Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-23

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All times shown according to UTC.

Time Nick Message
07:32 olass joined #bioclipse
07:32 olass moin
07:32 zarah hi olass
07:56 Gpox joined #bioclipse
07:56 egonw joined #bioclipse
08:02 egonw moin
08:02 zarah hello egonw, you fantastic person you
08:03 egonw Gpox: please let me kno w when you have time to discuss some issues regarding editors and non-IFile resources
08:10 Gpox tomorrow maby when i am in Uppsala? what is the issues?
08:14 egonw the issue is the following...
08:14 egonw I was working on opening  a new resource from in memory content
08:14 egonw NewMolecule, NewJavaScript
08:14 egonw which opens up an editor, but did not create a IFile resource yet
08:14 egonw like
08:14 egonw UntitledTextFile wizard
08:14 egonw which opens a new TextEditor
08:14 egonw now
08:15 egonw the problem is
08:15 egonw that
08:15 egonw the JavaScript editor (and XML-Lite editor too)
08:15 egonw require a IFile resource
08:15 egonw and I have not clue how to get those fixed
08:16 egonw to work like TextEditor and do not require a IFile ...
08:16 egonw I was hoping you had a clue
08:25 Gpox http://blog.eclipse-tips.com/2008/0​6/opening-editor-without-ifile.html
08:25 zarah Gpox's link is also http://tinyurl.com/dduo3j
08:26 Gpox it requiers that the editor uses taht way to get the data, which i dont think biolcipse editor dose
08:32 egonw Gpox: ok, great
08:32 egonw that link looks useful
08:34 rojasm joined #bioclipse
08:34 egonw Gpox: checked the blog...
08:34 egonw that sounds like a really useful template
08:51 masak joined #bioclipse
09:12 * olass is including balloon in bioclipse
09:13 olass I think 3D generation is so important
09:13 olass and will not be much work
09:13 olass and now I got licensing issues sorted out
09:13 olass now I need to figure out how to work with Fragments
09:14 olass a suitable exercise
09:14 olass for a monday morning
09:14 olass egonw: will be an xmpp service too :)
09:14 olass (I mean, why not?)
09:15 masak egonw: seen this? http://code.stanziq.com/strophe/
09:15 zarah masak's link is also http://tinyurl.com/5pb3u7
09:22 rojasm joined #bioclipse
09:39 edrin joined #bioclipse
09:40 edrin hi
09:40 zarah hi edrin
09:40 olass hi edrin
09:40 edrin hi olass
09:40 masak hi edrin
09:40 edrin hi masak
10:07 stain hi.
10:11 masak hi stain
10:12 olass hi stain
10:12 edrin egonw: around?
10:12 olass @seen egonw
10:12 zarah egonw was last seen 1 h 31 m ago in #farmbio saying 'but the closest I have been so far :)'
10:14 * olass has just found a new header directive in Eclipse manifest and is playing with it
10:14 olass Eclipse-ExtensibleAPI: true
10:15 olass very nice indeed
10:19 edrin olass: what does do?
10:19 olass allows for dynamic API extensibility from platform-specific fragments
10:19 olass (amongst others)
10:30 olass egonw: around?
10:34 edrin olass: there is a "is service on" xmpp app in svn now
10:34 olass yes, got your mail
10:34 edrin great :)
10:34 edrin it should return a code status of 0 if service was available
10:35 olass I previously implemented my own on the page http://ws1.bmc.uu.se:8080/hivrtpred/PredictHIVRT
10:35 zarah olass's link is also http://tinyurl.com/cc44jj
10:35 olass see top of that page
10:35 edrin ah cool :)
10:36 edrin olass: I really like this web page a lot1
10:36 edrin !
10:36 olass you do?
10:36 olass It's not so user friendly...
10:36 olass just made it very fast
10:36 edrin it's great
10:36 olass but it works :)
10:36 edrin it is userfriendly
10:38 edrin it's much easier to use such a page instead of a "fully blown graphic HTML" thing
10:38 edrin plain
10:38 edrin and easy
10:38 edrin just "citing" is missing
10:38 olass it's not published yet
10:38 edrin (a link to the pub)
10:38 edrin ok
10:38 olass the old is
10:38 olass there are two
10:38 olass mom
10:39 olass http://maradona.farmbio.uu.s​e/HIVProteasePredWeb/Predict
10:39 zarah olass's link is also http://tinyurl.com/cradzm
10:39 olass but not XMPP presence
10:39 edrin another webpage service i like much: http://ihg2.helmholtz-muen​chen.de/ihg/mitoprot.html
10:39 zarah edrin's link is also http://tinyurl.com/c474bx
10:39 olass I could set that up if we want it
10:39 edrin ok
10:39 olass edrin: yes, me too
11:15 olass egonw: what contenttypes exist now?
11:16 olass egonw: see bug #762
11:16 olass I'm a bit puzzled as to which I can use, and what that implies for dependencies
11:18 egonw look at the docs
11:18 egonw doc.developers
11:18 olass ok
11:18 olass did not know that info was there
11:18 egonw which contains HTML table with all content types we define in SVN
11:18 olass aah, super!
11:18 egonw well, you ask me to add it :)
11:19 olass egonw++
11:19 egonw .docs itself is pending...
11:19 olass well; I did not ask specifically for contenttypes
11:19 olass egonw: pending what?
11:19 egonw completion
11:19 olass :)
11:19 olass egonw: about mol2 support in cdk
11:19 olass what is the status?
11:21 egonw it should do your use case
11:22 olass ?
11:22 olass my use case?
11:22 olass I have not explained it yet...
11:23 olass my use case is: load and save in mol2 supporting most features
11:23 egonw ah, ic...
11:23 egonw no, that is not supported at this moment
11:23 olass ok
11:23 egonw the mol2 reader and write needs more attention for that
11:24 * olass wished that egonw would ge a grant to extend I/O in cdk
11:24 egonw yes, would be good to get this NIH grant
11:25 olass cdk needs good, stable I/O, which is a non-trivial task
11:26 egonw this is what the CDK-NIH grant is about, actually
11:27 egonw maintaince, stabilization of projects
11:27 olass great
11:36 egonw all: http://marian.musgit.com/projects_grepconsole.php
11:36 zarah egonw's link is also http://tinyurl.com/d65vd2
11:36 egonw sounds like a useful plugin
11:42 olass yes
11:42 olass if you try it, write some useful regexps on wiki
13:28 egonw olass: yes, I think I understand how the schema can be fixed
13:29 olass excellent
13:29 egonw please file a ticket on PZ
13:29 olass ok
14:36 egonw is anyone actually following: http://friendfeed.com/rooms/bioclipse
14:36 zarah egonw's link is also http://tinyurl.com/6bbxz5
14:36 egonw or using FF at all?
14:36 egonw a nice square Bioclipse logo would be nice...
14:38 * masak isn't
14:41 * olass neither
14:41 egonw was just wondering
15:00 egonw oh, btw: http://chemicalrcp.blogspot.com/2009/03/hi​ghlighting-console-output-in-eclipse.html
15:00 zarah egonw's link is also http://tinyurl.com/d88g2n
15:00 egonw olass: rather that than in the wiki
15:01 olass why so?
15:01 olass wiki is more convenient
15:01 egonw this may give me money
15:01 olass then other people can contribute more snippets
15:01 olass money?
15:01 olass how?
15:01 egonw via the adds in my blog
15:02 egonw two years left, and I can buy my first book :)
15:02 olass so you sacrifice other developers for that?
15:02 egonw no, only to the gods
15:02 egonw seriously...
15:02 egonw I do no have any useful regexp's yet...
15:55 egonw don't know...
15:55 egonw but was sent to it
15:55 egonw and I do not see a cc to me
15:55 egonw wrong window
16:12 CIA-58 bioclipse: egonw * r9442 /bioclipse2/trunk/plugins/net.bioclipse.​bibtexml/model/bibtexmlHandwritten.xsd: Given the entryType an ID
16:18 egonw mmm... can't wait to upgrade Pele to jaunty: semantic wikis, yeah :)
16:23 egonw masak: what was that link about fast typing again?
16:23 olass mmm... can't wait to go skiing this weekend
16:24 olass we all have our desires :)
16:24 egonw yeah, sounds nice!
16:25 egonw masak: ping
16:26 masak egonw: pong
16:26 * masak fetches
16:26 masak http://steve-yegge.blogspot.com/2008/09/​programmings-dirtiest-little-secret.html
16:26 zarah masak's link is also http://tinyurl.com/6f9lsz
16:31 egonw masak: the ping was actually about something else...
16:31 masak oh.
16:31 egonw about the manager documentation...
16:31 * masak read 'anger management' :)
16:31 egonw that has a name
16:32 egonw your leaking perspective
16:32 egonw either you're in an angry mood, or you consider me evil
16:32 egonw or so
16:32 masak :P
16:32 masak a Freudian misread, yes.
16:32 egonw no, that's angel management :)
16:33 masak what about the anger-manager documentation?
16:33 egonw yes, right
16:33 egonw umm...
16:33 egonw it seems we want that available from a plugin
16:33 masak want what available?
16:33 masak the Perl script?
16:33 egonw though I am actually thinking this belongs on a per plugin basis
16:33 egonw ah, no...
16:33 egonw the output
16:33 masak urk
16:34 egonw because it can generate HTML, right?
16:34 masak why?
16:34 masak yes, generate HTML is what it does.
16:34 egonw to be available as documentation?
16:34 masak well...
16:34 egonw so, that people can actually read the documentation?
16:34 masak but...
16:35 masak source code tends to drift away, and people tend not to update 20 HTML files, each one in its own module.
16:36 olass egonw: IMO it should really be in one plugin
16:36 egonw masak: that's where the perl script comes in
16:36 olass one docu plugin
16:36 olass really
16:36 egonw olass: yeah, fine
16:36 olass I am REALLY in favor of this
16:36 egonw that's where I am heading right now...
16:36 masak egonw: if it's per-module output you want, I can arrange that without a problem. but I don't really like the idea of committing those HTML files.
16:36 egonw just wanted to vent my thoughts...
16:36 egonw but it best aligns with masak's current script anyway
16:37 masak my script currently generates documentation for all plugins.
16:37 egonw masak: please talk to Ola as he does want it
16:37 egonw masak: yes, that's fine
16:37 masak but it can easily be modified to work on a per-plugin basis.
16:37 egonw ah, no forget that...
16:37 masak OK.
16:38 egonw where's the script?
16:38 masak olass: could you describe again what it is we want. I'm a bit slow today.
16:38 masak egonw: hold on.
16:38 egonw I'll move it into plugins/net.bioclipse.doc/ then
16:38 egonw create current HTML, commit
16:38 egonw and set up the toc.xml
16:38 olass a script in the net.bc.doc plugin
16:39 olass it should generate manager doc as HTML in the html dir
16:39 rojasm left #bioclipse
16:39 masak egonw: https://bioclipse.svn.sourceforge.net/svnroo​t/bioclipse/bioclipse2/trunk/manager-apidocs
16:39 olass and the toc.xml should hook this into the help system
16:39 egonw masak: ack, thanx
16:40 masak OK, you both seem to know what it is you want. :) feel free to move the script.
16:40 egonw masak++ for not using file extensions!
16:40 masak some paths may need changing to make it work on a new location.
16:40 masak I can do that after the move if you want.
16:40 egonw yes, please
16:40 egonw will ping
16:40 masak goodie.
16:41 * masak is not really here today
16:47 CIA-58 bioclipse: egonw * r9443 /bioclipse2/trunk/plugins/net.bioclipse.​bibtexml/model/bibtexmlHandwritten.xsd: Extracted complexType for entryType
16:52 egonw masak: is there anything special about YAML.pm?
16:52 egonw http://packages.ubuntu.com/search?searchon=​contents&keywords=YAML.pm&mode=exac​tfilename&suite=intrepid&arch=any
16:52 zarah egonw's link is also http://tinyurl.com/ce4jqr
16:52 egonw which one should I use ?!?!?
16:53 masak egonw: what do you mean, 'anything special'? it's a good hierarchical data storage format.
16:54 egonw Jaunty has 18 different copies of it...
16:54 egonw is it so version sensitive?
16:54 masak egonw: I'd recommend YAML::XS without more context.
16:54 masak egonw: I think it has gone through a few version cycles.
16:55 masak I've learned a little bit more about the history of YAML in the past two weeks than I think I really needed.
16:55 masak currently, YAML::XS is the way to go.
16:55 egonw not sure what ubuntu package that is in...
16:55 egonw that would be YAML/XS.pm, ritgh?
16:55 masak aye.
16:56 masak I know it's on CPAN, at least.
16:56 masak I'm heading to the store in a few minutes.
16:56 egonw ack, will email
16:56 egonw when done
16:57 masak sounds good.
16:57 egonw "Your format is silly:" :)
16:58 masak :P
16:58 masak someone's reading my code.
16:58 egonw no, the output actually
16:59 masak oh, it flags it as silly?
16:59 egonw Your format is silly: public interface IJsConsoleManager extends IBioclipseManager {
16:59 masak then someone introduced a case that my code doesn't cover.
16:59 egonw output of:
16:59 egonw bash run-the-whole-thing
16:59 masak aye.
16:59 masak I'll need to take a closer look at that.
16:59 egonw where does the output go?
17:00 masak egonw: to STDOUT.
17:00 masak but it isn't emitted until the end.
17:00 egonw I mean... the HTML
17:00 masak to STDOUT.
17:00 egonw mmm...
17:00 masak I usually pipe it.
17:00 masak write it to a file.
17:01 egonw ah, tidy not installed
17:01 egonw so everything went to /dev/null :)
17:01 masak uhm.
17:01 masak maybe I should check for tidy in the script.
17:01 * masak marks that as a TODO
17:01 egonw :)
17:02 * masak bikes to the store
17:12 CIA-58 bioclipse: egonw * r9444 /bioclipse2/trunk/ (17 files in 6 dirs): Concentrated script documentation in net.bioclipse.doc (fixes #742)
17:12 zarah bug #742 | http://tinyurl.com/dj5pzm
18:10 edrin left #bioclipse
18:18 CIA-58 bioclipse: ospjuth * r9445 /bioclipse2/trunk/plugins/net.bioclipse.balloon/: Initial import.
18:21 CIA-58 bioclipse: ospjuth * r9446 /bioclipse2/trunk/plugins/net.bioclipse.balloon/ (12 files in 7 dirs): Plugin for generating 3D conformations using Balloon. This plugin is for exposing platform-specific fragment.
18:22 CIA-58 bioclipse: ospjuth * r9447 /bioclipse2/trunk/plugins/net​.bioclipse.balloon.business/: Initial import.
18:24 CIA-58 bioclipse: ospjuth * r9448 /bioclipse2/trunk/plugins/net​.bioclipse.balloon.business/ (24 files in 11 dirs): Business code for calling Balloon via a BalloonManager.
18:26 CIA-58 bioclipse: ospjuth * r9449 /bioclipse2/trunk/plugins/net.bioclipse.jnati/: Initial import.
18:28 egonw olass: what's jnati
18:29 CIA-58 bioclipse: ospjuth * r9450 /bioclipse2/trunk/plugins/net.bioclipse.jnati/ (15 files in 8 dirs): Added plugin jnati for simplifying running native code from java.
18:29 egonw ah, ic...
18:29 egonw interesting...
18:59 CIA-58 bioclipse: egonw * r9451 /bioclipse2/trunk/plugins/n​et.bioclipse.ui.tests/src/ (2 files in 2 dirs): Added unit test for bug #708: test if the correct content type is detected
18:59 zarah bug #708 | http://tinyurl.com/ccvf9n
19:00 CIA-58 bioclipse: egonw * r9452 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Bind the CML editor to 5D CML files
19:05 CIA-58 bioclipse: ospjuth * r9453 /bioclipse2/trunk/plugins/net​.bioclipse.balloon_feature/: Initial import.
19:06 edrin joined #bioclipse
19:07 CIA-58 bioclipse: ospjuth * r9454 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon_feature/ (.project build.properties feature.xml): A feature to collect balloon fragments
19:10 CIA-58 bioclipse: ospjuth * r9455 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon.macosx/: Initial import.
19:11 olass joined #bioclipse
19:12 edrin hi olass
19:12 olass hi edrin
19:14 CIA-58 bioclipse: ospjuth * r9456 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon.macosx/ (22 files in 9 dirs): A fragment for running Balloon on Mac OS X.
19:14 CIA-58 bioclipse: ospjuth * r9457 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon.macosx/ (6 files in 2 dirs): A fragment for running Balloon on Mac OS X.
19:15 CIA-58 bioclipse: ospjuth * r9458 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon.tests/: Initial import.
19:20 edrin egonw: what do you think, the cml will tunnel through ejabberd successfully if you "adapt" the namespace thing?
19:23 egonw when we isolated the tool which causes the problem, we can mention that in the paper
19:23 egonw or did you make sure it is ejabberd already?
19:23 egonw olass: ping...
19:24 egonw olass: can you send me another set of ejabberd logs?
19:24 egonw edrin: it would be very nice if you could have xws4j output a time stamp in the log
19:41 olass egonw: in the middle of food now
19:41 egonw sure, no rush
19:41 olass will do as soon as I can
19:42 olass egonw: about the bibtexml schema...
19:42 olass an progress?
19:42 egonw dunno
19:42 egonw made a second commit
19:42 egonw see bug report
19:42 egonw please test
19:44 olass ok, will do
19:45 CIA-58 bioclipse: ospjuth * r9459 /bioclipse2/trunk/plugins/n​et.bioclipse.balloon.tests/ (16 files in 9 dirs): Tests for BalloonManager.
19:45 CIA-58 bioclipse: ospjuth * r9460 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon.linux/: Initial import.
19:45 CIA-58 bioclipse: ospjuth * r9461 /bioclipse2/trunk/plugins/n​et.bioclipse.balloon.linux/ (16 files in 9 dirs): A fragment for running Balloon on linux. Not implemented yet.
19:45 CIA-58 bioclipse: ospjuth * r9462 /bioclipse2/trunk/plugins/ne​t.bioclipse.balloon.win32/: Initial import.
19:46 CIA-58 bioclipse: ospjuth * r9463 /bioclipse2/trunk/plugins/n​et.bioclipse.balloon.win32/ (16 files in 9 dirs): A fragment for running Balloon on windows. Not implemented yet.
19:52 olass egonw: ejabberd.log sent
19:52 egonw TACK
19:52 olass ok, gotta go offline now
19:52 olass bye
19:52 olass cu tomorrow at BMC
19:54 edrin egonw: ok
19:54 edrin egonw: no, i do not know if it is ejabberd or JSO
19:54 egonw ack
19:54 edrin does the ejabberd log help?
19:54 egonw I hope so
19:55 edrin does it save all stanzas!?
19:57 edrin currently asking how they do it for PSI
19:58 egonw ack
20:02 edrin egonw: PSI serializes it first
20:02 egonw huh?
20:02 edrin they received stanzas
20:03 edrin what you see in the console was serialized first
20:03 egonw sure
20:03 egonw but therefore derialized too?
20:03 egonw deserialized ...
20:03 edrin i think so
20:04 egonw ok, that sucks
20:04 egonw from our point of view
20:04 egonw meaning that it still can be PSI
20:04 edrin yes
20:05 edrin i will try the pidgin im now
20:09 egonw ejabberd log is useless
20:09 egonw not messages
20:18 edrin exodus cannot show this large stanza...
20:18 edrin Pidgin as well
20:25 egonw :(
20:25 egonw meanwhile... I'm removing the use of default NS in the CML schema as dirty workaround
20:26 egonw that is, I hope it's a workaroun
20:26 egonw +d
20:37 edrin joined #bioclipse
21:10 edrin hehe
21:10 edrin :)
21:13 edrin egonw: i think it is at least ejabberd
21:13 edrin egonw: available?
21:13 egonw yes
21:13 egonw how so?
21:14 edrin because i could capture the result the server sent in a log file
21:15 egonw ok, edrin++
21:15 edrin saved the stanza, put the schema in file
21:15 edrin egonw: i used an old hax0r app of mine
21:15 egonw good
21:15 edrin found it on an old harddisk i have here
21:16 egonw :)
21:16 edrin i know that many liked it ;) i still do to
21:17 edrin ok
21:17 edrin egonw: http://codepad.org/Gept2XDi
21:17 edrin thus it's ejabberd
21:18 edrin of course in addition to that it can still be JSO, too
21:18 edrin but ejabberd is more important anyway
21:23 edrin egonw: do you have a minute to explain aleksey what might be wrong?
21:25 egonw yes
21:25 egonw channel?
21:26 egonw jabber?
21:29 edrin i will prepare a group chat channel
21:30 edrin egonw: it is xws@conference.jabber.org
21:30 egonw OK, let's hope PSI will not die this time :)
21:30 edrin heh
21:31 egonw nope
21:31 egonw it crashed again
21:31 edrin damn
21:31 egonw I make it to the window
21:31 egonw but when I then try to tpye
21:31 egonw it hangs :(
21:32 edrin is your psi up to date?
21:32 egonw dunno
21:32 egonw mom
21:32 edrin he is there now
21:32 egonw 0.12
21:32 edrin this should be current
21:33 edrin do you have another client available?
21:33 egonw trying
21:33 egonw kopete
21:34 egonw but that does not seem to support groups?
21:34 edrin damn
21:35 egonw did you get my chat message?
21:37 edrin he cant join irc
21:37 edrin egonw: try this: http://jwchat.org/
21:38 egonw and send my pwd unencrypted to a website I do not know?
21:38 egonw mmm...
21:38 edrin :)
21:38 edrin i know
21:39 edrin but no other idea now
21:39 egonw can't he just chat with me?
21:39 edrin you can change it
21:39 egonw egonw@jabber.org
21:39 edrin or create one at jwchat
21:39 egonw will do that
22:06 edrin damn
22:09 edrin hm
22:09 edrin thus it is JSO that must be fixed
22:10 egonw so it seems
22:13 egonw edrin: OK, uploaded a QSAR component with updated schema
22:16 edrin will try it
22:16 edrin now
22:18 edrin does it work for you?
22:18 egonw mmm... no
22:18 egonw sorry
22:19 egonw should have run my test client
22:19 edrin same here
22:19 edrin creates binding forever
22:19 egonw ProcessFactory.validateRunInput: could not create validator; function schemata correct?
22:19 edrin sorry
22:19 edrin ah
22:19 edrin ok, so there is an error
22:19 edrin in schema
22:19 egonw grmp...
22:20 egonw that's because of my hacking the schema I guess...
22:20 egonw not sure why the validating XML schema editor in Eclipse did not complain about it...
22:20 egonw hang on
22:20 edrin hm
22:20 edrin but actually it received the schema here ...
22:21 edrin strange
22:34 egonw edrin: please try now
22:34 egonw my test is working again
22:34 egonw fixed the schema
22:34 edrin ok
22:35 egonw I apparently forgot to upload the proper CML schema from the CDK to the QSAR component
22:36 edrin tack
22:36 edrin it's working
22:36 egonw creation of the binding?
22:36 egonw that's working?
22:36 edrin still creating but seems to work
22:36 egonw ok, so slow, but actually doing something
22:36 edrin takes a while
22:36 edrin yes
22:36 edrin it's slow for many schemata ;)
22:39 edrin and it is now extra slow because it has to do the stuff twice ;)... for i and o
22:39 egonw edrin: not good...
22:39 egonw well...
22:39 egonw I guess it cannot easily detect if the schema is the same
22:39 edrin yes
22:39 egonw MD5?
22:40 edrin well, one would have to code this
22:40 edrin not sure if that's worth it right now
22:40 edrin cml is really a big schema :)
22:43 edrin egonw: ok, binding was created successfully after ~ 5min ;)
22:43 egonw great!
22:43 egonw I'm happy we found the problem
22:43 edrin yeah, me too
22:43 egonw making a good unit test for the JSO hackers would be next...
22:43 edrin yes
22:44 edrin the guy who is doing JSO is linuxwolf

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