Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-13

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All times shown according to UTC.

Time Nick Message
00:33 wins joined #bioclipse
01:48 wins joined #bioclipse
05:31 wins joined #bioclipse
06:29 rojasm joined #bioclipse
06:33 egonw joined #bioclipse
06:37 egonw moin
06:37 zarah ni hao egonw
06:37 egonw rojasm: ping
06:40 rojasm hi egonw
06:40 rojasm how are you felling for some breakfast?
06:41 egonw yes
06:41 egonw in 10 minutes?
06:41 egonw I'm late
06:41 egonw just woke up 10 minutes ago
06:41 egonw worked on answering the questions for a Linux Magazine interview abou tthe CDK
06:41 egonw until some 1 o'clock UK time
06:42 rojasm don't worry!
06:42 egonw ummm
06:42 egonw make that 15
06:42 egonw mins
06:42 rojasm :)
06:42 egonw need to shower and pack too
06:43 egonw ok. afk for some minutes now
06:45 Gpox joined #bioclipse
07:02 CIA-40 bioclipse: goglepox * r10285 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
07:02 CIA-40 bioclipse: Added handling of ISubStructure selections
07:02 CIA-40 bioclipse: Fixes bug #1037
07:02 zarah bug #1037 | http://tinyurl.com/qechlm
07:02 olass joined #bioclipse
07:04 olass moin
07:04 zarah ni hao olass
07:04 CIA-40 bioclipse: ospjuth * r10286 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/domain/ISubStructure.java: Added copyright and license.
07:06 Gpox @pz 1037
07:06 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1037
07:58 * sneumann is checking out BC2 from SVN fo the first time ...
08:08 edrin joined #bioclipse
08:09 edrin hi#
08:09 sneumann morning
08:21 CIA-40 bioclipse: goglepox * r10287 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
08:21 CIA-40 bioclipse: Added propertyChangedListener to JChemPaintEditor
08:21 CIA-40 bioclipse: Resovles bug #650
08:21 zarah bug #650 | http://tinyurl.com/p7wtlu
08:22 jonalv joined #bioclipse
08:25 egonw joined #bioclipse
08:25 jonalv hi egonw
08:26 egonw hi jonalv
08:27 maclean joined #bioclipse
08:28 shk3 joined #bioclipse
08:37 CIA-40 bioclipse: ospjuth * r10288 /bioclipse2/trunk/ (39 files in 38 dirs): Set version to 2.0.0.B20090513
08:38 CIA-40 bioclipse: ospjuth * r10289 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Set version to 2.0.0.B20090513
08:41 rojasm joined #bioclipse
08:41 CIA-40 bioclipse: ospjuth * r10290 /bioclipse2/trunk/features/ (12 files in 12 dirs): Set version to 2.0.0.B20090513
08:42 masak joined #bioclipse
08:53 egonw joined #bioclipse
09:03 jonalv egonw: thanx for that beamer thingie btw. Did it work out of the box for you? It seems I am missing a whole lot of neded LaTeX packages... If I only knew how to install LaTeX packages... :(
09:11 egonw I have texlive installed
09:11 egonw at least you need the beamer package
09:11 egonw the thingy I send is only the stylesheet
09:13 olass jonalv: why don't you grab TexShop for mac?
09:14 jonalv egonw: yea I ahve beamer
09:14 jonalv I am missing pkg ztl and other strange stuff
09:14 jonalv I started trying to download .sty files on after another but gave up after a while...
09:14 jonalv olass: I don't know. I sthat better? I have some tex version...
09:14 jonalv olass: I think I installed LaTeX with macports..
09:14 egonw rojasm:
09:14 egonw jcl104.over.slf4j
09:14 egonw and
09:14 olass jonalv: probably does not matter
09:14 egonw slf4j.api
09:15 egonw jonalv: which latex distrib?
09:15 egonw tetex and texlive should both be fine
09:15 egonw but make sure you have the needed optional packages for those distribs
09:16 jonalv egonw: I honestly don't know. I think it's tetex becasue that's the only one I have heard of... :)
09:17 egonw ports--
09:17 * jonalv mutters something about how it probably would have "just worked"™ if he had been on Ubunut
09:17 jonalv |Ubuntu :)
09:18 olass lol... Ubunut
09:18 masak spelling errors are fewer on Ubuntu as well.
09:18 egonw ubernut?
09:20 masak mm, uber-nuts.
09:24 egonw you mean, like the huge blue obelisk?
09:24 * olass is going nuts
09:25 * jonalv tried starting up PowerPoint but it wanted an upgrade and since this piece of crap computer refuses to do upgrades I sort of got tired of all of it...
09:25 * jonalv is going nuts
09:26 * masak is thinking of opening the bag of peas on the desk
09:27 maclean wasabi peas?
09:29 masak maclean: you bet, mister!
09:29 maclean excellent
09:29 masak maclean: it's the nice lady who owns the sushi place who keeps throwing them on us.
09:30 maclean mmmm sushi
09:31 egonw mmm... sounds good
09:31 egonw can you help rojasm with logging trouble?
09:31 egonw he is not finding a class
09:31 egonw and trying to figure out how to get it working with slf4j stuff
09:32 jonalv egonw: Well I am not really having any succedss with LaTeX so maybe. What is the problem?
09:34 egonw mom
09:34 rojasm joined #bioclipse
09:34 egonw rojasm: explain the problem to jonalv please
09:37 rojasm I try to use the method :         IJumboSpectrum spectrum = (IJumboSpectrum)spectrummanager.loadSpectrum( new MockIFile(path));
09:38 rojasm this method is from net.bioclipse.spectrum plugin
09:38 rojasm but I am become some errors
09:40 jonalv rojasm: so you are writing a JUnit test?
09:40 rojasm notclassfound: org/slf4j/LoggerFactory
09:40 rojasm yes. I am using a unittest loading the file as a CMLSpectrum
09:41 jonalv rojasm: How are you running this test?
09:44 rojasm I am running no plugin test
09:45 jonalv oh how I hate logging...
09:45 jonalv perhaps you could try runnign the test as a plugin test?
09:45 jonalv just to see if that works...
09:45 jonalv egonw: could you show him how to set up a plugin test run config?
09:45 egonw yes
09:46 egonw but we need them to run as non-plugin tests right now
09:46 rojasm The thing is that when I run the spectrum.test doesn't fails for me
09:46 egonw as the functionality is not working when run as plugin yet
09:46 rojasm and this test has the same method
09:48 * jonalv is trying to think of some "vanilla flavour" JUnit test that might be using the logging framework when run...
09:48 jonalv but I don't really know what is working and what is not...
09:52 egonw ok, thanx
09:54 jonalv egonw: sry...
09:56 masak if I factor out code written in 2008 and 2009 into a new file, do I mark that file as "(c) 2008-2009" or just "(c) 2009"?
10:05 olass ask egonw
10:05 olass he usually has strong opinions on this
10:05 olass and long experience
10:06 olass masak: if you include some code from 2008, then IMO 2008-2009
10:06 olass but I guess it depends on how much of the code is from 2008
10:06 olass in reality, it matters very little
10:07 olass if it is not central code in an advanced algorithm
10:07 olass (which I assume it is not, since very little code like that exists in Bioclipse)
10:07 masak it's not.
10:08 masak it's the tab completion code, which I extracted so that it can be tested.
10:10 olass go for 2008-2009 I'd say, just to be sure
10:11 * olass is gone for 30 mins to buy a blue car
10:13 egonw masak: git log
10:14 masak egonw: I'll take that as a "2008-2009" answer.
10:14 masak I know the code itself is from 2008, mostly.
10:14 masak (see my original question.)
10:14 egonw masak: surely you can do some Perl magic here
10:14 masak now, let's not go overboard. :)
10:14 masak it's only one file.
10:14 egonw git log | perlgrep masak | perlgrep year | min & max | echo >> foo.java
10:14 egonw git log foo.java | perlgrep masak | perlgrep year | min & max | echo >> foo.java
10:15 masak uhm.
10:16 CIA-40 bioclipse: carl_masak * r10291 /bioclipse2/trunk/plugins/ (9 files in 6 dirs):
10:16 CIA-40 bioclipse: added many missing copyright headers
10:16 CIA-40 bioclipse: Fixed a typo and removed a few extra imports on the way.
10:16 masak lunch &
10:23 rojasm joined #bioclipse
10:24 CIA-40 bioclipse: miguelrojasch * r10292 /bioclipse2/trunk/_playground_/net.bioclipse​.medea/src/net/bioclipse/plugins/medea/core/ (CMLSpectrumCreator.java Medea.java):
10:25 CIA-40 bioclipse: miguelrojasch * r10293 /bioclipse2/trunk/_playground_/net.b​ioclipse.medea/META-INF/MANIFEST.MF: Added dependecies
10:29 CIA-40 bioclipse: miguelrojasch * r10294 /bioclipse2/trunk/_playgroun​d_/net.bioclipse.medea.test/ (4 files in 4 dirs): Added test for learning process in Medea
10:46 sneumann Hi there
10:46 sneumann I have a bugreport,
10:46 sneumann but am too lazy to edit the wiki or pelezilla, so here...
10:46 sneumann Bundle-Name: Bioclipse Scripting
10:46 sneumann net.bioclipse.jsexecution
10:47 sneumann which is not mentioned as dependency on
10:47 sneumann http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
10:47 zarah sneumann's link is also http://tinyurl.com/58kmzp
10:51 CIA-40 bioclipse: miguelrojasch * r10295 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (42 files in 12 dirs): Excluding the package not used. They consist meanly in wizards, action from Bioclispe1
10:53 sneumann so I probably got everything for the core bioclipse from SVN,
10:53 sneumann but on startup I get an java.lang.IllegalArgumentException: The System Bundle's start level can not be modified.
10:53 sneumann I'll check further and report a real question when back.
10:54 CIA-40 bioclipse: miguelrojasch * r10296 /bioclipse2/trunk/_playground_/net.bioclipse.medea​.test/src/net/bioclipse/medea/test/MedeaTest.java: updated to net.bioclipse.medea changes
11:06 shk3 added the plugin in the wiki in checking out bc2
11:07 CIA-40 bioclipse: shk3 * r10297 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (5 files in 4 dirs): made helper methods in manager privat
11:07 CIA-40 bioclipse: shk3 * r10298 /bioclipse2/trunk/plugins/net.bioclipse.​spectrum.test/src/net/bioclipse/spectrum​/business/test/SpectrumManagerTest.java: added a test
11:11 maclean sneumann : the last time that Stefan got this it was because his workspace directory did not have write permissions
11:12 maclean changing the permissions seemed to fix it.
11:13 egonw otherwise, try "Set as Target Platform" once more...
11:13 egonw which cures many different unrelated problem
11:13 egonw s
11:16 CIA-40 bioclipse: gilleain * r10299 /bioclipse2/trunk/_playground_/net.b​ioclipse.medea/META-INF/MANIFEST.MF: Removed bundle version constraints.
11:20 CIA-40 bioclipse: shk3 * r10300 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/lib/JCampParser.jar: jcamp opens files with more than 50 peaks
11:33 sneumann shk3: merci
11:37 sneumann egonw: "Set as Target Platform" helped
11:37 sneumann next thing: get speclipse and medea working from SVN
11:37 sneumann will report
11:43 sneumann zarah: tell egonw "Set as Target Platform" helped
11:43 zarah Consider it noted.
11:52 egonw joined #bioclipse
12:09 CIA-40 bioclipse: gilleain * r10301 /bioclipse2/trunk/cdk-externals/trunk/org.op​enscience.cdk.charges/src/org/openscience/cd​k/charges/GasteigerPEPEPartialCharges.java: Bond counts instead of atom counts.
12:10 CIA-40 bioclipse: miguelrojasch * r10302 /bioclipse2/trunk/_playground_/net.bioc​lipse.medea/src/net/bioclipse/medea/cor​e/learning/ExtractorProbability.java: modify path for picking the data directory
12:16 CIA-40 bioclipse: steinbeck * r10303 /bioclipse2/trunk/features/net.bio​clipse.medea_feature/feature.xml: Added some plugins needed
12:16 * olass has bought a car and regrets it already
12:17 egonw :(
12:17 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
12:17 egonw @msg
12:17 zarah egonw: 1 d 3 h 17 m 1 s ago, jonalv said http://wiki.bioclipse.net/index.ph​p?title=How_to_make_a_manager#The_.40PublishedClass_and_.40P​ublishedMethod_annotations
12:17 zarah egonw: 33 m 14 s ago, sneumann said "Set as Target Platform" helped
12:18 sneumann currently lost in figuring which dependencies medea pulls in.
12:19 egonw sneumann: ack
12:19 sneumann Not exactly lost, but chaining my way through
12:19 egonw sneumann: working on that
12:19 egonw it seems that shk3 has not been running things as features
12:19 egonw just tried to get it running on Chris machine, but that failed too
12:27 sneumann One minor annoyance are
12:27 sneumann DescriptionPathResourceLocationType
12:27 sneumann Manifest has no main sectionnet.bioclipse.cdk.busi​ness/META-INFMANIFEST.MFline 1Plug-in Problem
12:27 sneumann just after checkout
12:27 sneumann inserting a newline and saving the file fixes that
12:27 CIA-40 bioclipse: egonw * r10304 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (2 files in 2 dirs): Linked up the Medea prediction tool
12:28 CIA-40 bioclipse: egonw * r10305 /bioclipse2/trunk/cdk-externals/trunk/ (14 files in 5 dirs): Moved data files to the correct location (see CDK bug #2790735)
12:28 zarah bug #2790735 | http://tinyurl.com/okr234
12:28 egonw sneumann: adding the newline does not just trigger a refresh of the errors on the file?
12:29 egonw where should the newline be?
12:29 sneumann I added that just at the end of manifest
12:29 sneumann as a noop to trigger saving and re-eval
12:29 egonw sneumann: ack
12:29 egonw can you commit?
12:30 sneumann no
12:30 egonw ack
12:31 sneumann cdk.business has many cdk dependencies, do I need to check out these, or are there prepackaged jars somewhere ?
12:32 jonalv I think you need t ocheck them out
12:32 sneumann ah, they are in the externals ?
12:32 sneumann and cdk-externals ...
12:32 egonw some are
12:32 egonw right
12:33 egonw cannot reproduce the 'has no Main' section in cdk.business MANIFEST.MF
12:33 egonw and my version has a newline at the end...
12:33 egonw are you running Windows, or so?
12:34 sneumann Uck. You know me. Dont you ?!
12:34 egonw ic... well, don't think I can fix that...
12:34 sneumann nevermind, was only minor annoyance
12:37 edrin masak, jonalv: do you have a few minutes to try out the xws bc2 xmpp bundle following the instructions here? http://pele.farmbio.uu.se/xmpp​-services/index.php/Fist_steps
12:37 zarah edrin's link is also http://tinyurl.com/qrbqrr
12:38 egonw joined #bioclipse
12:39 jonalv edrin: okey I can do that
12:39 edrin :) great
12:42 CIA-40 bioclipse: miguelrojasch * r10306 /bioclipse2/trunk/cdk-externals/tru​nk/org.openscience.cdk.reaction/src​/org/openscience/cdk/reaction/type/ (2 files): Changing reaction center for some reactions
12:43 CIA-40 bioclipse: goglepox * r10307 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.control/src/org/open​science/cdk/controller/MoveModule.java:
12:43 CIA-40 bioclipse: Removed firing of structureChangedEvent
12:43 CIA-40 bioclipse: [jchempaint-primary@14591]
12:44 CIA-40 bioclipse: goglepox * r10308 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.render/src/org/opens​cience/cdk/renderer/RendererModel.java:
12:44 CIA-40 bioclipse: Added check for null to avoid NPE
12:44 CIA-40 bioclipse: [jchempaint-primary@14590]
12:44 jonalv edrin: org.mozilla.javascript.WrappedException: Wrapped net.bioclipse.xws.exceptions.XmppException: The client is not connected to the server. (line: #18)
12:44 jonalv net.bioclipse.xws.exceptions.XmppException: The client is not connected to the server.
12:44 CIA-40 bioclipse: goglepox * r10309 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
12:44 CIA-40 bioclipse: Clears external selection when structure changed or
12:44 CIA-40 bioclipse: selection is empty
12:46 edrin jonalv: ok, where did this happen?
12:46 jonalv edrin: Do I have to run the scriptsw manually?
12:46 edrin yes
12:46 jonalv oh
12:46 jonalv can't we have actions for running scripts? :)
12:46 jonalv in the cheat sheet :)
12:47 olass we have
12:48 egonw joined #bioclipse
12:48 olass jonalv: there is a RunScriptAction
12:48 jonalv edrin: do I have to run the script that connects before I can run the example script?
12:48 olass but it is not turned on since users should click "run" themselves
12:48 jonalv olass: cool
12:49 olass jonalv: I did this at the cdk workshop...
12:49 edrin we could but i think the js.execute() does this in the console and several scripts dont work in the console because they need dynamic import*
12:49 olass guess you were sleeping
12:49 jonalv olass: yes I thought so, that's why I was a bit suprised when I have to click myself... :)
12:49 olass edrin: right, and there is no JSEditor manager
12:49 edrin right
12:49 olass to click 'that' run button from API
12:49 edrin i know
12:50 edrin will come
12:50 * olass does not like this duplication but will live with it for now
12:50 jonalv edrin: first I connect, then I disconnect and then I try to run a script that requires me to be connected....
12:50 edrin jonalv: what machine are you on? does the following gist work: 47421 ???
12:50 olass edrin: I asked you to fix that
12:50 jonalv edrin: sort of unintuitive I think...
12:50 olass did you not do that?
12:51 sneumann where do I find net.bioclipse.inchi ? I found inchi.business in svn ...
12:51 olass edrin: I wrote you an email about that
12:51 jonalv edrin: took me a while to figure out what was going on... :)
12:51 edrin olass: manager API?
12:51 olass edrin: I wrote you an email about all scripts should start with connect()
12:51 edrin ah
12:51 edrin this
12:51 edrin right
12:51 edrin :)
12:51 olass you forgot?
12:51 edrin yes
12:51 edrin i forgot
12:51 olass :)
12:51 jonalv sneumann: I thought it would be there. IS it not?
12:51 olass jonalv: thanks for the catch
12:52 sneumann Ack, net.bioclipse.inchi == inchi.business
12:52 sneumann project name != svn directory
12:52 jonalv sneumann: oh that is not ideal
12:52 * olass agrees
12:53 jonalv sneumann: however I would prefer if we could leave it a lone until after the big merge tomorrow...
12:54 jonalv olass, edrin: Is it possible to write click to dosnload gist instead of "click to perform"?
12:54 edrin olass: i did this for most gists, just forgot the most important one
12:54 jonalv "click to download gist"
12:54 edrin jonalv: I dont know
12:54 CIA-40 bioclipse: egonw * r10310 /bioclipse2/trunk/_playground_​/org.openscience.cdk.qsarweka/ (15 files in 3 dirs): Version 1.2.2.9 of ChemoJava: API changed to Weka.setData(InputStream)
12:54 jonalv olass: do you know?
12:54 edrin jonalv: does the following gist work: 47421 ???
12:55 edrin olass: i updated the gist that was lacking connect()
12:55 jonalv edrin: org.mozilla.javascript.WrappedException: Wrapped java.lang.ClassCastException: org.apache.xmlbeans.impl.va​lues.XmlComplexContentImpl (line: #38)
12:55 jonalv java.lang.ClassCastException: org.apache.xmlbeans.impl.va​lues.XmlComplexContentImpl
12:55 jonalv
12:55 edrin damn!
12:56 jonalv edrin: it would be really cool if you would use the UserManager for storing the passwords :)
12:57 edrin indeed
13:00 edrin ok, i just got disconnected when running the script :) that's because someone else was using the account at the same time!
13:01 jonalv edrin: how does this long running things work?
13:02 edrin jonalv: did it work?
13:02 jonalv In the Console there is some output claiming that I can check status or terminate. How do I do that? There is also nothing in Bioclispe signalling that I am doing stuff...
13:02 edrin jonalv: i mean didn't it work?
13:02 jonalv edrin: I don't know if it wrked or not
13:03 edrin jonalv: after 3 minutes it reports the result
13:03 jonalv buit the JavaScript does not seem to be running any longer
13:03 jonalv |the JavaScirpt script
13:03 edrin jonalv: this script does not "put itself" in the Bioclipse very well....
13:03 edrin jonalv: it's demoing the xws4j API
13:04 edrin jonalv: it's running somewhere in the background, you cant see it anymore
13:04 edrin hidden
13:04 jonalv edrin: uhm can I be sure about that? Why doesn't it show up as all other JavaScripts?
13:04 edrin jonalv: this async API is not thought to be used for normal scripts atm...
13:05 edrin jonalv: it's like this...
13:05 jonalv edrin: is this a second JavaScript script started from within the first?
13:05 edrin the script adds code to the xws thread that the xws thread will execute when a job is done...
13:05 edrin jonalv: yes, exactly
13:05 sneumann When getting CDK for BC2, can I just stuff CDK-1.2.2 jars into a plugin project ? Or better get stuff from SVN ? Or is SVN outdated and I need git ?!
13:05 edrin jonalv: the second is the "listener"
13:06 shk3 joined #bioclipse
13:06 edrin jonalv: did the output reach your platform?
13:06 jonalv sneumann: SVN should be fine. We have not yet moved the git for Bioclipse
13:06 edrin i mean was the blast printed?
13:06 jonalv edrin: nope I can't see any output
13:06 jonalv edrin: And there is no way of knowing if I am still waiting for it?
13:06 CIA-40 bioclipse: shk3 * r10311 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (3 files in 2 dirs): update of source tab works
13:06 edrin jonalv: maybe someone else was disconnecting you by using the same account
13:07 edrin jonalv: unfortunately no..
13:07 * jonalv tries to run it again then...
13:07 edrin jonalv: wait a second!
13:07 jonalv edrin: too late
13:07 jonalv :)
13:07 egonw SVN is fine
13:07 edrin ok
13:07 egonw joined #bioclipse
13:08 edrin jonalv: please write down the session ID of the process before...
13:08 edrin the XWS- thing
13:08 jonalv XWS-18 and the new one XWS-19
13:08 egonw [15:06:57] <egonw> SVN is fine
13:08 egonw [15:07:07] <egonw> best to use the module bundles in cdk-externals/trunk
13:08 edrin ok...
13:08 jonalv edrin: now I got something back
13:09 edrin jonalv: with this script, by changing the variable of the session ID you can delete the old blast data on the process... please do this... : http://gist.github.com/106046
13:09 jonalv edrin: it would be good if the second listener script was run as a job as well...
13:09 edrin // Modify session ID here!
13:09 edrin var sessionID = "XWS-8";
13:09 edrin jonalv: I know... for bc it would be
13:10 edrin jonalv: the current sample scripts are just easy way to demo the xws4j api... in fact it is just using the plain xws4j api. if you understand the script you know how to use the xws4j library
13:12 edrin jonalv: did terminating the blast work?
13:13 jonalv edrin: it said "termination performed" so I guess so...
13:14 sneumann ack, I found cdk-externals/TRUNK/*
13:14 edrin jonalv: great :)
13:14 jonalv jupp
13:14 egonw sneumann: will check the wiki
13:14 egonw it's so difficult to keep those pages updated :(
13:16 olass jonalv: did we ever file a bug about BioObject implementing ISchedulingRule?
13:16 olass cannot find it...
13:16 jonalv olass: I guess not then...
13:16 egonw sneumann: saw that indentation in Checking_out_Bioclipse was broken regarding org.openscience.cdk.*
13:16 olass jonalv: have you thought more about it?
13:17 egonw sneumann: for MEDEA, you also need stuff from _playgroud_
13:17 olass jonalv: in the NWO this must be important...
13:17 jonalv olass: no not really. When we realise that we need it it should not be too hard to add though...
13:17 olass agreed
13:17 olass will file a bug anyway
13:17 jonalv oki
13:17 sneumann http://apps.sourceforge.net/mediawiki/cdk/ind​ex.php?title=Main_Page#Download_CDK_Releases
13:17 zarah sneumann's link is also http://tinyurl.com/4ln8ve
13:18 * jonalv keeps feeling that there might be strange threading issuses waiting for us out there...
13:18 sneumann has s is available (1.2.1 on Sourceforge), as well as a dev
13:18 sneumann whereas you already have 1.2.2
13:18 egonw I'm on it
13:21 egonw fixed
13:21 egonw the link actually is OK
13:21 egonw thanx
13:22 edrin jonalv: ok, everything except the HIV thing worked well?
13:23 jonalv edrin: gonna have a look at the second cheat sheet
13:24 jonalv edrin: oh maybe this is the first one...
13:24 jonalv edrin: uhm should they be run in a certain order if so maybe give them numbers?
13:24 CIA-40 bioclipse: egonw * r10312 /bioclipse2/trunk/_playground_/net​.bioclipse.medea/src/net/bioclipse​/medea/business/MedeaManager.java: Fixed import: package name was incorrect
13:28 edrin jonalv: no, you can run them in any order
13:31 jonalv egonw: does the gist manager add .js to all files now?
13:31 egonw if that was commited, yes...
13:31 jonalv okey
13:31 egonw but it is only supposed to go into the XMPP demo bundle
13:31 jonalv aha
13:31 egonw awaiting a better fix later
13:31 jonalv that explains why it works like that (I am in that bundle)
13:32 jonalv egonw: what would be a better fix?
13:32 jonalv edrin++ //Things seeem to be working
13:32 egonw jonalv: check PZ
13:33 egonw @pz gist
13:33 zarah [980] Error on exiting bioclipse when... http://tinyurl.com/q6x3wd
13:33 zarah [898] Adapt scripts on http://wiki.bi... http://tinyurl.com/cugxk5
13:33 zarah [263] Option to disable gist.load() s... http://tinyurl.com/qxnyn7
13:33 zarah [790] Mediawiki extension for Gists      http://tinyurl.com/odlbud
13:33 zarah [254] Remove /Virtual in favor of a f... http://tinyurl.com/q2xrxp
13:33 zarah Entire list (19) at http://tinyurl.com/p4vp3o
13:33 egonw @pz gist js
13:33 zarah [980] Error on exiting bioclipse when... http://tinyurl.com/q6x3wd
13:33 zarah [790] Mediawiki extension for Gists      http://tinyurl.com/odlbud
13:33 zarah [900] add net.bioclipse.test.gist        http://tinyurl.com/qa6nlq
13:33 zarah [922] Downloaded gists should save fi... http://tinyurl.com/qfgpuw
13:33 zarah [839] Download GIST NewWizard does no... http://tinyurl.com/qjygf3
13:33 zarah Entire list (9) at http://tinyurl.com/qmomhy
13:34 egonw mmm... none of these...
13:34 egonw @pz igist
13:34 zarah [1041] Introduce IGist & Gist with AP... http://tinyurl.com/o4sday
13:34 zarah Entire list at http://tinyurl.com/rbvpsm
13:34 egonw that's the one
13:34 egonw @pz 1041
13:34 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1041
13:34 jonalv egonw: would that help?
13:35 egonw yes
13:35 jonalv egonw: how? :)
13:37 egonw String IGist.getFileName() ?
13:38 jonalv egonw: ah that is the filename declared for the gist?
13:38 egonw what else?
13:38 egonw IGist is not a IFile like thing
13:38 CIA-40 bioclipse: egonw * r10313 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.dict/src/org/opensci​ence/cdk/dict/DictionaryDatabase.java: Removed debug to STDOUT
13:38 jonalv egonw: no idea. I am being stupid...
13:38 egonw no, curious
13:39 jonalv egonw: well, that too :)
13:39 CIA-40 bioclipse: miguelrojasch * r10314 /bioclipse2/trunk/_playground_/net​.bioclipse.medea/src/net/bioclipse​/medea/business/MedeaManager.java: forgot imports
13:40 CIA-40 bioclipse: ospjuth * r10315 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Clear all tests on change in JCP. Also removed some debugging code.
13:45 edrin jonalv: thanks for testing
13:46 jonalv edrin: I love testing :)
13:46 edrin great
13:50 CIA-40 bioclipse: miguelrojasch * r10316 /bioclipse2/trunk/_playground_/org.opensc​ience.cdk.qsarweka/src/org/openscience/ch​emojava/qsar/model/weka/J48WModel.java: Changed String path of the table for InputStream
14:11 CIA-40 bioclipse: egonw * r10317 /bioclipse2/trunk/cdk-externals/trunk​/org.openscience.cdk.dict/src/org/ope​nscience/cdk/dict/data/elements.owl: Duplicated data file, because it is not picked up by the DictionaryDatabase from the cdk.atomtype bundle (note added to CDK #2790735)
14:15 shk3 joined #bioclipse
14:17 sneumann OK, I got everything working _except_ medea
14:18 sneumann (Well, everything I wanted ;-)
14:18 sneumann DescriptionResourcePathLocationType
14:18 sneumann Bc_MEDEAPlugin.UNSET cannot be resolvedBc_MEDEAPlugin.javanet.bioclip​se.medea/src/net/bioclipse/pluginsline 116Java Problem
14:18 egonw_ joined #bioclipse
14:18 sneumann egonw: please check my last 4 lines in the logs
14:18 sneumann Ah, split personality.
14:19 sneumann Then check my last 4 lines right here ;-)
14:22 egonw_ yes, medea feature fixing is on my schedule...
14:24 sneumann Is net.bioclipse.seneca needed by medea.case somewhere ?
14:24 egonw_ yes
14:24 egonw_ but you do not need medea.case at this moment
14:24 sneumann "Close project" ;-)
14:26 egonw_ right
14:26 egonw_ that will come soon, I think
14:27 CIA-40 bioclipse: ospjuth * r10318 /bioclipse2/trunk/plugins/net.bioclipse.ds​/src/net/bioclipse/ds/model/IDSTest.java: Removed deprecated test method that took a TestRun as input.
14:28 CIA-40 bioclipse: ospjuth * r10319 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Adapted smarts tests for removed runWarningTest method.
14:28 sneumann Anything I can help with medea or testing  ?
14:29 CIA-40 bioclipse: miguelrojasch * r10320 /bioclipse2/trunk/_playground_/net.bioc​lipse.medea/src/net/bioclipse/medea/cor​e/learning/ExtractorProbability.java: remove imports
14:29 CIA-40 bioclipse: miguelrojasch * r10321 /bioclipse2/trunk/_playground_/net.biocli​pse.medea/src/net/bioclipse/medea/core/pr​ediction/AdministratorFilesReader.java: Changed String path of the table for InputStream
14:29 CIA-40 bioclipse: ospjuth * r10322 /bioclipse2/trunk/plugins/net.bi​oclipse.ds.dblookup.bursi/data/ (. cas_withprops.sdf): Added SDF with data for bursi lookup. Includes FP, inchi, and inchikey.
14:30 egonw_ joined #bioclipse
14:30 CIA-40 bioclipse: gilleain * r10323 /bioclipse2/trunk/_playground_/net.bio​clipse.medea.case/src/net/bioclipse/pl​ugins/extensions/WCCMedeaJudge.java:
14:30 CIA-40 bioclipse: - Wrong medea import line.
14:30 CIA-40 bioclipse: - Unimplemented judge method.
14:49 CIA-40 bioclipse: ospjuth * r10324 /bioclipse2/trunk/plugins/net.bioclipse.ds​/src/net/bioclipse/ds/model/IDSTest.java: Added Bioclipse Exception to runWarningTest().
14:49 CIA-40 bioclipse: ospjuth * r10325 /bioclipse2/trunk/plugins/​net.bioclipse.ds.dblookup/ (3 files in 2 dirs): Added a stub for ExactDBLookup based on Inchi and/or InchiKey.
14:50 CIA-40 bioclipse: ospjuth * r10326 /bioclipse2/trunk/plugins/net​.bioclipse.ds.dblookup.bursi/ (5 files in 3 dirs): Contributed an ExactDBlookup on preprocessed Bursi (=Ames) SDF.
14:53 CIA-40 bioclipse: egonw * r10327 /medea-paper/ (. trunk/): Set up folder for the MEDEA paper
15:00 CIA-40 bioclipse: egonw * r10328 /bioclipse2/trunk/_playground_/ (5 files in 3 dirs): Cleaning up reading from InputStream... not done yet, but need to catch plane now and want to share with Miguel
15:01 CIA-40 bioclipse: gilleain * r10329 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Rendering of arrows.
15:04 egonw_ catching plane
15:08 CIA-40 bioclipse: ospjuth * r10330 /bioclipse2/trunk/plugins/net.bioclip​se.ds.dblookup/META-INF/MANIFEST.MF: Export the impl package to make tests visible.
15:10 CIA-40 bioclipse: ospjuth * r10331 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.dblookup.bursi/plugin.xml: Renamed lookup test to exact.lookup.bursi since a nearest neighbour test will come soon.
15:10 maclean joined #bioclipse
15:13 shk3 joined #bioclipse
15:15 CIA-40 bioclipse: ospjuth * r10332 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Catch if a data file is missing from extension.
15:15 CIA-40 bioclipse: ospjuth * r10333 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.dblookup.bursi/plugin.xml: Declared data file for exact bursi lookup test extension.
15:16 CIA-40 bioclipse: ospjuth * r10334 /bioclipse2/trunk/plugins/net.bioclip​se.ds.dblookup/src/net/bioclipse/ds/d​blookup/impl/DBExactMatchTest.java: Throw exception if a required data file is missing from Test extension.
15:19 CIA-40 bioclipse: gilleain * r10335 /bioclipse2/trunk/ (4 files in 3 dirs):
15:19 CIA-40 bioclipse: - Getter/setter for the arrowHeadWidth.
15:19 CIA-40 bioclipse: - Tidied code in the AWTDrawVisitor.
15:25 CIA-40 bioclipse: ospjuth * r10336 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Fixed so the InchiKey is generated when asked for. Previously, both getInchi() and getInchiKey() returned the InChi.
15:42 CIA-40 bioclipse: ospjuth * r10337 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/model/TestHelper.java: Extended helper class to also read EP subelements 'parameter'.
15:45 CIA-40 bioclipse: ospjuth * r10338 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added stub for nearest neighbour DB lookup based on fingerprints. Requires a database file and a distance.tanimoto parameter declared in extension.
15:46 CIA-40 bioclipse: ospjuth * r10339 /bioclipse2/trunk/plugins/net.bioclipse.ds.test​s/src/net/bioclipse/ds/tests/TestDBLookup.java: Adde test for DBLookup exact and nearest neighbour.
15:52 CIA-40 bioclipse: ospjuth * r10340 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/n​et/bioclipse/ds/model/AbstractWarningTest.java: Made default toString() return the name of test.
15:52 CIA-40 bioclipse: ospjuth * r10341 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.dblookup.bursi/plugin.xml: Changed names of tests to separate exact matches from nearest neighbours.
16:28 CIA-40 bioclipse: carl_masak * r10342 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java:
16:28 CIA-40 bioclipse: [UIManager] whitespace therapy
16:28 CIA-40 bioclipse: - Removed excess empty lines
16:28 CIA-40 bioclipse: - Removed unused imports
16:28 CIA-40 bioclipse: - Aligned things vertically
16:28 CIA-40 bioclipse: - Shortened >80 char lines
16:29 CIA-40 bioclipse: - Removed stale commented-out code
16:29 CIA-40 bioclipse: carl_masak * r10343 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java:
16:29 CIA-40 bioclipse: [UIManager] fix #745
16:29 CIA-40 bioclipse: ui.remove now squals an IllegalArgumentException if the file is not there
16:29 CIA-40 bioclipse: to remove.
17:29 CIA-40 bioclipse: ospjuth * r10344 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationWorkbenchAdvisor.java: Automatic updates: Only install feature patches if contains a plugin that has greater version than the installed plugin. Hopefully fixes #943 but needs verification in released version.
17:29 zarah bug #943 | http://tinyurl.com/pcjhx7
17:32 olass edrin: hopefully r10344 resolves the auto install of feature patch that you experienced
17:33 olass it should (tested it here at least)
17:34 edrin ok
17:34 edrin olass: and the hivpred schema thing?
17:34 edrin hm
17:34 edrin going home soon
17:35 olass edrin: no success
17:35 olass I am stuck
17:35 olass really need your help
17:40 olass edrin: what jar is incorrect?
17:43 edrin olass: what jar?
17:43 edrin olass: no, i mean, i wonder what this problem is that the hivpred script is not working
17:43 edrin the cast exception
17:43 olass yes
17:43 olass do you not think it is the wrong jar?
17:44 olass some place?
17:44 olass maybe not ...
17:44 * olass is trying to reproduce
17:45 olass aaaah
17:45 olass edrin: progress
17:45 edrin oh?
17:45 edrin !?
17:46 olass it works if I do not have the se.uu.farmbio.hivpred plugin installed
17:46 olass hmmmmmmm
17:46 edrin ic
17:46 edrin is there xmlbeans in!?
17:46 edrin or some lib used by xmlbeans?
17:46 edrin causing incompatibility?
17:47 olass no idea
17:48 olass have no idea about xmlbeans, never used it
17:48 olass will probably need your help looking at it
17:50 olass but at least we have a start...
17:54 olass edrin: the hivpred plugin contributes a binding generated with EMF
17:54 olass edrin: could the script somehow get an instance of something that the hivpred plugin also provides?
17:56 olass EMF has quite some plugins in xml
17:57 olass se hivpred.model
17:57 olass no idea which could be conflicting
18:02 wins joined #bioclipse
18:07 olass edrin: still here?
18:11 edrin olass: yes
18:11 olass investigating an interesting lead
18:12 edrin is EMF having XMLBeans behind the scence?
18:12 olass no
18:12 olass looking at the deps now
18:13 olass nope
18:13 olass that was not it :(
18:14 edrin but it is for sure strictly depending on the presence of hivpred?
18:22 edrin olass: you are right, I can reproduce this error on my laptop when adding the hivpred plugins to the bc instance
18:22 olass must be some dep problem
18:22 olass or namespace issue
18:22 edrin olass: the problem must be associated with the hivpred plugin
18:23 olass I don't know enough of xml to resolve this
18:23 olass maybe egonw can help
18:23 olass (or you)
18:23 edrin namespace? no, it must be some lib that is also used by xmlbeans
18:23 olass what is reall ycausing the error?
18:23 olass I found 2 jars that were duplicated
18:23 olass 1) resolver.jar
18:24 edrin i think xmlbeans uses some lib
18:24 edrin ok
18:24 olass in hivpred.model: there is org.apache.resolver plugin
18:24 olass replaced the jar with the plugin
18:24 olass did not solve problem :(
18:24 olass so
18:25 edrin replaced the jar with the plugin -> what do you mean?
18:25 olass if there is an eclipse plugin: do not add a jar, use that plugin instead
18:25 olass ok?
18:25 edrin where?
18:26 olass there was a jar (resolver.jar) in net.bc.xws4j jars folder
18:26 olass hivpred.model added the eclipse plugin org.apache.resolver
18:26 olass they provide the same packages
18:26 olass (or similar at least)
18:26 olass I thought they could conflict
18:26 olass but that was not it
18:26 edrin ok, ic. olass suggestion to solve:
18:27 edrin olass: why do you think this is not the problem?
18:27 olass no idea
18:27 olass I am just guessing
18:27 edrin olass: suggestion:
18:27 olass incompatibility in deps in some way
18:28 edrin replace the resolver.jar in your eclipse installation/plugin with the resolver.jar from the xws4j plugin for now?
18:29 olass cannot do that
18:29 olass really no idea how
18:29 olass and should really be the other way around
18:29 olass please experiment you too
18:29 olass need to go offline now
18:29 olass see you tomorrow
18:29 edrin ciao
18:29 olass happy hunting
18:29 olass bye
19:22 edrin left #bioclipse
20:27 rojasm joined #bioclipse
20:39 CIA-40 bioclipse: miguelrojasch * r10345 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (data/ src/data/): Changed datat directory to src
21:14 CIA-40 bioclipse: miguelrojasch * r10346 /bioclipse2/trunk/plugins/​net.bioclipse.data.medea/: Initial import creating the plugin data.medea
21:46 CIA-40 bioclipse: miguelrojasch * r10347 /bioclipse2/trunk/plugins/​net.bioclipse.data.medea/ (18 files in 11 dirs): Initial import creating the plugin data.medea
21:47 CIA-40 bioclipse: miguelrojasch * r10348 /bioclipse2/trunk/_playground_/net.biocli​pse.medea/src/net/bioclipse/medea/core/pr​ediction/AdministratorFilesReader.java: Changed datat directory to src
22:23 CIA-40 bioclipse: miguelrojasch * r10349 /bioclipse2/trunk/plugins/​net.bioclipse.data.medea/ (5 files in 3 dirs): Added the molecule and the spectrum for the compound 30460-92-5 from Nist database
22:25 CIA-40 bioclipse: miguelrojasch * r10350 /bioclipse2/trunk/_playground_/​net.bioclipse.medea/plugin.xml: modified errors in the plugin
22:31 CIA-40 bioclipse: miguelrojasch * r10351 /bioclipse2/trunk/plugins/net.bioclipse.d​ata.medea/data/Javascripts/prediction.js: load molecule of the file instead of smiles
22:50 CIA-40 bioclipse: egonw * r10352 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added cdk.isConnected (fixes #1056)
22:50 zarah bug #1056 | http://tinyurl.com/pzfvj4
22:54 CIA-40 bioclipse: egonw * r10353 /bioclipse2/trunk/plugins/net.bioclipse.cdk.bus​iness.test/src/net/bioclipse/cdk/business/test/ (AbstractCDKManagerPluginTest.java CDKManagerTest.java): Added unit tests for bug #1006
22:54 zarah bug #1006 | http://tinyurl.com/qlaovx
22:54 CIA-40 bioclipse: egonw * r10354 /bioclipse2/trunk/plugins/ne​t.bioclipse.doc.developers/ (4 files in 2 dirs): Added build.xml to generate the HTML docs (requires perl + xsltproc, fixes #792)
22:54 zarah bug #792 | http://tinyurl.com/p44thy
22:56 CIA-40 bioclipse: egonw * r10355 /bioclipse2/trunk/ (14 files in 11 dirs): Implemented IMolecule.Property to indicate how urgent a property should be calculated (implements #1043)
22:57 CIA-40 bioclipse: egonw * r10356 /bioclipse2/trunk/plugins/ (7 files in 5 dirs): Made ICDKMolecule properties use IMolecule.Property (implements #1042)
22:57 CIA-40 bioclipse: egonw * r10357 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Removed two obsolete and unused methods; use instead getSMILES(IMolecule.Property.USE_CACHED)
22:58 CIA-40 bioclipse: egonw * r10358 /bioclipse2/trunk/plugins/ (9 files in 7 dirs): Refactored to use an InChI object, so that calculation of both the InChI and InChIKey of a molecule, will run the InChI generation only once
22:59 CIA-40 bioclipse: egonw * r10359 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated script for current API
22:59 CIA-40 bioclipse: egonw * r10360 /bioclipse2/trunk/plugins/net.biocli​pse.chemoinformatics/cheatsheets/Gen​eralChemoinformaticsCheatSheet.xml: Fixed typos and outdated info

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