Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-23

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All times shown according to UTC.

Time Nick Message
06:46 egonw_ joined #bioclipse
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07:11 viklund joined #bioclipse
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08:32 CIA-14 bioclipse: ospjuth * r4764 /branches/bioclipse2/bioinformatics/plugins/​net.bioclipse.biojava.business/src/net/biocl​ipse/biojava/business/BiojavaManager.java: Implemented DNAtoProtein and ProteinToDNA
08:44 jonalv joined #bioclipse
08:44 jonalv hi all
08:46 olas hi jonalv
09:05 * viklund is away: coffee
09:18 olas edrin: have you seen http://www.omg.org/technolog​y/documents/formal/lsae.htm
09:27 jonalv <http://wiki.bioclipse.net/index.php​?title=Building_a_recordable_plugin>
09:37 * viklund is back (gone 00:31:55)
09:37 masak joined #bioclipse
09:38 Annzi left #bioclipse
09:48 CIA-14 bioclipse: jonalv * r4765 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java: Simple reference generation test
10:11 * viklund is away: hämta plånbok
10:35 CIA-14 bioclipse: ospjuth * r4766 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.business​/src/net/bioclipse/biojava/business/ (BiojavaHelper.java BiojavaManager.java IBiojavaManager.java): Updated translation functionality. All except RNA I/O now works.
10:35 CIA-14 bioclipse: ospjuth * r4767 /branches/bioclipse2/bioinformatics/plug​ins/net.bioclipse.biojava.business.tests​/tests/net/bioclipse/biojava/business/ (BiojavaHelperTest.java BiojavaManagerTest.java): All tests now passes except those who require RNA input.
10:36 masak olas++
10:36 CIA-14 bioclipse: ospjuth * r4768 /branches/bioclipse2/bioinformatics/​plugins/net.bioclipse.biojava.ui/src​/net/bioclipse/biojava/ui/actions/ (5 files): Wrote translation actions for manager except for those who require RNA input.
10:45 Annzi joined #bioclipse
10:49 EskilA joined #bioclipse
11:12 egonw_ lunch time
11:33 edrin olas: no, i did not know this, what is this?
11:35 steinbeck joined #bioclipse
11:35 edrin hello steinbeck
11:35 steinbeck Cheers
11:53 * viklund is back (gone 01:41:50)
11:57 edrin olas: you there?
11:59 olas edrin: yes
12:00 edrin olas: the link you posted, what is it?
12:02 olas I donät know
12:02 olas just stumbled upon it
12:02 edrin ah
12:02 olas and thought you'd be interested in it
12:03 olas as it seems somewhat related to your XEP
12:03 edrin well, is it SOAP? i don't see the difference?
12:03 olas I have not read it
12:03 edrin hm
12:03 edrin ok
12:03 olas ignore it if it's irrelevant
12:04 edrin i think they define a way how to handle an asynchronous job via SOAP
12:49 CIA-14 bioclipse: jonalv * r4769 /branches/bioclipse2/ (8 files in 6 dirs): Created Bioclipse Exception and used it in the biojava manager
13:19 CIA-14 bioclipse: jonalv * r4770 /branches/bioclipse2/core/plugins/net.biocl​ipse.recording/src/net/bioclipse/recording/ (JSScriptGenerator.java Record.java): Simple reference support for script generation
13:41 CIA-14 bioclipse: jonalv * r4771 /branches/bioclipse2/core/plugins/​net.bioclipse.ui/src/net/bioclipse​/ui/views/ActionHistoryView.java: added newline between statements when opening editor with generated script
13:50 * viklund is away: journal club
13:53 jonalv <http://www.phdcomics.com/co​mics/archive/phd011408s.gif>
14:16 CIA-14 bioclipse: carl_masak * r4772 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
14:16 CIA-14 bioclipse: [ScriptGenerationTests.java]
14:16 CIA-14 bioclipse: * new test about escaping of \n, \t etc
14:25 CIA-14 bioclipse: carl_masak * r4773 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
14:25 CIA-14 bioclipse: [ScriptGenerationTests.java]
14:25 CIA-14 bioclipse: * corrected test a bit
14:26 CIA-14 bioclipse: carl_masak * r4774 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
14:26 CIA-14 bioclipse: [Record.java]
14:26 CIA-14 bioclipse: * satisfied escaping test
14:38 CIA-14 bioclipse: carl_masak * r4775 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
14:38 CIA-14 bioclipse: [ScriptGenerationTests.java]
14:38 CIA-14 bioclipse: * test now wants a lower-case first letter on made-up identifiers
14:38 CIA-14 bioclipse: * one test fails
14:42 CIA-14 bioclipse: carl_masak * r4776 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
14:42 CIA-14 bioclipse: [Record.java]
14:42 CIA-14 bioclipse: * satisfied test from r4775
14:42 CIA-14 bioclipse: * all tests now pass
14:52 * viklund is back (gone 00:58:50)
14:56 masak joined #bioclipse
15:21 CIA-14 bioclipse: carl_masak * r4777 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
15:21 CIA-14 bioclipse: [Record.java]
15:21 CIA-14 bioclipse: * Removed extraneous space in stringification
15:22 CIA-14 bioclipse: carl_masak * r4778 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
15:22 CIA-14 bioclipse: [Records.java]
15:22 CIA-14 bioclipse: * removed extraneous quotes in stringification
15:26 CIA-14 bioclipse: ospjuth * r4779 /branches/bioclipse2/bioinformatics/plugins/net​.bioclipse.biojava.business/src/net/bioclipse/b​iojava/domain/BiojavaSequenceCollection.java: Caught an NPE.
15:31 CIA-14 bioclipse: carl_masak * r4780 /branches/bioclipse2/core/plugins/net.bioclipse.l​ogging/src/net/bioclipse/logging/Activator.java:
15:31 CIA-14 bioclipse: [Activator.java]
15:31 CIA-14 bioclipse: * changed one ArrayList -> List (program against interfaces)
15:31 CIA-14 bioclipse: * rewrote while/iterator loop into foreach loop
15:31 CIA-14 bioclipse: * removed unused imports
15:31 CIA-14 bioclipse: carl_masak * r4781 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
15:31 CIA-14 bioclipse: [Record.java]
15:31 CIA-14 bioclipse: * removed unused import
15:32 egonw_ masak: good patches...
15:32 egonw_ maybe 'we' should set up Bioclipse Nightly...
15:33 CIA-14 bioclipse: carl_masak * r4782 /branches/bioclipse2/core/plugins/net.biocl​ipse.recording.tests/src/net/bioclipse/reco​rding/integrationTests/RecordingTest.java:
15:33 CIA-14 bioclipse: [RecordingTest.java]
15:33 CIA-14 bioclipse: * added generic types to raw types
15:33 egonw_ nightly trunk build, with PMD tests and other sorts of things we find useful
15:33 masak egonw_: there has been talk about that
15:34 masak I'm for it mainly because I think we need to win back our freedom from Eclipse
15:35 egonw_ olas pointed me to docs describing how to autobuild with Ant...
15:35 masak yes
15:35 egonw_ but just a selected set of PMD reports might be nice...
15:35 * masak doesn't understand
15:35 masak PMD?
15:35 egonw_ the tests are JUnit, right?
15:36 egonw_ so, those could be run too...
15:36 egonw_ ah...
15:36 egonw_ masak: check out:
15:36 egonw_ http://cheminfo.informatics.india​na.edu/~rguha/code/java/nightly/
15:36 egonw_ PMD is a tool to check code problems, possible bugs...
15:36 egonw_ also unused code
15:36 egonw_ and things that can be done better with Java5
15:36 masak cool!
15:36 egonw_ e.g. List instead of ArrayList
15:37 masak we want that!
15:37 egonw_ but CDK Nightly also runs the tests every night and reports on that
15:37 masak I'm all for letting machines teach us to code
15:38 egonw_ OK, I'll set something up to easily run the PMD tests...
15:38 masak woot
15:38 egonw_ but do not have the resources to set up a webpage for it
15:38 egonw_ time resources really
15:40 CIA-14 bioclipse: ospjuth * r4783 /branches/bioclipse2/bioinformatics/pl​ugins/net.bioclipse.biojava.ui.test/: Initial import.
15:40 CIA-14 bioclipse: ospjuth * r4784 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.ui.test/ (17 files in 9 dirs): Initial import.
15:41 jonalv olas: När man konverterar en fasta fil från DNA till R
15:41 jonalv noo
15:41 jonalv han drog
15:41 jonalv wrong language... sry
15:42 jonalv but still, he left...
15:42 CIA-14 bioclipse: carl_masak * r4785 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/src/net/bioclipse/ui/​editors/keyword/KeywordEditor.java:
15:42 CIA-14 bioclipse: [KeywordEditor.java]
15:42 CIA-14 bioclipse: * ArrayList -> List (code against interfaces)
15:42 CIA-14 bioclipse: * added generics
15:42 CIA-14 bioclipse: * removed debug comments
15:43 CIA-14 bioclipse: ospjuth * r4786 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (3 files in 3 dirs): Updated contentProvider to support unit tests.
15:49 CIA-14 bioclipse: carl_masak * r4787 /branches/bioclipse2/ (4 files in 4 dirs):
15:49 CIA-14 bioclipse: [build.properties in net.bioclipse.core,
15:49 CIA-14 bioclipse:  net.bioclipse.r,
15:49 CIA-14 bioclipse:  net.bioclipse.scripting,
15:49 CIA-14 bioclipse:  net.bioclipse.springBasedPrototypePlugin]
15:49 CIA-14 bioclipse: * included plugin.xml
16:19 egonw_ masak: still around?
16:19 egonw_ I'm about to commit PMD stuff to SVN...
16:20 egonw_ are you ready to give it a go?
16:20 egonw_ it only checks for unused code at this moment...
16:20 egonw_ which is in itself already quite useful
16:21 CIA-14 bioclipse: egonw * r4788 /branches/bioclipse2/ (9 files in 3 dirs): Added PMD QA set up
16:21 egonw_ (or someone else)
16:24 masak egonw_: I'm here
16:24 masak but a bit busy right now...
16:24 egonw_ in branches/bioclipse2
16:24 egonw_ check out pmd.xml and pmd/
16:24 masak ok
16:24 * egonw_ hopes masak has things on a local dir
16:24 egonw_ and imported into Eclipse
16:24 egonw_ instead of doing the checkout with eclipse
16:24 masak :)
16:25 masak maybe not...
16:25 masak but that's easily arranged
16:25 jonalv ah so that's how it's preferably done?
16:25 egonw_ depends
16:25 * jonalv should set it up like that sometime...
16:25 egonw_ for PMD you'll need to a checkout of the full bioclipse/branches/bioclipse2/ tree
16:25 masak just use command-line svn
16:25 masak egonw_: sounds worth a try
16:25 jonalv That means you can do command line svn
16:26 egonw_ :)
16:26 masak jonalv: it's not very hard
16:26 egonw_ jonalv: it's what those keyboards are for...
16:26 jonalv yes but you can't use the checked out tree directly in Eclipse
16:26 jonalv So I gave up...
16:27 egonw_ it's amazing that MS did not push the keyboard-less windows machine concept
16:27 egonw_ jonalv: no, you do have to import things...
16:27 masak there should indeed be a bridge between svn and subclipse...
16:27 egonw_ but that's quite easy...
16:27 egonw_ just point File->Import at the branches/bioclipse2/ dir
16:27 jonalv yes importing stuff is the way to go. I realise that now
16:27 masak oh
16:27 egonw_ and Eclipse will automatically detect all plugins
16:27 egonw_ by means of the .plugin files
16:27 egonw_ works lovely
16:28 egonw_ anyway... when you got there...
16:28 egonw_ run:
16:28 egonw_ ant -f pmd.xml
16:28 masak ok
16:28 masak I will
16:28 masak sooner or later, we will want to set this up on a server somewhere
16:29 egonw_ and you'll get a set of .xml and .html files in bioclipse2/reports
16:29 masak nice
16:44 masak egonw_: it worked!
16:45 masak cool
16:45 masak now we just need to set it up to run nightly on a server, too
16:58 egonw_ masak: and we need to decide which tests to run...
16:58 egonw_ there are plenty more
16:58 egonw_ see pmd.sf.net
16:58 egonw_ left hand menu
16:58 egonw_ gives a lot of rulesets
17:00 masak uh huh
17:01 masak feels like one would like to start with all turned on, and subsequently turn them of if we don't like them
17:02 masak wow, thery're matching using XML!
17:02 masak XPath, rather
17:02 masak that's very brave
17:05 egonw_ but works quite well...
17:05 egonw_ we can even make customized tests...
17:06 egonw_ e.g. for the CDK we are happy with longer variable names then the default test...
17:06 egonw_ ok, but got to go for dinner now
17:06 egonw_ mbbl
17:07 masak oki
17:45 CIA-14 bioclipse: jonalv * r4789 /branches/bioclipse2/ (8 files in 5 dirs):
17:45 CIA-14 bioclipse: Introduced BioObjectList that implements the Collection interface List.
17:45 CIA-14 bioclipse: Later on we should try to make it recordable as well. (no help from Spring this time though)
17:54 masak jonalv++
17:54 * jonalv is on deep water..
18:07 CIA-14 bioclipse: carl_masak * r4790 /branches/bioclipse2/bioinformatics/plugins​/net.bioclipse.biojava.business/src/net/bio​clipse/biojava/domain/BioObjectList.java:
18:07 CIA-14 bioclipse: [BioObjectList.java]
18:07 CIA-14 bioclipse: * removed @Overrides
18:18 CIA-14 bioclipse: jonalv * r4791 /branches/bioclipse2/ (7 files in 5 dirs): Moved the BioObjectList into net.bioclipse.recording. The best would be to have it in net.bioclipse.core but there is a circular reference problem. Maybe we should merge some plugins into one?
18:20 egonw joined #bioclipse
18:25 CIA-14 bioclipse: carl_masak * r4792 /branches/bioclipse2/core/plugins/net.​bioclipse.recording/src/net/bioclipse/​recording/domain/BioObjectList.java:
18:25 CIA-14 bioclipse: [BioObjectList.java]
18:25 CIA-14 bioclipse: * removed @Overrides
18:30 Annzi left #bioclipse
18:44 edrin left #bioclipse

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