Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-09-26

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All times shown according to UTC.

Time Nick Message
07:29 malick joined #bioclipse
08:01 thomasku joined #bioclipse
08:20 shk3 joined #bioclipse
08:28 jonalv joined #bioclipse
08:29 jonalv zarah: hi >(
08:29 zarah hello jonalv :)
08:30 shk3 hi jonalv
08:30 jonalv hm that was the wrong keys... :)
08:31 * jonalv is at the euroqsar2008 :)
08:32 shk3 did you hear christophs talk?
08:36 jonalv yea
08:37 jonalv it's been so many talks though :)
08:39 shk3 we hope to have some really usefull stuff in that area soon
08:39 jonalv cool
08:39 CIA-30 bioclipse: shk3 * r7094 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/contenttypes/CmlFileDescriber.java: If there are spectra in the cml, we assume it is a specmol file and not a molecule one
09:03 masak joined #bioclipse
09:19 CIA-30 bioclipse: carl_masak * r7095 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui/src/net/bioclipse/biojava/u​i/views/SequenceContentProvider.java: [SequenceContentProvider.java] removed unused imports
09:42 gilleain joined #bioclipse
10:17 egonw joined #bioclipse
10:32 rojasm joined #bioclipse
10:45 edrin joined #bioclipse
10:47 edrin hi
10:47 zarah hi edrin
10:49 masak hi edrin
10:49 edrin hi masak
10:50 CIA-30 bioclipse: carl_masak * r7096 /bioclipse2/trunk/plugins/net.bioclipse.​biojava.ui/src/net/bioclipse/biojava/ui/ (3 files in 2 dirs):
10:50 CIA-30 bioclipse: [Aligner] made a few things public, fiddled with ws
10:50 CIA-30 bioclipse: [AlignmentEditor] slight reordering
10:50 CIA-30 bioclipse: [AlignmentOutlinePage] dumped big chunks of code so that
10:50 CIA-30 bioclipse: the outline now shows a minimized version of the alignment
10:50 CIA-30 bioclipse: ...except it doesn't when I try to use ScrolledComposite
10:50 CIA-30 bioclipse: need to look more into that
10:50 masak lunch &
11:27 egonw hi all
11:27 zarah hi egonw
11:27 edrin hi egonw
11:30 masak hi egonw
11:30 zarah hi egonw
11:38 rojasm joined #bioclipse
11:42 edrin egonw: how is it un Uppsala?
11:45 CIA-30 bioclipse: carl_masak * r7097 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.rdfeditor/src/net/bioclipse/cd​k10/rdfeditor/editor/RDFEditor.java: [RDFEditor] a few indentation fixes, replaced some tabs with spaces
12:06 egonw edrin: still settling in :)
12:06 egonw brb
12:14 egonw joined #bioclipse
12:16 maclean joined #bioclipse
12:28 jonalv joined #bioclipse
12:31 jonalv hi
12:31 zarah hi jonalv
12:31 zarah jonalv: You have new messages. Write '@messages' to read them.
12:32 jonalv zarah: tell me...
12:32 zarah jonalv: masak said Spring 2.5 verkar coolt. http://en.oreilly.com/oscon200​8/public/schedule/detail/2511
12:38 jonalv edrin: hi, have you collected more questions? :)
12:38 edrin not yet, currently stressed with other things in the lab
12:38 jonalv aha okey
12:57 maclean hahaa! the springy osgish framework aop stuff recognises my plugin at last. hooray.
12:59 jonalv w00t
12:59 jonalv maclean: which plugin! :)
12:59 jonalv lol which pluign?
12:59 maclean Seneca.
12:59 maclean It's just a port. So I guess it's not really 'mine' yet. Still Egon's.
13:00 jonalv is it in the bioclipse repo?
13:00 maclean not until it has basic functionality, no.
13:01 maclean but pressing tab in the javascript console and seeing its name is nice.
13:01 jonalv yea :)
13:02 jonalv maclean++
13:02 maclean By the way, how do you specify paths in the console?
13:02 jonalv I am trying to have a look at the webservice manager by shk3 but I can't get it to turn up when I prexx tab... :(
13:03 maclean Yeah, he said that was a problem.
13:03 jonalv maclean: you can drag and drop files from the Bioclipse explorer
13:03 maclean Oh reeaaaalllly. Nice.
13:03 jonalv ta!
13:04 masak maclean: paths are specified with the workspace dir as implicit root, IIRC
13:04 maclean woah.
13:04 maclean that d'n'd is very good.
13:04 jonalv it's stwew wright in the afternoon now playing everywhere! :)
13:04 masak maclean: thanks :)
13:04 masak jonalv: :P
13:04 jonalv bbc2++
13:05 masak indeed
13:05 masak my day just got twice as enjoyable
13:06 jonalv shk3: ping
13:07 shk3 yes
13:07 jonalv I realise that people have a hard time callign the package containing the managers for business. But I don\t think scripting is a good alternative
13:07 jonalv I further think we should try to call it the same in all plugins
13:08 shk3 if you have time, you could start bc with the webservices plugin
13:08 jonalv it makes it much easier to switch between plugins
13:08 shk3 you then see the error
13:08 shk3 probably I miss something obvious
13:08 jonalv shk3: That's exaclty what I am trying to do. Not gotten it to work yet though... :(
13:09 shk3 ah, so it's not that obvious
13:09 jonalv but I had to look befroe I found the manager files. :(
13:09 jonalv Could we either have that code in a net.bioclispe.pluignname.business or make up another name and change all plugins we already have
13:10 maclean I thought that most plugins  did that anyway.
13:10 shk3 we can change that, no problem
13:10 shk3 I used the convention mostly,
13:10 shk3 just not in the webservices plugin
13:10 shk3 where I left things as they were
13:10 jonalv I have no suggestion for another name so I would prefer having net.bioclipsebc?webservices.scripts named net.bioclipse.webservices.business
13:10 shk3 probably not a good idea
13:10 jonalv those extra bc seems sort of superfluos too
13:10 shk3 sure
13:11 shk3 yes
13:11 shk3 we had it in bc1 a lot
13:11 shk3 but it's not needed
13:11 jonalv shk3: will you fix this? :)
13:11 shk3 yes
13:12 * jonalv is moving on to look at the actual code now :)
13:12 maclean hmmm. loading files using the paths provided by d'n'd is not working (on windows, at least - not tested on mac).
13:13 jonalv maclean: uhm in what whay are you loading the file when it doesn't work?
13:13 maclean I get these "Path must include project and resource name: " errors
13:14 maclean Oh, if I say 'jmol.load(...)' with the path as the arg.
13:14 maclean Or 'cdk.loadMolecule(...)'
13:14 jonalv please let me remind you people that we are trying to keep the source code in bioclipse 2 within 80 cols
13:14 maclean It's the ResourcePathTransformer
13:14 masak maclean: could you nopaste what it is you're writing
13:15 maclean nopaste?
13:15 masak http://nopaste.snit.ch/
13:15 masak or similar
13:15 jonalv maclean: okey Gpox who should be here next week I think is our export on eclispe resources, files and such but perhaps we can figure it out too...
13:16 maclean Well, it's short enough to go here:
13:16 maclean cdk.loadMolecule("\Sample Data\3D Structures\mol\alcohols\(2R)-butan-2-ol.mol")
13:16 jonalv (I think he should be here next week that is)
13:16 masak maclean: uh-uh, backslashes
13:16 masak maclean: you sure those shouldn't be double?
13:16 maclean The path is returned by drag/drop, sorry.
13:17 jonalv masak: you sure those shouldn't be "/"?
13:17 masak jonalv: I would've made them '/', yes
13:17 maclean If it shouldn't be in that format, then drag and drop should return the right thing...
13:17 masak maclean: aye
13:17 masak maclean: please try a few different variants
13:17 maclean It's line endings all over again :(
13:17 maclean (as it were)
13:17 masak if it turns out that '/' works whereas '\' doesn't, I'll change the dnd function
13:18 maclean trying it...
13:18 maclean now getting a "Could not handle" error.
13:18 jonalv I am pretty sure those are supposed to be "/"
13:18 masak jonalv: maybe maclean is running MS DOS
13:18 jonalv maclean: that means that it has tried 3 versions and given up
13:19 maclean Well, on windows "\" == "/"
13:19 * maclean is on XP
13:19 jonalv yea but those are urls if they are workspace relative and I think they are platform independent
13:19 masak maclean: I know DOS when I see it :)
13:20 jonalv but I am not great at that stuff...
13:21 jonalv shk3: Are you building something that is gonna use the webservices.downloadPDB method right now?
13:21 edrin i think windows vista is just a graphical frontend of DOS. i think they were not happy with the win2k kernel...
13:21 CIA-30 bioclipse: carl_masak * r7098 /bioclipse2/trunk/plugins/net.sourcef​orge.jseditor/src/net/sourceforge/jse​ditor/handlers/RunScriptHandler.java: [RunScriptHandler] now asks to save if script is unsaved
13:21 maclean Well, anyway, it doesn't work, whether I am using dos or not :)
13:22 edrin there are rumors that apple will switch back DOS, too...
13:22 masak edrin: they already did. it's called BSD Unix.
13:22 * maclean really is under the impression that I am on XP, not Vista.
13:22 jonalv shk3: I am starting to think that perhaps there also should be an alternative to download to a resource in the virtual project...
13:22 masak only it's 1e3 times better than DOS
13:23 jonalv well I am prettty sure that we have not done sufficiant testing on Windows and that there will turn up more Windows realated bugs
13:24 masak it's just so hard to find Windows users nowadays...
13:57 masak shk3: recent commits indicate that you still emit tab characters in bc2 code? have you imported tabless.xml?
13:59 CIA-30 bioclipse: carl_masak * r7099 /bioclipse2/trunk/plugins/net.bioclipse.webservic​es/src/net/bioclipse/webservices/Activator.java: [n.b.webservices/Activator] removed a few tab characters
14:02 jonalv shk3: which error message do you get when you try to start the webservices pluign?
14:03 edrin masak: I would like to add some common tools for js, should i create my own manager or do you suggest I modify code of the "js" manager ?
14:07 shk3 jonalv:
14:07 shk3 Caused by: java.lang.NullPointerException
14:07 shk3 at net.bioclipse.plugins.bc_webservices.script​s.WebservicesManagerFactory.setInitializati​onData(WebservicesManagerFactory.java:34)
14:07 shk3 is the error causing problems
14:08 edrin shk3: maybe it is related to this @ stuff (Spring and this stuff)
14:09 shk3 i set "insert spaces for tab" in the preferences, but this seems to have no effect
14:09 masak edrin: things that are related to Javascript in some way should go into 'js'. if the things you plan to add are not related to js, it's better to make a separate manager
14:10 edrin yes, that's my plan
14:10 edrin masak: some are, some are not
14:10 jonalv edrin, shk3: Yea it's related to "the Spring stuff" :)
14:10 jonalv I am looking at it a little like now but I get anotehr errormessage
14:11 edrin jonalv: maybe he did not declare this interface ;)
14:11 jonalv edrin: oh he did
14:11 edrin ok
14:11 jonalv edrin:  you don't like interfaces?
14:11 edrin yes, i like them
14:12 masak edrin: then add those who are to the 'js' manager
14:12 jonalv shk3: okey no I at least get the same error :)
14:13 masak and those that aren't to some other manager
14:13 CIA-30 bioclipse: carl_masak * r7100 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
14:13 CIA-30 bioclipse: [JsConsole] added say(message) as a bare-function wrapper
14:13 CIA-30 bioclipse: to js.say(message) in the js console
14:13 edrin shk3: as you already ported the web service plugin I think I would add some more to it
14:14 edrin masak: can a script check it's monitor as in bc1?
14:14 masak edrin: no, but it sounds intriguing
14:14 jonalv edrin, masak: I think we can do more cool stuffs with monitors, manager methods and scripts
14:14 edrin masak: that's one function I want to add
14:15 maclean cool stuff++
14:15 masak edrin: go right ahead. I'll review it once you've committed
14:15 edrin in bc1 the script could check if it was canceled: example: rhino.isCanceled()
14:15 maclean but of course, also : boring bugfixes++
14:16 masak karma bugfixes
14:16 zarah bugfixes has a karma of 1
14:16 edrin another thing I need is loading .jars at runtime
14:16 masak ooh
14:17 jonalv I would like to create a job when runnign a js script. Count the number of manager calls in the script. And give each maanger call in the script a subbprogressmnonitor with proportional amount of ticks
14:17 jonalv That would be awesome. But I am not sure about how easy it would be to do...
14:19 edrin :) sounds hard
14:20 masak jonalv: good luck. let me know how that works out.
14:20 maclean :)
14:20 jonalv so if the number of manager calls in a js-script is n then each manager call should get numberOfTicks/n ticks...
14:20 masak jonalv: how will you detect a manager call?
14:21 jonalv but I am not sure how easy it is to do these kind of things with js. Perhaps some other langugae is easier?
14:21 shk3 jonalv: changed package names in webservices plugin
14:21 shk3 shall I commit?
14:21 masak jonalv: static code analysis is hard, period
14:21 jonalv masak: that's the problem. We would need to inspect the code...
14:21 jonalv shk3: yea!
14:21 masak jonalv: consider the following situation:
14:22 masak myJs = js; myJs.print("hi")
14:22 masak that's a manager call
14:22 jonalv masak: That is VERY much frowned upon...
14:22 masak jonalv: no, and that's the thing
14:22 masak it's perfectly ok js code
14:22 jonalv why would you wanna do that?
14:23 masak I don't know
14:23 jonalv that's bad and ugly
14:23 masak but it's not illegal or anything
14:23 masak jonalv: no, it's neither bad nor ugly
14:23 jonalv look here if you wanan break things you always can
14:23 edrin btw. what do you think of an chat/irc plugin ? thus users can ask for help on-line
14:23 masak jonalv: that's not it. it's us having insufficient tools to cover all cases. we're at fault.
14:24 jonalv masak: what do you suggest hen?
14:24 masak edrin: not exactly core business for Bioclipse, but please go ahead
14:24 edrin ;)
14:24 masak jonalv: no, I'm not suggesting a hen. that would be the last resort
14:24 jonalv *then
14:24 jonalv :)
14:25 masak sacrificing hens is a very outdated development practice
14:25 CIA-30 bioclipse: shk3 * r7101 /bioclipse2/trunk/plugins/​net.bioclipse.webservices/ (52 files in 18 dirs): changed package name to bc2 convention
14:25 jonalv who said somethiong about sacrifing something? You are just avoiding my question!
14:25 jonalv masak: What do you suggest?
14:26 masak jonalv: yes. I think this is a bit like the Recorder thing: putting ourselves in the stickiest kind of trouble we can think of
14:26 masak but don't let me stop you :)
14:26 jonalv masak: You do realise that the first thing edrin started asking me about was just this...
14:26 CIA-30 bioclipse: shk3 * r7102 /bioclipse2/trunk/plugins/net.biocli​pse.webservices/src/net/bioclipse/we​bservices/WebservicesConstants.java: changed package name to bc2 convention
14:27 masak jonalv: I'm not saying it's not a wanted feature. I'm saying it's a very difficult problem.
14:28 jonalv masak, edrin: You are the JavaScript experts. How should we do with progressmonitors and scripting?
14:28 masak I'm not really an expert at progress monitors
14:28 masak so I don't really know
14:30 egonw ok, enough for me today
14:30 egonw bye all!
14:30 jonalv egonw: bye
14:31 masak egonw: bye
14:31 jonalv edrin: what are your inputs on this?
14:36 masak jonalv: another interesting thing: eval("js.print('hi')")
14:37 edrin jonalv: i would just give it no ticks... a script just has "running" and "finished" states
14:37 masak jonalv: what edrin said.
14:37 edrin you could add some pseudo ticker...
14:37 jonalv edrin: that's a good idea
14:37 edrin as in many other apps
14:37 edrin however I do not like pseudo tickers...
14:38 edrin that's just fooling the user...
14:38 jonalv We use the standard ticker. The method's has ticker functionality that are used when the methods are called from the gui
14:38 jonalv thing is that only one method is called then :(
14:38 jonalv qbaj'odub
14:38 jonalv sry...
14:38 masak jonalv: please keep discussion civil :)
14:38 * edrin must leave
14:38 jonalv I am having a little fight with my keyborad
14:38 edrin have a nice weekend
14:38 edrin left #bioclipse
14:39 maclean Yes, no imaginary curses.
14:39 jonalv that was supposed to be a glad smiley
14:39 masak jonalv: "happy"
14:39 jonalv masak: why?
14:39 masak jonalv: don't know. just is.
14:39 masak jonalv: so you're suffering from the illusion that you have a Swedish keyboard layout :)
14:39 masak that happens sometimes
14:40 jonalv oh well, I just blame everything on it being friday afternoon and me being tiered after a tugg week...
14:40 jonalv gah
14:40 jonalv a tuff week
14:40 masak "though"
14:40 maclean "tough"
14:41 jonalv :(
14:43 * jonalv is confused now...
14:43 masak maclean: aye, "tough"
14:44 maclean english is such a bastard language : dough, cough, ought.
14:44 jonalv I lik you people although parsing you sentences can be a bit tough sometimes though...
14:44 jonalv how many error where in that sentence?
14:44 masak jonalv: are you saying you lick us?
14:45 masak (I wouldn't)
14:45 jonalv that's one..
14:45 masak "parsing you sentences"?
14:45 maclean Gah. I can't see why the webservices plugin won't work. I say sacrifice the damn hen.
14:46 jonalv maclean: lol
14:46 jonalv maclean: I am have just updated. Gonna look at it again :)
14:47 masak maclean: no! don't sacrifice it now! we're saving the hen till just before release!
14:47 maclean Well, the xml files in the spring folder seem okay, the Manager seems okay.
14:47 * maclean puts the hen back
14:47 jonalv what is it with me fingers automagicly writing am as soon as I am wrtie Iam
14:47 jonalv |lol|
14:47 maclean ERROR_TOO_MANY_ERRORS
14:48 masak maclean: in your code or in jonalv's writings?
14:48 maclean Oh, it's just Friday. I dunno.
14:48 masak it's indeed Friday
14:48 jonalv it is very much friday
14:48 masak the Fridaiest Friday in a long time
14:50 jonalv masak: there is something fishy about that Activator...
14:51 masak jonalv: which Activator?
14:51 jonalv net.bioclipse.webservices
14:51 masak jonalv: ok
14:51 maclean it's final static PLUGIN_ID is private, for a start.
14:51 jonalv I think the problem is within in that. I am gonna compare it to another one and see what I find
14:52 maclean (but that's not the problem)
14:57 shk3 did that comparision
14:57 shk3 but perhaps you find someting
14:57 shk3 i didn't
14:57 jonalv I thinkI have found something else
14:57 maclean oh?
14:58 jonalv yea I got it showing up now
14:58 maclean oh?
14:58 shk3 ah?
14:58 shk3 oh?
14:58 jonalv The plugin should be activated when one of it's classes are loaded
14:58 jonalv commit pending
15:09 * shk3 is eagerly awaiting the commit
15:11 jonalv oh it should be in now
15:11 jonalv sry got phone...
15:11 maclean You phone in your commits? That must take ages!
15:11 jonalv lol
15:12 CIA-30 bioclipse: shk3 * r7104 /bioclipse2/trunk/plugins/net.bioclip​se.specmol/src/net/bioclipse/specmol/ (3 files in 2 dirs): added an action to check a spectrum
15:12 masak maclean: at least he's more accurate on the phone :P
15:12 maclean :)
15:19 CIA-30 bioclipse: shk3 * r7105 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (4 files in 3 dirs): added an action to check a spectrum
15:24 shk3 jonalv: thanks for fixing the script problem
15:25 jonalv shk3: np
16:09 CIA-30 bioclipse: shk3 * r7106 /bioclipse2/trunk/plugins/net.bioclip​se.nmrshiftdb/src/net/bioclipse/nmrsh​iftdb/wizards/ServerWizardPage.java: using preferences for the server
17:12 CIA-30 bioclipse: shk3 * r7107 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum/src/net/bioclipse/spectrum/​PeakLabelThresholdPreferencePage.java: improved the preference page
17:16 CIA-30 bioclipse: shk3 * r7108 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (5 files in 3 dirs): addedd a preference page
17:31 CIA-30 bioclipse: shk3 * r7109 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (html/assign.html html/check.html toc.xml): improved help

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