Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-11-24

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Time Nick Message
01:25 ilbot2 joined #bioclipse
01:25 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || http://www.youtube.com/watch?v=ZUBQknWUEYU
06:15 egonw joined #bioclipse
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09:35 CIA-57 bioclipse.core: Egon Willighagen 2.2.x * r87b61e4 / plugins/net.bioclipse.ui.business.te​sts/src/net/bioclipse/ui/business/te​sts/AbstractUIManagerPluginTest.java : Added unit test to assert that IUIManager.readFileIntoArray is working - http://bit.ly/4PYnZy
09:35 CIA-57 bioclipse.core: Egon Willighagen 2.2.x * rff5bd4b / plugins/net.bioclipse.ui.business.tests/src/net​/bioclipse/ui/business/tests/CoverageTest.java : Overwrite and implement the required getManagerInterface() method - http://bit.ly/5fH2Id
09:35 CIA-57 bioclipse.core: Egon Willighagen 2.2.x * r77296c9 / plugins/net.bioclipse.ui.business/src/ne​t/bioclipse/ui/business/IUIManager.java : Fixed test class name - http://bit.ly/7wYt26
10:13 samuell egonw: Do you know if you used something like "TDB" for implementing the RDF storage with Jena?
10:14 egonw not that I am aware off
10:14 egonw -f
10:14 egonw of
10:14 samuell Ok
10:43 jonalv CIA-57: wake up!
10:52 olass joined #bioclipse
10:53 olass hola
10:53 zarah saluton olass
10:53 olass SALUTON ZARAH!
10:53 olass zarah: sorry
10:53 zarah olass: excuse me?
10:53 olass zarah: no, excuse me!
10:53 zarah olass: I see.
10:54 olass zarah: you are the dumb one
10:54 zarah olass: no, YOU'RE the dumb one!
10:54 olass zarah: I see.
10:54 zarah olass: excuse me?
10:54 * olass gives up
11:20 sneumann__ jkutzer: xcms/inst/unitTests
12:27 * samuell can't get importing a jar from another plugin to work :(
12:28 samuell ....eventhough exporting it from the other plugin etc.
12:31 samuell Maybe there's more that needs to be set, than exporting in Manifest.mf
12:32 samuell Hmm... now I got one clue, which I will check up.
12:32 * samuell checks up his clue
12:49 masak joined #bioclipse
13:11 egonw joined #bioclipse
13:23 egonw moin
13:23 zarah oh hai egonw
13:23 * egonw is back online
13:29 jonalv oh hai egonw
13:31 egonw Gpox: do you still have patches lined up for bioclipse.cheminformatics?
13:32 egonw Gpox: I see two pull requests in my GH inbox, but nothing shows up after I fetched your branches and I compare...
13:32 egonw jonalv: I see yours too... will test that now
13:32 jonalv egonw: oh I have stuff, good
13:37 egonw jonalv: I see only one patch
13:38 egonw replacing the use of SubProgressMonitor by IProgressMonitor
13:38 jonalv egonw: yup
13:38 jonalv egonw: it's important...
13:38 jonalv :)
13:39 egonw yes, looks good to me...
13:39 egonw sounds like a unit test, btw
13:39 jonalv egonw: sry?
13:39 CIA-57 bioclipse.cheminformatics: jonalv 2.2.x * rca77a39 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/ICDKManager.java :
13:39 CIA-57 bioclipse.cheminformatics: Need to code against the general interface.
13:39 CIA-57 bioclipse.cheminformatics: Needed (and better) to code against the general interface IProgressMonitor instead of SubProgressMonitor - http://bit.ly/75J118
13:39 egonw a unit testing ensuring IProgressMonitor is used, and not an implementation of it
13:40 jonalv egonw: a unit test? Yea maybe the days we actually start caring about unittests...
13:40 egonw speak for yourself :)
13:41 jonalv let me rephrase that. Maybe the days we start running the unit tests auotmagicly on nightly builds
13:42 egonw well, you should run it before you submit any change
13:46 Gpox egonw: added some more patches and sent a new pullrequest
13:46 egonw Gpox: yes, please do update jcp-prim too
13:46 egonw yes, recieved the ping :)
14:08 samuell egonw: seems like I'm missing some source code:
14:08 samuell > var myStore = pellet.createTDBStore();
14:08 samuell java.lang.NoSuchMethodError:
14:08 samuell com.hp.hpl.jena.sparql.lib.Metad​ata.<init>(Ljava/lang/String;)V
14:09 samuell Trying now to locate jena.lib.sparql. Doesn't seem to be there at the files from sourceforge.
14:09 samuell jena.sparql.lib I mean.
14:10 egonw mom
14:10 egonw meanwhile, please check which version of jena is required by the tdb you downloaded...
14:11 samuell Will do
14:13 samuell I have quite a messy file structure in the com.hp.hpl.jena plugin though
14:13 egonw how so?
14:14 samuell I couldn't get the jars to work, so I tried importing the source code folders instead
14:14 egonw :(
14:14 egonw no, I will need it to use jars...
14:14 samuell Yeah, that would really be good
14:16 samuell The folder structure seem to easily become confusing otherwise... e.g. there is both a tdb package (with subpackages), and a com.hp.hpl.jena.tdb package...
14:16 samuell So, I think I better start over with setting this up.
14:16 samuell Trying with the jars again.
14:20 samuell But I'll obviously need some help with those...
14:22 egonw ok
14:22 egonw but feel try again
14:22 egonw just be persistent
14:22 egonw feel -> please
14:23 samuell Yep
14:25 samuell Btw, for all the jars that should be added, almost all of them were already available in com.hp.hpl.jena, but with different file names (for example without the version number)
14:26 samuell So, I'm not sure whether it is better to let it try to use the jars that are available already, or to have multiple copies of the same jars (with possibly minor version differences)
14:26 samuell Maybe go with the latter option for now... and clean up later?
14:27 egonw one copy of the same jar
14:27 samuell Ok, will try that
14:28 * jonalv is fighting to install mysql on his mac--
14:28 egonw mychem?
14:28 jonalv brunn
14:29 jonalv macports-- didn't really do the work
14:30 jonalv o hhang on
14:30 egonw didn't ubuntu install on that nice hardware?
14:30 jonalv seems it installed something called mysql5
14:30 jonalv which is started with mysql5 and not mysql
14:30 jonalv egonw: I haven't tried but I some day I probably will. I am getting tired of this operating system
14:31 jonalv it has desktops but they are so borken..
14:42 samuell egonw: Will I have to specify the used plugins from the pellet feature also?
14:43 egonw what do you mean?
14:43 samuell I mean, do I have to do any changes to the pellet feature's manifes.mf file
14:43 egonw does TDB depend on Pellet?
14:43 samuell Nope
14:43 samuell It will be Just the other way around
14:43 egonw no idea
14:43 egonw that is...
14:44 egonw you have not told me what you want to do
14:44 egonw so I have no clue you will need to do that
14:44 samuell And, well... I'm thinking it should be enough that pellet feature depends on the com.hp.hp.jena plugin
14:44 egonw it already does
14:44 samuell Yep
14:44 egonw it depends on the bioclipse.rdf feature
14:45 samuell I have now added the tdb jar(s) to the com.hp.hpl.jena plugin, and exported them (afais), but still cannot import the package com.hp.hpl.jena.tdb
14:45 samuell (from code in the pellet plugin)
14:46 egonw OK, check the bc wiki
14:46 egonw search for 'classpath horror'
14:46 samuell Ok :)
14:47 samuell Found it
14:57 samuell Hmm... for some reason, the plugin manifest editor won't open anymore :( (just opening in text mode, although telling it explicitly to open with the manifest editor)
14:57 samuell Eclipse--
14:58 samuell ... but that's life.
15:12 jonalv don't talk to me about life
15:12 jonalv google "life, don't talk to me about life"
15:12 zarah jonalv: http://en.wikiquote.org/wiki/The_H​itchhiker%27s_Guide_to_the_Galaxy
15:14 jonalv marvin++
15:21 dsurdyk joined #bioclipse
15:21 dsurdyk anyone there?
15:21 egonw hi dsurdyk
15:21 egonw yes
15:21 dsurdyk I could use a link to the bioinformatics repos.
15:22 dsurdyk that edrin was/is working
15:22 egonw mom
15:23 egonw there is a full list at: http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.2
15:23 zarah egonw's link is also http://tinyurl.com/yaxkhfy
15:23 egonw down the bottom of the page
15:23 egonw http://wiki.bioclipse.net/index.php?titl​e=Checking_out_Bioclipse_2.2#Other_Git_r​epositories_for_other_Bioclipse_Features
15:23 zarah egonw's link is also http://tinyurl.com/yaxkhfy
15:23 dsurdyk thats the list
15:23 dsurdyk i was looking for that - thanks
15:23 egonw welcome
15:27 dsurdyk while i'm at it - where can I find bioclipse.cda
15:28 dsurdyk bioclipse.cdk (it's an import for bioclispe.webservices)
15:29 samuell Things work better now... thanks egonw for the hints!
15:29 samuell (Can import the tdb package, from it's jar file)
15:29 egonw dsurdyk: is that a feature or a plugin?
15:29 egonw dsurdyk: but that should already be fixed I think...
15:29 egonw olass: ?
15:29 egonw olass: ping
15:30 dsurdyk one of the plugins from 2.2
15:30 dsurdyk i just DL it last night from GIT
15:30 olass egonw: pong
15:30 * olass is in tel
15:30 egonw olass: dsurdyk is wondering about .webservices needing .cdk
15:30 egonw but I do not remember the details and/or state of that
15:31 olass 2.2.0 branch?
15:31 olass 2.2.x branch?
15:31 dsurdyk yes
15:31 olass that should be fixed...
15:31 dsurdyk olass: I DL that from the branch last night - when was it fixed?
15:32 olass a while ago...
15:32 dsurdyk hmm - maybe not?
15:32 olass what is the problem? cdk depends on webservices?
15:32 dsurdyk other way around
15:32 olass mom, let me check
15:32 dsurdyk .webservices is looking for .cdk and can't find it
15:32 * olass is not in tel anymore
15:33 olass dsurdyk: can you confirm that you are not running master branch but 2.2.x?
15:33 olass I suspect this is only fixed in 2.2.x
15:33 olass we have not merged the bugfixes into master
15:34 egonw dsurdyk: check with 'git branch'
15:34 egonw or 'git status'
15:34 egonw olass: jonalv did a merge into master rather recently
15:35 olass egonw: how does it look with you? do you see any deps in webservices plugin for cdk?
15:36 olass I don't see any here
15:36 dsurdyk what is the git command to display where i did the checkout from?
15:36 dsurdyk git status only says "nothing to commit"
15:37 olass what does "git branch" say?
15:37 dsurdyk i'm pretty sure i got it from what is listed on http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.2
15:37 zarah dsurdyk's link is also http://tinyurl.com/yaxkhfy
15:37 dsurdyk * master
15:37 olass dsurdyk: yes, but after that you need to check out the 2.2.x branch
15:37 olass ah
15:37 dsurdyk ?
15:37 olass that is the problem
15:38 olass you are on master branch
15:38 egonw dsurdyk: do:
15:39 egonw git checkout -b 2.2.x origin/2.2.x
15:39 egonw ummm...
15:39 egonw first...
15:39 egonw dsurdyk: what is the output of: git remote -v
15:39 egonw ?
15:39 egonw if that looks like: origin git://...
15:39 egonw then my git checkout command is fine
15:39 dsurdyk 2 lines
15:40 dsurdyk one that has (fetch) at the end, one that has (push) at the end
15:41 dsurdyk now i get the following on "git branch"
15:41 dsurdyk *  2.2.x
15:41 dsurdyk master
15:41 olass dsurdyk: try the 'git checkout -b 2.2.x origin/2.2.x' and then type 'git branch' again
15:41 dsurdyk i'm assuming that is correct?
15:41 olass nice
15:41 olass yes
15:41 olass now you are on 2.2.x branch
15:41 dsurdyk great - thanks, and you should add that to the wiki
15:41 olass yup
15:41 olass dsurdyk: note that you need to refresh in Eclipse now
15:41 olass to make it pick up the branch change
15:42 olass (if you use Eclipse)
15:42 egonw dsurdyk: good point. Can you please file a bug report for that? I'm busy writing book chapters right now
15:43 egonw or change it in the wiki yourself?
15:43 egonw olass: can he create an account himself?
15:43 egonw or is that moderated?
15:43 samuell egonw: Olass will have to give him an account
15:43 olass I need to create wiki acounts..
15:43 egonw ah, ok
15:43 olass we were so spammed before :(
15:43 samuell (sry olass... )
15:44 egonw dsurdyk: so, if you want one, ask olas :)
15:44 olass samuell: no worries :)
15:44 olass dsurdyk: you want a wiki account?
15:44 dsurdyk alright - great
15:44 dsurdyk that broke everything now!!
15:44 olass :)
15:44 olass did you refresh everything in Eclipse?
15:44 dsurdyk yes
15:45 olass do you only have core feature checked out?
15:45 dsurdyk i just deleted it and reimported the projects... it's not finding org.eclipse
15:45 olass you probably need to switch to 2.2.x branch for all repos
15:45 egonw reset target platform too
15:45 dsurdyk thats what broke it all
15:45 dsurdyk mom
15:45 olass sorry, need to go offline for a while
15:45 olass brb
15:45 dsurdyk i'm going to start from scratch
15:46 egonw never mind that bug report
15:46 egonw updating the wiki
15:46 egonw bloody latex is not listening to me...
15:46 egonw got a SMILES which does not enter the latex source nicely ...
15:46 egonw need to escape something, but not sure what or how...
15:48 dsurdyk ?
15:49 sneumann__ egonw: does mchem \ce{} work with smiles ?!
15:49 dsurdyk not on my end
15:49 dsurdyk it did when he originally left the room though
15:50 egonw sneumann__: mchem?
15:50 dsurdyk "git-ing" now
15:52 sneumann__ egonw: texlive-science: /usr/share/texmf-texlive/t​ex/latex/mhchem/mhchem.sty
15:53 sneumann__ which works for sum formulae:
15:53 sneumann__ \ce{ C15H14O6}
15:54 egonw I'll try...
15:54 sneumann__ documentation does not mention smiles
15:56 dsurdyk alright...
15:57 sneumann__ egonw: it compiles, but looks utter crap.
15:57 dsurdyk i'm now clean, with a git-clone from 5 mins ago.  using the core eclipse (which you should change the documentation on -- it's called "Eclipse Classic 3.5.1" not "Eclipse SDK"
15:57 dsurdyk and I did the git checkout command for 2.2.x
15:58 dsurdyk I just ran the target platform... and it's still looking for .sdk
15:58 dsurdyk sorry... .cdk
15:59 egonw ok, please file a bug report
16:00 dsurdyk ok - will do
16:00 egonw you can work around it by also downloading and using the 2.2.x branch of the bioclipse.cheminformatics git repository
16:00 dsurdyk k
16:00 egonw olas did fix something related, but apparently not all instances of the problem...
16:00 dsurdyk thnx
16:01 dsurdyk there's also a birt dependency and its apparently not bundled with Eclipse Classic
16:01 egonw no, it is not
16:01 dsurdyk i'll throw it all in the bug rep.
16:01 egonw please file a bug report about that too...
16:01 egonw thanx
16:01 dsurdyk probably all the same - they're all related??
16:01 egonw no, not necessarily
16:02 dsurdyk ok - diff reports then
16:02 egonw please make them split up
16:02 egonw sneumann__: :(
16:02 dsurdyk if i had a wiki account, i could update the wiki without the bug report
16:03 dsurdyk (at least for the birt issue)
16:03 egonw well, I am not sure it should depend on BIRT at all
16:03 egonw I don't think that is intended
16:03 jonalv sry I just looked here. What shouldn't depend on BIRT?
16:05 dsurdyk ahh - the .cdk looks like a stale import and a stale manifest dependency list
16:05 egonw jonalv: bioclipse.core
16:05 jonalv egonw: does bioclipse.core depend on birt? How did this happend?
16:06 dsurdyk and bioclipse.birt has "org.eclipse.birt.report.v​iewer.utilities.WebViewer" as an import
16:06 jonalv egonw: That's wrong
16:06 egonw dsurdyk: yes, bioclipse.birt does depend on BIRT
16:06 dsurdyk as expected
16:06 egonw :)
16:06 egonw dsurdyk: but you do not see bioclipse.core depend on BIRT then, or do you?
16:07 dsurdyk no
16:07 dsurdyk not the core
16:07 dsurdyk all i meant was that the wiki should be changed to import BIRT like how you imported the "Apache Commons" add-on
16:08 dsurdyk since its part of the git checkout
16:08 samuell egonw: Git question: Should I create a separate branch for my additions to bioclipse.rdf, or just push master to my fork?
16:09 egonw dsurdyk: very much down the bottom there is some text about that
16:09 egonw arghh... does someone remember how to create an encoded pwd for /etc/shadow ?
16:09 egonw so that some remote person can send me a pwd ?
16:10 dsurdyk i think it was htpassword
16:10 dsurdyk or htpass
16:10 dsurdyk htpasswd
16:15 samuell egonw: Well, implementing file based RDF storage was the trick. 0.114 instead of 110 s :)
16:15 samuell egonw++
16:15 samuell (for retreiving all predicates, out of ~3500 triples)
16:16 samuell (trying now for the full dataset)
16:16 egonw nice :)
16:22 samuell Still very good results: 3.582 s for the full dataset. Will try to summarize things in a blog post.
16:22 egonw that's what I call a performance improvement :)
16:22 samuell :)
16:22 egonw and this compares to what in prolog?
16:22 samuell I have to check
16:22 egonw samuell: I think I have to make you co-author on the Bioclipse-RDF application note
16:23 egonw and add in the TDB support to the results
16:23 egonw looking forward to your patch ;)
16:23 samuell Oh... well, you decide... btw, there are refinements needed
16:24 samuell Like file path handling...
16:24 egonw always :)
16:24 samuell which I have to learn how you're doing it
16:24 samuell in Bioclipse.
16:24 samuell (The TDB takes full file paths.)
16:25 samuell Also, I wonder what is the policy of exporting libraries in a library plugin like com.hp.hpl.jena?
16:25 samuell I might have exported some unneeded packages now... when trying to get things to work
16:26 egonw no worries about that
16:26 samuell Ok
16:27 samuell Btw, implementing TDB was a no-brainer...
16:27 samuell I'm impressed with how easy it was.
16:28 * egonw hates the double, double escaping of regexp's in Java...
16:28 egonw someone must really hate human kind
16:28 samuell :)
16:28 egonw to come up with triple, double escaping
16:29 egonw I always find myself randomly adding \'s until it compiles...
16:31 dsurdyk left #bioclipse
16:57 samuell egonw: Gotta go, but I summarized the first test: http://saml.rilspace.com/content/file-b​ased-rdf-storage-in-pellet-first-tests
16:57 zarah samuell's link is also http://tinyurl.com/ylpfwl9
16:57 samuell Looking more into this tomorrow.
16:57 * samuell has to rush...
16:58 samuell Oops, the formatting of the code got screwed up :(
16:59 samuell (fixed now)
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