Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-03

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All times shown according to UTC.

Time Nick Message
01:08 stain joined #bioclipse
03:12 egonw joined #bioclipse
06:14 jonalv joined #bioclipse
06:49 CIA-46 bioclipse: jonalv * r5782 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Wrote tests for SMARTS query
06:54 thomas_ku joined #bioclipse
07:07 masak joined #bioclipse
07:08 malick joined #bioclipse
07:12 Gpox joined #bioclipse
07:18 rojasm joined #bioclipse
07:19 rojasm hi good morning! some body working with sdfEditor?
07:21 jonalv I think Gpox might be...
07:22 rojasm ok, thanks
07:23 jonalv huh?
07:24 egonw joined #bioclipse
07:25 jonalv rojasm, I am sorry in what why did I just help you?
07:27 rojasm Hi egonw
07:27 rojasm I was wandering how difficult could be to integrate for sdfEditor the
07:28 rojasm handling of reactions
07:28 egonw that would be a RDF editor
07:28 egonw interesting idea
07:28 egonw would not be overly hard to do
07:28 jonalv oh, I have no idea. Didn't even know SDF supported reactions
07:28 egonw SDF does not
07:29 egonw but RDF is to RXN what SDF to to MDL molfiles
07:29 egonw RDF/RXN is from MDL too
07:29 egonw and closely related
07:30 rojasm that means that for reaction integrations should be created an independent plugin
07:30 egonw right
07:30 rojasm mmm
07:30 egonw and me has no time for that this summer
07:31 egonw :(
07:31 rojasm I know
07:31 egonw rojasm: but, I can support your efforts if you want to take it forward...
07:32 rojasm I will think about. Because I think it could be a nice feature for eclipse
07:32 jonalv egonw: when it comes to SMARTS querying there can't be any such thing as a fingerprint help right?
07:34 egonw nope
07:50 jonalv egonw, org.openscience.cdk doesn't seem to export org.openscience.cdk.smiles.smarts
07:50 egonw jonalv: please make it so
07:53 jonalv egonw: I don't have commit bit to cdk... (that's where it is right?)
07:54 egonw yes
07:55 olas joined #bioclipse
07:57 jonalv egonw, can you fix? :)
07:57 olas hi all
07:57 egonw no, but will give you write access
07:57 masak :)
07:57 jonalv That works too
08:10 CIA-46 bioclipse: carl_masak * r5783 /bioclipse2/trunk/plugins/net.bioclipse.ui/​src/net/bioclipse/ui/editors/Aligner.java: [Aligner] scrolling now works (Gpox++)
08:13 egonw jonalv: go ahead, you got rw now
08:14 jonalv thanks
08:33 EskilA joined #bioclipse
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09:08 jonalv olas: you seem to have changed code without running the tests to realize that you broke one. I could be wrong but test CDKManagerTest.testCDKMoleculeFromIMolecule seems to fails after your commit rev#5776. Please after changing code in managers run the tests!
09:10 CIA-46 bioclipse: jonalv * r5784 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Implemented SMARTS querying. My test case doesn't work though. I have mailed about it to the cdk people. Maybe I have misunderstood how SMARTS works?
09:20 shk3 joined #bioclipse
09:28 CIA-46 bioclipse: ospjuth * r5785 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/colorers/ (. PropertyColorer.java): Added a colorer by property.
09:28 CIA-46 bioclipse: ospjuth * r5786 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/j​chempaint/ui/editor/IJCPBasedEditor.java: Updated with method to getChemModel()
09:29 CIA-46 bioclipse: jonalv * r5787 /bioclipse2/trunk/plugins/net.bioclipse.struct​uredb/src/net/bioclipse/structuredb/business/ (3 files): Added SMARTS querying to structuredb
09:29 CIA-46 bioclipse: ospjuth * r5788 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (9 files in 6 dirs): Started working on an EP for hooking in IAtomColorers by eclipse.
09:50 shk3 hi all
09:51 shk3 just checked out bc1, but can't start
09:51 shk3 java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
09:51 shk3 anybody an idea?
09:51 CIA-46 bioclipse: carl_masak * r5789 /bioclipse2/trunk/plugins/net.bioclipse.ui/​src/net/bioclipse/ui/editors/Aligner.java: [Aligner] added fixed column of names
09:52 masak shk3: you just missed the entourage going to sauna, er, lunch
09:52 shk3 coffe break
09:53 shk3 have been to personal department
09:57 shk3 i tried update classpath and clean and rebuild
09:57 shk3 but no luck
10:03 shk3 that's not a good start :-(
10:06 masak shk3: what do you need to do in bc1>
10:06 masak s/>/?/
10:07 masak olas: I don't think you should version a release '1.3.1+'
10:07 masak better to stick to numbers
10:07 shk3 i need to get that fucking nmrshiftdb product exported which has been ready for about a year
10:12 egonw joined #bioclipse
10:13 shk3 ah egonw,
10:13 shk3 I can't run bioclipse
10:13 shk3 java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
10:14 shk3 any idea apart from update classpath and clean wha
10:14 shk3 t I can do?
10:16 egonw shk3: really busy now... can't support you with that at this moment...
10:16 egonw anyone else?
11:01 Gpox joined #bioclipse
11:02 rojasm shk3 welcome again!
11:10 olas shk3 : WB!
11:12 olas shk3: have you updated CP?
11:12 olas have you set target platform?
11:12 * olas is really busy today, and tomorrow
11:14 jonalv shk3: Sorry I don't think I can be of much help with Bioclipse1...
11:22 shk3 hi ola
11:22 shk3 what is CP?
11:23 shk3 ah, classpath
11:23 shk3 did this
11:23 shk3 no help
11:23 shk3 where do I set target platform?
11:23 shk3 don't remember I ever did
11:23 jonalv shk3, target platform is for bioclipse 2
11:24 olas yes
11:24 olas oh, bc1?
11:24 olas sorry
11:24 * olas will not confuse anymore
11:27 shk3 hm, the bioclipse product has only listed net.bc.feature as a feature to constitute the product.
11:27 shk3 is this ok?
11:29 olas yes
11:29 olas all other features are loaded via UpsateSite
11:34 shk3 when I try to run nmrshiftdb application, I get "no application id found"
11:34 shk3 did you come across this?
11:34 jonalv is this the hibernate project?
11:35 shk3 no, the nmrshiftdb clien
11:35 shk3 t
11:36 jonalv so the "db" does not stand for database?
11:36 shk3 well, yes, but the database is on the server
11:36 jonalv I remember medling with the Hibernate project... :)
11:36 shk3 www.nmrshiftdb.org
11:37 shk3 the bioclipse app is just a frontend
11:37 shk3 and it has been ready for about a year or two
11:37 shk3 but it is not possible to export it
11:37 shk3 and publish it
11:37 shk3 and I am really getting angry about this
11:38 jonalv okey, I don't know. I guess olas might be able to help you when he finds some time later on...
11:38 shk3 I am lunch now
11:38 shk3 see you later
11:51 edrin joined #bioclipse
11:51 edrin hi
12:02 CIA-46 bioclipse: jonalv * r5790 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Changed to use propane instead in test. This works.
12:11 CIA-46 bioclipse: jonalv * r5791 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): switched to using propane and butane in SMARTS search tests. Now all tests passes in Structuredb.
12:42 shk3 application starts
12:42 shk3 ok so far
12:42 jonalv yey
12:43 shk3 olas: is it correct that jcp is not working on mac?
12:43 jonalv shk3, it is more or less working on mac in bioclipse 2. Som small problems left I think.
12:44 shk3 ok, but not in bc1?
12:44 jonalv Gpox, what's the current status? :)
12:44 jonalv shk3, I don't think there has been any backporting, no...
12:45 shk3 ok
13:50 CIA-46 bioclipse: ospjuth * r5792 /bioclipse2/trunk/plugins/net.bioclipse.cdk​10.jchempaint/src/net/bioclipse/cdk10/jchem​paint/ui/editor/mdl/MDLMolfileEditor.java: Always create coordinates, as GeometryUtil.has2Dcoordinates() thinks [0,0] for all should return true.
14:33 CIA-46 bioclipse: shk3 * r5793 /bioclipse/trunk/plugins/net.biocl​ipse.nmrshiftdb/src/bc_nmrshiftdb/​util/Bc_nmrshiftdbConstants.java: server changed
14:34 egonw joined #bioclipse
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17:01 CIA-46 bioclipse: ospjuth * r5794 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (7 files in 5 dirs): Fixed EP for adding colorerActions in JCP toolbar.
17:02 CIA-46 bioclipse: ospjuth * r5795 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (SDFEditor.java SDFJCPPage.java StructureTablePage.java): Adapted SDFEditor to be able to use Colorers.
17:12 olas left #bioclipse
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