:20 shk3 just the molecule doesn't make much sense
10:21 jonalv true
10:21 jonalv I think we haven't reached taht code yet...
10:21 jonalv all editors probably do their saving themself...
10:22 shk3 hm, looks like i need this
10:22 jonalv yea, maybe you should be the one to write it then :)
10:23 shk3 don't feel quite confident right now, but I will try
10:23 jonalv please have in mind the String String String version to be used from the console too
10:24 jonalv I think it will be two versions. one taking molecule, IFile, format string and one taking just strings
10:24 jonalv what do you think about that?
10:24 shk3 sounds good
10:30 edrin http://xkcd.com/456/
10:45 olas shk3,jonalv: I second this as well
10:46 olas editors now have their own parsing/saving
10:46 olas they should be refactored to use Manager methods instead
10:46 olas the Formats we had in BC1 are not implemented yet
10:52 shk3 just did an update
10:52 shk3 the loadMolecule(InputStream) in cdkmanager has been removed, it seems
10:53 shk3 I remember we said a streammethod should be there in such cases
10:53 shk3 or am I wrong?
10:53 shk3 i can use the IFile one anyway, so just for curiosity
10:55 olas IFile should be used
10:55 olas IFile and String
10:55 olas from the IFIle you can get the INputStream
10:55 olas we should not have INputStream in manager methods
11:00 shk3 good to know
11:00 CIA-49 bioclipse: ospjuth * r6346 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Added JSEditor and Quickimage to bioclipse-feature.
11:10 shk3 HELP!
11:10 shk3 I did an update and bioclipse no longer runs
11:12 shk3 ah, looks like plugins need to be added manually in run configuration ?!?
11:15 olas you can always fall back to the bioclipse.product and chhose "launch"
11:15 olas then add mroe plugins
11:16 shk3 it didn't launch for me without adding plugins
11:18 shk3 hm, my handler can no longer find the CDKManager
11:18 shk3 anything I need to do for that?
11:18 shk3 (it worked before the update)
11:22 olas is the plugin selected?
11:22 olas add required plugin?
11:22 olas dependencies ok?
11:23 shk3 looks like
11:23 shk3 cdk.ui depends on cdk.business and both are in the run configuration
11:25 olas what does the console log say?
11:26 shk3 lots of stuff
11:26 shk3 mainly related to logging
11:27 shk3 SEVERE: Pre refresh error
11:27 shk3 org.apache.commons.logging.​LogConfigurationException: org.apache.commons.logging.​LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@3acc67 for org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category) (Caused by org.apache.commons.logging.​LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@3acc67 for org.apache.commons.logging.impl.Log4JLogger (Caused by
11:27 shk3 java.lang.NoClassDefFoundError: org/apache/log4j/Category))
11:27 shk3 at org.apache.commons.logging.impl.LogFactory​Impl.newInstance(LogFactoryImpl.java:543)
11:27 shk3 and so on
11:28 shk3 short question: How do I install the sample data?
11:28 shk3 wanted to test this to close the bug.
11:30 shk3 olas: could you just tell me this, please?
11:31 shk3 anybody else?
11:31 olas shk3
11:31 olas mom
11:32 olas add the sample data plugin to run config
11:32 olas start
11:32 shk3 done
11:32 olas New... project... SampleDataProject
11:32 shk3 ah, thanks
11:32 shk3 works
11:32 shk3 will close bug
11:32 olas great
11:34 CIA-49 bioclipse: ospjuth * r6347 /bioclipse2/trunk/plugins/​net.sourceforge.jseditor/: Initial import.
11:35 shk3 i will try the savemolecule first
11:35 shk3 perhaps the manager not found resolves by itself
11:38 * shk3 is having lunch
11:39 CIA-49 bioclipse: ospjuth * r6348 /bioclipse2/trunk/plugins/​net.sourceforge.jseditor/ (79 files in 24 dirs): Added jseditor again as needed modifications to run in Bioclipse (hence svn externals is not an option).
11:39 CIA-49 bioclipse: ospjuth * r6349 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Removed unused editors (prev used for testing purposes).
11:57 CIA-49 bioclipse: jonalv * r6350 /bioclipse2/trunk/externals​/net.sourceforge.jseditor/: removed externals/net.sourceforge.jseditor we will use the one in plugins...
12:01 olas http://wiki.bioclipse.net/index.php​?title=Contenttypes_and_describers
12:01 zarah olas's link is also http://tinyurl.com/5b4bcf
12:01 jonalv Has anyone else noticed that we no longer have functioning logging?
12:02 olas no
12:03 olas but have not looked either
12:04 jonalv please do
12:06 olas how?
12:07 * olas successfully exported jseditor
12:07 jonalv uhm start bioclipse
12:07 olas :-)
12:07 jonalv nice
12:08 jonalv now we just need a play button :)
12:08 olas exactly
12:08 olas masak will fix that tomorrow I assume
12:08 jonalv edrin: Are you there?
12:08 edrin yes
12:08 jonalv olas: yea :)
12:09 jonalv edrin: I am looking at some js files in sampledata
12:09 edrin ok
12:09 jonalv you seem to have done some cool stuff
12:09 jonalv I am in related thoughts...
12:09 jonalv Especially the Multithradingscript I am looking at
12:10 edrin ok
12:10 jonalv I am thinking about how to get good status monitors on java scripts...
12:10 edrin i did this with eclipse jobs
12:10 jonalv Have you worked much with rhino?
12:11 jonalv Yea for the moment each managaer method start an Eclipse job
12:11 edrin i have been working with it
12:11 edrin ok
12:11 jonalv So each manager method keeps a monitor updated
12:12 jonalv (at least quite a few of them)
12:12 jonalv I am thinking we could use this for creating a big status bar for a complete script somethow
12:12 edrin i think this is in it, no?
12:13 jonalv if could get a parse tree or somthing from rhino we could count the number of manager method calls. And give each method an amount of ticks for the complete script
12:13 jonalv edrin: What\s in it what? :)
12:13 edrin yes
12:14 * edrin checks source
12:14 jonalv hm what's in what?
12:14 jonalv The thing is that we don't wanna parse javascript but perhaps rhino could do it for us...
12:15 edrin sure, that's what I did
12:15 edrin rhino is executing the script
12:15 edrin and
12:15 edrin as you were talking about the thread stuff
12:16 jonalv ah well you didn't quite catch the goory details here. I need to get the number of manager method calls in a given java script in order to allocate a correct amount of ticks for each manager call
12:19 jonalv uhm maybe you did anyway...
12:19 malic1 left #bioclipse
12:20 jonalv edrin: Do your javascript jobs have a worlking status bar? If so how is it updated?
12:21 * olas donät think we had a Monitor in bc1 for that
12:22 edrin sorry, was away
12:24 jonalv k
12:24 * jonalv would love t ohear the answer to the question anyway :)
12:25 edrin jonalv: yes, if you run a script in its own thread (via the button) then it gets an eclipse job with progress bar. within the script you cancheck if the user canceled the job, a function to update/change info in the progress view from within the script can be added in minutes...
12:26 jonalv edrin: okey but you are not doing any automagic ticking of the monitor. That is you arfe not automagicly calling the worked method?
12:27 edrin to check within the script if the script was canceled by the user (in progress view) you just do rhino.isCanceled();
12:28 edrin I do not like progress bars that progress even if the thread is not really progressing ...
12:28 edrin but someone could add a function like rhino.updateStatus(blah):
12:29 edrin why not just reuse rhino plugin in bc2 ?
12:30 jonalv I must admit that I don't know enough about it. But I am dowloading bioclipse 1 source to check it out right now
12:31 jonalv My feeling is that it will need to be adapted though
12:31 jonalv And my ideas was to do soem things a bit more crazy... :)
12:31 jonalv oh did I write crazy? I mean cool
12:31 jonalv :)
12:31 jonalv (only problem is that I have a feeling that my dream is unreachable...)
12:33 jonalv As I said my dream is to automagicly get a fully working status bar for all our manager based javascripts :)
12:34 CIA-49 bioclipse: goglepox * r6351 /bioclipse2/trunk/plugins/net.bioclipse.core/ (2 files in 2 dirs): Removes open editors to Virtual resources on startup. fixes: 2030492
12:35 jonalv Gpox++
12:36 olas nice
12:36 olas gotta run off for some time
12:36 olas be back later
12:36 olas left #bioclipse
12:51 shk3 I need a progress monitor for the getContent method of IFile.
12:52 shk3 Is there an example of this?
12:52 shk3 no idea right now, how monitors work.
12:52 jonalv hehe, did you see edrin's and my disussion? :)
12:53 jonalv shk3: in which method do you need it_
12:54 jonalv if you are in the manager method with the signature IFile, String, String you should add another paramter IProgressmonitor to that method. But I higly recommend this article for you:
12:55 jonalv http://www.eclipse.org/articles/Art​icle-Progress-Monitors/article.html
12:55 zarah jonalv's link is also http://tinyurl.com/6pyuhb
12:55 shk3 thanks
12:55 shk3 will look at it
12:56 shk3 I am in the manager method with ICDKMolecule, IFile, String
12:57 jonalv have a look at the method called loadMolecules
12:57 jonalv I think that one is ok but I might remmebr wrong now
12:59 shk3 looks good
13:03 edrin the bc1 web service plugin has a complete progress monitor as well
13:03 jonalv okey
13:04 jonalv I am in mac os x so I can't start two Eclipse instances and check out bc1 at the same time as bc2 though...
13:05 jonalv but it was progress monitors toghether with rhino I awas intrested in now
13:06 jonalv edrin: Do you think it's doable?
13:46 CIA-49 bioclipse: jonalv * r6352 /bioclipse2/trunk/plugins/net.bioclipse.ui/s​rc/net/bioclipse/ui/jobs/BioclipseJob.java:
13:46 CIA-49 bioclipse: Removed 1 of 2 error dialog popping up for the same error
13:46 CIA-49 bioclipse: Made the job return something even though it ran into exception
13:46 CIA-49 bioclipse: The js thread no longer get's stuck waiting for a returnvalue not comming if something goes wrong while running manager methods that should return something from now on.
13:46 jonalv ha black belt in long sentecnes for me :)
13:54 CIA-49 bioclipse: jonalv * r6353 /bioclipse2/trunk/plugins/net.b​ioclipse.data.sampledata/data/ (JavaScript/ misc/cmlspect.bib):
13:54 CIA-49 bioclipse: Removed javascript files that can't be used in bioclipse 2 from sampledata.
13:54 CIA-49 bioclipse: Removed bibtex file from sampledata
13:54 CIA-49 bioclipse: (these should be returned to sampledata if functionality able to used them are added/ported to bioclipse 2)
14:07 shk3 still getting the "Could not get the CDK manager" in my handler.
14:07 shk3 anybody an idea what to do?
14:08 shk3 cdk.business is there
14:13 jonalv in yur handler?
14:14 shk3 yes
14:14 jonalv shk3: how do I reproduce your problem?
14:14 shk3 the one I wrote for coordinate generation
14:14 shk3 not, right now
14:14 shk3 would need to commit
14:15 jonalv I don't really understand what you are doing...
14:15 jonalv brb
14:15 shk3 i added a generate2dcoordinates mathod to cdkmanager
14:16 shk3 I wrote a handler to call this from the context menu
14:16 shk3 when I try, i get cdkmanager not found
14:17 jonalv okey I think I would need to have a look at that handler...
14:19 shk3 i try to clean up things and commit
14:21 shk3 btw, do you think cdk.ui is the right plugin for the menu function?
14:21 jonalv probably
14:22 CIA-49 bioclipse: shk3 * r6354 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): added a generate2dcoordinates method
14:23 shk3 what are plans for the release?
14:23 CIA-49 bioclipse: shk3 * r6355 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (3 files in 2 dirs): the 2d coordinate generation (not yet ready)
14:23 jonalv well we are working on releasing on friday
14:25 shk3 hm, looks like lots of things to do
14:25 shk3 I tried jcp (in bc) today and found some problems
14:25 shk3 will file these
14:25 jonalv okey?
14:25 jonalv yea please do that
14:25 shk3 you could try the coordinate generation
14:25 shk3 everything should be in cdk.business and cdk.ui
14:25 jonalv oki
14:27 jonalv java.lang.ClassNotFoundException: net.bioclipse.jmol.actions.PdbAction, java.lang.ClassNotFoundException: net.bioclipse.jmol.actions.CmlAction
14:28 shk3 where?
14:28 jonalv http://paste2.org/p/53577
14:29 jonalv hum that's strange...
14:29 shk3 I don't get these
14:31 jonalv what file should I run it on?
14:32 shk3 a mol file
14:34 jonalv I get those errors once. ANd then nothing happens.
14:34 jonalv where should the newly generated file end up?
14:34 jonalv in the virtual project?
14:37 shk3 do you get the dialog?
14:37 shk3 new file or overwrite?
14:38 jonalv yea
14:38 shk3 it fails for me before that
14:38 shk3 so something is wrong with my configuration
14:38 jonalv oh
14:38 shk3 the new file thing is not yet implemented
14:38 shk3 what can be wrong here?
14:38 jonalv hm are you running from the product?
14:38 shk3 yes
14:39 jonalv are you having cdk on the console?
14:39 shk3 sorry, no
14:39 shk3 if I run from the product, it doesn't run
14:39 shk3 I opened the run config and added plugin
14:39 shk3 s
14:39 shk3 then it runs
14:39 jonalv that's intresting
14:39 shk3 I don't have the console
14:39 jonalv what plugins where missing?
14:39 shk3 another problem...
14:40 shk3 all
14:40 jonalv you don't have the console?
14:40 shk3 but it looks like you changed t features?
14:40 jonalv When did you try from the product last?
14:40 shk3 before the update at noon
14:41 jonalv It has been some refactoring the last days...
14:41 shk3 the console is also not in the views
14:41 jonalv are you running net.bioclipse.scripting.ui?
14:42 shk3 don't have that
14:42 shk3 is that a new plugin?
14:43 jonalv sort of
14:43 shk3 ok, getting it
14:44 shk3 perhaps that's the reason
14:44 shk3 other new stuff?
14:44 jonalv probably...
14:44 jonalv I am trying to think what wlse could be different
14:45 jonalv I an really recommend running svn from console and just import all plugins into workbench
14:45 jonalv at least if you don;t have very little ram in your computer...
14:45 jonalv :)
14:45 jonalv *I can really recommend
14:46 shk3 hm, no change
14:47 shk3 i get all plugins i do not yet have
14:52 jonalv yea woreth a try I guess :)
15:00 CIA-49 bioclipse: carl_masak * r6356 /bot/trunk/zarah.pl: [zarah] now responds a bit better to yes/no and lone question marks
15:00 zarah joined #bioclipse
15:13 jonalv shk3: any progress?
15:15 shk3 hm, has the target.platform plugin gone?
15:17 jonalv no :)
15:17 jonalv that one will stay :)
15:18 jonalv why?
15:18 jonalv doesn't eclipse ppick it up when you are trying to import?
15:19 jonalv I had that problem..
15:19 shk3 i can't see it in svn
15:19 jonalv I had to delete the plugins cataloguoe and redownload them to get it to work...
15:19 jonalv You are using subclipse to check out stuff right?
15:20 jonalv oh sry
15:20 jonalv not plugns
15:20 jonalv it is directly in trunk
15:20 shk3 right
15:20 shk3 so it seems I have got everything
15:20 jonalv https://www.datorbutiken.com/se/default.as​px?Product=ASEEEPCBL&amp;UrlTag=Newsletter
15:20 shk3 i try cleaning
15:20 jonalv but it is definlty there :)
15:20 shk3 an rebuilding
15:21 shk3 and setting target platform
15:21 jonalv http://bioclipse.svn.sourceforge.n​et/viewvc/bioclipse/bioclipse2/tru​nk/net.bioclipse.target.platform/
15:21 zarah jonalv's link is also http://tinyurl.com/5jt7xu
15:21 jonalv that was the right paste
15:21 jonalv :)
15:22 shk3 net.sf.jseditor gives errors for me
15:22 shk3 can I close this project or is it needed?
15:23 jonalv it is sort of needed but it is new
15:23 jonalv think you can close it
15:23 shk3 all the org.eclipse imports fail for me
15:23 jonalv there where some duplications with it
15:23 jonalv is your variant found in externals or in plguns?
15:24 shk3 plugins
15:24 jonalv *plugins
15:24 jonalv okey
15:24 jonalv that should be the good one
15:24 jonalv then I don't know what's going on
15:27 shk3 ah, when i start
15:27 shk3 i get a conflict for Create2dHandler
15:28 shk3 that's a pointer at least
15:28 jonalv k
15:29 shk3 ok, that was an artifact left behind
15:29 shk3 trying again...
15:30 shk3 !MESSAGE An error occurred while automatically activating bundle net.bioclipse.scripting (11).
15:30 shk3 org.osgi.framework.BundleException: The activator net.bioclipse.scripting.Activator for bundle net.bioclipse.scripting is invalid
15:30 shk3 Caused by: java.lang.NoClassDefFoundError: org/jruby/runtime/callback/InvocationCallback
15:30 shk3 DEBUG - java.lang.NoClassDefFoundError: net/bioclipse/scripting/ScriptingThread
15:31 shk3 that's what i get _now_ when trying to run the coordiante generation
15:32 jonalv huh jruby?
15:32 jonalv hm what has that got to do with anything?
15:32 shk3 no idea
15:33 shk3 the ScriptingThread is not found in
15:33 shk3 at net.bioclipse.ui.jobs.CreateJobAdvi​ce.invoke(CreateJobAdvice.java:57)
15:33 shk3 does that ring a bell?
15:33 jonalv can I try it?
15:33 jonalv yea I wrote that code this week
15:34 jonalv which is why I would want to try it here :)
15:34 shk3 try, well, i just run bc and try the coordinate generation
15:34 shk3 as you did
15:34 shk3 worked for you, but not for me
15:35 jonalv I hate to ask this but you of course have updated all plugins?
15:37 shk3 yes, but i will do it right now again
15:38 jonalv firing up my ubuntu machine to get a third view on this...
15:45 shk3 same problem
15:48 * jonalv is trying to recreate it on the other machine
16:18 shk3 jonalv:
16:19 shk3 the first error I get is the jruby stuff not found
16:19 jonalv shk3:
16:19 shk3 this is in at net.bioclipse.scripting.Activa​tor.<init>(Activator.java:28)
16:19 jonalv hm
16:19 shk3 perhaps scripting not being activated leads to scripting classes not found later
16:19 jonalv sounds very reasonable
16:19 shk3 where should the jruby stuff exist?
16:19 jonalv I am not sure
16:19 jonalv masak made that...
16:20 shk3 there is no jar in scripting which looks like jruby stuff
16:20 shk3 sorry, no, there is
16:20 shk3 jruby.jar
16:21 shk3 and the class is in there
16:21 shk3 why is it not found?
16:21 jonalv hm and why only not for you
16:22 shk3 i have updated and the only project having local differences is spectrum
16:26 shk3 i will do a new checkout
16:27 jonalv wow I tried an update classpath out of a hunch and now things are working much better
16:29 shk3 doesn't help for me
16:43 jonalv okey I can confirm your errors in Ubuntu
16:43 jonalv shk3
16:47 shk3 great
16:48 shk3 then it's not me being an idiot
16:48 jonalv shk3: I get the cml actions error when doing it on a cml file and your error on a mol file I think
16:48 shk3 didn't try cml
16:48 shk3 so it works on mac but not on ubuntu?
16:48 jonalv hang on
16:49 jonalv sry it took td to check out cdk via wireless... :)
16:49 jonalv *time
16:50 jonalv no I get the pdb error on mol files to
16:50 jonalv it complaints about jmol actions
16:51 shk3 hm
16:54 jonalv Windows behaves as Ubuntu
16:54 jonalv so it's just my mac installation behaving differently...
16:55 jonalv You will have to ask olas for help tomorrow
16:56 jonalv I am leaving now...
16:56 jonalv perhaps Gpox++ might come up with something too. He is usually good with this sorts of things
16:57 shk3 thanks anyway
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