Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-11

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All times shown according to UTC.

Time Nick Message
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08:14 edrin hi
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09:02 CIA-13 bioclipse: jonalv * r6143 /bioclipse2/trunk/plugins/ (7 files in 6 dirs):
09:02 CIA-13 bioclipse: Refactored the cdk manager to use IFile instead of InputStream and also added
09:02 CIA-13 bioclipse: some methods taking a "String-path" where such where lacking. This commit breaks
09:02 CIA-13 bioclipse: a few tests making them fail with the IleegalstateException "Workspace is
09:02 CIA-13 bioclipse: closed" when run as standard JUnit tests. It might be that some of them can be
09:02 CIA-13 bioclipse: run as plugin tests. I am currently thinking / planning for another solution to
09:02 CIA-13 bioclipse: this problem.
09:14 CIA-13 bioclipse: jonalv * r6144 /bioclipse2/trunk/plugins/ (5 files in 4 dirs):
09:14 CIA-13 bioclipse: made cdk.loadMolecule(String path) get an IFIle and call cdk.loadMolecule(IFile
09:14 CIA-13 bioclipse: file). Missed this in last commit. More tests will fail now if run as standard
09:14 CIA-13 bioclipse: JUnit tests. Some of them might pass as plugin tests but I am thinking on
09:14 CIA-13 bioclipse: another solution.
09:19 edrin no ola today?
09:29 jonalv edrin: it doesn\t seem so...
09:29 jonalv edrin: I don\t know ehere he is
09:30 shk3 hi jonalv
09:30 jonalv hi shk3
09:30 shk3 just trying to write a spectrum editor
09:30 shk3 this will combie the spectrum stuff from bc1
09:30 shk3 peaktable, charts, metadata editor etc.
09:31 shk3 does that sound reasonable?
09:31 jonalv aha
09:31 jonalv I guess
09:31 shk3 ok
09:31 jonalv I don't know much about spectrums...
09:31 shk3 olas said we should try to have things in an editor for one type of file
09:31 jonalv but they where different views in bc1?
09:31 shk3 which were in different views in bc1
09:31 shk3 yes
09:32 jonalv Yea I think it's better to have it in one editor
09:32 shk3 think so as well
09:32 shk3 just had a look at the jcp editor
09:32 shk3 rather complicated...
09:32 jonalv yea I guess
09:32 shk3 basically, I need the contributor and the editor and a number of editor pages, right?
09:32 jonalv the one in bioclipse...
09:33 shk3 yes, the bc2 one
09:33 jonalv Gpox had had a lot to say about that one. Not so much positive I think...
09:34 shk3 hm ok,
09:35 shk3 where is the file parsing done in the editor?
09:35 shk3 that should go in the editor, shouldn't it?
09:35 jonalv yea well at least IFile parsing :(
09:35 jonalv :)
09:35 * jonalv is still fighting with hte american jkeyboard... :/
09:38 shk3 isnt't the editorinput the thing the editor gets?
09:38 shk3 in the init method?
09:38 jonalv yea...
09:38 shk3 ah yes, and in createpages the parsing is done
09:38 shk3 ok, will try like this
09:39 jonalv I have heard the the jcp editor uses the constructor instead...
09:39 shk3 I imported a German keyboard
09:40 jonalv yea well swedish keyboards in mac requires three buttons for writing { and } so I am learning american instead :)
09:40 edrin uh
09:40 edrin do you know french keyborads?
09:40 jonalv nope
09:40 jonalv edrin: what about em?
09:41 shk3 positions of {}\@ are probably a bit better on the english ones
09:41 edrin the even put most norbal ABC letters just at different positions
09:41 shk3 that's an advantage indeed
09:41 jonalv yea they sure are :)
09:41 edrin normal
09:41 jonalv edrin: aouch...
09:41 shk3 well, the French, you know, are a bit ... different
09:41 jonalv might as well go dvorsak then :)
09:42 jonalv yea well they sure are... :)
09:42 edrin german keyboard is ok
09:42 shk3 pretty similar to the swedish one
09:42 shk3 I found
09:42 jonalv k
09:42 shk3 position of stuff like !/?;:
09:43 edrin although not three buttons for }
09:43 edrin and we need the
09:45 edrin there is no egon as well
09:48 jonalv nope
09:48 jonalv that reminds me though :)
09:49 jonalv They are at olas parents place
09:49 jonalv eating and having a nice time :)
09:49 jonalv egon is going home today
09:58 edrin oh egon is is Sweden?
09:58 jonalv yea
09:58 edrin ah
09:58 edrin you had a bicoclipse meeting there
09:59 jonalv yea I guess you can say that :)
09:59 jonalv There was some jcp work but I am not too involved in that
09:59 edrin discussing release plans of bc2?
10:00 jonalv All I got out of the days is that we are going to go for two versions of resource methods on managers
10:00 jonalv on taking an IFile and one taking a String
10:00 edrin ok
10:00 jonalv not really but I know olas want's a release soon
10:00 jonalv and who doesn't? :)
10:01 edrin release is always good
10:01 jonalv yea :)
10:01 jonalv I think we should have something that does something first though
10:01 edrin i think you are planing a chemoinformatic release first
10:03 jonalv yea that ws the plan
10:03 jonalv I think the jcp needs more work before a release of that though...
10:19 shk3 I get the impression quite a few bits which were in bc1 are still missing in bc2 but could be put in easily
10:19 shk3 like the 2d/3d coordinate generation
10:19 shk3 or did I miss them?
10:31 jonalv You are probably right
10:47 shk3 so we should just put in more functions if they are easy to do
10:47 shk3 and documentation is an important thing
10:47 shk3 I don't know what it is like in bc2 right now, but I suppose it can be improved
10:58 * shk3 is going strawberrypicking
11:32 jonalv sounds nice :)
12:38 CIA-13 bioclipse: jonalv * r6145 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb/src/net/bioclipse/structuredb/business​/ForConsoleDecoratedStructuredbManager.java: squeezed everything in on 80 cols
14:26 shk3 jonalv
14:26 shk3 having problems running my plugin
14:26 jonalv shk3: hm
14:26 shk3 org.apache.commons.logging classes are missing
14:26 shk3 any dependencies I need for this?
14:26 jonalv yup they sure are :)
14:26 jonalv what plugin need them?
14:27 shk3 well, I did a new plugin
14:27 shk3 for logging,
14:28 jonalv a new plujgin for logging? What was wrong with net.bioclipse.logging?
14:28 shk3 I imported org.apache.log4j
14:28 shk3 no, not for logging
14:28 shk3 for spectra
14:28 jonalv aha
14:28 shk3 do I need a dependency on net.bioclipse.logger?
14:28 jonalv no
14:28 jonalv I don't think sop
14:29 shk3 when running bc and using my plugin, i get a classdefnotfound
14:29 jonalv so your spectra things need commons.logging?
14:29 shk3 for org.apache.commons.logging
14:29 shk3 no
14:29 shk3 well, I didn not include it
14:30 shk3 the only class i am using is org.apache.log4j.Logger
14:30 shk3 is this correct for logging?
14:30 jonalv yea
14:30 jonalv is this commited?
14:30 jonalv can I test?
14:30 shk3 no, not commited
14:31 shk3 i hava a look again myself
14:31 shk3 and if i find nothing, i commit, ok?
14:31 jonalv yea
14:39 CIA-13 bioclipse: shk3 * r6146 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/: Initial import.
14:40 shk3 jonalv
14:40 shk3 here you are
14:40 shk3 try opening a jx file to see the problem
14:40 CIA-13 bioclipse: shk3 * r6147 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (46 files in 14 dirs): Initial import.
14:40 jonalv is there a jx file in the sample projet?
14:41 shk3 yes
14:41 shk3 in sample data
14:41 shk3 directory spectra
14:41 jonalv I will have a quick look. I need to get going soon
14:41 shk3 e. g. aug07.dx
14:41 shk3 thanks
14:41 shk3 sorry for bothering you
14:42 jonalv no problem
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14:45 jonalv just importing org.apache.commons.logging to the plugin seem to work
14:46 jonalv but I don't know where it comes from
14:46 jonalv maybe not so important right now?
14:46 shk3 yes, think so
14:46 shk3 will go on
14:46 shk3 thanks
14:46 jonalv should I commit that?
14:47 shk3 i will do with next commit
14:47 jonalv k
14:47 shk3 if that's ok
14:47 jonalv that works :)
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14:50 shk3 looks like opening the editor works...
14:50 shk3 now i just need to write the editor
14:56 jonalv hehe
15:01 jonalv okey, I am out of here. Next week I will be gone so see you in about 10 days :)
15:13 shk3 see you
15:18 shk3 jonalv: last question
15:18 shk3 ?
15:18 shk3 ok?
15:24 shk3 ok, solved it myself
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