Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-03

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All times shown according to UTC.

Time Nick Message
05:26 CIA-22 bioclipse: carl_masak * r5326 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java:
05:26 CIA-22 bioclipse: [JsConsoleView.java]
05:26 CIA-22 bioclipse: * "assimilated" method helpString
05:26 CIA-22 bioclipse: ** changed the name
05:26 CIA-22 bioclipse: ** removed some braces
05:26 CIA-22 bioclipse: ** added some empty lines
05:26 CIA-22 bioclipse: ** added a few preconditions
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08:04 jonalv Biomoby doesn't compile now. olas?
08:06 CIA-22 bioclipse: jonalv * r5327 /bioclipse2/trunk/plugins/net.bioclipse.​usermanager.tests/tests/net/bioclipse/us​ermanager/business/UserManagerTest.java: userManager.signOut -> userManager.logOut
08:14 egonw joined #bioclipse
08:15 jonalv hi egonw
08:19 CIA-22 bioclipse: ospjuth * r5328 /bioclipse2/trunk/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/services/DownloadSimpleMoby.java: Removed unused dependencies
08:19 olas hi egonw
08:19 olas how did your defence go?
08:24 egonw good
08:24 egonw we are now setting up our laptops for the CDK/chemometrics/metabolomics unconference
08:24 egonw kindly hosted at my old department
08:24 de_maas joined #BIOCLIPSE
08:25 CIA-22 bioclipse: jonalv * r5329 /bioclipse2/trunk/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/services/DownloadGenbankMoby.java: cleaned up imports and removed an unused reference to a class that my setup can't find)
08:26 jonalv egonw, sounds cool :)
08:26 egonw yeah, I hope so...
08:27 jonalv egonw, I know that you are always very busy and such but could you take a quick look at the data model for net.bioclipse.structuredb some time? I just want to know what you think and if something more could be needed...
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08:29 egonw jonalv: yeah, sure... please email me some details...
08:29 CIA-22 bioclipse: ospjuth * r5330 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/core/jobs/ActionJobWrapper.java: Updated with getter and setter for wrapped job.
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09:13 CIA-22 bioclipse: carl_masak * r5331 /bioclipse2/trunk/plugins/net.biocl​ipse.ui/src/net/bioclipse/ui/views/ (JsConsoleView.java ScriptingConsoleView.java):
09:13 CIA-22 bioclipse: [JsConsoleView.java]
09:13 CIA-22 bioclipse: * changed visual aspect of help strings
09:13 CIA-22 bioclipse: [ScriptingConsoleView.java]
09:13 CIA-22 bioclipse: * opened up MAX_OUTPUT_LENGTH to be protected
09:13 CIA-22 bioclipse: * note to self: this type of constant should probably be
09:13 CIA-22 bioclipse:  protected (or wider) from the start
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09:44 CIA-22 bioclipse: jonalv * r5332 /bioclipse2/trunk/plugins/net​.bioclipse.structuredb.tests/ (.classpath META-INF/MANIFEST.MF build.properties): added junit4 dependency
09:46 edrin joined #bioclipse
09:46 edrin hi
09:46 jonalv hi edrin
09:47 edrin hi jonalv
09:52 EskilA joined #bioclipse
09:57 edrin left #bioclipse
09:57 CIA-22 bioclipse: jonalv * r5333 /bioclipse2/trunk/plugins/net​.bioclipse.structuredb.tests/ (4 files in 3 dirs): Quick and dirty fix to my logging problems. I don't think this is the best way to go...
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12:12 CIA-22 bioclipse: carl_masak * r5334 /bioclipse2/trunk/plugins/net.bioclipse.us​ermanager/src/net/bioclipse/usermanager/pr​eferences/UserManagerPreferencePage.java:
12:12 CIA-22 bioclipse: [UserManagerPreferencePage.java]
12:12 CIA-22 bioclipse: * the "Delete" button was incorrectly sized
12:12 CIA-22 bioclipse: * fixed that
12:25 steinbeck__ joined #bioclipse
12:26 edrin hello egonw
12:26 edrin how was your defense?
12:27 egonw good
12:37 edrin egonw: so you are Doktor Egon now?
12:40 CIA-22 bioclipse: carl_masak * r5335 /bioclipse2/trunk/plugins/net.bioclipse.usermanag​er/src/net/bioclipse/dialogs/EditUserDialog.java:
12:40 CIA-22 bioclipse: [EditUserDialog.java]
12:40 CIA-22 bioclipse: * fixed bug #1932019
12:50 steinbeck__ joined #bioclipse
12:55 edrin egonw: anyway, congratulations :)
12:55 egonw oh, sorry...
12:55 egonw we're having a CDK unconference here...
12:55 egonw and got distracted
12:56 egonw yes, herr doktor jetz
13:30 EskilA congratulations, or as we say in #farmbio egonw++
13:38 egonw thanx
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13:53 CIA-22 bioclipse: jonalv * r5336 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): Made all written dao tests pass
14:01 olas nice!
14:01 olas time to write some more?
14:02 olas :-)
14:05 jonalv hehe
14:05 jonalv I realised that timestamping on auditing shouldn't be made in java by the client
14:05 jonalv it should be made in sql by the server
14:05 jonalv so I a going to try to change tha now
14:06 olas right
14:06 jonalv or should it?
14:06 jonalv hm..
14:07 jonalv that's not great either because that would mean that those fileds where nyll untill the object has been saved and reloaded...
14:08 jonalv I might just leave it...
14:08 jonalv What say you olas?
14:08 olas hmm
14:08 olas leave it for now
14:08 olas make a note
14:08 olas it's clearlyu not a prioritized task
14:08 olas file an RFE?
14:09 jonalv RFE?
14:12 olas Feature request
14:12 olas on SF
14:13 jonalv yea
14:13 olas hmm
14:13 olas Request For fEatures?
14:13 jonalv lol
14:20 jonalv I think someonw should go through all bugs directed to bioclipse 1 and close them and mark them as won't fix. What do you think?
14:20 egonw request for enhancement
14:21 egonw jonalv: or, postponed to bc2
14:21 egonw depending on the nature of the report
14:21 jonalv exactly if that would be possible
14:21 olas yes, I will do that
14:21 egonw or, close with 'fixed in bc2'
14:21 jonalv sure if that's the case yea :)
14:21 olas been thinking of that for some time
15:18 CIA-22 bioclipse: jonalv * r5337 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKChemFile.java CDKMolecule.java ICDKMolecule.java): olas++ came over and wrote ICDKMolecule from my computer
15:19 CIA-22 bioclipse: jonalv * r5338 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: forgot to commit...
15:21 rklancer joined #bioclipse
15:21 rklancer hi all
15:21 jonalv hi
15:21 rklancer hi jonalv...
15:22 rklancer I saw your frustration this morning, just sent you an email, hope it helps
15:23 jonalv I am not running osgi stuff when runnign these tests you know...
15:23 rklancer yeah i thought of that later
15:24 rklancer but it is one way to resolve the problem. Much simpler to check the "clear configuration area" checkbox, though
15:25 rklancer sorry it was 6 in the morning at the time, so I hope I'm forgiven if I didn't work that out in my head quick enough :)
15:25 jonalv there is no such tab for running JUnit tests...
15:25 rklancer ? let me check
15:26 jonalv I am happy for all help I can get :)
15:26 rklancer is the test working for you now or is this exception still a problem?
15:26 jonalv no exception for the moment but no logging eihter...
15:27 rklancer because of the slf4j.simple fix?
15:28 jonalv I can't run the tests right now ( borken code) but yea probably
15:28 jonalv or rather before that fix nothing worked...
15:29 jonalv running tests now...
15:29 jonalv I get the: WARN No appenders could be found
15:30 rklancer huh. I'm not getting the usual "junit test" option when I right click and select "run as..."
15:30 jonalv not?
15:30 jonalv what do you get? :)
15:31 rklancer run as... gives on option, "open run dialog"
15:31 rklancer pfft. as I've said I'm not sure how eclipse, pde, and junit work together, yet.
15:31 jonalv no, who is?
15:38 jonalv so you can't even run the tests?
15:39 rklancer yeah, strange..
15:39 jonalv and you are clicking the net.bioclipse.structuredb.tests project?
15:39 rklancer ok, I'm quitting and running eclipse -clean
15:39 rklancer always helps get the gremlins out :)
15:39 jonalv hehe
15:40 rklancer okay, I have the structuredb.tests project open, and opened up GenericDaoTest.java in my editor
15:41 rklancer right clicking on any of the test methods in the Outline view (or in the editor itself) gives me a "run as..." submenu with just one option, "Open Run Dialog"
15:41 rklancer hmm.
15:42 jonalv are you lacking some JUnit component?
15:45 rklancer well I wasn't the day before yesterday :(
15:46 jonalv hum can you run any other junit tests or?
15:47 rklancer worth asking
15:47 rklancer and of course the answer is yes
15:47 * rklancer smacks forehead
15:50 jonalv okey what was the great wisdom here? :)
15:50 rklancer nothing yet
15:50 rklancer but i'll tell you my hunch regarding the test
15:50 jonalv but you can run it now?
15:51 rklancer no, i think I'll take a few minutes to figure out the difference between structuredb.tests and other tests plugins
15:52 jonalv okey, /me wasn't even aware there was one...
15:56 CIA-22 bioclipse: jonalv * r5339 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (business/IStructuredbManager.java domain/Structure.java): the structuredb domain object Structure now implements IMolecule
15:57 CIA-22 bioclipse: jonalv * r5340 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/core/domain/ (IMolecule.java SmilesMolecule.java): olas++ came over and wrote some stuff from my computer
16:18 rklancer jonalv...
16:18 rklancer i was able to force a test to run. Do you run it by right-clicking and selecting "run as Junit Plug-in test"?
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16:27 rklancer anyway, if you do, I think if you scroll past "Run as Junit" stuff to "Open Run Dialog", then check the "clear config area" under the configuration tab (which should show up) then you should clear out the gremlins.
16:27 rklancer after removing slf4j.simple, of course
16:27 rklancer my hunch as to why your config got hosed, I couldn't reproduce
16:27 rklancer hello EskilA
16:28 EskilA hello
16:28 jonalv no I am not running JUnit plugin-in test
16:28 rklancer are you using the junit view?
16:28 jonalv I am running as junit test only
16:29 rklancer oh okay
16:29 rklancer hmm
16:29 rklancer aha
16:29 rklancer that does it...
16:29 rklancer ALTER TABLE Structure ADD FOREIGN KEY (library)    REFERENCES Library(id);
16:29 rklancer SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
16:29 rklancer SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
16:31 jonalv yea I saw that too
16:31 jonalv well I need to go...
16:32 jonalv sorry for not being very much help in this...
16:34 jonalv although it's actually me that needs help :)
16:34 jonalv anyway gtg
16:34 jonalv cya
16:35 rklancer (I fixed it...)
16:39 CIA-22 bioclipse: rklancer * r5341 /bioclipse2/trunk/plugins/net​.bioclipse.structuredb.tests/ (.classpath META-INF/MANIFEST.MF build.properties):
16:39 CIA-22 bioclipse: Fix for jonalv's test difficulties. (I hope.) Removed slf4j.api from
16:39 CIA-22 bioclipse: require-bundle headers in manifest. This was already resolved by the
16:39 CIA-22 bioclipse: import-package org.apache.commons.logging and apparently the osgi framework
16:39 CIA-22 bioclipse: didn't like seeing both. Removed previous slf4j.simple quickfix.
16:50 rklancer gtg...
17:39 CIA-22 bioclipse: rklancer * r5342 /bioclipse2/trunk/plugins/net​.bioclipse.structuredb.tests/ (.classpath META-INF/MANIFEST.MF build.properties): Not so fast. The "fix" I committed in r5341 isn't a fix at all. Still investigating...
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