Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-08

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All times shown according to UTC.

Time Nick Message
05:16 masak joined #bioclipse
07:31 Gpox joined #bioclipse
07:54 CIA-54 bioclipse: goglepox * r8151 /bioclipse2/branches/gpox-newMoleculeTable/: Extending compositTable with selection and multiple column support
08:35 CIA-54 bioclipse: ospjuth * r8152 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added missing method testLoadSaveMol for bug #197.
08:35 zarah bug #197 | http://tinyurl.com/8yeuwr
08:45 olass joined #bioclipse
08:46 olass moin
08:46 zarah hi olass
08:46 masak hi olass
08:46 olass hi masak
09:13 gilleain joined #bioclipse
09:13 gilleain mornin
09:14 masak good morning!
09:23 edrin1 joined #bioclipse
09:41 jonalv joined #bioclipse
09:55 zarah joined #bioclipse
10:06 jonalv Gpox++
10:19 edrin1 hi
10:19 zarah hi edrin1
10:22 * gilleain stops reading about tetragraphs and diacritics, and goes back to work...
10:39 CIA-54 bioclipse: carl_masak * r8153 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] reverted r8084
10:39 olass I have bad news
10:39 olass http://www.damnhandy.com/2008/11/29/eclipse-​on-mac-java-6-reveals-more-swt-shortcomings/
10:40 zarah olass's link is also http://tinyurl.com/6or7mh
10:40 olass seems we will not have Java 6 for some time
10:40 gilleain oh noes.
10:40 gilleain and I have just got a new 64bit mac...
10:42 gilleain and come to think of it, I downloaded java6, switched to it, and eclipse /seems/ to run. hmm.
10:42 olass well, there's hope I think
10:42 olass http://www.eclipse.org/swt/cocoaport.php
10:42 zarah olass's link is also http://tinyurl.com/3gp646
10:43 gilleain I guess I didn't switch *shrug*.
10:44 olass so we wait for Eclipse 3.5 I guess
10:46 gilleain guess so.
10:52 edrin1 olass: is there something to present data in bc2?
10:53 edrin1 for example to print it to some graphical rendering engine
10:53 edrin1 html page auto generation to visualize a dataset
10:53 gilleain what-what-what?
10:54 gilleain line graphs?
10:54 edrin1 no
10:54 edrin1 for example working with webservices
10:54 gilleain ok
10:54 edrin1 and the service returned a string array with sequences...
10:54 edrin1 how to visualize them in a general way?
10:55 edrin1 a nicely rendered page.. would be user friendly
10:55 gilleain hmmm.
10:55 edrin1 for example in html to show in a browser window
10:55 gilleain well I suppose that swt has browser plugins
10:56 edrin1 for example: public static void htmlDump(String input[]);
10:56 edrin1 but i mean the rendering engine...
10:57 gilleain so you make the html, and send it as a document to an editor that renders webpages, I guess.
10:57 edrin1 yep
10:57 edrin1 i was just curious if there is something
10:57 gilleain just as if I open an html file in eclipse, it opens in an editor.
10:57 edrin1 because this might be nice in some way
10:58 edrin1 eclipse can show html pages
10:58 gilleain yes
10:58 gilleain there is an editor called "Web Browser".
11:00 gilleain maybe necessary to install the web tools platform
11:04 gilleain org.eclipse.swt.browser.Brow​ser.setText("<html></html>")
12:29 olass edrin1, gilleain: We want the mozill browser in Eclipse
12:29 olass there are projects for this
12:29 edrin1 ok
12:29 olass for now, there is a Browser editor
12:29 olass we just haven't added the Mozilla browser yet
12:29 olass but the Browser should be fine for now
12:29 olass until we need more advanced mozilla features
12:33 CIA-54 bioclipse: ospjuth * r8154 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Added access to getWidget() as required to customize rendering in external plugins.
12:35 CIA-54 bioclipse: ospjuth * r8155 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/BaseObject.java: Added setResource() with no functionality.
12:49 * jonalv needs egonw
13:02 * olass needs coffee
13:02 gilleain Is the sourceforge bug tracker for bioclipse only visible to logged-in users?
13:03 gilleain It seems not to be available until I log in...
13:03 olass gilleain: dunno
13:03 olass but please use pelezilla
13:03 olass and mylyn
13:03 gilleain right, yes, I just remembered pelezilla
13:05 gilleain heh @google pelezilla
13:05 olass @pz
13:05 zarah olass: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
13:05 gilleain nono
13:05 gilleain @google pelezilla
13:05 zarah gilleain: http://www.weddingbee.com/2008/06/01/o​ne-lucky-day-weekend-bonus-pele-zilla/
13:06 olass yeah, saw that earlier :-)
13:06 gilleain top hit : wedding blog!
13:06 gilleain :)
13:06 olass lol
13:07 masak gilleain++
13:07 CIA-54 bioclipse: carl_masak * r8156 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/business/JsConsoleManager.java:
13:07 CIA-54 bioclipse: [JsConsoleManager]
13:07 CIA-54 bioclipse: * turned out that scripts run in the js editor were collapsed to one line
13:07 CIA-54 bioclipse: * consequently, '//' comments hid the rest of the script
13:07 CIA-54 bioclipse: * solved this by adding "\r\n" after each line
13:07 jonalv @google pelezilla site:uu.se
13:08 jonalv zarah: ping
13:08 zarah jonalv: pong
13:08 jonalv @google pelezilla site:uu.se
13:08 gilleain yay - (line feed bug fixes)++
13:08 zarah jonalv: No hits.
13:08 jonalv @google bugzilla site:uu.se
13:08 zarah jonalv: http://runestone.it.uu.se/bu​gzilla/describekeywords.cgi
13:08 masak gilleain: I blame the js editor in this case.
13:09 gilleain pesky js editor.
13:09 masak (js editor)--
13:17 gilleain huh.
13:17 gilleain org.mozilla.javascript.EcmaError: TypeError: Cannot find function calculateSmiles.
13:20 jonalv gilleain: what did you do? :)
13:20 masak gilleain: did you prefix it with a manager?
13:20 gilleain tried to run either of the sample data javascripts
13:21 masak gilleain: oh.
13:21 masak gilleain: I don't think those work, no.
13:21 masak never did.
13:21 gilleain oh right roffle.
13:21 * jonalv doesnt really know which scripts we are talking of...
13:22 masak those are bc1 scripts AFAIK.
13:22 gilleain extractsmilesAndMass.js
13:23 gilleain in Sample Data/Javascripts/
13:23 jonalv I wrote that. it _should_ work...
13:23 jonalv I wonder what has happended
13:24 gilleain I don't need it or anything, I was just randomly trying out features :)
13:25 gilleain aha!
13:26 gilleain it works if you change "mols.get(i).calculateMass()" to
13:26 gilleain "cdk.calculateMass(mols.get(i))"
13:29 masak gilleain++
13:30 gilleain also: I get better output on windows if I change '+ "\n"' to '+ "\r\n"'
13:38 masak gilleain: that's good news.
13:38 masak or something.
13:38 gilleain "or something" I would say.
13:50 masak http://bash.org/?328464
13:51 gilleain I love that one: "ur all freaks thats what u r"
13:52 edrin1 gilleain: to what group are you belonging to?
13:52 gilleain christoph's
13:54 edrin1 ah ok
13:56 olass edrin1: see @pz 229
13:56 olass @pz 229
13:56 zarah http://tinyurl.com/8gd5zk
13:56 olass edrin1: I cannot assign bugs to you yet because edrin has to set you as developer on pelezilla
13:56 olass I have bugged him to be admin as well
13:56 olass @tell egonw: Please make me admin on pelezilla
13:56 zarah Consider it noted.
13:57 edrin1 ok
13:57 olass edrin1: the good news is that I fixed my hivpred XMPP service
13:57 edrin1 olass: that's strange, for me it is working
13:57 olass will upload it now
13:58 olass edrin1: can you assign it to yourself?
13:58 edrin1 as far as i remember
13:58 olass hmm
13:58 olass will try again
13:58 olass actually worked now
13:59 olass mylyn did not find you however
13:59 olass but writing it explicitly worked
13:59 edrin1 bug reasigned ...
13:59 olass why aliban and not edrin?
14:00 jonalv gilleain: that javascript isn't working because someone (egonw) changed from Smiles to SMILES everywhere. (except in that script perhaps?)
14:01 jonalv at least I think so
14:01 gilleain hmm.
14:02 jonalv no actually it fails even before that
14:02 gilleain I "irc-committed" a fix a few minutes ago :)
14:02 gilleain "print(cdk.calculateMass(mols.get(i)) + "\n");"
14:02 jonalv what does that mean?
14:03 gilleain I mean that I typed it into the chat window :p
14:03 gilleain but I could /actually/ commit it if you like
14:03 * jonalv must have missed that...
14:03 jonalv please do that
14:07 gilleain oh, right, the smiles->SMILES change did work in the other script.
14:08 olass masak: the tab completion bug for case insensitive commands is really annoying
14:08 masak olass: working on that one.
14:08 olass great
14:08 masak it's 50% half almost done.
14:08 olass things are improving today
14:08 * olass is happy for that
14:08 olass edrin: I got an XMPP script for you to test
14:09 edrin1 ok?
14:09 edrin1 olass: the console is not working for me
14:09 edrin1 and running scripts does not really work either
14:09 olass can you run JS files?
14:09 olass why is that?
14:09 edrin1 it sometimes work
14:09 edrin1 s
14:10 olass edrin1: http://paste2.org/p/126620
14:10 edrin1 olass: i assigned some bugs to you
14:10 masak edrin1: maybe you got bitten by the '//' bug I just fixed.
14:10 olass seen them
14:10 edrin1 olass: there i reported some errors
14:10 olass reassigned most to masak
14:10 olass he's in charge of scripting and console
14:10 edrin1 for example print("asdasd") does not print to the console :)
14:10 olass for me it does
14:11 olass masak: did you hear this?
14:11 masak sure.
14:11 masak works here too.
14:11 masak edrin1: what operating system are you running?
14:11 olass edrin1: do you get exception?
14:11 edrin1 windows
14:11 masak edrin1: I see.
14:12 edrin1 olass: i am not home, i cant test
14:12 olass ok
14:12 edrin1 olass: what error do you get?
14:12 olass I get no error. What do you mean?
14:12 edrin1 olass: or does the script work for you?
14:12 olass it works!
14:13 edrin1 ah cool :)
14:13 edrin1 nice script!
14:13 olass I like it
14:13 olass I actually once wrote a plugin that displayed things nicely in jfreechart
14:13 olass will try to find it again
14:14 edrin1 olass: what happens if the sequence is > or < 99 AA? what if there are letteres that are no aminoacids?
14:14 olass nic egraphics are never wrong
14:14 olass edrin1: it complains
14:14 masak a møøse once bit my sister...
14:14 olass masak: mose bites are serious!
14:14 masak olass: I know!
14:15 olass or was that elks?
14:15 masak no, definitely møøse
14:15 masak Wi nøt trei a høliday in Sweden this yer?
14:15 olass edrin1: it has an AminoAcidValidator
14:15 masak See the løveli lakes
14:15 edrin1 ok :)
14:16 masak The wonderful telephøne system
14:16 masak And mani interesting furry animals
14:16 olass Holy grail?
14:16 masak aye.
14:16 * olass loves that movie
14:16 edrin1 olass: minimal thing: var rename resultObj  to var resultDoc ?
14:17 olass hmm
14:17 edrin1 not sever of course
14:18 edrin1 just because inputDoc is used, too
14:18 olass getOutputObject(result) should then in analogy be getOutputDocument(resukt)
14:18 olass right?
14:18 olass else it would be confusing
14:18 edrin1 olass: getOutputObject is a dummy function anyway. there should be another function in *this* iofactory that sounds like
14:19 edrin1 .getHIVPredInputDocument(output)
14:19 edrin1 something like this
14:19 edrin1 err
14:19 edrin1 .getHIVPredOutputDocument()
14:19 olass there is
14:20 olass but returns null
14:20 edrin1 huh?
14:20 olass try it yourself
14:20 olass here it returns null
14:21 olass will file you a bug
14:21 edrin1 olass: when you take a look in the binding files: there is the IoFactory.java , what does the code say?
14:21 olass mom
14:21 edrin1 (starting up my laptop
14:25 CIA-54 bioclipse: gilleain * r8157 /bioclipse2/trunk/plugins/net.bioclip​se.data.sampledata/data/Javascripts/ (extractsmiles.js extractsmilesAndMass.js): Some functions have moved or changed names, so fixing sample calls to those.
14:25 edrin1 olass: hypothetic the returned object is not valid for specified output definitions??
14:26 olass could be
14:26 olass don't you validate returned docs?
14:26 olass but they look good
14:26 edrin1 no
14:26 olass not?
14:27 edrin1 well, it is valid xml i suppose, and maybe the autogenerated function that wants to parse it has a problem ....
14:27 olass so what is wrong?
14:28 olass what don't you like?
14:29 edrin1 in my opinion the reason might be that it returned null because after parsing the output in XMLBeans the "validation to the output XML Schema" fails:
14:29 edrin1 like in ioFactory class
14:29 olass edrin1: it should throw a validation fails exception IMO
14:31 edrin1 getHIVPredOutputDocument(Element output) {
14:31 edrin1 XmlObject xs = parse(ouput);
14:31 edrin1 if (xs instanceof HIVPredOutputDocument)
14:31 edrin1 return (HIVPredOutputDocument) xs;
14:31 edrin1 return null;
14:31 edrin1 }
14:31 edrin1 olass: I fully agree, it should throw an exception
14:31 edrin1 if you filed the bug i will solve it
14:31 edrin1 file
14:32 edrin1 then it will throw an exception
14:32 olass edrin1: bug 230 is for you
14:32 olass @pz 230
14:32 zarah http://tinyurl.com/a3959c
14:33 edrin1 thx
14:34 olass so is 231
14:35 * olass will get a coffee and some chcolate
14:35 edrin1 olass: wait
14:35 edrin1 olass: can you see if the binding is generated ?
14:36 edrin1 in the binding folder?
14:41 edrin1 masak: question: when a script is run, are all commands run in a sequence? meaning one after the other?
14:41 masak edrin1: no.
14:41 masak edrin1: I don't see why people think that would work.
14:42 gilleain Some languages interpret like that, I think.
14:42 edrin1 that means if line 1 has a doThis(); and line 2 has a doThat(); it might happen that doThis() did not return or finish before doThat() is called !?
14:43 masak edrin1: I just hand over all control to the js interp.
14:43 edrin1 ok
14:43 masak edrin1: otherwise I'd have to do if statements and loops myself.
14:43 masak which seems like a bad idea.
14:43 edrin1 sure
14:43 edrin1 then it's ok
14:43 jonalv masak: good point
14:44 masak if someone wants to do the if statements and loops, that's ok by me.
14:44 jonalv I didn\t think of that...
14:44 jonalv )(
14:44 jonalv :)
14:45 CIA-54 bioclipse: carl_masak * r8158 /bot/trunk/zarah.pl: [zarah] now responds when people say 'mom' on the channel
14:45 masak zarah: reboot
14:45 zarah joined #bioclipse
14:45 masak mom
14:45 zarah mother!
14:45 masak zarah++
14:46 masak zarah: you're a smart girl.
14:46 zarah masak: Then why did you turn me down for that raise? Over.
14:46 * masak changes the subject
14:51 olass masak: mom
14:51 olass mom for masak
14:51 olass mom
14:51 zarah my son!
14:52 olass !
14:52 masak olass: she only does it in that case.
14:52 masak so, not very intrusive.
14:52 olass zarah: if you are my mother, who is my father?
14:52 zarah olass: I'm just a bot, you expect me to understand that?
14:52 masak she's playing innocent.
14:52 olass definitely
14:52 masak mom
14:52 zarah my son!
14:52 olass zarah: I'll figure it out
14:52 zarah olass: eh... wha'?
14:53 masak wow, me too?
14:53 olass does that make us brothers?
14:53 olass zarah: is it so?
14:53 zarah olass: I'm just a bot, you expect me to understand that?
14:53 masak olass: maybe just half-brothers, but still.
14:53 olass virtual brothers
14:54 masak forever!
14:54 olass mom
14:54 zarah dad!
14:54 olass ?
14:54 masak :D
14:54 olass that does not make sense
14:54 masak definitely not.
14:54 jonalv mom
14:54 zarah grandpa!
14:54 olass zarah: you are the stupid one
14:54 zarah olass: no, YOU'RE the stupid one!
14:54 olass zarah: you are the lying one
14:54 zarah olass: no, YOU'RE the lying one! :)
14:55 olass why not a smile in the first one?
14:55 masak she only smiles sometimes.
14:55 olass oh
14:55 masak zarah: you are the smile in the first one!
14:55 zarah masak: no, YOU'RE the smile in the first one! :)
14:56 jonalv zarah: you are like a parrot
14:56 zarah jonalv: excuse me?
14:56 masak jonalv: you're not playing by the rules!
14:57 jonalv zarah: you are the parotty one!
14:57 zarah jonalv: no, YOU are the parotty one! :)
14:57 masak zarah: you're the repetitive one!
14:57 zarah masak: no, YOU are the repetitive one! :)
14:57 masak zarah: no, YOU are the repetitive one! :)
14:57 zarah masak: oh, shut up :)
14:57 masak :)
14:57 masak zarah: oh, shut up
14:57 zarah masak: :)
15:05 jonalv zarah: mom
15:05 zarah jonalv: eh... wha'?
15:06 masak jonalv: it's not a command, it's a regexp.
15:06 jonalv masak: I am just exploring...
15:09 masak mom
15:09 zarah mom, I'm home!
15:10 olass masak: how do I echo to console in the simplest way?
15:10 CIA-54 bioclipse: jonalv * r8159 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs/ (876 files in 333 dirs): Merge branch 'master' into jonalv-merged
15:10 olass jonalv++ /FINALLY!
15:10 gilleain 876 files!!
15:11 masak jonalv++
15:11 gilleain jonalv++
15:12 jonalv gpox++
15:13 masak GPox++
15:17 gilleain so what was it all?
15:18 gilleain or, right n/m
15:26 jonalv gilleain: I merged all from trunk into the branch...
15:26 gilleain oh.
15:26 CIA-54 bioclipse: carl_masak * r8160 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: [ScriptingConsoleView] made tab completion case insensitive
15:54 CIA-54 bioclipse: carl_masak * r8161 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: [ScriptingConsoleView] updated JavaDoc a bit
16:24 CIA-54 bioclipse: carl_masak * r8162 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
16:24 CIA-54 bioclipse: [JsConsoleView] refined the search for methods to also recurse
16:24 CIA-54 bioclipse: through parent interfaces
16:40 masak @pz
16:40 zarah masak: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
16:44 olass off to the train, will check back later
16:44 olass bye
16:52 CIA-54 bioclipse: jonalv * r8163 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs​/plugins/net.bioclipse.scripting.ui/src/net/bio​clipse/scripting/ui/views/JsConsoleView.java:
16:52 CIA-54 bioclipse: [JsConsoleView] refined the search for methods to also recurse
16:52 CIA-54 bioclipse: through parent interfaces
17:21 CIA-54 bioclipse: jonalv * r8164 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs​/plugins/net.bioclipse.scripting.ui/src/net/bio​clipse/scripting/ui/views/JsConsoleView.java: fixed interface inheritance problem in man command
18:36 edrin1 left #bioclipse
21:16 adssss joined #bioclipse
21:57 CIA-54 bioclipse: edrin_t * r8165 /xws/trunk/xws4j-binding/src​/net/bioclipse/xws/binding/ (2 files in 2 dirs): added exception on error casting/parsing output
22:09 CIA-54 bioclipse: edrin_t * r8166 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (5 files in 3 dirs): adapted to throw exception if output "parsing"(class casting) in IoFactory fails
22:09 CIA-54 bioclipse: edrin_t * r8167 /xws/trunk/xws4j-binding/src/net/bioclipse​/xws/binding/tools/IoFactoryBuilder.java: bug fixed

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