Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-04

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All times shown according to UTC.

Time Nick Message
02:55 LaserJock left #cdk
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07:26 egonw moin
07:27 carsten Hallop
07:27 carsten -p
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07:31 thomas_ku moin
07:32 egonw hi thomas_ku
07:33 olas joined #cdk
07:34 egonw hi olas
07:34 egonw olas: what biomoby library are you using?
07:34 egonw what crash course tutorial in particular?
07:34 olas jmoby
07:34 egonw I found a Super-Easy MOBY Service Creation page...
07:34 olas looked at the client examples in jmoby
07:34 egonw but that had broken links...
07:34 olas never done a service yet
07:35 egonw ack
07:35 olas how did the JCP hackathlon turn out?
07:35 * egonw was looking into that yesterday...
07:35 egonw and will continue this week
07:35 egonw quite good...
07:35 egonw read my blog
07:35 olas I sure will
07:35 egonw I don't have the SWT demo done yet
07:36 olas ack
07:36 egonw but I do have bits of code in bioclipse svn -> playgroun/
07:36 egonw progz plugin
07:36 egonw but that code does not propagate the widget dimensions yet
07:36 egonw not so experienced with that
07:37 egonw imput welcome... hint, hint
07:39 olas is it an editor you are constructing or a view?
07:39 egonw view at the moment
07:39 egonw but that will chance
07:40 egonw now that the hackathon worked out so well
07:40 olas excellent
07:40 olas we need both a view and an editor
07:40 egonw but much of the editing functionality still needs to be ported to the new architecture
07:41 olas and into SWT
07:41 olas right
07:56 jpansanel moin
07:57 jpansanel egonw : http://chem-file.sourceforge.net/data​/alcohols/2-methylpropan-1-ol_fr.html works fine with Operator
07:57 lambdabot2 Title: 2-Methylpropan-1-ol, http://tinyurl.com/yog6uy
08:30 egonw jpansanel: mmm.. it does not show up with my Operator addon...
08:38 CIA-31 cdk: thomaskuhn * r8851 /trunk/cdk-taverna/src/main/java/org/openscience​/cdk/applications/taverna/CDKTavernaConfig.java: A small change to the default bioclipse naming! Now it uses on linux systems Biolcipse instead of bioclipse
08:40 CIA-31 cdk: thomaskuhn * r8852 /trunk/cdk-taverna/src/main/java/org/o​penscience/cdk/applications/taverna/ba​sicutilities/FileNameGenerator.java: Add a new method which allows the setting of the file name and path separately as two strings
08:41 CIA-31 cdk: thomaskuhn * r8853 /trunk/cdk-taverna/src/main/java/org/​openscience/cdk/applications/taverna/​bioclipse/BioclipseResultViewer.java: Change to the different bioclipse naming
08:42 CIA-31 cdk: thomaskuhn * r8854 /trunk/cdk-taverna/src/main/java/org/openscienc​e/cdk/applications/taverna/io/FileReader.java: Change the filereader to allow the multipe selection of files within the file chooser dialog
08:42 CIA-31 cdk: thomaskuhn * r8855 /trunk/cdk-taverna/src/main/java/org​/openscience/cdk/applications/tavern​a/io/action/FileReaderAction.java: Change the filereader to allow the multiple selection of files within the file chooser dialog
08:43 CIA-31 cdk: thomaskuhn * r8856 /trunk/cdk-taverna/src/main/java/o​rg/openscience/cdk/applications/ta​verna/io/ReadSMILESFromFile.java: Add a file chooser dialog to this file reader
08:44 CIA-31 cdk: thomaskuhn * r8857 /trunk/cdk-taverna/src/main/java/org/o​penscience/cdk/applications/taverna/io​/action/ReadSMILESFromFileAction.java: Add a file chooser dialog to this file reader
08:46 CIA-31 cdk: thomaskuhn * r8858 /trunk/cdk-taverna/src/main/java/org/openscience/c​dk/applications/taverna/io/WriteToMDLMolFile.java: Solves a problem of writing mol files from molecules which have the cdkconstant.title set
08:46 CIA-31 cdk: thomaskuhn * r8859 /trunk/cdk-taverna/src/main​/resources/cdk.properties: Change some naming of different workers
08:47 CIA-31 cdk: thomaskuhn * r8860 /trunk/cdk-taverna/src/main/resources​/META-INF/services/org.embl.ebi.escie​nce.scuflui.spi.ProcessorActionSPI: Register the action of the read SMILES from file worker
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08:49 CIA-31 cdk: thomaskuhn * r8861 /trunk/cdk-taverna/src/test/java/org/openscience/​cdk/applications/taverna/io/FileReaderTest.java: Update the test for using the multipe selection of files within the dialog
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08:50 CIA-31 cdk: thomaskuhn * r8862 /trunk/cdk-taverna/src/test/java/or​g/openscience/cdk/applications/tave​rna/io/ReadSMILESFromFileTest.java: Add a test for ReadSMILESFromFile worker
08:51 CIA-31 cdk: thomaskuhn * r8863 /trunk/cdk-taverna/src/test/resources/data/smiles/ (. allStructures.smi): Add a test file for the ReadSMILEFromFile worker
08:53 CIA-31 cdk: thomaskuhn * r8864 /trunk/cdk-taverna/pom.xml: Update to Version 0.4.0.0 for the upcoming new release
08:56 CIA-31 cdk: thomaskuhn * r8865 /trunk/cdk-taverna/pom.xml: Add a cdk-taverna repository
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10:02 jpansanel egonw : could you see something wrong in source ?
10:03 egonw no, not directly...
10:03 egonw but have not explored in detail
10:03 jpansanel with firefox and Operator, I see Resources(1)
10:03 jpansanel and this give me access to search on chemspider, pubchem, ...
10:03 egonw ok, good
10:07 egonw no, can't reproduce...
10:07 egonw just reinstalled Operator 0.8
10:08 egonw where do you see Resources anyawy?
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11:10 rojasm Christoph can I call you?
11:10 rojasm sorry: hi steinbeck
11:11 steinbeck Hi rojasm
11:11 steinbeck Miguel - not at the moment, unfortunately. Are you in Cologne?
11:12 rojasm I was this weekend
11:12 rojasm but not today
11:12 rojasm I spoke with Pascal
11:12 steinbeck Ack
11:13 rojasm But with skype is all easy :)
11:13 rojasm wenn you have time I would like to speak with you
11:16 steinbeck Right - at the moment I'm on an ISDN line and doing an Ubuntu Update. No bandwidth left for Skype. But I'll try to call you when I'm done.
11:17 rojasm perfect
11:17 steinbeck I opened a private chat window
11:17 rojasm my privat irc doesn't work :(
11:17 rojasm miguel.rojas.ch
11:18 rojasm is my nick
11:18 steinbeck ack
11:18 rojasm not complicate
11:19 steinbeck I'll first send you a request for exachange of online-information. mom
11:21 steinbeck ok, seems to have worked.
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11:50 jpansanel egonw : I've tried on nmrshift, but it doesn't work correctly
11:51 jpansanel attribut used is class and not property
11:51 CIA-31 bioclipse: biocoder * r3741 /trunk/playground/plugins/net.bioclips​e.ghemical/net.bioclipse.chart.test/: Test plugin for testing the net.bioclipse.chart plugin API
11:52 egonw right... nmrshifdb is not using RDFa... but microformats
11:52 egonw where do you see Resources anyawy?
11:52 egonw I got 'RDFa' in my tool bar
11:53 egonw http://torrez.us/services/rdfa/?url=http%​3A%2F%2Fchem-file.sourceforge.net%2Fdata%​2Falcohols%2F2-methylpropan-1-ol_fr.html
11:53 lambdabot2 http://tinyurl.com/yohy5u
11:54 egonw namespace does not show up
11:54 egonw but you do declare the prefix...
11:55 egonw http://www.w3.org/2007/08/pyRdfa/extract?ur​i=http%3A%2F%2Fchem-file.sourceforge.net%2F​data%2Falcohols%2F2-methylpropan-1-ol_fr.ht​ml&format=pretty-xml&submit=go%21
11:55 lambdabot2 http://tinyurl.com/ysgb4z
11:55 egonw that one also nicely extracts the RDF :)
11:55 jpansanel <html xmlns="http://www.w3.org/1999/xhtml" xmlns:chem="http://www.blueobelisk.org/chemistryblogs/">
11:55 CIA-31 bioclipse: biocoder * r3742 /trunk/playground/plugins/​net.bioclipse.chart.test/: Test plugin for testing the net.bioclipse.chart plugin API
11:55 lambdabot2 Title: XHTML namespace
11:55 egonw jpansanel: right
11:55 egonw that looks fine to me
11:55 egonw and since it works for your Operator, I'm sure your code is fine...
11:55 egonw just annoyed that it does not work for me :(
11:56 jpansanel sure ...
11:56 jpansanel but with my code, the page is no more xhtml-strict valid
11:58 egonw http://rdfa.info/2007/08/0​7/w3c-htmlrdfa-validator/
11:58 lambdabot2 Title: RDFa � Blog Archive � W3C HTML+RDFa Validator
12:03 CIA-31 bioclipse: biocoder * r3743 /trunk/playground/plugins/net.biocli​pse.chart.test/net.bioclipse.empty/:
12:06 CIA-31 bioclipse: biocoder * r3744 /trunk/playground/plugins/net.biocli​pse.chart.test/net.bioclipse.empty/: Test plugin for testing the net.bioclipse.chart plugin API
12:12 jpansanel egonw : on w3c, I've only two errors :
12:12 jpansanel about and property are not valid attribute
12:12 CIA-31 bioclipse: biocoder * r3745 /trunk/playground/plugins/​net.bioclipse.chart.test/:
12:14 egonw jpansanel: ack
12:14 egonw got to go now... we'll talk later...
12:15 egonw when I got my operator addon properly working...
12:15 egonw jpansanel: blog about it...
12:21 jpansanel ok
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14:13 CIA-31 blueobelisk: pansanel * r101 /structures/trunk/ (TODO tools/cmlwriter.py tools/xhtmlwriter.py): Fix RDF
14:26 CIA-31 cdk: thomaskuhn * r8866 /trunk/cdk-taverna/src/main/java/org/openscienc​e/cdk/applications/taverna/io/FileReader.java: Remove two system.out
14:28 CIA-31 cdk: thomaskuhn * r8867 /trunk/cdk-taverna/src/main/java/org/openscience/​cdk/applications/taverna/io/ReadMDLRXNFile.java: Add a file chooser dialog for this file reader
14:28 CIA-31 cdk: thomaskuhn * r8868 /trunk/cdk-taverna/src/main/java/org/​openscience/cdk/applications/taverna/​io/action/ReadMDLRXNFileAction.java: Add a file chooser dialog for this file reader
14:29 CIA-31 cdk: thomaskuhn * r8869 /trunk/cdk-taverna/src/main/java/o​rg/openscience/cdk/applications/ta​verna/io/ReadSMILESFromFile.java: Change the xml tag name
14:30 CIA-31 cdk: thomaskuhn * r8870 /trunk/cdk-taverna/src/main/java/org/op​enscience/cdk/applications/taverna/reac​tionenumerator/ReactionEnumerator.java: Add a try catch block
14:31 CIA-31 cdk: thomaskuhn * r8871 /trunk/cdk-taverna/src/main/java/org/op​enscience/cdk/applications/taverna/rend​erers/CreatePDFWith2DStructures.java: Remove a bug which produces more than one pdf
14:32 CIA-31 cdk: thomaskuhn * r8872 /trunk/cdk-taverna/doc/tutorial-data/ (aspirin.mol ethanol.mol): Change the titles of these files
14:32 CIA-31 cdk: thomaskuhn * r8873 /trunk/cdk-taverna/src/main​/resources/cdk.properties: Add the missing SDG
14:33 CIA-31 cdk: thomaskuhn * r8874 /trunk/cdk-taverna/src/main/resources​/META-INF/services/org.embl.ebi.escie​nce.scuflui.spi.ProcessorActionSPI: Register the action for the read mdl rxn files worker
14:33 CIA-31 cdk: thomaskuhn * r8875 /trunk/cdk-taverna/src/main/resources/META-​INF/services/org.openscience.cdk.applicatio​ns.taverna.scuflworkers.cdk.CDKLocalWorker: Add the missing SDG
14:34 CIA-31 cdk: thomaskuhn * r8876 /trunk/cdk-taverna/src/test/java/o​rg/openscience/cdk/applications/ta​verna/io/ReadMDLRXNFileTest.java: Add a test for the ReadMDLRXNFile's worker
14:43 CIA-31 cdk: thomaskuhn * r8877 /trunk/cdk-taverna/doc/ (4 files):
14:58 rojasm egonw: question
14:59 rojasm do you know other data for spectrum as
14:59 rojasm mzXML, mzData or CML
15:02 CIA-31 cdk: thomaskuhn * r8878 /trunk/cdk-taverna/example/ (10 files): Add new example workflows and remove the old ones because they will not work anymore
15:03 rojasm and MZML
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15:56 rojasm egonw: I am implementing as well the java class to mass to formula
15:57 rojasm But I don't think the method which is used from Rzepa works very fine
15:58 rojasm it has not sense if the results are C2H11 for 35 m/z
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16:46 egonw the nice thing of working in Cambridge is that people listen when you have something to say:
16:47 egonw one of Peter's blog posts hit SlashDot :
16:47 egonw http://yro.slashdot.org/arti​cle.pl?sid=07/09/04/1341248
16:47 lambdabot2 Title: Slashdot | Scientist Must Pay to Read His Own Paper
16:47 egonw cool to read the comments :)
16:50 carsten Stick with the chemistry, doc! Understanding the law isn't for you.
16:56 egonw :)
16:56 egonw well, the missed the point...
16:56 egonw he payed for the article being freely available...
16:57 egonw free as in free beer
16:57 egonw anyway...
16:57 egonw good for the Blue Obelisk this is...
16:57 egonw bye now, cu later
17:08 CIA-31 cdk: thomaskuhn * r8879 /trunk/cdk-taverna/ (ChangeLog ReleaseNotes): Update the ReleaseNotes and the ChangeLog for the new release
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