Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-08-05

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All times shown according to UTC.

Time Nick Message
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05:21 CIA-120 bioclipse.opentox: Egon Willighagen master * rd397786 / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Made test values final static Strings - http://bit.ly/ogxho8
05:21 CIA-120 bioclipse.opentox: Egon Willighagen master * r54e47ce / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Three more methods tested - http://bit.ly/nQFjLe
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05:37 CIA-120 bioclipse.opentox: Egon Willighagen master * rc2a8574 / (2 files in 2 dirs): Added unit tests for calculating descriptors - http://bit.ly/nqpglH
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05:50 CIA-120 bioclipse.opentox: Egon Willighagen master * r928dba3 / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Test method for searching data sets - http://bit.ly/oq9AQD
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06:09 CIA-120 bioclipse.opentox: Egon Willighagen master * r82a251a / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Test methods for listAlgorithms() and listDescriptors() - http://bit.ly/oOZBoX
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07:18 CIA-120 bioclipse.opentox: Egon Willighagen master * r9451239 / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Added test methods for the two search methods - http://bit.ly/nrXDVU
07:18 egonw_ is now known as egonw
07:21 egonw Gpox: ping
07:21 egonw Gpox: the satelites running the jobs are also on Hudson, right?
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07:21 egonw Gpox: that is, 'master' is just pele, correct?
07:22 Gpox yes
07:26 CIA-120 bioclipse.opentox: Egon Willighagen master * r6ac4d71 / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Fixed server to use - http://bit.ly/o6Wqjz
07:38 CIA-120 bioclipse.opentox: Egon Willighagen master * r34611ae / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Fixed previous commit: 'fixed' the wrong test :( - http://bit.ly/pIVxhZ
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08:30 CIA-120 bioclipse.opentox: Egon Willighagen master * ra9411af / plugins/net.bioclipse.opentox/src/net/bioclipse​/opentox/api/MolecularDescriptorAlgorithm.java : Provide some feedback on what is going on - http://bit.ly/plU4kt
08:30 CIA-120 bioclipse.opentox: Egon Willighagen master * r27ab872 / (3 files in 2 dirs): Return the bool returned by OpenSSO - http://bit.ly/qXUUUf
08:30 olass egonw++ thanks for updates
08:41 CIA-120 bioclipse.opentox: Egon Willighagen master * r18e807a / plugins/net.bioclipse.opentox.test/​src/net/bioclipse/opentox/test/Abst​ractOpentoxManagerPluginTest.java : Fixed unit test: use the OT URI, not the BODO URI (bloody fucking idiot I am) - http://bit.ly/mS6F84
08:42 olass hehe
08:43 egonw the .js I had used a different call on the stringmatrix ... get(1,1)
08:43 egonw I replaced that by using get(1,"desc")
08:43 egonw so, based on column name, because sometimes the server decides to return them in a different order
08:43 egonw so 1,1 is not very stable
08:44 olass indeed
08:44 egonw expect that I picked the wrong column name :(
08:44 olass lol
08:44 egonw nina just mentions weirdness with the TUM services...
08:44 egonw might be related to your issues
08:45 olass I asee
08:45 olass well, let's not dig too depp at this time
08:45 egonw http://pele.farmbio.uu.se/jenki​ns/job/Bioclipse.test.opentox/
08:45 olass it demonstrates well that errors in services propagate
08:46 olass nice trend!
08:46 olass going down...
08:46 egonw remaining unit tests are not false positives...
08:46 egonw so, all is good regarding the BC/OT stuff now
08:46 olass ok, what is still failing?
08:46 olass testSearchModule?
08:46 olass what is that?
08:47 egonw read closely
08:47 olass read where?
08:47 olass sea36.util.config.Configuration)
08:47 egonw well, I suggest anything you read :)
08:47 egonw yes: InChI not loading
08:47 olass ok
08:48 egonw the other one is the BC testing framework buggy
08:48 egonw @pz false positive
08:48 zarah [3058] The core manager testing testP... http://tinyurl.com/44w6azb
08:48 zarah Entire list at http://tinyurl.com/3huryhm
08:48 egonw @pz inchi
08:48 zarah [3021] JNI-InChI in target platform n... http://tinyurl.com/42oxjco
08:48 zarah [3048] inchi still doesn't load properly http://tinyurl.com/4355ef7
08:48 zarah [3024] Check and potentially fix InCh... http://tinyurl.com/3eutao7
08:48 zarah Entire list at http://tinyurl.com/3hm2gfa
08:48 olass hmm, I see we get 2 errors for each error, JavaTest and JavascriptTest in the junit reports....
08:48 olass a bit annoying
08:48 egonw but important
08:48 egonw one tests the manager in a GUI environment
08:49 egonw the other in the JS evn
08:49 egonw env
08:49 olass can we not have two test suites?
08:49 egonw they are
08:49 olass well, maybe that's not good either..
08:49 egonw wrapped in a third one
08:49 olass ok
08:49 egonw but, one test may fail in one env and not in the other
08:50 egonw we had that in the past
08:50 egonw we've become better :)
08:50 egonw they either fail in both or in none now :)
08:54 olass it's just that four errors look much worse than 2... it is in >95% of the cases only 2 issues...
08:54 egonw :)
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08:55 egonw then again... 30 tests look much better than 15 :)
08:55 olass hehe
08:55 olass goes both ways
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10:56 zaetnick cande: ping
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11:51 * samuell can't find where my bioclipse plugin stores it's preference page values :(
11:51 samuell (have checked the relevant bioclipse workspace folder/.metadata/.plugins ... but no folder fo my plugin there :/
11:59 egonw wouldn't that go into a general folder, using the central prefs system?
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12:09 samuell Hmm, didn't find it in my eclipse workspace either
12:13 samuell Not a too big issue though ... bigger problem is that I didn't succeed to specify default values for my preference page which uses fieldeditors ...
12:14 samuell I guess I'll find out sooner or later, though ...
12:15 CIA-120 bioclipse: Samuel Lampa master * r29c78e0 / (4 files in 4 dirs): Added button to update Galaxy ToolConfigs on damand, in JobInfoView (+10 more commits...) - http://bit.ly/ruwPxl
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13:38 samuell how do you guys set default preferences?
13:39 samuell (For a preference page using fieldeditors)
13:43 zaetnick Activator.getDefault().getPreferenceStore()
13:43 zaetnick .setDefault(net.bioclipse.r.business
13:43 zaetnick .Activator.PREF_R_HOME, R_HOME);
13:44 samuell zaetnick, Ok ... You do that on the preference page itself (which method?), or in the activator?
13:45 zaetnick it is in RBUsinessManager in this case
13:45 samuell Ok, right ...
13:45 zaetnick in the activator we've declared this: public final static String PREF_R_HOME = "PREF_R_HOME";
13:45 samuell Ok
13:45 samuell I tried to use the method I tried to use the method initializeDefaultPreferences(IPreferenceStore store) in the activator
13:46 samuell (as said in a tutorial for the normal pref pages) ... but it is never run in my case
13:46 samuell ... but I guess I should try something like your code above
13:46 samuell Thanks btw! :)
13:47 zaetnick well, I got help from Ola with this... not completely sure if it's relevant for your case but hope it helps
13:48 samuell Trying now ...
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13:50 samuell zarah, tell zaetnick: Yep, that did the trick! :)
13:50 zarah Consider it noted.
13:50 samuell zaetnick++
13:52 CIA-120 bioclipse: Samuel Lampa master * re975a27 / (2 files in 2 dirs): Properly set default prefernces - http://bit.ly/o8atyX
13:54 CIA-120 bioclipse: Samuel Lampa master * rb5b627f / plugins/net.bioclipse.hpc/src/net/bioclip​se/hpc/preferences/HPCPreferencePage.java : Remove semantically redundant code - http://bit.ly/o0CmiR
14:03 CIA-120 bioclipse.cheminformatics: Arvid Berg 2.5.x * radfe0bf / (2 files):
14:03 CIA-120 bioclipse.cheminformatics: Added extractSDFile method with IProgressMonitor
14:03 CIA-120 bioclipse.cheminformatics: Implemented progress to advance one tick per molcule that is scaned - http://bit.ly/nQpZLB
14:03 CIA-120 bioclipse.cheminformatics: Arvid Berg 2.5.x * r7e5a8d6 / plugins/net.bioclipse.cdk.ui.sdfeditor/src/ne​t/bioclipse/cdk/ui/wizards/ExtractWizard.java :
14:03 CIA-120 bioclipse.cheminformatics: Run extractFromSDFile in a job
14:03 CIA-120 bioclipse.cheminformatics: Solves bug 3039 - http://bit.ly/oRUJl2
14:03 zarah bug #3039 | http://tinyurl.com/3q7b99k
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14:33 Topic for #bioclipse is now #bioclipse An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse
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14:34 Topic for #bioclipse is now #bioclipse An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse
14:51 Juul left #bioclipse
14:52 CIA-120 bioclipse: Samuel Lampa master * rdb2434c / (3 files in 3 dirs): Moved setDefaultPreferences to HPCApplication - http://bit.ly/mPXGak
14:52 CIA-120 bioclipse: Samuel Lampa master * r64ab994 / (2 files in 2 dirs): Should 'add' the field as well, and set default value - http://bit.ly/ojcJYZ
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18:17 Topic for #bioclipse is now #bioclipse An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse

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