Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-15

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All times shown according to UTC.

Time Nick Message
06:22 olass joined #bioclipse
06:44 olass hej
06:47 edrin joined #bioclipse
06:47 edrin hi
06:47 zarah hi edrin
06:59 egonw joined #bioclipse
07:06 edrin hi olass, egonw
07:06 olass hi edrin
07:12 Gpox joined #bioclipse
07:24 rojasm joined #bioclipse
07:31 CIA-40 bioclipse: edrin_t * r10449 /bioclipse2/trunk/plugins/net.bioc​lipse.xws4j/META-INF/MANIFEST.MF: xmlbeans packages are exported...
07:33 sneumann joined #bioclipse
08:21 egonw OK, going to try to get some work done now...
08:22 jonalv joined #bioclipse
08:25 steinbeck joined #bioclipse
08:26 steinbeck egonw: the connection just dropped and I cannot reconnect.
08:26 steinbeck I'm in Heidelberg and my meeting starts now. I'll call back later
08:28 egonw ok
08:28 egonw cu later then
08:28 jonalv note to self: when editing wiki pages, remember to save from time to time and not only click preview
08:30 jonalv :(
08:41 edrin joined #bioclipse
08:41 CIA-40 bioclipse: goglepox * r10450 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Changed listener collection to ListenerList
08:42 CIA-40 bioclipse: goglepox * r10451 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
08:42 CIA-40 bioclipse: Changed tabs into spaces and removed traling spaces
08:42 CIA-40 bioclipse: And removed some lines
08:44 CIA-40 bioclipse: goglepox * r10452 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Moved CDKMolecule referenc to JCPWidget
08:46 CIA-40 bioclipse: goglepox * r10453 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (6 files in 2 dirs): Replaced deprecated WorkbenchPlugin.getDefault().getWorkbench() with PlatformUI.getWorkbench()
08:47 egonw_ joined #bioclipse
08:48 CIA-40 bioclipse: goglepox * r10454 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (7 files in 2 dirs): Removed unused handlers and commands from jchempaint
09:13 steinbeck_ joined #bioclipse
09:41 Gpox joined #bioclipse
09:45 steinbeck joined #bioclipse
09:49 rojasm joined #bioclipse
09:58 rojasm joined #bioclipse
10:04 jonalv SVN--
10:10 egonw_ :)
10:10 egonw_ what's up?
10:14 egonw_ jonalv: http://wiki.bioclipse.net/index.php?title=​Http://wiki.bioclipse.net/index.php%3Ftitl​e%3DHow_to_make_a_manager_2&rcid=2529 ??
10:14 zarah egonw_'s link is also http://tinyurl.com/pf6m48
10:14 egonw_ what's that about?
10:14 egonw_ :)
10:17 jonalv egonw_: I am writing about how to make a manager following the latest way of doing it :)
10:17 egonw_ sure
10:17 egonw_ but note the page title
10:17 egonw_ you are writing *two* pages
10:17 jonalv egonw_: what about it?
10:17 egonw_ see:
10:17 egonw_ http://wiki.bioclipse.net/index.​php?title=Special:Recentchanges
10:17 zarah egonw_'s link is also http://tinyurl.com/r5nb59
10:17 egonw_ see what you edited yesterday
10:17 egonw_ and what today
10:18 jonalv wtf
10:18 egonw_ :)
10:19 jonalv hm
10:19 egonw_ that might explain that "I need to save, and not just preview" ?
10:19 jonalv what to do now? :(
10:19 egonw_ copy/paste ?
10:19 jonalv egonw_: well I guess that explains that problem as well
10:19 egonw_ the wikitext content of the last into yesterday's page
10:19 jonalv can I delete pages?
10:19 egonw_ yes, think so
10:20 Gpox joined #bioclipse
10:27 jonalv egonw_: okey better now I guess...
10:27 jonalv :)
10:27 jonalv yikes...
10:38 masak joined #bioclipse
10:45 edrin hello masak
10:45 masak edrin: hello.
11:07 CIA-40 bioclipse: ospjuth * r10455 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Update Version to 2.0.0.B20090515
11:07 CIA-40 bioclipse: ospjuth * r10456 /bioclipse2/trunk/features/ (12 files in 12 dirs): Update Version to 2.0.0.B20090515
11:13 CIA-40 bioclipse: ospjuth * r10457 /bioclipse2/trunk/plugins/ (17 files in 17 dirs): Update Version to 2.0.0.B20090515
11:14 CIA-40 bioclipse: ospjuth * r10458 /bioclipse2/trunk/plugins/ (18 files in 16 dirs): Update Version to 2.0.0.B20090515
11:14 CIA-40 bioclipse: ospjuth * r10459 /bioclipse2/trunk/ (6 files in 6 dirs): Update Version to 2.0.0.B20090515
11:15 CIA-40 bioclipse: ospjuth * r10460 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (4 files in 2 dirs): Update Version to 2.0.0.B20090515
11:25 olass jonalv: around?
11:25 olass jonalv: did you update any spring jars for the NWO?
11:26 olass it seems the spring jars were originally built using java 1.6
11:26 olass maybe they were before too
11:26 olass so maybe no problem
11:26 olass however
11:26 olass I cannot export right now
11:26 olass no idea why :(
11:26 olass jonalv: ping me when back
11:35 CIA-40 bioclipse: ospjuth * r10461 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Update Version to 2.0.0.B20090515
11:36 jonalv olass: sry trying to eat a little. No I ahve not changed any spring jars. They are what they have been all the time
12:06 jonalv joined #bioclipse
12:38 shk3 joined #bioclipse
12:39 shk3 egonw_: you mentioned that we should run from features
12:39 shk3 I tried again yesterday, but it doesn't work for me
12:39 shk3 if I run from plugins, it's all fine
12:39 shk3 I stick with running from plugins then.
12:40 shk3 I test the speclipse feature with the download version when I export to make sure it runs
12:40 edrin shk3: me too
13:22 CIA-40 bioclipse: shk3 * r10462 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/src/net/bioclipse/spe​ctrum/editor/SpectrumEditor.java: save as has original file set as default
13:26 edrin jonalv: could you find out what's wrong?
13:27 jonalv edrin: I am sort of busy with a dep problem that only shows up when building and not when running from Eclipse...
13:27 shk3 these are tricky problems as well
13:28 shk3 good luck with that
13:28 edrin jonalv: ic
13:28 jonalv shk3, edrin: what problem exactly are you referring to?
13:28 edrin the problem you are working on :)
13:28 shk3 I referred to your dep problem
13:29 shk3 just wanted to express my sincere sympathy with you
13:30 edrin @pz 1070
13:30 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1070
13:31 edrin jonalv: and could you trace this problem
13:31 jonalv edrin: trace?
13:32 jonalv edrin: I am trying to solve it
13:32 jonalv edrin: I ahve a working teori but I am not sure yet...
13:32 edrin jonalv: that's what i mean :)
13:32 jonalv edrin: what do you mean with trace?
13:32 edrin what is your theory?
13:32 rojasm can someone commit to svn.bioclipse?
13:32 rojasm I get this error :
13:32 rojasm svn: MKACTIVITY of '/svnroot/bioclipse/!svn/act/58c67​844-2101-0010-8632-712414b5a29c': 403 Forbidden (https://bioclipse.svn.sourceforge.net)
13:33 jonalv that theSpring core bundle exists in two versions
13:33 edrin rojasm: I had this, too...
13:33 edrin rojasm: your account was disabled
13:33 rojasm oo
13:33 edrin rojasm: ask ola
13:34 jonalv I am trying with upgrading to latest version of spring DM now. It might fix the problems. If not,  at least we have updated to the latest afterwards... :)
13:34 shk3 I have a problem which seems to be caused by new world order.
13:34 shk3 has somebody some minutes to advise on that?
13:34 shk3 not necessarily now
13:34 shk3 later would be fine.
13:34 jonalv I removed all old Spring stuff and there looked like two different naming schemes where there som we might have had two different versions...
13:35 jonalv shk3: maybe you could write a mail about it? Then I can anser when I find time + everyone else can read it as well...
13:35 shk3 sure
13:36 edrin jonalv: interesting
13:39 egonw_ shk3: yes, you should run with features
13:39 egonw_ I mentioned it Wed morning again
13:39 egonw_ because I was still around for helping getting it going
13:39 egonw_ that would have been the time to ask me around it
13:39 egonw_ remote debugging is just trickier
13:39 egonw_ but would love to help make it work for you too
13:40 rojasm olass: could you give access to svn.bioclipse when it is possible? Thanks
13:40 olass ?
13:40 olass rojasm: what you mean?
13:41 rojasm When I try to make a commit I get this error
13:41 shk3 jonalv: email sent
13:41 rojasm svn: MKACTIVITY of '/svnroot/bioclipse/!svn/act/58c67​844-2101-0010-8632-712414b5a29c': 403 Forbidden (https://bioclipse.svn.sourceforge.net)
13:41 olass strange
13:41 olass mom
13:41 rojasm I guess it is because I don't have access
13:41 olass looking at it
13:41 rojasm oo thanks
13:42 olass rojasm: you were right
13:42 olass must have been missed after yesterday's merge
13:42 olass turned it on again
13:42 olass sorry for the inconvenience
13:42 rojasm no worry
13:42 olass should work now I hope
13:43 rojasm perfect thanks
13:44 CIA-40 bioclipse: miguelrojasch * r10463 /bioclipse2/trunk/_playground_/ (9 files in 5 dirs): Added test for MedeaManager class
13:50 shk3 jonalv: I found the loadReactions method in icdkmanager still have a progress monitor.
13:50 shk3 shouldn't that be removed for nwo?
13:50 jonalv shk3: there is another method that does not take an progressmonitor too right?
13:51 * jonalv is not sure how the calling code looks but since both are there the caller can choose....
13:51 shk3 no
13:51 shk3 only with progressmonitor
13:52 olass shk3: please let jonalv focus on the critical export bug
13:52 shk3 ok
13:53 shk3 please have a look at my email if you have time
13:53 CIA-40 bioclipse: miguelrojasch * r10464 /bioclipse2/trunk/_playground_/net.bioclipse.me​dea.test/src/net/bioclipse/medea/business/test/ (MedeaManagerPluginTest.java MedeaManagerTest.java): Changed using SpectrumManager instead of the ISpectrumManager to load Spectra in the test classes. Added test for learning MS
13:55 jonalv I hate logging. My Eclipse refuses to acknowlede jcl104.over.slf4j jar file for me...
13:55 jonalv where cna I cry out? :/
13:59 edrin jonalv: pastebin
14:01 egonw_ gist?
14:01 olass a very big trumpet?
14:02 * egonw_ is now finally booting Eclipse for BC2 manager code clean up for the managers for which he is assigned responsible
14:03 egonw_ will do:
14:03 egonw_ move tests in non plugin test to PluginTest classes
14:03 egonw_ remove the non-plugin ones
14:03 egonw_ update wiki with new statistics
14:03 egonw_ file bug reports for failing tests
14:03 egonw_ fix manager method helps (where not using params="Type foo, Type bar" format, but with description too
14:04 egonw_ and other things I think of later
14:04 jonalv everything has changed name in this new Spring version...
14:04 egonw_ such as:
14:04 egonw_ make a start with writing unit tests based on Jonathan's new wiki pages
14:04 jonalv guys this is gonan take a while to get some order to
14:04 jonalv I just managed to get Bioclispe booting. No managers at all...
14:04 egonw_ jonalv: can you update me on this?
14:05 egonw_ Bioclipse was booting, what has changed?
14:05 jonalv egonw_: Eclipse sucks
14:05 jonalv egonw_: Just because it boots from Eclispe doesn't mnean it can be exported
14:05 jonalv egonw_: When exporting we get strange error
14:05 jonalv egonw_: probably becasue Spring core bnundle exists in multiple versions
14:06 jonalv egonw_: to resolve this I am switching t olatest version of Spring all over
14:06 jonalv egonw_: MUCH has changed in newest Spring version. So things are not working
14:06 jonalv egonw_: that's about it...
14:07 jonalv + the orm bundles used bu structuredb was not in this newest Spring version either so when I am gonna do structuredb I am gonan get all the problems again...
14:08 egonw_ ic
14:08 egonw_ what version was BC2 in SVN using, and how come Ola had a different version?
14:08 jonalv egonw_: huh?
14:08 jonalv egonw_: No there where appharently multiple version in bc svn
14:09 egonw_ ah, ok
14:09 * egonw_ was not aware we had spring in svn
14:09 egonw_ rojasm: ping
14:09 egonw_ rojasm: looked at your last patch
14:09 jonalv egonw_: the jar files are in the target platform. you knew that...
14:09 egonw_ rojasm: but you need to change the way you instantiate the managers, and use ISpectrumManager as type, and the plugins Activator to get a copy for it...
14:10 egonw_ rojasm: shall I make the modifications?
14:10 egonw_ jonalv: the target platform in bioclipse2/ root?
14:10 egonw_ I was not aware there were jars there...
14:10 jonalv egonw_: jars is about all that's there. What did you think it contained?
14:11 egonw_ the config file by which we hit 'Set as target platform'
14:11 egonw_ now that you mention it... I think I actually must have seen the jars...
14:13 egonw_ @tell rojasm ping me when you get back
14:13 zarah Consider it noted.
14:29 edrin cu#
14:29 edrin left #bioclipse
15:31 CIA-40 bioclipse: egonw * r10465 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/ (3 files in 2 dirs): Merged tests from CDKManagerTest into AllCDKBusinessTestsSuite and removed the first (all tests should be run as plugin test)
15:51 edrin joined #bioclipse
15:53 edrin jonalv: did you manage to solve the problem?
15:53 jonalv edrin: no
15:54 edrin hm...
15:55 jonalv mhm, it's tricky to find out what the problem is about since it works perfectly fine to run it from within Eclipse... :(
15:55 edrin indeed...
15:56 edrin does it complain when you try to create the build or when you try to run the build
15:57 edrin jonalv: maybe it could help to checkout bc in a new installed eclipse/empty workspace?
15:57 jonalv edrin: in what way would that help?
15:57 edrin jonalv: i have notice strange errors that I could not solve until i did this
15:57 jonalv okey
15:57 edrin i still don't know why this helped me several times...
15:58 jonalv well I might give that a try on monday when nothing else works
15:58 edrin ok
15:58 jonalv I need to leave in a couple of minutes now anyway
15:58 edrin what must i click to create a build and where does the error occur ?
15:59 edrin jonalv: sorry, we have dinner now
15:59 edrin cu
17:26 CIA-40 bioclipse: shk3 * r10466 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): adopted reaction methods to nwo by removing progress monitors, added empty constructor to cdkreaction
17:35 CIA-40 bioclipse: shk3 * r10467 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (4 files in 3 dirs): synchronisation of tabs and save/save as works, except update of reactioneditor page, still nwo problem there.
17:48 CIA-40 bioclipse: egonw * r10468 /bioclipse2/trunk/plugins/ (8 files in 5 dirs):
17:48 CIA-40 bioclipse: Updated unit testing framework for the NWO.
17:48 CIA-40 bioclipse: * refactored to use a AbstractBioManagerFramework that allow getting the manager and its interface
17:48 CIA-40 bioclipse: * API unit testing is no longer done by a manager test class, but cannot done in plugin manager,
17:48 CIA-40 bioclipse:  so in a new APITest class
17:48 CIA-40 bioclipse: * removed the empty AbstractNewWorldOrderManagerTest
18:42 CIA-40 bioclipse: egonw * r10469 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Fixed params='' fields (and some whitespace clean up)
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