Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-13

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Time Nick Message
07:07 egonw joined #bioclipse
07:27 CIA-55 bioclipse: egonw * r8786 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: Uploaded Jmol bug fix release 11.6.16
07:49 CIA-55 bioclipse: egonw * r8787 /bioclipse2/trunk/cdk-externals/trunk/ (30 files in 10 dirs): Updated from jchempaint-primary (commit 14177)
08:15 Gpox joined #bioclipse
08:15 egonw hi Gpox
08:15 egonw Gpox: I have updated JCP from jchempaint-primary
08:15 egonw with the help of gilleain
08:18 CIA-55 bioclipse: egonw * r8788 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.control/src/org/opensc​ience/cdk/controller/ControllerHub.java: Fixed two NPE sources
08:27 olass joined #bioclipse
08:27 olass moin
08:27 olass hi
08:27 olass @ping
08:27 zarah olass: pong
08:28 egonw olass: does any data_install extension get it's own project?
08:28 egonw or do all end up in a single project?
08:28 olass drugbank creates its own project, if that's what you mean
08:29 egonw ok, that's indeed what I wanted to know
08:29 egonw because it still also has a DrugBank folder...
08:29 olass there are menas for this in the recent changes of the EP
08:29 egonw which is kind of redundant then
08:29 olass yes
08:29 olass please remove that one
08:29 egonw will fix that
08:29 olass it SHOULD work
08:29 olass please file bug if it doesn't and I'll fix it
08:30 egonw btw: http://pele.farmbio.uu.se/bioclipse/docs/eps/
08:30 zarah egonw's link is also http://tinyurl.com/czt988
08:30 olass the key thing here is that you can reuse the net.bc.data wizard
08:30 egonw it does, irght?
08:30 olass I saw that
08:30 egonw you did that, not?
08:30 olass nice
08:30 olass yes
08:31 olass Egon: this is nice
08:31 olass but it is not really what bug 318 was about
08:31 olass maybe I made myself unclear
08:31 olass will comment in bug
08:32 egonw oh... yes, please do :)
08:32 olass I mean, the docs are REALLY great
08:32 egonw good we now verify things actually being fixed :)
08:32 olass indeed
08:34 egonw Gpox, olass: I tried the CDKMolecule property source last night
08:34 egonw but did not get it to work
08:34 egonw CDKMOlecule getAdapter() is not called
08:34 egonw not even the BioResource.getAdapter
08:34 olass BioResource is BC1
08:34 olass BioObject
08:34 egonw BioObjet ?
08:34 egonw the super class of CDKMolecule
08:34 olass hmm
08:34 olass hmm
08:34 olass that used t owork...
08:34 olass Gpox: do you know anything about this?
08:35 egonw it works for selections in the Outline
08:35 egonw but I don't get it working for things in the MDLmolfile editor
08:35 egonw Gpox: and I did not see properties either when I selected an entry in the SDFEditor
08:35 egonw so, this morning I'll focus on Pref pages...
08:36 CIA-55 bioclipse: goglepox * r8789 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintView.java: Changed how JChemPaintView reacts on selections resolves bug #15
08:36 zarah bug #015 | http://tinyurl.com/5nrsdv
08:36 CIA-55 bioclipse: goglepox * r8790 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculeTable.java: Removed deprecated class
08:36 Gpox Is there a CDKMoleculePropertySource?
08:36 zarah Gpox: You have new messages. Write '/msg zarah @messages' to read them.
08:36 egonw ah, maybe this fix also does help my bug...
08:37 egonw Gpox: no, I made CDKMolecule implement IPropertySource
08:37 egonw at least as a start
08:37 egonw Gpox: but since getAdapter() was not being called... I could not get it to pass an new class anyway
08:41 Gpox how do you check that?
08:41 Gpox is the PropertySource changes commited?
08:42 Gpox because getAdapter in CDKMolecule is called for IPropertySource
08:42 egonw no, did not commit, because it did not work
08:43 egonw break point
08:43 egonw in CDKMolecule.getAdapter()
08:43 egonw Gpox: yes, that's what I guessed... but it did not happen :(
08:43 egonw OK, I'll try again... in particular, commit 8789 looks relevant...
08:44 egonw Gpox: something else...
08:44 egonw we really need drawing on an empty canvas working, not necessarily today, but at least for 2.0
08:44 Gpox no i only changed things in JChemPaintView
08:44 egonw Gpox: oh :(
08:44 egonw ok
08:49 steinbeck joined #bioclipse
08:49 steinbeck moin
08:50 egonw hi steinbeck!
08:50 steinbeck Hi egonw
09:14 olass egonw, Gpox: I need to build beta2 today
09:15 olass Could you settle with finishing up at 13?
09:15 egonw olass: yes, sounds good
09:15 olass Gpox?
09:17 olass I just want to make sure you have no open refactorings at that time that would compromize the beta2 release
09:17 olass but I know, you work in patches so that should not be a problem
09:18 Gpox ok
09:26 olass egonw: How about that BO data repository?
09:26 olass we had that in bc1
09:27 olass since it is SO easy to add more data, compiling a feature/plugin with data takes 3 minutes
09:27 egonw will ask jerome on #cdk
09:27 olass please do
09:27 egonw but, yes, we can still distrib the data from bc1
09:27 olass sure, just check it is not in sample-data
09:28 olass I have a feeling that there is some overlap
09:28 egonw yes, very likely
09:29 olass AFAIK, sample data took some sample data from BO
09:29 olass well, I did I guess :-)
09:30 olass egonw: should I set it up for BC2?
09:30 olass I think I will do it faster than you...
09:32 egonw yes,please do
09:32 egonw olass: use version 2.1
09:32 egonw see this blog item:
09:32 egonw http://pansanel.blogspot.com/2008/01​/chemical-structures-release-21.html
09:32 zarah egonw's link is also http://tinyurl.com/agzjve
09:33 egonw no, there should be a newer one...
09:33 olass egonw: can you look into how to generate Javadoc API for Bioclipse in Eclipse? It should be straightforward...
09:33 olass and should be part of the Help
09:33 olass ok, will file a bug :-)
09:34 egonw of a developers feature?
09:34 egonw sounds good
09:34 olass hmm
09:34 egonw was thinking the same thing
09:34 olass API for all plugins
09:34 olass like Eclipse does
09:34 egonw yes, but should not end up in bioclipse by default
09:34 olass indeed
09:34 olass right
09:34 olass I see your point
09:35 olass Eclipse is for development, Bioclipse is for working :-)
09:35 egonw right
09:35 olass a devel feature would be nice
09:35 olass will file a bug
09:35 olass cdk-debug could go in there
09:35 olass right?
09:36 olass hmm, maybe not
09:36 olass that would require dep to cdk
09:36 egonw right, no need for that
09:36 olass on the other hand, a devel feature might be OK to require some libs
09:36 olass right
09:36 olass a chemoinfo-devel feature in the future
09:36 olass :-)
09:36 egonw 2.1 does seem to be the latest version:
09:36 egonw http://pansanel.blogspot.com/2008/01​/chemical-structures-release-21.html
09:37 zarah egonw's link is also http://tinyurl.com/agzjve
09:37 egonw https://sourceforge.net/project​/showfiles.php?group_id=169897
09:37 olass is this the latest?
09:37 egonw yes, it seems so
09:37 egonw but I know he was talking to carsten about an update
09:37 olass I hate SF links with https...
09:43 olass egonw: a question
09:43 olass jpansanel calls it "chemical structures"
09:43 olass can we really call it BO data repository then?
09:44 egonw yes
09:44 egonw see the blue obelisk web site
09:44 egonw it's listed there
09:44 egonw btw, I like the idea of a Blue Obelisk dinner in Stockholm
09:45 olass yes
09:55 olass egonw: so id=net.bioclipse.data.blueobelisk and name "Blue Obelisk Data Repository" is good?
09:56 olass or "Blue Obelisk Chemical Structures Repository"?
10:01 egonw second, please
10:02 olass ok
10:13 olass egonw: I might need your help with this after all
10:14 egonw just put a pref page in the wrong plugin :(
10:14 olass I need to remove all non-mol/cml files from the BO data
10:14 olass I am not so fluent with bash/unix commands
10:14 egonw I am...
10:14 olass could you help me?
10:14 egonw please commit
10:14 egonw file a bug report
10:14 olass will do
10:14 egonw will finish the current bug fix I am working on...
10:15 olass ok
10:15 egonw first
10:16 CIA-55 bioclipse: ospjuth * r8791 /bioclipse2/trunk/plugins/net​.bioclipse.data.blueobelisk/: Initial import.
10:25 edrin joined #bioclipse
10:29 egonw oi oi oi...
10:30 egonw another new bug :(
10:30 egonw guys, we *really* need unit testing...
10:31 olass yes
10:33 olass we have unit testing
10:33 olass it's just not extensive
10:34 olass and I donät understand why people don't run it
10:34 olass just because it is not run automatically doesn't mean you can't run it manually!
10:34 egonw well... and the plain lack of unit tests...
10:35 egonw in the CDK, each new bug first results in a new unit test
10:35 egonw in bioclipse we just 'fix' it...
10:35 egonw so it can easily get broken later again, without anyone noticing
10:35 olass I know
10:35 olass this is something we really should improve in the future
10:52 olass egonw: this commit will take a while
10:53 olass getting really slow UL speed
10:53 egonw ok
10:53 olass at 10 % now...
10:54 olass grrr SF is so damn SLOW sometimes!
11:21 CIA-55 bioclipse: ospjuth * r8792 /bioclipse2/trunk/plugins/net.b​ioclipse.data.blueobelisk/data/ (3434 files in 33 dirs): Updated BO data repo 2.1. Contains non-molecule files that needs removal.
11:29 egonw OK, done with the first CDK pref page
11:29 egonw fixing bug 300 along the line
11:30 CIA-55 bioclipse: egonw * r8793 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fixed a NPE: just assume zero implicit hydrogens if atom type is not recognized
11:32 egonw quote "People fear computers becoming smarter and taking over the world, but currently computers are not very smart and they already have taken over the world! "
11:33 egonw from: http://friendfeed.com/e/0d59cf14-1622​-b278-677c-e60e5b311ffc/Artificial-In​telligence-researcher-Pedro-Domingos/
11:33 zarah egonw's link is also http://tinyurl.com/bkzqs5
11:33 CIA-55 bioclipse: egonw * r8794 /bioclipse2/trunk/cdk-externals/trun​k/org.openscience.cdk.libiocml/src/ (4 files in 3 dirs): Patched the CMLWriter to have the option to not output the XML declaration
11:34 CIA-55 bioclipse: egonw * r8795 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (5 files in 2 dirs): Added a preference page for how to output CML with CDKMolecule.getCML()
11:35 CIA-55 bioclipse: egonw * r8796 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Rewrote code to do nice indentation again, but without the XML declaration which broken embedding of the CML in other snippets earlier (fixes #300)
11:35 zarah bug #300 | http://tinyurl.com/cgqh23
11:44 egonw http://www.steinbeck-molecular.de/steinblog​/index.php/2009/02/13/open-notebook-science​open-drug-discovery-at-gdch-nation-meeting/
11:44 zarah egonw's link is also http://tinyurl.com/ae6zee
11:44 egonw check out the speaker list ;)
11:47 olass looks great
11:47 olass congrats
11:54 jonalv joined #bioclipse
11:54 jonalv oh hai
11:54 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
11:55 egonw hej jonalv
11:56 egonw olass: do you want *all* HTML removed?
11:56 egonw or shall we keep in the _en.html ?
11:57 egonw nevermind
11:57 egonw all the data in the HTML should be part of the CML anyway
11:57 egonw if not, we'll file bug reports
11:57 egonw the HTML should really just be a derive from the CML
12:09 egonw olass: removing the HTML is slow too :)
12:10 egonw Gpox: is there a reason why there are not icons for:
12:10 egonw 1. deleting atoms and bonds
12:10 egonw 2. drawing other rings in addition to benzene?
12:15 egonw olass: ping
12:15 egonw how are we doing in terms of the time?
12:15 egonw we're past the commit deadline now...
12:15 egonw the HTML removal commit is still in progress...
12:17 jonalv edrin: Could you write a doctors certificate for me describing that it is not good for my health to be forced into writing my lab repports using MS Word? ;)
12:18 egonw hahaha...
12:18 edrin oh is it not?
12:18 jonalv I am pretty sure itäs doing bad thing to my blood pressure
12:19 jonalv :)
12:19 edrin jonalv: here we even have to do it with a MS Word running on a remote desktop windows machine we have to connect to... sometimes in 16 colors only.
12:19 edrin this is doing bad things on our blood pressure
12:20 jonalv but... why?
12:20 olass egonw: pong
12:20 olass I still need one hour probably
12:20 egonw ok
12:20 olass and then some testing
12:20 edrin and it gets even worse when we have to use the Adobe Photoshop on the remote machine in 16 colors, and dragging&dropping stuff on a remote screen is very evil, too
12:21 olass jonalv: is it possible for you to test on windows?
12:21 olass in 1-2 hours?
12:21 jonalv olass: technically yes, schematically no not really
12:21 edrin jonalv: this is because of our system admin.................
12:21 olass jonalv: practivally is sufficient answer
12:21 jonalv olass: I might be able to take a quick test run
12:21 olass ok
12:22 olass soudns good
12:22 olass just see if it boots in enough
12:22 olass it's just a beta2
12:23 edrin this means, everyone here has a core 2 duo machine, with Windows 2000 running, we are not allowed to install *any* software, only a MS Word 6.0 (from 1995?) is preinstalled. everything else must be done on the remote desktop...
12:23 olass egonw: my subclipse seriously broke things with bo data repo
12:23 olass were you able to cehck it out?
12:24 edrin they are doing this to save time... this way they have to install stuff only on one server
12:24 egonw yes, no problem
12:24 olass all data?
12:24 olass how big was it?
12:25 egonw dunno
12:25 olass ok
12:25 CIA-55 bioclipse: ospjuth * r8797 /bioclipse2/trunk/plugins/net​.bioclipse.data.blueobelisk/ (13 files in 8 dirs): Updated for src files in bo data.
12:25 egonw ~5MB
12:25 egonw 5.4
12:25 olass damn
12:26 egonw jonalv: ping
12:26 olass hmmm
12:26 jonalv egonw: yes?
12:26 egonw olass: too, actually
12:26 egonw trying to run the CDKManagerTest
12:26 egonw and it fails on CDKMOlecule.toString
12:26 egonw because that is using the Activitor
12:26 olass sry, no time
12:27 egonw which is actually null
12:27 egonw which means that when we do things properly, unit testing only from a PluginTest makes sense
12:27 jonalv egonw: yes it would mean that, or you could mock
12:28 olass egonw: that is what I have been telling you all the time :-)
12:28 olass but unit tests are important too
12:28 olass as they run fast
12:29 egonw yeah, but not if they fail if run incorrectly
12:29 CIA-55 bioclipse: egonw * r8798 /bioclipse2/trunk/plugins/net.b​ioclipse.data.blueobelisk/data/ (2182 files in 32 dirs): Removed HTML (fixes #485)
12:29 zarah bug #485 | http://tinyurl.com/csxx3y
12:29 egonw hahahaha...
12:29 egonw 2128 files :)
12:30 olass was that the nasty hack?
12:32 egonw no, that's behind us already
12:36 egonw olass: sorry...
12:37 egonw but there are a few bugs in the CDKManager/CDKMolecule which really needs fixing...
12:37 olass ok
12:37 egonw so, I hope I indeed still have 23 minutes
12:37 olass no worries
12:37 olass it must be today
12:37 olass and I have to leave at like 17
12:37 egonw and I won't bother sending bug reports to the authors this time
12:37 olass just do it :-)
12:38 olass I am struggling here too
12:45 CIA-55 bioclipse: egonw * r8799 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Fixed unit test: actually test something; removed use of toString() which always fails with a NPE when not run as plugin test
12:46 CIA-55 bioclipse: egonw * r8800 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Don't set the Prefs ahead of initialization, but in the constructor. Fixes a NPE
12:47 CIA-55 bioclipse: egonw * r8801 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Reuse local constructors to increase consistency
12:47 CIA-55 bioclipse: egonw * r8802 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Take into account the use case where the manager is used, but not in a plugin setting (as with CDKManagerTest)
12:48 CIA-55 bioclipse: egonw * r8803 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Fixed a unit test: -> UNIT TESTS ARE SUPPOSED TO TEST SOMETHING <- (come on, that's basic, not??)
12:48 egonw olass: yes, getting foul again
12:49 olass :-)
12:49 olass you have my support
12:52 egonw and right now... all tests of the CDKManagerPluginTest fail
12:52 egonw because I cannot instantiate a CDKManager
12:53 egonw jonalv: ping
12:53 jonalv egonw: yes
12:53 egonw jonalv: where did we put that call again, to force loading of a manager earlier this week?
12:53 jonalv egonw: I can't remember
12:54 egonw ok
12:54 egonw neither do I
12:54 jonalv in the beforeclass?
12:54 egonw I'll search
12:54 egonw yes, that sounds like it
12:54 egonw tack!
12:55 egonw jonalv: it actually fails just after our net.bioclipse.ui.Activator.getDefault()
12:55 egonw so that was not a fix, but a mere conincidence that it worked after adding that line :(
12:55 jonalv egonw: is this a pluign test_
12:56 egonw yes
12:56 jonalv k
12:57 olass egonw: what version is the drugbank plugin?
12:57 egonw dunno... copied something from another plugin
12:57 olass oh
12:57 egonw Bsomething, I guess
12:57 olass ok, will use bioclipse versioning then
12:57 olass no, I mean the actual data
12:58 egonw oh
12:58 olass does it have a version?
12:58 egonw umm... no idea when we copied it
12:59 olass ok
12:59 olass will be bc versioning for now then
13:00 egonw yes
13:05 CIA-55 bioclipse: ospjuth * r8804 /bioclipse2/trunk/plugins/net​.bioclipse.data.blueobelisk/ (6 files in 3 dirs): Added extension of EP to install BO data repo. Solves bug #486.
13:05 zarah bug #486 | http://tinyurl.com/celc3e
13:06 CIA-55 bioclipse: ospjuth * r8805 /bioclipse2/trunk/plugins/ (14 files in 13 dirs): Set version to 2.0.0.B20090213. This is Beta2 release, taking versioning in parts.
13:07 egonw f**k
13:07 CIA-55 bioclipse: ospjuth * r8806 /bioclipse2/trunk/plugins/net​.bioclipse.data.blueobelisk/ (build.properties plugin.xml): Updated name and build.props to include data on export.
13:10 olass EGONW: ABOUT THE INCHI PLUGIN
13:10 olass oops
13:10 olass did not mean to shout
13:10 olass caps lock horror
13:10 olass anyways
13:10 egonw right...
13:10 olass egonw: how about the inchi plugin?
13:10 egonw mom
13:10 olass you were talking about an easy fix
13:11 egonw yes
13:11 egonw jonalv: ping
13:11 olass 30 mins?
13:11 olass more?
13:11 egonw jonalv: what was that osgi> command line again to list plugin states?
13:11 egonw olass: yes, should work...
13:11 jonalv egonw: ss
13:13 egonw jonalv: ACTIVE is good, right?
13:13 jonalv egonw: uhm depends on whether you want it to be running...
13:13 olass masak: around?
13:14 egonw oh... OK, right
13:14 egonw so, not good :(
13:14 egonw RUNNING should be the state... ok
13:14 egonw ok, that's the problem then
13:14 egonw sort of fits the picture...
13:14 jonalv olass: I think I see masak in #farmbio
13:14 egonw cdkbla.Activator.getDefault() returns null...
13:14 olass right
13:14 egonw for I don't know what reason :(
13:18 CIA-55 bioclipse: egonw * r8807 /bioclipse2/trunk/plugins/net.bioclipse.gi​st/src/net/bioclipse/gist/Activator.java: Fixed the error message: correct manager name
13:18 jonalv Is olas building next Bioclipse relase today?
13:18 olass yes
13:18 olass in 30 mins
13:19 egonw can anyone else try to run CDKManagerPluginTest, please?
13:19 CIA-55 bioclipse: egonw * r8808 /bioclipse2/trunk/plugins/net.bioclipse.​inchi.business.test/src/net/bioclipse/in​chi/business/test/InChIManagerTest.java: Added unit test for situations where not stereochemistry is given: creating InChI should not fail on that
13:19 jonalv and the webservices? WSDb+fetch. Are they going in?
13:19 olass jonalv: why do you ask?
13:19 jonalv "pz 464
13:20 jonalv @pz 464
13:20 zarah http://tinyurl.com/afd97m
13:20 jonalv @pz 463
13:20 zarah http://tinyurl.com/djs457
13:20 egonw how do I get a manager to send a message to the console?
13:21 jonalv egonw: use js.print
13:21 egonw js is which manager?
13:21 jonalv the javascript manager
13:21 olass jonalv: it is a beta2
13:21 jonalv okey
13:21 olass RC it would not
13:22 olass ok with you?
13:22 olass we have many otehr bugs open...
13:22 * jonalv dives back into receptor lab now
13:22 olass I agree it is not good
13:22 egonw olass: inchi is in
13:22 egonw fixed the problem
13:23 olass great
13:23 olass egonw++
13:24 egonw can anyone else try to run CDKManagerPluginTest, please?
13:24 egonw can anyone else try to run CDKManagerPluginTest, please?
13:24 egonw can anyone else try to run CDKManagerPluginTest, please?
13:24 zarah can anyone else try to run CDKManagerPluginTest, please?
13:25 olass egonw: ok
13:25 CIA-55 bioclipse: egonw * r8809 /bioclipse2/trunk/plugins/net.bioclipse.​inchi.business.test/src/net/bioclipse/in​chi/business/test/InChIManagerTest.java: Fixed the unit test: the correct InChI
13:25 CIA-55 bioclipse: ospjuth * r8810 /bioclipse2/trunk/ (18 files in 18 dirs): Set version to 2.0.0.B20090213. This is Beta2 release, second half of plugins.
13:26 CIA-55 bioclipse: egonw * r8811 /bioclipse2/trunk/plugins/net.biocli​pse.inchi.business/src/net/bioclipse​/inchi/business/InChIManager.java: Don't fail if we get a warning: that just typically indicates missing info on the input, such as undefined stereo centeres (see InChIManagerTest.testGenerateStereo())
13:26 egonw on one hand it is nice, two days of just hacking after a while of just meeting and writing...
13:26 egonw but then again...
13:27 egonw you find so many stupid bugs all over the place
13:29 olass ok egonw, did run it
13:29 olass I see failures
13:29 egonw but it runs?
13:30 olass sure
13:30 egonw well.. not here...
13:30 olass it can be a mess
13:30 egonw ok, what is the fail rate?
13:30 olass this is how I solve it
13:30 olass hmm
13:30 olass 11 Errors 1 fails total is 49
13:30 olass set target platform
13:31 egonw ack will try
13:31 olass in run config, remove all, add required plugins 2 times, run
13:31 olass perhaps create a new run config
13:31 olass but yes, it runs here
13:33 edrin jonalv: is your web service bug still active?
13:33 jonalv edrin: I guess so
13:34 edrin jonalv: so downloading file fails?
13:34 edrin or opening the file?
13:34 jonalv edrin: I can try again...
13:34 edrin or only if the file was only downloaded  2x ?
13:34 jonalv gah now it deletes all html files I just saw it downlaod last time I rebased
13:34 jonalv what are you people doing_
13:34 edrin or the file was "incomplete" deleted in the meantime?
13:35 edrin jonalv: ?
13:35 edrin why html files?
13:35 olass jonalv: read commit messages and you will understand
13:35 edrin is this plugin related?
13:36 maclean joined #bioclipse
13:36 jonalv edrin: I was talking about rebasing Bioclipse
13:37 edrin rebasing? what does this mean?
13:37 jonalv zarah: google git rebase
13:37 zarah jonalv: http://www.kernel.org/pub/softwa​re/scm/git/docs/git-rebase.html
13:38 CIA-55 bioclipse: ospjuth * r8812 /bioclipse2/trunk/features/ (5 files in 5 dirs): Set version to 2.0.0.B20090213. This is Beta2 release, features.
13:39 olass edrin: why have you set LGPL on net.bc.jseditor?
13:39 olass we only have EPL on our plugins here
13:40 olass Can I change it?
13:40 olass if not we cannot have the plugin in Bioclipse
13:40 edrin oh it should be EPL?
13:41 olass edrin: yes, that is an official demand on all our core bioclipse plugins
13:41 edrin sure, i will change it at weekend then
13:41 olass I am building now
13:41 edrin ok
13:41 olass please change now
13:41 olass else it will miss beta2 release
13:41 edrin i cant, i am not home
13:41 olass :-(
13:41 olass sry
13:41 edrin you can change it if you want
13:41 olass ok, will do
13:42 edrin how does the license look?
13:42 olass EPL?
13:42 edrin olass: in webservice plugin, there are some files with lgpl, too
13:42 egonw edrin: that is no problem
13:42 edrin why not?
13:42 jonalv edrin: it seems to be working now
13:42 egonw as long as the BC related code it EPL
13:42 olass edrin: I have told you many times we use EPL in Bioclipse
13:42 olass we link in LGPL
13:43 edrin ah
13:43 edrin ok
13:43 olass ok?
13:43 olass good
13:43 edrin yes sure
13:43 egonw edrin: that is no problem <- if is is third party stuff
13:43 olass all our code is EPL
13:43 edrin ok, dont mind
13:43 edrin dont even know epl
13:43 olass linked in libs (like cdk or xws4j) can be LGPL as far as I'm concerned
13:43 olass @gg eclipse public license
13:43 zarah olass: http://www.eclipse.org/legal/epl-v10.html
13:44 edrin olass: yes, i was talking about some source .java files in the webservice plugin... there are very few of them that have the same header...
13:45 olass please change them as soon as you can
13:45 edrin i think for example the ResourceCreator file
13:45 olass will file yopu a bug
13:45 edrin jonalv: ok, if it is working, can you disable the bug?
13:45 olass edrin: are you really reading your bug list on a regular basis?
13:45 olass need to know if I can rely on that
13:46 olass when it comes to releases
13:46 edrin i think so
13:47 edrin i get emails
13:47 olass you need to review it constantly
13:47 edrin how can i see bugs assigned to me?
13:47 olass you donät get emails for everything
13:47 olass :-(
13:47 olass I guess that answers my question....
13:48 olass @pz
13:48 zarah olass: Pelezilla is at http://bugs.bioclipse.net
13:48 egonw grmp...
13:48 egonw my patch won't commit...
13:48 olass click Search existing bug reports
13:48 olass edrin: this is for you
13:48 edrin yes
13:48 edrin and then?
13:48 olass in box Email adresses,. Bug ....
13:49 edrin Zarro Boogs found.
13:49 olass in left textarea, write "aliban"
13:49 edrin i am logged in
13:49 olass [14:51] < olass> in left textarea, write "aliban"
13:49 edrin Zarro Boogs found.
13:49 olass in Status, I usually select NEW, ASSIGNED, and REOPENED
13:50 olass and in Target I click "2.0" to only see bugs for the 2.0 release
13:50 edrin olass: yes, this i somehow got
13:50 olass I see your bugs
13:51 edrin and what did you enter?
13:51 olass aliban
13:51 olass [14:52] < olass> in Status, I usually select NEW, ASSIGNED, and REOPENED
13:52 olass http://pele.farmbio.uu.se/cgi-bin/bugzilla/bugl​ist.cgi?query_format=advanced&amp;short_desc_ty​pe=allwordssubstr&amp;short_desc=&amp;long_desc​_type=substring&amp;long_desc=&amp;bug_file_loc​_type=allwordssubstr&amp;bug_file_loc=&amp;dead​linefrom=&amp;deadlineto=&amp;bug_status=NEW&am​p;bug_status=ASSIGNED&amp;bug_status=REOPENED&a​mp;emailassigned_to1=1&amp;emailtype1=substring​&amp;email1=aliban&amp;emailassigned_to2=1&amp;​emailreporter2=1&amp;emailcc2=1&amp;emailtype2=​substring&amp;email2=&amp;bugidtype=include&amp​;bug_id=&amp;votes=&amp;chfieldfrom=&amp;
13:52 edrin ah advanced search
13:52 zarah olass's link is also http://tinyurl.com/cha64r
13:52 olass sure
13:54 edrin ok, they are all resolved I think, except the writing sample scripts
13:54 CIA-55 bioclipse: ospjuth * r8813 /bioclipse2/trunk/plugins/net.biocl​ipse.jseditor/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090213 and updated props for JSeditor plugin.
13:54 edrin back in 10 min
13:54 olass edrin: please mark as resolved
13:55 CIA-55 bioclipse: ospjuth * r8814 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Replaced net.sf.jseditor with net.bioclipse.jseditor.
13:56 maclean olass: can I close #430
13:56 maclean + ?
13:56 olass why do you ask me?
13:56 maclean @bug 430
13:56 olass mom
13:56 zarah http://tinyurl.com/dbhapw
13:56 maclean I ask you on the grounds that you opened (and re-opened :) it...
13:56 olass maclean, no , please mark as fixed
13:57 maclean oky
13:57 olass then I see it, and then I will try it
13:57 olass then close it
13:57 olass :-)
13:57 maclean or reopen it...
13:58 olass @tell masak: js.jar exists in net.bioclipse.jseditor but also in net.bioclipse.scripting.
13:58 zarah Consider it noted.
13:58 olass @tell edrin: js.jar exists in net.bioclipse.jseditor but also in net.bioclipse.scripting.
13:58 zarah Consider it noted.
13:58 olass grr
13:59 olass lets hope it is the same version at least
13:59 maclean egonw : so can I set bug #482 to FIXED? I saw you updated cdk-external.
13:59 CIA-55 bioclipse: ospjuth * r8815 /bioclipse2/trunk/plugins/net.bio​clipse.jseditor/build.properties: Updated build to include icons.
14:00 egonw @pz #482
14:00 zarah http://tinyurl.com/b36k93
14:00 egonw yes, maclean fixed that
14:00 maclean ok
14:01 egonw hahahaha
14:01 egonw though ola asked about that one being FIXED
14:01 egonw which I addressed you in third person when replying :)
14:01 maclean yeah thought so
14:01 maclean :)
14:01 egonw olass: plugin unit test failed, because the workspace was messed up... deleting it solved it...
14:02 egonw olass: I get 12 failures too...
14:02 CIA-55 bioclipse: ospjuth * r8816 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/ (5 files in 4 dirs): Removed js.jar from jseditor as it should depend on net.bc.scripting which provides this jar.
14:02 egonw checking them now
14:02 olass ok
14:02 olass good
14:02 maclean by the way, about the oval highlight, Gpox - is the intention to have an circle for each bond (so 2 for a double bond, 3 for a triple..)?
14:03 egonw oh.. btw, can you check rendering of triple bonds?
14:03 egonw it fails for me
14:03 egonw jonalv: I got for UnsupportedOperation fails in CDKManagerPluginTest
14:03 jonalv egonw: four?
14:04 maclean in bioclipse-jcp?
14:05 * maclean assumes so, and will test there
14:05 maclean I know it works in swing-jcp, so it's probably the renderer options
14:06 egonw maclean: yes, rendering opts in bc-jcp is up next for me
14:07 maclean I can do that - do you want the facade approach of a published method for each option?
14:07 maclean (only the sensible ones - the user should not be setting the scale, or the color map, I think)
14:08 egonw I think everything should be available from the command line...
14:08 egonw even scale...
14:08 maclean hmmm, I don't
14:08 egonw GUI will only contain save stuff...
14:08 egonw zoom: yes, scale: no
14:09 egonw color map -> what's that then?
14:09 egonw not how atoms are colored,
14:09 maclean zoom - for sure
14:09 * olass is building now
14:09 egonw but an internal map of allocated colors?
14:09 CIA-55 bioclipse: ospjuth * r8817 /bioclipse2/trunk/plugins/​net.bioclipse.ui/toc.xml: Fixed incorrect Help paths.
14:09 egonw that should indeed not be visible
14:09 maclean egonw : exactly
14:09 egonw OK, that calls for a split up of rendering options...
14:10 egonw of implementation specific stuff
14:10 egonw and user settable stuff
14:10 egonw -t
14:10 maclean egonw : well, that's what the internal RenderingParameters was for :)
14:11 olass @tell masak: output from running JSEditor is not in Javascript Console
14:11 zarah Consider it noted.
14:13 egonw maclean: btw, sure, you're welcome to implement your suggestion
14:13 maclean hmmm, forgot about that - invalid thread access.
14:13 egonw maclean: but I don't want to keep you too much from CASE stuff
14:13 maclean egonw : okay, will do
14:13 egonw but it's your call
14:14 edrin olass: it is the same version
14:14 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
14:15 olass edrin: I have replaced it
14:15 edrin olass: will the xws4j plugin be in the release?
14:15 olass see r8816
14:15 olass release is SF release
14:15 olass xws4j will be on update site, yes
14:15 edrin ah
14:15 edrin then
14:15 edrin there is still one problem
14:16 edrin we must find a way to "import" the exports of xws4j in the jseditor and scripting console plugin
14:16 edrin at runtime
14:17 edrin as we do not want everything to depend on xws4j
14:17 olass edrin: this is too late for anything
14:17 olass no time
14:17 edrin otherwise we can not use the Async API of xws4j  in bioclipse scripting
14:17 olass if things don't work, it will not go on update site
14:17 olass deadline was yesterday, as you know
14:17 edrin olass: the thing works
14:18 olass ok
14:18 edrin olass: i am talking about a general issue
14:18 olass please, not now
14:18 olass too busy with release
14:18 edrin ok
14:18 olass file a bug or write email
14:18 edrin is it a release candidate or a beta?
14:18 olass beta2
14:18 edrin ah ok
14:18 olass that's why webservices can go
14:18 edrin i will write an email
14:18 olass and jseditor
14:19 olass since they really do not live up to demands of an RC
14:19 olass with open bugs
14:19 olass in pelezilla
14:19 olass and untested
14:22 CIA-55 bioclipse: gilleain * r8818 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java:
14:22 CIA-55 bioclipse: - 'Highlight radius model' is no longer used.
14:22 CIA-55 bioclipse: - 'Bond distance' is now specified in screen space, not model space.
14:23 maclean egonw : that fixes the double/triple bonds.
14:23 egonw ok, thanx... great
14:23 egonw olass: it's too late for the release, I guess?
14:24 maclean :( sorry olass, I read the thing earlier about only sending patches...
14:24 olass not yet
14:24 olass have not built final
14:24 edrin olass: did the test of webservice work for you?
14:24 olass taking things step by step
14:24 olass edrin: no time now
14:24 edrin ok
14:24 * olass is building
14:25 olass and testing
14:25 olass edrin: I got a pdb
14:25 olass so that sort of worked
14:25 edrin yes
14:25 olass but managers still have failing tests
14:25 edrin good
14:25 edrin do they?
14:25 olass last I ran them
14:25 olass maclean: we are not using patches yet
14:26 maclean ok
14:26 edrin i could not figure out why the tests did not work
14:26 olass edrin: part is that cdk cannot parse pdb
14:26 edrin i dont even know what they test ;)
14:26 edrin ah
14:26 edrin ok, this i cannot change
14:27 olass it's a cdk thing
14:27 olass filed for 2.1
14:28 olass but please make the tests test that the manager actually works for a number of test cases
14:28 olass without using cdk
14:28 olass theu MUST pass in order to make 2.0.0
14:28 olass but you can test them in other ways
14:28 edrin ok
14:28 olass like e.g. compare to an already downloaded pdb
14:29 olass ok, final call
14:29 olass I am syncing for binary build
14:30 olass all is well so far
14:30 olass have tested a binary on mac
14:30 olass egonw: can you test on linux?
14:30 egonw yes
14:30 olass in 10 mins or so I guess
14:33 CIA-55 bioclipse: ospjuth * r8819 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Final bioclipse.product for beta2.
14:34 egonw A20090123 -> A20090213 ... subtle... took me some seconds to spot it :)
14:35 olass B
14:35 CIA-55 bioclipse: ospjuth * r8820 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: bioclipse.product now has correct version as well: 2.0.0.B20090213
14:36 olass egonw: I never learn: are you on 32 bit or 64?
14:36 egonw 32
14:36 olass good
14:40 olass Bioclipse2beta2 is ~63 Mb
14:40 olass for download
14:41 egonw link?
14:42 egonw 5 bioclipse paper cites now
14:43 egonw 3 self-cites, 1 broad revies, 1 real
14:43 olass on pele
14:43 egonw it's a start
14:43 olass /home/ola/bioclipse/.
14:43 egonw ack
14:43 olass linux version is there in 30 secs
14:43 olass oh no
14:43 olass :-(
14:43 olass 6 mins...
14:44 egonw ah, I can see it grow
14:44 olass ok
14:44 egonw 50MB to go
14:46 edrin egonw: do you have PMIDs of the articles citing bc ?
14:47 egonw DOIs
14:47 edrin whatever
14:47 edrin links
14:47 edrin url pls
14:47 egonw 10.1021/ac070741j
14:47 edrin :)
14:47 egonw no, not even DOIs for all
14:47 egonw WoS is not everything...
14:48 edrin hm
14:48 edrin google fails
14:48 zarah edrin: http://failblog.org/
14:48 egonw edrin: will email
14:48 edrin :)
14:48 egonw google fails?
14:48 zarah egonw: http://failblog.org/
14:48 egonw on what?
14:48 edrin with the 10.1021/ac070741j
14:49 egonw why not resolve the normal way:
14:49 egonw dx.doi.org/DOI
14:49 egonw thus: dx.doi.org/10.1021/ac070741j
14:50 edrin ok, got it
14:50 olass egonw: UL finished, please test
14:51 egonw olass: downloading
14:51 egonw ETA: 4m
14:52 edrin egonw, olass: plz read&comment&add to the manuscript outline today/weekend saturday morning,
14:52 edrin i want to compile stuff together
14:52 egonw yes
14:52 egonw edrin: BC2 beta is almost done...
14:52 edrin next week two medics are coming back and need help from me
14:52 olass what do you mean with compile stuff together?
14:52 egonw after that it's a week of a lot of writing..
14:52 egonw including yours
14:52 edrin ok
14:53 edrin olass: i will add citations, reformat stuff
14:53 edrin update wiki
14:53 edrin prepare wiki rather
14:54 edrin next week an other project will start, and this will consume my time
14:56 egonw olass: ping
14:57 egonw olass: in the welcome screen... the text is in between the background and the icons -> unreadable
14:57 egonw btw, intro++
14:57 egonw really nice work!
14:58 edrin oh
14:59 egonw installing new features -> points to a general welcome cheat sheet... intentional, or just missing proper cheat sheet?
14:59 edrin thx, got your mail
14:59 edrin egonw: <-
15:00 egonw ack
15:01 olass egonw: that is an eclipse error, nothing we can do about it
15:01 egonw ah, OK
15:01 egonw was just wondering...
15:02 olass egonw: it runs?
15:02 olass in 40 secs you can test the update site
15:03 egonw yes, it runs...
15:03 egonw and I did not spot regressions
15:03 olass any errors?
15:03 egonw extractsmiles.js does not work
15:04 olass file bugs
15:04 olass ut's a beta2
15:04 olass now I will upload to SF
15:04 egonw yes, sounds like a good plan
15:04 olass have to assume win version works
15:04 jonalv oh hai
15:04 egonw will take forever too :)
15:04 olass yes
15:04 jonalv was there a windows verison?
15:04 jonalv did someone test that one?
15:04 olass no
15:04 olass can you?
15:04 egonw olass: please put them on pele
15:05 olass ok
15:05 egonw all, then I can continue upload
15:05 jonalv yea I can. can I have a link?
15:05 egonw olass: better...
15:05 egonw I'll upload them all...
15:05 edrin extractsmiles.js <- is this run in the jseditor?
15:05 egonw so that you can spend the last 40 minutes on writing a blog item
15:05 olass egonw: yes, that is better
15:05 egonw edrin: yes
15:05 olass great
15:05 * olass is uploading to pele
15:05 olass need to build 3 more versions as well :-)
15:06 egonw right
15:06 edrin egonw: are other .js working in jseditor?
15:06 olass edrin: it is probably an error of the script
15:06 edrin egonw: did it not work because of jseditor?
15:06 egonw edrin: dunno... did not test that
15:06 edrin ok, so other .js are working
15:06 egonw will explore later
15:06 olass jonalv: ETA 6 mins for win version on pele
15:06 jonalv oki
15:07 olass egonw: please test update site
15:07 olass I cannot do it here
15:07 olass seems to work
15:07 olass but no time to DL all
15:07 egonw olass: tested drugbank feature
15:08 egonw that worked fine
15:08 olass please test all
15:08 edrin egonw: did you test it from .js script?
15:08 egonw olass: doing so...
15:09 egonw I do miss a few things
15:09 egonw I think
15:09 olass :-)
15:09 egonw CDK Feature
15:09 olass ?
15:09 olass that is not in release
15:09 egonw why not?
15:09 olass mom
15:09 olass but easy to add if you like
15:10 olass does inchi work?
15:10 olass any other feature you are missing?
15:10 olass well, too late ti remove inchi now anyways
15:10 egonw inchi should work fine now
15:11 olass "should" :-)
15:11 olass please test xmpp
15:11 egonw tested it on a few entries in the DrugBank SDF
15:11 egonw the thing why it was failing so much...
15:11 egonw it has a feature to fail on warnings...
15:11 olass test on a file in sampledata with only 2D coordinates
15:11 egonw for example when the input is not clear on stereochemistry
15:12 egonw which it often is not
15:12 olass ok
15:12 egonw and I had it fail on that
15:12 egonw but fixed that
15:12 egonw seems to work fine
15:12 olass good
15:12 olass how is 2D editing?
15:12 egonw good
15:12 egonw I like the moving of selections
15:12 olass I don't
15:12 egonw there are a few remaining issues...
15:12 olass indeed
15:12 egonw like drawing on an empty canvas
15:12 edrin egonw: is the jseditor working "in general" ?
15:13 olass edrin: it send s output to  some rhino console instead of JSConsole
15:13 olass bad
15:13 egonw no, JSeditor is not working
15:13 edrin olass: no, not bad, we were discussing this
15:13 egonw Wrapped org.eclipse.core.runtime.AssertionFailedException: null argument: (line: #1)
15:13 olass edrin: did you not test the jseditor?
15:14 edrin i did, it worked for me
15:14 olass exporting to binary?
15:14 edrin egonw> Wrapped org.eclipse.core.runtime.AssertionFailedException: null argument: (line: #1) <- that's an error in the script
15:14 olass egonw: add a new js line
15:14 olass js file
15:14 olass cdk.fromSMILES("CC").getCML()
15:14 olass that worked for me
15:14 maclean olass : you don't like the moving of selections?
15:14 edrin egonw: create a .js file and add xmpp.connect();
15:15 maclean whyfor not?
15:15 jonalv @pz
15:15 zarah jonalv: Pelezilla is at http://bugs.bioclipse.net
15:15 egonw confirmed
15:15 olass maclean: it should not highlight in outline when a user hovers over an atom
15:15 egonw the scripts are bad
15:15 egonw not the editor
15:15 olass AND
15:15 edrin phuuu
15:15 egonw can't see the difference yet, though
15:15 maclean olass : that's not moving of selections.
15:15 olass ah
15:15 olass ok
15:16 olass hovering over a symbol is not indicated currently
15:16 olass that is a major thing for me
15:16 maclean indicated how?
15:16 maclean it's indicated with a highlight element
15:16 olass hover over a bond -> indicated
15:17 olass hover over an atom not rendered as a symbol -> indicated
15:17 olass hover over an atom rendered as a symbol -> not indicated
15:17 egonw olass: I think that's because the highlite is smaller than the symbol
15:17 egonw I see that now and then too
15:17 maclean yes
15:18 maclean this is why
15:18 olass well, it's bad now
15:18 maclean also, it's underneath
15:19 edrin olass: regarding the "printing to another console issue" we were discussing this, and i think we agreed that it is totally confusing if a scipt prints to the jsconsole
15:19 olass ok, if you and masak agrees on it then I'm fine with it
15:19 edrin i think so
15:19 edrin masak: aruond?
15:19 edrin no
15:19 olass no
15:19 edrin jonalv: do you remember?
15:19 jonalv edrin: no not really
15:20 olass edrin: I'd really like you to make things certain in the future
15:20 jonalv edrin: where shoudl output go then?
15:20 edrin jonalv: on a console for scripts run from editor
15:20 olass edrin: please send email to bioclipse-devel discussing things
15:20 egonw olass: the whitespace of the symbol needs to be transparent...
15:20 edrin i am currently writing one
15:20 olass egonw: I just want it to work
15:20 olass spare me the details :-)
15:21 * olass donät know a thing about 2D drawing
15:21 jonalv edrin: I think I remember saying that you and masak should come up with a solution. Anyway that's what I think now.
15:22 CIA-55 bioclipse: gilleain * r8821 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Bumped up the highlight distance to make it visible under atom symbols.
15:22 olass juuuust a bit too late
15:22 maclean egonw: no the symbol has to have an opaque background in order to write over the bonds
15:22 maclean oops
15:23 maclean sorry
15:23 olass egonw: could you please tag?
15:23 edrin i think we said that it makes sense to not queue all scripts in one loop to have the possibility of parallel scripts, and that it makes sense to not print stuff from the editor to the console, because this does not make sense as these are two independent contexts
15:23 olass that last commit will sort of be in the wrong place...
15:24 olass edrin: masak is not here
15:24 olass please use email
15:26 edrin olass: one thing we should change is the two options: run in main thread and run in its own thread, I agree
15:31 * egonw making the tag
15:31 egonw not entirely correct
15:31 egonw as it will contain the two patches from gilleain
15:32 CIA-55 bioclipse: egonw * r8822 /bioclipse2/tags/2.0.0.B20090213/: Tagged the second beta release
15:32 maclean oh well, there's always the rc. :)
15:32 egonw indeed
15:33 maclean and anyway, my last commit brought out a bug in the highlight generator...
15:34 egonw :)
15:35 maclean Gpox didn't say, but do we really want a circle per bond for the highlight?
15:35 maclean it kind of makes a lozenge shape for double bonds
15:35 egonw one single oval, I'd say
15:35 maclean ah good - that's what I've just changed it to :)
15:36 maclean (sorry Gpox...)
15:36 Gpox no it was just to visulaize the highlight radius trying to fix the context menu
15:37 Gpox It used to use the bond generator and change the width
15:37 Gpox dunno where that whent
15:38 maclean it was making an anonymous visitor, and visiting all the generated line elements, then making an oval element for each
15:38 egonw olass: don't forget the solaris version
15:38 jonalv olass: ETA Windows version?
15:38 egonw jonalv: -10m
15:39 egonw jonalv: on pele
15:39 maclean but, the main thing was that most parameters are now specified in screen space, and then scaled down to model space when needed
15:39 egonw home/ola/bioclipse/bioclipse-2.0​.0.B20090213.win32.win32.x86.zip
15:39 maclean like double highlightRadiusModel = model.getHighlightDistance() / model.getScale()
15:39 jonalv in ten minutes?
15:39 egonw no, 10minutes ago
15:39 jonalv oh
15:40 * jonalv stops waiting then :)
15:40 egonw :)
15:44 egonw beta2 uploaded to SF
15:45 egonw win32, os/x, linux, 32bit only at this moment
15:45 egonw olass: can we still expect 64bit and solaris flavors?
15:48 maclean oh!
15:48 maclean it's Friday 13th
15:49 maclean no wonder I forgot my passcard...
15:49 jonalv hm the jchempaint teditor is named cml file editor. Is that really correct? Can it handle a cml file with multiple molecules? Can it handle a cml file with a spectrum? egonw ?
15:49 egonw see wiki.bioclipse.net
15:49 egonw no, it cannot
15:49 maclean cml file with mol+spectrum = specmol?
15:49 edrin jonalv: is the jseditor working for you?
15:49 egonw it's still CML
15:50 egonw it's *a* CMLEditor
15:50 egonw not *the* CMLEditor
15:50 jonalv edrin: I only tried the js scripts in the example. They seems outdated.. :(
15:50 edrin jonalv: what means outdated? maybe i did something wrong?
15:50 edrin jonalv: i wrote a mail to the dev listregarding scripting and the dynamic import?
15:51 jonalv edrin: yes?
15:51 edrin jonalv: does this explain why we need this dynamic addition of libs
15:51 edrin ?
15:51 * jonalv reads edrins mail....
15:52 jonalv edrin: "Julian Kölle"? (How many names do you have?)
15:52 edrin this is my mailing list mail
15:54 maclean huh. 'switch workspace' now works...sortof...except that it doesn't seem to actually switch
15:54 olass cool
15:54 olass maclean: file a bug for shk3
15:54 maclean ok
15:54 CIA-55 bioclipse: ospjuth * r8823 /bioclipse2/trunk/features/net.bi​oclipse.cdk_feature/feature.xml: Updated version for release.
15:55 jonalv edrin: yea, but I am afraid I personally don't know what to do...
15:56 edrin it is a really complicated thing
16:02 egonw olass: can we commit to trunk again?
16:02 olass have you tagged?
16:02 * jonalv feels that he already has his hands in enough complicated stuff with AOP and managers in Bioclipse...
16:03 egonw maclean, Gpox: I hacked up a pref page for JCP with the default bond color, but it is not hooked up to the JCP manager yet
16:03 egonw olass: yes
16:03 olass please go ahead
16:03 maclean ok
16:03 * olass is uploading files to pele
16:03 * olass is also writing a blog post to announce bioclipse2-beta2
16:03 egonw olass: good
16:04 egonw I'll post them to SF then...
16:04 olass will be very similar to beta1 :-)
16:04 olass yup
16:04 egonw good :)
16:04 olass great
16:04 egonw olass: make sure to mention:
16:04 egonw the new welcome page
16:04 olass indeed
16:04 CIA-55 bioclipse: egonw * r8824 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (5 files in 2 dirs): Added template for JCP preferences
16:04 egonw the new demo data
16:04 egonw and the lots of bugs fixed since beta
16:04 egonw 1
16:05 CIA-55 bioclipse: egonw * r8825 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchemp​aint/src/net/bioclipse/cdk/jchempaint/preferences/ (JChemPaintPreferencePage.java PreferenceConstants.java): Preference bond color (not linked to the JCPManager yet...)
16:05 egonw olass: you did the solaris one too?
16:05 egonw sparc or i386 (or even both)?
16:06 * egonw will soon install OpenSolaris on a virtual machine
16:07 olass sparc
16:07 olass yes, I did
16:07 olass eclipse only supports sparc/gtk2 it seems
16:07 maclean hmmm egonw: PreferenceConstants.P_BOOLEAN not found
16:08 olass egonw: please test update site again, added cdk feature
16:09 egonw maclean: ack, comtting fix now
16:09 egonw olass: ack
16:09 maclean oki
16:09 CIA-55 bioclipse: egonw * r8826 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.jchempaint/src/net/bioclipse/cdk/jchempain​t/preferences/PreferenceInitializer.java: Compile fix... refactor/rename of field clearly had not worked :(
16:10 egonw URL of the second update site?
16:10 egonw is that update2?
16:10 egonw that's the bioclipse2 update site, right?
16:10 egonw should I use that one?
16:11 egonw ah, indeed
16:11 egonw I see the CDK Feature now
16:15 jonalv hm there is a Services menu un the top menu now. It has a Biocinformatics service called clustalwLocal. This seems a bit strange...
16:18 * egonw is going to make a walk
16:19 egonw olass: please email any left over jobs regarding the release...
16:19 egonw I'll do the remaining upload to SF anyway...
16:19 egonw but if there is other stuff... just email me
16:19 jonalv egonw: are there new tags in pelezilla for bugs in the new release?
16:19 egonw jonalv: good one...
16:19 egonw please file a bug report...
16:19 egonw will add those later tonite too
16:19 jonalv lol
16:19 jonalv oki
16:22 olass egonw++
16:30 CIA-55 bioclipse: gilleain * r8827 /bioclipse2/trunk/cdk-externals/trunk/org.ope​nscience.cdk.render/src/org/openscience/cdk/r​enderer/generators/HighlightGenerator.java: Single oval per bond, scaled to suit the screen.
16:40 CIA-55 bioclipse: gilleain * r8828 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Use the default parameters as much as possible.
16:48 edrin jonalv: egonw managed to get a Wrapped exception in the current beta, [16:13:18] <egonw> Wrapped org.eclipse.core.runtime.AssertionFailedException: null argument: (line: #1)
16:49 edrin jonalv: you can ask him how he did it
16:49 edrin jonalv: you could also try a script with the following content:
16:49 edrin xmpp.connect();
16:50 edrin (in a .js file run with the jseditor)
16:50 edrin as you probably do not have account data set, it will throw an exception ...
16:50 jonalv edrin: but what does the editor do to create those exceptions and do we want that in the console somehow?
16:51 edrin the exceptions are not from the editor, they are from the script
16:51 edrin meaning, a manager call throws an exception because the there was an error
16:52 jonalv yea but what wraps it_
16:52 edrin it is wraped with an excpetion thrown by the rhino context i think
16:53 edrin you push in a script in rhino, rhino compiles and runs it, rhino detects exceptions in the script, aborts, and throws its own exception that wraps the exception in the scripts
16:53 edrin did i get it?
16:53 jonalv okey so perhaps we are unwrapping them?
16:54 edrin you mean remove the "wrap" in the text line?
16:54 edrin in sense of 'cosmetics' ;) ?
16:55 jonalv what? No I don't know...
16:55 edrin "perhaps we are unwrapping them" this is what i did not get
16:56 jonalv I mean perhaps masak unwrapped them in his console...
16:57 edrin and what comes out then?
16:57 edrin jonalv: what happens if you type xmpp.connect() in the console ?
16:57 jonalv you get: Could not create default client: the plug-in has set invalide account data in
16:57 jonalv preferences.
16:57 jonalv that is the message
16:57 jonalv which is sort of what we thought was the best idea...
16:57 jonalv perhaps it is not...
17:00 edrin well
17:00 edrin i think for a console it is good
17:00 edrin because a console is more interactive than a script
17:01 jonalv yes
17:02 edrin if one is writing a more complex script the user most likely knows some background of the API he/she is using, more detailed info is helpful here
17:03 jonalv yup
17:03 jonalv I am giving up now. cya.
17:03 edrin CU
17:03 edrin cu
17:03 edrin caps
17:35 CIA-55 bioclipse: gilleain * r8829 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Rendering options methods.
17:51 maclean feck
18:05 egonw maclean: I'll check that 8829 patch tonite and hack it up with the prefs page in bc2
19:26 edrin egonw: what are you currently doing?
19:26 edrin isn't the release already released?
19:26 edrin /the beta
19:27 egonw doing some last BC2 uploads...
19:27 egonw no, there are many tastes now...
19:27 egonw e.g. OS/X for PPC, Solaris for Sparc
19:27 edrin tastes?
19:27 edrin tasks?
19:27 edrin ah ok
19:27 edrin fucking experiment failed!
19:29 egonw https://sourceforge.net/project/sho​wfiles.php?group_id=150681&amp;pack​age_id=286282&amp;release_id=660851
19:29 egonw 7 different downloads
19:43 maclean joined #bioclipse
19:44 edrin cu later guy
19:44 edrin guys
19:44 edrin left #bioclipse
19:58 CIA-55 bioclipse: gilleain * r8830 /bioclipse2/trunk/ (21 files in 5 dirs): Minor changes to accommodate cleanup of RendererModel use by generators.
20:10 maclean hmmm. no margin.
20:28 CIA-55 bioclipse: gilleain * r8831 /bioclipse2/trunk/cdk-externals/trunk/org.opensci​ence.cdk.render/src/org/openscience/cdk/renderer/ (RendererModel.java RenderingParameters.java): Make the atom radius (used for compact atom elements) a double rather than an int.
20:29 CIA-55 bioclipse: gilleain * r8832 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Atom radius should be a double, not an int.
20:31 CIA-55 bioclipse: gilleain * r8833 /bioclipse2/trunk/cdk-externals/trunk/​org.openscience.cdk.render/src/org/ope​nscience/cdk/renderer/Renderer.java: Respect the model margin parameter.
20:36 egonw hi maclean
20:36 maclean hi
20:36 maclean been adding stuff
20:36 egonw yes, noticed
20:36 egonw was doing some pelezilla admin stuff...
20:36 egonw fixing the Version field
20:36 maclean oh right
20:37 egonw you did not like reflection right... then don't read Jim's blog:
20:37 egonw http://wwmm.ch.cam.ac.uk/blogs/downing/?p=289
20:37 zarah egonw's link is also http://tinyurl.com/dbxtf8
20:38 maclean ooh argh! my precious eyes!
20:38 maclean reflection = good
20:38 maclean reflection in java = aargh!
20:39 maclean it's just so hard to read, and that makes it dangerous
20:39 egonw true
20:40 * egonw is trying to figure out how to hook up the pref page with the new JCPmanager commands
20:40 maclean ah, right yes I forgot to d othat
20:40 maclean btw, if you see any missing preferences, say now
20:40 egonw now?
20:40 egonw next week fine too?
20:41 maclean well, sure :)
20:41 egonw I think I found something...
20:41 maclean I just meant that now's a good opportunity
20:41 egonw btw, these pref pages are brilliant...
20:41 egonw so looking forward to just making a JChemPaint branding of bioclipse
20:43 maclean Rajarshi is driving forward usability of the code :)
20:43 egonw yes, he had quite some experience with the old renderer
20:43 egonw good to have them do test driving...
20:43 egonw btw, I (electronically) met today a PhD in Stockholm (BO ML)
20:43 egonw who did a basic chemical editor:
20:43 maclean oh?
20:44 egonw really basic
20:45 maclean I think every chemist who programs makes a chemical editor at some point
20:45 egonw yes, guess so :)
20:45 maclean now, with the cdk, they can all do it more easily!
20:45 maclean :)
20:47 egonw indeed
20:47 egonw we'll need to start writing some tutorials...
20:48 egonw maybe something for a tutorial at the CDK workshop...
20:48 egonw btw, I'll start a "Bioclipse for CDK Developers" series in my blog...
20:48 maclean well, I will try and re-write these essay emails I've been sending to the list.
20:48 egonw :)
20:48 egonw or convert them to CDK News papers
20:48 maclean I think a nice test case would be an editor for peptides.
20:49 egonw that reminds me...
20:49 egonw we need a template mode...
20:49 egonw with a nice Bioclipse View with a list of templates...
20:50 egonw just a MOleculesTable
20:50 maclean oh definitely
20:50 egonw or maybe buttons...
20:50 egonw depending on the size...
20:50 egonw mmm...
20:50 maclean hmm. auto-generated buttons?
20:50 egonw possibly
20:51 egonw ah, missing prop: default bond color
20:51 egonw or am I overlooking that one?
20:51 maclean ah, yes, I've missed out colors
20:51 egonw it's the one field I actually now have in the pref page :)
20:51 maclean I didn't know how those would work on the command line
20:51 egonw indeed
20:51 maclean maybe they shouldn't be published?
20:51 egonw I have jcp.newPoint2d(x,y)
20:52 egonw I can imagine a jcp.newColor(R,G,B)
20:52 maclean true
20:53 egonw and font?
20:53 egonw is that available?
20:53 maclean ah no
20:53 maclean only double and bool ones
20:53 maclean jcp.makeFont?
20:53 egonw will get back on that...
20:53 egonw not sure what FontFieldEditor has :)
20:54 maclean ooh h-bonds
20:54 egonw yes, that would be nice too...
20:54 egonw HBondGenerator
20:54 egonw but no support for that in the CDK just yet
20:54 egonw post 1.2
20:54 maclean sure
20:54 egonw grmp...
20:54 egonw I really need to get that release out...
20:57 maclean oops message to cdk-jcp list bounced :)
20:57 egonw I can approve
20:57 egonw shall I?
20:58 egonw or not?
20:58 egonw it's the size...
20:58 egonw it did not bounce... it's merely on hold for manual approval...
20:58 maclean nah, don't bother - I forwared it to rajarshi
20:58 egonw OK, I just have to hit the button
20:58 maclean oh right, thatnks
20:58 egonw well, it has nice screenies...
20:59 egonw accepted
20:59 maclean \o/
21:00 maclean right, I'm off to watch NCIS, have a good evening egonw
23:58 edrin joined #bioclipse

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