Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-26

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Time Nick Message
05:07 egonw joined #bioclipse
05:15 rojasm joined #bioclipse
05:18 egonw_ joined #bioclipse
05:21 rojasm moin
05:21 zarah hello rojasm, you fantastic person you
05:26 egonw_ hi rojasm
06:08 rojasm hi egonw_
06:09 rojasm I am almost finish with the reaction plugin and after I switch to medea plugin to bring it to end
06:09 egonw rojasm++
06:11 rojasm But  with reaction pathway I have still some incompatibilities with JCP. e.g. defining the coordinates.
06:14 egonw ah, you had bad weather this morning? :)
06:14 egonw ok
06:32 rojasm incredible scary.
06:33 Gpox joined #bioclipse
06:34 rojasm luckily today night I was so tired that I felt to sleep anyway.
06:45 rojasm doesn't someone how to get a specific Editor?
06:45 egonw yes
06:46 egonw let me check
06:46 rojasm oh thanks
06:46 egonw mmm... trying to remember where such code is used
06:48 rojasm there is the mehtod findEditor from getActiveWorkbenchWindow().getActivePage()
06:49 rojasm but then you need a IEditorInput and that you can only get when you have one editor already. I thinkg
06:50 egonw no, that's not needed
06:52 egonw OK, will send you a few patches
06:52 egonw which do a similar thing
06:52 egonw not in SVN yet
06:53 egonw not entirely finished yet
06:54 rojasm ok thanks egonw
06:54 egonw sent
06:55 rojasm received
06:55 rojasm thanks
07:43 jonalv joined #bioclipse
07:56 jonalv zarah: morning
07:56 zarah jonalv: I did not understand that
07:56 jonalv zarah: sry
07:56 zarah jonalv: eh... wha'?
08:16 shk3 joined #bioclipse
08:52 edrin joined #bioclipse
09:03 sneumann_ joined #bioclipse
10:22 CIA-40 bioclipse: shk3 * r10729 /bioclipse2/trunk/plugins/net.b​ioclipse.data.seneca/data/hko2/ (. hko2.sjs mzdiv-813_c.cml mzdiv-813_c.jdx): another seneca example
10:33 egonw joined #bioclipse
10:38 sneumann_ joined #bioclipse
10:39 Gpox joined #bioclipse
10:45 maclean joined #bioclipse
11:10 masak joined #bioclipse
11:19 CIA-40 bioclipse: shk3 * r10730 /bioclipse2/trunk/features/net.bi​oclipse.seneca_feature/.project: wrong name in .project
11:20 jonalv @ps runAllTestAs
11:21 jonalv @pz runAllTestAs
11:21 zarah [1109] Verify manager calls with Bioc... http://tinyurl.com/os2w86
11:21 zarah Entire list at http://tinyurl.com/olmec7
11:21 jonalv @pz error when running tests
11:21 zarah jonalv: Zarro boogs found.
11:25 CIA-40 bioclipse: carl_masak * r10731 /bot/trunk/zarah.pl: [zarah.pl] now asks 'did you mean @pz?' on @ps
11:25 masak @reboot
11:25 jonalv @ps
11:25 zarah joined #bioclipse
11:25 jonalv @ps
11:25 zarah jonalv: Did you mean '@pz' or '@pelezilla'?
11:25 jonalv zarah: knows what I mean but mocks me!
11:25 zarah jonalv: eh... wha'?
11:26 jonalv |zarah knows what I mean and mocks me
11:26 jonalv :(
11:26 masak zarah++
11:33 shk3 hi jonlav
11:34 shk3 when I try using the update site, I get lots of errors.
11:34 shk3 did you have a look at the update site?
11:34 jonalv shk3: me too but olass marked my bug report as invalid so you will have to ask him...
11:35 shk3 is he around?
11:35 jonalv @ps update site
11:35 zarah jonalv: Did you mean '@pz' or '@pelezilla'?
11:35 jonalv gah
11:35 jonalv @pz update site
11:35 zarah [71] Bioclipse2 lacks a QualityAssura... http://tinyurl.com/6gmsm5
11:35 zarah [4] Not able to save molecule to othe... http://tinyurl.com/rxh8d3
11:35 zarah [142] experimental updatesite lacks d... http://tinyurl.com/qtwhsw
11:35 zarah [818] Test Cytoscape3 in Bioclipse2      http://tinyurl.com/cozuxl
11:35 zarah [1018] Parsing the ChEBI SDF file mis... http://tinyurl.com/phtfxe
11:35 zarah Entire list (9) at http://tinyurl.com/oh9mj9
11:36 CIA-40 bioclipse: ospjuth * r10732 /bioclipse2/trunk/plugins/net.bioclipse.ds.test​s/src/net/bioclipse/ds/tests/TestDBLookup.java: Updated unit test to call manager methods with uijobs one by one.
11:37 shk3 another question: I want to save a number of molecules to an sdfile and then open them.
11:38 shk3 if I do cdkmanager.saveSDFile
11:38 shk3 and then
11:38 shk3 uimanager.open
11:38 shk3 the file does not open correctly.
11:38 shk3 is it possible this is becuase of job stuff?
11:38 shk3 ie the saveSDFile being executed in background and the open
11:38 shk3 being called before the file is actually created?
11:46 CIA-40 bioclipse: ospjuth * r10733 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Added check that throws exception if signatures creation failed.
11:46 olass joined #bioclipse
11:46 olass hi
11:46 zarah oh hai olass
11:47 olass jonalv: could you update and run the test again?
11:50 jonalv olass DSExcpetion SignSicRunner.java row 443
12:01 olass yes, that is what should happen
12:01 olass hmm
12:01 olass maybe should catch that in test
12:02 jonalv olass: or declare that the test should throw that excpetion
12:07 * jonalv feels like he has had his brains smashed out by a slice of lemon, wrapped 'round a large gold brick. How would a test that tests that a manager method is actually run as a job look?
12:07 olass join the job at some point?
12:08 jonalv olass: I don't get a reference to the job
12:09 olass then it is not so easy I guess
12:09 jonalv mhm
12:09 jonalv thanks for the moral boost... :)
12:10 maclean morale
12:13 shk3 hi olass
12:13 olass hi shk3
12:13 olass hi all others too
12:13 shk3 can anybody comment on my problem with sdfile creation?
12:13 olass what bug?
12:14 masak maclean: a 'moral boost' is whay you get when all your sins are forgiven. :)
12:14 masak s/whay/what/
12:15 shk3 [12:37] <shk3> another question: I want to save a number of molecules to an sdfile and then open them.
12:15 shk3 [12:38] <shk3> if I do cdkmanager.saveSDFile
12:15 shk3 [12:38] <shk3> and then
12:15 shk3 [12:38] <shk3> uimanager.open
12:15 shk3 [12:38] <shk3> the file does not open correctly.
12:15 shk3 [12:38] <shk3> is it possible this is becuase of job stuff?
12:15 shk3 [12:38] <shk3> ie the saveSDFile being executed in background and the open
12:15 shk3 [12:38] <shk3> being called before the file is actually created?
12:15 shk3 not sure if it's a bug
12:15 shk3 it might be me doing something wrong.
12:19 jonalv shk3: I am not sure. Could you explore further? Your theori sure is plausible though. MAybe we shuldn't run save as a job?
12:20 shk3 hm
12:20 shk3 is my understanding correct that this saveSDFile call ends up in the methos with IProgressMonitor?
12:20 shk3 in nwo
12:21 jonalv shk3: I think so
12:21 shk3 ok
12:21 jonalv shk3: is there another method it could be calling?
12:21 shk3 I will try some debugging to veryfy this
12:22 shk3 only one saveSDFile in the manager
12:22 jonalv if it fins a method with identival method signature it will run it otherwise and if not it will start translations and adding progressmonitors and such stuff
12:25 shk3 ok
12:26 shk3 so if we want to have a choice, we need both methods and use the right one?
12:26 shk3 because in my use case, it should be blocking
12:26 olass shk3: please file this as a bug
12:27 maclean joined #bioclipse
12:28 shk3 ok
12:28 shk3 olass: another question
12:29 shk3 software update in beta5 seems to be totally broken now.
12:29 shk3 Are you aware of this?
12:40 olass no
12:41 olass we have nothing on update site
12:46 shk3 but I do
12:46 olass no
12:46 olass you have another update site
12:46 shk3 I think we want to encourage people to write for bioclipse
12:46 olass ?
12:46 shk3 so we need to make sure this works
12:46 shk3 right
12:46 shk3 but it's not my site which is broken
12:47 shk3 (at least I believe it's not)
12:47 shk3 I get npes when I just call the function in beta5
12:48 olass shk3: file a bug for me
12:48 shk3 ok
13:00 CIA-40 bioclipse: goglepox * r10734 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java: Added methods for setting and getting properties for molecules in SDFIndex
13:12 CIA-40 bioclipse: egonw * r10735 /bioclipse2/trunk/plugins/net.bioclipse.rdf/sr​c/net/bioclipse/rdf/business/RDFManager.java: Fixed a NullPointerException: SPARQLs without filter and OPTIONAL clauses can lead to null nodes
13:18 CIA-40 bioclipse: ospjuth * r10736 /bioclipse2/trunk/plugins/net.bioclipse.ds/sr​c/net/bioclipse/ds/business/IDSManager.java: Declared exceptions on IDSManager interface.
13:19 CIA-40 bioclipse: ospjuth * r10737 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (model/TestRun.java ui/views/TestsView.java): Added fields for success/failure and error message for TestRuns and populated them upon test completion.
13:19 CIA-40 bioclipse: ospjuth * r10738 /bioclipse2/trunk/plugins/net.bioclipse.ds.test​s/src/net/bioclipse/ds/tests/TestDBLookup.java: Catch DSExceptions to not make test fail when an individual test fails to run.
13:21 CIA-40 bioclipse: ospjuth * r10739 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): A missing ID update from 19 to 20 for release beta5 on NWO.
13:22 CIA-40 bioclipse: ospjuth * r10740 /bioclipse2/trunk/plugins/net.bioc​lipse.inchi/META-INF/MANIFEST.MF: A missing ID update from 19 to 20 for release beta5 on NWO.
13:24 CIA-40 bioclipse: ospjuth * r10741 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Set ID to 20090526 for testing update site with experimental feature.
13:24 CIA-40 bioclipse: ospjuth * r10742 /bioclipse2/trunk/features/net.biocli​pse.experimental_feature/feature.xml: Set ID to 20090526 for testing update site with experimental feature.
13:27 CIA-40 bioclipse: ospjuth * r10743 /bioclipse2/trunk/features/net.biocli​pse.experimental_feature/feature.xml: Removed dep to core patch.
13:35 olass shk3: I fixed the update site problem, please confirm and close bug 1112.
13:36 shk3 thanks
13:36 olass shk3: thanks for the bug report
13:36 olass did not understand how severe this was
13:37 shk3 do I need to get a new download?
13:38 CIA-40 bioclipse: ospjuth * r10744 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Removed redundant requires directive.
13:39 shk3 no longer errors, but still requesting that core.patch for me
13:39 olass shk3: you need to remove that from speclipse feature dependencies
13:40 olass jonalv: could you update and run TestDBLookup again? I hope I have fixed the exception now so you can run it...
13:41 shk3 I don't just get it with speclipse
13:41 CIA-40 bioclipse: jonalv * r10745 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Wrote test for problem described in bug: #1109
13:41 zarah bug #1109 | http://tinyurl.com/os2w86
13:42 shk3 sorry, can't find a depency to that in speclipse
13:42 shk3 chemoinformatics and baloon seem to have the dependeny
13:43 shk3 or do I need to donwload a new beta5?
13:43 jonalv olass: oki
13:43 olass shk3: yes
13:44 olass shk3: this info was in the release announcement
13:44 shk3 ok
13:44 shk3 sorry
13:44 olass shk3: since the NWO is a larage change
13:44 olass large
13:44 jonalv olass: which commit would that be that should have fixed things?
13:44 shk3 mom
13:44 olass hmm
13:44 shk3 I have a beta5 from friday
13:44 shk3 I realized this is needed
13:45 olass jonalv: 10738
13:45 shk3 did you update today, to fix the dependency?
13:45 olass shk3: I set up the update site today
13:45 shk3 ok
13:45 olass fixed dep on friday
13:45 shk3 thanks
13:45 olass so no core patch dep now
13:45 olass (I hope)
13:45 shk3 then I do a download
13:46 olass jonalv: still no luck?
13:46 jonalv olass: I get a DSException on row 443 of SignSicRunner
13:50 shk3 olass: works fine now
13:52 CIA-40 bioclipse: carl_masak * r10746 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java:
13:52 CIA-40 bioclipse: [JsThread] 'cancel' action now resets 'jsRunning' boolean
13:52 CIA-40 bioclipse: This makes the js console not hang on the next request. However, the canceled
13:52 CIA-40 bioclipse: script is not stopped, only abandoned. The next action still has to wait for
13:52 CIA-40 bioclipse: the previous action to finish, even though it was canceled.
13:53 CIA-40 bioclipse: shk3 * r10747 /bioclipse2/trunk/plugins/net.bio​clipse.spectrum/build.properties: css stuff for cheat sheet contribution to welcome was not included in build
14:08 sneumann_ Hi, just for the records: a fresh checkout of BC2 is working for me here. Took a while, I probably had leftovers from before NWO around.
14:09 masak sneumann_++
14:17 CIA-40 bioclipse: jonalv * r10748 /bioclipse2/trunk/plugins/net.bioclip​se.core.tests/src/net/bioclipse/manag​ers/tests/JavaManagerMethodTest.java: code cleanup
14:20 sneumann_ egonw: not getting rdf to work.
14:20 sneumann_ DEBUG - org.mozilla.javascript.EcmaError: ReferenceError: "rdf" is not defined. (unnamed script#1)
14:20 sneumann_ How to get the plugin / feature ? I have them in workspace, and tried to
14:20 egonw using the rdf.product?
14:20 sneumann_ ... 2) run the rdf.product
14:20 egonw which is in net.bioclipse.rdf_feature
14:20 sneumann_ in the rdf_feature
14:21 egonw :)
14:21 egonw ok...
14:21 egonw what errors in the Eclipse console
14:23 rojasm joined #bioclipse
14:23 sneumann_ None.
14:24 egonw please use a pastebin for the full output
14:24 sneumann_ Hm. Features dont complain if the plugins are not there ?
14:25 maclean that's right.
14:25 egonw but bioclipse typically does upon boot
15:41 CIA-40 bioclipse: ospjuth * r10749 /bioclipse2/trunk/plugins/net.bi​oclipse.core/src/net/bioclipse/ (4 files in 2 dirs): Updated BioclipseJob to also feature a completeResult method since might not always want to return partial results in a list.
16:00 CIA-40 bioclipse: ospjuth * r10750 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (8 files in 3 dirs): Rewrote running of tests to not throw exceptions on failure but return an ErrorResult object.
16:01 CIA-40 bioclipse: ospjuth * r10751 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java DBNearestNeighborTest.java): Adapted runWarningTest(...) to return ErrorResult and not throw exceptions on failure.
16:02 CIA-40 bioclipse: ospjuth * r10752 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Adapted runWarningTest(...) to return ErrorResult and not throw exceptions on failure.
16:02 CIA-40 bioclipse: ospjuth * r10753 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Adapted runTest() to return ErrorResult and not throw exceptions.
16:03 CIA-40 bioclipse: ospjuth * r10754 /bioclipse2/trunk/plugins/net.bioclipse.ds.test​s/src/net/bioclipse/ds/tests/TestDBLookup.java: Updated test for no exceptions but ErrorResult on running DSTests.
16:15 CIA-40 bioclipse: ospjuth * r10755 /bioclipse2/trunk/plugins/net.bioclipse.ds/sr​c/net/bioclipse/ds/business/IDSManager.java: Made methods identical to take advantage of NWO.
16:20 CIA-40 bioclipse: ospjuth * r10756 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/src/net/bioclipse/managers/tests/​AbstractManagerMethodDispatcherTest.java: Updated to support completeResults in partialReturner.
16:37 CIA-40 bioclipse: ospjuth * r10757 /bioclipse2/trunk/plugins/net.bioclipse.ds.test​s/src/net/bioclipse/ds/tests/TestSignSIc.java: Wrote test for running SignSic as UIJob. runInUI() never reached, filed as bug 1117.
16:37 zarah bug #1117 | http://tinyurl.com/pvdzdw
16:47 CIA-40 bioclipse: ospjuth * r10758 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/jobs/BioclipseJob.java: Added catch if returnValue != null when doing partial return. To be verified in bug 1113 by jonalv.
16:47 zarah bug #1113 | http://tinyurl.com/oz6acu
16:53 CIA-40 bioclipse: miguelrojasch * r10759 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (7 files in 3 dirs): Synchronization the new structure created with the box.
17:14 edrin left #bioclipse
17:20 sneumann_ joined #bioclipse
17:31 rojasm can I with JCP-Bioclipse introduce other element like Mg?
17:32 rojasm with right mouse I can only add the typical elements CNOFClS blabla
17:34 maclean Hmmm. There's a periodic table in swing-jcp.
17:34 rojasm ups I don't find. do I need some specific plugin?
17:34 maclean I'm looking for it
17:35 maclean I was sure that I saw something about it in the commit history...
17:37 maclean hmmm. no, can't find anything. ask arvid, I suppose.
17:37 rojasm thanks anyway. Don't worry
17:37 rojasm not very important now
17:45 egonw it's a View
17:45 egonw mom, I'll try to find it
17:47 maclean cdk.ui.periodictable?
17:47 egonw guess so
17:47 egonw but I don't see it in my list of views
17:47 egonw mmm
17:47 maclean I didn't have it checked out, so I wasn't surprised not to see it.
17:48 egonw it is listed in the plugin.xml
17:48 egonw ah...
17:48 maclean hmmm.
17:48 egonw but it is a new plugin
17:48 egonw ok, it's not in the cheminfo feature
17:52 egonw and it does not seem operational yet
17:52 egonw I think he scheduled it for 2.0 though
17:52 egonw as Arvid for details...

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