Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-12

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All times shown according to UTC.

Time Nick Message
00:18 CIA-55 bioclipse: edrin_t * r8748 /bioclipse2/trunk/plugins/​net.bioclipse.webservices/ (9 files in 6 dirs): resolved naming of web service result folder, result is now opened in editor
05:01 sneumann_ joined #bioclipse
07:15 egonw joined #bioclipse
07:31 Gpox joined #bioclipse
07:37 egonw moin Gpox
07:37 egonw Gpox: I need your help
07:37 Gpox ok
07:37 egonw please check bug 460
07:38 egonw the ICDKAdapterFactory is parsing each file selected (not opened) in the navigator
07:39 olass joined #bioclipse
07:39 egonw even 1GB file and files it cannot parse at all
07:39 olass @sen edrin
07:39 olass @seen edrin
07:39 zarah edrin was last seen 11 h 52 m 50 s ago in #bioclipse saying 'egonw: ?'
07:40 olass egonw: you seen edrin?
07:40 egonw he was online last nite
07:40 egonw not seen today yet
07:40 olass we wre
07:41 olass we were supposed to have a skype call 8.30...
07:41 olass I guess he forgot
07:41 egonw oops
07:41 egonw so did I
07:41 olass :-)
07:41 egonw OK, heading to the skype phone now
07:41 olass I overslept :-)
07:41 egonw just in case he shows up
07:41 olass well
07:41 olass you at BMC?
07:42 olass oj, you have a separate skype phone?
07:42 olass cool
07:42 olass :-)
07:42 olass egonw: I need breakfast
07:42 olass call me if he shows up
07:43 egonw ok
07:44 egonw olass: yeah, and the coolest thing is that it looks like laptop :)
07:51 olass_ joined #bioclipse
08:18 olass grr. olas had not timed out :-(
08:19 olass karma olas
08:19 zarah olas has a karma of 46
08:19 olass karma olass
08:19 zarah olass has a karma of 11
08:19 olass karma zarah
08:19 zarah zarah has a karma of 57
08:19 olass same!
08:19 olass karma jonalv
08:19 zarah jonalv has a karma of 67
08:20 olass karma masak
08:20 zarah masak has a karma of 57
08:20 olass karma Gpox
08:20 zarah Gpox has a karma of 45
08:20 olass karma egonw
08:20 zarah egonw has a karma of 50
08:20 olass karma perl
08:20 zarah perl has a karma of 0
08:20 olass !
08:20 egonw hahaha
08:20 egonw OpenBabel fails on the DrugBank file too...
08:20 olass you really should tell drugbank suppliers...
08:21 olass I'm sure they'd appreciate it
08:21 egonw yes, I know...
08:21 egonw Joerg blogged about SDF support in BioClipse...
08:21 olass oh?
08:21 olass positive?
08:22 egonw SDF failed for him
08:22 egonw will give you link, hang on...
08:22 olass @seen edrin
08:22 zarah edrin was last seen 12 h 35 m 42 s ago in #bioclipse saying 'egonw: ?'
08:23 egonw http://miningdrugs.blogspot.com/2009/02/​life-science-are-it-guys-getting-it.html
08:23 zarah egonw's link is also http://tinyurl.com/cjqn6u
08:24 olass too bad it didn't work
08:24 egonw yes
08:24 egonw I asked him to email me
08:24 egonw so that I can fix his use case
08:24 olass egonw++
08:25 egonw OB seems to like to latest DrugBank download
08:39 CIA-55 bioclipse: goglepox * r8749 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (MoleculesIndexEditorInput.java SDFAdapterFactory.java): Removed use of BioclipseStore in SDFAdapterFactory
08:39 CIA-55 bioclipse: goglepox * r8750 /bioclipse2/trunk/plugins/net.bio​clipse.inchi.business/plugin.xml: removed adapting to ICDKMolecule in inchi menu entry
08:41 egonw yeah, bioclipse boots again :)
08:42 egonw olass: OK, the DrugBank file is fixed
08:43 egonw removed all spurious new lines
08:43 olass nice
08:52 jonalv joined #bioclipse
08:52 jonalv oh hai
08:53 jonalv hi
08:53 jonalv zarah: are you there?
08:53 zarah jonalv: are you making fun of me?
08:53 jonalv zarah: you are managing that fine by yourself
08:53 zarah jonalv: are you talking to *me*?
08:54 masak joined #bioclipse
08:55 egonw olass: DrugBank can now go back into the release
08:55 egonw can I readd it to the Data Feature?
08:56 olass well
08:56 olass things have changed a bit
08:56 olass let me do it and verify it
08:56 olass hmm
08:56 CIA-55 bioclipse: egonw * r8751 /bioclipse2/trunk/plugins/net.bioclipse.data​.drugbank/data/DrugBank/small_mol_drugs.sdf: Fixed our DrugBank SD file: removed empty entries (zero atoms), and removed all spurious new lines
08:56 olass no
08:56 olass please fo it
08:56 olass just remembered I fixed it earlier :-)
08:57 olass fo=do
08:57 egonw sorry, can't follow you
08:57 egonw what has changed?
08:57 CIA-55 bioclipse: egonw * r8752 /bioclipse2/trunk/plugins/net.bioclipse.data​.drugbank/data/DrugBank/small_mol_drugs.sdf: Removed two more empty records
08:57 egonw you fixed it earlier? how? what?
08:57 CIA-55 bioclipse: egonw * r8753 /bioclipse2/trunk/plugins/net.biocl​ipse.tests/src/net/bioclipse/tests/ (2 files): Removed test suites outside the release
09:05 edrin joined #bioclipse
09:05 edrin hi
09:07 masak privet, edrin.
09:07 edrin hi
09:09 olass hi edrin
09:09 jonalv @pz jchempaint ediotr does not recognize 0 atom fioles
09:09 zarah http://tinyurl.com/d3cnq7
09:10 jonalv @pz jchempaint ediotr does not recognize 0 atom files
09:10 zarah http://tinyurl.com/d3cnq7
09:10 masak hm.
09:10 masak jonalv: try a broader search
09:10 masak @pz jchempaint atom
09:10 zarah [455] Adding bonds and atoms is not i... http://tinyurl.com/b39lhn
09:10 zarah [170] Cannot open zero-atoms template... http://tinyurl.com/aalgxr
09:10 zarah [166] Custom coloring of molecules in... http://tinyurl.com/cfcod8
09:10 zarah [167] Custom visualization of changed... http://tinyurl.com/bk3y89
09:10 zarah [165] Color atoms and bonds in JCP fr... http://tinyurl.com/5q4sks
09:10 zarah Entire list (6) at http://tinyurl.com/d3kxgw
09:11 masak @pz recognize atom
09:11 zarah masak: Zarro boogs found.
09:11 masak strange that she only answers 'zarro boogs' sometimes.
09:13 olass egonw: I think we should have a separate drugbank feature
09:14 olass that better demonstrates how data can be provisioned for bioclipse
09:14 egonw olass: ha, you really like the 150 CDK plugins, don't you? ;) now you want 150 features too... nice
09:14 olass haha
09:14 olass you disagree?
09:14 egonw yes
09:14 olass so drugbank is sample data?
09:14 egonw I want 200 plugins, and 175 features :)
09:15 olass lol
09:15 egonw seriously, sounds good
09:15 olass bug for you coming up
09:15 egonw I hope it comes with a nice blog post to show how other can do it too?
09:15 egonw OK
09:15 olass it will, in time
09:16 olass for now, we have: http://wiki.bioclipse.net/index.php?title​=Contributing_a_data_plugin_to_Bioclipse
09:16 zarah olass's link is also http://tinyurl.com/dhzfvm
09:16 olass but will definitely be a nice blog post prior to bc2.0
09:17 egonw might be nice for Planet Eclipse
09:18 olass indeed
09:18 olass but there are some issues to sort out also
09:25 olass Gpox: I closed bug #327 (context menu adaptation).  Context menu has several errors though. I assume this is already being worked upon and has bugs assigned?
09:26 olass Add hexagon throws exception for example
09:27 Gpox no, no bugs on that
09:27 olass ok
09:27 olass Gpox: I really would like hovering to be visualized when Symbols are being hovered upon
09:27 olass so hard to see what you right-click on
09:28 olass that, however, has already been filed
09:28 olass egonw: What does the JCP menu action "Update implicit hydrogens" do?
09:28 olass nothing visual at least...
09:28 egonw recalculates the implicit hydrogens
09:28 egonw depends on you actually showing the implicit hydrogens
09:29 egonw a renderer option
09:29 egonw for which I have the Pref Pane bug
09:29 olass ok
09:29 olass just wondered
09:29 egonw yeah, no problem
09:29 egonw just explaining :)
09:32 jonalv @pz context manu jmol
09:32 zarah jonalv: Zarro boogs found.
09:32 jonalv @pz context menu jmol
09:32 zarah [310] Option to export open Jmol as i... http://tinyurl.com/b8vbf8
09:32 zarah [322] Jmol lacks a context menu          http://tinyurl.com/bn36ho
09:32 zarah Entire list at http://tinyurl.com/bu5kzw
09:39 masak egonw: "You must determine a target milestone for bug 425 if you are going to accept it. Part of accepting a bug is giving an estimate of when it will be fixed." Is it possible to make this error message slightly less condescending? :)
09:39 edrin jonalv: did my fixes resolve your problems?
09:40 jonalv edrin: sry, which bug are you reffering to?
09:40 * jonalv has created so many bugs lately...
09:40 masak also, the alternatives "2.0" and "2.1" makes the selection slightly bogus.
09:40 egonw masak: no idea
09:40 masak I read those two as "soon" and "later" :)
09:42 egonw olass: did you set that message yourself, or is that a BZ default?
09:42 olass what msg?
09:44 masak olass: the latter, I think.
09:45 masak it's large text on a red background, so it feels like I did something very wrong each time I run into it.
09:45 olass ah
09:45 olass no, did not set that
09:45 masak the rest of bz looks much better nowadays.
09:45 olass just required target
09:45 olass seems mylyn has not built in support for that I guess
09:46 olass < masak> I read those two as "soon" and "later" :) <- I guess you are right
09:46 masak maybe this'll be the thing that brings me over to mylyn :)
09:46 olass in principle everything might go in bc 2.1 since it is not clearly defined yet...
09:46 olass but I agree it is confusing :-)
09:47 olass how do I sort bugs on priority in mylyn?
09:47 olass Gpox?
09:47 egonw they are with me automagically
09:47 olass hmm, maybe here too
09:48 Gpox Choose sort in the view menu
09:48 olass ah
10:00 CIA-55 bioclipse: egonw * r8754 /bioclipse2/trunk/plugins/net.bioclipse.chemoinfor​matics/src/net/bioclipse/chemoinformatics/wizards/ (3 files): Set a default file name (implements part 2 of #461)
10:01 CIA-55 bioclipse: egonw * r8755 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: Made titles use the Eclipse scheme (fixes part 2 of #461).
10:03 egonw John Overington just joined the BlueObelisk mailing list
10:04 jonalv @tell edrin no I can not get the WSDb-fetch to work at all now :(
10:04 zarah Consider it noted.
10:07 edrin jonalv: what does it say?
10:07 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
10:08 edrin @msg
10:08 zarah edrin: 3 m 15 s ago, jonalv said no I can not get the WSDb-fetch to work at all now :(
10:08 jonalv edrin: nothing :(
10:08 edrin what does it do? what did you do?
10:08 jonalv I tried with that fasta that was suggested in the dialgo
10:08 jonalv nothing happended at all
10:08 jonalv or rather
10:08 jonalv I got the dialog with the result
10:08 jonalv but when I clicked finish it just cloased and then nothing happended
10:08 edrin and then?
10:08 edrin oh
10:09 jonalv the resource was not saved to foler and no editor was opended and no stacktrace was printed
10:09 edrin can you try with pdb?
10:09 jonalv see the bug
10:09 edrin huh?
10:09 jonalv I tried with pdb but it complained about missing the fasta file
10:09 jonalv which was doenlwoaded earlier and which I remoed
10:09 edrin pdb has nothing todo with fasta
10:10 jonalv I must be able to remove downloaded resources from that foler right?
10:10 edrin jonalv: ah, you deleted the fasta file?
10:10 edrin yes
10:10 jonalv yea I didn't want it any longer...
10:10 edrin how did you delete the file?
10:10 edrin with the bioclipse Explorer?
10:10 jonalv by delete in the context menu of Bioclipse explorer
10:10 edrin hm...
10:11 edrin and then it complained about missing this file!?
10:11 jonalv yup
10:11 jonalv (when I was downloading the pdb)
10:11 edrin ok, but this is not the webservice plugin then
10:11 jonalv (which is very strange...)
10:11 jonalv okey?
10:11 edrin this is the explorer not deleting files properly on your platform
10:12 edrin at least that's what I guess
10:12 jonalv uhm but just tell me what that has todo with dowloading that pdb resource. I mean it's not the same resource
10:13 edrin i think the eclipse navigators do not show you "the" files in the directory, but rather the entries in a database which reflect the files that eclipse thinks they exist in this directory...
10:13 jonalv olass: can you comment on this?
10:14 edrin jonalv: it most likely thought that the file already exists (because eclipse thinks it exists)
10:14 edrin and therefore did nothing
10:14 edrin jonalv: if you try the thing again, but change the final filename a little bit, i bet it works
10:14 maclean joined #bioclipse
10:14 edrin can you try?
10:15 jonalv I just removed the project and restarted
10:15 jonalv now I got two files there...
10:15 olass edrin: that is correct
10:15 edrin ah, ok, i now got it. it is different, the other way round
10:16 olass eclipse manages the workspace
10:16 olass that is why you need to "refresh"
10:16 olass at some points
10:16 olass it is stored as metadata
10:16 jonalv afk
10:16 edrin jonalv: its probably the other way round. you did not really delete the file but you deleted only the file-name from the eclipse database... ths it could not create the file ;)
10:19 jonalv okey
10:19 jonalv I am heading for lunch now
10:21 masak lunch &
10:21 jonalv lunch &
10:26 olass joined #bioclipse
10:45 egonw masak: using Perl again...
10:46 maclean hei egonw
10:46 egonw hi maclean
10:47 maclean I have a feeling that some of these fresh bugs in bioclipse-jcp could be solved by merging recent changes from jcp-primary...
10:47 egonw maclean: yes, agreed
10:47 egonw need to do that indeed
10:47 maclean ok, just thought I'd mention it - saw your merge plan :)
10:48 egonw good
10:48 egonw I hope you like it
10:48 maclean I do!
11:06 olass @tell jonalv: I'd like your decision on bug #475
11:06 zarah Consider it noted.
11:07 egonw olass: doing some work in HTML-izing extension points
11:07 olass great
11:07 egonw as I sort of need it for the CML content types anyway
11:07 * olass is updating the Bioclipse Help
11:07 olass so booring
11:08 olass but must be done
11:08 * egonw wonders if masak did get to proofreading stuff
11:08 olass likely not
11:14 * jonalv is back
11:14 jonalv zarah: ping
11:14 zarah jonalv: pong
11:14 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
11:15 jonalv @pz 475
11:15 olass @tell shk3: please attend to bug #476 asap.
11:15 zarah http://tinyurl.com/amp4rs
11:15 zarah Consider it noted.
11:16 olass jonalv: wanted your commment on that
11:17 maclean olass: shk is in Germany til tues
11:17 jonalv Do anyone here have any feelings regarding the ActionHistory view?
11:17 olass jonalv: is it working?
11:17 olass do we have a fully working use case?
11:17 jonalv olass: uhm define working please :)
11:17 olass not failing?
11:17 olass does what it is expected to do?
11:17 jonalv I haven't tried it in a long time
11:18 olass test it and document it if you have time
11:18 jonalv I don't think it is crashing but I am pretty sure that it doesn't do all that it is intended to do
11:18 olass well, it's your decision
11:18 olass I cannot judge if it should go in 2.0
11:19 jonalv perhaps postpone it
11:19 jonalv it's very untested stuff
11:19 olass ok, please uncomment it and file a bug for 2.1 t obring it back
11:22 CIA-55 bioclipse: ospjuth * r8756 /bioclipse2/trunk/plugins/net.bi​oclipse.usermanager/plugin.xml: Placed log in and log out actions in same menubar path so no separator between them in File menu.
11:22 olass jonalv: how can I tell if a user is logged in?
11:22 olass a pointer please?
11:23 jonalv olass: 475
11:23 jonalv wtf
11:23 olass ?
11:24 jonalv coyping from the new js console is borken. masak
11:24 olass oh, file urgent bug
11:24 olass important
11:25 jonalv masak: userManager.isLoggedIn()
11:25 jonalv olass: userManager.isLoggedIn()
11:25 * jonalv is confused now...
11:26 olass jonalv: why?
11:26 jonalv olass: it was just temporaily.
11:27 olass what was?
11:27 olass logged in?
11:27 olass will it be moved?
11:27 olass and to where?
11:27 jonalv it wasn't masak who should have that usermanager information it was you...
11:27 jonalv LOL
11:27 olass what information?
11:27 olass hmm, ok
11:28 jonalv olass: I am sorry I have really messed up this converation...
11:28 olass :-)
11:28 * olass will have lunch now
11:28 jonalv oki
11:28 olass in the afternoon I will work more on Help
11:28 olass then build rc1
11:28 olass or if we call it beta2
11:28 jonalv I think beta2 might be a better name
11:29 olass rc1 sounds much more finished than the current state IMO
11:29 jonalv I don't think we are ready for a RC
11:29 olass me neither
11:29 olass @lunch
11:36 CIA-55 bioclipse: carl_masak * r8757 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: various @PublishedMethod anno cleanups
11:41 masak olass: you're committing tabs. stop that.
11:42 maclean whitespace crime! :)
11:43 * masak ponders a version of Minority Report which prevents whitespace crime before it happens
11:43 Gpox i think it is called git
11:43 maclean well, they would just alter your eclipse editor profile, so that would be quite easy
11:43 CIA-55 bioclipse: egonw * r8758 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/business/IJmolManager.java: Updated text to make clear the optimized structure is not saved to file (addresses #478)
11:44 zarah bug #478 | http://tinyurl.com/bux9oa
11:44 masak Gpox++
11:44 masak maclean: aye.
11:44 masak but they'd do it before you hit the commit button.
11:44 maclean git predict-future ... I knew it!
11:45 masak it's been there since 1.5.1, come on!
11:45 maclean joined #bioclipse
11:45 masak maclean: did the precrime unit get to you? :)
11:46 maclean note to self : plugin network cable before shutting off wireless
11:46 masak hah
11:48 * olass is blushing
11:49 olass I change Eclipse too often :-(
11:49 egonw same here
11:49 egonw even switching workspace already looses the templates :(
11:50 masak egonw: only if you do it the wrong way.
11:50 egonw enlighten me
11:50 masak olass: 's OK. just don't do it again. :)
11:50 masak egonw: there's some clone capability.
11:50 masak jonalv++ is said to know the details.
11:50 * jonalv looks innocent
11:51 egonw and he's good at it
11:52 * maclean is intrigued, and wishes to subscribe to the newsletter
11:52 CIA-55 bioclipse: carl_masak * r8759 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
11:52 CIA-55 bioclipse: Revert "Added code to propagate focus from output to input on click. Not sure if this is desired behaviour, so placed TODO for masak and commented on bug #262."
11:52 CIA-55 bioclipse: This reverts commit e6a260c3f9734d363b6c844111526afc78dafe13. We don't want
11:52 CIA-55 bioclipse: to do it like this.
11:52 zarah bug #262 | http://tinyurl.com/b2vxgo
11:52 * olass imported tabless.xml (again)
11:53 masak maclean: in Soviet Russia, the newsletter subscribes to YOU!
11:53 maclean :)
11:55 masak and it is not intrigued in the slightest.
11:59 egonw masak: did you make any progress with integrating HTML?
11:59 egonw from managers, and other docs?
11:59 maclean I should stop reading a long argument about how to comment code, and do some work...
11:59 masak egonw: hm, haven't really looked at it yet.
11:59 masak but I'm between tickets now, so I'll take a look.
12:00 egonw no hurry, just wondering...
12:00 egonw I got another HTML generator around the corner
12:01 masak OK.
12:02 * jonalv is falling in love with jmol.minimize it's so cool :)
12:02 egonw hahaha
12:05 egonw olass: ping
12:05 olass pong
12:05 egonw olass: which extension points you want reports about?
12:05 * jonalv heads off to write a lab repport :/
12:05 olass hmm, all in release I guess
12:30 * egonw shall now update JCP in BC2
12:31 egonw which should fix several bugs
12:31 CIA-55 bioclipse: egonw * r8760 /bioclipse2/trunk/ (.gitignore ep2html.xslt makeExtensionsHTML.perl): Added a script to summarize the use of extension points (fixes #318)
12:31 zarah bug #318 | http://tinyurl.com/bjy687
12:48 masak egonw: http://gist.github.com/62605
12:48 masak egonw: taking a look at the source to see if I can pinpoint the errors myself.
12:49 egonw oh...
12:49 egonw mom
12:49 masak egonw: do I have your permission to change this file?
12:49 masak you're doing some things inefficiently.
12:49 egonw I suggest adding a -p here and there
12:50 egonw 'mkdir -p'
12:50 masak aye.
12:50 masak I'll do that first, and then attack the general structure of the script.
12:50 egonw ok
12:50 masak I see my Perl lecture will be much appreciated :)
12:50 masak s/Perl lecture/forthcoming Perl lecture/
12:51 masak left #bioclipse
12:51 masak joined #bioclipse
12:51 masak augh, Emacs :P
12:51 egonw oh, looking forward to that
13:03 masak wow, ^R (reverse-interactive-search) in bash FTW
13:04 olass Eclipse 3.5 M5 is released
13:04 olass we can REALLY soon move to java 1.6
13:04 olass http://download.eclipse.org/eclipse/downloads/d​rops/S-3.5M5-200902021535/eclipse-news-M5.html
13:04 zarah olass's link is also http://tinyurl.com/aepm7m
13:06 masak egonw: oh, and if you find heredocs hard to read, it might be because your editor doesn't satisfy all your colour-coding needs.
13:08 egonw right
13:08 maclean block selection, eh. hmmm.
13:08 masak maclean: what about it?
13:09 maclean in the new eclipse
13:09 masak ooh
13:09 masak that does come in handy sometimes
13:09 egonw that's cool
13:09 egonw the one feature of jEdit I missed in Eclipse
13:10 maclean ooh constructor completion!
13:13 egonw and detection of dead code
13:13 egonw PDE Tools->Internationalize...
13:14 egonw finally we get to make a Swedish Bioclipse
13:14 maclean oh good?
13:14 maclean And a Cornish one, of course. And Manxian.
13:14 masak Lojban Bioclipse.
13:15 egonw olass: when do you plan to make the switch? before or after 2.1?
13:16 olass no idea
13:17 olass not now
13:17 egonw clearly not now
13:19 masak egonw: cp: plugins/net.bioclipse.ui/html/developers/*: No such file or directory
13:19 egonw add a mkdir
13:19 CIA-55 bioclipse: carl_masak * r8761 /bioclipse2/trunk/makeHelpWebsite.pl:
13:19 CIA-55 bioclipse: [makehelp] changed "rm -Rf" to "rm -Rf output"
13:19 CIA-55 bioclipse: phew.
13:19 masak egonw: do you have a directory developers locally? I don't.
13:20 CIA-55 bioclipse: carl_masak * r8762 /bioclipse2/trunk/makeHelpWebsite.pl:
13:20 CIA-55 bioclipse: [makehelp] used "mkdir -p" pattern everywhere
13:20 CIA-55 bioclipse: instead of checking if there's already a dir from Perl with -d, which has a
13:20 CIA-55 bioclipse: number of shortcomings. there could for example be a non-dir there, making
13:20 CIA-55 bioclipse: the mkdir command fail silently.
13:20 masak egonw: add a mkdir so I can copy all the files from an empty directory? why?
13:20 egonw check the bioclipse1 folder
13:20 egonw there must have been sometihng
13:20 masak erm.
13:20 egonw rm -Rf is one thing
13:21 egonw but I'm not a complete idiot
13:21 masak I didn't say so.
13:21 masak I'm just trying to figure out what the script tries to do, and asking questions along the way.
13:22 egonw hehehe
13:22 masak right now I'm wondering why it gives error when trying to copy from a nonexistent directory.
13:22 egonw it's been a long while since I wrote this...
13:22 masak "add a mkdir" is a surreal reply to that.
13:22 egonw it's a kind of archeology
13:22 egonw sorry...
13:22 egonw I though you meant the target did not exist
13:23 egonw not that the source did not exist
13:23 masak it might, or it might not.
13:23 masak cp dies before that.
13:23 masak no, I think it exists.
13:24 egonw masak: svn co bioclipse/bioclipse/trunk
13:24 egonw cd bioclipse/bioclipse/trunk
13:24 egonw find . -name developers
13:24 * masak does that, somewhat reluctantly
13:24 masak I thought my job was to integrate scripts, not to do archeology... :P
13:25 egonw programming is partly archeology
13:25 masak yes, but these are your ruins...
13:25 egonw you're digging into history to figure out what the *peep* a piece of code is supposed to do
13:26 masak yes, that seems to be what I'm doing.
13:27 maclean I like code archeology.
13:28 egonw masak: it's not always as easy as writing Perl6
13:28 maclean But not in perl.
13:30 masak egonw: my complaint doesn't concern the exact choice of language, it's that this seemingly simple task suddenly expanded into a lot of yak shaving.
13:30 masak still checking out bc1.
13:30 egonw ah, that's where filing bugs comes in ...
13:31 masak I could do that. it's your script, after all.
13:32 egonw yes, sounds almost logical
13:32 * masak makes it so
13:32 egonw did you touch makeExtensionsHTML.perl already?
13:32 egonw will fix some things per your suggestions in that one too then
13:33 masak great.
13:33 masak no, didn't touch it.
13:33 masak haven't seen it yet, in fact.
13:35 masak but I'll probably keep touching makeHelpWebsite.pl though.
13:39 CIA-55 bioclipse: egonw * r8763 /bioclipse2/trunk/ep2html.xslt: Added bookmarks
13:45 CIA-55 bioclipse: egonw * r8764 /bioclipse2/trunk/makeExtensionsHTML.perl: Rewrite: use system() not backticks; use proper OPEN syntax
13:49 CIA-55 bioclipse: carl_masak * r8765 /bioclipse2/trunk/makeHelpWebsite.pl:
13:49 CIA-55 bioclipse: [makehelp] replaced `` command quotes with system()
13:49 CIA-55 bioclipse: The `` form should generally only be used when one is interested in the
13:49 CIA-55 bioclipse: output from the system command. There was one such occurrence in the script,
13:49 CIA-55 bioclipse: which I left alone.
13:57 grandm44 joined #bioclipse
13:58 CIA-55 bioclipse: goglepox * r8766 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Added accessor for properties coulmumns
13:59 CIA-55 bioclipse: goglepox * r8767 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui.sdfeditor/src/net/bioclipse/cdk/ui/​sdfeditor/editor/PropertySelector.java: Class for editing properties shown in molecule table
14:01 CIA-55 bioclipse: carl_masak * r8768 /bioclipse2/trunk/makeHelpWebsite.pl: [makehelp] corrected array initialization
14:01 CIA-55 bioclipse: goglepox * r8769 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (4 files):
14:01 CIA-55 bioclipse: Added page for editing visible properties in molecules table
14:01 CIA-55 bioclipse: fixes bug #174
14:01 zarah bug #174 | http://tinyurl.com/79fbdp
14:12 CIA-55 bioclipse: ospjuth * r8770 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (18 files in 9 dirs):
14:12 CIA-55 bioclipse: Usermanager plugin fixes:
14:12 CIA-55 bioclipse: * Renamed packages to start with net.bioclipse.usermanager
14:12 CIA-55 bioclipse: * Rewrote menu extensions to use org.eclipse.ui EP with Commands and Actions
14:12 CIA-55 bioclipse: * Implemented a propertytester to test if logged in an filter menu activation based on this
14:12 CIA-55 bioclipse: * Added menu option icons
14:12 CIA-55 bioclipse: Solves bug #188.
14:12 zarah bug #188 | http://tinyurl.com/ch6om7
14:25 maclean joined #bioclipse
14:32 masak olass: re #477. you're funny.
14:32 olass ?
14:32 masak olass: first you destroy the scripting console with a focus-changing commit...
14:32 masak ...and then you charge me to fix it.
14:32 masak :)
14:32 olass aha, it was ME who broke it!
14:32 olass hmm
14:32 olass well
14:32 masak I suppose so.
14:32 masak I will look at it.
14:33 olass technically it was you who uncommented my commmented out code if you remember?
14:33 masak no, I removed it all.
14:33 olass I said: "please revert all my changes"
14:33 masak I did.
14:33 olass hmm, then it wasn't me, right?
14:33 masak maybe not. I will look. :)
14:33 olass :-)
14:34 masak jonalv++ reported the same bug through the air earlier today.
14:34 masak it was then I realized that I still hadn't reverted your commit.
14:35 masak olass: no, worksforme.
14:35 olass jonalv reported it
14:35 olass not me
14:35 masak you were probably suffering from your own commit. :P
14:35 masak olass: ah, ok.
14:35 masak then you're not as funny as I thought. :P
14:43 edrin joined #bioclipse
14:56 CIA-55 bioclipse: egonw * r8771 /bioclipse2/trunk/ (ep2html.xslt makeExtensionsHTML.perl): More info: file extensions, plugin (with link to SVN)
15:01 olass egonw: around?
15:02 egonw yes
15:02 egonw about the InChI stuff...
15:02 olass it would be extremely nice if as much HTML as possible for a release could be generated
15:02 egonw when I do it...
15:02 olass ok?
15:02 egonw I see it complains about ambigous stereocenters...
15:03 egonw that's easy to work around...
15:03 egonw and probably best...
15:03 egonw it should not fail on that type of error
15:03 egonw will fix that
15:03 olass super
15:03 egonw olass: yes, agreed
15:03 olass then we can keep it in release
15:03 egonw wrt to the HTML bits
15:03 olass good
15:03 egonw masak is integrating scripts
15:03 olass super
15:03 * olass is working with the help sections
15:06 egonw about triple stores scalability: http://esw.w3.org/topic/LargeTripleStores
15:06 zarah egonw's link is also http://tinyurl.com/4m4oox
15:06 egonw 9.8 billion triples is the current edge
15:06 egonw though they estimate that system scales to 60B
15:06 egonw should be enough for everyone :)
15:07 egonw Gpox++
15:07 egonw really cool Headers TAB in the SDF editor
15:08 olass If I have time I will build beta2 today, else early tomorrow
15:08 olass will work in evening today
15:18 * egonw is updating JCP to the latest version
15:22 maclean great
15:22 egonw I guess we need some jcp/controllerhub support for making atoms radicals and add lone pairs, right?
15:23 maclean hmmm, yes true
15:23 egonw OK, no compile errors
15:25 egonw mmm... I'm seeing a few problems in JCP-SWT... :(
15:25 maclean oh?
15:26 egonw wrt to selections...
15:26 maclean yup?
15:26 egonw it does not change 'mode'...
15:26 egonw e.g. cannot lasso...
15:26 egonw also deselect does not work properly
15:27 egonw btw, rendering is *really* nice !
15:27 maclean well that's good at least
15:27 egonw 'highlight' is too small...
15:27 egonw it also highlights in the Outline...
15:27 egonw that's nice too...
15:27 maclean outline highlight is nothing to do with me
15:28 egonw I know
15:28 maclean size of highlight is controlled by setHighlightRadius(X)
15:28 maclean where X is in screen space
15:28 egonw still cannot draw on an empty pane :(
15:29 maclean hmmm.
15:29 maclean stacktrace?
15:29 egonw not sure what to do...
15:29 egonw revert, or apply changes...
15:29 egonw not sure if the current code in bc2 svn has the getclosestatom problems...
15:29 maclean well, I'm eager to fix these problems.
15:33 egonw reverted...
15:33 egonw will test what SVN has now...
15:33 egonw and see if that is better
15:34 olass masak: around?
15:34 egonw maclean: it is...
15:34 egonw current SVN has fewer bugs...
15:34 masak olass: aye.
15:34 olass masak: can zarah tell multiple people at the same time?
15:34 masak olass: no.
15:34 olass ok
15:34 masak you have to do it the hard way.
15:34 maclean >:-|
15:34 masak s/hard/"hard"/
15:35 olass @tell masak: please add yourself to page http://wiki.bioclipse.net/index.php?ti​tle=Bioclipse_Developers&amp;Itemid=20
15:35 zarah olass's link is also http://tinyurl.com/b2stnn
15:35 zarah Consider it noted.
15:35 olass @tell jonalv Please add yourself to page http://wiki.bioclipse.net/index.php?ti​tle=Bioclipse_Developers&amp;Itemid=20
15:35 zarah olass's link is also http://tinyurl.com/b2stnn
15:35 zarah Consider it noted.
15:35 maclean egonw: I think it's better to update and fix, than to revert
15:35 egonw just reverting locally...
15:35 olass @tell Gpox Please add yourself to page http://wiki.bioclipse.net/index.php?ti​tle=Bioclipse_Developers&amp;Itemid=20
15:35 egonw meaning...
15:35 zarah olass's link is also http://tinyurl.com/b2stnn
15:35 zarah Consider it noted.
15:35 masak @clear
15:35 zarah masak: Messages cleared.
15:35 egonw will not update to the latest JCP in BC2 now
15:36 egonw maclean: will need to talk to Gpox tomorrow why the new JCP is so much worse...
15:36 maclean sigh, ok.
15:36 egonw maclean: if you like...
15:36 egonw I could send you the changes
15:36 maclean ok!
15:36 olass I guess this setlles things. I will release tomorrow
15:36 egonw maybe you spot obvious problems...
15:36 olass just too many things in the air now
15:37 maclean egonw: quite possibly
15:37 egonw ok, hang on
15:37 edrin joined #bioclipse
15:38 masak olass: added.
15:39 olass masak: added what?
15:39 masak olass: myself to said list.
15:39 olass great
15:39 masak glad to be of help.
15:45 egonw maclean: #482
15:45 egonw @pz #482
15:45 zarah http://tinyurl.com/b36k93
15:45 maclean takk
15:46 masak olass, edrin: could either of you check lines 62..73 of plugins/net.bioclipse.webservices/src/net/bioclip​se/webservices/business/IWebservicesManager.java ?
15:46 egonw s#kk#ck#g
15:46 olass masak: would it be possible to generate a HTML list of all plugins and all features in SVN?
15:46 masak olass: absolutely.
15:46 olass the wiki page http://wiki.bioclipse.net/index.php?title=Plugins is hopelessly outdated...
15:46 zarah olass's link is also http://tinyurl.com/alwvxm
15:46 masak olass: I don't doubt it.
15:47 masak olass: find plugins/ -type d -depth 1
15:47 olass edrin: could you please check masaks webservices request?
15:47 egonw masak: that perl script does better...
15:47 egonw it just lists all plugins that are in features...
15:48 masak egonw: ok.
15:48 masak olass: what egonw said.
15:48 olass hmm, how do we get a small description into the list from the plugins?
15:48 masak olass: copy+paste?
15:48 olass I want the name, id, and a small description of what it does
15:48 olass can we not generate this HTML page in some way?
15:49 edrin masak: ok, looked at it
15:49 olass hmm, maybe things will not change overly much from now on...
15:49 edrin and now?
15:49 olass :-)
15:49 masak olass: better to generate wiki markup if it's to be on the wiki
15:49 olass true
15:49 masak edrin: notice how annotations are embedded in JavaDoc?
15:49 olass ah, that might be me
15:49 masak edrin: that makes my Perl script very confused.
15:49 masak olass: ok.
15:49 olass I commented it out since it should not be a published m,ethid
15:50 masak olass: when in doubt, delete.
15:50 masak do not comment out.
15:50 olass hmm, ok
15:50 masak please.
15:50 olass edrin: might you delete the annotations please?
15:50 edrin i cant i am not at home
15:50 masak I'll do it.
15:50 edrin sure
15:51 masak olass: even if commenting out the annotations would have been a good idea, you cannot have things like that inside a JavaDoc comment.
15:52 masak JavaDoc comments have syntax, just like the rest of Java.
15:52 olass ok ok
15:53 masak I'm not saying it just to nag. I'm saying it because my script dies when someone does that.
15:53 CIA-55 bioclipse: carl_masak * r8772 /bioclipse2/trunk/makeHelpWebsite.pl: [makehelp] removed depr bareword filehandles
15:54 CIA-55 bioclipse: carl_masak * r8773 /bioclipse2/trunk/plugins/net.bioclipse​.webservices/src/net/bioclipse/webservi​ces/business/IWebservicesManager.java:
15:54 CIA-55 bioclipse: removed JavaDoc-commented annotations
15:54 CIA-55 bioclipse: The manager documentation script picked these up as disturbances in the force.
15:55 egonw olass: there is no sample data feature, right?
15:55 egonw just the plugin
15:55 egonw which is int he bioclipse_feature
15:55 egonw correct?
15:55 * masak STR there's a sampledata feature
15:55 olass yes there is
15:55 egonw ah..
15:56 egonw indeed
15:56 egonw but not named _feature
15:56 egonw overlooked it
15:56 masak rename it! :)
15:56 olass the plugin net.bc.data has a very small sample data collection
15:56 olass which is extended by net.bc.data.sampledata plugin
15:56 olass but requires downloading
15:57 egonw olass: OK, drugbank feature depends on the features: bioclipse_feature, chemoinformatics_feature and smapledata_feature
15:57 olass no
15:57 olass not sampledata feature
15:57 egonw no?
15:57 egonw oh...
15:57 olass no
15:57 egonw that's the larger one?
15:57 olass no need for that
15:57 egonw in which feature is .bioclipse.data then?
15:57 olass bioclipse-feature
15:57 egonw that was sort of the question
15:57 egonw ok, good
15:57 egonw that's what I had to start with :)
15:57 olass did not understand that
15:57 olass sry
15:58 egonw I was not clear
15:58 egonw he, it's dinner time...
15:58 egonw need sugards
15:58 egonw need sugars
15:58 olass :-)
15:59 maclean mmm sugards
15:59 maclean (sorry, they sound good :)
16:00 CIA-55 bioclipse: egonw * r8774 /bioclipse2/trunk/features/ne​t.bioclipse.drugbank_feature/ (. .project build.properties feature.xml): Added the DrugBank feature (fixes #466)
16:00 zarah bug #466 | http://tinyurl.com/adtlte
16:12 masak maclean++
16:12 * masak wants sugards too now
16:12 maclean specifically, biscuity ones
16:12 masak mm, biscuity sugards...
16:13 maclean I found the problem in selections, and it's due to over-clever reflection magic. People : I recommend against reflection in java! It's not the language for it...
16:15 * maclean goes to the shops
16:15 masak maclean: you'll have to elaborate, but I'll take your word for it.
16:22 CIA-55 bioclipse: carl_masak * r8775 /bioclipse2/trunk/manager-apido​cs/parse-file-for-annotations:
16:22 CIA-55 bioclipse: [managerdocs] reduced some repetition
16:22 CIA-55 bioclipse: Perl++
16:22 CIA-55 bioclipse: carl_masak * r8776 /bioclipse2/trunk/manager-apido​cs/parse-file-for-annotations:
16:22 CIA-55 bioclipse: [managerdocs] fixed expressions so that it works
16:22 CIA-55 bioclipse: I'm not 100% sure, but it might have previously collected only the first hit,
16:22 CIA-55 bioclipse: instead of all of them.
16:23 egonw masak: ping
16:23 masak egonw: pong
16:23 * egonw is doing some more EP HTML conversion
16:23 masak ok.
16:23 egonw so please don't touch that perl script right now
16:24 masak I won't.
16:24 masak I'm in manager-docs
16:24 egonw ack
16:24 masak egonw: btw, I'd appreciate a review of those scripts, if you have time sometime.
16:25 egonw ok, file a bug report
16:25 egonw otherwise I'd forget
16:26 masak egonw: what's the observable? a paragraph of text?
16:26 egonw no, something you can measure
16:26 egonw 'observe'
16:26 masak I can measure text in paragraphs :)
16:27 egonw yeah, char counts...
16:27 egonw could be
16:27 egonw what's the context?
16:27 masak egonw: the ticket you asked me to create just now.
16:28 egonw oh sorry...
16:28 egonw 'the', not 'a'
16:28 * masak rolls his eyes patiently
16:28 egonw hehe... be nice to me, ok ...
16:28 masak :P
16:29 egonw umm...
16:29 egonw "provide comment on scripts" ?
16:29 masak ok, works.
16:29 * masak creates
16:29 * egonw is happy to see someone cares about observables...
16:29 egonw and the concept being used in bug reports
16:30 * masak doesn't like bugs that cannot be removed due to vagueness
16:30 masak s/removed/resolved/
16:30 maclean egonw : fixed the selection stuff.
16:30 egonw cool
16:30 maclean but can't reproduce the highlight problems
16:31 egonw shall I apply arvid's oval bond selection patch to jcp?
16:31 egonw to jcp-prim?
16:31 egonw if you apply your patches, I could try another update
16:32 maclean apply my patches to jcp-primary?
16:32 maclean it's like a 3 line change, anyway - just a missing constructor
16:32 egonw yes, please
16:32 maclean righto
16:33 egonw otherwise the patch may get lost later on...
16:33 egonw like I about overlooked the oval bond patch
16:33 egonw the thing is...
16:33 egonw I just overwrite whatever jcp control/ render/ code is in BC2 with that from jcp-prim
16:33 maclean I noticed with the oval bond selection that you get double ovals for double bonds
16:33 egonw not really apply patches
16:33 maclean hah! that's what I did too
16:34 egonw :)
16:34 maclean as I couldn't get your patch to apply
16:35 egonw that does not suprise me :)
16:35 edrin egonw: the article?
16:35 edrin :)
16:36 egonw edrin: sorry... still on my list for today :(
16:36 egonw my list is too long at this moment...
16:36 egonw really sorry about that...
16:36 edrin I expected this ..
16:36 edrin heh
16:36 egonw will try tonite... really...
16:36 edrin ok ;)
16:39 egonw maclean: how's that patch actually fixing problems?
16:39 egonw that was what you said about introspection?
16:39 maclean yup
16:39 egonw ic...
16:39 egonw ok...
16:40 maclean shk3 changed the constructor so that the relay handler could be added to the selection
16:40 CIA-55 bioclipse: carl_masak * r8777 /bioclipse2/trunk/manager-apido​cs/parse-file-for-annotations: [managerdocs] that variable should be an array
16:40 maclean reflection isn't bad as such, it's just that you don't get compile-time errors...
16:41 egonw indeed
16:41 maclean and it's so cumbersome in java that it's hard to ducktype or whatever
16:42 egonw maclean: how's the opinion on the UK on the Wilders case?
16:42 egonw he's an idiot...
16:42 egonw let me make that clear...
16:42 maclean he has strange hair
16:43 maclean (that's not the uk opinion)
16:43 egonw yes, that should be enough indeed...
16:43 egonw but that's just marketing...
16:43 egonw I'm sure he has a trademarket on it :)
16:43 egonw I share that opinion
16:43 maclean there was something about a muslim mp...
16:43 egonw yeah, he is disallowed to enter the UK
16:43 egonw but no clue why...
16:44 egonw if he would have been able to enter...
16:44 egonw they could not have disallowed him to speak to the parliament or so?
16:44 egonw and show his movei
16:44 egonw which is stupid, btw...
16:44 egonw and on his website anyway
16:45 egonw the problem is that he takes these things really to massage the public
16:45 egonw and getting votes for his intifada against the islam
16:45 egonw wrong idea, good politician :(
16:47 egonw you know, the dangerous combination...
16:47 egonw and the UK does not seem to know how to handle it...
16:47 egonw not that the NL really does...
16:47 maclean hmmm. milliband is claiming the "fire in crowded theater" defence
16:50 egonw milliband?
16:51 maclean oh uk politician
16:51 egonw ah, ok
16:51 * egonw reading news.bbc now
16:52 maclean I don't see why expressing an opinion, however repellant, should be banned.
16:52 egonw no, neither do I
16:53 egonw I mean, any MP would directly understand how stupid the movie is anyway...
16:53 egonw and Wilders has just what he wanted now...
16:53 egonw media attention
16:53 maclean one of our diplomats was recently charged when he went on a rant about the Israelis in a gym - undiplomatic, but not arrestable
16:53 egonw and focus on his movie
16:58 stain maclean: also his boss was jewish.. not very strategic
16:59 stain wasn't he like the Middle East envoy or something?
16:59 stain (or is that Blair?)
16:59 maclean oh it was extremely stupid
16:59 maclean yes, he was :)
17:00 stain that's why I never connect my headphones to the TV in the gym.. I always make silly comments like that at home towards the TV
17:01 egonw OK, dinner now
17:01 egonw bbl
17:03 maclean @tell egonw http://gist.github.com/62731
17:03 zarah Consider it noted.
17:18 masak I'm doing something wrong with Perl's sort function, and I can't figure out what.
17:19 olass masak: is Perl hard to understand?
17:19 masak olass: generally, no.
17:19 maclean hhahaaa
17:19 masak I could explain this code to you in a minute or so.
17:19 masak thing is, it doesn't work. :P
17:19 maclean <=>
17:19 masak and I don't know why.
17:19 masak maclean: alphabetic, so 'cmp'
17:20 maclean ahhh
17:20 masak but yes.
17:20 masak I have this expression:
17:20 masak $h->{$a}{Namespaces}[0] cmp $h->{$b}{Namespaces}[0]
17:20 masak and I've printed those values to see that they indeed contain what I think they do.
17:20 maclean ok
17:20 masak but The Thing Still Won't Sort.
17:21 maclean could you pasebin the code?
17:21 masak sure.
17:22 masak http://gist.github.com/62746
17:22 masak oh, and the Load function is from YAML
17:23 masak it returns a hash of stuff.
17:23 maclean sure
17:23 maclean hmmm. it sure looks like it should work
17:24 masak good. that makes two of us.
17:25 maclean although its a long time since I did any perl.
17:25 maclean is Namespaces a variable name
17:25 masak no, it's a hash key semi-deep in $h
17:25 maclean it can't be, as it has no sigl
17:25 masak keys autoquote in {} in Perl.
17:26 maclean oh right - dwim
17:26 masak or something.
17:26 masak I want to solve this before I go swimming.
17:27 maclean so @managers is returned unsorted?
17:27 masak yes.
17:27 masak that is, it's not sorted according to the order I expect.
17:28 masak in fact, it seems to be in the order it came in.
17:28 maclean right right
17:29 masak if I loop over 'map { $h->{$_}{Namespaces}[0] } keys %{$h}', it prints the values I want to sort on.
17:29 masak this is highly peculiar!
17:29 maclean it is
17:30 masak it reports them as scalars, so there's nothing funny going on.
17:30 masak could this be a bug in Perl 5.8.8?
17:30 maclean could be
17:30 masak I'll try and factor the YAML out of it and reproduce it.
17:30 maclean multilevel data structures or so
17:33 masak the bug survived the factoring-out. making a gist out of it and hitting the closest #perl channel.
17:34 maclean ok
17:34 masak :/
17:35 masak it didn't, however, survive being placed in a separate script file.
17:35 masak I'm dealing with high-level deamons here.
17:35 maclean : {
17:37 masak ah, but I found the line that I need to include to re-reproduce the bug. :)
17:37 masak it's this one:
17:38 masak my $a = join "", <>;
17:38 maclean hmm
17:39 masak do tell me if I'm missing something important here.
17:39 masak also, feel free to try and reproduce it.
17:39 maclean well <> is stdin, right? So you get "allthelinesofafilejammedtogether"?
17:40 masak maclean: yes, but note that I never use that variable.
17:40 masak OH!
17:40 masak AH!
17:40 masak nevermind.
17:40 maclean ok
17:40 masak :(
17:40 masak "never call a variable $a in your Perl program"
17:40 masak damn.
17:40 maclean why?
17:40 masak because it's magical.
17:40 masak it's used in &sort
17:41 maclean should have known
17:41 maclean hah! (sorry)
17:41 maclean this is why I use python...
17:41 masak I really should have known...
17:41 masak this is why I use Perl 6...
17:42 maclean true :)
17:42 masak but once again, the scientific method prevails!
17:42 masak science++
17:42 maclean http://community.activestate.co​m/faq/perls-magic-sort-variable
17:42 zarah maclean's link is also http://tinyurl.com/dngn9w
17:42 maclean $b as well, apparently
17:43 masak yes, naturally.
17:43 masak in Perl 6, those are $^a and $^b, but it's really much more beautiful than that.
17:44 maclean then again, in python I have made the mistake of using 'file' as a variable
17:44 masak it works \o/
17:44 maclean yay!
17:45 masak http://pele.farmbio.uu.se/manager-docs/
17:45 zarah masak's link is also http://tinyurl.com/aqykgf
17:47 masak swimming, here I come!
17:47 CIA-55 bioclipse: carl_masak * r8778 /bioclipse2/trunk/manager-apido​cs/parse-file-for-annotations: [managerdocs] now finds managers' namespaces
17:48 CIA-55 bioclipse: carl_masak * r8779 /bioclipse2/trunk/manager-apidocs/render-as-html:
17:48 CIA-55 bioclipse: [managerdocs] now sorted by namespace name
17:48 CIA-55 bioclipse: Also, kids: never call a global variable $a or $b in a Perl 5 program. It took
17:48 CIA-55 bioclipse: me far too long to find why the sorting was broken.
18:08 CIA-55 bioclipse: ospjuth * r8780 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (45 files in 11 dirs): Much work on Welcome/Intro and general Bioclipse Help.
18:21 CIA-55 bioclipse: ospjuth * r8781 /bioclipse2/trunk/plugins/net.bioclipse.ui/html/ (6 files in 4 dirs): Added a general overview of the Bioclispe workbench in Help.
18:37 maclean olass : is there a way to restore the welcome screen once you've been using bioclipse for a while?
18:39 maclean hmm, if I could switch the workspace, then I could..
18:59 egonw back
18:59 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
18:59 egonw @msg
18:59 zarah egonw: 1 h 56 m 9 s ago, maclean said http://gist.github.com/62731
19:00 maclean it's one option...
19:00 egonw looks good
19:00 egonw on the other hand
19:00 egonw this does not allow recording...
19:00 maclean oh?
19:01 egonw r.bla = x
19:01 egonw it's not a procedural call...
19:01 egonw so Spring can't pick it up, I think
19:01 egonw that is...
19:01 maclean well it works nicely, anyway
19:01 egonw this doesn't go via a manager
19:01 maclean ahh.
19:02 egonw maybe that is not needed...
19:02 maclean well.
19:02 egonw but could be a nice way to define stylesheets for htings
19:02 egonw ACS has a stylesheet for 2D chem diagrams
19:02 egonw and people need to use that
19:02 maclean true
19:04 maclean oh, and I forgot to add jcp.updateView() to the gist...
19:04 egonw yes
19:05 egonw but I had that in mind nevertheless
19:05 egonw obvious
19:05 egonw will try to update jcp-prim tonite...
19:05 egonw but want to finish a bit of xslt magic first
19:06 maclean fair enough
19:20 egonw olass: "Text Editor Wee" ??
19:21 egonw OK, one culprit down
19:21 egonw oh, and let's not forget "Text Editor Wee2" :)
19:25 maclean dammit. fit-to-screen doesn't work properly.
19:49 * egonw is only making slow progress... :(
19:57 olass egonw: haha
19:57 olass remnants
19:57 olass wil lremove them
19:58 egonw OK, got some reasonable starting point for EP documentation...
19:58 egonw hang on...
19:58 egonw uploading to Pele now...
19:58 CIA-55 bioclipse: ospjuth * r8782 /bioclipse2/trunk/plugins/net.​bioclipse.ui/html/glance.html: Fixed spelling error.
19:59 egonw http://pele.farmbio.uu.se/bio​clipse/docs/eps/ep.index.html
19:59 zarah egonw's link is also http://tinyurl.com/d4cwxn
20:00 egonw enough room for improvement... making cross links etc
20:00 egonw but should give a good summary of things
20:02 egonw http://intellectualcramps.blogspot.com/2009/02​/how-to-build-xsl-tools-with-ant4eclipse.html
20:02 zarah egonw's link is also http://tinyurl.com/clmjse
20:02 egonw that looks quite good!
20:02 egonw really clean
20:02 egonw for building bioclipse...
20:04 maclean_ joined #bioclipse
20:10 egonw @tell masak  http://pele.farmbio.uu.se/bioclipse/docs/eps/
20:10 zarah egonw's link is also http://tinyurl.com/czt988
20:10 zarah Consider it noted.
20:12 CIA-55 bioclipse: egonw * r8783 /bioclipse2/trunk/ (ep2html.xslt makeExtensionsHTML.perl): More EPs are now supported and summarized in HTML
20:16 * edrin gone
20:16 edrin left #bioclipse
20:31 olass ok, gotta go
20:31 olass cu tomorrow
20:31 olass bye
20:45 CIA-55 bioclipse: egonw * r8784 /bioclipse2/trunk/ep2html.xslt: 1. Use ID of no name is available; 2. report some details for script contributions
20:45 CIA-55 bioclipse: egonw * r8785 /bioclipse2/trunk/makeExtensionsHTML.perl: Having the EP id is more informative then its main element
21:30 egonw grmph...

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