Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-06

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All times shown according to UTC.

Time Nick Message
06:46 olass joined #bioclipse
06:46 olass moin
06:46 zarah privet olass
06:50 masak joined #bioclipse
07:01 Gpox joined #bioclipse
07:52 edrin joined #bioclipse
07:53 edrin hi
07:53 zarah privet edrin
07:53 edrin morning
07:55 masak privet
07:58 jonalv joined #bioclipse
07:58 jonalv hi
07:58 zarah oh hai jonalv
08:01 masak oh hai jonalv
08:30 CIA-58 bioclipse: jonalv * r9592 /bioclipse2/trunk/plugins/net.biocl​ipse.specmol/src/net/bioclipse/spec​mol/business/SpecmolManager.java: I am not an author of the SpecmolManager
08:33 shk3 joined #bioclipse
08:40 shk3 hi all
08:40 zarah hi shk3
08:41 shk3 how are things going for bioclipse2?
08:42 egonw joined #bioclipse
08:46 jonalv o/
08:46 shk3 what does that mean?
08:46 egonw that's Yoda with a light saber
08:46 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:47 egonw @msg
08:47 zarah egonw: 2 d 15 h 46 m 28 s ago, maclean said I had to comment out the section of the net.bioclipse.cml plugin's plugin.xml where it mentions "org.eclipse.wst.xml.core.catalogContributions" as I can find no way to fix it.
08:47 egonw @tell maclean: as long as you do not commit, please file a bug report about the lack of any decent documentation about which plugin/feature to install to get that dependency
08:48 zarah Consider it noted.
08:48 egonw @tell maclean: sorry about the inconvenience
08:48 zarah Consider it noted.
08:59 CIA-58 bioclipse: ospjuth * r9593 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Rewrote QsarResult to contain the DescriptorType, not just the descriptorID since we can have multiple combos of ontologyID + parameter.
08:59 CIA-58 bioclipse: ospjuth * r9594 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated cdk descriptor calc and tests to return required descrptorType.
09:32 jonalv olass: is only Brunn using the UserManager or is there some other plugin?
09:32 olass I think only brunn
09:33 jonalv there seems to be a bug in it butif only brunn is affected then I think I will note it and leave it for later...
09:42 olass ok
09:43 CIA-58 bioclipse: ospjuth * r9595 /bioclipse2/trunk/plugins/net.bioclip​se.qsar.ui/src/net/bioclipse/qsar/ui/ (4 files in 3 dirs):
09:43 CIA-58 bioclipse: * Fixed removal of descriptors to remove results and providers if needed
09:43 CIA-58 bioclipse: * Refactored out preferences to QsarHelper for caching state of descr/mol combos
09:43 CIA-58 bioclipse: * Fixed builder to build non-built descriptors even if unchanged
09:43 CIA-58 bioclipse: * Adapted to API change for DescriptorResults to hold DescriptorType, not just ID
09:43 CIA-58 bioclipse: * Updated DescriptorPage to not cache QsarModel since changed in Builder did not propagate
09:50 CIA-58 bioclipse: ospjuth * r9596 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorsPage.java MoleculesPage.java QsarEditor.java): Updated MoleculesPage to not cache QsarModel but always get latest from QsarEditor. Solves sync prob when builder has changed results.
09:57 CIA-58 bioclipse: ospjuth * r9597 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Refactored out removal of descriptors to Manager.
10:18 CIA-58 bioclipse: ospjuth * r9598 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (OverviewPage.java QsarEditor.java ResponsesPage.java): Updated OverviewPage and ResponsesPage to not cache QsarModel but always get latest from QsarEditor. Solves sync prob when builder has changed results.
10:51 jonalv egonw: do you know of a Jmol command that will give me what is selected?
10:52 egonw there is a get state command somewhere
10:52 egonw this might give you what is selected too
10:54 jonalv egonw: okey, do you know where?
10:55 egonw not off the top of my head
10:56 jonalv oki
11:20 CIA-58 bioclipse: ospjuth * r9599 /bioclipse2/trunk/plugins/net.bioclipse.qsar.​ui/src/net/bioclipse/qsar/ui/QsarHelper.java: Removed logging for preferences.
11:27 CIA-58 bioclipse: carl_masak * r9600 /bot/trunk/zarah.pl: [zarah] now allows colon between 'bug' and digits
11:27 masak zarah: reboot, please.
11:28 zarah joined #bioclipse
11:28 CIA-58 bioclipse: jonalv * r9601 /bioclipse2/trunk/plugins/net.bioc​lipse.jmol/src/net/bioclipse/jmol/ (7 files in 4 dirs):
11:28 CIA-58 bioclipse: Now Jmol actions are run on selections if anything is selcted, if nopthing is selected "select all" will be run before the action just as before. Fixes bug #603.
11:28 CIA-58 bioclipse: Also changed way of avoiding loop when responding to Jmolselections. Added a boolean so this should be as good as bullet proof. (yes I found a case when the old fix didn't work...)
11:28 zarah bug #603 | http://tinyurl.com/d63pu5
11:33 jonalv @pz writing things to jmol console
11:33 zarah jonalv: I couldn't find anything on 'writing things to jmol console' in the database.
11:33 jonalv @pz writing  jmol console
11:33 zarah jonalv: Zarro boogs found.
11:34 masak @pz writing jmol console
11:34 zarah masak: I couldn't find anything on 'writing jmol console' in the database.
11:34 * masak prefers 'Zarro boogs found'
11:48 jonalv egonw: does Jmol create a new thread for each script or is there one thread processing each script?
11:48 egonw dunno
11:48 jonalv :(
11:49 * jonalv is trying to figure out what to do about @pz 726
11:49 jonalv zarah?
11:49 jonalv zarah: ping
11:49 zarah jonalv: pong
11:50 jonalv zarah: bug 726
11:50 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=726
12:16 CIA-58 bioclipse: jonalv * r9602 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/splash.bmp: updated Copyright notice to 2006-2009
12:17 jonalv oh that fixed 531
12:17 jonalv bug 531
12:17 jonalv zarah: bug 531
12:17 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=531
12:17 jonalv zarah--
12:18 CIA-58 bioclipse: ospjuth * r9603 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.model/ (5 files in 3 dirs): Set default response value to NaN.
12:23 shk3 hi everybody
12:23 shk3 what are plans for the release right now?
12:23 shk3 anything I can help with?
12:25 olass shk3: documentation and cheatsheets
12:25 olass shk3: could I assign a cheatsheet in cheminfo to you?
12:25 shk3 I would do my best
12:25 olass mom
12:26 shk3 we should cross-read our stuff
12:26 shk3 but I will have a go
12:26 olass shk3: see bug #349
12:26 olass @pz 349
12:26 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=349
12:27 olass shk3: then there is documentation in help system
12:27 olass maybe you could help egonw with some simple documentation on JCP?
12:27 olass that is bug #735
12:28 shk3 I can do for jcp
12:28 shk3 and perhaps for cdk
12:29 shk3 other plugins really need to be done by those people who did them
12:30 olass indeed
12:30 olass I have given out tickets for this
12:31 olass but egon is so busy, would be great if you could help him out a bit
12:31 olass and you know cdk and jcp very well :)
12:38 egonw shk3: I would indeed much appreciate if you could copy/paste some drawing documentation...
12:38 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
12:39 egonw menu docs are less relevant, as they are different, AFAIK
12:39 egonw @msg
12:39 zarah egonw: 2 m 1 s ago, jonalv said We need to book that half hour for fixing bug 688: Bring back the Jmol view.
12:39 egonw jonalv: later...
12:39 egonw the original VRNT plan (beaf up the science bits, but do not change too much) did not work out...
12:40 egonw so, now actually considerably rewriting the application
12:40 egonw this is top priority
12:40 egonw until that is done, no CDK, no Bioclipse, and nothing much else
12:41 egonw maybe, if lucky, some sleep here and there
12:46 shk3 egonw: I will try to do jcp and cdk documentation as much as possible
12:46 shk3 and you should then look at it
12:47 egonw keep in mind that the CDK manager documentation is available already from the plugin net.bioclipse.doc
12:48 egonw and that that will be complemented with example scripts from our gist collection
12:48 egonw please file a ticket at Pele when you are done and I can check it
13:22 shk3 major problems:
13:23 shk3 when I create a new document the bond length is way to large,
13:23 shk3 so drawing makes a mess
13:23 shk3 and neither the element symbols in the toolbar nor the hover-and-press-button are there,
13:24 shk3 so it seems the context menu is the only option you have for changing element.
13:24 shk3 too complicated if you have to change like 10 Os and Ns in your new structure.
13:25 jonalv for me the tool works but only for one atome a time...
13:25 shk3 which tool?
13:26 jonalv we are talking about jchempaint here are we not?
13:26 shk3 yes
13:26 shk3 jcp in bc
13:26 jonalv second from the left
13:26 shk3 ah right
13:26 shk3 the cycle symobl
13:26 shk3 that exists as well
13:27 shk3 it's for one atom only
13:27 shk3 how should it work for several ones?
13:27 shk3 what should that look like from the users perspective to change more than one, I mean?
13:28 jonalv I don't know
13:28 jonalv but you where talking about chaning 20 atoms...
13:28 masak I don't know exactly when, but zarah turned 1.5 kLOC recently.
13:28 jonalv so I trioed to find an easy way
13:28 shk3 ah sorry
13:28 jonalv I think best would be context meny on multiple selection...
13:28 shk3 in swing jcp we have buttons for them
13:29 shk3 so you choose O and do click, click, click
13:29 shk3 but that's not a major problem.
13:29 shk3 The cycle symbol is ok
13:29 shk3 another problem: Is there any way to set a symbol not in cycle symbol and the context menu?
13:30 shk3 How do I set e. g. Selenium?
13:30 * jonalv has no idea...
13:30 jonalv Gpox: ?
13:30 masak three cheers for zarah!
13:30 zarah hooray! hooray! hooray! :)
13:30 masak :)
13:32 Gpox There is a bug about that
13:32 shk3 good
13:32 shk3 will put a TODO into help
13:35 jonalv do anyone know about a manager method that should be run as a job but which is not working on a file?
13:39 edrin left #bioclipse
13:44 * jonalv takes that as a no and downproritices the bug related to such methods...
13:45 masak jonalv: I can imagine such a method, but I don't know of any.
13:45 jonalv masak: about the same here...
13:49 shk3 what's the reason for doing a net.bc.doc plugin?
13:50 shk3 shouldn't documentation be in the respective plugins?
13:50 masak shk3: not all of it, I think.
13:52 shk3 hm, right now it's empty
13:53 egonw shk3: no, it's just that the autogeneration is not yet triggered by Eclipse... (ticket filed and assigned to me)
13:54 shk3 ah
13:54 shk3 ant that generates scripting doc from the managers?
14:01 egonw yes
14:01 shk3 thanks
14:02 shk3 another question:
14:02 egonw except that it is Perl, and there is no ant wrapper
14:02 shk3 net.bc.cdk.jcp defines several editors,
14:02 shk3 including one which has no contentTypeBinding
14:02 shk3 what is this for?
14:03 egonw the answer to that is pending
14:03 egonw think along the line of:
14:03 egonw MDL molfile has meta data, which you might want to edit in an extra tab
14:04 egonw likewise CML can contain an InChI, but does not by default...
14:04 egonw an extra tab could support that rather useful feature
14:05 egonw need to checkout a house in the nearby area now...bbl
14:06 shk3 right. but what has the extra editor to do with it?
14:06 shk3 anyway,
14:06 shk3 I see all jcp editors have the same ID
14:06 shk3 doesn't seem to do harm, but looks odd.
14:12 CIA-58 bioclipse: shk3 * r9604 /bioclipse2/trunk/plugins/net​.bioclipse.spectrum/toc.xml: better not start label with The
14:17 CIA-58 bioclipse: jonalv * r9605 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/business/JmolManager.java: Fixed a NullPointerException that occured in some circumstances
14:19 CIA-58 bioclipse: jonalv * r9606 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src/​net/bioclipse/jmol/actions/RunScriptHandler.java: only add "select all" "select none" around non select scripts as well as only when nothing is already selected.
14:26 CIA-58 bioclipse: ospjuth * r9607 /bioclipse2/trunk/features/ (2 files in 2 dirs):
14:29 CIA-58 bioclipse: ospjuth * r9608 /bioclipse2/trunk/plugins/net.bioclipse.qsar/sr​c/net/bioclipse/qsar/business/QsarManager.java: Remove descriptorresults if resource is removed.
14:30 CIA-58 bioclipse: ospjuth * r9609 /bioclipse2/trunk/plugins/net.bioclip​se.qsar.ui/src/net/bioclipse/qsar/ui/ (5 files in 3 dirs): Overviewpage now shows synced content.
14:47 jonalv I have lost my Bioclipse workspace!
14:47 jonalv I had stuff there :(
14:48 jonalv I hate this operating system
14:50 jonalv olass: ?
14:50 olass yes?
14:51 olass ask shk3
14:51 olass he's in charge of that
14:51 jonalv do you know if it is gone forever?
14:51 olass did you say 'clear workspace' ?
14:51 shk3 starting from eclipse?
14:51 jonalv olass: no
14:51 jonalv shk3: yes
14:51 olass then it should be around
14:51 olass search the computer
14:52 jonalv olass: seems we have changed default location now
14:52 shk3 this should still be defined via the run configuration
14:52 shk3 but it's not
14:52 olass yes, that is shk3's doing
14:52 jonalv I looked at the old location but I can't find anything... :(
14:52 shk3 I check this
14:52 shk3 everybodyl blaming poor shk3 :-(
14:52 jonalv I am not blaming anyone I just wonder if my data is lost...
14:53 masak FWIW, I think /Users/masak/bioclipse-workspace is a less-than-ideal default location for the Bioclipse Workspace on Mac OS X.
14:53 shk3 don't think so
14:53 masak maybe I should write that in the email thread? :)
14:53 jonalv I had an example js script there which I was working on to include in Bioclispe example data...
14:53 shk3 have a look if ${workspace_loc}/../runtime-bioclipse.product is still on your disk
14:53 shk3 if yes, it's not lost
14:54 jonalv shk3: sry? It has changed...
14:54 shk3 yes
14:54 jonalv masak: what is wrong with that location?
14:54 shk3 but the workspace used to be ${workspace_loc}/../runtime-bioclipse.product
14:54 shk3 in the run config
14:54 masak jonalv: it belongs to the user, not to applications.
14:55 shk3 this directory should still be there even if not used
14:55 masak http://www.codinghorror.com​/blog/archives/001032.html
14:55 zarah masak's link is also http://tinyurl.com/2rruve
14:55 jonalv masak: I don't understand what you are saying. If I used Bioclipse and wanted to browse the files in the bioclipse workspace from outside that is where I would look for the folder.
14:55 jonalv masak: where would you look?
14:56 masak jonalv: the "Application Support" folder.
14:56 shk3 right now, in home/bioclipse-workspace
14:56 masak that's where things like this belong.
14:56 masak that's what it's for.
14:56 jonalv masak: application support is whre things that you should not touch belongs
14:56 masak that's how all responsible applications do.
14:56 masak jonalv: no, it's not.
14:56 jonalv masak: yes it is, it screams don't touch me when you browse that area of the computer
14:57 jonalv I mean common, Application support
14:57 masak jonalv: did you read the linked blog post?
14:57 jonalv masak: no I missed that, where?
14:57 masak jonalv: jonalv: I think it's bad to put
14:57 masak jonalv: jonalv: I think it's bad to put
14:57 masak argh!
14:57 masak http://www.codinghorror.com​/blog/archives/001032.html
14:57 zarah masak's link is also http://tinyurl.com/2rruve
14:57 jonalv masak: a case of the stutters?
14:58 masak yes, Firefox is too slow.
14:58 masak it doesn't react to my Copy shortcut.
14:58 masak jonalv: I think it's bad to put things in the user's home directory.
14:58 masak it's bad both for philosophical and practical reasons.
14:59 olass masak, jonalv: I wrote about this in bioclipse-devel
14:59 masak the latter because the user might not be aware that anything in her home directory is needed by an application.
14:59 olass did you not see these emails?
14:59 masak olass: aye.
14:59 masak didn't react, though.
14:59 olass I got the impression that all liked it apart from me
14:59 masak I must have been busy with other things.
14:59 olass :)
14:59 jonalv olass: I sae those mails yes and I did not disagree. I just wonder if my old data is gone now...
14:59 masak I'm reacting now. :P
14:59 olass jonalv: can you not search your computer?
15:00 jonalv olass: no :(
15:00 olass ok
15:00 jonalv I hate this operating system...
15:00 olass unix?
15:00 masak FWIW, I cannot find my old dir either.
15:00 jonalv well I guess that explains why my searches have failed...
15:00 olass user.home/Library/Application Support/Bioclipse
15:00 olass that was the old default
15:01 olass user.home/Library/Application Support/Bioclipse/Bioclipse-workspace maybe
15:01 olass (this is all from memory)
15:01 masak olass: I like that.
15:01 olass yes
15:01 shk3 just sent an email to the list
15:01 shk3 regarding this.
15:01 olass but shk3 did not agree and removed it
15:01 olass even though he's not on mac ;)
15:02 olass shk3: sory for blaming you
15:02 jonalv I don't have that folder...
15:02 olass I guess it is good to have same on linux and mac
15:02 jonalv it must have been removed somewhow...
15:02 olass I am happy with any place, as long as we decide it and stick with it
15:02 jonalv masak: where would you expect it on linux?
15:02 masak jonalv: /dev/null? I don't know...
15:03 shk3 olass: I would need to research how to detect platform in code.
15:03 masak jonalv: maybe /usr/share or something.
15:03 shk3 then it would be no problem to use that location on mac.
15:03 masak jonalv: but Linux file hierarchies are somewhat hairy...
15:03 * jonalv is beginning to think that Eclipse does it right and begins by asking where to save the shit...
15:03 shk3 I don't really mind
15:04 masak jonalv: I'd like a T-shirt with "Where can I save my shit?" written on it.
15:04 olass jonalv: default is home.dir/workspace
15:05 olass we decided home.dir/bioclipse-workspace
15:05 olass shk3: am I correct?
15:05 jonalv olass: and I like that
15:05 shk3 yes
15:05 shk3 for all platforms
15:06 * masak doesn't like, for the above reasons
15:07 CIA-58 bioclipse: shk3 * r9610 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (8 files in 2 dirs): created help for jcp
15:10 shk3 egonw: you saw my commit?
15:11 egonw 9160?
15:11 egonw 9610...
15:11 egonw yes
15:11 egonw please still file a ticket
15:11 * jonalv mourns his old data...
15:11 shk3 sure
15:11 jonalv anyone know where I can get the big.sdf again?
15:11 shk3 which plugin should the chemoinformatics cheat sheet go into?
15:11 shk3 from cdk
15:12 shk3 test data
15:12 masak jonalv: you should ask Magnus for a backup.
15:12 shk3 shall I email it to you?
15:12 jonalv masak: haha
15:12 masak jonalv: no, really.
15:12 masak that's what they're for.
15:12 jonalv shk3: oh that would fill up my inbox sort...
15:12 masak restoring lost data.
15:14 jonalv bah, /me goes and pays Magnus a visit...
15:16 egonw jonalv: next time... use a content version system on top of the backups
15:16 egonw that saves you some swearing from Magnus
15:16 egonw acutally ...
15:16 egonw dunno if he swears...
15:16 egonw but it will save you some funny looks at least :)
15:17 masak he might recoice, or just laugh.
15:17 masak or do a funny dance.
15:17 masak the "It's time to retrieve jonalv's backups" dance.
15:17 * jonalv just realises what time it is...
15:17 masak or maybe he won't be there.
15:18 CIA-58 bioclipse: shk3 * r9611 /bioclipse2/trunk/plugins/net.bioclipse.spectr​um/cheatsheets/GeneralSpectrumCheatSheet.xml: wrong title
15:18 jonalv egonw: a content management system on my entire disk?
15:18 jonalv egonw: this wasn't even in my home folder you know...
15:18 egonw jonalv: yeah, why not?
15:19 jonalv egonw: are _you_ having that?
15:19 * masak has it for his homedir
15:19 egonw I have all the important bits in a cvs, yes
15:19 masak egonw and CVS! hah!
15:19 jonalv I didn't even know that the Application Data folder existed much less that it was important
15:19 jonalv I hate this OS...
15:27 masak ignorance is a strange reason for hate.
15:27 masak not an uncommon one, though.
15:40 jonalv masak: skit på dig!
15:40 CIA-58 bioclipse: jonalv * r9612 /bioclipse2/trunk/plugins/net.bioclipse​.data/data/Javascripts/jmolExample.js: added an example script jmolExample.js to example data. It makes a 3d model for glucose from SMILES and does some fancy visualization in Jmol.
15:40 masak jonalv: you are so full of hate today.
15:45 CIA-58 bioclipse: shk3 * r9613 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (html/sdfEditor.html toc.xml): will fill this soon, this is just to make sure the filename is fixed
15:51 jonalv three cheers for masak on his namesday
15:51 zarah hooray! hooray! hooray! :)
15:52 masak \o/
15:52 masak jonalv: I think you're the second person to ever use the 'three cheers' function in zarah.
15:53 olass three cheers for masak on his namesday!
15:53 zarah hooray! hooray! hooray! :)
15:53 olass that makes me the third :)
15:53 masak aye. :)
15:53 masak three cheers for three people using the 'three cheers' function!
15:53 zarah hooray! hooray! hooray! :)
15:53 masak it gets old quickly, though. :)
15:53 jonalv very...
15:54 jonalv copycats
15:54 jonalv Ö=
15:54 jonalv oh
15:54 jonalv hm
15:54 jonalv swedish
15:54 jonalv :)
16:05 CIA-58 bioclipse: shk3 * r9614 /bioclipse2/trunk/plugins/net.bioclipse.spectr​um/cheatsheets/GeneralSpectrumCheatSheet.xml: correct numbering
16:07 shk3 the chemoinformatics feature says it includes something called net.bc.inchi.
16:07 shk3 but there is only net.bc.inchi.business
16:07 shk3 or am I missing something?
16:19 CIA-58 bioclipse: ospjuth * r9615 /bioclipse2/trunk/plugins/net.bioclip​se.qsar.ui/src/net/bioclipse/qsar/ui/ (builder/QSARBuilder.java editors/QsarEditor.java): Updated new builder to generate CSV containing the dataset.
16:42 CIA-58 bioclipse: shk3 * r9616 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (6 files in 4 dirs): added a chemoinformatics cheat sheet
16:48 CIA-58 bioclipse: shk3 * r9617 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (3 files in 2 dirs): put cheat sheet into welcome
17:01 CIA-58 bioclipse: shk3 * r9618 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/html/concepts.html: added something about workspace switching
18:58 edrin joined #bioclipse
18:58 olass joined #bioclipse
18:58 olass hi edrin
18:58 edrin hi ola
19:01 * shk3 is leaving for today
19:58 edrin left #bioclipse

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