Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-04

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All times shown according to UTC.

Time Nick Message
06:27 Gpox joined #bioclipse
06:27 egonw joined #bioclipse
06:46 olass joined #bioclipse
06:47 olass moin
06:47 zarah oh hai olass
06:47 egonw moin
06:47 zarah saluton egonw
07:27 edrin joined #bioclipse
07:27 edrin hi
07:27 zarah hi edrin
07:29 edrin olass, egonw: did you get my mail?
07:30 egonw yes
07:30 egonw edrin: drop OME, go for 6 schema
07:33 edrin ok
08:36 jonalv joined #bioclipse
08:36 egonw hi jonalv
08:36 jonalv oh hai
08:36 zarah privet jonalv
08:36 jonalv all good today?
08:47 rojasm joined #bioclipse
09:29 egonw mmmm... pele is up 156 days now....
09:29 egonw sounds like a new Ubuntu release :)
09:29 jonalv egonw: that's nice
09:29 * jonalv is still running 8.04 at home... :)
09:29 egonw average load: 0.37
09:29 egonw not sure for the peroid over which that was calculated
09:29 jonalv is that %?
09:30 egonw [0,1]
09:30 jonalv oh are we using that much?
09:30 jonalv I thought we where hardly using it at all...
09:30 egonw quite a few things run there now
09:31 egonw the XMPP services (cdk, rdf, qsar)
09:31 egonw pelezilla
09:31 jonalv ah cool
09:31 egonw planet bioclipse
09:31 egonw CDK Nightly *5 or so
09:31 jonalv you have nightly build there :)
09:31 egonw right :)
09:31 egonw planet cdk
09:31 egonw busy machine
09:32 egonw I really should start about backups...
09:32 egonw start think
09:33 jonalv yes... :)
09:38 * jonalv <- lunch
11:18 jonalv egonw: PING!
11:19 egonw PPPPOOOONNNNNGGGG
11:19 egonw CAN YOU SHOUT A BIT HARDER?
11:19 jonalv egonw: have you changed BioclipseException from extending RuntimeException to extending Exception?
11:19 egonw TOO MUCH RAIN
11:19 egonw INTERFERING WITH IP TRAFFIC
11:19 jonalv HAVE YOU?
11:19 egonw ummm...
11:19 egonw I hope not
11:20 egonw that sounds like a scary change
11:20 jonalv your name is on that row in my git blame
11:20 egonw mom
11:21 jonalv egonw: If you have made this I would like you to explain why...
11:21 egonw yeah, interested too...
11:22 egonw mmm... part of the commit
11:22 egonw that moved things into a new hierarchy...
11:22 egonw so, /me is off the hook
11:22 egonw also check the last line
11:22 egonw and lines 1, 3-12
11:22 egonw my name is there only because I move that class into a new location
11:23 egonw March 2008!
11:23 egonw phew...
11:23 egonw jonalv: you scared me!
11:23 jonalv egonw: okey, so who do I blame then?
11:23 egonw why blame
11:23 egonw March 2008...
11:24 egonw that's ancient history
11:24 egonw that is
11:24 egonw is has not been a RuntimeException after that...
11:24 egonw ever
11:24 egonw what makes you think it was not a mere Exception from the start?
11:24 * egonw looks up previous location of that file
11:25 egonw 4981
11:25 egonw that's the commit
11:25 egonw that's over 5000 commits ago :)
11:26 jonalv egonw: I rewrote that class and I am pretty sure I made it a RuntimeException
11:26 jonalv or am I just confused here?
11:27 egonw dunno
11:28 Gpox @pz 1000
11:28 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1000
11:28 egonw Gpox++
11:29 jonalv egonw: you are right it seems like it has never been a Runtimeexcetion...
11:29 jonalv egonw: but I was so sure..
11:29 egonw Gpox: will look into that problem
11:29 jonalv egonw: I could have betted highly on that
11:30 egonw a shame we didn't :)
11:31 jonalv hehe
12:09 olass egonw: did shk3 implement tanimoto in CDKManager?
12:13 egonw I have not seen such patch yet
12:13 egonw may have missed it
12:18 olass where is he btw?
12:18 egonw dunno
12:19 olass egonw: what is the difference between inchi and inchiKey?
12:19 olass (I know I have asked before)
12:19 egonw inchikey == hash of inchi
12:19 egonw inchi -> unique
12:19 egonw inchikey not
12:19 egonw inchi = long
12:19 egonw inchikey = short
12:20 olass how long is inchi?
12:20 olass on average?
12:20 egonw no idea
12:20 egonw I can tell you later this week
12:20 egonw based on the pubchem data
12:20 olass :)
12:20 egonw it is now loading the data into mysql
12:20 egonw well, some data
12:21 egonw inchi + cid
12:21 egonw should have added inchikey too, I guess
12:21 egonw mmm... maybe should reboot
12:21 olass when use inchi and when inchikey?
12:21 egonw always inchi
12:21 olass first compare inchikey, then inchi?
12:22 olass to speed up?
12:22 egonw speed up what?
12:22 olass a qeuery?
12:22 egonw yes
12:22 olass finding exact mathes
12:22 egonw inchikey must be the same, and if then inchi must be the same too
12:22 olass so isomorphism is not required?
12:22 egonw huh?
12:23 egonw you are talking about exact matches...
12:23 olass yes..?
12:23 olass please explain
12:23 egonw well, if the are exact matches, that implies isomorphic
12:23 olass what is exact match?
12:23 olass and what is isomoprh?
12:23 * olass is confused
12:24 egonw isomorphic -> same chem graph
12:24 egonw exact match -> isomorphic and same stereo, etc
12:24 olass what is etc here?
12:24 olass apart from stereo?
12:25 egonw EZ isomerism
12:25 olass does an MDL molfile store these values?
12:25 egonw etc -> not just atom parities
12:25 egonw they can
12:27 masak joined #bioclipse
12:28 olass egonw: got a minute?
12:32 masak olass: in r9673, you changed "Copyright 2008" to "Copyright 2009". I don't know how important it is, but common practice seems to be "Copyright 2008-2009".
12:33 olass masak: right
12:33 olass must have made a mistake there
12:33 olass what was it about?
12:33 olass what file?
12:33 masak in other places in the Bioclipse code, I actually see "2008-2009".
12:33 masak olass: just go to the commit in question :)
12:33 olass how?
12:34 masak olass: svn log -v
12:34 masak svn log -v -r9673
12:35 olass svn: '.' is not a working copy
12:35 olass that's what I get
12:35 masak olass: are you perchance running git-svn?
12:35 masak olass: if not, are you in the right directory?
12:35 olass masak: what is the right dir?
12:36 masak olass: a bc2 source dir...?
12:36 olass any?
12:36 olass I am in bc2 workspace root
12:36 masak preferably the top one with svn.
12:36 masak olass: the workspace is not a source dir.
12:36 olass mbpro:net.bioclipse.ui ola$ svn log -v -r9673
12:36 olass svn: This client is too old to work with working copy '.'; please get a newer Subversion client
12:37 olass masak: sorry
12:37 * olass will wait for git
12:37 * masak checks what file it was
12:37 masak olass: meanwhile, get a newer SVN client. :)
12:37 olass how?
12:37 * masak rolls eyes
12:37 olass MOHAHAHA
12:38 masak olass: you could try Googling for it.
12:38 olass seriously
12:38 olass macports?
12:38 masak probably.
12:38 olass port upgrade svn
12:38 masak aye.
12:38 olass arrh
12:38 masak might be 'subversion' or something, though.
12:39 olass aye.
12:39 masak olass: the file was bioclipse2/trunk/plugins/net.bioclip​se.data.sampledata/about.properties
12:39 olass thx
12:40 masak np
13:07 olass Gpox: is a SDFRandomAccessWriter filed as a bug? Cannot find it...
13:07 olass iterate over GB SDF, calculate properties for individual molecules and then saving them on the fly, not keeping the entire file in memory...
13:08 olass egonw: maybe this is a CDK bug?
13:09 egonw Gpox: use MDLWriter
13:09 egonw you can use writeMolecule(cdk.interfaces.IMolecule) to append entries
13:09 olass egonw: append?
13:09 egonw but updating a single entry is indeed not possible...
13:09 egonw if that is what is intended
13:09 olass right
13:09 egonw ic
13:10 egonw no idea how to do that
13:10 olass so a new file need be created, but then it works?
13:10 olass egonw: it does not keep all in memory then?
13:10 olass sounds promising
13:11 egonw no, it does not
13:11 egonw but there is an immense amount of IO
13:11 egonw because one has to copy the whole file...
13:12 olass upon completion, yes
13:12 olass or what?
13:12 egonw guess so...
13:12 egonw I can imagine that upon replacing, you write the new items first
13:12 egonw and upon completion copy all entries from the old files which have not been replaced
13:12 egonw but doing it while keeping order sounds much more tricky...
13:12 egonw but again
13:13 egonw I really don't think this is something we should focus too much on
13:13 egonw this is what structuredb is about
13:13 olass egonw: we don't have structuredb :(
13:14 olass but I see your point
13:14 egonw no, and we don't have props changes for SDF yet
13:14 olass not yet
13:24 edrin left #bioclipse
13:24 edrin joined #bioclipse
13:45 olass joined #bioclipse
13:45 olass egonw: looking fwd to comments on the bugs I submitted today
13:45 egonw yes
13:46 * egonw is working on fixing bug 1000
13:46 * masak 1002
13:46 masak embarassing... :)
13:46 jonalv @pz 1002
13:46 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1002
13:46 * olass is on bug #845
13:47 masak olass++ # nice bug report.
13:47 olass :)
13:47 jonalv olass++ // 1002 is a very nice bug repport
13:47 olass \o/
13:47 * masak is quicker, and can spell
13:47 masak :)
13:47 jonalv masak: I must remmebr to not say things out loud that I plan to say
13:47 jonalv |write
13:48 masak jonalv: aye, do so. :)
13:48 * jonalv fails too c why the isnult was nicassari
13:55 egonw OK, 500 thousand structures in the PubChem copy on Pele now
13:55 egonw of the 25M
13:56 egonw cid, inchi, inchikey
13:57 egonw so, nothing much to see really
13:58 jonalv egonw: are you making a copy of PubChem on pele?
13:58 egonw as side effect of doing some analysis on it, yes
13:58 jonalv poor pele
14:00 masak olass: I should have a test for something like bug #1002...
14:01 egonw jonalv: poor pele?
14:01 jonalv pele is working hard these days...
14:03 olass masak: what do you mean?
14:03 masak olass: I mean, it's not a GUI-related thing, and it can be tested against regressions.
14:03 olass ok, please write a test if you like
14:04 masak olass: essentially, that means that the next time this occurrs, the tests will catch it before a human does. :)
14:04 masak ...which is a good thing.
14:04 egonw masak: that's what I asked about last time...
14:04 egonw masak: how can we ensure a JS command works properly
14:04 egonw which involves catching thrown exceptions and output
14:05 masak egonw: well, that's slightly different.
14:05 masak egonw: this bug was 100% console-related.
14:05 egonw how so?
14:05 egonw what is differnt?
14:05 masak egonw: it didn't even involve the GUI parts of the console.
14:05 egonw so?
14:05 egonw please explain
14:05 masak egonw: this has nothing to do with JS.
14:05 egonw I do not understand
14:05 masak egonw: it's just the tab completion of the console.
14:06 egonw ah, just harder to make a unit test for?
14:06 masak egonw: I can see how I could make a regression test out of #1002.
14:06 masak that's my point.
14:06 masak with JS and/or GUI involved, I don't see how, really.
14:06 masak but this one's easy.
14:08 CIA-40 bioclipse: carl_masak * r10047 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
14:08 CIA-40 bioclipse: [ScriptingConsoleView] fixed #1002
14:08 CIA-40 bioclipse: The condition for allowing 'help' and 'man' as alternative tab completions
14:08 CIA-40 bioclipse: was too permissive. It allowed not only these alternatives in the first
14:08 CIA-40 bioclipse: position, but also when it had encountered a dot, and the whole term was
14:08 CIA-40 bioclipse: in the first position. Forbade the latter case.
14:10 edrin masak: I want to provide the javascript tools in jsexecution as a manager, do you have something against this?
14:11 masak edrin: what are those tools, more exactly?
14:11 * masak does not have such good overview over jsexecution
14:19 edrin various hack functions
14:19 edrin they are documented
14:20 edrin hm no
14:20 jonalv egonw: newly rebased version of my brnach available on pele now if you are intrested
14:20 masak edrin: 'various hack functions' sounds not-too-desirable... :) but I don't see the harm in providing access to them through a manager.
14:20 edrin cant make them an interface
14:20 edrin err an
14:20 edrin manager
14:20 masak edrin: no?
14:20 masak then what, in effect, is your question?
14:21 * jonalv walks by
14:21 edrin they currently need the ThreadSafeConsoleWrap
14:21 * masak is lost
14:22 edrin masak: the problem at the moment is that i have an object "jst" (javascripttools) that can be used in js from editor but is not available in jsconsole
14:22 masak edrin: uhm.
14:22 edrin the most important thing why is that
14:22 masak yes.
14:22 jonalv edrin: why is that?
14:23 edrin when running a script i have this console for it where it prints to. and it makes sense that a script can print to its indivivual console...
14:23 jonalv edrin: oh you don't know
14:24 edrin i wanted to add an option later that a script when executed spawns its own console...
14:24 jonalv edrin: uhm are you saying that each script has it's own individual console now?
14:24 edrin no, not yet
14:24 jonalv ah
14:24 edrin but maybe later as an option, (dropdown button)
14:24 * jonalv hasn't kep up (he lives in a branch for the moment)
14:24 edrin it would then also make sense to have multiple jsconsoles
14:25 edrin while you do something in console 1 you can do another thing in console 2
14:25 edrin same for js from editor
14:25 edrin "parallel scripting"
14:26 edrin anyway, each script needs a way to print to its log-console
14:26 edrin jonalv, masak: are you using MacOS X?
14:26 jonalv I am still not entirely sure that I want a zillion of JavaScript consoles for inout and then another zillion of consoles for output. edrin, masak: Why was it you two couldn't play along in the same console again?
14:26 masak edrin: aye.
14:26 * jonalv primarily works on OS X
14:27 masak jonalv: which console is it that you want, mine or edrin's? :P
14:27 edrin jonalv: can you checkout current xws4j and try one of Ola's gists ? he has problems with it and we must know if this is really a platform issue
14:27 jonalv masak: honestly I am not sure I care which one but I do want the functionality found in yours...
14:28 masak jonalv: noted.
14:28 masak jonalv: well, I'm not sure I want output from the outside in mine.
14:28 masak jonalv: so that might actually be the issue.
14:28 jonalv edrin: yes as it happends I just rebased so I should have the latest xws4j here, what do you want me to try?
14:29 olass jonalv or masak: could one of you try to run the gist 47421 and report if it works or throws exception?
14:30 olass sry for pasting in wrong channel
14:30 olass it should have gone here
14:30 jonalv olass: what features do I need?
14:30 olass gist
14:30 olass xws4j
14:30 olass oh
14:30 CIA-40 bioclipse: egonw * r10048 /bioclipse2/trunk/cdk-externals/trunk/ (12 files in 12 dirs): Placed packages with data files only in Export-Package too (fixes #1000, I think)
14:30 olass gist is in core
14:30 jonalv olass: isn't gist in core?
14:30 zarah bug #1000 | http://tinyurl.com/ca645a
14:30 jonalv :)
14:30 edrin jonalv: you need xws4j plugin only
14:31 edrin jonalv: you must setup an xmpp account in bioclipse preferences
14:31 jonalv edrin: okey is there a wiki page for that?
14:32 edrin jonalv: no, but it is easy, ola can tell you a test account for ws1
14:32 edrin jonalv: just open preferences...
14:32 edrin and add the test account
14:32 jonalv I am there
14:32 jonalv edrin: what test account?
14:33 edrin test@ws1.bmc.uu.se is the test account
14:33 edrin pwd
14:33 edrin test
14:33 edrin ;)
14:33 Gpox egonw++
14:33 egonw Gpox: it works now?
14:33 jonalv edrin: uhm there is no account field... there is a server and a Jabber ID field...
14:33 Gpox yes
14:33 egonw good :)
14:33 egonw weird that this has not shown up before
14:34 edrin jonalv: jabber ID is test@ws1.bmc.uu.se and server is ws1.bmc.uu.se
14:35 jonalv edrin: the error handling could use some help here...
14:36 edrin jonalv: what is the problem?
14:36 jonalv I wrote the adress wrong and only got a decent error on the console in Eclipse...
14:37 jonalv the Consoile in Bioclipse only said somethign about a wrapped exception but not the actual exception that told me what went wrong...
14:37 edrin the jsconsole?
14:37 edrin xmpp.connect() ?
14:37 edrin or from jseditor ?
14:38 edrin or the xmpp log/debug console?
14:38 jonalv anyway I get a Predicted susceptibility on masak's Javascript Console
14:38 jonalv when I do it right
14:38 edrin olass: you see?
14:38 edrin jonalv: happy to hear this!
14:38 jonalv edrin: yes on the consoel know as only "Console" it looks a bit like this:
14:38 olass ?
14:38 olass what was wrong?
14:39 jonalv org.mozilla.javascript.WrappedException: Wrapped java.lang.reflect.UndeclaredThrowableException (line: #23)
14:39 jonalv olass: I missed an e in uu.se the first time...
14:39 jonalv edrin: that error message could be better...
14:39 olass ok, the gist works with you?
14:40 jonalv olass: yup
14:40 jonalv at least I think so
14:40 edrin jonalv: indeed the error message could be better
14:40 olass edrin: much could be improved with error handling in xws
14:40 jonalv I am not entierly sure what it should do...
14:40 edrin i know
14:40 masak edrin: if you want inspiration, the js console already looks inside wrapped exceptions.
14:40 jonalv edrin: but in Eclipse I get: Caused by: java.net.UnknownHostException: ws1.bmc.uu.s
14:41 edrin well, actually jonalv it should print this :/
14:41 jonalv edrin: if you did the error handling the way the rest of Bioclispe does using masak++s code for it then that inforation would be there...
14:41 edrin olass: the gist works at jonalv's MacOSX
14:41 olass ok
14:41 jonalv edrin: okey
14:41 egonw jonalv: .se?
14:42 jonalv egonw: that was not so easy to understand...
14:42 egonw [16:40:47] <jonalv> edrin: but in Eclipse I get: Caused by: java.net.UnknownHostException: ws1.bmc.uu.s
14:42 edrin jonalv: how does the jsconsoel do this? do you have a wiki that tells me how to get the thing in the wrap?
14:42 masak edrin: JsConsoleView.java:97-107
14:42 jonalv edrin: ask masak but I think there is a method somewhere that you can simply just call
14:44 masak edrin: that method actually does two things: (1) unwraps the exception to the innermost throwable, or one being a BioclipseException
14:44 edrin masak: for example if I use the js.print() method from the editor run script it would print to the jsconsole, right? I guess you wont like this, do you?
14:45 edrin masak: ok, will implement this function
14:45 masak (2) returns the message, or in the case of a non-BioclipseException, the exception name plus the message
14:45 masak edrin: re js.print(). it will, and I don't mind that.
14:46 masak edrin: that's an explicit transgression. those are ok :)
14:46 edrin masak: ok, but wouldn't it be better to direct the js.print() to the "associated" console?
14:48 masak edrin: no, because 'js' here means 'the JS console'.
14:48 masak edrin: cf 'js.clear()'
14:48 edrin ah
14:49 edrin maybe rename the js then to jsc (like jsconsole) ?
14:50 egonw console.print() ?
14:50 edrin i would have expected js to be javascript
14:50 masak edrin: unless you have something competing for that manager name, I would advise against renaming 'js'. :)
14:50 edrin although the js.print() would also be logical if it prints to the 'associated' console
14:50 masak egonw: 'console' might be confusing, since there are a fair amount of consoles...
14:51 egonw true
14:51 jonalv masak, edrin: Could you take a few moments and explain to me how you want all these consoles to interact?
14:51 edrin masak: in fact i like a js. with some helper functions (for example those available in the jst. right now)...
14:51 * jonalv is sort of lost among all consoles...
14:52 masak edrin: the less state we have to mix into our basic constructs, the better, I think.
14:52 masak jonalv: interact?
14:52 masak jonalv: there's a bunch of consoles, and the nice things about them is that the don't interact, for the most part.
14:53 jonalv masak: yea, it sounds to me as if edrin wants JavaScript consoel to write in and another for printing stuff in
14:53 jonalv and then multiple instances of such pairs
14:53 jonalv that will mean many consoles...
14:53 jonalv and pairwise interaction
14:53 * masak does not want
14:54 jonalv edrin: maybe I missunderstood?
14:54 edrin jonalv: no, i do not want two consoles
14:55 edrin all i mean that in principle each script should finally have its personal location to print to, so that if you run different scripts they do not mix things up
14:56 edrin for example if the jseditor would support multiple instances (while each gets its personal javascript newly created instance) i would just push the script in a newly created instance of it
14:57 edrin unfortunately the jsconsole is currently avaialble as a singular instance, and it has a global javascript instance
14:58 edrin running different scripts on the same javascript instance is not logical, impossible to debug scripts this way, and no lines
14:58 edrin where the error is
14:59 jonalv edrin: can't we add lines?
15:00 edrin jonalv: where?
15:00 jonalv edrin: to the error messages in the JavaScript console...
15:01 jonalv or did I miss something?
15:01 edrin jonalv: in my opinion it is a fundamental principal that each single script should primarily run in its own javascript instance, otherwise you could mix up variables (objects)
15:02 masak edrin: we're moving in that direction, yes.
15:02 edrin jonalv: for example you do script 1: var text = "blah"; and then script2: js.print(text);
15:02 masak edrin: not quite there yet. the full move over to that reality is slated for 2.1.
15:02 CIA-40 bioclipse: ospjuth * r10049 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (2 files in 2 dirs): Implemented checkboxes to enable/disable auto updates on startup in the prefs Update Sites page. Solves bug #845.
15:02 zarah bug #845 | http://tinyurl.com/crwjj2
15:02 masak edrin: there's a pz ticket about it.
15:02 edrin if you run script 1 first and 2 second this works, other way round it does not ...
15:03 edrin jonalv: do you understand?
15:03 jonalv edrin: yes offcourse, but the important thing is that you can\t rung them simultanesosly
15:03 * olass wants to rung scripts simultaneously
15:03 edrin I did not get this :(
15:03 masak jonalv: see?
15:03 edrin why cant i simultan?
15:03 jonalv edrin: there is not way to start both those script at the same time
15:03 olass rung?
15:03 masak jonalv: perfect example of lack of spelling preventing comprehension. :)
15:04 jonalv masak: it's not like I wasn't trying
15:04 jonalv masak: I was
15:04 masak jonalv++ # for trying
15:04 olass :)
15:04 edrin jonalv: sureyou can, each must have its personal javascript instance
15:04 olass edrin: that is 2.1
15:04 masak olass++ # for being up-to-date
15:05 olass edrin: there are bugs about this in pelezilla
15:05 jonalv edrin: but as of now you can't run them simultanously and that is the important thing
15:05 edrin olass: for jsconsole, yes, jseditor can run scripts in parallel, but they all print to the same console (and that's a thing i want to fix at some point as an option for running a script)
15:05 jonalv edrin: if you are so careless that you use an uninitilaised variable in your scripts then you have yourself to blame as of now...
15:06 olass I see
15:06 edrin ?
15:06 olass edrin: I want content assistance in the jseditor!
15:06 olass it is hard to write scripts now :(
15:06 edrin back in 3 minutes
15:06 jonalv edrin: who was that "?" for?
15:06 edrin olass: indeed, one needs a way to record scripts in the console and save them as .js :)
15:07 olass there are bugs for this
15:07 edrin you have yourself to blame as of now... <- what do you mean
15:07 * edrin back in 3 minutes
15:07 edrin student's waiting
15:07 olass keep 'em waitin ;)
15:07 olass (students are used to that)
15:07 olass (me too)
15:09 jonalv edrin: I was refering to your second script: "js.print(text);" It uses the variable text without initlialising it first. That isn't exaclty good practise, but I think it's a feature and not a bug that it actually happends to remember whatever was in text last time...
15:15 egonw http://pele.farmbio.uu.se/pubchem/
15:15 zarah egonw's link is also http://tinyurl.com/crnw4d
15:16 jonalv egonw: what's that?
15:16 egonw try it
15:16 jonalv egonw: I am looking at it
15:16 egonw it won't bite (much)
15:16 edrin back
15:16 olass egonw: how try?
15:16 jonalv egonw: how many atom types are there? :)
15:16 olass egonw: about commenting on the bugs?
15:17 olass you promised this thing would not delay bc2 release
15:17 * olass is waiting for egonw's comments
15:17 * egonw is meanwhile working on bugs...
15:17 olass sounds good
15:17 edrin jonalv: yes, but that's what i wanted to show... you write a script that must not work by itself, but it could work
15:17 egonw but sometimes one has to wait for a git checkout etc
15:17 olass :)
15:17 olass anyway
15:17 egonw or bioclipse to boot
15:17 edrin jonalv: but in my opinion it must not work
15:17 olass egonw: how do we try it?
15:17 olass I see the page
15:18 olass how do I interact with it?
15:18 egonw hang on...
15:18 olass in Bioclipse?
15:18 egonw adding such help
15:18 olass is there a gist?
15:18 egonw olass: yes, was thinking about that...
15:18 jonalv edrin: okey you might be right but isn't that how things are working now anyway?
15:18 egonw adding Bioclipse script snippets to those HTML pages
15:18 edrin jonalv: of course one may use such a feature, but the logical step first is to have them seperate...
15:19 olass egonw: while you add those snippets, please comment on the bugs
15:19 olass or we talk about them tomorrow
15:19 edrin olass: wait
15:19 edrin what is the status of the gist?
15:19 * olass feels there will be many meeings tomorrow
15:19 edrin is it working now?
15:19 olass edrin: what gist?
15:19 edrin your gist
15:19 edrin teh hivpred
15:19 olass nope
15:20 olass does not work
15:20 edrin why does it not work?
15:20 olass not here
15:20 olass edrin: what do you mean why?
15:20 olass I have reported that many times...
15:20 edrin olass: do you have another XMLBeans in one of your running plugins?
15:20 egonw http://pele.farmbio.uu.se/pubchem/?cid=161073
15:20 olass no idea
15:20 zarah egonw's link is also http://tinyurl.com/cltue5
15:20 olass edrin: how can O tell?
15:20 olass I
15:20 edrin maybe it's like egon suggested, multiple
15:21 edrin olass: clean workspace? eclipse is behaving strange sometimes...
15:21 edrin damn
15:22 edrin anyway,
15:23 egonw http://pele.farmbio.uu.se/pu​bchem/atomtyping/?element=C
15:23 zarah egonw's link is also http://tinyurl.com/dhmqmb
15:24 jonalv egonw: that seems intresting but I am not sure I understand, does it not recognize c as in carbon?
15:24 egonw because: atom type != element type
15:24 egonw it does recognize it as carbon
15:24 egonw but not a C++ carbon
15:25 egonw who would want to recognize C++ anyway :)
15:25 jonalv C--
15:25 jonalv C--
15:25 egonw yeah, that one is quite unlikely too
15:26 jonalv but what does it mean? Is it the same thign as C2+?
15:26 egonw yes
15:26 jonalv egonw: okey and why don't people write C2+ then?
15:26 * jonalv ducks
15:27 egonw some do
15:27 egonw matter of taste
15:27 egonw some have taste, others not
15:27 jonalv so do they write C--- as well?
15:28 egonw masak: ummm...
15:28 egonw masak: ping
15:28 masak egonw: um, pong
15:28 egonw masak: are you sure your patch does what you think it does??
15:28 egonw TAB now deletes the whole line
15:28 masak egonw: :)
15:29 masak I'm pretty sure I test-drove it...
15:29 egonw well, there you have it...
15:29 egonw you have to test-drIve it ...
15:29 egonw :)
15:29 edrin olass: do you have a non dev version of bc installed? like the last bc2 rlease? does the gist work with this version?
15:29 shk3 joined #bioclipse
15:29 masak egonw: so, if you type 'inchi.' and then press TAB... does it get deleted then?
15:29 egonw shk3: humph.com ?
15:30 egonw masak: mmm... it seems to work now...
15:30 egonw let me reboot ...
15:30 egonw bc2 that is
15:31 masak *phew*
15:31 egonw oh... getting all sorts of class not found in the console...
15:31 egonw OK, never mind...
15:31 masak :)
15:31 * masak 's honour is saved, for this time
15:31 shk3 what is humph.com?
15:32 egonw [17:29:38] --> shk3 (n=shk3@ns.humph.com) has joined #bioclipse
15:32 shk3 ah
15:32 egonw shk3: you tell me
15:32 shk3 don't know
15:32 masak humph.
15:32 egonw :)
15:32 jonalv shk3: _what_ the heck is humph.com?
15:32 shk3 don't know
15:32 egonw ah, using some wireless network?
15:32 shk3 using wireless
15:32 shk3 yes
15:32 shk3 mayday today
15:33 jonalv lol
15:33 masak May the Fourth be with you!
15:33 masak :D
15:34 jonalv masak++ //nice one
15:34 shk3 what is biolist for?
15:34 * masak loses his good mood
15:34 shk3 to do some serious talk
15:34 jonalv shk3: recording
15:34 masak :(
15:35 shk3 and it's used like list?
15:35 jonalv shk3: more like ArrayList or LinkedList
15:36 shk3 yes
15:36 shk3 thats what i mean
15:36 shk3 like a list implementation
15:36 egonw http://pele.farmbio.uu.se/pubchem/?cid=161073
15:36 egonw now with Bioclipse Script
15:36 jonalv shk3: however there is one method still not implemented... :(
15:36 zarah egonw's link is also http://tinyurl.com/cltue5
15:36 jonalv shk3: subList is not working. subList is magical
15:37 shk3 I don't worr about that right now
15:37 jonalv shk3: it can probably be fixed but it's not done yet anyway...
15:37 edrin masak: do you also have Mac OS X?
15:38 masak edrin: seems so.
15:38 edrin does ola's script work on your last bc2 beta release? or on your dev snapshot?
15:38 masak edrin: they furnish us with one of those Apple computers and let us frolic in the fields.
15:39 masak edrin: I can test on bleeding if you like.
15:39 edrin ok, test on bleeding
15:39 olass I think it is just my comp that fails :(
15:39 masak olass: dåligt. :)
15:39 edrin olass: if so that would be good
15:39 olass yes
15:40 olass (and no)
15:40 edrin yes
15:40 masak (and no)
15:40 edrin maybe it's the eclipse version ?
15:40 edrin hm
15:40 edrin masak: you will have to setup an xmpp account
15:41 masak edrin: ok. I'm including the xmpp plugin now.
15:41 edrin ok
15:42 edrin in bc preferences of xmpp specify test@ws1.bmc.uu.se as JID and ws1.bmc.uu.se as server
15:42 edrin and the password is
15:42 edrin guess what
15:42 edrin ;)
15:42 CIA-40 bioclipse: shk3 * r10050 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (3 files in 2 dirs): added tanimoto calculation
15:43 masak edrin: I don't seem to have the xmpp plugin in my workspace. importing...
15:43 edrin ok
15:44 masak um, what exactly is it that I'm looking for?
15:44 masak there's no n.b.xmpp
15:44 masak as far as I can see.
15:44 CIA-40 bioclipse: shk3 * r10051 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: added tests for tanimoto calculation
15:44 edrin masak: xws4j
15:44 edrin sorry
15:44 shk3_ joined #bioclipse
15:44 masak ah.
15:44 edrin n.b.xws4j
15:44 masak that one I did see.
15:47 masak script seems to work here.
15:47 masak it spat out a chunk of XML.
15:49 egonw olass: what's up with your system?!?
15:50 olass egonw: ?
15:50 egonw well, if the script works for masak too...
15:50 egonw why does it fail for you
15:50 egonw OS/X is apparently not the problem either
15:50 olass no idea
15:50 masak olass: check your settings.
15:50 olass what setting?
15:50 masak Preferences > XMPP
15:50 egonw olass: otherwise, we'll align outputs tomorrow
15:50 edrin no
15:51 olass masak: that is no problem
15:51 edrin the xmpp settings are ok
15:51 masak ok.
15:51 olass I get a classcastexception
15:51 edrin it's an obscure classpath issue, maybe associated with the eclipse version?
15:51 edrin hm...
15:51 edrin that's why we must take care that the scripts work with the bc2 beta xws version, too
15:53 jonalv olass: so what error are you getting?
15:53 olass I get a classcastexception
15:54 edrin olass: maybe it's like egon suggested, there is another XMLBeans somewhere in the installation?
15:54 olass how can I tell?
15:54 olass gah
15:54 olass now the gist works
15:54 olass very very strange
15:54 edrin huh!?
15:55 edrin yeah!
15:55 masak o_O
15:55 * olass does not like this
15:55 olass what changed?
15:55 * masak thinks olass had a setting wrong, but doesn't dare admit it
15:55 egonw it just turned 5:55
15:55 olass setting wrong?
15:55 egonw those 666 people have it all wrong
15:56 olass there is no setting for xmlbeans AFAIK
15:56 masak olass: like, the server set to "google.com" or something.
15:56 egonw any good programmer starts at 0
15:56 masak egonw: still, that only yields 665.
15:56 egonw ah, no digit-wise, of course
15:56 egonw you're not getting it either
15:56 olass well well
15:56 egonw :)
15:56 * olass is happy it works
15:56 egonw anyways...
15:56 egonw same here
15:56 egonw only took half a day :)
15:57 olass egonw: did you comment on the bugs?
15:57 * egonw is away for dinner
15:57 egonw nope, not yet
15:57 masak how convenient.
15:57 * olass has asked all day
15:57 olass @slap egonw
15:57 * zarah throws some pointy lambdas at egonw
15:57 egonw what for?
15:57 olass :)
15:57 * egonw is commenting on bugs
15:57 egonw not good?
15:58 olass egonw++ //plåster på såren
15:58 masak (Open Sores)++
15:59 egonw shk3_: can you please comment on bug #1003 ?
16:00 egonw shk3_: and tell me if you agree with the name change?
16:00 egonw shk3_: if you do, please comment in bug report and I will apply the name change
16:00 egonw OK, I think that were all reports
16:00 egonw bbl
16:00 egonw meanwhile, enjoy the Bioclipse Script at: http://pele.farmbio.uu.se/pubchem/?cid=161072
16:00 zarah egonw's link is also http://tinyurl.com/clgm62
16:00 egonw jonalv: that's a nice c+++
16:01 egonw or c3+, if you prefer that notation
16:01 egonw (btw, what are they thinking?!?!?!)
16:01 olass who are they?
16:01 masak but they!
16:01 egonw olass: btw, very much input appreciated on BMC/PCM/group/UU/whatever branding, in terms of logos etc
16:02 olass egonw: what do you mean?
16:02 olass how that webpage should be branded?
16:02 * jonalv feels totally lost now...
16:02 * olass too
16:03 olass "very much input appreciated" < does that mean a little input is not appreciated?
16:04 * olass is angry abot default preferences not being set
16:04 * masak is angry about hyphens
16:04 * jonalv is angry too
16:04 jonalv uhm
16:04 jonalv about
16:04 jonalv uhm
16:05 * masak is angry about jonalv's apparent indecision
16:05 jonalv ah I am angry about my new API not workign togehter with my old API for Bioclipsejob
16:12 masak my tabComplete() method is too tangled. :/
16:13 * olass is still angry
16:13 * masak is furious
16:14 * olass is calmer now since the default prefs seem to work again
16:14 masak olass: things seem to work very intermittently at your place today.
16:15 olass well, this thing I at least fixed myself...
16:16 masak olass: ah :)
16:17 shk3__ joined #bioclipse
16:18 olass shk3__: how is the tanimoto coming along?
16:18 olass shk3__: and could it be related to bug 1001?
16:18 olass if so, please comment in the bug if you have further suggestions
16:22 CIA-40 bioclipse: ospjuth * r10052 /bioclipse2/trunk/plugins/net​.bioclipse.balloon.business/ (4 files in 3 dirs): Implemented a preference page for balloon to set Timeout. Solves #997.
16:24 * olass is hungry
16:24 * jonalv too
16:24 * olass is angry for being hungry
16:24 jonalv but first swimming :)
16:25 * olass is swimming in bugs
16:25 olass actually it's not too bad
16:25 jonalv good
16:25 * olass is looking forward to tomorrows status meeting
16:25 * olass is looking forward to tomorrow's status meeting
16:26 olass jonalv: can you make it to 09.30?
16:26 * jonalv is afraid of tomorrows status meeting
16:26 * masak is unsure he'll be able to make it to 90:30 tomorrow
16:26 jonalv olass: okidoki, masak: can you?
16:26 masak s/90/09/
16:26 olass ok
16:26 masak I'll sure try.
16:27 olass masak: ok
16:28 shk3__ olass: tanimoto is there
16:28 shk3__ just in manager
16:28 shk3__ will work on ui tomorrow
16:28 olass great
16:29 olass see bug 1001 too
16:29 olass @bug 1001
16:29 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1001
16:30 olass oh, I see you have
16:34 shk3__ yes
16:35 shk3__ I thought arvin was working on a dynamic extension of the editor.
16:35 shk3__ that would clash with your suggestion, I think.
16:35 shk3__ we need only one, probably.
16:52 olass shk3__: not at all
16:52 olass my suggestion had nothing to do with the editor
16:52 olass it COULD be used with it but no dependency at all
16:59 edrin cu later
16:59 edrin left #bioclipse
17:03 Gpox but pretty much suggests the same functionality
17:07 shk3_ joined #bioclipse
17:17 CIA-40 bioclipse: shk3 * r10053 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (5 files in 3 dirs): added an icon to intro item
17:17 CIA-40 bioclipse: shk3 * r10054 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (5 files in 3 dirs): added an icon to intro item
17:20 CIA-40 bioclipse: shk3 * r10055 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/configextension.xml: added an icon to intro item
17:40 olass egonw: is php not installed on pele?
17:40 egonw http://pele.farmbio.uu.se/pu​bchem/atomtyping/?element=Ac
17:40 egonw that is php
17:40 zarah egonw's link is also http://tinyurl.com/d6jnpp
17:40 olass hmm
17:49 edrin joined #bioclipse
17:57 CIA-40 bioclipse: goglepox * r10056 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/business/JChemPaintManager.java: Moved cleanup code to not run synchronous on the ui thread
17:57 CIA-40 bioclipse: goglepox * r10057 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added key to for changing atom to hydrogen in JCPEditor
19:19 sneumann_ joined #bioclipse
19:39 CIA-40 bioclipse: egonw * r10058 /bioclipse2/trunk/plugins/net.bioclipse.c​hemoinformatics/src/net/bioclipse/chemoin​formatics/util/ChemoinformaticUtils.java: Removed PDB from list of supported formats, as we do not officially support PDB yet (scheduled for 2.1, fixes #998)
19:39 zarah bug #998 | http://tinyurl.com/cbtmkh
19:40 CIA-40 bioclipse: egonw * r10059 /bioclipse2/trunk/plugins/net.b​ioclipse.chemoinformatics.test/ (13 files in 7 dirs): Added missing test suite
19:41 CIA-40 bioclipse: egonw * r10060 /bioclipse2/trunk/plugins/net.bioclipse.c​hemoinformatics/src/net/bioclipse/chemoin​formatics/util/ChemoinformaticUtils.java: Refactored to use a List<String> to create cleaner code
20:45 olass left #bioclipse

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