Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-14

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All times shown according to UTC.

Time Nick Message
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09:26 thomas_ku moin
09:27 egonw hi thomas_ku
09:28 jonalv hi all
09:28 thomas_ku hi all
09:29 jonalv btw egonw I have read he major part of Tobias thesis now
09:29 egonw ah, good
09:31 jonalv It seems that the Hibernate project mostly has been about fighting against the Bioclipse Biresource structures...
09:31 jonalv I also realised that that project will not be easily integrated into Bioclipse 2
09:31 egonw possibly...
09:32 egonw we have all been fighting the Bioclipse Bioresource structures :)
09:32 egonw partly because it was a moving target :)
09:32 jonalv ah
09:32 jonalv okey
09:33 jonalv Have you seen our short mail to the bioclipse list yet? :)
09:33 egonw yes
09:33 egonw but just 'seen'
09:33 egonw not read yet...
09:33 egonw just printed it...
09:33 jonalv okey
09:36 thomas_ku_ joined #cdk
10:40 egonw OK, cdk is 999 commits away from the 10k commits
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14:54 egonw thomas_ku: trying to get mvn2 to compile against at CDK trunk
14:55 egonw I hope to see compile errors :)
14:56 egonw thomas_ku: around?
14:57 egonw yeah, I got my compile errors :)
15:01 thomas_ku egonw: yes I am
15:02 egonw [WARNING] POM for 'org.openscience:cdk:pom:1.1.0.20080114:compile' is invalid. It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM. for project org.openscience:cdk at /home/egonw/.m2/repository/org/openscience​/cdk/1.1.0.20080114/cdk-1.1.0.20080114.pom
15:02 egonw any comments on that?
15:02 egonw something wrong with the version number?
15:04 thomas_ku it looks like the version number you used is not suported within maven 2
15:06 egonw ah... the thingy was not in the maven repos...
15:06 egonw so the bla.pom in ~/.m2 is not a proper .pom file
15:06 thomas_ku ok
15:07 thomas_ku did you choose the option generate pom during the installation of the cdk.jar file?
15:08 egonw cool
15:08 egonw now it works :)
15:08 egonw even picked up by the maven plugin in eclipse
15:08 egonw no
15:08 egonw just copied the file
15:09 egonw but the .pom in ~/.m2 was a HTTP 404 message that the file did not exist
15:09 egonw hacked it up, staring from the template for the cdk-1.0.2.pom
15:09 egonw anyway...
15:09 egonw 14 errors now
15:10 thomas_ku that ok so far
15:12 egonw [INFO] BUILD SUCCESSFUL
15:13 egonw that was easy
15:13 egonw so, back to the problem of how to deploy it :)
15:13 thomas_ku ;-)
15:20 egonw what was the 'goal' for uploading to the repos again?
15:20 egonw cdk-taverna.de in your case?
15:22 thomas_ku mom
15:24 thomas_ku so the thing is that if you want to use the plugin installation mechanism of taverne you have to have such a repo
15:24 thomas_ku you can install all these things also locally
15:25 thomas_ku within the repositories there have to be the jar within a maven repo structure and the configuration files which Taverna will read
15:26 egonw yeah, I'm hacking something up locally now... on my local Apache server
15:27 thomas_ku a description what is needed can you find here:  http://www.mygrid.org.uk/userma​nual1.7/publishing_plugins.html
15:27 egonw thomas_ku: there is no ro FTP access to that server, correct?
15:28 egonw wget picks up lot of garbage for m2/release_repository/
15:28 egonw wanted to make a local mirror
15:28 thomas_ku from the cdk-taverna server?
15:28 egonw yes
15:28 thomas_ku mom
15:29 thomas_ku can you start your skype acount?
15:29 egonw yes
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15:50 egonw thomas_ku: OK, attempting to install CDK-Taverna 0.4.2.0 now :)
15:51 thomas_ku ohhhh I hope it will work
15:51 egonw so do I
15:51 egonw not for 1.7 though
15:51 egonw no idea what I need to do for that
15:53 thomas_ku not so much you have to change only the version of taverna at two positions
15:54 thomas_ku within the pom file and within the plugin configuration file
15:54 egonw right
15:54 egonw Q:
15:54 egonw where's the cdk-taverna jar on the website?
15:54 egonw should that be in release_repository/ too?
15:54 thomas_ku yes
15:54 egonw mmm...
15:54 egonw it did not copy that :(
15:55 egonw ok, another try
15:55 thomas_ku one mom
15:55 * egonw hopes Thomas has some bandwith left :)
15:55 thomas_ku oh yes no problem
15:56 thomas_ku it should be here /m2/release_repository/org/openscience/cdk​/applications/taverna/cdk-taverna/0.4.1.0/
15:56 egonw yeah, found it...
15:56 egonw had during the wget from the FTP server trouble with disk space...
15:56 egonw resumed... but that clearly did not work out nicely
15:56 egonw mmm
15:56 egonw no, that was not the problem
15:57 egonw recursive depth??
15:57 thomas_ku what?
15:57 egonw ok, depth=10 is better
15:57 egonw it truncated the FTP grab at recursive level 4 or 5 or so
15:58 thomas_ku ah ok
15:58 egonw therefore not recursing into cdk/applications
16:01 egonw OK, here goes...
16:01 * egonw is booting T 1.6.2
16:01 egonw and hopes his existing cdk-taverna 0.4.1.0 is not making trouble
16:02 egonw mmm... no new plugins :(
16:02 egonw ah...
16:02 egonw "An update is available for this plugin" :)
16:02 thomas_ku that's normal
16:02 thomas_ku oh good
16:02 egonw had to press 'Find Updates' first... even after adding my localhost as second plugin site
16:03 thomas_ku hopefully it will be installed without problems ;-)
16:03 egonw now, after restarting the Plugin Manager I was able to Update...
16:03 egonw no errors reported in the GUI
16:03 egonw a big stacktrace on the command line
16:04 thomas_ku thats good so far
16:04 thomas_ku that not good
16:04 egonw but that's for one of the web services :)
16:04 thomas_ku ;-)
16:04 thomas_ku ok than you have to restart
16:04 egonw ok, was just about to do that...
16:04 egonw feels logical...
16:05 egonw mmm...
16:06 thomas_ku problems?
16:06 egonw it's still populating...
16:06 egonw but I don't see the CDK local processors yet
16:06 thomas_ku do you see any other local processors?
16:06 egonw yes
16:06 thomas_ku that's not goo
16:06 thomas_ku d
16:07 thomas_ku they will not show up than...
16:07 egonw right :(
16:07 thomas_ku did you got any error messages?
16:07 egonw org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
16:07 egonw at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
16:07 egonw at org.apache.xerces.jaxp.Docum​entBuilderImpl.parse(Unknown Source)
16:08 thomas_ku really no idea where these messages came from....
16:08 thomas_ku can you look into the log file of taverna?
16:08 thomas_ku if there are some strange informations about a problem
16:09 egonw will try reinstall T1.6.2 first
16:09 egonw nothing much one could mess up with those .pom files
16:10 thomas_ku do that
16:11 egonw it's downloading itext
16:11 egonw jcp
16:11 egonw the cdk-taverna jar
16:11 egonw jai
16:12 egonw cdk 1.1.0.20080114
16:12 egonw it tries all at mobycentral first :)
16:12 thomas_ku yes I now that
16:12 thomas_ku ah
16:13 thomas_ku you have to change the cdk version within the pom file of jchempaint
16:13 egonw no
16:13 egonw not?
16:13 egonw did not update the JCP version
16:13 egonw so, that one still depends on 1.0.2
16:13 egonw well, will surely likely break...
16:13 thomas_ku yes
16:13 egonw but then again, maybe not...
16:13 egonw because the APIs did not change
16:14 egonw ok, restarting T1.6.2
16:14 thomas_ku or you have to build a jcp jar from the trunk and than install everything on your local repo  again
16:15 thomas_ku and I suggest not to mention the cdk-taverna plugin site so that it only knows your local one!
16:15 egonw OK, I forgot to put the new CDK version on my local Apache server :)
16:16 egonw cool
16:16 egonw got this stacktrace now:
16:17 egonw java.lang.ClassNotFoundException: org.openscience.cdk.applications.t​averna.qsar.descriptors.molecular.​ValenceCarbonConnectivityOrderZero
16:17 egonw at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:195)
16:17 egonw at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:154)
16:17 egonw ...
16:17 egonw that's becuase I have not removed the lines in the registry for those nodes yet :)
16:17 thomas_ku ah ok
16:17 thomas_ku so now they show up?
16:17 egonw and the local services is populated with CDK stuff now :)
16:17 egonw yes :)
16:17 thomas_ku :-)
16:18 * egonw is trying the InChI node :)
16:19 thomas_ku I have to cook now bbl
16:20 egonw ok, cu
16:20 egonw btw, InChI does not seem to work :(
16:20 egonw oh, crap...
16:20 egonw this one I have seen before:
16:21 egonw java.lang.ClassNotFoundException: org.openscience.cdk.applic​ations.taverna.CMLChemFile
16:21 egonw at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:195)
16:32 thomas_ku egonw: can you test if other cdk worker do their work properly
16:32 egonw will try
16:33 egonw now going home
16:33 thomas_ku ok cu later
16:33 egonw but it's that same stupid stacktrace as earlier... :(
16:33 egonw cu later
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17:16 jonalv did egonw leave?
17:16 jonalv :(
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