Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-29

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All times shown according to UTC.

Time Nick Message
04:46 egonw joined #bioclipse
05:51 olass joined #bioclipse
05:52 olass moi
05:52 olass moi moi mukkulat
06:05 olass egonw: is there a command to create a new empty CDKMolecule from script?
06:06 olass like: mol=cdk.newMolecule()
06:06 olass which gives a new empty molecule
06:07 olass egonw: I will file a bug since I couldn't find it
06:27 egonw ok, good
06:27 egonw there is no such method right now
06:27 egonw i can imagine it to be useful
06:28 sneumann moin
06:28 zarah hello sneumann, you fantastic person you
06:29 sneumann the mzML polugin / Editor I mentioned yesterday is ready as a set of eclipse plugins
06:29 sneumann and I have a feature that is not really working, i.e. the plugins dont show up in BC2
06:29 sneumann Should I put up the tarballs somewhere ?
06:36 egonw commit to bioclipse svn?
06:37 egonw tgz is fine too
06:42 egonw olass: ping
06:42 olass pong
06:42 egonw olass: plugins do not have a clear mechanism for stating the license, do they?
06:42 egonw that kind of sucks
06:42 olass licenses are on feature basis
06:42 sneumann Hm, there is a place in the copyright
06:42 olass which is reasonable
06:43 olass since users install features and accept license at that time
06:44 olass egonw: I'd like to discuss bug 1128 when Gpox comes online
06:44 egonw olass: so, I'll have to introduce a Jena feature
06:44 egonw ah, no better idea
06:44 egonw a Pellet feature
06:44 egonw and have the RDF feature include Jena
06:45 egonw that's fine
06:45 egonw olass: ack
06:45 egonw sneumann: where?
06:45 olass egonw: what are you talking about?
06:45 egonw olass: legal talk
06:45 olass Jena?
06:45 olass are you referring to my bug about jen?
06:45 olass jena?
06:45 egonw bug about jena?
06:45 egonw did not see that...
06:46 olass [08:47] < egonw> olass: so, I'll have to introduce a Jena feature
06:46 egonw @pz jena
06:46 olass why?
06:46 zarah [1107] Use SPARQL to set up descripto... http://tinyurl.com/n55t8e
06:46 zarah [1137] RDFManager should propagate re... http://tinyurl.com/lz46fk
06:46 zarah [1106] Migrate descriptor ontology pa... http://tinyurl.com/n6v8xg
06:46 zarah Entire list at http://tinyurl.com/lne8oq
06:46 egonw Pellet is AGPL
06:46 olass egonw: what are you talking about?
06:46 egonw so, currently the whole RDF feature is AGPL
06:46 olass so
06:46 egonw if your QSAR plugin would use the RDF right now
06:46 sneumann for the mzML stuff I'd need developer status in BC2. Does that need any "New Maintainer" process ?
06:46 egonw it would be AGPL too
06:46 olass sneumann: no, it is straightforward
06:47 olass but you need a SF user account
06:47 olass @gg AGPL
06:47 sneumann sneumann;-)
06:47 egonw we only need your credit card information
06:47 zarah olass: http://www.fsf.org/licensi​ng/licenses/agpl-3.0.html
06:47 olass yes, and expiry date
06:47 egonw olass: Affero GNU Public License
06:47 sneumann Hm, lets look up jhgjh.jhgjhg.ru for some valid numbers ;-)
06:47 egonw == GPL + clause
06:47 egonw clause += if you use this on a website, and made modifications, you must make those AGPL too
06:48 egonw sneumann: :)
06:48 egonw sneumann: did you test against RyanAir?
06:49 olass egonw: qsar plugin will be EPL
06:49 egonw right
06:49 egonw so I need to split up the Jena part from the Pellet part in the RDF features
06:49 egonw Jena uses a BSD like license
06:49 olass egonw: I now have Jena in teh QSAR plugin
06:49 egonw so, making a Pellet feature will remove the copylefting
06:50 olass what is pellet?
06:50 egonw Jena does simple SPARQL too...
06:50 egonw enough for your needs
06:50 olass ok
06:50 egonw but not the good stuff Pellet does
06:50 olass will there be a jena manager?
06:50 egonw pellet is a RDF reasoning engine
06:50 sneumann Um, I the mzML stuff copied as much of the formal stuff from QSAR as possible, i.e. currently it is EPL as well. It has EMF generated Code. Should I change that ?
06:50 egonw olass: there already is... it's called 'rdf'
06:50 egonw sneumann: EPL+clause would be best
06:51 egonw that is the default for Bioclipse
06:51 olass sneumann: EPL would be best
06:51 egonw we only use GPL for plugins when 3rd part libs require that
06:51 olass as little as possible
06:51 egonw sneumann: mind the EPL+clause
06:51 egonw see the BMC Bioinformatics paper on the details of this clause
06:51 olass actually, don't think we have any left now... do we?
06:51 egonw GPL?
06:51 olass egonw: is there any GPL in bioclipse2?
06:51 egonw BioJava
06:51 olass no
06:52 olass LGPL
06:52 egonw ChemJava
06:52 egonw ChemoJava
06:52 egonw BioJava is LGPL?
06:52 olass ChemoJava: never heard of
06:52 egonw when did that happen?
06:52 olass egonw: yes
06:52 olass they changed license
06:52 egonw ChemoJava := GPL bits of the CDK
06:52 egonw ah, ic
06:52 olass soem time ago
06:52 egonw did not know that
06:52 egonw well, have not looked at BioJava in a long time :)
06:52 egonw Pellet is AGPL
06:53 egonw in some future point, I hope to do a OpenBabel plugin
06:53 egonw to further unite the BlueObelisk kommun around Bioclipse
06:54 olass egonw: in short, how does AGPL differ from EPL?
06:54 egonw AGPL == GPL with some extra clauses
06:54 egonw roughly speaking
06:55 olass ok
06:55 egonw olass: did you give sneumann write acces yet?
06:55 olass oh
06:55 * olass does now
06:55 egonw good boy
06:55 egonw :)
06:55 egonw otherwise I would have done it
06:57 olass sneumann: I added you as developer to Bioclipse
06:57 olass Welcome!
06:57 egonw olass: what's the 2.0.0 release bug report again?
06:57 olass ?
06:57 olass what you mean?
06:57 egonw we should make a Google Map with development sites
06:57 egonw ummm
06:57 egonw the bug
06:57 egonw that
06:57 olass 73 you mean?
06:57 egonw the one which depends on all bugs that must be fixed before release
06:57 egonw @pz 73
06:58 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=73
06:58 egonw yep, that's the one
06:58 egonw tack
07:02 * olass will have a late breakfast now
07:06 Gpox joined #bioclipse
07:07 * egonw is starting some RDF refactoring
07:07 egonw but will first commit his StructureRDF plugins
07:21 CIA-40 bioclipse: egonw * r10823 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb.rdf/ (19 files in 9 dirs): Template for a RDF-backed structureDB
07:21 CIA-40 bioclipse: egonw * r10824 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb.rdf/ (6 files in 3 dirs): Renamed things properly
07:22 CIA-40 bioclipse: egonw * r10825 /bioclipse2/trunk/features/net.bi​oclipse.structuredb.rdf_feature/ (. .project build.properties feature.xml): Feature for this RDF-backed version
07:22 CIA-40 bioclipse: egonw * r10826 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb.rdf/ (7 files in 5 dirs): OK, now properly recognized: apparently it needs a unique interface to be loaded correctly.
07:23 CIA-40 bioclipse: egonw * r10827 /bioclipse2/trunk/plugins/net.b​ioclipse.structuredb.rdf.tests/ (15 files in 8 dirs): Setting up a test suite
07:24 CIA-40 bioclipse: egonw * r10828 /bioclipse2/trunk/plugins/net.bioclipse.st​ructuredb.rdf/src/net/bioclipse/structured​b/rdf/business/IStructureRDFManager.java: Also extend the IBioclipseManager interface
07:24 CIA-40 bioclipse: egonw * r10829 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Towards unit testing...
07:25 egonw always nice to sit back and let 'git svn dcommit' do the work
07:25 egonw excellent opportunite to read up with literature
07:25 CIA-40 bioclipse: egonw * r10830 /bioclipse2/trunk/plugins/net.b​ioclipse.structuredb.rdf.tests/ (10 files in 3 dirs): Added test data and setUp method for manager tests
07:25 egonw or to discuss bugs with olass and Gpox
07:25 egonw hint, hint
07:25 CIA-40 bioclipse: egonw * r10831 /bioclipse2/trunk/plugins/net.bioclip​se.structuredb.rdf.tests/.gitignore: Ignore the autogenerated logs dir, though not sure where that comes from...
07:25 olass hard to discuss when git clutters the console
07:26 CIA-40 bioclipse: egonw * r10832 /bioclipse2/trunk/externals/com.hp.h​pl.jena/jars/slf4j-simple-1.5.0.jar: Added missing library the bundle needs: a slf4j implementation
07:26 egonw hej, that SVN, all right...
07:26 egonw not gits fault
07:26 olass lol
07:26 egonw :)
07:26 olass Gpox, egonw: about bug 1128
07:26 CIA-40 bioclipse: egonw * r10833 /bioclipse2/trunk/ (5 files in 5 dirs): Implemented createDatabase and added two matching unit tests
07:27 olass especially Gpox, could you elaborate on the solution?
07:27 olass I understand theproblem
07:27 olass but don't really see how it can be resolved
07:27 CIA-40 bioclipse: egonw * r10834 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Worked on adding molecules, but RDF manager does not allow me to add RDF yet
07:27 Gpox @pz 1127
07:27 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1127
07:28 olass @pz 1128
07:28 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1128
07:28 CIA-40 bioclipse: egonw * r10835 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb.rdf/ (2 files in 2 dirs): Very loosy storage of a molecule: just the name. But it is a start
07:28 Gpox create a CDKMolecule and use ui.open() ?
07:28 egonw I don't understand why JCPEditor could not support IStorageEditorInput...
07:28 olass Gpox: that was my suggestion too
07:28 CIA-40 bioclipse: egonw * r10836 /bioclipse2/trunk/plugins/net.bioclipse.structu​redb.rdf.tests/src/net/bioclipse/structuredb/rd​f/business/tests/StructureRDFManagerTest.java: Throw RuntimeException instead of failing: this better distinguishes between unimplemented tests and actual failing tests
07:28 egonw I don't understand that solution either...
07:28 egonw how does that help in the code of the JCPEditor?
07:29 CIA-40 bioclipse: egonw * r10837 /bioclipse2/trunk/plugins/net.bioclipse.structured​b.rdf/src/net/bioclipse/structuredb/rdf/business/ (IStructureRDFManager.java StructureRDFManager.java): Added structrdf.getStore() so that we have access to the raw RDF too
07:29 olass that is two manage rcalls...
07:29 Gpox to convert fromm CML to CDKMolecule i use the cdk manager and there is no loadMolecule(InputStream...
07:29 egonw ah, ok
07:29 CIA-40 bioclipse: egonw * r10838 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb.rdf.tests/src/testData/TestData.java: Removed obsolete file
07:29 egonw now I understand the problem
07:29 egonw what about reading the CML from the inputstream into a String?
07:29 egonw or byte[] ?
07:29 Gpox But i don't understand why you need a string store
07:29 egonw which is better
07:29 CIA-40 bioclipse: egonw * r10839 /bioclipse2/trunk/plugins/net.b​ioclipse.structuredb.rdf.tests/ (2 files in 2 dirs): Use a local test db, so that I can make an assertion on the database triple count
07:29 egonw because NewMoleculeWizard
07:30 egonw we said we wanted to edit a molecule without first having to save a file
07:30 egonw 'we' that is
07:30 CIA-40 bioclipse: egonw * r10840 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): DBMolecule Id and Name are now roundtripped
07:30 olass yes, create a molecule in memory and decide where to save on first save call
07:31 olass and 'save' should fwd to 'Save as...'
07:31 egonw Gpox: like the NewJavaScriptWizard
07:31 olass indeed
07:31 Gpox inf p3erformFinish() do new CDKMolecule() and ui.open(molecule, cmlEditorId)
07:32 olass Gpox: it is one solution
07:32 egonw (ha... Eclipse software is now mostly developed in Linux! :)
07:32 olass but the problem is, ui.open() does not have save, only save as
07:32 olass (maybe that can be chaned?)
07:32 egonw and does not force using the right editor
07:32 Gpox ICDKMolecule.setResource()
07:33 olass but there is no resource, right?
07:33 egonw the JCPEditor needs hacks anyway...
07:33 Gpox it dose if you give it the editor id
07:33 egonw it needs to know when to redirect doSave() to doSaveAs()
07:33 egonw if it is not a IFileStorageEditorInput thingy
07:33 olass here is a use case: A user wants to draw a molecule and search for this as a substructure in an SDFile. He should not have to create and save a new file for this.
07:33 egonw Gpox: ack
07:33 Gpox if it don't have a resource then how can you do save() ?
07:34 egonw because it triggers saveAs()
07:34 olass right, then it should fwd to save as
07:34 olass and default to File
07:34 egonw Gpox: please check the JsEditor
07:34 egonw (lower case s)
07:35 olass in fact, the best thing would be if ui.open(mol, "jcp") would have 'save' enabled and forwarding to 'Save as'
07:35 olass but I don't know is that's feasible
07:35 olass Gpox: what do you think?
07:35 Gpox in doSave on JCPEditor if(molecue.getresource() == null ) doSaveAs()
07:36 egonw Gpox: yes, that would likely help
07:37 Gpox it's been there since the end of april
07:38 egonw does it...
07:38 egonw ok, then it does not help... :(
07:38 egonw but
07:38 egonw maybe that is because it does not set the molecule properly when opening
07:39 egonw Gpox: would it help if I added cdk.loadMolecule(InputStream) ?
07:39 egonw would that solve everything?
07:44 Gpox mol = cdk.fromSMILES("CC"); ui.open(mol); works but ui.open(mol,"net.bioclipse.cd​k.ui.editors.jchempaint.cml") dose not
07:46 Gpox or rather it stopped working
07:47 Gpox while it would be nice to support IStorageEditorInputs I think getting ui.open to work would be better
07:48 egonw Gpox: well, I think we will need IStorageEditorInputs for StructureDB too
07:52 Gpox maybe but structureDB is not in 2.0 and ui.open is
07:52 egonw sure
07:52 egonw I don't know what the easiest solution for now is
07:53 Gpox i have a look at it
07:57 Gpox olass: about bug 813 I had it yesterday on the train and this morning now i updated and it works a gain
07:57 sneumann_ joined #bioclipse
07:57 olass @pz 813
07:57 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=813
07:57 jonalv joined #bioclipse
07:58 * olass updates again
07:59 olass Gpox: It could be related to bug 1135. I would like jonalv to comment on this
07:59 olass jonalv: we are talking about bug 813
07:59 egonw your daily fri afternoon mood changer: http://www.qwghlm.co.uk/toys/dailymail/
07:59 zarah egonw's link is also http://tinyurl.com/mn9tl
08:00 egonw I feel my exhaustion just melt away
08:00 jonalv olass: ye I just saw that one
08:00 sneumann_ Back to license stuff. Ola has his plugins with
08:01 sneumann_ https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk/plugi​ns/net.bioclipse.qsar.model/plugin.xml
08:01 sneumann_ are made available under the terms of the Eclipse Public License v1.0
08:01 sneumann_ This is EPL but I dont see "+ clause"
08:02 sneumann_ So is it fine if I add n.b.mzml.* with that ?
08:03 jonalv olass: I am not saying it's not the same problem but it does look a bit different to me...
08:03 olass ok
08:04 jonalv olass: I think this method is called with the right arguments and still fails
08:04 olass Gpox: I updated and get this error (bug 813) every time
08:05 jonalv olass: while 1135 actually calls the manager method with the wrong arguments.
08:05 olass jonalv: there is something strange going on here...
08:05 olass I think there are some corner cases in teh dispatcher
08:05 olass possible related to threading
08:06 olass but 813 I get every time
08:06 jonalv olass: my opinion too. I don't think it's the same problem
08:07 jonalv olass: but then again, I could be wrong...
08:08 olass I must do my presentation for monday
08:08 olass jonalv: but I am here to help if I can
08:09 jonalv olass: okey I am going through my bugs now and then I am gonna dive in for another debug session of 1135..
08:09 olass sounds good
08:15 CIA-40 bioclipse: sneumann * r10841 /bioclipse2/trunk/plugins/​net.bioclipse.mzml.model/: Initial import of mzML generated from mzML.xsd 1.1.0 RC6
08:17 sneumann_ If this commit is basically fine, I can continue with the other mzML.* plugins.
08:17 jonalv olass: is the exclude / include test working yet?
08:17 sneumann_ Um, asking me ?
08:17 sneumann_ ah, no.
08:19 olass jonalv: no
08:20 jonalv olass: I am sort of drowning in information here, a bit too many tests running... :)
08:20 olass jonalv: comment them out in plugin.xml
08:20 olass in the ds plugins ending with .bursi
08:21 CIA-40 bioclipse: sneumann * r10842 /bioclipse2/trunk/plugins/net​.bioclipse.mzml.model.edit/: Initial import of mzML generated from mzML.xsd 1.1.0 RC6
08:23 egonw sneumann: please file me a bug report on pelezilla to review your plugins
08:26 CIA-40 bioclipse: sneumann * r10843 /bioclipse2/trunk/plugins/net.​bioclipse.mzml.model.editor/: Initial import of mzML generated from mzML.xsd 1.1.0 RC6
08:27 jonalv olass: regarding 1135, I get the error even if running only one test.
08:28 olass you commented some out?
08:28 CIA-40 bioclipse: goglepox * r10844 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (2 files in 2 dirs):
08:28 CIA-40 bioclipse: Added synchronized when reading molecules
08:28 CIA-40 bioclipse: Resolves bug #813
08:28 zarah bug #813 | http://tinyurl.com/r4u3b9
08:29 CIA-40 bioclipse: sneumann * r10845 /bioclipse2/trunk/plugins/net​.bioclipse.mzml.model.tests/: Initial import of mzML generated from mzML.xsd 1.1.0 RC6
08:34 CIA-40 bioclipse: ospjuth * r10846 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Made debugging of failing tests a bit nicer.
08:36 sneumann_ @pz 1142
08:36 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1142
08:36 sneumann_ cool
08:37 egonw thanx
08:37 egonw please do commit the feature too
08:37 egonw btw, I guess we should now educate you in how to set up an Update Site in Halle :)
08:38 olass egonw: a wiki page for this would be nice
08:38 olass it is actually very easy
08:39 olass I could write it in 5 mins
08:39 egonw OK, will file a bug report
08:39 olass thx
08:39 egonw this is important for community building
08:39 egonw acutally
08:39 * olass will do it now
08:39 olass but please file the bug
08:39 egonw just saw yesterday that Bill Gates says sane things too
08:39 egonw e.g. he focused MS very much in building a developers community to work on top of MS stuff
08:40 egonw like we plan to do after 2.0 too
08:40 egonw olass: tack
08:41 egonw @pz 1143
08:41 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1143
08:41 egonw sneumann: yes, nice feature...
08:42 egonw we only need to educate zarah to report the bug title too
08:42 egonw as in:
08:42 egonw @pz wiki
08:42 zarah [898] Adapt scripts on http://wiki.bi... http://tinyurl.com/cugxk5
08:42 zarah [1143] Write wiki page on how to set ... http://tinyurl.com/m95o7h
08:42 zarah [800] Refactor ValidateCMLManager int... http://tinyurl.com/c6u9hj
08:42 zarah [805] Refactor SpecmolManager into th... http://tinyurl.com/c4yf5o
08:42 CIA-40 bioclipse: sneumann * r10847 /bioclipse2/trunk/features/net​.bioclipse.massspec_feature/: Initial import, feature adapted from net.bioclipse.rdf_feature
08:42 zarah [830] Generate3D using CDK should hav... http://tinyurl.com/c9bheu
08:42 zarah Entire list (27) at http://tinyurl.com/ljkmq8
08:42 egonw sneumann: oh... ambitious!
08:43 egonw massspec_feature :)
08:43 egonw going for the big fish directly :)
08:44 sneumann_ It's an invitation to provide more plugins
08:44 egonw :)
08:44 egonw message received
08:44 sneumann_ I can do n.b.mzData and n.b.mzXML as well
08:44 egonw have been pondering about a chemistry-aware spreadsheet plugin for MS
08:44 sneumann_ Then, if the connection to R is working
08:44 egonw ah, yes...
08:44 egonw indeed...
08:45 sneumann_ you can extract spectra from th mz* stuff
08:45 egonw then we hook up all our components
08:45 sneumann_ and pass them to xcms
08:45 egonw visuzalize and elucidate structures with CDK and MEDEA features
08:45 egonw visualize spectrum with Speclipse
08:45 sneumann_ So following NWO we have World Domination (tm)
08:46 sneumann_ Question:
08:46 sneumann_ How do features work ?
08:46 sneumann_ My ms_feature has the mzml* plugins
08:46 sneumann_ in feature.xml
08:46 sneumann_ and I thought I could just add ms_feature to
08:46 egonw you run bioclipse using features
08:46 egonw yes, to bioclipse.product
08:46 sneumann_ exactly.
08:47 egonw did you link content-types to the editor ?
08:47 egonw ok, will check that...
08:47 egonw need to finish this RDF/Pellet refactoring first...
08:47 egonw will then look at it
08:47 egonw meanwhile...
08:47 egonw can someone please set up a Google Map with pointers for the sites where Bioclipse plugins are developed?
08:47 egonw perhaps using KML?
08:48 egonw or do that KML-mashup with the CIA bot to make a google map of the locations from where the last 200 commits were made from?
08:49 sneumann_ The ms_feature does not show up in the running BC2
08:49 sneumann_ http://pastebin.com/m4549a9a7
08:49 sneumann_ and yes, I have file extensions mzml registered with the editor
08:50 sneumann_ actually, can I register multiple extensions ? mzml, mzML, ...
08:50 sneumann_ or even peek into the XML to check which editor to use ?
08:50 egonw yes, just comma separated
08:50 egonw yes, better even that
08:50 egonw mom...
08:51 egonw net.bioclipse.cml/plugin.xml
08:51 egonw line 63-77
08:51 egonw notice the use of <describer>
08:52 egonw sneumann: do you have example files?
08:52 egonw if so, please do make a 'sample data' plugin too
08:53 egonw sneumann: that output looks good
08:53 egonw all those feature lines
08:53 egonw are coming from the automatic checking of update sites
08:57 sneumann_ http://msbi.ipb-halle.de/updateSite/
08:57 zarah sneumann_'s link is also http://tinyurl.com/kppsnr
08:57 olass sneumann_: http://wiki.bioclipse.net/index.php?title=​How_to_set_up_an_update_site_for_Bioclipse
08:57 sneumann_ This is still from BC1 in 2007 v:-)
08:57 zarah olass's link is also http://tinyurl.com/mmb7f7
08:57 sneumann_ This is still from BC1 in 2007 :-)
08:57 olass egonw: http://wiki.bioclipse.net/index.php?title=​How_to_set_up_an_update_site_for_Bioclipse
08:57 zarah olass's link is also http://tinyurl.com/mmb7f7
08:57 olass there you go
08:58 egonw thanx
09:00 egonw olass: what's the option again to disable the update site chekcing?
09:00 egonw -noUpdate does not seem to have effect
09:01 olass egonw: it really should...
09:01 egonw I am expecting a typo or so
09:01 egonw cannot find the details in the wiki
09:01 olass -noupdate
09:01 olass eller -noUpdate
09:02 egonw mmm... ok
09:02 egonw program arugment?
09:02 egonw right?
09:03 egonw ok, works fine
09:03 egonw either casing...
09:03 olass nope, checking toLowercase()
09:03 egonw can't find anymore what I did earlier, so not sure what I did wrong :(
09:04 olass egonw: could this be related to bug 1120?
09:04 olass I have that one assigned
09:04 egonw @pz 1120
09:05 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1120
09:05 olass please comment with your behaviour
09:05 CIA-40 bioclipse: sneumann * r10848 /bioclipse2/trunk/ (512 files in 39 dirs): Initial import of mzML generated from mzML.xsd 1.1.0 RC6
09:05 egonw perhaps
09:05 egonw I am using an older WS here
09:05 egonw so should indeed have been a saved state
09:06 CIA-40 bioclipse: jonalv * r10849 /bioclipse2/trunk/plugins/net.bi​oclipse.core/src/net/bioclipse/ (3 files in 2 dirs): Performed genreal thread safetying and worked around symptoms described in bug: #1135. I do not understand what was wrong but now it seems the method is always called with the right arguments. Fixes bug: #1135.
09:07 zarah bug #1135 | http://tinyurl.com/mqoe9l
09:13 egonw jonalv: ping
09:13 jonalv egonw: pong
09:13 egonw I have a weird error:
09:14 jonalv egonw: yey, yet another weird error...
09:14 jonalv \o/
09:14 jonalv :/
09:14 jonalv egonw: okey shoot
09:14 egonw http://bioclipse.pastebin.com/m16b6cb34
09:14 zarah egonw's link is also http://tinyurl.com/m846ue
09:14 olass jonalv++ //1135 seems resolved
09:14 olass at least it works here
09:15 jonalv olass: good
09:15 egonw but I am sure the pellet.Activator does have a getDefault()
09:15 olass did you resolve teh bug?
09:15 egonw wait
09:15 olass yes
09:15 egonw I'll update first...
09:15 jonalv egonw: what is pellet?
09:15 egonw @gg pellet rdf clark
09:15 zarah egonw: http://clarkparsia.com/weblog/page/2/
09:16 egonw reasoning engine
09:17 jonalv egonw: okey, is it commited?
09:17 egonw no
09:17 egonw was wondering if you saw something special about the stack trace
09:18 jonalv egonw: well no I can't say I do. But I guess I could have a look at the code and ssee if I get the same error here...
09:18 sneumann_ Most annoying eclipse "feature": it forgets the most recently used directory in "import existing project into workspace"
09:19 sneumann_ Trying to get the UpdateSite running (again)
09:19 sneumann_ Problems during export
09:19 sneumann_ Problems parsing the feature file:/home/sneumann/eclipse-bioclipse/features/ne​t.bioclipse.chemoinformatics_feature/feature.xml.
09:19 sneumann_ Problems parsing the feature file:/home/sneumann/eclipse-bioclipse/features/ne​t.bioclipse.chemoinformatics_feature/feature.xml.
09:20 sneumann_ Why does "build all" (and also "build", for that matter) try to parse other features ?
09:20 sneumann_ They're not mentioned in Site.xml
09:21 egonw jonalv: commits being made as we speak
09:21 egonw sneumann: weird
09:21 egonw sneumann: commiting the Pellet stuff...
09:21 sneumann_ might be related to the fact that my ms_feature is not working in first place ?
09:21 egonw will then look at your feature
09:21 egonw :)
09:22 CIA-40 bioclipse: egonw * r10850 /bioclipse2/trunk/plugins/net.bioclipse.rdf/ (4 files in 2 dirs): Removed all bits that require Pellet, so that this plugin is plain EPL+clause again
09:22 CIA-40 bioclipse: ospjuth * r10851 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Further decrease of debugging in DS when running tests as jobs.
09:23 CIA-40 bioclipse: egonw * r10852 /bioclipse2/trunk/plugins/net.bioclipse.rdf/sr​c/net/bioclipse/rdf/business/RDFManager.java: Made this helper method public static and added JavaDoc
09:24 CIA-40 bioclipse: egonw * r10853 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: With the AGPL Pellet bits removed, the RDF feature is EPL+clause again
09:25 CIA-40 bioclipse: egonw * r10854 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Removed unused dependency
09:26 egonw 9 out of 10 warmest spring in NL are after 1990
09:26 egonw the two hottest in 2007 and 2009
09:26 egonw how so, no global warming?
09:27 egonw april second hottest in 300 years
09:27 CIA-40 bioclipse: egonw * r10855 /bioclipse2/trunk/ (28 files in 11 dirs): Set up the Pellet plugin and feature (licensed AGPL v3), with links to the clarkparsia.com website
09:27 olass egonw: you like the cold?
09:27 egonw let's rephrase it... the ~1600 ice age is finally over
09:27 egonw oh, yes, much better here in sweden
09:28 egonw a nice ~22 degrees on average for last and coming week
09:28 olass you should consider moving even further to the north
09:28 egonw bit cold yesterday
09:28 egonw but Mon should make up :)
09:28 olass lol
09:28 egonw olass: yes, saw that
09:28 egonw 25+ in lapland
09:28 egonw there is always reykyavik
09:29 egonw I promised when 24+ I'd take a dive in our pool
09:29 egonw seems that Sunday is the day
09:29 egonw pool == pond
09:29 egonw last chance anyway
09:30 olass egonw: don't waste that chance
09:30 olass sry I can't help with the moving
09:30 egonw yes, no worries
09:30 egonw jonalv and masak will help
09:30 olass jonalv is a good swimmer
09:31 egonw and two friends any father in law
09:31 egonw should be enough
09:31 olass he is actually semi-professional
09:31 olass jonalv that is
09:31 egonw in house moving?
09:31 olass an old pro in swimming
09:31 jonalv olass: lier
09:31 egonw yeah, half understood something about that
09:31 egonw jonalv: details?
09:31 olass jonalv: you are too modest
09:31 egonw jonalv: olympic junior champ of 1996 ?
09:32 jonalv egonw: it's all in olas head.
09:32 egonw yes, that happens on fridays
09:32 egonw did I mention yet this nice site:
09:32 egonw http://friendfeed.com/dullhunk/c67ad​5c8/daily-mail-o-matic-qwghlm-co-uk
09:32 olass jonalv almost made the paralympics team
09:32 zarah egonw's link is also http://tinyurl.com/nzfkjl
09:32 egonw hahahaha
09:32 egonw for being a IT programmer?
09:33 jonalv egonw: yes I think you mentioned it...
09:33 olass egonw: YES
09:33 jonalv "ARE SINGLE MOTHERS STEALING FROM YOUR PETS?" :)
09:40 egonw oh, and check out there ontology...
09:41 egonw the classify everything
09:42 egonw in a real DailyMail fashion
09:42 egonw something either causes cancer
09:42 egonw or cures it
09:42 jonalv egonw: link
09:43 egonw http://dailymailoncology.tumblr.com/
09:43 zarah egonw's link is also http://tinyurl.com/8k4rxt
09:43 egonw try aspirin
09:44 jonalv egonw: that is true
09:45 jonalv egonw: I stumbled upon that during my course earlier this year...
09:49 * jonalv @ lunch
10:00 CIA-40 bioclipse: egonw * r10856 /bioclipse2/trunk/plugins/net​.bioclipse.pellet/plugin.xml: Removed content-types already defined in the net.bioclipse.rdf plugin
10:01 egonw BioList is now?
10:01 egonw RecordableList or so, right?
10:02 egonw mmm... no
10:03 egonw ah, it is
10:09 CIA-40 bioclipse: egonw * r10857 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Compile errors for recent API changes
10:18 egonw ummm... Compile *fixes* :)
10:38 egonw jonalv: please ping when you are back
10:42 CIA-40 bioclipse: egonw * r10858 /bioclipse2/trunk/plugins/net.bioc​lipse.pellet/src/net/bioclipse/pel​let/business/IPelletManager.java: Tuned summaries a bit towards RDF
10:43 CIA-40 bioclipse: egonw * r10859 /bioclipse2/trunk/plugins/net.bioc​lipse.pellet/src/net/bioclipse/pel​let/business/IPelletManager.java: Added DOI to further literature
10:46 egonw @tell jonalv please have a look at running the rdf.product after adding (locally) the pellet feature
10:46 zarah Consider it noted.
10:46 egonw @tell jonalv and let me know what you think could be the reason pellet.Activator.getDefault() is not found...
10:46 zarah Consider it noted.
11:21 egonw uppsala: ping
11:23 CIA-40 bioclipse: sneumann * r10860 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.massspec/: Initial import, adapted from net.bioclipse.data.sampledata
11:23 egonw sneumann++
11:24 * egonw had some feature does not boot problems too...
11:24 egonw with the Pellet feature
11:25 sneumann_ Solution was ?
11:25 egonw no solution yet
11:25 CIA-40 bioclipse: sneumann * r10861 /bioclipse2/trunk/plugins/n​et.bioclipse.data.massspec/ (22 files in 12 dirs): Initial import, adapted from net.bioclipse.data.sampledata
11:26 sneumann_ Which feature depends on ms sample data ? The MS feature or the sampledata feature ?
11:27 egonw MS feature
11:28 sneumann_ and the data.ms plugin pulls in its dependency n.b.sampledata, I hope
11:29 egonw add the sampledata feature to depdency for the massspec feature
11:33 sneumann_ just looked at your rdf.product (from yesterday)
11:33 sneumann_ it has
11:33 sneumann_ <product name="Bioclipse" id="net.bioclipse.ui.product" ...>
11:33 sneumann_ so rdf.product is_a disguised bioclipse.product just with a different plugin/feature list ?
11:36 CIA-40 bioclipse: sneumann * r10862 /bioclipse2/trunk/features/ne​t.bioclipse.massspec_feature/ (feature.xml massspec.product): Added dependency on net.bioclipse.data.massspec
11:41 sneumann_ Seems that my updateSite problem is related to the fact that not all cheminformatics_feature plugin dependencies are there.
11:42 sneumann_ How do you guys keep everything in the workspace and dont loose overview of xxx plugins ?
11:43 jonalv Ctrl + Command + T
11:43 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
11:43 jonalv zarah: tell me
11:43 zarah jonalv: 57 m 15 s ago, egonw said please have a look at running the rdf.product after adding (locally) the pellet feature
11:43 zarah jonalv: 56 m 51 s ago, egonw said and let me know what you think could be the reason pellet.Activator.getDefault() is not found...
11:46 egonw sneumann: yes, rdf.product is currently just a convenience .product to not have to add the features again and again
11:46 egonw sneumann: unfortunately, we do loose overview
11:46 egonw speclipse has (had) some missing plugin trouble too
11:50 egonw jonalv: I can find nothing what can cause this...
11:51 egonw I started with the net.bioclipse.rdf plugin which has a manager too...
11:51 egonw and that one has no problems
11:51 egonw I 98% I have updated all important fields
11:51 egonw and cannot find the mistake I made
11:59 jonalv egonw: that is a very strange exception
11:59 jonalv _very_
11:59 egonw yes, thought so too
12:00 jonalv egonw: however I ahve two classes named net.bioclipse.pellet.Activator in my workspace. Taht might be related...
12:00 egonw you do?
12:00 egonw really?
12:01 jonalv egonw: the second one is in org.mindswap.pellet and is written by you...
12:01 egonw ok
12:01 egonw I see it
12:01 egonw thanx
12:01 jonalv egonw: np
12:02 egonw at some point I did check Open-Type *.pellet.Activator
12:02 egonw and that *did* say one net.bioclipse and one org.mindswap.pellet.Activator
12:02 egonw so, did not check the actual plugin src/ fodler of org.mindswap...
12:02 egonw how deceptive Eclipse can be
12:02 egonw eclipse--
12:02 egonw jonalv++
12:02 egonw for looking at the problem
12:02 jonalv :)
12:03 jonalv I should have a look at shk3's problem with progressmonitor and running seneca job
12:03 jonalv but I don't really know where to start..
12:04 jonalv "IS POLITICAL CORRECTNESS HURTING THE QUEEN?"
12:04 egonw :)
12:05 egonw sneumann: solution to my feature boot problem: two files with the same name on the classpath
12:13 jonalv egonw: Rob Shellhorn was that your student?
12:14 * jonalv whished he had a better memory...
12:18 egonw yes
12:18 jonalv egonw: there are some strange code here...
12:18 egonw the ebi guys have already done massive tweaking and bending
12:19 jonalv DeterministicStructureElucidationJob and StochastivStructureElucidationJob, I need some help understand I fear...
12:19 egonw not sure if I still recognize the code
12:19 egonw sure
12:19 jonalv egonw: can I patch it?
12:19 egonw I know what the idea *was*...
12:19 egonw that's Chris' group to say
12:19 jonalv egonw: actually I don't care what it's doing it's just the way it treats the monitors...
12:19 egonw since it is not working, I guess they would appreciate
12:20 jonalv egonw: first thing I spotted was the way it almost but not quite dealt with the possibility of being handled null instead of a monitor...
12:28 jonalv gah I don't understand ths code
12:28 jonalv :(
12:32 egonw as said...
12:32 egonw the ebi guys already had a good go at it...
12:32 egonw but if you point me to a particular class, I could have a look
12:33 jonalv egonw: Well I merely wonder what it is that makes the javascript monitor be reset...
12:33 jonalv something strange must be done...
12:34 jonalv ..in that code
12:34 jonalv and I can barely figure out what calls what...
12:38 jonalv egonw: on row 140 in StochasticStructureElucidationJob the subTask is given 10000 ticks. As far as I can see these ticks are never tocked. That is: Where is monitor.worked called?
12:40 egonw originally, the idea was that each generated structure would cause one tick
12:40 egonw this clearly got lost
12:41 jonalv egonw: so it creates exactly 10000 structres?
12:42 egonw the MoleculeAnnealerAdapter is new
12:42 egonw actually...
12:42 egonw the monitor *is* used
12:42 egonw line 232-251
12:43 egonw but no tick it seems
12:43 jonalv egonw: exactly
12:44 egonw but I agree... that 10000 should be linked to the MoleculeAnnealerAdapter
12:44 egonw file a bug report
12:44 jonalv egonw: for who?
12:44 egonw gilleain
12:44 jonalv oki
12:51 sneumann [14:05] <egonw> sneumann: solution to my feature boot problem: two files with the same name on the classpath
12:51 egonw sneumann: looking at your code right now
12:51 egonw problem 1:
12:51 egonw you must not depend on JRE 1.6
12:51 sneumann in some of the plugins of my feature ?
12:51 sneumann Ack.
12:51 egonw our OS/X developers don't have Java 1.6
12:52 egonw commiting a fix now
12:52 sneumann merci
12:52 jonalv whats gilleans adress on bugzilla?
12:53 egonw http://pele.farmbio.uu.se/cgi-bin/bugzilla/editu​sers.cgi?action=list&amp;matchvalue=login_name&a​mp;matchstr=&amp;matchtype=substr&amp;groupid=7
12:53 zarah egonw's link is also http://tinyurl.com/nlltj3
12:53 jonalv egonw: Sorry, you aren't a member of the 'editusers' group, and you don't have permissions to add or remove people from a group, and so you are not authorized to add, modify or delete users.
12:54 egonw hahaha
12:54 egonw ah, did not know this as confidential data :)
12:54 egonw mom
12:54 CIA-40 bioclipse: egonw * r10863 /bioclipse2/trunk/externals/org.mindswap.pellet/ (5 files in 4 dirs): Renamed the activator to not conflict with that of net.bioclipse.pellet
12:55 CIA-40 bioclipse: egonw * r10864 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Don't depend on JRE 1.6 (OS/X needs 1.5)
12:56 jonalv @pz 553
12:56 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=553
12:57 egonw sneumann: ping
12:57 egonw sneumann: which plugin has the content types?
12:57 egonw is that .editor?
12:57 egonw well, it has an editor indeed
12:57 egonw but no content type
12:58 egonw sneumann: I cannot find the content types
12:58 sneumann_ Not yet committed
12:58 egonw oh
12:58 sneumann_ shot in the blue, comming now
12:59 egonw BSOD?
12:59 sneumann_ but with 800+ (or so) plugins workspace building is pretty slow ...
12:59 egonw ah, right
13:00 egonw working sets helps
13:00 egonw and I can also recommend using different workspaces for different projects
13:00 egonw I sometimes have 3 eclipses open at the same time
13:00 sneumann_ The latter I have
13:00 egonw how do you get 800 plugins...
13:00 egonw that will make olass jealous
13:00 egonw olass: right? :)
13:00 sneumann_ the first I try to figure. I had a cdk-external Working Set, but it is gone ?!
13:01 sneumann_ maybe a bit fewer ...
13:01 olass *grmpf*
13:01 * olass does not like the current plugin explosion
13:02 jonalv olass: why not?
13:02 olass too many plugin != difficult to mange
13:02 olass manage
13:02 CIA-40 bioclipse: egonw * r10865 /bioclipse2/trunk/plugins/net.bi​oclipse.data.massspec/.project: Fixed project title in .project
13:02 jonalv I think big plugins are hard to manage as well
13:03 CIA-40 bioclipse: sneumann * r10866 /bioclipse2/trunk/plugins/net.biocl​ipse.mzml.model.editor/plugin.xml: Adding content type extension point
13:03 olass yes, there is a tradeoff
13:03 jonalv I guess much code is hard to manage...
13:03 olass our plugins folder is growing large in SVN
13:03 olass but things will change anyway after the move to git
13:03 jonalv cool
13:04 sneumann_ OK, I see now MANIFEST Bundle-RequiredExecutionEnvironment: J2SE-1.5 in my mzml.*
13:04 sneumann_ but eclipse project still has 1.6 ?
13:05 egonw mmm...
13:05 egonw my patch only touched .classpath
13:05 * sneumann_ modifying "workspace settings"
13:08 CIA-40 bioclipse: egonw * r10867 /bioclipse2/trunk/features/net.bioclip​se.massspec_feature/massspec.product: Fixed application: should be bioclipse.ui.application
13:12 CIA-40 bioclipse: sneumann * r10868 /bioclipse2/trunk/plugins/net.bioclipse.data​.massspec/data/massspec/tiny.pwiz.1.1.mzml: Added first mzML file
13:12 masak joined #bioclipse
13:12 masak oh hai
13:12 zarah oh hai masak
13:12 masak oh hai zarah
13:13 egonw hi masak
13:13 egonw hows' the hacking in Stkhlm ?
13:13 egonw btw, here's patch, specifically for you:
13:13 jonalv hi masak
13:13 egonw (please review)
13:13 egonw (should I file a bug report as reminder?)
13:14 CIA-40 bioclipse: egonw * r10869 /bioclipse2/trunk/plugins/ (5 files in 4 dirs):
13:14 CIA-40 bioclipse: Added support for multiple DOIs:
13:14 CIA-40 bioclipse: * refactored .doi() to return a String[] because the DOI specs allow so many characters
13:14 CIA-40 bioclipse:  a 'X'-separated list is impossible
13:14 CIA-40 bioclipse: * added a PublishedClass.doi field
13:14 CIA-40 bioclipse: * added output of DOI info for 'man <MANAGER>'
13:14 masak egonw: people seem pleased with getting to know Perl 6, but the meeting kinda wound down before we got to the hackathon part. :)
13:14 masak egonw: might be best to file a bug report, yes.
13:15 egonw ack
13:15 CIA-40 bioclipse: sneumann * r10870 /bioclipse2/trunk/features/net.bioc​lipse.massspec_feature/feature.xml: Added update site to massspec_feature
13:15 masak egonw: I hope to be able to look at it during the weekend.
13:15 egonw yeah, no worries
13:15 masak jonalv: oh hai
13:15 egonw it's just a root kit
13:15 masak egonw: oh, good.
13:20 sneumann_ [14:51] <egonw> problem 1:
13:20 sneumann_ and number 2 ?
13:21 egonw 2: data plugin had the wrong .project project name
13:21 egonw 3: missing content type
13:21 egonw with that fixed
13:21 egonw I can now see if it works here... :)
13:22 sneumann_ !MESSAGE Missing required bundle org.eclipse.emf.ecore.xmi_0.0.0.
13:23 egonw ok, that's an easy fix
13:24 egonw here it is.
13:24 egonw :
13:28 egonw ...
13:28 CIA-40 bioclipse: egonw * r10871 /bioclipse2/trunk/features/net.bioc​lipse.massspec_feature/feature.xml: Added missing EMF feature
13:28 maclean joined #bioclipse
13:28 maclean
13:29 jonalv o/
13:30 maclean I backlogged, jonalv, and saw complaints about my code! I was shocked, shocked! And at the same time not surprised at all :)
13:30 maclean The monitors subticks are not being done properly, eh?
13:30 jonalv maclean: so it's your code? I wasn't really sure...
13:31 jonalv maclean: you got a bug ticket about it anyway..
13:31 maclean well, it's hard to say by now. egon, me, shk, ...
13:31 maclean I think it was messed up by me when trying to shoehorn visual feedback into monitors.
13:32 maclean I'll take a look, anyway.
13:35 masak maclean: just held a talk about Perl 6: http://masak.org/carl/stockholm.pm/perl6.pdf
13:35 zarah masak's link is also http://tinyurl.com/lx5jmh
13:35 * maclean takes a gander
13:36 masak "it's Moose, not Goose!"
13:36 maclean :)
13:37 maclean http://en.wiktionary.org/wiki/gander
13:37 zarah maclean's link is also http://tinyurl.com/m4wsty
13:37 jonalv TotoiseSVN--
13:38 jonalv SVN--
13:38 jonalv svn--
13:38 jonalv windows--
13:38 * jonalv afk //tortosisesvn is working...
13:39 maclean does 'a' xx 3 enforce list context?
13:40 masak maclean: yes.
13:41 maclean I made the mistake of doing "[[0]] * n" the other day in python, and got a list of n references to the same list. I felt foolish.
13:42 maclean ooh eqv looks good.
13:43 maclean hmm, actually, no it doesn't, it loos inconvenient, but probably more correct. anyway, I'll stop thinking aloud now...
13:43 egonw masak: please tell maclean about that git PDF book thingy
13:44 masak maclean: a couple of seconds ago, egonw said about that git PDF thingy
13:44 maclean there are git books in the sanger library
13:44 egonw sneumann: editor sort of working for me now
13:44 maclean :)
13:44 egonw simple tree with file content
13:44 masak egonw: http://www.newartisans.com/2008​/04/git-from-the-bottom-up.html
13:44 zarah masak's link is also http://tinyurl.com/cf6fjv
13:44 masak um, maclean: http://www.newartisans.com/2008​/04/git-from-the-bottom-up.html
13:44 maclean masak: tack.
13:44 zarah masak's link is also http://tinyurl.com/cf6fjv
13:45 maclean I had better gin up on git.
13:45 CIA-40 bioclipse: egonw * r10872 /bioclipse2/trunk/features/net.bioc​lipse.massspec_feature/feature.xml: Added missing plugin dependencies
13:46 egonw ok, busy now...
13:46 egonw bbl
13:46 sneumann_ bye
13:46 egonw sneumann: please test
13:46 sneumann_ will do
13:47 shk3 joined #bioclipse
13:48 maclean oh my yes : "@fib = 1,1 ... &[+]" -nice.
13:49 masak aye.
13:50 maclean lazy evaluation, though, I hope :)
13:50 jonalv <jonalv> egonw: Sorry, you aren't a member of the 'editusers' group, and you don't
13:50 jonalv have permissions to add or remove people from a group, and so you are not
13:50 jonalv authorized to add, modify or delete users.
13:50 jonalv <egonw> hahaha                                                                  [14:54]
13:50 jonalv <egonw> ah, did not know this as confidential data :)
13:50 jonalv <egonw> mom
13:50 jonalv <CIA-40> bioclipse: egonw * r10863 /bioclipse2/trunk/externals/org.mindswap.pellet/ (5
13:50 jonalv files in 4 dirs): Renamed the activator to not conflict with that of
13:50 jonalv net.bioclipse.pellet
13:50 jonalv <CIA-40> bioclipse: egonw * r10864 /bioclipse2/trunk/plugins/ (4 files in 4 dirs):
13:50 jonalv Don't depend on JRE 1.6 (OS/X needs 1.5)                               [14:55]
13:50 jonalv <jonalv> @pz 553                                                                [14:56]
13:50 jonalv <zarah> http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=553
13:50 jonalv <egonw> sneumann: ping                                                          [14:57]
13:50 zarah jonalv's link is also http://tinyurl.com/mpnd2v
13:50 jonalv <egonw> sneumann: which plugin has the content types?
13:50 jonalv <egonw> is that .editor?
13:50 jonalv <egonw> well, it has an editor indeed
13:50 jonalv <egonw> but no content type
13:50 jonalv <egonw> sneumann: I cannot find the content types                               [14:58]
13:50 jonalv <sneumann_> Not yet committed
13:50 jonalv <egonw> oh
13:51 jonalv <sneumann_> shot in the blue, comming now
13:51 jonalv <egonw> BSOD?                                                                   [14:59]
13:51 jonalv <sneumann_> but with 800+ (or so) plugins workspace building is pretty slow ...
13:51 jonalv <egonw> ah, right
13:51 jonalv <egonw> working sets helps                                                      [15:00]
13:51 jonalv <egonw> and I can also recommend using different workspaces for different projects
13:51 jonalv <egonw> I sometimes have 3 eclipses open at the same time
13:51 jonalv <sneumann_> The latter I have
13:51 jonalv <egonw> how do you get 800 plugins...
13:51 jonalv <egonw> that will make olass jealous
13:51 jonalv <egonw> olass: right? :)
13:51 jonalv <sneumann_> the first I try to figure. I had a cdk-external Working Set, but it is
13:51 jonalv gone ?!
13:51 jonalv <sneumann_> maybe a bit fewer ...                                               [15:01]
13:51 jonalv <olass> *grmpf*
13:51 jonalv * olass does not like the current plugin explosion
13:51 jonalv <jonalv> olass: why not?                                                        [15:02]
13:51 jonalv <olass> too many plugin != difficult to mange
13:51 jonalv <olass> manage
13:51 jonalv <CIA-40> bioclipse: egonw * r10865
13:52 jonalv /bioclipse2/trunk/plugins/net.bi​oclipse.data.massspec/.project: Fixed project
13:52 jonalv title in .project
13:52 jonalv <jonalv> I think big plugins are hard to manage as well
13:52 jonalv <CIA-40> bioclipse: sneumann * r10866
13:52 jonalv /bioclipse2/trunk/plugins/net.biocl​ipse.mzml.model.editor/plugin.xml: Adding
13:52 jonalv content type extension point                                           [15:03]
13:52 jonalv <olass> yes, there is a tradeoff
13:52 jonalv <jonalv> I guess much code is hard to manage...
13:52 masak jonalv: dåligt.
13:52 jonalv <olass> our plugins folder is growing large in SVN
13:52 jonalv <olass> but things will change anyway after the move to git
13:52 jonalv <jonalv> cool
13:52 jonalv <sneumann_> OK, I see now MANIFEST Bundle-RequiredExecutionEnvironment: J2SE-1.5 in my
13:52 jonalv mzml.*                                                              [15:04]
13:52 jonalv <sneumann_> but eclipse project still has 1.6 ?
13:52 jonalv <egonw> mmm...                                                                  [15:05]
13:52 jonalv <egonw> my patch only touched .classpath
13:52 jonalv * sneumann_ modifying "workspace settings"
13:52 jonalv <CIA-40> bioclipse: egonw * r10867
13:52 jonalv /bioclipse2/trunk/features/net.bioclip​se.massspec_feature/massspec.product:
13:52 jonalv Fixed application: should be bioclipse.ui.application                  [15:08]
13:53 jonalv <CIA-40> bioclipse: sneumann * r10868
13:53 jonalv /bioclipse2/trunk/plugins/net.bioclipse.data​.massspec/data/massspec/tiny.pwiz.1.1.mzml:
13:53 jonalv Added first mzML file                                                  [15:12]
13:53 jonalv *** masak (n=user@gw.iis.se) has joined channel #bioclipse
13:53 jonalv <masak> oh hai
13:53 jonalv <zarah> oh hai masak
13:53 jonalv <masak> oh hai zarah
13:53 jonalv <egonw> hi masak                                                                [15:13]
13:53 jonalv <egonw> hows' the hacking in Stkhlm ?
13:53 jonalv <egonw> btw, here's patch, specifically for you:
13:53 jonalv <jonalv> hi masak
13:53 jonalv <egonw> (please review)
13:53 jonalv <egonw> (should I file a bug report as reminder?)
13:53 jonalv <CIA-40> bioclipse: egonw * r10869 /bioclipse2/trunk/plugins/ (5 files in 4 dirs):
13:53 jonalv [15:14]
13:53 jonalv <CIA-40> bioclipse: Added support for multiple DOIs:
13:53 jonalv <CIA-40> bioclipse: * refactored .doi() to return a String[] because the DOI specs
13:53 jonalv allow so many characters
13:53 jonalv <CIA-40> bioclipse:  a 'X'-separated list is impossible
13:53 jonalv <CIA-40> bioclipse: * added a PublishedClass.doi field
13:54 jonalv <CIA-40> bioclipse: * added output of DOI info for 'man <MANAGER>'
13:54 jonalv <masak> egonw: people seem pleased with getting to know Perl 6, but the meeting kinda
13:54 jonalv wound down before we got to the hackathon part. :)
13:54 jonalv <masak> egonw: might be best to file a bug report, yes.
13:54 jonalv <egonw> ack                                                                     [15:15]
13:54 jonalv <CIA-40> bioclipse: sneumann * r10870
13:54 jonalv /bioclipse2/trunk/features/net.bioc​lipse.massspec_feature/feature.xml: Added
13:54 jonalv update site to massspec_feature
13:54 jonalv <masak> egonw: I hope to be able to look at it during the weekend.
13:54 jonalv <egonw> yeah, no worries
13:54 jonalv <masak> jonalv: oh hai
13:54 jonalv <egonw> it's just a root kit
13:54 jonalv <masak> egonw: oh, good.
13:54 jonalv <sneumann_> [14:51] <egonw> problem 1:                                          [15:20]
13:54 jonalv <sneumann_> and number 2 ?
13:54 jonalv <egonw> 2: data plugin had the wrong .project project name                      [15:21]
13:54 jonalv <egonw> 3: missing content type
13:54 jonalv <egonw> with that fixed
13:54 jonalv <egonw> I can now see if it works here... :)
13:54 jonalv <sneumann_> !MESSAGE Missing required bundle org.eclipse.emf.ecore.xmi_0.0.0.   [15:22]
13:55 jonalv <egonw> ok, that's an easy fix                                                  [15:23]
13:55 jonalv <egonw> here it is.                                                             [15:24]
13:55 jonalv <egonw> :
13:55 jonalv <egonw> ...                                                                     [15:28]
13:55 jonalv <CIA-40> bioclipse: egonw * r10871
13:55 jonalv /bioclipse2/trunk/features/net.bioc​lipse.massspec_feature/feature.xml: Added
13:55 jonalv missing EMF feature
13:55 jonalv *** maclean (n=maclean@host86-151-33-224.range86-151.btcentralplus.com) has joined
13:55 jonalv channel #bioclipse
13:55 jonalv <maclean> yø
13:55 jonalv <jonalv> o/                                                                     [15:29]
13:55 jonalv <maclean> I backlogged, jonalv, and saw complaints about my code! I was shocked,
13:55 jonalv shocked! And at the same time not surprised at all :)                 [15:30]
13:55 jonalv <maclean> The monitors subticks are not being done properly, eh?
13:55 jonalv <jonalv> maclean: so it's your code? I wasn't really sure...
13:55 jonalv <jonalv> maclean: you got a bug ticket about it anyway..                        [15:31]
13:55 jonalv <maclean> well, it's hard to say by now. egon, me, shk, ...
13:55 jonalv <maclean> I think it was messed up by me when trying to shoehorn visual feedback into
13:55 jonalv monitors.
13:55 jonalv <maclean> I'll take a look, anyway.                                             [15:32]
13:56 jonalv <masak> maclean: just held a talk about Perl 6:
13:56 jonalv http://masak.org/carl/stockholm.pm/perl6.pdf                            [15:35]
13:56 jonalv <zarah> masak's link is also http://tinyurl.com/lx5jmh
13:56 zarah jonalv's link is also http://tinyurl.com/lx5jmh
13:56 jonalv * maclean takes a gander
13:56 jonalv <masak> "it's Moose, not Goose!"                                                [15:36]
13:56 jonalv <maclean> :)
13:56 * olass is back from Systembolaget
13:56 jonalv <maclean> http://en.wiktionary.org/wiki/gander                                  [15:37]
13:56 zarah jonalv's link is also http://tinyurl.com/m4wsty
13:56 jonalv <zarah> maclean's link is also http://tinyurl.com/m4wsty
13:56 jonalv <jonalv> TotoiseSVN--
13:56 jonalv <jonalv> SVN--                                                                  [15:38]
13:56 jonalv <jonalv> svn--
13:56 jonalv <jonalv> windows--
13:56 jonalv * jonalv afk //tortosisesvn is working...
13:56 jonalv <maclean> does 'a' xx 3 enforce list context?                                   [15:39]
13:56 jonalv <masak> maclean: yes.                                                           [15:40]
13:56 jonalv <maclean> I made the mistake of doing "[[0]] * n" the other day in python, and got a
13:56 jonalv list of n references to the same list. I felt foolish.                [15:41]
13:56 jonalv <maclean> ooh eqv looks good.                                                   [15:42]
13:56 jonalv <maclean> hmm, actually, no it doesn't, it loos inconvenient, but probably more
13:56 jonalv correct. anyway, I'll stop thinking aloud now...                      [15:43]
13:57 olass joined #bioclipse
13:57 jonalv <egonw> masak: please tell maclean about that git PDF book thingy
13:57 jonalv <masak> maclean: a couple of seconds ago, egonw said about that git PDF thingy  [15:44]
13:57 jonalv <maclean> there are git books in the sanger library
13:57 jonalv <egonw> sneumann: editor sort of working for me now
13:57 jonalv <maclean> :)
13:57 jonalv <egonw> simple tree with file content
13:57 jonalv <masak> egonw: http://www.newartisans.com/2008​/04/git-from-the-bottom-up.html
13:57 zarah jonalv's link is also http://tinyurl.com/cf6fjv
13:57 jonalv <zarah> masak's link is also http://tinyurl.com/cf6fjv
13:57 jonalv <maclean> masak: tack.
13:57 jonalv <masak> um, maclean: http://www.newartisans.com/2008​/04/git-from-the-bottom-up.html
13:57 zarah jonalv's link is also http://tinyurl.com/cf6fjv
13:57 jonalv <zarah> masak's link is also http://tinyurl.com/cf6fjv
13:57 jonalv <maclean> I had better gin up on git.                                           [15:45]
13:57 jonalv <CIA-40> bioclipse: egonw * r10872
13:57 jonalv /bioclipse2/trunk/features/net.bioc​lipse.massspec_feature/feature.xml: Added
13:57 jonalv missing plugin dependencies
13:57 jonalv <egonw> ok, busy now...                                                         [15:46]
13:57 jonalv <egonw> bbl
13:57 jonalv <sneumann_> bye
13:57 jonalv <egonw> sneumann: please test
13:57 jonalv <sneumann_> will do
13:58 jonalv *** shk3 (n=shk3@nat8018.ebi.ac.uk) has joined channel #bioclipse               [15:47]
13:58 jonalv <maclean> oh my yes : "@fib = 1,1 ... &[+]" -nice.                              [15:48]
13:58 jonalv <masak> aye.                                                                    [15:49]
13:58 jonalv ERC> I think I hate tortoisesvn
13:58 jonalv huh what's going on here?
13:58 olass my IRC is seriously messed up
13:58 jonalv masak: mhm
13:58 rojasm joined #bioclipse
13:58 jonalv zarah: huh?
13:58 zarah jonalv: please rephrase or stop trying to be witty :)
13:59 jonalv olass: you can say that again...
13:59 jonalv zarah fast as a snail...
14:01 masak jonalv: was that really necessary? :P
14:01 jonalv masak: :þ
14:02 * jonalv is still trying to get tortoisesvn to update Bioclipse checkout... :/
14:13 jonalv tortoisesvn--
14:13 olass jonalv: teh name implies it is slow
14:13 jonalv olass: yes...
14:13 olass use rabbitsvn
14:14 olass or cheetahsvn
14:14 jonalv @gg rabbitsvn
14:14 zarah jonalv: http://svn.haxx.se/dev/archive-2006-03/0458.shtml
14:14 olass lol
14:18 maclean joined #bioclipse
14:20 maclean is the irc regurgitation flood over?
14:20 maclean (seems like it...)
14:26 CIA-40 bioclipse: ospjuth * r10873 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Updated to really clear tests when clearAction is run.
14:33 CIA-40 bioclipse: goglepox * r10874 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/ChoiceGenerator.java: Made ChoiceGenerator work like a group generator
14:34 CIA-40 bioclipse: goglepox * r10875 /bioclipse2/trunk/ (3 files in 3 dirs):
14:34 CIA-40 bioclipse: New view to be able to view which generators are being used.
14:34 CIA-40 bioclipse: [jchempaint-primary] synced r14599
14:35 CIA-40 bioclipse: goglepox * r10876 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Changed getAdapter() so it only adapts to the active editor if it is of the right type
14:36 olass Gpox++ //fixes a lot of issues!
14:38 * egonw firing up the BBQ
14:38 egonw to celebrate the last day in this nice house :(
14:38 egonw bye (again)
14:38 olass bye egonw
14:58 jonalv @pz 766
14:58 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=766
15:04 jonalv Do anyone know what plugin contributes the "New molecule" wizard?
15:23 jonalv zarah: ask egonw row 1036 in plugins/net.bioclipse.cdk.jchempaint/plugin.xml. A new wizard with the name "Molecule (2)", what's the idea behind that name?
15:24 zarah Consider it noted.
15:29 jonalv @pz 1149
15:29 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1149
15:29 jonalv zarah: tell egonw http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1149
15:30 zarah jonalv's link is also http://tinyurl.com/l53rgc
15:30 zarah Consider it noted.
15:30 * jonalv is glad he is not living in Hammersmith
15:31 jonalv queue queue queue, always queue (or tube shut downs...)
15:31 jonalv bbc2++
15:34 olass jonalv: see bug 1128 for the New Molecule bug
15:35 jonalv @pz 1128
15:35 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1128
15:36 jonalv olass: I hate the fact that these thigns are not fixed yet...
15:36 olass jonalv: the combo is your bug, right?
15:36 jonalv olass: yes I got that one somehow...
15:37 olass do you have more urgent things than that?
15:37 jonalv olass: no, not any longer
15:37 jonalv olass: thanks for asking :)
15:37 olass lol
15:37 olass jonalv++ //closed a lot of urgent bugs recently
15:38 * olass has a few too :(
15:38 jonalv olass: I just don't quite feel up for starting to work on that a friday 20 mins to six...
15:38 olass really true
15:38 * olass expects RC1 on tuesday
15:38 olass that gives us monday to work on things for RC1
15:38 jonalv I want a combo box and I want a little field with a short descriptive text for each file format
15:39 jonalv (for the one selected in the combo box)
15:39 olass would be nice
15:39 olass actually, not only nice, but necessary
15:39 jonalv olass: yes
15:39 jonalv and the save as dialog in jchempaint should have that as well
15:43 egonw jonalv: ping
15:43 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
15:43 egonw @msg
15:43 zarah egonw: 19 m 56 s ago, jonalv said row 1036 in plugins/net.bioclipse.cdk.jchempaint/plugin.xml. A new wizard with the name "Molecule (2)", what's the idea behind that name?
15:43 zarah egonw: 13 m 55 s ago, jonalv said http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1149
15:44 egonw jonalv: 1149 is a dup
15:44 egonw see 1126
15:44 jonalv egonw: sort of...
15:44 jonalv @pz 1126
15:44 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1126
15:44 egonw no, not sort of... exact dup
15:44 jonalv egonw: oh
15:44 jonalv so the bug you gave me then?
15:44 jonalv these two sort of conflict...
15:45 egonw conflict?
15:45 jonalv egonw: but yes I agree, better to open the editor and then have the combo box when saving. That's the right way of doing things...
15:45 egonw well, that was what was designed before :)
15:46 jonalv egonw: I have a bug about adding a combo box to the wizard you have a bug about removing...
15:46 egonw I'm just implementing :)
15:46 egonw jonalv: dunno about that one
15:46 jonalv egonw: so I guess I might as well skip adding a combo box to it then since it\s sheduled for deletion...
15:46 egonw I just commented on 1149
15:46 egonw that has not been decided yet
15:47 egonw depends on whether Gpox gets the wizards to work with the JCPEditor
15:47 egonw ok, bye again
15:47 egonw back to BBQ
15:47 jonalv egonw: what has not been secided?
15:48 jonalv I think I am giving up for today
15:50 Gpox I believe there is a simple solution to 1127, 1128 but it might spawn another bug i haven't had time to look at it
15:51 olass Gpox: sounds promising
15:51 jonalv @pz 1127
15:51 jonalv @pz 1128
15:51 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1127
15:51 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1128
16:22 CIA-40 bioclipse: ospjuth * r10877 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Try to get TestsView to work in MolTable. Gives strange behavior with respect to structuredChanged events.
16:26 CIA-40 bioclipse: goglepox * r10878 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added periodic table view to chemoinformatics feature
16:26 CIA-40 bioclipse: goglepox * r10879 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java: Added method for retrieving resource form SDFileIndex
16:27 CIA-40 bioclipse: goglepox * r10880 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/src/net/bio​clipse/cdk/ui/sdfeditor/business/ (IMoleculeTableManager.java MoleculeTableManager.java): Added method for saving IMoleculesEditorModels
16:27 CIA-40 bioclipse: goglepox * r10881 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Implemented save and saveAs
16:44 CIA-40 bioclipse: ospjuth * r10882 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Store selection and re-set it after an automatic recalculation following complete rerun of tests.
17:08 CIA-40 bioclipse: goglepox * r10883 /bioclipse2/trunk/plugins/net.bioclipse.cdk.j​chempaint/src/net/bioclipse/cdk/jchempaint/ge​nerators/ClosestToCenterOfMassGenerator.java:
17:08 CIA-40 bioclipse: Added null check on atom in ClosesToCenterOfMassGenerator
17:08 CIA-40 bioclipse: Fixes NPE when opening a empty model
17:08 CIA-40 bioclipse: goglepox * r10884 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
17:08 CIA-40 bioclipse: Changed usage of widget.getMolecule() to getCDKMolecule()
17:08 CIA-40 bioclipse: This is so that the chemodel is synced with the
17:08 CIA-40 bioclipse: CDKMolecuel
17:09 CIA-40 bioclipse: goglepox * r10885 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (2 files in 2 dirs):
17:09 CIA-40 bioclipse: Changed wizard to use ui.open(BioObject,editorID)
17:09 CIA-40 bioclipse: Some clean up is left to do from old implementation
17:09 CIA-40 bioclipse: Fixes bugs #1127, #1128
17:09 olass Gpox++
17:09 olass !
17:24 * olass will quit for the weekend now
17:25 olass see you all on monday
17:25 olass bye
18:55 sneumann_ joined #bioclipse
21:10 egonw joined #bioclipse
21:20 egonw moin
21:20 zarah oh hai egonw
21:20 egonw just checking email
21:20 egonw and messages with zarah
21:21 egonw @msg
21:21 zarah egonw: You have no new messages.
21:21 egonw zarah: tack
21:21 zarah you're welcome, egonw :)
22:17 edrin joined #bioclipse

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