Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-17

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All times shown according to UTC.

Time Nick Message
05:52 egonw joined #bioclipse
06:01 CIA-40 bioclipse: egonw * r10479 /bioclipse2/branches/bioclipse-xmp​p/plugins/net.bioclipse.jseditor/ (26 files in 8 dirs):
06:01 CIA-40 bioclipse: Revert "copy from trunk": no copy/paste from trunk, which will pull in too much NWO stuff.
06:01 CIA-40 bioclipse: This reverts commit 10477.
06:02 CIA-40 bioclipse: egonw * r10480 /bioclipse2/branches/bioclipse-xmp​p/plugins/net.bioclipse.gist.test/ (11 files in 3 dirs):
06:02 CIA-40 bioclipse: Revert "copy from trunk": no copy/paste from trunk which will pull in too much NWO stuff.
06:02 CIA-40 bioclipse: This reverts commit 10476.
06:03 CIA-40 bioclipse: egonw * r10481 /bioclipse2/branches/bioclipse-x​mpp/plugins/net.bioclipse.gist/ (15 files in 7 dirs):
06:03 CIA-40 bioclipse: Revert "copy of trunk": no copy/paste from trunk which would pull in too much NWO specifics.
06:03 CIA-40 bioclipse: This reverts commit 10475.
06:13 CIA-40 bioclipse: egonw * r10482 /bioclipse2/branches/bioclipse-xmpp/plugins/ (295 files in 97 dirs):
06:13 CIA-40 bioclipse: Revert "will be replaced with current version": no copy/paste from trunk which would copy in too many NWO changes.
06:13 CIA-40 bioclipse: This reverts commit 10474.
06:49 egonw_ joined #bioclipse
07:28 CIA-40 bioclipse: egonw * r10483 /bioclipse2/trunk/plugins/ (8 files in 2 dirs):
07:28 CIA-40 bioclipse: Updated test evironment for the Gist manager.
07:28 CIA-40 bioclipse: * added missing test class annotation to IGistManager
07:28 CIA-40 bioclipse: * added missing copyright/license headers
07:28 CIA-40 bioclipse: * added test suite for APITest and ConverageTest
08:35 edrin joined #bioclipse
11:26 edrin left #bioclipse
11:33 edrin joined #bioclipse
11:41 egonw joined #bioclipse
11:41 edrin hi again egon
11:41 edrin egonw: i sent you a mail
11:55 egonw ah, ok
11:55 egonw will check
12:04 egonw OK, four patches being commited
12:05 CIA-40 bioclipse: egonw * r10484 /bioclipse2/branches/bioclipse-xmpp/plugins/n​et.bioclipse.xws4j/cheatsheets/xmppgists.xml:
12:05 CIA-40 bioclipse: Replaced hivpred gist with bioschemata gist in xmppscripts cheatsheet.
12:05 CIA-40 bioclipse: git-svn-id:
12:05 CIA-40 bioclipse:  https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@10444 fcb5ba71-d80d-0410-8237-ba3920747fcc
12:05 CIA-40 bioclipse: Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc>
12:06 CIA-40 bioclipse: egonw * r10485 /bioclipse2/branches/bioclipse-xmpp/plugins/net​.bioclipse.jseditor/src/net/bioclipse/jseditor/ (RhinoConsole.java actions/RunRhinoScriptAsJobAction.java):
12:06 CIA-40 bioclipse: nowthe js editor console is shown when a script is run
12:06 CIA-40 bioclipse: git-svn-id:
12:06 CIA-40 bioclipse:  https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@10447 fcb5ba71-d80d-0410-8237-ba3920747fcc
12:06 CIA-40 bioclipse: Author: edrin_t <edrin_t@fcb5ba71-d80d-0410-8237-ba3920747fcc>
12:07 CIA-40 bioclipse: egonw * r10486 /bioclipse2/branches/bioclipse-x​mpp/plugins/net.bioclipse.xws4j/ (4 files in 3 dirs):
12:07 CIA-40 bioclipse: removed .jar that is not needed...
12:07 CIA-40 bioclipse: git-svn-id:
12:07 CIA-40 bioclipse:  https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@10448 fcb5ba71-d80d-0410-8237-ba3920747fcc
12:07 CIA-40 bioclipse: Author: edrin_t <edrin_t@fcb5ba71-d80d-0410-8237-ba3920747fcc>
12:07 CIA-40 bioclipse: egonw * r10487 /bioclipse2/branches/bioclipse-xmpp/plugins​/net.bioclipse.xws4j/META-INF/MANIFEST.MF:
12:07 CIA-40 bioclipse:  xmlbeans packages are exported...
12:07 CIA-40 bioclipse: git-svn-id:
12:07 CIA-40 bioclipse:  https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@10449 fcb5ba71-d80d-0410-8237-ba3920747fcc
12:07 CIA-40 bioclipse: Author: edrin_t <edrin_t@fcb5ba71-d80d-0410-8237-ba3920747fcc>
12:12 egonw edrin: if there are more you want backported, let me know...
12:12 edrin ok, no, i think that's it
12:12 egonw I had no merge conflicts, but keep in mind this was down automagically by git...
12:12 egonw I only copied the four patches you requested...
12:12 edrin to build one must cheout the whole thing right?
12:13 egonw now going to take a nap
12:13 egonw huh?
12:13 egonw yes
12:13 egonw just like running
12:13 edrin bone appetite
12:13 edrin yes
12:13 edrin how will build? me, ola? you?
12:14 egonw I don't know how
12:14 edrin ok
12:14 egonw done it once, but would not be able to reproduce
12:14 edrin ok
12:18 egonw ok, bbl
13:30 shk3 joined #bioclipse
13:46 egonw joined #bioclipse
13:49 edrin left #bioclipse
14:25 CIA-40 bioclipse: egonw * r10488 /bioclipse2/trunk/plugins/ (6 files in 3 dirs):
14:25 CIA-40 bioclipse: Updated testing framework for the InChI manager:
14:25 CIA-40 bioclipse: * added a suite for non-plugin tests
14:25 CIA-40 bioclipse: * updated test class annotation in IInChIManager
14:25 CIA-40 bioclipse: egonw * r10489 /bioclipse2/trunk/plugins/ (5 files in 2 dirs):
14:25 CIA-40 bioclipse: Updated testing framework for NWO:
14:25 CIA-40 bioclipse: * Added APITesting
14:25 CIA-40 bioclipse: * Added suite for non-plugin tests
14:25 CIA-40 bioclipse: * Updated test class annotation in ICDKDebugManager accordingly
15:11 CIA-40 bioclipse: egonw * r10490 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (IJavaCDKManager.java IJavaScriptCDKManager.java): Added missing copyright/license headers
15:12 CIA-40 bioclipse: egonw * r10491 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (8 files in 3 dirs):
15:12 CIA-40 bioclipse: Converted the ValidateCML manager to the NWO:
15:12 CIA-40 bioclipse: * added IJava/IJavaScript interfaces
15:12 CIA-40 bioclipse: * updated the Activator to have return method for both
15:12 CIA-40 bioclipse: * updated a few methods in the same class that used the Activator
15:13 CIA-40 bioclipse: egonw * r10492 /bioclipse2/trunk/plugins/ (11 files in 3 dirs):
15:13 CIA-40 bioclipse: Updated testing framework for ValidateCMLManager for the NWO:
15:13 CIA-40 bioclipse: * add suites for plugin and non.plugin tests
15:13 CIA-40 bioclipse: * factored out tests into an abstract class
15:13 CIA-40 bioclipse: * added plugin test classes for the Java and JavaScript environment
15:13 CIA-40 bioclipse: * update test class annotation in IValidateCMLManager
15:20 edrin joined #bioclipse
15:23 shk3 hi egonw
15:24 egonw hej shk3
15:24 shk3 i am trying to convert the seneca manger to nwo
15:24 shk3 it seems there is only a context.xml now
15:24 shk3 there used to be a context-osgi.xml as well
15:24 shk3 but this seems to be gone?
15:24 egonw one .xml file is fine
15:24 shk3 ok
15:25 egonw though most seem to use context-osgi.xml as file name
15:25 shk3 ah
15:25 egonw the content can be in one file
15:25 shk3 cdk has context.cml
15:25 egonw use the cdk.business context xml file as template
15:25 egonw don't think it matters
15:25 shk3 that's what I am trying
15:25 egonw just converted ValidateCMLManager to use context-osgi.xml
15:25 egonw it still had two files
15:26 egonw I can talk you try the content
15:26 shk3 if the seneca running is in the manager, nice thigs can be scripted
15:26 shk3 like running multiple times and doing statistics
15:26 shk3 I give it a try and will ask if something is unclear
15:26 shk3 but need to go the toilette first
15:28 egonw indeed
15:28 egonw scripting is a big plus of bc2
15:28 * egonw needs to go make dinner really soon
15:31 CIA-40 bioclipse: egonw * r10493 /bioclipse2/trunk/plugins/net.bioclipse.cdk.bus​iness.test/src/net/bioclipse/cdk/business/test/ (AllCDKManagerPluginTests.java AllCDKManagerTests.java): Added missing unit test suites for CDKManager
15:32 CIA-40 bioclipse: egonw * r10494 /bioclipse2/trunk/plugins/net.biocl​ipse.tests/src/net/bioclipse/tests/ (4 files): Updated for new suites added in the last few commits
15:36 shk3 don't worry
15:36 shk3 we will continue tomorrow
15:38 edrin egonw: i managed to create a bc build from trunk
15:47 shk3 is a factory needed for the manager?
15:53 egonw yes
15:53 egonw for the JS one, I think
15:53 egonw to allow getting the JS flavor working for the Java Console
15:54 egonw edrin++
15:55 egonw edrin: let me know if I need to test a bundle... make sure to make a 64 bit one
15:55 edrin egonw: i still have a classloader problem...
15:55 edrin with xmlbeans
15:56 edrin egonw: that means, the script in the build still does not work...
16:30 shk3 looks like I got things running
16:35 shk3 uppsala++ for nwo
17:43 CIA-40 bioclipse: ospjuth * r10495 /bioclipse2/trunk/features/net.bio​clipse.xws4j_feature/feature.xml: Removed old dep to core_patch.
17:52 rojasm joined #bioclipse
17:52 egonw hi rojasm
17:52 egonw rojasm: ping
17:52 * egonw is converting the MedeaManager to the NWO
18:02 rojasm ei egonw
18:02 zarah rojasm: You have new messages. Write '/msg zarah @messages' to read them.
18:03 egonw hej rojasm
18:03 egonw good you are online
18:03 egonw got big MedeaManager patches around...
18:03 egonw which I will commit shortly
18:04 rojasm Oh perfectly I am trying to update my home computer with Bioclipse repository
18:04 egonw ack
18:04 rojasm But I thought that MedeaManager was already update to the new NOW
18:05 egonw no
18:06 egonw because on Wed/Tue the NWO architecture was not merged with trunk uet
18:06 egonw yet
18:09 rojasm Meanwhile I will try to update the prediction of the intensities
18:11 rojasm egown thanks for taking care of the update in Medeaplugin for the NOW version
18:11 egonw no worries
18:11 shk3 joined #bioclipse
18:12 egonw I started the manager
18:12 egonw so, my responsiblity to fix it too
18:13 rojasm hi shk3 stefan
18:13 egonw rojasm: plugin tests currently fail because if issues in the Spectrum plugin
18:13 shk3 hi miguel
18:13 egonw shk3: didn't you commit the JumboSpectrum constructor without arguments?
18:14 shk3 thought so
18:14 egonw shk3: that's the stacktrace indicating for the Medea unit tests...
18:14 egonw yes, thought so too...
18:14 shk3 mom
18:14 shk3 checking
18:14 egonw same here
18:14 egonw I see only, public JumboSpectrum(CMLSpectrum spectrum)
18:14 shk3 ok
18:14 shk3 will commit
18:15 shk3 starting eclipse
18:15 egonw BTW, the source does not have any copyright/license header
18:15 egonw while at it... ?
18:15 shk3 it does
18:15 shk3 here
18:15 shk3 :-)
18:15 egonw ic
18:15 egonw good, commit will fix too then :)
18:15 shk3 saw that yesterday
18:17 shk3 somehow my changes must have got lost
18:17 shk3 I don't have them even locally
18:17 shk3 strange
18:19 shk3 ok, that should do it
18:20 CIA-40 bioclipse: shk3 * r10496 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/domain/ (IJumboSpectrum.java JumboSpectrum.java): JumboSpectrum needs empty constructor
18:21 egonw shk3: please check the bioclipse-devel ML archive of last week for the proper header template
18:22 CIA-40 bioclipse: egonw * r10497 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (7 files in 4 dirs):
18:22 CIA-40 bioclipse: Converted the MedeaPlugin to be conform the NWO:
18:22 CIA-40 bioclipse: * added IJavaScriptMedeaManager and IJavaMedeaManager interfaces
18:22 CIA-40 bioclipse: * updated the activator with get methods for both
18:22 CIA-40 bioclipse: * update the Spring configuration
18:22 CIA-40 bioclipse: * added test class annotation to IMedeaManager
18:23 CIA-40 bioclipse: egonw * r10498 /bioclipse2/trunk/_playground_/net.bioclipse.me​dea.test/src/net/bioclipse/medea/business/test/ (9 files):
18:23 CIA-40 bioclipse: Updated the MedeaManager unit tests for the NWO architecture:
18:23 CIA-40 bioclipse: * added missing APITest
18:23 CIA-40 bioclipse: * added Java/JavaScript set up for running the functional test
18:23 CIA-40 bioclipse: * added suites for running the plugin and non-plugin test
18:23 CIA-40 bioclipse: shk3 * r10499 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/src/net/bioclipse/spe​ctrum/editor/SpectrumEditor.java: after save as, the editor works on the new file and not the old one
18:34 CIA-40 bioclipse: shk3 * r10500 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/domain/ (IJumboSpectrum.java JumboSpectrum.java): new header template
18:36 rojasm I have still in the plugin structuredb some errors regarding with NWO. Are they essential?
18:36 egonw no
18:36 egonw you can close that project
18:37 egonw jonathan has not had time yet to update that manager
18:39 rojasm ok
18:39 rojasm perfect now with any errors
18:46 egonw rojasm: question...
18:46 egonw how can I get a MF with charges starting from a IAtomContainer
18:46 egonw with Iatom's with formal charges?
18:48 egonw OK, more than enough for today
18:49 egonw going to finish watching Young Frankenstein
18:49 egonw cu tomorrow
18:53 rojasm using MolecularFormulaManipulator
18:53 rojasm I mail you
19:05 egonw ok, thanx!
19:05 * egonw failed to shut down machine and watch tv
19:32 edrin egonw: available?
19:32 egonw sort of :)
19:32 edrin egonw: i have a question
19:34 egonw sure, go ahead
19:36 edrin regarding the managers, is the @GuiAction still working?
19:37 edrin egonw: this is really a strange error, it happens only in the build
19:38 edrin it seems it sometimes does not find the xmlbeans package on the classpath...
19:38 egonw might @GuiAction be NWO stuff?
19:38 egonw not sure about that
19:39 edrin egonw: i dont know...
19:39 edrin i just wonder why this error always happens
19:39 edrin i mean sometimes happens
19:40 edrin !MESSAGE An internal error occurred during: "Javascript - Gists109331.0.js".
19:40 edrin !STACK 0
19:40 edrin java.lang.NoClassDefFoundError: org/apache/xmlbeans/XmlString
19:40 edrin at java.lang.Class.getDeclaredMethods0(Native Method)
19:40 edrin at java.lang.Class.privateGetDeclaredMethods(Unknown Source)
19:40 edrin at java.lang.Class.privateGetPublicMethods(Unknown Source)
19:40 edrin at java.lang.Class.getMethods(Unknown Source)
19:40 edrin at org.mozilla.javascript.JavaMembers​.discoverAccessibleMethods(JavaMem
19:40 edrin ers.java:385)
19:40 edrin this happens only sometimes
19:41 egonw I have no clue
19:42 edrin egonw: do you know, is there a way to check if there is another xmlbeans hidden somewhere on the classpath that might be used sometimes and then fails?
19:42 egonw can you email me what buttons to hit, to reproduce it...
19:42 egonw how often I have to hit it too
19:42 edrin egonw: i always reproduce it this way:
19:42 egonw since it does not happen each time
19:43 edrin i start the build with having the old workspace deleted before, then i click tutorial in the welcome screen, then the XMPP tutorial
19:43 edrin i follwo the instructions, when i finally get to the downloaded gist and run it, it fails ~ 50%
19:44 edrin if it does not fail the first time and i click the run button again it might fail with 50% chance
19:44 rojasm1 joined #bioclipse
19:51 egonw I will try tomorrow morning
19:54 edrin ok
20:02 rojasm joined #bioclipse
20:23 CIA-40 bioclipse: egonw * r10501 /bioclipse2/trunk/plugins/ (8 files in 5 dirs):
20:23 CIA-40 bioclipse: Set up to use the new world order:
20:23 CIA-40 bioclipse: * added IJava/IJavaScriptRDFManager interfaces
20:23 CIA-40 bioclipse: * merged and updata Spring config files
20:23 CIA-40 bioclipse: * have Activator return both manager flavors
20:23 CIA-40 bioclipse: * have the factory return the JS version
22:52 edrin left #bioclipse

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