Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-08

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Time Nick Message
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08:39 olass moin
08:39 zarah privet olass
08:39 olass oh hai
08:39 zarah oh hai olass
08:39 olass hola
08:39 zarah saluton olass
08:39 olass zarah: oh shut uå
08:39 zarah olass: please rephrase or stop trying to be witty :)
08:39 olass zarah: oh shut up
08:39 zarah olass: :)
08:43 egonw joined #bioclipse
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09:16 CIA-57 bioclipse.qsar: Egon Willighagen master * r292ba70 / plugins/net.bioclipse.qsar/src/net/bioc​lipse/qsar/business/OntologyHelper.java : Updated for change in the RDF manager: createStore() -> createInMemoryStore() - http://bit.ly/dnEaV0
09:16 CIA-57 bioclipse.qsar: Egon Willighagen master * ra21c779 / plugins/net.bioclipse.qsar/src/net/bioc​lipse/qsar/business/OntologyHelper.java : Updated for changes in the IRDFManager: List<List<String>> replaced by IStringMatrix - http://bit.ly/cWom0v
09:17 jonalv joined #bioclipse
09:24 egonw scientific visualization special nature methods issue: http://www.nature.com/nmeth​/journal/v7/n3s/index.html
09:24 zarah egonw's link is also http://tinyurl.com/ygtve44
09:35 samuell joined #bioclipse
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10:37 olass egonw: ping
10:37 egonw pong
10:37 olass my cheminfo does not compile in master
10:37 olass complains about BioclipseLoggingTool
10:37 egonw what is the complaint?
10:38 olass must implement bla bla many methods
10:38 olass I updated org.op.cdk
10:38 egonw update org.openscience.cdk
10:38 egonw oh...
10:38 egonw cehcking
10:38 olass a new branch?
10:38 egonw see email
10:38 egonw yes, irght
10:39 olass what email?
10:39 olass to devel?
10:39 egonw http://github.com/egonw/org.ope​nscience.cdk/tree/bioclipse2.4
10:39 zarah egonw's link is also http://tinyurl.com/ygcl8zn
10:39 egonw yes, bioclipse-devel
10:39 olass why new branch?
10:39 * olass is confused with always having to switch branch
10:39 olass can we not have one for development?
10:42 olass so where do I get the plugin net.sourceforge.nattable.c​ore;bundle-version="2.0.0" ?
10:42 olass it is a dep in sdfeditor
10:42 olass Gpox: do you know?
10:42 olass it seems it is not in repo
10:43 olass egonw: do you know?
10:44 olass oh, target platform updated
10:44 olass :(
10:44 egonw yes
10:44 Gpox olass: are you developing against master? try to set the target platform
10:44 egonw the need for another branch is that the org.openscience.cdk is a shared repos
10:45 egonw the branch will disappear shortly again, now that the required patch is in CDK master
10:45 olass it is just so cumbersome to always have one hour of startup time since you don't know what the latest branch is, and need to look up various emails etc...
10:46 olass can we not have one point where we write what branch should be used?
10:47 egonw yeah, that would be nice
11:07 olass egonw: ok, so where are the xest plugins?
11:07 olass org.eclipse.zest.core is missing
11:07 olass why is this not in the repo?
11:07 olass damn
11:07 egonw birt, emf is not either, is it?
11:08 olass it should be in target platform I suppose
11:08 olass ok, et it from software update form eclipse?
11:08 olass ok
11:08 egonw would it then not be part of the main bioclipse distrib too?
11:08 egonw yes
11:08 egonw reset target platform after installation
11:09 * olass really dislikes the current build steps
11:10 * olass wants buckminster
11:10 egonw buckminster++
11:10 olass no zest found on galileo
11:10 olass ok, what now?
11:10 egonw http://www.eclipse.org/gef/updates/
11:10 zarah egonw's link is also http://tinyurl.com/y872ymq
11:11 olass oh, a separate update site?
11:11 egonw apparently
11:11 olass no, this page says "3.4 install manager"
11:11 olass we are running 3.5
11:12 olass does it work anyway?
11:13 egonw yes
11:13 egonw http://download.eclipse.org/​tools/gef/updates/releases/
11:13 zarah egonw's link is also http://tinyurl.com/yflkceg
11:13 egonw lists versions for 3.2, 3.3, 3.4 and 3.5.2
11:13 olass and which should I get?
11:14 olass it says in manifest: org.eclipse.zest.core version 1.2.0
11:14 olass GEF SDK 3.5.2 provides zest 1.1.2
11:14 olass no way to get zest.core plugin info from this
11:15 olass egonw: is the toolkit enough?
11:15 olass or do I need the SDK?
11:16 egonw toolkit should be enough, I think
11:16 egonw olass: then file me a bug report to remove that 1.2 dep
11:16 egonw that was automatically added anyway
11:17 olass ok
11:17 egonw I think jonalv said it worked with his older version too, which is likely also 1.1.2
11:17 egonw not sure where my 1.2 comes from
11:17 egonw eclipse really sucks here
11:17 olass 1.1.2 is feature version
11:17 olass 1.2 is plugin version
11:17 olass might differ
11:19 egonw oh, ic
11:22 olass ok, removing the hardcoded version dep solved it
12:02 olass @tell egonw: http://www.slideshare.net/ospjuth/building​-a-flexible-infrastructure-with-bioclipse-​open-source-and-federated-cloud-services
12:02 zarah olass's link is also http://tinyurl.com/yb6qqvu
12:02 zarah Consider it noted.
12:14 olass @ask egonw: are you involved in http://www.taverna.org.uk/2010/01/​19/chemtaverna-project-under-way/ ?
12:14 zarah olass's link is also http://tinyurl.com/y92a2rg
12:14 zarah Consider it noted.
13:07 olass @tell egonw you have no idea how long it took me to figure out that you are using Java 1.6 in teh chembl plugin. It just died silently. Please make sure all Java 1.6 is removed, we have a poilicy for this in the Bioclipse project and even though that might change very soon it is still valid.
13:07 zarah Consider it noted.
13:12 olass @tell egonw: please see bug 1906, it is blocking my progress on QSAR-ChemBL
13:12 zarah Consider it noted.
13:22 CIA-57 bioclipse.core: Ola Spjuth master * r5fd03d0 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : Added -consolelog and -noupdate since devel in master. - http://bit.ly/b31hQd
13:22 CIA-57 bioclipse.core: Ola Spjuth master * rb34ae43 / features/net.bioclipse.platfor​m_feature/bioclipse.gtk2.18.sh : Added gtk-linux-startscript. Solves #1836. - http://bit.ly/aVQZ6g
13:29 egonw joined #bioclipse
13:31 egonw moin
13:31 zarah saluton egonw
13:31 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
13:31 egonw @msg
13:31 zarah egonw: 5 d 2 h 56 m 40 s ago, jonalv asked Why does the JenaRDFLiteral not have the value of the actual literal?
13:31 zarah egonw: 4 d 22 h 15 m 16 s ago, jonalv pinged
13:31 zarah egonw: 1 h 28 m 28 s ago, olass said http://www.slideshare.net/ospjuth/building​-a-flexible-infrastructure-with-bioclipse-​open-source-and-federated-cloud-services
13:31 zarah egonw: 1 h 16 m 42 s ago, olass asked are you involved in http://www.taverna.org.uk/2010/01/​19/chemtaverna-project-under-way/ ?
13:31 zarah egonw: 23 m 30 s ago, olass said you have no idea how long it took me to figure out that you are using Java 1.6 in teh chembl plugin. It just died silently. Please make sure all Java 1.6 is removed, we have a poilicy for this in the Bioclipse project and even though that might change very soon it is still valid.
13:31 zarah egonw: 18 m 38 s ago, olass said please see bug 1906, it is blocking my progress on QSAR-ChemBL
13:31 olass egonw: ping
13:31 egonw pong
13:32 olass I get VERY verbose debugging for cheminformatics now
13:32 olass is this deliberate?
13:32 egonw I guess you are at DEBUG level?
13:32 olass what do you mean?
13:32 egonw CDK emits quite a lot at debug level indeed
13:33 egonw how are the bioclipse logging levels defined?
13:33 egonw perhaps bioclipse debug it not generally debug?
13:33 olass logger.debug, logger.warn
13:33 olass logger.info
13:33 egonw right...
13:33 egonw regular log4j kind of stuff
13:33 olass yes
13:33 egonw same for the CDK
13:34 egonw no, not involved in ChemTaverna
13:34 egonw had not heard of it before
13:34 olass but doing anything now results in very VETY ong debugging
13:34 olass see: http://paste2.org/p/706941
13:34 olass and that is just the last part
13:34 olass what I did was:
13:35 olass in console: cdk.getInfo("/demo/aziridine.cml")
13:35 egonw yes, that will trigger quite some debug info
13:35 olass it seems to to some very long initialization that was not the case before
13:35 edrin joined #bioclipse
13:35 egonw yeah, the isotope factory has lazy initialization
13:35 edrin hi
13:35 egonw and long indeed
13:35 zarah oh hai edrin
13:35 egonw hi edrin
13:35 olass can you start this up in plugin activator in background thread?
13:36 olass it blocks the UI now
13:36 egonw the isotope factory?
13:36 egonw yes, think so...
13:36 olass thanks
13:36 olass will file you a bug
13:36 egonw yeah, the debugging to console when running from eclipse makes things really slow...
13:36 egonw the eclipse console is not particularly smart it seems
13:37 olass could you please remove the verbose debugging?
13:37 egonw olass: sorry about that Java6 stuff...
13:37 egonw eclipse is stupid about that too...
13:37 olass it's OK, just took long to find out...
13:37 egonw it sneaks those things in silently
13:37 egonw what verbose debugging do you want me to remove?
13:37 olass cdk debugging
13:38 olass it floods my console
13:38 egonw yes, that's debug mode...
13:38 olass so, how do I switch it off?
13:38 egonw file a feature request for that please...
13:38 egonw for 2.4
13:38 olass ?
13:38 olass it was not there in 2.2
13:38 egonw for a switch
13:38 olass no, I want to shut it off
13:39 olass forever
13:39 egonw with default 'off' if you like
13:39 olass I can't debug my code now
13:39 olass since CDK floods it
13:39 egonw no, I need it for debugging purposes...
13:39 egonw then turn of debug messages?
13:39 olass how do I switch it off in my local checkout?
13:39 olass how?
13:39 egonw why do we have a debug mode if we do not use it?
13:39 egonw dunno...
13:39 egonw I did not write the Bioclipse logger functionality
13:39 olass egonw: how do I switch off CDK debugging so I can see other debug messages?
13:40 olass it was not like this before, clearly you have changed something
13:40 egonw jonalv, Gpox: do you know how to switch Bioclipse from debug logging to mere info, or warn?
13:40 egonw yes, I changed that....
13:40 egonw see the commit messages
13:40 olass egonw: what did you do to get it like this?
13:40 egonw I need this info to debug user bugs
13:40 olass what commit message?
13:40 egonw route CDK logging to the Bioclipse logging facilities
13:40 olass can you please try to be helpful?
13:40 egonw yes, I am...
13:41 egonw but you're not the only one to please
13:41 olass I am trying to do my part for your paper
13:41 olass but your manager does not work
13:41 olass and I cannot debug things
13:41 egonw I offered a switch to turn off CDK debugging... I can make a preference option for that
13:42 olass ok, let me know when that is fixed and bug 1906 is resolved too
13:42 olass for now I cannot go on
13:43 egonw looking at 1906 now...
13:43 egonw we had that before, right?
13:43 egonw do you remember what we had to do to fix that on your machine?
13:56 egonw jonalv: ping
13:59 olass egonw: no, I have never seen that error before
14:00 jonalv egonw: pong
14:01 egonw olass: mmm... I'm sure I did see it before... it's probably xerces again...
14:01 egonw jonalv: how can I trigger something to happen in the background when the Activator is being run...?
14:01 egonw jonalv: is one of those methods being run in the background already?
14:02 jonalv egonw: I guess you could spin of athread from the start method in the activator
14:02 egonw jonalv: or should I fire up a separate background thread from the Activator constructor?
14:02 olass can you reproduce?
14:02 olass egonw: I do this in the QSAR activator
14:02 jonalv egonw: I might need to know a bit more about what you want to do...
14:02 olass it reads the BODO in background
14:03 jonalv olass: so if soemthing needs it before it is done than that thing waits?
14:03 egonw olass: checking...
14:03 olass I have a wait in the manager for all things depending on it
14:04 egonw olass: which qsar plugin?
14:04 olass hmmm
14:04 olass will have to see
14:05 olass qsar.ui Activator
14:05 olass it spawns a job
14:05 olass however, as jonalv says, you ned to implement a join() for all methods depending on it
14:06 olass so maybe not so easy in the case of IsotopeFactory
14:06 egonw setting up an Activator... will that block the UI?
14:06 olass ?
14:06 olass jonalv?
14:06 jonalv egonw: start methods of Activator should finnish fast
14:07 egonw yeah, so I fire up a separate thread
14:20 olass egonw: how will you wait for it?
14:20 egonw not
14:21 olass ok
14:21 egonw if it is not finished, it will try to initialize again...
14:21 egonw it might even do this twice...
14:21 egonw there is threading risk
14:21 egonw but the moment should of actually registering the read data is short...
14:24 egonw Gpox: ping
14:24 Gpox egonw: pong
14:24 egonw I'm looking at the JCP prefs page
14:24 egonw I have a listener there?
14:24 egonw correct?
14:24 egonw that redraws JCP when the pref field has changed?
14:24 egonw GenerateLabelPrefChangedLisener
14:25 egonw (note the missing 't' in the class name :)
14:25 egonw is that the proper way to listen to changed parameters?
14:25 egonw and not to use performOK()?
14:27 Gpox duno
14:27 egonw ok
14:28 Gpox there was someting witht he integration with the context menu
14:30 Gpox And the generated label fix for a bug so I don't know how thought through the implementation is for the whole preferences problem
14:30 egonw no, worries
14:31 egonw I was looking for a mechanism to enable/disable routing CDK message (info, debug, etc...) to the Bioclipse logger ...
14:31 egonw but with performX() I can do it too
14:32 egonw I think
14:32 egonw testing now
14:37 olass egonw: the 1906 is still there, right?
14:38 egonw @pz 1906
14:38 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1906
14:38 egonw @bugzilla 1906
14:38 olass [14:43] < egonw> looking at 1906 now...
14:38 egonw yes, it's still there...
14:39 olass ok, ping me if resolved
14:44 CIA-57 bioclipse.core: Ola Spjuth master * rfbad9f0 / plugins/net.bioclipse.ui/plugin.xml :
14:44 CIA-57 bioclipse.core: updated welcome screen from 2.0 to 2.
14:44 CIA-57 bioclipse.core: Solves #1838. -
14:44 CIA-57 bioclipse.core: Ola Spjuth master * r1b91c85 / (3 files in 3 dirs):
14:44 CIA-57 bioclipse.core: Added "Install Sample Data" to Help menu.
14:44 CIA-57 bioclipse.core: Solves #1899. - http://bit.ly/djvzWe
14:45 egonw argh... too much important email
14:45 egonw overload...
14:46 egonw oh crap
14:46 egonw ok, this solution is not going to work
14:46 egonw CDK is being to smart
14:46 egonw next iteration
15:02 CIA-57 bioclipse.cheminformatics: Egon Willighagen master * r2613ad3 / (6 files in 4 dirs): Added option to enable CDK debugging 2 the Bioclipse Logger (fixes #1909)
15:02 zarah bug #1909 | http://tinyurl.com/y9wekz5
15:07 egonw olass: ping
15:07 egonw olass: I got to leave now...
15:07 egonw I have no clue about 1906...
15:07 olass pong
15:07 olass :(
15:07 egonw I see no missing deps
15:07 egonw it works here
15:07 olass ack...
15:08 egonw o
15:08 olass will be problematic for me to implement
15:08 egonw try the rdf.sparqlRemote method
15:08 egonw myexperiment has some examples
15:08 olass how?
15:08 egonw otherwise ask annzi
15:08 olass about what?
15:08 egonw test if sparqlRemote() works at all...
15:08 olass ok
15:09 olass annzi: how do I test this?
15:09 egonw check the BSL workflows first, please
15:09 egonw on myexperiment.org
15:09 annzi olass: do you want to test a certain query or what?
15:10 olass annzi: you tell me
15:10 egonw annzi: sparqlRemote() does not work at his machine
15:10 olass anthing I guess
15:10 egonw I need to know if that method is not working inseide the ChEMBLManager
15:10 egonw or not at all
15:10 olass egonw: rdf.ui has Java 1.6 in it
15:10 olass can you please fix?
15:11 annzi ok, I haven't tried it my self yet..but I guess you are still running through rdf.sparqlRemote()?
15:13 egonw olass: file a bug report
15:13 egonw got to run now
15:13 olass ok
15:13 annzi *looking into it now*
15:13 egonw will be back after 20:00
15:13 egonw olass: please let me know by email if sparqlRemote() works at all
15:13 olass yes
15:14 olass annzi: just let me know how to try it out
15:25 olass annzi: help?
15:25 annzi olass: I think it is something wrong with the question
15:25 olass you can't get it to work either?
15:25 annzi trying to figure out what
15:25 annzi no
15:25 olass good
15:25 * olass wonders why it works with egonw
15:25 annzi I get an empty list..
15:25 olass I get a stacktrace
15:26 annzi which method do you run?
15:26 annzi qsar?
15:26 olass chembl.getActivities(10885)
15:26 olass see bug 1906
15:26 olass @1906
15:26 olass @pz 1906
15:26 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1906
15:28 annzi olass: sorry but that one works for me…I must have written a competely wring id nr..
15:28 olass strange it does not work here...
15:28 olass :(
15:29 olass what branch are you running of rdf?
15:29 olass master?
15:29 annzi yes
15:34 olass ok, can you give me a query to test with sparqlRemote()
15:34 olass annzi?
15:34 annzi olass: of course
15:35 annzi I will send you the same query to obtain activities. 1 min
15:38 olass thx
15:38 annzi olass:  var sparql = "\
15:38 annzi PREFIX blueobelisk: <http://www.blueobelisk.orgchemistryblogs/> \
15:38 annzi PREFIX chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> \
15:38 annzi SELECT DISTINCT ?act \
15:38 annzi WHERE {\
15:38 annzi ?activ chembl:type ?act; \
15:38 annzi chembl:onAssay ?ass. \
15:38 annzi ?ass chembl:hasTarget\
15:38 annzi <http://rdf.farmbio.uu.se/chembl/target/t10885>. \
15:38 annzi }";
15:39 annzi rdf.sparqlRemote("http://rdf.farmbio.uu.se/chembl/sparql/", sparql)
15:39 zarah annzi's link is also http://tinyurl.com/y8tfzgc
15:39 zarah annzi's link is also http://tinyurl.com/yggj5aw
15:39 zarah annzi's link is also http://tinyurl.com/yb9r9vb
15:39 zarah annzi's link is also http://tinyurl.com/y8ocpuv
15:39 olass annzi: please, pastebin
15:39 annzi ok
15:39 olass annzi: please, pastebin
15:40 annzi http://pastebin.com/XUnkcnBC
15:41 annzi olass: hope it works
15:43 olass same error
15:43 olass javax.xml.stream.FactoryConfigurationError: Provider
15:43 olass com.bea.xml.stream.MXParserFactory not found
15:45 annzi olass: did you check out the whole rdf project now or did you just update it?
15:45 olass git pull
15:47 annzi same here
15:54 annzi olas: btw do you have javax.xml 1.3.4?
15:54 olass how can I tell?
15:55 olass and where should I have it?
15:55 annzi it should be in your workspace in eclipse as a plug-in
15:56 olass yes I have
15:56 olass but there is no dep to it from jena
15:57 olass there is a dep in rdf_feature
15:57 olass ok, I'm stuck
15:58 olass annzi: can you send me a string serialization of what the chembl.getActivities(10885) returns?
15:58 annzi sure,
15:59 annzi olass: [IC50, ND, Ki, Activity, Inhibition, Phorbol displacement, Selectivity, PKC,
15:59 annzi Ratio, ID50, Selectivity ratio]
16:13 olass annzi: what does this lien give you:
16:13 olass chembl.getQSARData( 10885,"IC50" )
16:14 olass can you send me a pastebin of the serialization?
16:14 olass so I know what I am dealing with..
16:26 olass annzi?
16:27 annzi olass: http://pastebin.com/08ghQYMj
16:28 olass danke
16:28 annzi np
17:39 edrin left #bioclipse
18:43 annzi joined #bioclipse
19:00 sneumann joined #bioclipse

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