Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-15

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
06:58 Gpox joined #bioclipse
07:03 egonw joined #bioclipse
07:07 olass joined #bioclipse
07:14 olass RC2 release: http://sourceforge.net/project​/showfiles.php?group_id=150681
07:14 zarah olass's link is also http://tinyurl.com/ndzz64
07:14 olass I will blog and announce once we check that it runs on linux,windows
07:15 olass egonw: would it be possible for you to DL and see that it opens on linux?
07:15 egonw moin
07:15 olass I will do the same on windows and mac
07:15 zarah oh hai egonw
07:15 egonw yes
07:15 olass moin egonw
07:15 olass egonw: at BMC?
07:15 egonw yes
07:15 egonw need to send some faxes
07:15 egonw explore more mobile broadband options
07:16 egonw etc, etc
07:16 egonw busy day
07:16 egonw and bad night
07:16 olass yup
07:16 egonw the rain flooded our basement
07:16 olass why bad night?
07:16 olass oh no!
07:16 egonw with pellet burner
07:16 sneumann joined #bioclipse
07:16 egonw no big damage
07:16 olass much rain now
07:16 egonw but did not hit my bad before 02:00
07:17 egonw the worst seems over now
07:17 egonw ok, bbl
08:07 jonalv joined #bioclipse
08:08 jonalv olass: RC2 today?
08:20 CIA-40 bioclipse: goglepox * r11335 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/src/net/bio​clipse/cdk/ui/sdfeditor/business/ (IMoleculeTableManager.java MoleculeTableManager.java): Added calcualteProperties(ICDKMolecule ...)
08:21 CIA-40 bioclipse: goglepox * r11336 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java: Sync properties when saving moleucles to SDFIndexEditorModel
08:22 CIA-40 bioclipse: goglepox * r11337 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 2 dirs):
08:22 CIA-40 bioclipse: Sync properties when switching form JCP page
08:22 CIA-40 bioclipse: Fixes bug #1280
08:22 zarah bug #1280 | http://tinyurl.com/nmd5b8
08:24 CIA-40 bioclipse: goglepox * r11338 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java:
08:24 CIA-40 bioclipse: Added canceled check to calculateProperty()
08:24 CIA-40 bioclipse: Solves bug #1291
08:24 zarah bug #1291 | http://tinyurl.com/n6wev8
08:29 jonalv @pz 1267
08:29 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1267
08:32 shk3 joined #bioclipse
08:33 shk3 hi olass
08:33 shk3 what happened to rc2?
08:36 sneumann IRC logs say done this morning 07:00,
08:37 sneumann and to be announced after testing on linux and other arches.
08:37 sneumann That's how I interpreted it
08:37 shk3 ah indeed
08:37 shk3 its now online
08:37 shk3 i am going to test
08:40 shk3 sneumann: do you want to have your update site preconfigured in bc?
08:42 shk3 hm, when I try to install Mass Spectrometry Feature
08:42 shk3 it says
08:42 shk3 it needs org.eclipse.platform 3.3.0
08:44 olass shk3: I just updated the update site
08:44 olass but please make sure your bundles do not list requirements with specific versions
08:44 olass look in manifest.mf in text format
08:45 shk3 well, I think sneumann got trapped by that
08:45 shk3 it's indeed dangerous
08:45 sneumann I did not specify specific versions myself,
08:45 sneumann that was all eclipse magic.
08:46 shk3 yes
08:46 shk3 that's the problem
08:46 shk3 eclipse tries to be clever
08:46 sneumann How to disabled that, so the next run wont add it again ?
08:46 shk3 so you need to edit the files
08:46 shk3 and remove versions
08:46 sneumann no problem
08:46 sneumann which one ?
08:46 sneumann which ones ?
08:46 shk3 (except you really need a specific one, of course)
08:46 sneumann the individual features / plugins ,
08:46 sneumann or the update site descriptions ?
08:47 shk3 features/plugins
08:47 sneumann ack.
08:47 shk3 don't think the update site has any
08:51 CIA-40 bioclipse: ospjuth * r11339 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (exec/signatures-linux32 permissions.properties): Use correct signatures file and updated permissions.properties for this version.
08:55 CIA-40 bioclipse: shk3 * r11340 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: added licence agreement etc.
09:00 CIA-40 bioclipse: goglepox * r11341 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (3 files):
09:00 CIA-40 bioclipse: MolTable checks for IColorProvider and colors the text acrodingly if found
09:00 CIA-40 bioclipse: I had to copy TextCellPainter form nattable to be able to override the painting behaviour for the text.
09:00 CIA-40 bioclipse: Fixes bug #1286
09:00 zarah bug #1286 | http://tinyurl.com/mst8yq
09:06 sneumann Hm, I went through all my plugins MANIFESTs, no trace of version requirements
09:06 shk3 somewhere there must be a dependency to this platform thing
09:07 shk3 i have a look
09:07 sneumann The feature.xml has version="0.0.0"
09:07 shk3 did you download rc2 and try to install your feature?
09:08 shk3 ah, I do not have the org.eclipse.platform feature in the download
09:08 shk3 and it is not on update site
09:08 shk3 so what is this about?
09:08 shk3 do you really need it?
09:09 sneumann Stuff is autogenerated, I have no clue where it got in.
09:09 sneumann I guess it is via the EMF stuff ?
09:09 shk3 looks like
09:09 shk3 emf depends on it
09:10 shk3 i try to configure an upate site for that
09:11 sneumann There are other EMF based plugins in BC2, they probably need that as well.
09:11 olass shk3: why on earth would you want to bundle org.eclipse.platform??
09:12 shk3 me?
09:12 shk3 not at all
09:12 olass ??
09:12 olass [11:11] < shk3> ah, I do not have the org.eclipse.platform feature in the download
09:13 shk3 I want to install sneumanns feature
09:15 egonw joined #bioclipse
09:17 olass why does JCP rendering look so much worse on windows than on linux?
09:18 sneumann olass: my UpdateSite/content.xml has
09:18 sneumann <unit id='org.eclipse.emf.feature.group' version='2.4.0.v200806091234' singleton='false'>
09:18 olass sneumann: you should go through your dependencies, I do not think you require that plugin
09:18 sneumann <required namespace='org.eclipse.equinox.p2.iu' name='org.eclipse.platform.feature.group' range='[3.3.0.v20061208-Fj22sCYGm0XDWm3,4.0.0)'/>
09:18 Gpox because it is developed on a mac
09:18 olass Gpox: Touché ;)
09:18 olass is it java2d for win that is not good?
09:19 Gpox JCP in bioclipse uses SWT
09:20 Gpox Maybe I should boot windows and see how rc2 runs on windows 7
09:20 olass ;)
09:20 jonalv Gpox: good idea
09:21 * olass wonders how difficult it would be to improve the rendring of bonds=lines on windows
09:25 sneumann could my dependencies be imported through <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/> ?
09:25 sneumann Otherwise I cannot find anything explicit.
09:27 sneumann_ joined #bioclipse
09:28 shk3 I can't find an update site for this 3.3.0 version
09:29 shk3 where is this classpathentry in?
09:30 shk3 what I did for speclipse feature is to add all plugins needed on plug-ins tab and to make it depend on net.bioclipse.chemoinformatics feature
09:31 shk3 no features included
09:43 CIA-40 bioclipse: goglepox * r11342 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (MoleculeTableContentProvider.java MoleculeTableViewer.java):
09:43 CIA-40 bioclipse: Added an empty row at the bottom of molTable
09:43 CIA-40 bioclipse: Adds an extra row to the moleculesTable so that
09:43 CIA-40 bioclipse: all molecules are shown. Also added a check in the
09:43 CIA-40 bioclipse: provider to stop it from trying to find a molecule
09:43 CIA-40 bioclipse: for this empyt row.
09:43 CIA-40 bioclipse: Solves bug #862
09:44 zarah bug #862 | http://tinyurl.com/mks68u
09:50 egonw olass: SF download linux 64 bit works for me
09:50 olass great
09:53 CIA-40 bioclipse: goglepox * r11343 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/src/net/bio​clipse/cdk/ui/sdfeditor/business/ (IMoleculeTableManager.java MoleculeTableManager.java):
09:53 CIA-40 bioclipse: Removed creageSDFIndex(InputStream ...)
09:53 CIA-40 bioclipse: Clean up of code that should no longer be there
10:02 shk3 the 32 bit works as well
10:11 sneumann_ Hm, cant be the <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
10:12 sneumann_ you'd have the problem as well:
10:12 sneumann_ net.bioclipse.specmol/.classpath:<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
10:13 shk3 ah, this is in .classpath of a plugin
10:13 shk3 the .classpath files are autogenerated
10:13 shk3 never edited these
10:14 sneumann_ and not used by the plugin dependencies
10:14 sneumann_ but I thought they could give me a hint
10:18 sneumann_ There are other plugins using EMF, such as
10:18 sneumann_ net.bioclipse.qsar.ui/META-INF/MANIFEST.MF
10:20 shk3 I think qsar is experimental and not part of the update sie
10:21 shk3 so it might be the problem was not yet noted
10:22 sneumann_ net.bioclipse.bibtexml.edit/META-INF/MANIFEST.MF: org.eclipse.emf.edit;visibility:=reexport
10:25 shk3 also not part of update site
10:25 shk3 sorry
10:27 shk3 I would think it should be enough to have an update site for this 3.3.0 platform thing
10:27 shk3 if emf needs it, well, then the user needs to donwload
10:27 shk3 it
10:27 shk3 but I can't find that
10:27 shk3 3.4.0
10:27 shk3 yes
10:27 shk3 but not 3.3.0
10:28 sneumann joined #bioclipse
10:28 olass egonw: would it be possible for you to tag SVN for RC2?
10:29 olass best would be the version at midnight sun/mon swe time
10:29 olass 11334 AFAIK
10:30 * olass is having lunch
10:32 shk3 sneumann: found the right site
10:32 shk3 now missing org.eclipse.jdt.launching
10:33 sneumann Umpf. Dependency hell.
10:33 egonw olass: ack
10:33 olass egonw: thanks
10:33 * egonw is preoccupied with finding mobile internet options
10:33 olass shk3: jdt is java development tools
10:33 egonw can't work from home properly otherwise
10:34 egonw git is fine
10:34 olass just so you know
10:34 egonw but does not help compensate for the missing virtual bookshelf called Google :(
10:34 * olass does not understand why Java Development Tools is needed wither
10:34 olass either
10:34 jonalv egonw: you should do: internet.clone() :)
10:34 olass egonw: I understand
10:34 olass git download internet
10:34 shk3 ok
10:34 shk3 I can install
10:35 jonalv what is needing JDT?
10:35 egonw sudo aptitude install internet
10:35 egonw cool
10:35 shk3 emf
10:35 sneumann org.eclipse.jdt.debug_3.4.1.v20081216_r342
10:35 jonalv I think emf is doing somet on the fly compiling
10:35 sneumann Export-Package: ... Export-Package:
10:35 sneumann Export-Package: ...  org.eclipse.jdt.launching
10:36 sneumann Maybe EMF does that if you on-the-fly add new stuff to your models
10:36 sneumann which I don't do
10:36 sneumann Open for suggestions how to trum these
10:36 sneumann Open for suggestions how to trim these
10:37 shk3 well, the update is large, but seems to work
10:37 jonalv sneumann: sry for stumbling in in the middle of things but why can't you have those deps?
10:38 sneumann shk3 had problems installing because of missing deps.
10:38 sneumann So either those update sites need to be configured
10:38 sneumann or deps trimmed down. The first is probably easier
10:39 jonalv yea I ahve a feeling trimming down that dep is not so easy...
10:39 shk3 seems to work
10:39 sneumann cool.
10:40 shk3 I could add yours and the 3.3.0 update site to default sites
10:40 jonalv egonw: ping
10:40 sneumann Maybe enable that a day after 2.0 release ?
10:40 shk3 you can then install by hitting calculate dependencies button on the update dialog
10:40 sneumann So it can linger a bit more in devel state ?
10:40 shk3 I thought it would be done automatically
10:40 shk3 but it seems not
10:41 egonw jonalv: pong
10:41 jonalv egonw: when I do help cdk I get some DOIs
10:41 egonw good
10:41 egonw but not only DOIs I hope...
10:41 jonalv egonw: It would be nice to have a look at those in Bioclipse somehow...
10:41 egonw the methods too, right?
10:41 egonw jonalv: yes, try 'doi cdk'
10:42 jonalv egonw: ah, that was not so easy for a little jonalv to understand...
10:42 shk3 sneumann: devel state is fine
10:42 egonw olass: would you mind if I add that to the output?
10:43 shk3 we could still add the update site, I think
10:43 jonalv egonw: this DOI stuff should I file feature requests to you about it?
10:44 sneumann shk3: ack, go ahead. What are versioning suggestions for plugins ?
10:44 sneumann My feature has 2.0.0.rc2 atm, and plugins 1.0.0
10:45 egonw jonalv: yes, good idea
10:45 egonw cc olass
10:45 shk3 versioning is to be in line with bc, I suppose
10:45 shk3 ie 2.0.0.rc2 right now
10:45 shk3 if you go for the release
10:45 shk3 if not,have your own schema
10:45 shk3 I would think
10:51 shk3 sneumann: what name would you like for your update site?
10:51 shk3 mass spectrometry update site?
10:51 shk3 ipb update site?
10:52 sneumann probably the latter, there will be other MS providers (Miguel, ...) as well.
10:52 shk3 ok
10:52 CIA-40 bioclipse: egonw * r11344 /bioclipse2/tags/2.0.0.RC2/: Tagged 2.0.0 RC2
10:56 shk3 egonw, rojas1: do we have the reaction plugins on an update site?
10:56 egonw olass: I asked to put MEDEA on experimental, right?
10:58 CIA-40 bioclipse: shk3 * r11345 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (BioclipseConstants.java prefs/UIPreferenceInitializer.java): added the ipb halle update site
11:06 shk3 I could probably external testers for that, but they would need a not-so-hard-to-use download possibility
11:06 shk3 source checkout is not an option, I believe
11:07 egonw shk3: did you check if MEDEA is on the experimental update site?
11:08 olass egonw: I think we decided that MEDEA should be hosted at EBI
11:08 shk3 can't find it
11:08 egonw olass: ah, OK
11:08 shk3 hm
11:08 egonw rojas1: or in Leiden?
11:08 shk3 sounds like me has to do something
11:09 egonw shk3: please ask Miguel what he wants
11:09 egonw being his project
11:09 shk3 yes
11:09 shk3 I think this is the best
11:09 olass egonw: yes, now that I remember, you suggested hosting in Leiden
11:09 egonw time to make a google map with Bioclipse update sites :)
11:09 olass indeed :)
11:10 jonalv egonw:  feel free to add RC2 to pelezilla...
11:10 egonw done
11:11 jonalv @pz 1294
11:11 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1294
11:28 olass shk3: next time, please file a bug for me to add stuff to net.bioclipse.ui. ok?
11:28 olass adding an update site must really work
11:28 olass and be tested
11:29 egonw which reminds me...
11:29 shk3 hm ok
11:29 egonw do we have a manager test to add update sites?
11:29 egonw ummm
11:29 olass since this is tyhe first time, I don't want to (by mistake) release RC3 with something incorrect
11:29 egonw do we have a manager *command* to add update sites?
11:29 olass no
11:29 olass we should
11:29 olass fiel a bug
11:29 olass file
11:29 egonw will do
11:30 shk3 I can revert that
11:30 shk3 if you like
11:30 olass is the update site online?
11:30 olass and working?
11:30 olass tested on different OS?
11:30 olass if so, leave it
11:30 olass if not, please revert
11:31 olass I am in no position to judge the quality of medea
11:31 egonw users can easily add an update site the graphical way...
11:31 olass exactly
11:31 shk3 I will revert
11:31 olass ack
11:31 shk3 going to lunch now
12:05 rojasm joined #bioclipse
12:06 shk3 olass: which platforms do you test on and how?
12:06 olass shk3: ?
12:07 olass the ones we build for... or what do you mean?
12:07 olass we all try to help out
12:07 olass I don't test personally on all platforms, if that's what you suggest
12:07 shk3 well, because you said I should do that?
12:07 olass I never said that
12:08 olass I asked if it was tested on all supported platforms
12:08 olass I never sugegsted you to do it
12:08 olass if it does not run on linux 64 bits, then that must be fixed
12:08 shk3 well, if we all do it together, how can it be done without committing?
12:08 shk3 sorry, I am confused
12:09 olass shk3: I am repsonsible for core
12:09 olass I commit there
12:09 shk3 ok
12:09 shk3 no problem
12:09 olass I do not commit to speclipse without asking you
12:09 shk3 good to know
12:09 shk3 I wouldn't mind you doing...
12:09 olass ;)
12:10 olass well, I think you would the week before an important release...
12:10 olass I sort of feel I want control at this time
12:10 shk3 sure
12:10 olass hoep you agree with me
12:10 olass right
12:10 olass it's just so many things in the air now
12:11 olass so no offense intended
12:11 shk3 didn't think it was intended
12:11 olass good :)
12:15 CIA-40 bioclipse: shk3 * r11346 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (BioclipseConstants.java prefs/UIPreferenceInitializer.java): reverted to 11345
12:24 jonalv I keep getting eror along the lines  "java.lang.IllegalArgumentException: Could not handle /Virtual/dnaiso.js" :(
12:24 jonalv Am I the only one having probl;ems with Virtual?
12:25 egonw will try
12:37 CIA-40 bioclipse: egonw * r11347 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: Added some inline pointers on what to do with these DOIs (fixes #1293)
12:37 zarah bug #1293 | http://tinyurl.com/nhk7lq
12:50 egonw olass: please fix commit #11209
12:50 egonw you deleted important files in net.bioclipse.doc.developers
12:51 olass egonw: fix?
12:51 olass egonw: please revert it
12:52 egonw revert being commited
12:52 olass thx
12:52 CIA-40 bioclipse: egonw * r11348 /bioclipse2/trunk/plugins/ne​t.bioclipse.doc.developers/ (9 files in 4 dirs):
12:52 CIA-40 bioclipse: Revert "Set version to 2.0.0.RC2."
12:52 CIA-40 bioclipse: This reverts commit d246f85c4355213b4200d23bb0fe99a91314daa2.
12:53 olass egonw: I must have made a mistake there
12:53 egonw yeah, think so
12:54 egonw next release you'll update the version numbers anyway
12:54 olass true that
13:14 egonw "//masak,jonalv,egonw: I deliberately did not use a loop to annoy you!"
13:14 * egonw is not amused
13:16 jonalv egonw: what is this?
13:16 * olass vaguely remember that...
13:17 egonw MdlMolFileCoordinatesDescriber line 72
13:18 CIA-40 bioclipse: goglepox * r11349 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java:
13:18 CIA-40 bioclipse: If requested path is part of 'Virtual' create it.
13:18 CIA-40 bioclipse: Sovles bug #1262
13:18 zarah bug #1262 | http://tinyurl.com/nhee68
13:22 olass Gpox++
13:23 egonw olass: permission asked to tune that class to support 0D MDL molfiles
13:23 olass sounds wonderful
13:23 olass what is the use case?
13:23 olass oh
13:23 olass no coords in molfile
13:23 egonw your 1061 bug report
13:24 olass right
13:24 olass egonw++
13:24 * olass is a bit stressed today and cannot think clearly
13:24 * olass probably needs more coffee
13:25 egonw that means: permission granted?
13:25 olass of course
13:25 olass why not?
13:25 olass we should fix bugs...
13:27 olass jonalv++ //Good testing, many good bug reports
13:32 CIA-40 bioclipse: egonw * r11350 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (2 files in 2 dirs): Added missing MDL molfile (0D) content type (fixes #1308 and #1061)
13:32 zarah bug #1308 | http://tinyurl.com/l5bqh2
13:34 CIA-40 bioclipse: goglepox * r11351 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: JCP sends a selection event when strucuture changed
13:36 Gpox jonalv: bug 1306 back to you
13:36 jonalv @pz 1306
13:36 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1306
13:37 jonalv Gpox: how do I select an atom in the jchempaintedtior?
13:37 Gpox click the move button in toolbar and click a atom
13:38 jonalv Gpox: no that moves the atom
13:39 Gpox use the lasso then
13:39 jonalv ah
13:39 Gpox and it won't mve if you dont drag i belive
13:39 jonalv Gpox: I don't know how to fix 1306
13:40 Gpox In the properties view when SMILES/INCHI is claculated check for an empty molecule
13:41 egonw ICDKMolecule.getAtomContainer().getBondCount() == 0
13:41 egonw or getAtomCount()
13:43 jonalv oh sry
13:43 jonalv not 1306 then
13:43 jonalv yea 1306
13:44 jonalv Gpox: it's about jchempaint sending different events when I add carbons and when I add rings
13:45 jonalv Gpox: and when I do clear it doesn't work as well
13:45 Gpox I am talking about the stacktrace in that bug
13:46 jonalv Gpox: I have fixed that part
13:46 Gpox good, and i have fixed tha other part
13:46 Gpox r11351
13:47 Gpox where is your commit?
13:47 jonalv Gpox: pending
13:47 jonalv mom
13:47 jonalv hang on...
13:48 jonalv here is the bug ticket anyway:
13:48 jonalv @pz 1307
13:48 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1307
13:49 jonalv I hate this stupid operating system
13:49 jonalv When I start a program  Iwant a freaking window
13:49 jonalv grr
13:50 egonw who wrote ICDKManager.create(IMOlecule) ?
13:51 jonalv beats me, egonw: git blame?
13:51 egonw 149a08df (jonalv
13:52 CIA-40 bioclipse: jonalv * r11352 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Only calcualte inchi and smiles if the molecule contains any atoms. Fixes bug: #1307
13:52 zarah bug #1307 | http://tinyurl.com/nvo43t
13:52 jonalv egonw: cool, what have I done now?
13:52 egonw :)
13:52 egonw you added create(IMolecule)
13:52 jonalv egonw: maybe
13:52 egonw 5660
13:52 jonalv egonw: why?
13:52 egonw no, for sure
13:52 egonw anyway...
13:52 egonw I want to rename it to:
13:52 egonw asCDKMolecule()
13:52 egonw or convertToCDKMolecule()
13:52 jonalv egonw: by all means
13:53 jonalv I like as variant
13:53 jonalv but
13:53 jonalv LOL
13:53 jonalv it does actually create a new one always right?
13:53 egonw :)
13:53 jonalv otherwise I am fucked
13:53 egonw no
13:53 jonalv oh
13:53 jonalv it doesn'?
13:54 egonw if the input already is a ICDKMOlecule
13:54 egonw it just returns that
13:54 jonalv yikes...
13:54 jonalv NOOO
13:54 egonw != clone
13:54 jonalv egonw: what is the name of the clone method then?
13:54 egonw dunno
13:54 * jonalv is using it as a clone method...
13:54 egonw have not seen one int he CDKMnaager
13:54 jonalv we need a clone method
13:54 egonw OK, here comes RC4
13:55 jonalv RC4?
13:55 egonw metaphorically speaking
13:55 egonw no pun intended
13:57 egonw shk3: ping
13:57 egonw shk3: can you please upload the test file for bug 1273 ?
13:57 egonw want to test my fix
13:57 jonalv egonw: so can you rename that method and create a method that does the clone thingie?
13:57 egonw jonalv: file me a bug report please
14:00 shk3 mom
14:03 egonw jonalv: not sure what /Virtual problem you were talking about earlier
14:03 egonw but I now notice I do not have a /Virtual in trunk!
14:03 egonw RC2 looked fine
14:03 egonw but what happened to it?
14:03 jonalv egonw: beats me it just disapeared..
14:04 shk3 egonw: attached file to bug
14:04 egonw thanx
14:04 shk3 I had that yesterday
14:04 shk3 virtual disappeared suddenly
14:04 shk3 but I could not reproduce this
14:09 CIA-40 bioclipse: egonw * r11353 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fixed calculation of massing by taking into account implicit hydrogens (fixes #1273)
14:09 zarah bug #1273 | http://tinyurl.com/njxzxm
14:16 jonalv how do I remove the calcualte inchi actions from the contextmenu in jchempaint?
14:17 egonw the plugin.xmo
14:17 egonw .xml
14:17 egonw jonalv: the clone
14:17 egonw happy with ICDKMolecule to ICDKMolecule ?
14:18 jonalv egonw: yea I guess that works
14:18 egonw it's important though
14:18 egonw the above could simply clone IAtomContainer
14:18 egonw cloning of IMolecule would require CML intermediate
14:19 jonalv egonw: it's olass who always tries to make things work on IMolecule level but a clone methog on the cdkmanager should definitly do only a cdkmolecule clone if you ask me...
14:20 jonalv to be honest I don't see how anything else would work...
14:20 egonw yes, 100% agreed
14:20 egonw everything else can go via CML by default
14:21 jonalv egonw: Which plugin.xml would that be? I can't find it in pluign.xml in jchempaint...
14:22 egonw OK, try:
14:22 egonw net.bioclipse.doc.developers/doc/ep.foo.html
14:23 jonalv egonw: my delopers project does not have a doc folder... :(
14:24 egonw make it clean
14:24 jonalv egonw: BUILD FAILED
14:24 jonalv /Users/jonathan/Work/git/bioclipse2/plugins​/net.bioclipse.doc.developers/build.xml:6: Execute failed: java.io.IOException: perl: not found
14:25 jonalv :(
14:25 egonw oh no
14:25 egonw not that again
14:25 egonw you do have Perl installed?
14:26 jonalv egonw: yes
14:26 jonalv which perl
14:26 jonalv /opt/local/bin/perl
14:26 jonalv
14:31 jonalv egonw: but where could it be? It has to in a plugin that depends on the net.bioclipse.inchi plugin right?
14:34 jonalv Would anyone know where the generate inchi action is contributed?
14:34 jonalv This pluign system makes it impossible to find things...
14:34 jonalv :(
14:36 Gpox net.bioclipse.cdk.ui maybe
14:36 rojasm joined #bioclipse
14:38 egonw jonalv: can you please test this:
14:38 egonw 1. cdk net.bioclipse.doc.developers
14:38 egonw 2. ant
14:39 jonalv egonw: huh what exaclty do you want me tod do with the developers project?
14:39 CIA-40 bioclipse: egonw * r11354 /bioclipse2/trunk/plugins/ (16 files in 12 dirs): Renamed ICDKManager .create to .asCDKMolecule (fixes #1309)
14:39 zarah bug #1309 | http://tinyurl.com/l92xhy
14:39 egonw 1. *cd* net.bioclipse.doc.developers
14:40 egonw cd, not cdk :)
14:40 jonalv egonw: ah you want me to run ant from the commandline :)
14:40 egonw yes, some call it like that :)
14:41 jonalv egonw: I get a zillion errors: No such file or directory
14:41 jonalv then it says BUILD SUCCESSFUL
14:41 egonw ok, that's called progress
14:41 egonw please copy/paste the full output somewhere
14:43 jonalv egonw: http://gist.github.com/130140
14:43 egonw ha, your xpath installation is broken
14:44 jonalv egonw:  you think? :)
14:44 egonw you'll have to fix that your self
14:44 egonw e.g. install Ubuntu
14:44 jonalv egonw: what id xpath?
14:44 jonalv egonw: hwo do I fix that?
14:44 jonalv I hate this operating system
14:45 egonw sorry, no clue
14:45 egonw OS/X is not my speciality
14:58 CIA-40 bioclipse: ospjuth * r11355 /bioclipse2/trunk/plugins/ (10 files in 9 dirs):
14:58 CIA-40 bioclipse: * Added a submenu for Decision Support calculators
14:58 CIA-40 bioclipse: * Moved all property calculators to new menu
14:58 CIA-40 bioclipse: * Updated column=property names
15:00 rojasm joined #bioclipse
15:01 egonw jonalv: ping
15:01 egonw jonalv: can you drop by please?
15:01 olass joined #bioclipse
15:03 * olass is backlogging
15:11 CIA-40 bioclipse: egonw * r11356 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added requested ICDKManager .clone(ICDKMolecule) method (implements #1312)
15:23 egonw Caused by: org.eclipse.core.internal.r​esources.ResourceException: Resource '/file:/home/egonw/var/Pro​jects/hg/bioclipse/Test2' does not exist.
15:23 egonw that resource name should not have a / at the start
15:23 egonw save is broken now
15:24 CIA-40 bioclipse: goglepox * r11357 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java:
15:24 CIA-40 bioclipse: Made CalculatePropertyHandler care about the order of the ids supplied to it.
15:24 CIA-40 bioclipse: Resolves bug #1313
15:24 zarah bug #1313 | http://tinyurl.com/mf3zrt
15:24 egonw Gpox, olass: ping
15:24 olass pong
15:24 Gpox pong
15:24 egonw [17:23:39] <egonw> Caused by: org.eclipse.core.internal.r​esources.ResourceException: Resource '/file:/home/egonw/var/Pro​jects/hg/bioclipse/Test2' does not exist.
15:24 egonw [17:23:49] <egonw> that resource name should not have a / at the start
15:24 egonw [17:23:57] <egonw> save is broken now
15:25 egonw critical bug introduced some patch introduced this afternoon, I guess
15:25 olass not good
15:25 CIA-40 bioclipse: ospjuth * r11358 /bioclipse2/trunk/plugins/net.biocli​pse.ds.lipinski/src/net/bioclipse/ds​/lipinski/impl/RuleOfFiveTest.java: cdk.create is renamed to cdk.asCDKMolecule()
15:33 CIA-40 bioclipse: goglepox * r11359 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java: Put check if project exists back into ResourcePathTransformer.parseRelative
15:36 sneumann_ joined #bioclipse
15:42 olass I have problems drawing molecules from scratch
15:42 olass resulting in JCP errors
15:42 olass egonw: does drawing molecules from scratch work for you?
15:42 olass I ad benzene, add some carbons, delete some carbins, add explicit/implicit hydrogens
15:42 olass after wditing a while, I run into errors
15:43 olass oh
15:43 egonw I think I had that too
15:43 olass it's undo/redo probably
15:43 egonw forgot to file a bug report
15:43 egonw I had a stacktrace
15:43 egonw also new
15:43 olass no
15:43 olass not undo/redo...
15:45 olass ok, here is a stacktrace:
15:45 rojasm joined #bioclipse
15:45 CIA-40 bioclipse: egonw * r11360 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Removed calculate InChI menu's, as the InChI is now available form the properties view (fixes #1259)
15:45 zarah bug #1259 | http://tinyurl.com/nfpttp
15:46 CIA-40 bioclipse: goglepox * r11361 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java: Now adds new calculated columns as third column
15:47 olass Gpox, egonw: http://paste2.org/p/267345
15:49 Gpox did you remove some 2d coordinates?
15:50 olass maybe
15:50 olass I just did some basic editing in JCP
15:50 olass ad/remove carons
15:50 olass add carbons
15:53 Gpox another thing is that show implicit hydrogens apears to do nothing when showEndCarbons is false
15:59 * olass have not seen that menu alternative
16:05 Gpox no menu alternavie and it is on by default
16:05 egonw jonalv and I are seeing serious JCP problems
16:05 egonw with drawing
16:06 egonw molecules disappearing
16:06 egonw or
16:06 egonw major trouble with IAtomContainer's changing
16:06 egonw incorrect pointers
16:06 egonw that sort of crap
16:07 egonw one problem
16:07 egonw is moving
16:08 egonw stop moving a structure
16:08 egonw make the molecule disappear
16:11 CIA-40 bioclipse: ospjuth * r11362 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/ui/views/DSView.java: Unregister all JCP propertylisteners on dispose().
16:11 Gpox ControllerHub realy need to be refactored
16:15 olass I guess that is a major undertaking?
16:16 Gpox moving fixed
16:16 CIA-40 bioclipse: goglepox * r11363 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.control/src/org/open​science/cdk/controller/MoveModule.java:
16:16 CIA-40 bioclipse: Move atom nowhere
16:16 CIA-40 bioclipse: The atom is moved with the ChemModelRelay to get a coordinatesChanged event
16:16 CIA-40 bioclipse: [jchempaint-primary] r14615
16:16 olass Gpox: DS reading properties is now broken
16:17 olass must have happened in the resourcepathtransformer/virtual fix
16:17 olass will file a bug
16:19 olass Gpox: bug 1316
16:20 olass hmm
16:22 olass has inchi property key changed?
16:23 olass nope
16:29 rojas1 joined #bioclipse
16:47 CIA-40 bioclipse: goglepox * r11364 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml:
16:47 CIA-40 bioclipse: Readded InChI calculator
16:47 CIA-40 bioclipse: fixes bug #1316
16:47 zarah bug #1316 | http://tinyurl.com/nkvo2e
16:49 Gpox egonw--
16:49 egonw he, I'm just following orders
16:51 egonw oh... ic...
16:51 egonw I think I get it...
16:51 egonw <Calculator> is not a pop up
16:51 egonw egonw--
16:51 egonw sorry
16:52 * egonw will just redirect bug reports to Arvid again
16:52 egonw more efficient
17:06 rojasm joined #bioclipse
17:27 sneumann_ joined #bioclipse
18:08 Gpox joined #bioclipse
20:16 CIA-40 bioclipse: ospjuth * r11365 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.lipinski/build.properties: Added folder 'icons' to build.properties
20:25 sneumann_ joined #bioclipse
21:05 CIA-40 bioclipse: lc69 * r11366 /bioclipse2/trunk/plugins/net.bioclip​se.ds/cheatsheets/gettingstarted.xml: Added text to explain how to generate a report.
21:05 olass joined #bioclipse
21:49 CIA-40 bioclipse: ospjuth * r11367 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (6 files in 3 dirs): Fixed bug that meant consensus was always negative in SDF consensus calculation. Also added ugly hack to color negative as blue for DB exact matches when results=0.

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary