Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-05

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All times shown according to UTC.

Time Nick Message
00:18 mgerlich joined #bioclipse
06:44 olass joined #bioclipse
06:50 Gpox joined #bioclipse
07:20 jonalv joined #bioclipse
07:26 sneumann joined #bioclipse
07:35 egonw joined #bioclipse
07:36 egonw moin
07:36 zarah hi egonw
07:36 egonw jonalv: ping
07:36 jonalv egonw: pong
07:36 egonw jonalv: I solved a few duplicate plugins in the git repositories
07:37 jonalv egonw: yes I saw that
07:37 jonalv egonw++
07:48 egonw olass: btw, my eclipse is fucked up again...
07:48 egonw I again cannot run unit tests
07:48 egonw no bloody clue what is happening :(
07:48 olass egonw: did you update the versions in the plugins?
07:48 egonw no, just woke up
07:48 olass ok
07:48 egonw will do that first
07:48 olass let me know
08:06 sneumann @zarah: tell shk3 that MetFrag filters non-CHNOPS compounds atm.
08:21 egonw olass: ping
08:22 egonw 2.0.1.v20090805 ?
08:22 olass egonw: sounds good
08:34 jonalv sneumann: I am afraid zarah does not recognise commands like that
08:35 egonw sneumann: use @tell
08:36 jonalv zarah: tell sneumann you can do it like this
08:36 zarah Consider it noted.
08:36 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r5d08ef3 / (14 files in 14 dirs): Increased version to 2.0.1.v20090805 - http://bit.ly/yVvia
08:36 jonalv @tell sneumann or you can do it like this
08:36 zarah Consider it noted.
08:37 * jonalv hopes sneumann is around otherwise he will probably wonder what "it" is when he reads that... :)
08:59 CIA-63 bioclipse.structuredb: jonalv master * r34f430c / plugins/net.bioclipse.structuredb/src/net/bioc​lipse/structuredb/DBMoleculesEditorModel.java : removed (at least partly) fixed TODO comment and fixed layout - http://bit.ly/MWQ3n
08:59 CIA-63 bioclipse.structuredb: jonalv master * r1100386 / plugins/net.bioclipse.structuredb/src/net/bioclip​se/structuredb/persistency/dao/DBMoleculeDao.java : Cache for number of molcecules in database and annotation. - http://bit.ly/8Fm24
09:19 sneumann @tell shk3 that MetFrag filters non-CHNOPS compounds atm.
09:19 zarah Consider it noted.
09:19 zarah sneumann: You have new messages. Write '/msg zarah @messages' to read them.
09:20 egonw jonalv: ping
09:21 jonalv egonw: pong
09:21 egonw structuredb seems to need nb.services
09:21 egonw which git repos is that in?
09:21 * jonalv is getting OutOfMemory Exceptions and think that HSQLDB eats memory... :(
09:21 jonalv egonw: core?
09:22 egonw jonalv: are you using the file backend for hsqldb ?
09:22 egonw sorry for the obvious question :)
09:22 jonalv egonw: I sure hope so :)
09:22 jonalv egonw: it uses huge amount of memory while processinga question and then it goes down again when it is done
09:22 egonw no, .core does not have nb.services
09:23 egonw ic...
09:23 jonalv hm where is it then?
09:23 jonalv not in structuredb?
09:23 egonw I see it in SVN
09:23 egonw no, not it bioclipse.structuredb
09:24 egonw bla... it tooks very long for them to review our comments on the xmpp paper :(
09:25 jonalv egonw: no where did you find a dep to net.bioclipse.services?
09:25 jonalv egonw: I can't find that
09:25 egonw mom
09:25 egonw eclipse is rebooting after EMF install
09:26 egonw structuredb
09:26 egonw mmm...
09:27 egonw I'll update
09:28 egonw ok, solved
09:28 egonw sorry
09:29 jonalv good
09:29 * egonw needs to think about to update efficiently all his local repos in the morning
09:30 jonalv is there a reason for Bioclipse to only use 512 MB at most?
09:30 * jonalv want all memory he can get his hands on
09:30 egonw no, I guess that should be the minimum ?
09:30 jonalv as it is now Bioclipse woill never use more than 512 MB...
09:31 egonw file a bug report
09:32 jonalv egonw: what good will that do?
09:33 egonw that the default gets increased?
09:33 egonw or the max removed?
09:34 jonalv egonw: Well I want to remove the max. Question is. how do one do that?
09:36 egonw http://dev.eclipse.org/newslists/​news.eclipse.tools/msg06327.html
09:39 jonalv egonw: yes but what I wanted to do was the reverse
09:39 jonalv egonw: however I fear that is not possible
09:39 jonalv We might need an installation process for Bioclipse where the user can specify how much memory Bioclispe should use...
09:42 egonw well, I guess you could remove that feature or set it to 4GB ?
09:43 jonalv egonw: if I remove it it will use Java default value which I think is 128MB
09:43 jonalv if I set it to 4GB and the actual computer only have 2GB I don't know what will happend...
09:44 jonalv huge amounts of swapping?
09:46 egonw yes, likely
09:46 egonw anyway...
09:46 egonw as far as I know
09:46 egonw you can set this easily in the bioclipse.ini
09:46 egonw or what's it called...
09:46 jonalv hence we need an individual memory usage for each computer
10:00 egonw miguelrojasch: ping
10:00 egonw @tell miguelrojasch please pull changes from my bioclipse.medea fork
10:00 zarah Consider it noted.
10:00 egonw @tell miguelrojasch it has a number of compile fixes, needed after our hack session two weeks ago
10:01 zarah Consider it noted.
10:03 CIA-63 bioclipse.structuredb: jonalv master * re4c5dea / plugins/net.bioclipse.structuredb/src/net/bioclip​se/structuredb/persistency/dao/DBMoleculeDao.java : decreased chache size from 200 to 10 for molecule browsing. Now I am able to browse molecules without OutOfMemoryExceptions on my machine. - http://bit.ly/1YGddf
10:03 egonw jonalv++
10:04 jonalv bu calling it fast would be a lie...
10:05 * jonalv @ lunch (all by himself... :(
10:21 egonw wow! I just saw a screenshow of win7... it looks like Kubuntu!
10:22 egonw if you can't beat them, join them?
10:34 * egonw hopes he now has all the EMF features installed that he needs for qsar.ui
10:43 shk3 joined #bioclipse
11:09 egonw Gpox: please let me know what info on http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2 was not working for you
11:09 zarah egonw's link is also http://tinyurl.com/58kmzp
11:10 Gpox git clone git@github.com:olas/bioclipse.core.git
11:11 egonw tack
11:11 egonw fixed that
11:17 egonw http://wiki.bioclipse.net/index.php?titl​e=Checking_out_Bioclipse_2#Other_Git_rep​ositories_for_other_Bioclipse_Features
11:17 zarah egonw's link is also http://tinyurl.com/58kmzp
11:18 egonw not sure who asked about a list of Git repositories again, but here it is
11:33 * jonalv don't want to write the code for converting from ms to days hours minutes and seconds... :(
11:43 olass @pz
11:43 zarah olass: Pelezilla is at http://bugs.bioclipse.net
11:45 olass egonw: bug 1460 is 2.1.0 release
11:46 olass please have a look
11:46 olass If we can get it out tomorrow, that would be great
11:47 egonw no dep on JOELib-QSAR ?
12:09 samuell joined #bioclipse
12:09 egonw hi samuell!
12:09 samuell Hi!
12:09 zarah hi samuell
12:10 samuell Hi all! (getting started trying to set up my dev environment.)
12:11 egonw did you find the wiki page?
12:11 samuell Yeah. So far it seems the "Articles" page ( http://wiki.bioclipse.net/index​.php?title=Development_articles ) is the place to start...
12:11 zarah samuell's link is also http://tinyurl.com/nczwl3
12:13 egonw samuell: also: http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
12:13 zarah egonw's link is also http://tinyurl.com/58kmzp
12:13 samuell Thanks
12:14 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r75fa83c / plugins/net.bioclipse.cdk.ui.sdfeditor/plugin.xml : Added menu to all SDF types, as the base-type if a content type of IFile's is apparently not checked by the 'property' org.eclipse.core.resources.contentTypeId - http://bit.ly/12t55O
12:14 olass egonw: did you create net.bioclipse.business?
12:14 olass is this in 2.0.x or master?
12:14 egonw net.bioclipse.business?
12:14 olass yes?
12:14 olass jonalv: are you responsible for this?
12:15 * olass has never seen it
12:15 egonw neither have I
12:15 olass jonalv: ping
12:15 jonalv olass: pong
12:15 jonalv olass: where?
12:15 olass core repo
12:15 olass you have it?
12:15 egonw no
12:15 egonw what is that?
12:15 olass no idea
12:16 olass it was gone here
12:16 olass but I did see it
12:16 * egonw has never seen that plugin
12:16 olass ok, will remove it if none of you two know about it
12:16 olass no idea where it came from
12:17 jonalv git log plugins/net.bioclipse.business
12:17 olass jonalv: wrong window
12:17 jonalv Added a 'bioclipse' manager to provide some helper methods oriented at users who like more info (addresses #1284)
12:17 jonalv seems like egonw did that...
12:17 olass he saus he did not
12:17 olass so I removed it
12:18 egonw ah...
12:18 egonw right
12:18 * egonw wonders why it does not show up in his git checkouts
12:18 olass it's gone now
12:18 egonw now I remember...
12:18 olass gone, baby, gone
12:18 jonalv there is a PlatformManager in that plujign
12:18 olass bye bye net.bioclispe.business
12:18 olass *poof*
12:18 jonalv written by egonw
12:19 jonalv egonw: was that not something that we were using?
12:19 jonalv it contains stuff like openURL and link to Bioclipse planet and bug manager
12:20 jonalv olass: are you removing it? Why?
12:20 * jonalv rather liked that stuff...
12:20 olass wel.. seems like people did not want it
12:20 olass [14:17]  * egonw has never seen that plugin
12:21 jonalv olass: who did not want it?
12:21 jonalv olass: when does never seen mean do not want?
12:21 olass well if egon created it and never seen it, then why keep it?
12:21 olass *poof*
12:21 jonalv olass: because I liked it? :)
12:21 olass jonalv: then resurrect it
12:21 egonw I added this for support like:
12:22 egonw license()
12:22 egonw copyright()
12:22 egonw pending one bug report
12:22 olass so in master
12:22 olass not 2.0.x
12:22 olass (which was my original question)
12:22 egonw I did not remember the name of the plugin I had added that too
12:22 olass :)
12:22 jonalv yea it's not 2.0.x stuff
12:22 * olass is just kidding and will bring the plugin back to life
12:22 olass if git can do that on my machine
12:25 olass CIA-63?
12:25 olass CIA-63: ping
12:25 olass CIA-63--
12:25 * egonw wonders why the CIA is ignoring olass
12:25 olass zarah: slap CIA-63
12:25 zarah go slap CIA-63 yourself
12:25 olass :(
12:26 olass zarah: slap CIA-63
12:26 * zarah places her fist firmly on CIA-63's jaw
12:26 olass that's better
12:27 olass egonw: are the update sites not migrated to git?
12:28 olass egonw: really no worry, just asking
12:28 egonw no, don't think so
12:28 olass ok
12:28 * olass will use subclipse, an old friend, again
12:30 olass egonw: where is net.bc.sdk_feature?
12:30 olass not in git?
12:30 egonw where should it belong?
12:30 egonw .core ?
12:30 * egonw hates Eclipse
12:31 egonw the unit testing worked for half a day
12:31 egonw maybe installing EMF broke it
12:31 * egonw has no clue what
12:31 * jonalv is trying to import the 1gb file again this time he has added a time left estiamtion feature
12:32 jonalv hm 3 hours
12:34 jonalv maybe that's not too bad
12:34 olass coffee break?
12:34 jonalv what do you people think? Three hours for importing a 1 gig sd file into Structuredb?
12:35 jonalv hm 3.5 hours now... :(
12:35 olass jonalv: sounds like much
12:35 olass depends on what performance you get when using it
12:35 jonalv It's calculating SMILES and figerprints for 193617 molecules...
12:35 olass jonalv: did you analyze the bittlenecks with yourkit?
12:35 olass jonalv: we said skip SMILES...
12:36 olass see how much that reduces
12:36 jonalv olass: yea we were considering that. I have not done anything about that yet though
12:36 olass egonw: I guess we caould have sdk in core repo, and we should IMO have the updatesites there too
12:36 olass jonalv: ack
12:36 jonalv hm, now it says 4 hours
12:36 olass where will it end?
12:37 jonalv must have been some really slow molceuls there and maybe it has started to garbage collect now...
12:37 olass jonalv: I suggest to comment out SMILES and try again
12:38 * jonalv grabs some water and sees what it estimates when he get back
12:38 jonalv olass: I can't simply do that. I will get Null error when trying to save molecules without SMILES
12:38 olass save "" then
12:38 jonalv yea I guess...
12:38 jonalv afk brb
12:46 * jonalv tests without SMILES now...
12:46 shk3 egonw: can I come back to your problems yesterday?
12:46 zarah shk3: You have new messages. Write '/msg zarah @messages' to read them.
12:46 shk3 sorry, I was distracted yesterday
12:47 shk3 the edit account does not work if a field is empty, right?
12:47 CIA-63 bioclipse.core: Ola Spjuth 2.0.x * rd91be90 / (2 files in 2 dirs): Create feature patch for 2.0.1 with net.bc.core plugin in it with updated version. - http://bit.ly/MSWmV
12:47 jonalv more like 1.5 hours now it seems
12:47 egonw shk3: yes, it seems so
12:47 shk3 ok, will look at that
12:47 shk3 is your password working?
12:48 egonw jonalv: 3 hours... that's 18 molecules a second
12:48 egonw shk3: not the last time I tried
12:48 egonw shk3: I tried changing it, hoping that would trigger a sync or so...
12:48 jonalv egonw: you think that is good or bad?
12:48 egonw but without success
12:49 egonw jonalv: no clue
12:49 egonw jonalv: it's not blazing fast
12:49 shk3 ok, I will test
12:49 shk3 it works locally
12:49 shk3 so if it does not work, it must be a server config problem
12:49 egonw jonalv: I guess it should be able to get it at least 5 times as fast
12:49 egonw jonalv: you could try a simple CDK prog, to do it from the command line
12:50 jonalv I guess...
12:51 jonalv Gpox: are you going to be in UA tomorrow?
12:51 egonw then you know of the slowlyness is in the CDK or in Bioclispe/HSQLDB
12:52 jonalv egonw: yourkit already indicated that SMILES calcualtion was a huge part of it
12:52 jonalv and it cut the time in about half when I remopved it...
12:54 Gpox yes
12:55 jonalv I want some help with the molecules editor, properties and stuff...
12:56 CIA-63 bioclipse: shk3 * r11721 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/SpeclipsePerspective.java: added the compare spectrum view to speclipse perspective
13:00 egonw olass: it seems that github is a bit overloaded...
13:00 egonw too successful
13:00 egonw fortunately, they are planning server upgrades
13:00 olass :)
13:00 olass needed
13:01 egonw indeed
13:02 egonw yeah, the unit tests run again...
13:02 egonw what a pain
13:02 * egonw feels stupid as the solution is so obvious
13:16 * jonalv has a small blackout
13:16 jonalv I am trying to push my last commit to github
13:16 jonalv but is says everything is up to date
13:17 egonw it is probably right
13:17 jonalv egonw: but the commit does not exist on github...
13:17 egonw I noticed just a minute ago that the web frontend is somewhat lacking
13:17 egonw I had the exact same problem with a commit I made about 30mins ago :)
13:17 jonalv hm but I got no info in here eihter
13:18 egonw try: git fetch
13:18 egonw and then boot gitk or gitk
13:18 egonw and check the labels
13:19 jonalv hm I guess I managed to push it then...
13:19 jonalv github--
13:21 egonw jonalv: lack of computing power
13:21 jonalv I know how that feels...
13:21 egonw the 'free server' user community is rather demanding
13:21 egonw which is why SF is also so slow
13:22 * egonw recommends people to check out 'tig' ... a git command line util, but then like gitx and gitk
13:23 jonalv yea I sae that. I just fon't think I need yet another git visualiser. Or do I?
13:23 * olass is uploading 2.0.1 to update site
13:24 * jonalv can't spell today it appears...
13:25 * olass has made his first tag: '2.0.1' with git
13:25 olass \o/
13:25 jonalv olass++
13:27 CIA-63 bioclipse.core: Ola Spjuth 2.0.x * r737b7e2 / (3 files in 3 dirs): Updated core.ui plugin/about and added to feature_patch. - http://bit.ly/rkSFR
13:29 CIA-63 bioclipse.core: jonalv master * r879fce0 / plugins/net.bioclipse.core/src/net/bi​oclipse/core/util/TimeCalculater.java : Created a util class for converting milliseconds to a humanly readable string. - http://bit.ly/fs7SB
13:29 CIA-63 bioclipse.core: jonalv master * rc55d64a / (3 files): Merge branch 'master' of git@github.com:olas/bioclipse.core - http://bit.ly/bA9eN
13:30 * jonalv ducks and covers
13:32 jonalv olass: What was that question regarding operationCancelledException btw?
13:34 jonalv olass: I am looking at the code but I can't see how you could end up in any trouble. What was the situation you thought about?
13:34 CIA-63 bioclipse.structuredb: jonalv master * r28a7ae4 / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : Added time remaining estimation for addStructuresFromSDF. - http://bit.ly/a4U8n
13:38 olass jonalv: how do I send a cancel in a manager calll?
13:38 olass if I just return, then I signal everything is OK
13:39 jonalv olass: throw OperationCancelledException
13:40 jonalv olass: if you have a monitor that is
13:40 jonalv olass: if you don't then throw something else
13:40 jonalv olass: but I suppose since you have cancel then you ahve a monitor...
13:41 jonalv olass: actually I think the Eclipse api defines "just returning" as okey to do in that situation thoguh. To what do you signal theat everything is okey?
13:41 jonalv olass: I don't think anything is listening...
13:44 olass let's talk IRL next time at BMC
13:57 jonalv @pz molecules table context menu
13:57 zarah [1458] Export behavior from molecules... http://tinyurl.com/nfjzq8
13:57 zarah [331] Extract subset of MoleculesTabl... http://tinyurl.com/ljn374
13:57 zarah [1153] Change visible columns in Mole... http://tinyurl.com/lf96qw
13:57 zarah Entire list at http://tinyurl.com/l86ppo
13:57 jonalv @pz table context menu
13:57 zarah [1458] Export behavior from molecules... http://tinyurl.com/nfjzq8
13:57 zarah [331] Extract subset of MoleculesTabl... http://tinyurl.com/ljn374
13:57 zarah [1181] Trouble with Jchempaint undo      http://tinyurl.com/mjs96p
13:57 zarah [1378] Refactor moltable to work with... http://tinyurl.com/nbk8rk
13:57 zarah [1153] Change visible columns in Mole... http://tinyurl.com/lf96qw
13:57 zarah Entire list at http://tinyurl.com/lekaln
14:02 egonw http://chem-bla-ics.blogspot.com/2009/08/​running-bioclipse-plugin-unit-tests.html
14:02 zarah egonw's link is also http://tinyurl.com/ngrcal
14:02 egonw might be of interest to others too
14:03 egonw what ?!?!
14:03 egonw do you know the solar flares of our sun?
14:03 jonalv egonw: what about em?
14:03 egonw well, every star has that...
14:04 egonw and they actually have pictures now of Betelgeuze with flares:
14:04 egonw http://www.eso.org/public/outreac​h/press-rel/pr-2009/pr-27-09.html
14:04 zarah egonw's link is also http://tinyurl.com/r32kyw
14:04 * jonalv thinks that StructureDB might not be hopelessly bad after all.
14:04 jonalv just need some input on the topic of what to do with it...
14:05 jonalv egonw: artista impression it sais on the pictures...
14:05 egonw yeah, but not all
14:05 egonw http://www.eso.org/gallery/v/ESOPIA​/Stars/phot-27b-09-fullres.tif.html
14:05 zarah egonw's link is also http://tinyurl.com/nbjmxa
14:05 olass jonalv++
14:05 egonw that's the real thing
14:07 jonalv okey
14:10 olass jonalv: can you do substructure search on the database?
14:11 jonalv olass: only from commandline and I don't know if it is workign right now :)
14:11 olass ah :)
14:11 jonalv but I think it does
14:11 jonalv I am not sure how one want to do that from the gui
14:11 jonalv dropping a molecule feels like adding it not searching for it...
14:12 olass jonalv: I'm not so sure
14:12 egonw jonalv: I agree
14:12 olass How about a dialog asking for what to do?
14:12 olass upon drop?
14:12 egonw jonalv: if one drops a query....
14:13 jonalv I ewar people will get crazy about dialogs....
14:13 olass jonalv: in any case there must be a context menu option "query"
14:13 jonalv olass: drops a query? Where would the user get a query to frop?
14:13 olass which opens a dialog
14:13 jonalv olass: yea that's probably a safe place to start...
14:14 olass jonalv: jonalv that was egon saying that
14:14 egonw a query editor
14:14 olass not me
14:14 * olass prefers a query dialog
14:14 olass well, maybe both?
14:14 jonalv olass: oh sry
14:15 jonalv egonw: where do the user get a query to drop?
14:15 egonw a query editor has the advantage that you can save it...
14:15 egonw say, in a folder, together with the search results...
14:15 jonalv egonw: what is a query editor?
14:15 olass sounds like a more advanced use case
14:15 egonw @gg editor
14:15 zarah egonw: http://en.wikipedia.org/wiki/Editing
14:15 olass @gg egon
14:15 zarah olass: http://en.wikipedia.org/wiki/Egon_Spengler
14:16 jonalv egonw: no I mean how would it look?
14:16 egonw query := something you want to search for ?
14:16 olass @gg image egon
14:16 zarah olass: http://commons.wikimedia.org/wiki/Fi​le:Egon_Herbert_Ein%25C3%25B6der.png
14:16 jonalv egonw: what sort of query
14:16 jonalv olass: yes I ahve substructure search
14:16 * jonalv runs multiple StructgureDB commans simultansously here... o/
14:16 * olass want substructure in a gui action from context menu
14:16 olass jonalv++
14:17 jonalv I have only done it on different databases yet though...
14:17 jonalv olass: okey I do a context menu action for doinga substructure search. How do you get a structure in?
14:17 olass open a dialog
14:17 jonalv what happends when you run the action?
14:17 egonw jonalv: a specialize JCP editor
14:18 egonw for editing SMARTS structures
14:18 olass let user select a file from workspace
14:18 olass that is the easiest
14:18 jonalv olass: okey
14:18 olass more advanced: JCP (as egon suggests)
14:18 olass but take the easy first IMO
14:18 jonalv yes first walk and then run
14:18 olass indeed
14:18 olass then jump
14:19 olass last: fly
14:19 olass overkill: nirvana
14:19 olass jonalv: there is a contentprovider for molecules in workspace
14:19 olass in net.bc.cheminformatics if I'm not mistaken
14:20 jonalv olass: I will look at it later
14:20 jonalv olass: I realised that I really need a toString method on my dbmolecules
14:20 jonalv the result from the substructure search on the console looks very bad...
14:20 jonalv structuredb.subStructureSearch("profiling", cdk.fromSMILES("CCC=C"));
14:21 jonalv [{DBMolecule}, {DBMolecule}, [.....]
14:21 olass if you need a dialog for selecting molecules in workspace, see: SelectMoleculesPage.java in qsar.ui plugin
14:21 jonalv olass: yes I will look at that
14:23 egonw bioclipse 2.0.0 is picking up the 2.0.1 updates
14:23 egonw and now downloading them
14:23 jonalv w00t
14:24 jonalv :)
14:24 * egonw has fingers crossed...
14:24 jonalv btw has anyone made sanity chacks like that all commits in the 2.0.x branch are in the 2.1 branch?
14:24 olass nope
14:24 jonalv |checks
14:24 olass jonalv: please check yourcommits
14:24 olass thx
14:25 * egonw suggests... git log 2.0.x..master
14:25 jonalv olass: what's wrong with my commits?
14:25 olass egonw: could you briefly have a look at bug 1428?
14:25 olass jonalv: wrong?
14:25 jonalv olass: yea, in what way do you want me to check them?
14:25 olass as in that you have committed them to master as well?
14:25 * jonalv sees no reason for why they wouldn't be okey...
14:26 olass jonalv: why do you ask then?
14:26 egonw olass: ack
14:26 jonalv olass: well I am not the only one working on it am I?
14:26 olass jonalv: almost only your commits in 2.0.1 release...
14:26 jonalv olass: and it's always possible to make erros
14:26 olass yes
14:27 olass true
14:27 egonw olass: does not sounds like a bug for Gpox to fix
14:27 olass no
14:27 olass I have no idea who filed it to him
14:27 olass egonw: this is a serious bug
14:27 egonw for the 2.1 release?
14:28 olass do you know what causes it?
14:28 jonalv hm I need a Bioclispe restart to see if my fix is working but my import still has about 1 hour left to run :/
14:28 egonw no
14:28 egonw not now
14:28 egonw would need to explore that...
14:28 egonw now working on the PubChem XML bug
14:28 olass thanks
14:29 olass If 1428 can make 2.0.2 I'd be very happyy
14:30 jonalv olass++
14:31 olass jonalv: thanks, but for what?
14:31 jonalv Bioclipse 2.1
14:31 jonalv uhm 2.0.1
14:31 olass :)
14:31 jonalv gah this versioning system is complicated :)
14:31 egonw olass: please make a 2.0.2 bug report and add a depends
14:32 olass egonw: already done that :)
14:32 olass @pz 1466
14:32 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1466
14:32 egonw tack
14:32 olass also assigned the formula bug to you (1428)
14:33 * olass will now fix his things for 2.1.0 release
14:37 CIA-63 bioclipse: shk3 * r11722 /bioclipse2/trunk/plugins/net.bioclipse​.data.speclipse/data/speclipse/assinged spectra/ (Maaranolide_G.xml Manaarenolide_G.xml): renamed file with correct chemical name
14:38 egonw bioclipse 2.0 update seemed to have worked well
14:38 egonw olass++
14:39 olass great
14:41 jonalv olass: do you know how to add a doubleclicklistener to the CNF so that I can open a label by doubleclicking on it?
14:41 egonw olass: do I have commit rights to bioclipse.data ?
14:41 olass jonalv: no
14:41 jonalv Common Navigator Framework really make things more complicated...
14:41 olass egonw: will check
14:41 egonw otherwise, I'll do a pull request
14:42 olass egonw: now you have
14:42 egonw tack
14:42 olass please push
14:48 egonw done
14:54 jonalv I hate Eclipse Common Navigaot Framework
14:55 egonw which is why people use the Common Navigator Framework instead? :)
14:56 * jonalv sticks out his tongue at egonw
14:56 jonalv :(
14:56 * egonw stables it to carl's table
14:56 egonw staples
14:56 jonalv ouch that hurts :)
14:58 egonw jonalv: I have the following CDKManager method:
14:58 egonw public ICDKMolecule fromString(String molstring)
14:58 egonw throws BioclipseException, IOException {
14:58 egonw I can change this into
14:58 egonw fromString(String molstring, IProgressMonitor monitor)
14:58 egonw without problems, right?
14:59 jonalv egonw: you might want to keep the throws BioclipseException part
14:59 jonalv I think
14:59 jonalv uhm
14:59 jonalv olass: do you remember?
14:59 egonw yeah, did not intend to change that
14:59 egonw just left that out for brevity
14:59 * jonalv 's brain has quit working...
15:02 olass jonalv: remember what?
15:02 * jonalv is gonna take a break and walk over to Ica hoernan and shop for some throat tablets
15:03 olass jonalv: been talking to much?
15:03 jonalv olass: how we agreed that it was with manager methods and exceptions..
15:03 olass well
15:03 olass you can throw what you want
15:03 olass but all except BioclispeException can not be caught
15:03 jonalv yea that sounds familiar
15:04 olass since they will be wrapped in some other exception by spring...
15:04 jonalv egonw: did that answer your question?
15:04 olass UndeclaredThrowableExc I think
15:04 olass you can still catch that
15:04 olass I guess
15:05 olass but does not seem reasonable to throw exceptions that will be eaten by Spring anyway, IMHO
15:05 jonalv well but this is off course not the case when the method id run as a job
15:05 jonalv then you don't get any exceptions at all
15:05 olass oh
15:05 olass why not?
15:05 jonalv olass: because that is in another thread
15:05 olass we need to discuss this
15:05 olass IRL as said
15:06 jonalv you can't throw exceptions between threads and you can't return between threads without lockingthe first calling thread and if that thread is the ui thread you are int trouble. For the millionth time... :)
15:06 * jonalv afk
15:14 egonw jonalv: what question?
15:17 olass egonw: where did org.openscience.cdk.renderer.Renderer move?
15:18 egonw org.openscience.cdk.renderextra
15:18 * samuell is getting headache from the Windows GUI Git client he downloaded
15:19 * egonw does not have suggestions for an alternative GUI
15:19 olass egonw: previously I did:         renderer.paintMolecule(mol, new AWTDrawVisitor(g2));
15:19 olass what now?
15:20 olass do you have a pointer?
15:20 egonw but you could try the command line git utils with Cygwin
15:20 egonw olass: what plugin, what class?
15:20 * samuell is thinking about setting up an ubuntu virtual machine as dev env instead
15:20 olass ds plugin, class ReportHelper.java
15:20 egonw samuell: yeah, good alternative
15:20 olass net.bioclipse.ds
15:21 samuell So, you are mostly using macs? Anybody running linux?
15:21 * egonw is
15:21 egonw ubuntun jaunty
15:21 * olass is on Mac
15:21 egonw see my blog: chem-bla-ics.blogspot.com
15:22 samuell egonw: Ok
15:22 samuell egonw: Good, then I have a source for wupport :)
15:22 olass egonw: about the renderer..
15:22 olass help?
15:22 olass you seem to have changed a lot
15:22 samuell (support)
15:23 * olass wants to get rid of compile errors in DS
15:23 olass ah
15:23 * olass changed paintMolecule to paint()
15:23 olass dunno if it works, but compiles anyway :)
15:25 egonw olass: I guess that is the proper fix
15:25 egonw olass: additionally...
15:25 egonw remove dep on renderextra
15:25 egonw and have only renderbasic and renderawt
15:25 olass ok
15:25 egonw and replace Renderer by AtomContainerRenderer
15:25 egonw (which is in renderbasic)
15:25 egonw should make it faster
15:33 jonalv hi samuell, bye samuell
15:34 olass :)
15:35 egonw Gpox: ping
15:36 Gpox egonw: pong
15:36 egonw Mark just emailed on cdk-jchempaint...
15:36 egonw can you please reply?
15:36 egonw in particular on the shift issue?
15:36 egonw and if you are indeed deliberately not using the renderer shift functionality?
15:39 egonw (which would just mean that we should integrate the approaches)
15:45 jonalv @pz 3d view
15:45 zarah http://pele.farmbio.uu.se/cgi-​bin/bugzilla/show_bug.cgi?id=3
15:46 samuell joined #bioclipse
15:47 olass egonw: could you please remove all CDKException from ICDKManager?
15:47 olass Else I always need to import org.openscience.* plugins to use CDK
15:47 egonw I guess I can do that in 2.1
15:47 olass thanks
15:47 olass will file a bug
15:48 egonw thanx
15:49 olass egonw: what cdk plugin is the CDKException in?
15:49 olass I need to import that just to call "Save"
15:49 egonw try: Ctrl-Shift-T
15:49 olass and then?
15:50 egonw type
15:50 egonw CDKException
15:50 egonw open it and see what plugin it is in
15:50 olass is that cdk.module?
15:50 egonw yes, that too
15:59 jonalv hm seems that if not HSQLDB is allowed to shut down properly it does not start fast enough for Bioclipse to not time out while waiting. I wonder if this will be a problem...
16:00 olass jonalv: likely
16:00 olass you need a progress bar so user sees it is initializing
16:02 jonalv I need something myself. I can't get it to start again.. :(
16:07 shk3 egonw: I try to get nightly working again, systems shut down the server it was running on
16:07 shk3 it seems git needs curl (whatever this is) in our case.
16:07 olass anyone who knows how to write a temp molecule file that I can load with CDK ?
16:07 shk3 is this correct?
16:07 olass Gpox?
16:07 olass egonw?
16:07 olass jonalv?
16:08 * olass hates /Virtual
16:08 egonw @gg curl
16:08 zarah egonw: http://curl.haxx.se/
16:08 jonalv olass: yes?
16:08 shk3 can't you do it the normal way?
16:08 olass jonalv: how write a temp mol file?
16:08 jonalv olass: there is some java feature for creating a file that is removed when the jvm dies
16:09 jonalv olass: hang on
16:09 olass jonalv: does that work with IFIle?
16:09 jonalv olass: I guess you can create an IFile that points to it yea
16:09 olass cdk.loadMolecule() and cdk.saveMolecule() does not work with stuff outside of workspace
16:09 jonalv olass: but there might be some other Eclipse way of doing it...
16:10 jonalv olass: http://www.exampledepot.com/eg​s/java.io/CreateTempFile.html
16:10 zarah jonalv's link is also http://tinyurl.com/l9us7e
16:10 olass jonalv: [18:10] < olass> cdk.loadMolecule() and cdk.saveMolecule() does not work with stuff outside of workspace
16:10 jonalv olass: maybe...
16:11 egonw shk3: what is correct?
16:11 jonalv olass: then you will have to ask Gpox
16:12 shk3 that the configuration at pele requires git to be compiled with curl support
16:12 shk3 I get:
16:12 shk3 error: git was compiled without libcurl support.
16:12 shk3 fatal: Don't know how to fetch from http://pele.farmbio.uu.se/g​it/jchempaint-primary.git/
16:12 zarah shk3's link is also http://tinyurl.com/l7zegy
16:12 shk3 I thought you might be able to say "yes, get this curl" or so
16:12 egonw shk3: no, clue...
16:12 egonw I did not compile git...
16:12 egonw used the .deb
16:12 shk3 I have to :-(
16:13 shk3 thanks anyway
16:13 jonalv shk3: have you compiled git yourself?
16:13 jonalv shk3: it probably picks up Curl if it is installed at compile time...
16:13 egonw shk3: http://packages.ubuntu.com/jaunty/git-core
16:13 zarah egonw's link is also http://tinyurl.com/my95go
16:13 egonw it seems it indeed is built with curl support
16:14 shk3 i will ask systems for curl
16:14 egonw what OS is your machine running?
16:14 * shk3 going to watch cricket
16:15 jonalv shk3: you too?
16:15 * jonalv doesn't even know what that game is all about
16:15 egonw like all games: winning
16:16 jonalv fair enough
16:16 * jonalv just removed all his hsqldbdatabase files... :(
16:28 CIA-63 bioclipse.balloon: Ola Spjuth master * r61bc3d4 / .gitignore : Added .gitignore - http://bit.ly/10Rgdu
16:36 * jonalv heads home
16:49 egonw_ joined #bioclipse
16:51 CIA-63 bioclipse.structuredb: jonalv master * r3d731ea / plugins/net.bioclipse.structuredb/src/net/b​ioclipse/structuredb/domain/DBMolecule.java : Wrote a toString method for DBMolecule so that they look nice when printed on the console - http://bit.ly/1NBUt
17:16 CIA-63 bioclipse.balloon: Ola Spjuth master * re575b8c / (4 files in 3 dirs): Implemented list of molecules as input and output. Added .gitignore. Solves bug 1463. - http://bit.ly/4DYLJP
17:16 zarah bug #1463 | http://tinyurl.com/lqzfhc
17:47 egonw joined #bioclipse
18:07 sneumann joined #bioclipse
18:27 olass egonw: I am getting stressed
18:28 olass 2.1.0 seems to need quite some work
18:28 olass I might need to release a devel version that does not work
18:28 olass that would be bad
18:29 olass do you think it feasible to solve all subbugs of 1460 before end of friday?
18:29 olass brb
18:29 CIA-63 bioclipse: shk3 * r11723 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (11 files in 3 dirs): code cleanups
19:17 samuell left #bioclipse
19:48 samuel joined #bioclipse
23:22 CIA-63 bioclipse.core: Egon Willighagen master * r4841b7c / (95 files in 3 dirs): Uploaded CDK 1.3.0.0bioclipse2 from http://pele.farmbio.uu.se/cgi-bin/g​itweb.cgi?p=jchempaint-primary.git - http://bit.ly/HHltR
23:22 zarah CIA-63's link is also http://tinyurl.com/m2blz3

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