Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-29

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All times shown according to UTC.

Time Nick Message
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07:50 olas joined #bioclipse
07:50 olas hi
07:50 zarah hi olas
07:50 olas zarah: any messages for me?
07:50 zarah olas: that was not so easy for a little bot to understand
07:51 olas zarah: you are old enough, stop complaining.
07:51 zarah olas: you've just exceeded my capabilities :/
07:51 olas zarah: dz
07:51 zarah you're welcome, olas :)
07:52 olas (memory like a goldfish)
07:59 masak indeed
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08:21 CIA-30 bioclipse: ospjuth * r6792 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/ (5 files in 3 dirs): Rewrote descriptor invocation to operate on new DescriptorInstance with one DescriptorImpl and N DescriptorParameters.
08:22 CIA-30 bioclipse: ospjuth * r6793 /bioclipse2/trunk/plugins/net.bioclipse​.qsar.test/src/net/bioclipse/qsar/test/ (DummyCalculator.java business/TestQsarManager.java): Updated tests to work on DescriptorInstance.
08:22 CIA-30 bioclipse: ospjuth * r6794 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.qsar/src/net/bioclipse/cdk/qsa​r/impl/CDKDescriptorCalculator.java: Implemented CDK calculation on DescriptorInstance.
08:23 CIA-30 bioclipse: ospjuth * r6795 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar.test/src/net/bioclips​e/cdk/qsar/test/TestCDKQsar.java: Wrote tests for testing same descriptor with different parameters in same calculation using CDK.
08:23 olas progress!!
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08:37 masak olas++
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09:26 CIA-30 bioclipse: ospjuth * r6796 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (7 files in 4 dirs): Added preference and preference page with new UpDownListEditor to order descriptor providers.
09:30 CIA-30 bioclipse: ospjuth * r6797 /bioclipse2/trunk/plugins/net.bioclipse.qsar​.ui/src/net/bioclipse/qsar/ui/editors/old/: Removed unused classes.
09:32 CIA-30 bioclipse: shk3 * r6798 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/views/SpectrumCompareView.java: avoids "widget is disposed" error
09:34 masak aha, so outline pages are provided through an adapter. I see.
09:34 shk3 yes
09:34 shk3 could have told you, did this myself recently...
09:35 shk3 just need to add selections in the outline
09:35 shk3 and in the editor
09:35 shk3 to reflect each other
09:35 masak shk3: the unknown unknowns are always hardest to detect :)
09:38 maclean Ahh yes, the Rumsfeld Doctrine.
09:40 maclean To be found here : http://politicalhumor.about.com/c​s/quotethis/a/rumsfeldquotes.htm
10:17 CIA-30 bioclipse: shk3 * r6799 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (3 files in 3 dirs): labels were never displayed for peaks with no y value given
10:24 CIA-30 bioclipse: shk3 * r6800 /bioclipse2/trunk/plugins/net.biocl​ipse.data.sampledata/data/spectra/ (spectrum2-invalid.xml spectrum2.xml): one example had an invalid namespace - both examples are now in
10:56 CIA-30 bioclipse: gilleain * r6801 /bioclipse2/trunk/plugins/net.bioclipse.​spectrum/src/net/bioclipse/spectrum/cont​enttypes/CmlSpectrumFileDescriber.java: Converted throwing error to returning INVALID as a workaround for a bug to do with jdx.
10:57 CIA-30 bioclipse: ospjuth * r6802 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/ (3 files in 2 dirs): Refactored out hardcoded element names to QsarConstants interface.
10:57 CIA-30 bioclipse: ospjuth * r6803 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (5 files in 3 dirs): Initialize preferences for provider order from Providers extension point.
10:57 CIA-30 bioclipse: ospjuth * r6804 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/ (2 files in 2 dirs): Added tests for QSAR preferences.
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11:28 CIA-30 bioclipse: ospjuth * r6805 /bioclipse2/trunk/plugins/ (10 files in 8 dirs): Refactored preferences to net.bc.qsar as needed in QSARManager. PreferencePage stays in qsar.ui.
11:28 CIA-30 bioclipse: ospjuth * r6806 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/ (2 files in 2 dirs): Added test for getPreferredImpl for descriptorID.
11:38 CIA-30 bioclipse: ospjuth * r6807 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Refactored out preference helper methods from initializer to its own class.
11:55 malic1 joined #bioclipse
12:08 CIA-30 bioclipse: ospjuth * r6808 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Refactored preference to store provider Name instead of ID for better visualization in prefs page.
12:58 CIA-30 bioclipse: ospjuth * r6809 /bioclipse2/trunk/plugins/ (5 files in 2 dirs): Working on Add descriptors. Spring exception. Commit for jonalv to check.
13:27 CIA-30 bioclipse: ospjuth * r6810 /bioclipse2/trunk/plugins/net.bioclipse​.qsar/META-INF/spring/context-osgi.xml: Tog bort wrapInProxyAdvice eftersom det kastade Spring stacktraces.
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13:37 CIA-30 bioclipse: jonalv * r6811 /bioclipse2/trunk/plugins/net​.bioclipse.qsar.ui/.project: fixed project naming in .project file for net.bioclipse.qsar.ui. I hope there is no more place the same error...
13:40 stain thomas_ku: I see you are hitting the myExperiment train :-))
13:41 stain or who is it posting..
13:42 stain thomas_ku: do you know rougly how many users there are of cdktaverna..?
13:44 CIA-30 bioclipse: ospjuth * r6812 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (6 files in 3 dirs): Replaced icon with 16x16.
13:46 jonalv Okey I am on Ubuntu now. (Feels great) and I canät get net.bioclipse.cdk.jchempaint to compile. something about: Unbound classpath container: 'JRE System Library [JVM 1.5.0 (MacOS X Default)]' in project 'net.bioclipse.cdk.jchempaint'ne​t.bioclipse.cdk.jchempaintBuild pathBuild Path Problem
13:46 jonalv can anyone comment? :)
13:46 maclean Remove it, and add the appropriate linux system library.
13:46 olas oh
13:46 maclean I get that too.
13:46 de_maas left #bioclipse
13:46 jonalv remove what?
13:47 olas this is a mac <--> linux issue
13:47 olas in manifest, remove Java version requirement
13:47 olas just remove it
13:47 maclean In the Libraries tab of the configure build properties.
13:47 olas 1.5.0 is what it is on Mac, and on linux it's java 1.5
13:49 jonalv removing it from manifest didn't seem to help
13:51 maclean Well, to get it to build, I seem to have altered the .classpath
13:52 jonalv okey can't we commit this and get it to work on all systems without fiddling?
13:52 maclean From path="org.eclipse.jdt.launching.JR​E_CONTAINER/org.eclipse.jdt.intern​al.launching.macosx.MacOSXType/JVM 1.5.0 (MacOS X Default)"/
13:53 maclean To : org.eclipse.jdt.launching.JRE_CONTAINER"
13:53 maclean jonalv: I agree.
13:55 jonalv Gpox: is it alrigt if maclean commits that?
13:56 Gpox yes
13:56 jonalv maclean, go ahead then :)
13:56 maclean okey. doing so that.
13:58 CIA-30 bioclipse: gilleain * r6813 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/.classpath: Wasn't building on non-mac platforms
14:07 olas jonalv: after you removed it from manifest, you must update classpath
14:07 olas (this is always the case)
14:08 jonalv aaahhha
14:09 jonalv olas, skype?
14:10 olas ok
14:15 CIA-30 bioclipse: shk3 * r6814 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (5 files in 5 dirs): it seems that using cmlpeak instead of cmlelement at these places breaks jcamp parsing - no idea why
14:22 jonalv Gpox, it seems net.bioclipse.cdk.jchempaint isn't exporting SWTRenderer which is needed by the sdfeditor. can you confirm?
14:32 CIA-30 bioclipse: ospjuth * r6815 /bioclipse2/trunk/plugins/ (12 files in 2 dirs): Updated propertySources and UI to display last selected entity in FormsPage with 2 viewers. Parameter properties now available in DescriptorInstances.
14:38 Gpox yes i can
14:38 CIA-30 bioclipse: goglepox * r6816 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: Added net.bioclipse.cdk.jchempaint.widgets to MANIFEST.MF
14:42 olas left #bioclipse
14:43 CIA-30 bioclipse: ospjuth * r6817 /bioclipse2/trunk/plugins/net.bioclipse​.qsar/src/net/bioclipse/qsar/descriptor​/model/DescriptorPropertySource.java: Added new prop src.
14:52 CIA-30 bioclipse: shk3 * r6818 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (18 files in 7 dirs): cleaned up code, removed warnings etc.
14:56 CIA-30 bioclipse: shk3 * r6819 /bioclipse2/trunk/plugins/net.bioclipse.spectrum​/src/spok/parser/JcampToCMLSpectrumMapper.java: replaced deprecated method
15:16 malic1 left #bioclipse
15:40 thomas_ku hi Stain
15:40 thomas_ku yes that me who hit myexperiment
15:40 thomas_ku no I have really no idea about how many user
15:40 thomas_ku but I fear that there are not so many
15:43 maclean christoph suggested that I might use cdk-taverna for some specrum analysis that I am doing.
15:44 thomas_ku oh cool
15:44 thomas_ku would be nice
15:44 maclean I have taverna itself running, but I haven't installed the cdk plugin
15:44 maclean yet
15:48 maclean hmmmm.
15:50 thomas_ku that should not be a problem...
15:51 maclean sorry, yes I did that - just figuring out how to use it!
15:51 maclean Stefan noted that you can set things as boring/interesting :)
15:52 thomas_ku yes thats true but this option is only usefull if you have a large number of worker and you want to show only some of them
15:52 maclean hmm. okay.
15:52 maclean I'm trying to work out where the cdk stuff is, now that I have installed it...
15:53 thomas_ku you must restart taverna after the installation
15:53 maclean ahhhh. I had that feeling. thanks.
15:53 thomas_ku than the cdk worker are within the local worker
15:53 thomas_ku all in the folder cdk
15:54 maclean perhaps taverna could prompt the user for restart, like eclipse does?
15:54 thomas_ku yes that would be better
15:55 maclean also, it would be nice to turn off these service discovery things, or have them lazily connect as needed. but anyway.
15:55 maclean aha! I see the cdk in local services.
15:57 thomas_ku you can turn of the service discovery within the mygrid.properties file in the config folder
15:57 maclean ahhh. that's good.
15:57 maclean anyway, I'll try it out, and get back to you if I have problems - is that ok?
15:58 thomas_ku that's fine with me
15:59 thomas_ku for a frist introductin you can also use the tutorial from cdk-taverna it is a bit outdated but many things should work
15:59 maclean I'm beginning to think that I should read some docs :)
15:59 thomas_ku you can find it http://downloads.sourceforge.net/cdk/​cdk-taverna-tutorial-data_V0.4.0.zip?​modtime=1188919050&amp;big_mirror=0 here
16:00 thomas_ku or read some taverna doc that also ok
16:02 maclean no, the tutorial seems to be good, I'll dive in.
16:03 thomas_ku I will be offline now! Not sure if I am online this weekend! But on Monday I am back. Or write an email if you have more questions....
16:04 maclean Okay, will do.
16:04 thomas_ku than have fun....
16:05 thomas_ku bye
17:16 shk3 bye all
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