Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-12-11

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
05:52 masak joined #bioclipse
06:11 egonw joined #bioclipse
07:24 CIA-60 bioclipse.core: Egon Willighagen 2.2.x * rc15522f / (1269 files in 127 dirs): Added Xerces 2.9.0 as bundled by the Eclipse Orbit project - http://bit.ly/4OjHe1
07:45 Gpox joined #bioclipse
08:05 sneumann joined #bioclipse
08:14 egonw moin
08:14 zarah ni hao egonw
08:14 * egonw is writing unit tests for the Pellet plugin for Bioclipse
08:15 egonw anticipating an upgrade to Jena 2.6.2 with matching Pellet and TDB
08:29 olass joined #bioclipse
09:20 olass egonw: how did teh Xerces problem go?
09:20 egonw dunno
09:20 olass I see that as the only blocker for RC3..
09:20 egonw did you get my email about unit tests?
09:20 egonw I'm working on it though
09:20 olass yes
09:21 egonw struggling with the ever nasty classpath eclipse cleaning
09:29 egonw snow predicted for tomorrow ... nice :)
09:30 * olass wants clear skies for his bandy game
09:30 egonw :)
09:30 egonw giving up...
09:30 egonw will set up a separate ARQ plugin then :(
09:31 egonw blah
09:31 egonw and I was so much hoping to finish the installation of Hudson on Pele today :(
09:37 egonw and my bloody 3G connection is so bloody slow now and then :(
09:38 egonw more now, than then, lately :(
10:02 sneumann <egonw> and I was so much hoping to finish the installation of Hudson on Pele today :(
10:03 sneumann Over here it was merely dropping the war in place ...
10:03 egonw right
10:03 egonw I also need to set up the proxy
10:03 egonw it's not much work
10:03 egonw but has lower priority
10:47 olass egonw: ping
10:49 olass egonw: my bioclipse.cheminformatics is not matching upstream bioclipse.cheminformatics. How can this happen? If I do pull "upstream 2.2.x", it says: "already up to date" but "git log" says differently...
10:49 egonw no sure...
10:49 egonw if you have nothing special in your branch, you could make a fresh branch
10:49 olass how can I tell if all my commits are present in upstream?
10:50 olass egonw?
10:51 egonw good question...
10:51 egonw you could run a grep
10:51 egonw mom
10:52 olass hmm
10:52 egonw see: http://gitster.livejournal.com/30195.html
10:52 zarah egonw's link is also http://tinyurl.com/yeav4nf
10:52 olass how about "git log 2.2.x..upstream/2.2.x" ?
10:52 egonw yes, but I thought you said that was not in agreement with 'git update'?
10:53 egonw so, I would not use that approach myself then
10:53 olass what is 'git update' ?
10:53 olass I use 'git pull'..
10:53 egonw that's what I meant
10:53 olass hmm..
10:54 olass egonw: did you apply my patches with updated copyright headers?
10:54 egonw yes, I did
11:17 egonw OK, factored out ARQ
11:17 egonw the RDF manager tests run again
11:17 egonw next up: Pellet
11:19 * egonw is downloading Pellet 2.0 which will take some 20 minutes, so getting lunch and more coffee
11:19 egonw make that 30 mins :(
11:32 egonw 15mins left
11:39 olass egonw: 15 mins lunch + 15 mins coffee?
11:40 egonw lunch is done, coffee half way...
11:40 egonw 25% left to go for the Pellet download :)
11:40 egonw so, things are on schedule :)
11:40 olass :)
12:14 samuell joined #bioclipse
12:28 egonw grmp...
12:38 egonw for no apparent reason the plugin unit test suites do not run anymore
12:39 egonw log4j not found ??
12:44 masak it's always logging, isn't it.
12:44 egonw "Multiple problems have occurred" ...
12:44 egonw lovely...
12:45 egonw one is that Eclipse seems to hang now :)
12:45 egonw so, I can't even see *what* the other problems are :)
12:47 masak egonw: they are beyond the Turing event horizon. :P
12:47 egonw so is the RC3 release
12:47 masak yup.
12:48 jonalv joined #bioclipse
12:49 egonw Bioclipse cited in: "ENFIN - A European network for integrative systems biology" in COMPTES RENDUS BIOLOGIES
12:50 egonw samuell: you might find interesting: http://www3.interscience.wiley.com/journal​/122582072/abstract?CRETRY=1&amp;SRETRY=0
12:50 zarah egonw's link is also http://tinyurl.com/y977tb2
12:50 masak \o/
12:53 egonw my 2010 goals: H-index=9, first paper with 100 citations
12:53 * egonw tries another time to reset target platform
12:54 samuell egonw: Session Cookie Error
12:54 samuell problem with the link ...
12:54 egonw DOI: 10.1002/mrc.2512
12:54 egonw so, try:
12:54 egonw http://dx.doi.org/10.1002/mrc.2512
12:54 zarah egonw's link is also http://tinyurl.com/y92qhte
12:55 samuell egonw: Cool, thanks! :)
12:57 egonw grpmh...
12:57 egonw resetted target platform...
12:57 egonw and now I get a red cross on the xerces bundle
12:58 egonw indicating I need to put a few more plugins from Eclipse Orbit into bioclipse.core/externals ...
13:01 egonw ok, resetting target platform once more
13:03 egonw I think I opened Pandora's box
13:18 masak I hate when that happens.
13:28 egonw well, it beats the LHC black holes
13:31 egonw :(
13:32 masak on #perl6 yesterday, people theorized that if LHF is an acronym for 'Low-Hanging Fruit', then LHC should mean 'Low-Hanging Chocolate'. :)
13:33 egonw no, I think, it strictly speaking an acronym for French of 'Low-Flying Birds', IIRC :)
13:33 egonw or low-flying bird-droppings or so...
13:33 egonw something like that
13:33 egonw but my french is a bit rusted
13:33 egonw meanwhile...
13:33 egonw still no functional plugin test suites :(
13:34 egonw OK, going to get some fresh air first now...
13:35 egonw before I start smashing in windows
13:35 egonw and yelling at Eclipse
14:00 egonw ok, getting fresh air did not magically solve the log4j not found
14:00 olass Gpox: can you run the plugin unit test egon is trying to run?
14:27 olass egonw: how do I delete a pushed branch on github from command line?
14:28 egonw add a : in front of the branch name
14:28 olass git push origin :toremove ?
14:28 egonw right
14:28 olass thx
14:28 * egonw is getting missing bundles for net.bioclipse.webservices
14:29 olass what bundles?
14:29 egonw javax.mail
14:29 egonw and
14:29 egonw javax.activation
14:29 egonw are those really needed?
14:29 olass there was a bug about this..
14:29 egonw they are in Orbit, I think
14:29 olass my Eclipse picks them up from teh Eclipse plugins
14:29 egonw I can add them
14:30 olass what is Orbit?
14:30 egonw to bioclipse.core/externals
14:30 olass might be a good idea..
14:30 olass give it a try
14:30 egonw an Eclipse subproject to bundle third party libs
14:30 egonw OK
14:30 * olass don't mind as it will not affect file size; they are already bundled with an export anyway
14:31 egonw indeed
14:31 egonw btw...
14:31 olass egonw: you are still struggling with the Xerces problem?
14:31 egonw Mark made a platform independent InChI library...
14:31 egonw olass: yes, I am
14:31 olass ading the xerces to externals did not solve things?
14:31 egonw well... the xerces problem seems solved
14:31 egonw but
14:31 egonw the tests no longer running, I cannot verify it really, really works
14:32 egonw so, struggling with confirming that the xerces problem is fixed :)
14:32 olass :)
14:32 olass have you pushed?
14:32 egonw yes, that did seem to solve the problem
14:32 egonw no, waiting for this confirmation
14:32 egonw last thing i want is to not just brake my environment
14:32 egonw but that of everyone :)
14:32 egonw break
14:32 egonw not brake
14:32 olass sounds good
14:45 CIA-60 bioclipse.structuredb: jonalv master * r3fe29ad / (13 files in 8 dirs): SQL query for properties names, also table indexes - http://bit.ly/7XvhWu
14:46 CIA-60 bioclipse.core: Egon Willighagen 2.2.x * re26a818 / (516 files in 73 dirs):
14:46 CIA-60 bioclipse.core: Added javax.xml and javax.activation from the Eclipse Orbit project,
14:46 CIA-60 bioclipse.core: required by the core feature, but not in a core Eclipse 3.5 download - http://bit.ly/6S4y2L
14:46 egonw @pz javax.mail
14:46 zarah egonw: I couldn't find anything on 'javax.mail' in the database.
14:46 egonw @pz javax mail
14:46 zarah egonw: Zarro boogs found.
14:47 egonw olass: do you remember if that problem was filed in pelezilla?
14:47 olass sorry, don't remember
14:48 egonw no worries
14:48 olass judging from your query it seems not
14:48 egonw indeed
14:48 egonw and if there is a report, it will show up at some time
14:48 egonw ok, another attempt to run the plugin test unit suite
14:49 egonw unit test plugin suite
14:49 egonw test suite unit plugin
14:49 egonw something like that
14:51 egonw argh.....
15:06 egonw ok, back to the xerces problem
15:11 egonw and fixed again
15:11 egonw back to the log4j problem
15:12 egonw ok, pushing xerces now
15:13 CIA-60 bioclipse.core: Egon Willighagen 2.2.x * r218003c / (473 files in 63 dirs): Added javax.xml 1.3.4 from the Eclipse Orbit project - http://bit.ly/7888UE
15:13 CIA-60 bioclipse.core: Egon Willighagen 2.2.x * r6582d97 / (167 files in 15 dirs): Added org.apache.xml.serializer 2.7.1 from the Eclipse Orbit project - http://bit.ly/5X02jU
15:13 CIA-60 bioclipse.core: Egon Willighagen 2.2.x * ra4a0e7a / (102 files in 23 dirs): Added org.apache.xml.resolver 1.2.0 from the Eclipse Orbit project - http://bit.ly/4XHL38
15:14 CIA-60 bioclipse.core: Egon Willighagen 2.2.x * r5be0aff / (792 files in 193 dirs): Removed CVS folders - http://bit.ly/6ApWk2
15:26 olass egonw: ping
15:27 egonw pong
15:27 olass I thought I'd wipe and start all over with bioclipse.cheminformatics. How do I do this?
15:27 egonw define wipe
15:27 olass erase?
15:27 olass completely remove?
15:27 egonw the 2.2.x branch or the whole repos clone?
15:27 olass whatever is needed..
15:28 egonw \rm -Rf bioclipse.cheminformatics
15:28 egonw and then git clone
15:28 olass yes, and then?
15:28 olass so I don't need to remove my github fork?
15:28 egonw ah... ummm... yes
15:28 egonw that too
15:28 egonw just delete your github fork
15:29 egonw and make a fresh fork
15:29 olass ok
15:29 olass will do
15:29 egonw OK, pushed all the changes
15:29 egonw but...
15:29 egonw still cannot run the test suites...
15:29 egonw bioclipse boots fine
15:30 egonw but the plugin test suites fail with the message that log4j cannot be found :(
15:30 egonw http://gist.github.com/254273
15:30 egonw does anyone still here spot something wrong?
15:31 egonw that is... except for the stacktraces, obviously :)
15:31 egonw argh...
15:31 egonw now I see it...
15:32 egonw it always helps if you try to explain what goes wrong!
15:32 egonw bloody run product is wrong!
15:32 egonw not set to bioclipse :(
15:33 egonw ah, but still have the log4j exception
15:33 olass you should see that since the console does not echo "starting Bioclipse...." and so on
15:33 olass oh :(
15:34 egonw updated the gist
15:35 egonw should I run a product
15:35 egonw or run an applicatino?
15:35 Gpox -Dlog4j.debug
15:35 * egonw googles for the wiki page
15:35 egonw @google bioclipse test suite run
15:35 zarah egonw: http://planet.bioclipse.net/
15:35 egonw nope :(
15:38 egonw http://wiki.bioclipse.net/index.php?t​itle=How_to_write_JUnit_plugin-tests
15:38 zarah egonw's link is also http://tinyurl.com/yb49qd2
15:38 egonw that's the one
15:40 egonw wow
15:41 egonw cdk plugin test suite is running again
15:41 egonw puzzled why...
15:41 egonw including org.openscience.cdk.log4j solved it...
15:42 egonw but that CDK module is optional!
15:47 CIA-60 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rdca9727 / plugins/net.bioclipse.cdk.busi​ness.test/META-INF/MANIFEST.MF : Added a apparently important dependency, despite it being optional. Got the CDK plugin unit test suite running again. - http://bit.ly/7DdgKL
15:49 olass egonw: the project com.hp.hpl.jena.arq does not compile here
15:49 egonw what error?
15:50 olass e
15:50 olass xerces errors
15:50 olass import cannot be resolved "org.apache.xerces.impl.xpa​th.regex.RegularExpression"
15:50 egonw you included the new bundles?
15:50 egonw did clean classpath
15:50 egonw set target platform
15:51 egonw PDE clean classpath
15:51 egonw project celan up
15:51 egonw at least twice?
15:51 olass did it once..
15:51 olass will do again..
15:52 olass seems to resolve it... strange..
15:52 olass why twice?
15:52 olass no
15:52 olass same error
15:56 olass no, the jena and jena.arq refuse to pick up xerces
15:56 olass the plugin is there
15:57 olass there is a deo
15:57 olass there is a dep
15:59 olass egonw: help!
16:02 egonw I briefly had that too
16:02 egonw my local .classpath was changed
16:03 egonw when I reverted to the version in the repos, refresh in Eclipse, and the problem disappeared
16:03 egonw please try tha
16:03 egonw t
16:03 samuell joined #bioclipse
16:06 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * ra23a899 / externals/com.hp.hpl.jena.arq/META-INF/MANIFEST.MF : There is no arq.jar anymore, and no need to export the command line utilities - http://bit.ly/8WyiOp
16:08 egonw samuell: can you check out the new bioclipse.rdf code?
16:08 egonw and let me know if it works for you?
16:08 samuell egonw: Sure!
16:08 egonw samuell: it has the new Jena 2.6.2, Pellet 2.0.0 and ARQ 2.8.2 in a separate bundle
16:08 egonw in particular, let me know if the new .arq compiles for you...
16:09 egonw it does for me, but not for olass
16:09 samuell Ok, but it will all come along when checking out bioclipse.rdf ?
16:09 egonw you also need to update bioclipse.core
16:10 samuell Ok
16:10 egonw which also has new bundles
16:11 samuell hmm ... is there a hard pull in git, or do I need to go backward in history first, and then pull your changes?
16:12 samuell -f maybe
16:12 samuell Well, I'll delete the whole folder.
16:14 samuell 2.2.x branch of core?
16:14 samuell I guess ...
16:15 egonw 2.2.x
16:16 samuell Ok ... starting up eclipse now, so will see what happens.
16:20 samuell Could not start ... starting to read the log now ( http://bioclipse.pastebin.com/m1f87e4f8 )
16:20 zarah samuell's link is also http://tinyurl.com/ydy4hvv
16:21 egonw samuell: set the bioclipse.product properly
16:21 samuell Maybe becuase I run java 6 ^^
16:21 egonw it often resets to not use attempting to start the bioclipse product and application
16:21 egonw open bioclipse.product
16:21 egonw and check the Product definition
16:22 egonw Product: net.bioclipse.ui.product
16:22 egonw Application: net.bioclipse.ui.application
16:22 egonw olass: how
16:22 egonw olass: how's it going?
16:22 olass refreshing...
16:23 samuell egonw: net.biocilpse.ui.application is not available in the second row
16:24 egonw ha, I had that last week too !
16:24 egonw it fixed itself at some point
16:24 samuell Ok, will keep refreshing things
16:24 egonw for no apparent reasons
16:24 olass egonw: a question
16:24 egonw sure
16:24 olass I am in rdf branch 2.2.x
16:25 olass git status says:
16:25 olass Your branch is ahead of 'upstream/2.2.x' by 35 commits.
16:25 olass how can that possibly be?
16:25 egonw do you have a fork?
16:25 egonw what's the output of 'git remote -v' ?
16:25 olass yes
16:25 egonw samuell: http://en.wikipedia.org/wiki/Semantic_reasoner
16:25 zarah egonw's link is also http://tinyurl.com/yete9s3
16:26 olass origingit@github.com:olas/bioclipse.rdf.git
16:26 olass upstreamgit://github.com/egonw/bioclipse.rdf.git
16:26 olass I can accept ahead of origin, but not ahead of upstream!
16:26 egonw olass: seems a rebase gone bad?
16:26 olass nope, I do not rebase
16:26 egonw yes, weird indeed
16:26 olass I just do "git pull upstream 2.2.x"
16:26 samuell egonw: thx for the link
16:27 egonw olass: did you check you were in the 2.2.x branch when you pulled?
16:27 egonw I guess you're in master
16:27 olass nope, I am in 2.2.x
16:27 egonw mmm...
16:27 olass and I get your commits
16:27 olass last is: There is no arq.jar anymore, and no need to export the command line utilities
16:27 egonw yes, same here
16:28 egonw try this:
16:28 egonw git fetch upstream
16:28 egonw that might solve it
16:28 samuell I found out that I did indeed check out the master of bioclipse.rdf, so trying again
16:28 olass but still, gitx says upstream/2.2.x is on Moved plugins to the bioclipse.social repository and into the Bioclipse Social Feature (fixes #1656)
16:28 egonw olass: that would explain it:
16:28 egonw yes, actually makes sense
16:28 egonw what happened is:
16:28 olass yes
16:28 egonw you pulled in those changed with 'pull' directly into your 2.2.x
16:28 olass that solves it
16:29 olass why?
16:29 egonw but it did not update your local upstream/2.2.x too
16:29 olass why not?
16:29 egonw perhaps you do not have them linked?
16:29 egonw but I'm guessing here...
16:29 olass they are in .git/confgig
16:29 egonw I always do this:
16:29 egonw git fetch upstream
16:30 egonw git log ..upstream/2.2.x
16:30 egonw and verify patches
16:30 egonw then I pull from my local clone with:
16:30 egonw git merge upstream/2.2.x
16:30 egonw (though I have 'upstream' typically called goglepox and olas
16:30 egonw )
16:31 olass right
16:31 olass ok, refreshing again...
16:31 olass did you say remove the .classpath?
16:32 olass egonw: sounded like you had a solution for the xerces not being picked up by jena and jena.arq..
16:32 egonw yes, delete it and get the copy from the repository
16:32 egonw or do:
16:32 egonw git checkout .classpath
16:32 egonw to reset it to the repository version
16:33 samuell I still got problems: http://bioclipse.pastebin.com/m3d8bb00a
16:33 zarah samuell's link is also http://tinyurl.com/y8j79nv
16:33 egonw yes!
16:34 egonw last classpath issue resolved
16:34 olass egonw: still no luck
16:34 egonw RDF and Pellet unit test suites work here !
16:34 olass egonw: can you paste your classpath for the jena and jena.arq?
16:34 * egonw fears the day is not over yet :/
16:34 egonw olass: hang on
16:35 * samuell used git branch 2.2.x, git checkout 2.2.x, and then, git pull origin 2.2.x, for bioclipse.core and bioclipse.rdf
16:36 egonw olass: do another pull on bioclipse.rdf
16:36 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * r9cb8bef / plugins/net.bioclipse.pellet/META-INF/MANIFEST.MF : Oops... had accidentally changed that version - http://bit.ly/54tcaq
16:36 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * rb1493c1 / externals/com.hp.hpl.jena/build.properties : These jars are no longer present - http://bit.ly/6WLOvm
16:37 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * ra0e667c / externals/org.mindswap.pellet/META-INF/MANIFEST.MF : Updated version number to match the jars; added missing dependency on ARQ 2.8.2 - http://bit.ly/5qeHVP
16:37 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * rfde1dfd / plugins/net.bioclipse.pellet​.tests/META-INF/MANIFEST.MF : Added missing dependency on the pellet libraries - http://bit.ly/7NACfa
16:37 egonw and see if that helps
16:37 * samuell got "java.lang.RuntimeException: No application id has been found."
16:37 egonw samuell: yep, that's the problem I had last week...
16:38 egonw do plenty of refreshes, classpath updates, PDE cleans and resets of target platforms
16:38 olass lol
16:38 samuell or. sorry (after I fixed the fields in the product config file):, "java.lang.RuntimeException: Application "net.bioclipse.ui.application" could not be found in the registry."
16:38 egonw samuell: as said, I had that too, but was gone today again
16:38 samuell Ah ... yes the target platform update I had forgotten
16:38 egonw olass: ok, the state here:
16:39 egonw rdf + pellet is now working with xerces 2.9.0
16:39 egonw next step for me: install EMF (again)
16:39 egonw and get the QSAR plugins to compile
16:39 samuell egonw: How do I do classpath update?
16:39 olass egonw: still no luck here with jena classpath :(
16:39 * samuell feels I have forgot something ...
16:40 egonw menu: Project -> Clean
16:40 olass egonw: please paste your .classpath for the jena plugin in pastebin
16:40 egonw select all plugins
16:40 egonw olass: right
16:40 egonw mom
16:40 olass samuell: right-click > PDE tools > Update classpath
16:40 samuell right click where, on all projects?
16:40 egonw http://gist.github.com/254321
16:40 egonw samuell: any project
16:41 egonw then select in the dialog *all* plugins
16:41 samuell Ok
16:41 egonw olass: other is: http://gist.github.com/254324
16:42 olass hmm, there is no xerces mentioned there?
16:42 egonw org.eclipse.pde.core.requiredPlugins?
16:42 olass what is that?
16:42 egonw line 4
16:42 egonw in both files
16:43 * samuell don't have "net.bioclipse.ui.application" available in that drop-down :(
16:43 egonw still not? :(
16:43 egonw samuell: try rebooting eclipse?
16:43 olass egonw: I don't understand what's wrong
16:43 egonw samuell: I do not know what fixed it here
16:43 samuell ok
16:43 egonw olass: eclipse
16:44 olass egonw: maybe...
16:45 egonw olass: you're .classpath files were the same?
16:45 olass yes
16:46 egonw mmm :(
16:46 egonw you imported all new bundles in .core/externals ?
16:46 olass yes
16:46 olass verified
16:47 olass the jena plugins refuse to find apache
16:47 olass but I have xerces
16:47 olass in my eclipse installation too
16:47 olass it does not pick up _any_ xerces
16:47 egonw :(
16:48 egonw samuell: do you get compile errors on the jena and jena.arq projects?
16:48 samuell I don't come that far ...
16:48 samuell It's missing thie net.bioclipse.ui.application "from the registry"
16:48 egonw but you need that only for booting bioclipse
16:49 egonw not to see if you get compile errors... or?
16:49 olass egonw: did you update the features for all new plugins too?
16:49 olass if not, please do..
16:49 samuell ah
16:50 egonw olass: the two deps for .webservices were already listed
16:50 samuell egonw: I don't see a jena.arq project ...
16:50 olass egonw: seriously, I cannot make them compile
16:50 egonw .cheminformatics/externals/com.hp.hpl.jena.arq
16:50 olass I will have to give up soon :(
16:50 egonw olass: I believe you
16:51 olass so no RC3 then
16:51 olass :(
16:51 egonw olass: I wish I knew what the difference between your and my workspace were
16:51 olass me too
16:51 olass xerces is behaving badly on mac
16:52 egonw no, rdf_feature is not updated
16:52 egonw doing that now
16:52 samuell egonw: Well, in the file system I have ./bioclipse.rdf/externals/com.hp.hpl.jena.arq/ but not inside bioclipse
16:52 samuell eclipse i mean
16:52 egonw please add it
16:52 samuell Ah, :)
16:52 samuell Good idea
16:53 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * ra1764ee / features/net.bioclipse.rdf_feature/feature.xml : Added Xerces and deps to RDF feature - http://bit.ly/7NYR76
16:54 egonw olass: please verify you have all of those 4 plugins
16:54 egonw that I just added to the RDF feature
16:55 olass yes I do
16:55 egonw damn
16:55 olass why is there no xerces jar?
16:55 olass have you upacked that?
16:57 egonw no, this is the way Orbit bundles it
16:57 egonw but indeed, it looks like it is unpacked
16:57 egonw tree with .class files
16:58 egonw OK, got to go get dinner...
16:58 egonw will be right back after that
16:59 egonw olass: BTW, PCM target: http://www.medit-pharma.com/
16:59 * egonw is meanwhile installing EMF
16:59 egonw bbl
17:00 egonw and will think on how to further debug the situation in olass workspace ...
17:02 * samuell is still getting java.lang.RuntimeException: Application "net.bioclipse.ui.application" could not be found in the registry.
17:05 * samuell got it running now, when I discarded changes done by classpath updates et.c. by running git checkout -a
17:05 samuell no, git checkout ./*
17:09 * olass has to run off now for the weekend
17:09 olass bye!
17:10 samuell egonw: No compile errors on jena and jena.arq
17:19 samuell egonw: Up running and doing pellet.reason with an InMemoryStore now :)
17:24 egonw yes, TDB is next up
17:28 samuell Ok
17:28 samuell btw, I found out that andy on the pellet-users list was right that one cannot use abbreviations in the rdf:datatype attribute value
17:29 samuell I got it working when changing xsd:decimal to the full URI
17:29 samuell Also there's a problem with empty hasShifts, but I made them 0.0 for the moment
17:32 samuell (So, the hasShifts look like so now:
17:32 samuell <nmr:hasShift rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">17.6</nmr:hasShift>
17:32 zarah samuell's link is also http://tinyurl.com/erkmb
17:32 samuell )
17:35 * samuell got to grab some food. Checking back in a while, before turning to exam studies.
18:44 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * r8387a10 / plugins/net.bioclipse.structu​redb.rdf/META-INF/MANIFEST.MF : Removed hardcoded versions - http://bit.ly/8SyI7t
18:44 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * r59d6feb / (2 files in 2 dirs): Synchronized with StructureDB APIs - http://bit.ly/7I0h8U
19:57 egonw joined #bioclipse
20:30 samuell joined #bioclipse
20:43 egonw hi samuell
20:43 samuell hello
20:43 zarah oh hai samuell
20:45 egonw samuell: is there a reason why the TDB model is created in the Pellet manager and not in the RDF manager ?
20:47 samuell Well, I implemented it there since pellet already had it's "createStore" function, so was thinking that it is best to do a variation on  that one
20:47 egonw ah, but RDFManager has a createStore too...
20:47 samuell Yes, and I thought there might be some differences
20:47 samuell and I was interested in using pellet
20:47 egonw there indeed are
20:47 samuell And they are?
20:47 egonw in that sense... there is perhaps room for a TDB manager
20:48 egonw pellet has a model preset with OWL knowledge
20:48 samuell Ah, ok
20:49 samuell Ok, so I guess it was some of those predicates I saw when "exporting all predicates" earlier ...
20:49 egonw yes, possibly
20:49 samuell (They looked OWL:ish)
20:50 samuell Ok
20:56 ChanServ joined #bioclipse
20:56 egonw joined #bioclipse
20:56 CIA-60 joined #bioclipse
20:56 ilogger2 joined #bioclipse
21:02 egonw samuell: ping
21:02 samuell pong
21:02 egonw TDB is back in:
21:02 egonw [12/11/09 21:54] <CIA-60> bioclipse.rdf: Samuel Lampa 2.2.x * r28fd9b8 / (6 files in 4 dirs): Added file based RDF Storage, via Jena TDB library
21:03 samuell Is that a question?
21:05 egonw no, a notification :)
21:05 samuell Ah, nice
21:05 samuell So, it's working?
21:05 egonw seems so:
21:05 egonw > store = pellet.createStore("/Test/store.tdb")
21:05 egonw RDFStore (Pellet / Jena TDB): 0 triples
21:05 samuell Cool :)
21:06 samuell Looking forward to try it
21:06 egonw yes, please give it a try...
21:06 * egonw is going offline...
21:07 egonw enough worked for today...
21:07 samuell Indeed
21:07 samuell Thanks a lot for fixing the TDB stuff :)
21:08 * samuell is pulling now
21:10 samuell launching Bioclipse ...
21:10 egonw OK, email me if it does not work
21:10 egonw bye!
21:11 samuell Yep, bye!
21:18 samuell Well, by some reason the pellet manager doesn't get started ... but we can look into that later
21:19 samuell (Or if you mail me your product file, since I guess it is that which is messed up)
21:20 samuell (but it's late now...)
21:21 samuell (It's probably just a lot of refreshing that is needed, as usual)
21:23 samuell Ah, there's a pellet.product ... will look for differences with that and my blipkit.product ...
21:56 ChanServ joined #bioclipse
21:56 CIA-60 joined #bioclipse
21:56 ilogger2 joined #bioclipse
22:48 egonw joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary