Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-05

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All times shown according to UTC.

Time Nick Message
06:19 sneumann joined #bioclipse
07:34 Gpox joined #bioclipse
07:55 sneumann joined #bioclipse
08:16 egonw joined #bioclipse
08:23 annzi joined #bioclipse
08:24 sneumann hi
08:24 zarah saluton sneumann
08:25 egonw http://condensedconcepts.blogspot.com/2010/02​/nature-publishes-17-parameter-fit-to-20.html
08:25 zarah egonw's link is also http://tinyurl.com/ydzb7g7
08:25 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:26 egonw @msg
08:26 zarah egonw: 17 h 53 m 10 s ago, sneumann said that I didn't do anything, but cdk stuff in metfrag works
08:26 zarah egonw: 17 h 13 m 33 s ago, sneumann said that the classNotFound is back. I didn't do anything. Really.
08:26 sneumann :-)
08:26 sneumann It worked once ...
08:26 egonw yes, classpath issues do come back occusionally... for no apparent reasons
08:27 egonw happens to all of us
08:27 egonw umm...
08:27 egonw there are some trickes...
08:27 egonw menu: Project -> Clean...
08:27 sneumann did that.
08:27 egonw and right click on Project in Pkg Explorer...
08:28 egonw PDE Tools... -> Update Classpath ...
08:28 sneumann That I'll try
08:28 egonw and of course, right click and Refresh...
08:28 sneumann I have refresh workspace on startup
08:28 egonw then, try the Set Target Platform
08:28 sneumann yup
08:28 egonw in target-platform.foo
08:28 egonw and refresh...
08:28 sneumann and all of that in random order ;-)
08:28 egonw repeat those a few times in random order...
08:28 egonw indeed!
08:28 egonw you know it already!
08:29 egonw the random is crucial :)
08:29 sneumann not the PDE ...
08:29 sneumann although that probably sets classpath in the eclipse and not the running metware.product
08:30 sneumann just added methods for setAccuracy, score, scores and ffragments
08:40 annzi1 joined #bioclipse
08:42 sneumann egonw: PDE stuff helped. Or something else did.
08:42 sneumann Interface question:
08:42 sneumann score(spec, molecule) and scores(spec, molecules)
08:42 sneumann Best thing to use are IMolecule and not IAtomContainer ?
08:44 egonw yes, manager API should use the *Bioclipse* IMolecule (not the CDK IMolecule)
08:45 sneumann and IMoleculeSet
08:45 egonw then, when you need the CDK molecule... use the CDK manager
08:45 egonw which has a method like asCDKMolecule
08:45 egonw which returns ICDKMolecule, which has getAtomContainer()
08:45 egonw there is a Bioclipse IMoleculeSet?
08:46 egonw Gpox: ?
08:46 egonw not List<IMolecule> ?
08:46 sneumann IMoleculeSet is in CDK :-(
08:46 sneumann So I'll use List<Molecules> or Container<Molecules> ?
08:47 egonw yes, and please file a report for needing CDKManager.asList(IMoleculeSet)
08:55 annzi joined #bioclipse
09:24 egonw annzi: I need to rewrite the RDF creation of ChEMBL today, in order to load it on the new server
09:24 egonw annzi: the new Virtuoso 6.1 does not load the old db
09:24 egonw and since I need to add the protein classification, use the ChEBI id, and a bit more in the RDF graphs anyway...
09:25 egonw sneumann: also incorporating the recent MB updates in my eclipse WS now
09:38 egonw "SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets"
09:38 egonw DOI:
09:38 egonw 10.1021/ci900416a
09:39 egonw @tell jonalv: http://pubs.acs.org/doi/abs/10.1021/ci900416a
09:39 zarah egonw's link is also http://tinyurl.com/ykeco9p
09:39 zarah Consider it noted.
09:41 annzi egonw: what is needed for me to access the db from bioclipse?
09:41 egonw nothing much
09:41 egonw rdf.remoteSPARQL()
09:41 egonw annzi: e.g http://www.myexperiment.org/workflows/927
09:42 zarah egonw's link is also http://tinyurl.com/yzdpr7l
09:42 egonw http://www.myexperiment.org/workflows/921
09:42 zarah egonw's link is also http://tinyurl.com/yd7j5q2
09:42 egonw http://www.myexperiment.org/workflows/928
09:42 zarah egonw's link is also http://tinyurl.com/yg75hsv
09:42 egonw http://www.myexperiment.org/workflows/889
09:42 zarah egonw's link is also http://tinyurl.com/l6od5e
09:42 egonw annzi: note the numbers at the end
09:42 egonw myexperiment.load(927)
09:42 egonw etc
09:42 egonw or something like that
09:44 annzi egonw: ok, and the old db work for now right, so I can work with it until you are done
09:49 egonw yeah, I hope to have the new one up and running by Monday
09:50 egonw annzi: perhaps you can blog today about running some SPARQL queries on other resources, like DBPedia and Bio2RDF... around chemistry questions
09:50 egonw or perhaps that LinkedFDA resource
09:50 egonw and I'd appreciated if you'd upload your Bioclipse scripts to MyExperiment
09:51 egonw so that people can easily download and reproduce them
09:52 annzi ok
10:03 olass joined #bioclipse
10:03 olass hi
10:03 zarah oh hai olass
10:03 egonw hi olass
10:03 olass hi egonw
10:31 Gpox joined #bioclipse
10:40 masak joined #bioclipse
11:06 jonalv joined #bioclipse
11:06 jonalv oh hai
11:06 zarah oh hai jonalv
11:06 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
11:07 annzi egonw: what does this error mean? com.hp.hpl.jena.sparql.res​ultset.ResultSetException: skipToHead: Unexpected
11:07 annzi tag: {http://www.w3.org/1999/xhtml}html
11:08 jonalv egonw: I saw your mail. Sadly I can totally no join in on thursday... :(
11:09 egonw jonalv: ack
11:09 egonw annzi: can you put up the full error with stacktrace on a pastebin?
11:09 egonw or at gist.github.com
11:10 * jonalv actually thinks this suck. I have teaching all next week. IS that date set in stone? :)
11:10 egonw yes it is
11:10 annzi egonw: it is the full error
11:11 egonw please put the script on gist
11:25 sneumann Is there any way to open a molecule I created in JS in a viewer / Editor ?
11:26 sneumann mol=cdk.fromSMILES("C1C(OC2=CC(=​CC(=C2C1=O)O)O)C3=CC=C(C=C3)O");
11:32 egonw ui.open(mol)
11:35 sneumann worked, thanks
11:49 sneumann egonw, what did you do the other day about those access restriction problems,
11:49 sneumann I have more of them (Access restriction: The method getList() from the type CMLElements<CMLPeakList> is not accessible due to restriction on required library  )
11:49 egonw import the proper plugins
11:49 egonw mom
11:49 sneumann and don't wont you all the time to clean that up.
11:49 sneumann and don't want you all the time to clean that up.
11:50 egonw add dep on plugin:
11:50 sneumann import and not bundle-require ?
11:50 egonw org.xmlcml.cmlxom
11:50 egonw and that that one to the feature
11:50 egonw as well as:
11:50 egonw net.bioclipse.xom
11:51 egonw or perhaps that is already in the platform_feature
11:51 egonw in that case, you need not add it to the metfrag_featue
11:51 egonw annzi: did you post your BSL script somewhere?
11:52 sneumann yup, in the plugin was enough
12:01 annzi egonw: I added as text on gist
12:01 egonw URL?
12:03 annzi http://gist.github.com/295724
12:10 egonw annzi: what happens if you run that SPARQL directly on the end point?
12:11 egonw and not via Bioclipse?
12:13 annzi it works via endpoint http://pele.farmbio.uu.se/chembl/snorql/?que​ry=PREFIX+chem%3A++++%3Chttp%3A%2F%2Fwww.blu​eobelisk.org%2Fchemistryblogs%2F%3E+%0D%0A%0​D%0ASELECT+DISTINCT+%3Fmol+%3Fsmil+WHERE+{%0D%0A%3Fmol+a+chembl%3ACompound%0D%0AOPTIONAL+{​%3Fmol+chem%3Asmiles+%3Fsmil}%0D%0A}%0D%0ALIMIT+5
12:13 zarah annzi's link is also http://tinyurl.com/yeepnza
12:13 annzi but not via Bioclipse
12:14 egonw ah, indeed!
12:14 egonw the problem is in line 17
12:14 egonw you have to fix that line
12:14 egonw then you should be fine
12:15 egonw mmm... education in rhyme
12:15 annzi haha
12:21 annzi yes of course, now I see
12:27 egonw OK, I think I got the N3 format done now for the activities table
12:28 egonw annzi: http://gist.github.com/295746
12:29 egonw well, almost
12:29 egonw as I realize I should use ChEBI ids here too :(
12:31 annzi great, I think this kind of thinking is amazing
12:37 annzi egonw: is it hard to do the things you do now?
12:38 * egonw is not sure what annzi is referring too
12:38 egonw thinking comes naturally
12:39 egonw well, I guess it's what they say... 10% inspiration, 90% transpiration
12:39 egonw but we have deoderant for that
12:41 annzi :)
12:57 egonw annzi: ok, the activities N3 is now using the ChEBI id for the molecules
12:57 egonw data being dumped as N3 as we speak
12:57 egonw was 1.1GB in RDF/XML format
12:57 egonw should be smaller now
13:01 egonw Gpox: made progress with Hudson?
13:02 Gpox Hudson is up and running
13:02 egonw URL?
13:02 Gpox http://pele.farmbio.uu.se:8080/hudson/
13:02 zarah Gpox's link is also http://tinyurl.com/yfujver
13:03 egonw no apache proxy yet?
13:03 egonw will set one up then
13:03 egonw hang on
13:10 egonw http://pele.farmbio.uu.se/hudson/
13:10 zarah egonw's link is also http://tinyurl.com/yf9nyk4
13:10 egonw mmm... no, that's not right
13:12 egonw Gpox: ping
13:12 egonw Gpox: that's the admin interface
13:12 egonw I don't think we want to expose admin menus on pele.farmbio.uu.se :)
13:13 egonw Gpox: what would the URL for build reports?
13:14 * olass get a "Not Found" on http://pele.farmbio.uu.se/hudson/
13:14 egonw yes, disabled it agin
13:14 olass ack
13:15 egonw because it had all sorts of admin menus
13:15 egonw and seemingly allowing me to change stuff
13:15 egonw [02/05/10 14:12] <egonw> I don't think we want to expose admin menus on pele.farmbio.uu.se :)
13:16 olass we should expose the reports
13:16 egonw yes, and only that
13:16 olass egonw: could we set up http://internal.pele.farmbio.uu.se?
13:16 zarah olass's link is also http://tinyurl.com/ydcjxxs
13:16 olass with only access from UU subnet..
13:21 egonw possibly
13:22 egonw crap... that did not work :(
13:27 sneumann here we go again,
13:27 sneumann Caused by: java.lang.NoClassDefFoundError: org/openscience/cdk/tools/man​ipulator/AtomTypeManipulator
13:27 sneumann at net.bioclipse.metfrag.business.BioClipseConve​nience.metFrag(BioClipseConvenience.java:136)
13:27 sneumann so atomtypemanip is in o.o.cdk.standard
13:27 sneumann which is required-bundle of n.b.metfrag
13:27 sneumann refresh is done, target platform, PDE classpath.
13:28 egonw menu, project, clean ?
13:29 egonw then repeat everything twice
13:29 egonw and make use the to it in the correct random order, otherwise you have to start from scratch
13:31 sneumann sigh. Is there a button for "random order" ?
13:36 egonw no, and just thinking about it, makes you have to restart too :)
13:37 egonw ah good... the N3 triples are coming in...
13:38 egonw SELECT DISTINCT * from activities, compounds WHERE activities.molregno = compounds.molregno;
13:38 egonw that was not really a good idea
13:38 egonw 2.4M and 0.5M each...
13:38 egonw not too much, but not something that works on pele :)
13:54 CIA-71 bioclipse.metabolomics: Steffen Neumann master * r17a2149 / (5 files in 3 dirs): now with adapter between ISpectrum, IMolecule and MetFrag - http://bit.ly/bk5BpI
14:04 sneumann http://www.myexperiment.org/workflows/1039
14:04 zarah sneumann's link is also http://tinyurl.com/yh4t5rm
14:04 sneumann Untested, since I still have classpath issues :-(
14:08 egonw no worries
14:10 sneumann also pull my d.i.metfrag
14:10 sneumann hangon, different NPE :-)
14:10 sneumann Caused by: java.lang.NoClassDefFoundError: org/apache/log4j/Category
14:11 sneumann WARN - Bioclipse JsExecution Plug-in: Failed to get a service: Plug-in "net.bioclipse.business" was unable to execute setInitializationData on an instance of "net.bioclipse.business.Biocl​ipsePlatformManagerFactory".
14:11 sneumann Sigh.
14:11 egonw sneumann: that is the one thing that begs for an Import-Package:
14:12 egonw but the n.b.metfrag already has that, not?
14:13 sneumann import what ?
14:14 * sneumann gives up for now.
14:16 egonw Import-Package: org.apache.log4j
14:33 CIA-71 chembl.rdf: Egon Willighagen master * r1d5ebe4 / compounds.php : Create RDF for all compounds again - http://bit.ly/c2Cdpj
14:33 CIA-71 chembl.rdf: Egon Willighagen master * re4ebb93 / activities.php :
14:33 CIA-71 chembl.rdf: Rewritten to emit N3, and few URI changes:
14:33 CIA-71 chembl.rdf: * emit N3, which is much smaller
14:33 CIA-71 chembl.rdf: * use ChEBI as molecule ID, as requested by ChEMBL team
14:33 CIA-71 chembl.rdf: * changed URIs for resources format to be happy in the N3 world
14:33 CIA-71 chembl.rdf: * URI domain leaks new Virtuoso server - http://bit.ly/9ZxHMS
15:15 de__maas joined #bioclipse
15:15 egonw hi de__maas
15:16 de__maas Hi Egon , how's life.
15:16 egonw good
15:16 egonw stressed, but having fun
15:17 egonw doing cool stuf :)
15:17 de__maas in bioclipse or unrelated?
15:30 egonw bioclipse, cdk, rdf ... molecular chemometrics :)
15:30 de__maas Aha, I'm fighting with CDK in knime, seems like they still are using an early version.
15:41 olass egonw: if you had time to look at the MCSS unit test patch I sent that would be really appreciated...
15:42 olass I suspect you will sovle it with a quick fix
15:42 * olass knows that egonw is wise in the ways of science
15:43 olass "- A duck!"
16:13 de__maas left #bioclipse
17:01 olass joined #bioclipse
17:02 olass wb olas
17:16 egonw_ joined #bioclipse
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18:18 egonw__ joined #bioclipse
18:26 sneumann joined #bioclipse
19:13 sneumann egonw__: completely wrecked the metfrag product, http://pastebin.com/m13120928
19:13 sneumann while bioclipde product works fine ?!
19:15 sneumann only logging seems broken, JS still works.
19:33 olass sneumann: where is the git repo and what branch are you running?
19:33 * olass has a minute over
19:34 * olass has fixed a few logging problems over the years
19:35 olass sneumann: let me know
19:36 * olass will isten in from time to time this evening
19:54 egonw__ olass: ping
19:55 olass egonw: pong
19:56 egonw do I have write permissions for bc.statistics?
19:56 egonw can I apply a few patches?
19:56 egonw those in bug 1789 ?
19:56 olass sure
19:56 olass we need to decide about that repo
19:56 olass some plugins are deps from core
19:56 olass and should be moved IMO
19:57 egonw such as?
19:57 olass matrixeditor among other
19:57 olass will give you write access to bioclipse.statistics
19:57 * olass will pursue the bioclipse github account next week
19:57 olass forgot to follow that up with Jarl
19:58 olass will write it on my todo for next weel
19:58 olass will write it on my todo for next week
19:58 egonw have you mailed github yet?
20:00 olass done
20:00 olass yes
20:00 olass got sort of a half answer..
20:00 olass need to go offline for a while
20:00 olass ttl
20:00 egonw ack, cu later
20:44 sneumann_ joined #bioclipse
20:51 CIA-71 chembl.rdf: Egon Willighagen master * r87d64eb / (compounds.php docs.php): Converted to spit N3 - http://bit.ly/c7Y9W7
22:29 egonw joined #bioclipse
22:45 egonw joined #bioclipse

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