Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-19

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All times shown according to UTC.

Time Nick Message
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09:09 CIA-30 bioclipse: goglepox * r8373 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java: Added some comments relates to bug #179
09:09 zarah bug #179 | http://tinyurl.com/6nnv93
09:09 jonalv joined #bioclipse
09:10 jonalv hi
09:10 zarah saluton jonalv
09:10 jonalv &names
09:10 jonalv zarah: seen masak
09:10 zarah masak was last seen 2 d 20 h 21 m 4 s ago in #bioclipse saying 'ok, s[/][\\]g, then.'
09:10 jonalv :)
09:15 gilleain joined #bioclipse
09:15 egonw joined #bioclipse
09:15 jonalv hi egonw
09:15 gilleain hei all
09:15 egonw moin
09:15 zarah saluton egonw
09:24 edrin joined #bioclipse
09:24 edrin hi
09:24 zarah oh hai edrin
09:24 edrin ?
09:25 gilleain ?
09:26 egonw hi edrin
09:26 edrin egonw, olass, do you have a second?
09:27 olass yes
09:27 edrin ok
09:27 olass need to teach in 30 mins
09:27 olass but got time until then
09:27 edrin ok, it's short
09:28 edrin egonw?
10:23 maclean joined #bioclipse
10:54 masak joined #bioclipse
10:54 olass hi masak
10:54 masak OH HAI
10:54 zarah saluton masak
10:55 maclean ohhh. it's esperanto.
10:55 masak zarah: you're the internationally aware one!
10:55 zarah masak: no, YOU'RE the internationally aware one!
10:56 maclean heh
11:05 edrin masak: the console is working well for me now
11:05 masak edrin: \o/
11:05 masak @pz 244
11:05 zarah http://tinyurl.com/axjm5g
11:05 edrin masak: could you add two things to do me favor ?
11:06 masak can I close this one?
11:06 masak edrin: I think I can. which ones?
11:06 edrin yes
11:06 * masak closes
11:06 egonw yeah :)
11:06 egonw masak++
11:07 masak this is shaping up to be a good day.
11:07 edrin masak: 1. I would like to see what command was sent to the console in the console text, too (like js>) so i know what output is associated with what command
11:07 masak 1. consider it done. it is already request #1 from people.
11:07 edrin masak: 2.) please add a record() function... like a .recordStart(filename) .recordStop()
11:08 masak edrin: will discuss this with jonalv, but yes, that seems likely.
11:09 masak edrin: it affects recording of both GUI and console actions, right?
11:09 edrin masak: the file could then be opened in the js editor for cleanup...
11:09 edrin masak: no, mainly just the console
11:10 masak edrin: so GUI actions are always recorded?
11:10 edrin masak: the idea is, one could discover a xmpp service in the console (exploiting tab completion) and when you succeeded you can clean the code for a nice script
11:10 edrin masak: it's not for recording GUI, just for teh script you type
11:11 edrin i can explain later, must continue now
11:11 masak edrin: ok, so it's totally separate from the current recording function?
12:01 masak @tell edrin jonalv and I would like an email to the mailing list, clarifying the recording function a bit more.
12:01 zarah Consider it noted.
12:01 edrin ok
12:01 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
12:01 edrin @msg
12:01 zarah edrin: 18 s ago, masak said jonalv and I would like an email to the mailing list, clarifying the recording function a bit more.
12:02 masak I'll do (1) now.
12:03 Gpox to me it sounds like it is the smame thing only different ways to achieve the same result
12:04 masak Gpox: aye, might well be.
12:06 edrin yes
12:06 edrin masak: it is the same thing, just without gui stuff
12:06 edrin masak: i can explain here
12:06 edrin masak, for example...
12:07 edrin in the bc console you can create a binding for a service
12:07 edrin like: iof = xmpp.getIoFactory(ioschemata);
12:07 edrin now you can tab complete functions in iof:
12:08 edrin for example:
12:08 edrin indoc = iof.getMyServiceInputDoc();
12:08 edrin indoc.setProteiSequence("asdasda");
12:08 edrin *ups, spelling error*
12:08 edrin indoc.setProteinSequence("asdasda");
12:09 edrin result = f.invokeSync(indoc, 30000);
12:09 edrin ...
12:09 edrin recordStop();
12:09 edrin now i can work on the recorded script...
12:09 masak edrin: have you tried doing this with the existing tools? just curious.
12:09 edrin and delete the wrong spelled line: indoc.setProteiSequence("asdasda");
12:10 edrin masak: there is a tool to do this?
12:10 masak edrin: yes.
12:10 edrin ok? where?
12:10 masak edrin: there's the Action History view.
12:10 edrin oh, havent seen this
12:10 edrin ok, then i do not need 2
12:10 masak :)
12:11 edrin masak: and exceptions are now printed to the console :)?
12:11 masak edrin: probably not.
12:11 masak one thing at a time :)
12:11 edrin ok
12:12 edrin but this i would like still
12:12 masak me too.
12:20 CIA-30 bioclipse: carl_masak * r8374 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: [ScriptingConsoleView] commands are now echoed to output
12:21 CIA-30 bioclipse: carl_masak * r8375 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] pulled together a few lines. vanity commit.
12:21 masak git-svn++
12:21 masak oops :)
12:21 masak @karma svn
12:21 zarah svn has a karma of 2
12:21 masak (git-svn)++
12:21 masak @karma git-svn
12:21 zarah git-svn has a karma of 3
12:22 masak git++
12:22 maclean what (if anything) is it possible to do with js.eval from the console?
12:22 maclean (I know what eval is, btw :)
12:23 maclean eg I can't do js.eval("print('hello')"); can I?
12:24 maclean oh, wait, I can.
12:24 edrin yes you can
12:24 edrin eval is part of ECMAscript definitions
12:25 maclean but I have to go js.eval("print('hello');"); to avoid eclipse console errors
12:25 maclean yeees. but I am allowed to do any eval-ing with it, or is there some sort of sandbox?
12:26 masak maclean: I didn't know about the semicolon thing. care to create a ticket for that?
12:27 edrin masak: that's not a bug
12:27 masak edrin: ok.
12:27 maclean It's a feature? :)
12:27 edrin maclean: why do you want to use eval at all?
12:27 maclean I don't, necessarily, but it is there...
12:28 masak :)
12:28 maclean I guess I was thinking of js.eval("def my_func(args) {...")
12:29 edrin ah
12:29 maclean for user-defined-functions
12:29 edrin well, we should definitely discuss a way to design recursive scripting .
12:29 edrin with how to pass input/output to a script
12:30 edrin but this we should do later
12:30 edrin well
12:30 maclean yes, certainly. just curious, is all.
12:33 masak your ideas are intriguing.
12:42 masak olass: when is this week's weekly meeting?
12:43 olass thursday
12:43 masak ah, good.
12:43 olass hmmm
12:43 olass wait, must check with all
12:43 olass is friday OK as well?
12:43 masak yes. :)
12:44 olass egonw: would friday be OK with you?
12:44 egonw I plan to be at BMC on Wed, Thu and Fri
12:44 olass ok, good
12:45 olass I am not sure I'll be here thursday
12:45 olass so let's have the meeting on friday, shall we?
12:45 masak oh! Friday before noon is ok. afternoon not so good.
12:45 olass masak: I know
12:45 olass fri 09.30?
12:45 masak (there's this girl who keeps wanting to see me on Friday afternoons)
12:45 masak olass: 09:30 is fine.
12:46 olass masak: pleasant friday-problem
12:46 masak olass: aye :)
12:46 * olass is joanalv's teacher so he knows that jonalv is free on friday
12:46 masak haha
12:46 olass :-)
13:54 grandm44 joined #bioclipse
13:55 grandm44 hi
13:55 zarah privet grandm44
13:55 maclean hello
13:55 zarah hi maclean
14:02 grandm44 I updated to the last snapshot, went thru all steps (target platform, plugins and configuration in bioclipse.product), but I still have a blank editor when I open a CML or MDL file.
14:03 egonw what platform are you running?
14:03 grandm44 linux 64
14:03 grandm44 java 5
14:04 grandm44 and last ganymede release
14:04 grandm44 I can try under windows if you think it might work
14:06 egonw 32bit?
14:06 egonw that's the only thing I can see differently right now...
14:07 maclean hmmm. I haven't tried b/c on my new 64bit mac yet...
14:07 grandm44 I have a x64 XP... with a 32 bit jdk
14:08 egonw the file does open properly in a Text Editor, or the XML-Lite editor?
14:08 grandm44 On one line, but I can read it, yes
14:11 egonw ok, that's CML then
14:12 egonw ok, any ERROR on the Eclipse console?
14:14 grandm44 http://bioclipse.pastebin.com/m7e39d864
14:14 zarah grandm44's link is also http://tinyurl.com/7fa8wx
14:15 grandm44 maybe lines 588 and after
14:16 egonw yes, that could very well be a problem
14:16 maclean lots of 'logging not found' stuff
14:16 egonw yes, not good either
14:16 egonw grandm44: you are booting Bioclipse via features, right?
14:17 egonw guys, we really need to make that "org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category))" a FAQ item :)
14:18 grandm44 I run BC from the "run configurations" menu, if it is what you mean
14:20 egonw can you try to run it via bioclipse.product?
14:20 maclean Also, to install the eclipse sdk (or pde, I think).
14:20 egonw in eclipse:
14:20 egonw Ctrl-Shift-R
14:20 egonw then type bioclipse.product
14:20 egonw then open the Configuration tab
14:20 egonw and add these features:
14:21 egonw net.bioclipse_feature
14:21 egonw net.bioclipse.chemoinformatics_feature
14:21 egonw net.bioclipse.cml_feature
14:21 egonw net.bioclipse.jchempaint_feature
14:21 egonw and then click the Launch button in the top right corner (green button with white triangle)
14:22 grandm44 Seems to work !
14:22 egonw good :)
14:25 grandm44 thanks :)
14:33 masak joined #bioclipse
14:37 maclean aargh. eclipse sdk, why takest you so long to install?
14:39 masak Java applications are space efficient.
14:41 maclean Hmmm. Gnomic words. Oracular, even.
14:41 maclean Anyway, no, it's just hanging at 58%. grr.
14:41 masak Java is also fast, secure, and portable.
14:42 masak it adheres to the principle "Write Once, Run Anywhere".
14:42 * masak experiences some kind or ironygasm
14:42 maclean :)
14:42 masak 'sargasm', perhaps...
14:43 maclean "Sargassum is a genus of generally planktonic (free-floating) macroalgae (seaweed) in the order Fucales." (wikipedia)
14:44 masak oops.
14:44 masak unless they, also, are sarcastic when they write that.
14:44 maclean double-s
14:44 masak oh, 'sargasSUm'
14:44 masak I see.
14:44 masak yes, heard about those.
14:45 maclean http://www.urbandictionary.​com/define.php?term=sargasm
14:45 zarah maclean's link is also http://tinyurl.com/5ckn87
14:46 masak yup. I think I got it from there originally. I subscribe to their Daily Urban Word service.
14:46 maclean Me too. Some are pretty dull, or hyper-specific, but there's the occasional gem.
14:48 masak aye
14:57 maclean right. so a minimal bioclipse install (feature, core, logger, scripting, scripting.ui, target.platform, ui, ui.business) works on osx_64
14:57 masak great news.
14:59 maclean Well, just thought I would check. Did you get a new laptop on Fri?
14:59 masak I did. I'm giving it basic training as we speak.
15:00 maclean good, good : "drop and give me 20 Mflops!"
15:00 masak stuff like that, yes.
15:04 egonw grandm44: on linux 64 bit too, right?
15:04 egonw can the 64bit users please test InChI?
15:04 egonw e.g. with this script:
15:04 egonw http://gist.github.com/33421
15:04 maclean I saw there was a release
15:05 jonalv joined #bioclipse
15:05 jonalv hi
15:05 zarah hello jonalv, you fantastic person you
15:05 jonalv and news
15:05 jonalv ?
15:05 jonalv :)
15:06 masak :)
15:07 jonalv anything going on?
15:07 masak jonalv: no, not much. :)
15:08 masak just installing things over here.
15:09 jonalv ah new computer :)
15:09 masak aye :)
15:14 grandm44 egonw: yes
15:15 egonw inchi works?
15:15 egonw on 64bit?
15:15 egonw perfect :)
15:15 grandm44 I tested your code, entered it in the javascript console : http://bioclipse.pastebin.com/m2fb1a839
15:15 zarah grandm44's link is also http://tinyurl.com/7tpp8a
15:15 egonw ah, ok... it did not work :(
15:15 grandm44 unfortunately, it seems i doesn't work
15:15 grandm44 it
15:16 egonw ok, but thanx for testing!
15:16 grandm44 no problem
15:16 grandm44 just ask when you need
15:29 masak joined #bioclipse
15:52 maclean egonw : gist 33421 seems to work on osx_64
15:53 egonw ok good
15:53 egonw so mixed experience with 64bit jni-inchi
15:53 maclean some log4j skwawks in the console, but otherwise fine.
15:55 shk3 does anybody here have on opinion on the undo/redo issue?
15:55 egonw Gpox: did you have a look at undo/redo in eclipse?
15:55 egonw I have not gotten around to that :(
15:56 Gpox I have read a litle
15:56 shk3 well, you need to have that IUndoableOperation implemented
15:56 shk3 and then there is a undo/redo stack
15:56 masak how can one tell if one is running osx_64?
15:56 shk3 under Bioclipse administration
15:57 maclean masak: hmmm moment, bitte.
16:00 maclean hmmm. I'm sure there was a way...
16:03 maclean system_profiler ?
16:03 masak aye, and then?
16:04 maclean yeees. it doesn't say, does it.
16:05 masak :)
16:23 lc joined #bioclipse
16:23 egonw hi lc
16:23 lc hi
16:23 zarah hi lc
16:24 lc left #bioclipse
16:25 egonw bye lc
16:28 grandm44 :)
16:34 olass short visit
16:34 maclean huh.
16:34 maclean http://www.appleinsider.com/article​s/08/08/26/road_to_mac_os_x_10_6_sn​ow_leopard_64_bits.html&page=2
16:34 zarah maclean's link is also http://tinyurl.com/6hcxah
16:35 maclean snow leopard will be a 64 bit kernel, leopard is only 32 bit.
16:35 masak ok, thank you very much.
16:36 maclean Executive summary : the situation is complicated.
16:37 masak :)
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19:39 CIA-30 bioclipse: egonw * r8376 /bioclipse2/trunk/plugins/net.b​ioclipse.ioformats/plugin.xml: Added the 4 PubChem XML formats we care about
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