Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-11

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
07:27 rojasm joined #bioclipse
08:03 Annzi joined #bioclipse
08:12 steinbeck joined #bioclipse
08:21 olas joined #bioclipse
08:41 egonw joined #bioclipse
09:13 jonalv joined #bioclipse
10:20 EskilA joined #bioclipse
10:36 olas steinbeck: I just proposed a place
10:36 olas feel free to add wherever you want
10:39 masak joined #bioclipse
10:45 EskilA_ joined #bioclipse
10:52 steinbeck_ joined #bioclipse
11:13 edrin joined #bioclipse
11:32 steinbeck left #bioclipse
12:42 thomas_ku joined #bioclipse
12:48 * jonalv summons olas
12:49 shk3 joined #bioclipse
12:51 edrin what's up with olas?
12:51 jonalv I think he is writing something...
12:51 edrin a paper?
12:52 jonalv an application for money...
12:52 edrin ah, I c...
12:54 masak hi shk3!
12:54 shk3 hi
12:54 shk3 we had a power failure in my company...
12:55 masak tough
12:55 masak are you running on battery now?
12:55 shk3 I am at home
12:56 masak ah
12:56 shk3 did we talk about the database/hibernate plugin?
12:56 masak gosh, I hope not
12:56 masak what about it?
12:57 shk3 the id stuff?
12:57 masak hm
12:57 shk3 did you rename it?
12:57 masak no...
12:57 shk3 or somebody else
12:57 masak maybe jonalv
12:57 shk3 ah ok
12:57 shk3 probably
12:57 jonalv yes guilty I am...
12:57 masak yoda? is that you?
12:57 shk3 I will change it's id to net.bioclipse.hibernate
12:57 shk3 ok?
12:57 jonalv great
12:57 shk3 and change references as well
12:57 jonalv So is it actually doing something or what?
12:57 shk3 to avoid clashes witht the new n.bc.database plugin
12:58 shk3 it is supposed to do something
12:58 shk3 you can save and search stuff in there
12:58 jonalv olas said that it was left behind...
12:58 shk3 but it's not quite intuitive
12:58 jonalv what is "stuff"?
12:58 shk3 hm, Tobias did it
12:58 shk3 molecule/spectra
12:58 jonalv okey
12:58 shk3 not sure about the status
12:58 shk3 but it worked
12:58 jonalv I am working on something similar...
12:59 jonalv :)
12:59 shk3 i just change the id and then we can fade it out
12:59 jonalv Or rather was before bioclipse 2 took all my attetntion not spent on Brunn...
12:59 shk3 what's brunn?
13:00 jonalv It's a laboratory information system for bioclipse that I ahve been working on for quite some thime now...
13:00 edrin do you know what Tobias is doing right now?
13:00 jonalv It's becoming open source and heading out on a sourceforge site at the moment
13:00 jonalv althugh sf had some bugs so it's currently a bit stalled...
13:01 shk3 tobias is with a company
13:01 shk3 doing lab journals
13:01 shk3 can't remember the name
13:01 jonalv No I am not sure but he has left the Bioclipse poject I am afrraid...
13:01 shk3 lab systems for bc sounds good
13:01 jonalv so it is for working with micro titer plates
13:02 jonalv and currenlty rather specialised for the lab here.
13:02 jonalv And terrible slow... It uses Hibernate
13:02 egonw spoke with tobias yesterday
13:02 egonw very short though
13:02 jonalv but almost no lazy loading.. :/
13:02 egonw he has not had any time...
13:02 egonw but still following the mailing list
13:03 jonalv It needs some heavy refactoring into lazy loading...
13:03 jonalv okey, cool so we might not have seen the last of him?
13:04 edrin ah
13:04 edrin and Miguel?
13:04 shk3 still working an his phd thesis
13:04 edrin ioh
13:04 shk3 or he might have cancelled that
13:04 shk3 he is in leiden
13:04 shk3 leyden
13:04 edrin ic
13:04 shk3 not sure
13:04 shk3 about spelling
13:06 shk3 coming back to database stuff:
13:06 shk3 our idea was to have that plugin
13:06 jonalv is there any documentation for how that Hibernate plugin works somewhere?
13:06 shk3 other plugins could provide hibernate mapping files for their resources
13:06 shk3 and there is one for each db system hsql etc.
13:07 jonalv yes there is a world outside Hibernate you know...
13:07 shk3 so you could save everything to the same db
13:07 shk3 something like this
13:07 egonw edrin: miguel is here (rojasm)... ask him instead of shk3 :)
13:07 shk3 I am just trying if it works
13:07 masak jonalv: do you think we need js tab completion inside `` quotes inside R mode?
13:07 jonalv I am actively switching from Hibernate into ibatis me..
13:07 jonalv masak: it would be cool
13:07 masak grrr
13:08 * masak mutters under his breath
13:08 masak I'll try
13:08 edrin ah ok
13:08 jonalv well I have no problem with a hibernate plugin doing such stuff as long as it stays there
13:09 jonalv For example the hsqldb.jar can not be in it though because I don't want to have the hibernate jars for my stuff...
13:09 jonalv There is also the problem of getting everything to work smothly toghether...
13:09 shk3 yes
13:10 shk3 i am happy with having something better
13:10 jonalv Is anyone working with Hibernate in Bioclipse now?
13:10 shk3 don't think so
13:10 shk3 as I said, the usability was poor
13:10 jonalv Except for me that is... :)
13:11 jonalv But brunn is not in the bioclipse repo even though it is for bioclipse...
13:11 jonalv olas and me have been thinking about a general view for searches
13:11 shk3 that was one component of our database ideas
13:11 jonalv That could be searches in databases and searches on other places...
13:12 shk3 we thought the databses could be nodes in the resource browser
13:12 shk3 and result sets as well
13:12 edrin http://xkcd.com/ really strange...
13:12 masak all of them?
13:12 masak or any special comic?
13:12 jonalv yes our talks have been somewhat on the same line but with search results in a separate view...
13:12 edrin as a result of this a few houres old cartoon there are already new search entries in google...
13:13 edrin just the current one
13:13 edrin "Died in a blogging accident"
13:13 masak :)
13:13 jonalv shk3: You have seen: <http://wiki.bioclipse.net/ind​ex.php?title=Database_plugin>?
13:14 shk3 hm, the hiberante plugin doesn't compile for me right now
13:14 jonalv and: <http://wiki.bioclipse.net/i​ndex.php?title=Structure_DB>
13:14 shk3 I will try to get its status evaluated
13:14 jonalv good initiative, I am actually curious... :)
13:14 shk3 the problem was having the dbs in the resource navigator
13:15 shk3 is that we would have them as resources
13:15 jonalv yes that will work better in bioclipse 2
13:15 shk3 this would mean they would need to be parsed etc.
13:15 shk3 might be a problem with many entries
13:15 shk3 as you might have them in a db
13:15 jonalv I don't think we should go there at all...
13:15 * egonw wonders is there is no existing database plugin for RCP... on project level that is
13:16 jonalv egonw, which functionality are you thinking about?
13:16 jonalv I don't think it is very general...
13:17 egonw db support
13:17 jonalv You want to interact with each database in a different manner
13:17 egonw right
13:17 jonalv please define what you mean when you say "db support"
13:17 egonw but there is SVN support on project level too..
13:17 egonw never mind
13:17 jonalv yes isn't it nice :)
13:18 jonalv shk3, are you interested in working with the database part of bioclipse?
13:19 * jonalv more or less got that part in his lap by ola...
13:19 CIA-20 bioclipse: carl_masak * r4661 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
13:19 CIA-20 bioclipse: [JsConsoleView.java]
13:19 CIA-20 bioclipse: * now js tab completion works in R mode, too
13:19 CIA-20 bioclipse: * however, there is no R variable/method tab completion
13:19 CIA-20 bioclipse:  this might be possible, but so far, all completion
13:19 CIA-20 bioclipse:  occurs on js names, even in R mode
13:25 shk3 ok, the hibernate plugin is trying to work when included in bc, but fails with an npe if adding a molecule to the db
13:25 CIA-20 bioclipse: carl_masak * r4662 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
13:25 CIA-20 bioclipse: [JsConsoleView.java]
13:25 CIA-20 bioclipse: * made a few variables static
13:25 shk3 I will have a look if I can fix it, else we should drop it
13:25 shk3 don't think there is a reason to spend much time on it
13:26 jonalv no I don't think so either
13:26 jonalv But do you have a diagram over it's object model?
13:26 jonalv how many tables are there?
13:26 jonalv what are they?
13:27 jonalv And are the ones I have defined toghether with olas at <http://wiki.bioclipse.net/i​ndex.php?title=Structure_DB> doing more or less the same thing?
13:28 jonalv That project is har all daos working
13:28 jonalv has all...
13:28 jonalv And is ready for adding of a Spring layer and then it needs some GUI of course... :)
13:29 shk3 sounds good
13:29 shk3 don't think there is documentation for Tobias' stuff
13:29 jonalv I am actually looking forward to continue that project
13:29 shk3 the tables are defined in the hibernate files (if I understood hibernate correctly)
13:29 shk3 I will look at the bug
13:30 shk3 Do we have a possibility to depricate plugins?
13:30 jonalv it is my second database project so it is feeling great :)
13:30 jonalv yes that's right
13:30 shk3 move them to an "attic" directory or so
13:30 shk3 similar to playground?
13:30 jonalv I could check out it and have a look at the Hibernate files but I am not sure it's worth it....
13:31 jonalv don't think so
13:31 jonalv How it it usually done? egonw?
13:31 shk3 let me have a look first if that's ok
13:31 shk3 if I feel like it could be done easily I wil tell you
13:31 egonw_ joined #bioclipse
13:33 egonw_ I second a bioclipse/attic/plugins set up
13:33 egonw_ however, before moving *anything* in there...
13:33 jonalv yes?
13:34 egonw_ it should be approved by the mailing list...
13:34 shk3 sure
13:34 shk3 and by the other
13:34 shk3 = author
13:34 jonalv That is a very slow and bureaucratic way of doing things...
13:35 egonw_ he... it's an open source project...
13:35 olas joined #bioclipse
13:35 egonw_ you can't just remove things other worked on hard just like that
13:35 jonalv It's not removed
13:35 jonalv it's svn it's still there
13:35 olas what have I missed?
13:36 jonalv besides if we can't do some cleaning of half finnished projects that no one is working on we are going to drown in half finnished projects that no on dears to touch
13:37 jonalv Just me oppinion...
13:37 egonw did you read Tobias PhD thesis?
13:38 jonalv aouch
13:38 jonalv =)
13:38 egonw ok, good
13:38 egonw next question please :)
13:38 shk3 I also think we need some process of getting rid of stuff
13:38 shk3 this is not to blame Tobias or so
13:38 jonalv what do you suggest that we do then?
13:38 shk3 but some projects just might be unfinished and some other project is doing the same
13:38 egonw shk3: right, that process is the mailing list
13:39 shk3 yes indeed
13:39 egonw at this moment, 1. you have no idea if someone is using it
13:39 shk3 I fully agree
13:39 egonw 2. you have no idea about the functionality
13:39 egonw 3. you have no idea about the state of completion
13:40 egonw and to just say, OK I do not understand the code, so let's stuff it away, is a bit lame
13:40 egonw he, I used the word 'lame'...
13:40 jonalv All I know is that it claimed to be a database plugin but was full of Hibernate stuff...
13:40 egonw first time ever
13:40 egonw :)
13:40 jonalv :)
13:41 masak :)
13:41 shk3 the problem is a
13:41 shk3 Could not read mapping document from URL: bundleentry://118/src/net/bioclipse/​model/PersistedDBCDKResource.hbm.xml
13:41 shk3 this document is in n.bd.cdk.database
13:41 jonalv that must be from all the movig around
13:41 shk3 anybody an idea why it's not found?
13:41 shk3 where does the 118 come from?
13:42 jonalv probably something the osgi framework put's there
13:42 jonalv it might be the bundle identity
13:42 jonalv but I am not sure
13:43 jonalv so shk3 how much experience have you got with Hibernate?
13:43 shk3 the code for building the url looks
13:43 shk3 good
13:43 shk3 nothing hardcoded in there
13:43 shk3 jonalv: none
13:44 shk3 to be exact
13:44 jonalv but it isn't hibernate that isn't working?
13:44 shk3 used torque a lot
13:44 shk3 well, I think hibernate isn't finding that mapping file
13:44 shk3 but I am just guessing
13:44 jonalv I am considering joining you in the checking out of this thing.
13:44 shk3 great
13:44 jonalv egnow: Where can I get Tobias phd thesis?
13:45 shk3 mom
13:46 shk3 http://kups.ub.uni-koeln.de/f​rontdoor.php?source_opus=2080
13:47 * jonalv is hoping this is english now...
13:48 shk3 yes
13:50 shk3 jonalv: do you want to join me trying to find the problem?
13:50 shk3 I can tell you how to reproduce the problem
13:51 jonalv well I feel that I should ahve a look at what he has done firt. I am going to give a short status rapport to my professor in 25 mins and I really have alot to do but yes I think I should. Do you have time on monday for this?
13:51 shk3 sure
13:52 shk3 take your time
13:52 shk3 will you be in the chat monday evening?
13:52 jonalv yes
13:52 jonalv or rather when does monday evening start?
13:53 shk3 well, at 6 pm?
13:54 jonalv sure
13:54 shk3 great
13:55 shk3 so see you then
13:55 jonalv I will need to bring something to eat but we could have a look at it then
14:12 shk3 egonw: you commented out the code for sdf parsing, right?
14:12 egonw_ joined #bioclipse
14:21 shk3 egonw_?
14:23 egonw_ yes
14:25 shk3 did you comment out the sdf code in bioclipse?
14:25 shk3 before the release?
14:26 egonw_ Ola discovered problems...
14:26 egonw_ so the decision was made...
14:26 egonw_ but we want it back in asap
14:26 shk3 I would like to fix that
14:26 egonw_ that would be great
14:26 shk3 can you tell me where the code is?
14:27 egonw_ I don't think the code was removed...
14:27 egonw_ just outcommented the hooks in the plugin.xml
14:27 egonw_ so check:
14:27 egonw_ net.bioclipse.cdk.ui/plugin.xml
14:27 egonw_ I think
14:27 shk3 thanks
14:27 egonw_ please write up in the wiki how it is supposed to work...
14:28 egonw_ to ensure that with the next release we test it properly...
14:28 egonw_ Ola and I might have misunderstood things...
14:28 egonw_ stupid thing is, I'm not sure anymore what was broken...
14:28 shk3 the problem was all children had same name
14:29 shk3 and could not be opened
14:29 egonw_ oh, right
14:29 egonw_ I fixed that
14:29 egonw_ there was something else, we discovered afterwards...
14:30 shk3 oh really
14:30 shk3 doesn't seem to be in plugin.xml of cdk.ui
14:30 egonw mom
14:31 shk3 it is
14:31 shk3 sorry
14:31 egonw ah, ok good :)
14:31 shk3 but not commented out
14:32 shk3 i try what happens
14:32 egonw huh?
14:32 egonw yeah, please do
14:42 shk3 looks like no children are created
14:44 CIA-20 bioclipse: carl_masak * r4663 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
14:44 CIA-20 bioclipse: [JsConsoleView.java]
14:44 CIA-20 bioclipse: * indented and documented regular expression
14:44 egonw shk3: do you have all the required plugins?
14:45 shk3 odd:
14:45 shk3 plugin xml stays at revision 4448 for me,
14:45 shk3 although there are newer ones
14:45 shk3 replace doesn't help
14:56 shk3 ok, done.
14:56 shk3 no children are created.
14:57 shk3 I can't find where it is done.
14:57 shk3 should be in sdfresource, shouldn't it?
14:57 shk3 the parseResource() of sdfresource is rather ... well ... simple.
14:58 egonw wasn't it was using the ChildResourceCreator thingy...?
14:58 egonw sorry... don't have access to the source right now...
14:58 egonw in the process of fixing some hardware/install trouble on my machines at hom
14:58 egonw +e
14:58 shk3 that's done via an extension point, right?
14:58 egonw right
14:59 egonw firing up my work desktop (via nx)
15:08 shk3 there is no childResourceExtractor entry for the sdf and it looks like ther never was
15:16 egonw mmm... can't nx into my work desktop
15:16 egonw will try from my laptop when it's done fixing vista
15:17 shk3 do you know where you changed stuff to fix the numbering of child resources?
15:17 Annzi left #bioclipse
15:52 CIA-20 bioclipse: jonalv * r4664 /branches/bioclipse2/ (2 files in 2 dirs): made BioObject into abstract class
16:07 rojasm left #bioclipse
16:08 shk3 exit
16:56 egonw joined #bioclipse
17:13 olas left #bioclipse
18:37 edrin left #bioclipse
18:49 egonw joined #bioclipse
20:09 edrin joined #bioclipse
20:14 edrin hi egon
20:18 egonw hi edrin
20:18 egonw was just about to log out...
20:18 egonw busy day tomorrow...
20:18 egonw cu

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary