Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-23

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All times shown according to UTC.

Time Nick Message
06:26 thomas_ku joined #bioclipse
06:27 CIA-58 bioclipse: ospjuth * r5685 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.ui/ (18 files in 9 dirs): Provides molecule content via CDK10 and makes SDFiles expandabe in Navigator.
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08:38 CIA-58 bioclipse: ospjuth * r5686 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (6 files in 3 dirs): Added a content outline for SDFiles. If clicked in outline, selects corresponding row in structureTable.
08:51 CIA-58 bioclipse: ospjuth * r5687 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.sdfeditor/src/net/bioclipse/cdk10/sdfeditor/ (editor/StructureTablePage.java outline/SDFOutlinePage.java): Changes in selections in StructureTable and Outline are now synchronized.
09:18 CIA-58 bioclipse: ospjuth * r5688 /bioclipse2/trunk/plugins/ (5 files in 2 dirs): Synchronized JCPPage with selections in outline, table, and toolbar.
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09:29 CIA-58 bioclipse: ospjuth * r5689 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFJCPPage.java: Removed debug line.
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11:34 rojas1 thanks for the updated sort in sdf editor
11:34 rojas1 is perfect
11:39 CIA-58 bioclipse: ospjuth * r5690 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (3 files): It is now possible to edit indivudual properties in the SDFileEditor. doSave() and doSaveAs() are not yet implemented.
11:40 olas rojas1: :-)
11:41 rojas1 other point maybe!
11:41 olas what?
11:42 olas please come with more suggestions
11:42 rojas1 would it be difficult to create the function zoom the structures
11:42 olas hmm
11:42 olas maybe and maybe not
11:42 olas file a bug
11:43 olas my idea was that images should resize when table column changed width
11:43 olas but not impl yet
11:43 olas would that be ok?
11:43 olas (It's just an image after all)
11:43 * olas is afk for 15 mins, must run to the police and get a new Passport
11:44 rojas1 yes but if you are interested in too know some groups functionals that it contains it is a bit difficult when die image is too small
12:15 olas I could set two modes, small and large
12:15 olas rojas1
12:16 olas would that be OK?
12:17 rojas1 I remember I was a viewMolecule is it works wit ?
12:24 olas rojas1: I don't understand your last sentence
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13:23 rojas1 I saw that sdf Editor has a single entry view
13:28 olas yes
13:30 rojas1 but it works for the first click
13:30 rojas1 I mean the first selection
13:30 rojas1 if afterwords I selected other it doesn't work
13:32 rojas1 And in Bioclipse there is into chemoinformatics group teh 2D-structures view. Is it synchronized with the sdfEditor?
13:33 olas hmm, I'm not sure
13:33 olas but it should be
13:33 olas let me check
13:33 olas no
13:34 olas but I assume it could be
13:34 rojas1 I think I updated all project already?
13:34 olas only problem is: different versions of CDK
13:34 olas CDK10 and CDK are not the same
13:34 olas please file a bug report about structure2DView synchr with SDFileEditor
13:34 olas I'll look at it later
13:34 rojas1 ok!
13:39 egonw joined #bioclipse
13:39 olas egonw: hi
13:39 olas egonw: one quick question
13:39 egonw hi olas
13:39 egonw sure
13:39 olas It seems to me that the MDLReader does not write properties to file
13:40 olas could that be so?
13:40 olas I can read in the properties with the MDLReader
13:40 olas but not write them using MDLWriter
13:40 egonw yeah, a roundtripping issue
13:40 egonw you need to use the Map
13:40 olas huh?
13:40 egonw mom
13:40 rojas1 done olas
13:41 olas rojas1: good
13:42 olas egonw: I have worked a lot on the ADFeditor
13:42 olas it's looking good now!
13:42 olas 2 issues remain
13:42 olas 1)
13:42 egonw is the sync working?
13:42 olas sort of
13:43 olas it works here
13:43 egonw MDLWriter.setSdFields(Map)
13:43 egonw ok
13:43 olas but I simply can't get DoubleClick to appropriately switch tab
13:43 egonw will try it here then
13:43 olas good
13:43 olas ?
13:43 egonw ic
13:43 olas oh
13:43 olas what does that method do?
13:44 egonw allow you to write properties to MDL SD files
13:44 olas oh
13:44 olas ok
13:45 olas so I set the property values that should be written
13:45 olas I se now
13:45 olas hmm, I vote for doing this automatically
13:45 olas but hey, it's your writer
13:45 * olas will test it now
13:46 olas egonw: must all mlecules have the same properties for it to be a valid SDFile?
13:46 egonw olas: file a feature request
13:46 egonw no, don't think so
13:46 olas me neither
13:46 olas this is a bug
13:46 olas I will file a bug
13:50 CIA-58 bioclipse: egonw * r5691 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Don't silently eat exceptions
13:52 egonw I liked the swedish add for the army with the rubick cube
13:52 egonw http://zie.nl/media/web/1554/rubikus
13:53 * egonw wonders that, say, every 2/5 times it goes wrong... like with real officers...
13:53 olas egonw: what should the sdfMap contain?
13:53 * egonw also wonders that this might be the swedish guantanomo bay practices
13:53 olas not just property names?
13:53 olas key -> values
13:54 olas what is key and what is value here?
13:54 egonw key = prop name
13:54 egonw value is straight forward, not?
13:54 olas no
13:54 olas it's for the writer
13:55 olas but the mols have different values
13:55 olas for the same property
13:55 olas like "ID"
13:55 olas please explain this
13:55 egonw oh... ummm this is at MDL level...
13:55 egonw one Map, one molecule
13:55 olas I thoughjt I'd just initialise the sdfMap with some IP's
13:55 egonw not sure about the SD writer...
13:55 egonw mom
13:55 olas damn
13:56 olas ok, will file a serious bug
13:56 olas unless you have a solution?
13:56 egonw I could hack something up...
13:56 olas Cubes are very important in War, donät you agree?
13:56 egonw but please start a discussion on cdk-devel
13:56 olas please do
13:57 olas my proposal is: add all props as entries in SDFile
13:57 * egonw was thinking "donät" was Swedish...
13:57 olas because that is what you get when you use the reader
13:57 egonw but it seems just to be a typo?
13:57 egonw or my keyboard config is wrong or so?
13:57 olas what do you mean now?
13:57 egonw olas: that option has been discussed in the past, not sure why that changed any more...
13:58 egonw (never mind)
13:58 egonw should I import cdk10.ui too now?
13:58 egonw or is that still in progress...
13:58 olas not necessary
13:58 egonw I get no errors without it
13:58 egonw ok
13:59 olas ok, so no quick solution to my problem?
13:59 olas then here comes the bug and mail to cdk-devel
13:59 egonw sure, I could easily hack up a custom writer...
13:59 egonw no problem
13:59 egonw in cdk10.sdfeditor...
13:59 olas I need some thing else too
13:59 egonw ?
13:59 olas do as you like
13:59 olas I think it should go into cdk
13:59 olas anyways
14:00 olas if JCP get's edited, we need to setDirty = true in JCPPage
14:00 egonw yes, eventually...
14:00 egonw but this is an API change, so should be carefully discussed...
14:00 olas I am on Mac, and can't do this
14:00 egonw in particular, because the current API was deliberately chosen
14:00 olas ok
14:00 olas please hack something up for Bioclispe in cdk10.sdfeditor then
14:01 egonw setDirty() should automatically happen already...
14:01 egonw works at least for the MDLEditor
14:01 olas ok, please test it too
14:01 olas for SDFeditor
14:01 olas sincle entry page
14:01 egonw ok
14:01 olas edit should bring up asterix, does it do that?
14:01 egonw yes
14:02 olas good
14:02 olas in a min you can test to save it too
14:02 egonw olas: you should really get yourself a VMWare with windows and/or linux
14:02 egonw olas: where is the current save code?
14:03 CIA-58 bioclipse: ospjuth * r5692 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.sdfeditor/src/net/bioclipse/cdk10/sdfeditor/ (CDK10Manager.java editor/SDFEditor.java): Implemented doSave(). CDK's MDLEditor doesn't save properties automatically, FIXME placed in CDK10Manager for egonw.
14:03 olas egonw: will do that after I migrate to Leopard
14:04 olas see commit btw for pointer
14:04 egonw ack, thanx
14:04 olas will get coffee while you look at this :-)
14:04 olas I think we're getting there
14:04 olas I'm gonna do a nice screencast really soon :-)
14:05 egonw cool
14:05 * egonw found some software to do that too...
14:05 egonw but it was not working properly for my machine yet...
14:21 * egonw will now try to replace net.bioclipse.cdk with org.openscience.cdk
14:22 egonw and is looking forward to no more svn:externals problems
14:24 egonw so far so good
14:24 egonw net.bioclipse.cdk.business and nb.jmol are happy with it
14:25 olas how 'bout cdk10?
14:25 olas Did you fix that SDFileWriter?
14:26 egonw would need to figure out versioning first then...
14:26 olas or should I file you a bug?
14:26 egonw oh, cr**
14:26 egonw I tihnk I forgot to do the 'git svn dcommit'...
14:26 * olas was sort of waiting...
14:26 egonw mom
14:26 egonw hang on
14:28 olas sure
14:30 CIA-58 bioclipse: egonw * r5693 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.s​dfeditor/src/net/bioclipse/cdk10/sdfeditor/io/ (. SDFWriter.java): Added a SD file writer that outputs all IMolecule.getProperties()
14:30 CIA-58 bioclipse: egonw * r5694 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Use org.openscience.cdk from CDK SVN directly, instead of the net.bioclipse.cdk wrapper with svn:externals
14:31 * egonw kinds urges Uppsala (and all other BC2 developers), to check out org.openscience.cdk from CDK SVN (which is cdk/trunk/), and import that in there Eclipse Bioclipse2 development workspace
14:32 * egonw will now edit the BC2 wiki page a bit :)
14:32 olas will do that now
14:32 egonw please verify that it works for you too, so that I can remove net.bioclipse.cdk
14:32 olas ok
14:34 olas egonw: there's no org.openscience.cdk!
14:34 olas please create that folder
14:34 olas else we might run into naming issues
14:34 olas right?
14:35 egonw just import <cdksvn>/cdk/trunk
14:35 egonw https://cdk.svn.sourceforge​.net/svnroot/cdk/cdk/trunk
14:35 egonw that provides the org.openscience.cdk plugin
14:35 olas hmm
14:36 olas I need to manually set the name then
14:36 egonw no
14:36 olas don't like that
14:36 olas ?
14:36 egonw it should be picked up from project.xml
14:36 olas oh
14:36 egonw .project
14:36 egonw not project.xml
14:36 olas sweet
14:36 egonw <projectDescription>
14:36 egonw <name>org.openscience.cdk</name>
14:37 olas why org.openscience.cdk instead of net.sf.cdk?
14:37 egonw historical
14:37 egonw check www.openscience.org
14:37 olas what is openscience?
14:37 olas k
14:37 egonw it's a website set up by Dan Gezelter, of Jmol fame
14:37 egonw a long time ago
14:41 olas cdk checkout at 84%
14:41 olas quite a large checkout
14:46 * jonalv has the complete cdk repo checked out. That was quite a large checkout that he doesn't now why he did. Since he uses the sourceforge browse svn feature anyway for looking things up :)
14:46 egonw there are large test files...
14:46 egonw and a large (broken) 3D template library for ring systems
14:47 olas could they not be in an additional plugin?
14:47 olas I mean, we need to package CDK for delivery with Bioclipse
14:47 olas and we want to keep that size as low as possible
14:47 olas and broken 3D modeling templates are not desired
14:48 egonw the 3D stuff was in net.bioclipse.cdk too
14:48 olas what you say, egonw?
14:48 egonw via the svn:externals
14:48 olas not good
14:48 egonw we should control what enters the .jar via the config files
14:48 olas yes
14:48 olas good idea
14:57 egonw olas: I still have that grey screen problem :(
14:57 CIA-58 bioclipse: goglepox * r5695 /bioclipse2/trunk/plugins/net.bioclipse.services/ (8 files in 4 dirs): Added functionality for updating the tree view when new services is added.
15:00 olas :-(
15:00 jonalv Gpox++
15:01 olas Gpox++
15:04 * egonw has to make dinner now
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