Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-02-15

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Time Nick Message
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07:50 CIA-91 bioclipse.data: Egon Willighagen master * rfa50a9d / (4 files): Added an update site - http://bit.ly/eo8C0R
07:53 CIA-91 bioclipse.data: Egon Willighagen master * r6eb6d65 / (8 files in 2 dirs): Renamed the update site, removing the .extra - http://bit.ly/euux0v
07:58 CIA-91 bioclipse.data: Egon Willighagen master * r69f540f / features/net.bioclipse.data_site/feature.xml : Removed the dependency for now - http://bit.ly/gyIonL
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09:25 egonw impressed with the progress of the egit plugin
09:26 egonw wondering though how to push commits to a remote repos
09:29 * egonw is trying to figure out how to update .cquery and/or .rmap files to make buckminster aware where to find the statistics feature
09:30 CIA-91 bioclipse.core: jonalv master * r15b605c / (5 files in 4 dirs):
09:30 CIA-91 bioclipse.core: global replace "s/Bioclispe/Bioclipse/g;"
09:30 CIA-91 bioclipse.core: Hm, maybe this should be done in all repos? It's a bit too easy to spell Bioclipse Bioclispe... :( - http://bit.ly/gcbAOD
09:30 egonw jonalv++
09:31 Gpox jonalv++
09:31 jonalv I like the easy karma++
09:31 jonalv me++
09:31 egonw oh, I got more then :)
09:31 egonw there is cheap #cdk karma too...
09:31 egonw but for bioclipse:
09:31 egonw http://pele.farmbio.uu.se/hudson/​job/Bioclipse.core/60/consoleText
09:32 egonw search that file for "Warning:"
09:32 jonalv wow :)
09:32 egonw or start with a search for MANIFEST.MF
09:32 egonw then you onlt get the configuration issues
09:33 * jonalv goes back to lab repports
09:33 egonw like: Warning: file /home/hudson/jobs/Bioclipse.core/workspace/extern​als/com.thaiopensource.jing/META-INF/MANIFEST.MF, line 10: The 'Eclipse-AutoStart' header is deprecated, use 'Bundle-ActivationPolicy'
09:33 egonw jonalv--
09:33 * jonalv might be procrastinating lab repports
09:33 jonalv egonw: procrastination can be good? right?
09:33 jonalv :)
09:34 egonw yeah, but not always good for the procrastinator
09:34 jonalv true
09:34 egonw particular if the procrastinator needs a thesis or a Nature Foo publication
10:10 Gpox egonw: http://pele.farmbio.uu.se/cgi-bin/gitwe​b.cgi?p=buckminster-pele.git;a=summary
10:10 zarah Gpox's link is also http://tinyurl.com/6kwolhx
10:11 Gpox http://pele.farmbio.uu.se/buckmin​ster-web/p2/LastSuccessfulBuild/ this is a agregated site for some of the hudson builds
10:11 egonw oh, cool!
10:12 egonw Gpox++ (for doing the aggregation site!)
10:12 egonw it's not yet created on Hudson, or is it?
10:12 Gpox pleas use the git repo for updating cquerys and rmaps
10:13 jonalv Gpox++
10:13 jonalv Gpox++
10:13 egonw Gpox++
10:13 zarah Gpox++
10:13 jonalv I can make Gpox++ machine go bing
10:13 jonalv oh not now :(
10:14 jonalv ob by the way: Bing is probably a trademark of Microsft corporation
10:14 egonw Gpox: can we make /var/www/buckminster-web a git checkout?
10:15 egonw or should I push to the repos? but then how can I make quick changes and test them?
10:16 Gpox it is magic (or a post-receive hook)
10:16 egonw well done!
10:17 egonw should we not move this repos to GitHub, or is there sensitive info?
10:17 Gpox it is verry pele specific
10:18 Gpox in the future the nessesary rmap and cquery probably should reside in thier respectiv git repo
10:23 egonw ok
10:23 egonw cloning
10:38 egonw Gpox: OK, giving it a spin now... for bioclipse.social
11:27 sneumann is now known as sneumann_
11:34 egonw mmm... that's a less common nick change
11:35 egonw @tell jonalv can you please check of bioclipse.pharmbio and bioclipse.social are registered with the CIA ?
11:35 zarah Consider it noted.
11:38 CIA-91 bioclipse.social: Egon Willighagen 2.4.x * ra3625fb / (4 files): Added an update site - http://bit.ly/ff8Glp
11:38 CIA-91 bioclipse.social: Egon Willighagen master * r9a5e63f / plugins/net.bioclipse.myexperiment/src/net/bioclip​se/myexperiment/business/MyExperimentManager.java : Updated for the move of IStringMatrix from rdf to core - http://bit.ly/i6kwHZ
11:38 CIA-91 bioclipse.social: Egon Willighagen master * r824ad0f / (2 files in 2 dirs): Import rather depend on JUnit - http://bit.ly/f3zjzD
11:38 CIA-91 bioclipse.social: Egon Willighagen master * r3733093 / (5 files in 5 dirs): Merge branch '2.4.x' - http://bit.ly/etVJnK
11:38 CIA-91 bioclipse.social: Egon Willighagen master * ra3625fb / (4 files): Added an update site - http://bit.ly/ff8Glp
11:38 CIA-91 bioclipse.social: Egon Willighagen master * rbcbfc53 / (4 files): Added an update site - http://bit.ly/hq5KV2
12:18 egonw I just love to see Hudson in action :)
12:18 egonw how it works it way through recompiling all jobs
12:19 egonw Gpox: we might need to consider build dependencies...
12:19 egonw something that depends on the RDF functionality...
12:19 egonw should it depend on bioclipse.rdf or bioclipse.test.rdf ?
12:19 egonw the latter might in fact make sense
12:20 egonw only if no regressions are found should downstream projects be recompiled... right?
12:29 egonw @tell Gpox do you also have a good back up approach for all the hudson configuration?
12:29 zarah Consider it noted.
12:32 CIA-91 bioclipse.chembl: Egon Willighagen master * rea9e3dd / features/net.bioclipse.chembl_feature/feature.xml : Also depends on the MOSS feature - http://bit.ly/hw1Jsx
12:51 egonw when I boot bioclispe from eclispe I get tons of OSGi message now...
12:51 egonw how do I silence that?
12:53 Gpox logback.xml
12:53 zarah Gpox: You have new messages. Write '/msg zarah @messages' to read them.
12:54 Gpox -Dlogback.configurationFile​=/path/to/logback-test.xml
12:54 egonw Gpox: oh, that sounds familiar ...
12:54 Gpox http://logback.qos.ch/manual/joran.html
12:55 egonw like -Dlogback.configurationFile=/ne​t.bioclipse.logback/logback.xml ?
12:56 Gpox no if you want to override stuff in logback.xml but don't whant them to get commited by mistake
12:57 egonw like -Dlogback.configurationFile=/net.b​ioclipse.logback/logback-egon.xml then?
12:57 egonw as VM argument?
12:58 Gpox yes to run configuration that you start bioclipse with
12:59 egonw mmm... is there a wiki page about this?
12:59 egonw zarah: do you have @wiki powers?
12:59 zarah egonw: I'm just a bot, you expect me to understand that?
13:00 Gpox probably not
13:00 egonw zarah: to search bioclipse wiki pages?
13:00 zarah egonw: eh... wha'?
13:00 jonalv zarah: I have a feeling egonw things you should be able to searc hthe bioclispe wiki
13:00 zarah jonalv: Hokay. You provide the commits, I provide the "should"-ing
13:00 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
13:01 jonalv @massage
13:01 zarah jonalv: 1 h 25 m 52 s ago, egonw said can you please check of bioclipse.pharmbio and bioclipse.social are registered with the CIA ?
13:02 jonalv egonw: yup they are listed
13:02 jonalv egonw: are they not working?
13:03 egonw social is in fact...
13:03 egonw pharmbio not sure yet...
13:03 egonw did not see the commits earlier
13:04 egonw jonalv++ (for checking, tahxn!)
13:05 jonalv karma
13:05 zarah jonalv has a karma of 271
13:05 egonw karma
13:05 zarah egonw has a karma of 204
13:05 egonw olass: just ignore
13:08 egonw Gpox: and how do I need to tune that file to not see those OSGi messages?
13:08 egonw I changed at line 32 INFO -> WARN
13:08 egonw but that did not help
13:09 Gpox <logger name="package" level="ERROR" />
13:10 olass karma
13:10 zarah olass has a karma of 140
13:10 egonw like line 27
13:10 egonw ?
13:10 olass :(
13:10 olass karma olas
13:10 zarah olas has a karma of 51
13:10 olass *morr*
13:12 egonw argh...
13:12 egonw of course i have to put logback-egon.xml in the bundle binary too
13:14 egonw Gpox: so, where do I add the -D optino then? VM Arguments, right?
13:15 Gpox product or run configuration that is run
13:15 egonw bioclipse.product -> Launching tab -> VM Arguments ?
13:15 egonw that's where I placed it...
13:16 Gpox try renaming it logback-test.xml
13:18 egonw bope
13:18 egonw nope
13:20 egonw 14:20:50,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [/net.bioclipse.logback/logback-test.xml]
13:20 egonw 14:20:50,899 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback-test.xml] at [bundleresource://2.fwk170​07273:1/logback-test.xml]
13:20 Gpox full path maybe
13:20 egonw 14:20:51,004 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.springframework] to ERROR
13:20 egonw 14:20:51,004 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting additivity of logger [org.springframework] to true
13:21 egonw so, it does pick it up
13:21 egonw and sets the springframework to ERROR
13:21 egonw but I still get them :(
13:23 egonw the format also seems different...
13:24 egonw so, Spring is using a different logging approach, so that the logback settings are not applicable?
13:25 Gpox might be a missing bundle try to find and include slf4j ... Log4j bridge
13:25 Gpox it might be missing
13:27 egonw log4j.over.slf4j?
13:28 egonw that's included as plugin in the core_feature
13:35 egonw Gpox: there are still a few logger.properties in bioclipse plugins
13:35 egonw can that cause havoc?
13:36 egonw adding to all of them:
13:36 egonw log4j.logger.org.springframework=FATAL
13:37 egonw nothing helped :/
13:58 Gpox compare to the headless branch jonalv enabeld more logging there for spring for troubleshooting
14:06 egonw https://github.com/bioclipse/biocli​pse.core/blob/HEADLESS/plugins/net.​bioclipse.logback/src/logback.xml ?
14:15 * egonw is annoyed... I know this used to work for me too in the past :/
14:35 Gpox egonw: searchf or a logback-test.xml if that is on the classpath it will be picked up before the logback.xml, but I think the property should override them all
14:36 Gpox open 'Run Configurations' and check that the property is set there for the bioclipse configuration
14:37 egonw the log indicates it is found
14:37 egonw and that it sets org.springframework to WARN
14:37 egonw but still it shows INFO messages
14:37 egonw do you want to check the full log?
14:38 Gpox it might help, I have not time to run bioclipse right now. But I could take a look at the log and see if I notice anythin od
14:39 egonw https://gist.github.com/827596
14:50 Gpox egonw: org.springframework.osgi.extender.internal] to ERROR . Try to set org.springframework osgi.extender.internal seams to specific
14:50 egonw sure :)
14:51 egonw I listed org.springframework first
14:51 egonw but then I though that maybe the problem was that it was not recursive ...
14:51 Gpox and it might be picking up some other logback-test.xml
14:51 egonw hence the specific one
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15:30 CIA-91 org.openscience.cdk: Egon Willighagen bioclipse2.6 * r7a3a431 / (2 files): Proper initialization at the primary renderer too. Commited upstream as: https://github.com/egonw/cdk/commit/d1​63bb2d36aeb31830813e1cf66facf16d787435 - http://bit.ly/hwBtSb
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19:17 samuell My SWT widgets won't keep their size even thouch I do textField.setSize(240, 32);
19:17 samuell :(
19:17 samuell (etc ...)
19:20 egonw :)
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19:32 * samuell solved it!
19:35 egonw samuell++
19:41 samuell :)
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20:40 ydgin Hi, Sonya
20:40 Sonya Hi :)
20:41 ydgin is now known as Evgeny
20:44 Evgeny Hello, everybody
20:46 Evgeny Egon and Ola told me about that channel. And if my questions shouldn't be here - tell me please where I can find the answers :)
20:47 Evgeny The first one may be sounds quit strange, but... Does anybody created the new atom type able to show in Jmol?
20:49 Evgeny And another one from Sonya )
20:51 Sonya Um... that was unexpected :) The question is: why are there two essentially parallel hierarchies of interfaces in CDK and bioclipse (IMolecule etc), and how do I convert from one to another - if, for example, I have a bioclipse Molecule, and want to get a CDK AtomContainer.
20:54 Evgeny We know about the CDKMolecule (to convert from CDK to Bioclipse) and ability of conversion from Bioclipse to CDK through CML. But is it clear?
21:01 jonalv Sonya: to get the atomcontainer just use the getAtomContainer method on CDKMolecule
21:02 jonalv or have I missed something?
21:05 Sonya left #bioclipse
21:05 jonalv Evgeny: she left? :(
21:06 Evgeny I think till morning )
21:06 jonalv oki
21:06 jonalv zarah: tell Sonya  to get the atomcontainer just use the getAtomContainer method on CDKMolecule, or have I missed something?
21:06 zarah Consider it noted.
21:09 Evgeny I think Sonya can use IAtomContainer to convert from Bioclipse molecule to CDK one, thanks!
21:10 jonalv Evgeny: the CDKMolecule is basically just a wrapper around an AtomContainer
21:14 Evgeny So, it is quit simple to make a CDK molecule from Bioclipse one using CDKMolecule(molecule)
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21:15 Evgeny And for Bioclipse IMolecule molecule from CDK IMolecule one should use getAtomContainer and the corresponding constructor...
21:16 jonalv_ uhm, I lost connection for a while
21:17 jonalv_ I don't have the code infont of me right now
21:17 Evgeny Ok. And Sonya asked about the necessity of IMolecule hierarchy both in CDK and Bioclipse. The question is why not to use all Molecules from CDK extending them if needed?
21:20 Evgeny Maybe such a question is difficult or silly, but in a few words?
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22:02 olass Evgeny: still there?
22:04 olass Bioclipse domain objects are interfaces which are general, and CDK is just one possible implementation of the bioclipse IMolecule
22:04 olass that they have the same name is pure coincidental
22:05 olass in principle you could have e.g. a JoelibMolecule implementation of a bioclipse.IMolecule
22:06 olass there is a SMILESMolecule, which is the most simple implementation of a net.bioclipse.IMolcule
22:06 olass if you need more cheminformatics functionality, go for the CDKMolecule (which is the CDK implementation of net.bioclipse.IMolecule)
22:06 olass hop this helps
22:06 * olass is going to bed now
22:06 olass by
22:07 olass bye
22:07 Evgeny Ok, bey
22:07 Evgeny bye :)
22:07 olass :)
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