Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-21

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Time Nick Message
05:44 Gpox joined #bioclipse
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07:30 edrin joined #bioclipse
07:36 olas joined #bioclipse
07:36 olas moin
07:36 zarah hi olas
07:50 olas it's time for a new Bioclipse release
07:51 olas well, actually only an updated update site
08:00 jonalv joined #bioclipse
08:01 jonalv hi
08:01 zarah hi jonalv
08:01 jonalv zarah?
08:01 jonalv :)
08:07 egonw joined #bioclipse
08:11 egonw moin
08:11 zarah hi egonw
08:17 edrin hi olas
08:17 zarah edrin: You have new messages. Write '@messages' to read them.
08:17 edrin olas: can you test the SampleClient ?
08:17 edrin zarah: @messages
08:17 zarah edrin: are you making fun of me?
08:17 edrin @messages
08:17 zarah edrin: 19 h 7 m 10 s ago, olas said ping me when you get back
08:18 edrin olas: the component you must run yourself, too. it must have testFunctions activated and the coffee machine sample loaded...
08:19 edrin please checkout current version of SampleClient, xws4j and xws4j-coffee-machine-sample...
08:19 olas edrin: will do
08:19 edrin the SampleClient will test the component in several modes ...
08:19 olas currently updating bioclipse2 checkout...
08:19 olas takes a while :-)
08:21 edrin olas: in SampleClient.java maybe you should comment out the runAsyncTest((IService)xitem); because this will call a delayed function 200 times in parallel...
08:21 edrin takes a while ;)
08:21 olas haha
08:21 olas good point
08:21 olas does it work fine?
08:21 edrin or you reduce NUMBEROFTHREADS = 200; to NUMBEROFTHREADS = 5;
08:21 edrin for me it did
08:22 edrin but i really do not know if this solves the problem you observed...
08:22 olas I will use your java client as stub otherwise
08:23 olas and build it up step by step until it works
08:23 edrin ok
08:25 edrin olas: you could mail me your client code if you want
08:25 olas now?
08:26 olas you have time now?
08:26 edrin not much, a few minutes
08:26 olas ok
08:26 egonw edrin: is the PDF still up to date?
08:26 olas will email you if it doesn't work
08:27 edrin egonw: maybe :)
08:27 jonalv egonw, olas: sushi today?
08:27 edrin egonw: why?
08:27 olas not me, I got box
08:27 egonw edrin: because I really need to start writing services too
08:27 edrin egonw: i changed some things...
08:27 edrin egonw: ok
08:27 egonw jonalv: no, got box too
08:28 egonw two boxes actually
08:28 jonalv egonw is gonna work late?
08:28 jonalv :)
08:30 edrin egonw: i think the pdf should still work
08:31 egonw ack
08:31 edrin egonw: but there is now ISimpleProcessListener... making async client dev simpler... you can use it instead of IProcessListener and then you do not have to take care about terminating remote processes in the client
08:32 egonw ok, good :)
08:32 edrin egonw: you can also take a look on the SampleClient:
08:32 edrin http://bioclipse.svn.sourceforge.net/viewvc/biocli​pse/xws/trunk/xws4j-sample-client/src/sample/clien​t/SampleClient.java?revision=7334&view=markup
08:32 zarah edrin's link is also http://tinyurl.com/6l9ggh
08:32 edrin this is java
08:33 edrin olas: when starting sample client:
08:33 egonw edrin: will you be around the full day?
08:33 edrin Usage: java SampleClient <clientJID> <pwd> <host> <port> <serviceJID>
08:33 edrin note:<serviceJID> must be xws.ayena.de
08:33 edrin egonw: I will be around
08:33 shk3 hi
08:33 zarah hi shk3
08:34 edrin but have to do other things, too
08:34 shk3 trying the qsar stuff
08:34 shk3 I can add molecules and descriptors
08:34 shk3 but the overview page still says 0 molecules and 0 descriptors
08:34 shk3 what to do?
08:36 edrin shk3: do you have access to the follwing article:
08:36 edrin http://www.ncbi.nlm.nih.gov/pubmed/18927​489?ordinalpos=1&amp;itool=EntrezSystem2​.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubm​ed_DefaultReportPanel.Pubmed_RVDocSum
08:36 zarah edrin's link is also http://tinyurl.com/6brlnt
08:36 olas joined #bioclipse
08:38 shk3 edrin: no, doesn't look like
08:41 edrin ok :(
08:41 edrin thx
08:42 shk3 olas: how is the qsar interface supposed to work?
08:44 olas interface?
08:45 shk3 the ui
08:45 shk3 I can
08:45 shk3 define molecules
08:45 shk3 and descriptors
08:45 shk3 but not do a calculation
08:46 olas just save it
08:46 olas it should be done in background automatically
08:46 olas and produce dataset.csv
08:46 olas but really not finished yet
08:46 olas please try it when I make the release
08:47 olas I'll also make a tutorial
08:47 olas hopefully VERY soon, but not 100% sure
08:47 olas glad you try it though
08:47 olas does it not build the dataset.csv?
08:47 shk3 nothing happening for me
08:47 olas did you start a QSAR project?
08:47 olas does the project have an overlay (small R) ?
08:47 shk3 ah yes, the dataset.csv is there
08:48 olas ok
08:48 olas if you install the matrix plugins, you can open it
08:48 shk3 the overview page of qsar.xml still says 0 molecules etc.
08:48 olas it's not 100% in sync yet
08:48 shk3 yes indeed
08:48 olas overview page and add responses from file are 2 key parts not finished
08:49 olas the rest sort of works
08:49 olas but no caching done yet
08:49 olas so complete rebuild if something changes
08:49 olas which can take time..
08:53 olas egonw: which CDK plugins are required in bioclipse2 released so far?
08:54 olas are they indicated in chemoinfo_feature?
08:54 egonw they should be
08:54 egonw I did that
08:54 egonw ok, git-svn fetch/rebase updated
08:54 egonw mom, let me check
08:54 olas so the feature should be up2date?
08:56 egonw yes
09:02 olas edrin: around?
09:03 olas Running your sample client gives me an error
09:03 olas hmm momen
09:04 edrin ok
09:05 olas oh, my bad
09:05 olas seems to be working fine I guess
09:05 edrin ? but
09:05 olas need to run component correctly
09:05 edrin ok :)
09:06 olas hmm
09:06 olas I noticed something
09:06 olas Component really does not care what jar you run in FUNCTION_JARS
09:07 olas it just uses the IFunctions it finds on classpath
09:07 edrin could be
09:07 olas I ran with my coffe.cfg but hivpred on classpath
09:07 olas service published: hivpred
09:07 edrin huh?
09:07 edrin no, this cant be
09:07 olas if you say so...
09:08 edrin the functions are actively loaded according to .jar in config
09:08 edrin are you sure?
09:09 olas replacing the classpath with coffee, now I see the correct coffee services. Same coffee.cfg
09:09 edrin huh?
09:09 olas Now your client runs fine!
09:10 edrin hm, this suggests th function loading code is corrupt...
09:10 olas ok, gives me something to build upon
09:10 olas I suggest you look at it and try to reproduc ethe error
09:11 olas I have reproduced it here 2 times now
09:11 edrin yes
09:11 edrin strange
09:11 edrin well, in fact a problem could be that it looks for the same package and function...
09:12 edrin hm...
09:12 edrin ah
09:12 edrin yes, i think i know...
09:12 olas your client never dies?
09:12 olas it never exits here...
09:12 edrin could be :)
09:13 edrin i think it does not die because the socket thread is still runnning...
09:13 olas exactly
09:13 edrin can you try a client.disconnect() ?
09:13 olas sure
09:13 edrin maybe it exits then?
09:15 olas edrin: yes, it exits now correctly
09:16 edrin olas: i think the problem is that the function .jar should not be in the classpath. maybe it gets confused this way
09:17 edrin if everything works in theory your component should be able to export your hiv.jar and coffeemachine .jar in parallel if you specify both in the config
09:17 CIA-52 bioclipse: jonalv * r7336 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb.tests/tests/net/bioclipse/structuredb/ (2 files in 2 dirs): [Structuredb] Added a few more tests related to PropertyChoice / ChoiceProperty relation
09:20 shk3 olas: sorry, have been for coffee
09:20 shk3 is there a connection of the qsar plugin and the molecule table?
09:21 shk3 can you view molecules and their results in the table?
09:22 olas no
09:22 olas not yet
09:23 olas would be nice
09:23 thomasku joined #bioclipse
09:24 shk3 hm, I think that's essential
09:24 shk3 I wrote an email to the list once about this
09:27 shk3 the email was called "Thoughts about QSAR in Bioclipse"
09:28 shk3 I think it's important to get this right
09:31 egonw olas: how so I run a feature again?
09:31 olas add it to bioclipse.prodcut
09:31 olas then run the product
09:31 egonw ack
09:32 egonw mmm... me notices he is starting to wonder when his new laptop arrives
09:35 CIA-52 bioclipse: jonalv * r7337 /bioclipse2/trunk/plugins/net.bioclip​se.structuredb/src/net/bioclipse/stru​cturedb/domain/ChoiceProperty.java: [Structuredb] Made the newly added test assertion in the domain tests pass
09:40 olas edrin: client.getFunction() does return a Service
09:41 olas not a Function
09:41 olas is that so?
09:41 olas and why?
09:44 maclean joined #bioclipse
09:47 shk3 olas: christoph and me thought about having a Bioclipse presentation at the free software session at gcc
09:47 shk3 right now, I think it would be better to wait till bc2 is ready
09:47 shk3 there isn't much point in presenting bc1 and bc2 is not ready, I feel.
09:47 shk3 what do you think?
09:49 olas_in_office_e yeah, I think so too
09:52 olas shk3: if you have other presentations, maybe you could include a slide or two about bioclipse?
09:52 olas else we should focus on getting BC2 out
09:53 shk3 no other presentations
09:54 edrin olas: ?really? it should return a IFunction
09:54 olas hmm, it returns a Service
09:55 olas will try again
09:55 * edrin looks in his code
09:55 edrin no, it should return a IFunction
09:56 edrin olas: IFunction func = client.getFunction("xws.ayena.de", "testFunction");
09:56 olas will try again
09:56 * jonalv -> lunch
09:59 olas so: IFunction hivFunction = client.getFunction(serviceJID, functionName);
09:59 olas and hivFunction.discoverSync(45000);
09:59 olas is that the way to go?
10:00 olas or does getFunction actually get it syncronously?
10:00 olas edrin?
10:00 olas do I need to to discover earlier?
10:01 olas or no need to discover if I have the function?
10:01 olas Can I validate it then?
10:01 * olas is off for lunch
10:01 olas ttl
10:40 egonw_ joined #bioclipse
10:44 olas egonw_: coffee
10:45 egonw_ 5mins?
10:47 edrin was for lunch
10:48 edrin olas: client.getFunction() just creates a Function. in fact it is not a must to discover it...
10:49 edrin you could in fact directly use it...
10:50 edrin discovery is just for "validating", "identifying" or "finding" Services and functions
10:51 edrin for example you can create an IXmppItem x = client.getXmppItem(); and then check if it is just *some* item, a Service or a Function by discovering it...
10:51 edrin or you can get the supported functions of a Service
10:52 edrin to validate a function you should do this:
10:53 edrin IXmppItem x = client.getXmppItem(jid, functionname);
10:53 edrin x = x.discoverSync(30000);
10:55 edrin if (x instanceof IFunction) {
10:55 edrin IFunction f = (IFunction)x;
10:55 edrin f.invokeSync(null, 30000);
10:55 edrin }
11:01 egonw shk3: what is the ref (bibtex) for your CDK News paper on the JCP applet?
11:09 egonw ah... cdk/doc/refs/cdknews.bib :)
11:10 egonw mmm... not updated :(
11:20 shk3 i don't think I have bibtex for it
11:23 egonw in any format?
11:23 egonw just issue number would already safe me work
11:27 jonalv joined #bioclipse
11:27 jonalv hi
11:27 zarah hi jonalv
11:27 egonw shk3: art35
11:27 egonw I think I found it
11:28 egonw CDK News 3.1
11:31 egonw Kuhn S: An Applet Release of JChemPaint. CDK News 2006, 3:21–23.
11:31 jonalv google  Kuhn S: An Applet Release of JChemPaint. CDK News 2006, 3:21–23
11:31 zarah jonalv: No hits.
11:31 jonalv :(
11:31 masak joined #bioclipse
11:31 egonw google An applet release of jchempaint
11:31 zarah egonw: http://almost.cubic.uni-koeln.de/cdk/jcp/applet/
11:32 egonw google cdk news
11:32 zarah egonw: http://sourceforge.net/project/showfiles.ph​p%3Fgroup_id%3D20024%26package_id%3D124796
11:33 egonw mmm... would have like it to show up cdknews.org :(
11:33 masak you can't bribe Google.
11:33 masak unless you're China.
11:36 jonalv google cdknews
11:36 zarah jonalv: http://www.rsc.org/images/CSte​inbeck_May08_tcm18-127435.pdf
11:37 maclean woah. that showed up in my chat as a pdf image. that's a neato.
11:37 maclean Er, an image linked to a pdf, that is.
11:37 egonw :)
11:37 masak maclean: using a web-based IRC client?
11:37 egonw nice presentation, btw
11:38 maclean colloquy
11:38 maclean anyway, lunchhh.
11:39 masak ah, colloquy
11:39 jonalv I tried colloquay, these was something wrong with it regarding links
11:39 * jonalv cant remember now...
11:39 charlgren joined #bioclipse
11:39 masak jonalv: they showed up as images? :)
11:40 jonalv masak: uhm that wasn't it
11:41 charlgren joined #bioclipse
11:48 egonw olas: the cheminfo feature is working for me
11:48 olas good
11:48 olas will try it later today
11:56 egonw http://gist.github.com/18284
11:57 egonw sort of pastebin, but then with versioning and forking :)
12:00 egonw how can I, from the JS Console, 'open' an object I have just created?
12:12 edrin egonw: in case you want to play with the xws with scripting console: the xws4j plugin still has the old xws4j.jar, thus there is a bug when using invokeSync() on a delayed function...
12:13 edrin (it does not return the result... )
12:13 edrin it is fixed in the current trunk xws4j
12:14 edrin but the rest should be fine, only minor changes...
12:19 malick joined #bioclipse
12:22 egonw ok
12:22 egonw I think I'm going to have to delay it until tomorrow :
12:22 egonw :(
12:25 maclean joined #bioclipse
12:26 egonw Gpox: there is this code for saveMol2():
12:26 egonw CDKMangere.java:line878
12:26 egonw Gpox: can you check if it is using the correct way of creating resources...
12:26 egonw I guess not, as it is not using any info on projects or workspace
12:27 egonw jonalv: btw, I think it did not show up upon autocomplete as it is missing from the ICDKManager interface?
12:27 Gpox egonw: no it don't use resources
12:28 jonalv egonw: if it isn't in the interface and not a @publishedMethod then it won't show up no...
12:30 egonw Gpox: a patch for that method to use project info would be much appreciated ;)
12:30 egonw where is the deparment meeting?
12:40 CIA-52 bioclipse: carl_masak * r7338 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
12:40 CIA-52 bioclipse: [JsConsole]
12:40 CIA-52 bioclipse: * running R commands or 'help' didn't result in
12:40 CIA-52 bioclipse:  reactivation of the prompt, which resulted in havoc
12:40 CIA-52 bioclipse: * now fixed
12:54 egonw masak++
12:55 masak thank you. the problem seemed trivial, then difficult, then easy, before I solved it. :)
12:56 masak turns out that ths js console hsa now entirely departed from the internal console API of returning strings from execueted commands.
12:57 masak "help", "js", "R" now all return the empty string
12:58 masak (besides, I'm thinking of removing the R mode from the js console)
13:00 egonw masak: right, and have a dedicated console for that...
13:00 egonw masak: when you do that, one for Jmol Script would be nice too
13:01 masak egonw: meeting now.
13:01 egonw indeed :(
13:01 egonw bbl
13:01 masak egonw: having the ability to call from js might still be nice, though
13:47 edrin f
14:25 jonalv zarah: ping
14:25 zarah jonalv: excuse me?
14:26 masak whoa, gotta fix that :)
14:26 masak zarah: you should say "pong" when people say "ping" to you :)
14:26 zarah masak: Hokay. You provide the commits, I provide the "should"-ing
14:27 masak zarah: hokay.
14:27 zarah masak: so, basically.
14:29 egonw hahaha... so, basically :)
14:29 masak :)
14:30 masak zarah: you're the funny one!
14:30 zarah masak: no, YOU are the funny one! :)
14:34 CIA-52 bioclipse: carl_masak * r7339 /bot/trunk/zarah.pl: [zarah] now pongs on pings
14:34 jonalv zarah: ping
14:34 zarah jonalv: excuse me?
14:34 masak zarah: restart, dear
14:34 olas joined #bioclipse
14:35 zarah joined #bioclipse
14:35 masak @ping
14:35 zarah masak: pong, dear
14:35 edrin pung
14:35 masak zarah: thanks, dear
14:35 zarah you're welcome, masak :)
14:35 jonalv zarah: pong
14:35 zarah jonalv: I'm just a bot, you expect me to understand that?
14:35 jonalv zarah: ping
14:35 zarah jonalv: pong
14:35 edrin huh
14:35 olas edrin: pung?
14:36 jonalv zarah: you pang?
14:36 zarah jonalv: I did not understand that
14:36 edrin well, was just testing Eliza
14:39 Julio joined #bioclipse
14:39 Julio left #bioclipse
14:40 olas pung in swedish is not that nice
14:43 masak she's not an Eliza...
14:45 edrin pung what does it mean?
14:46 masak edrin: scrotum
14:46 masak well, originally just "bag"
14:46 edrin oh
14:46 edrin ok
14:47 edrin in german commics you see it sometimes as a synonym for ping and pong...
14:48 edrin i am sorry :)
14:48 masak s'ok
14:48 egonw hahah
14:48 masak we're metropolitan enough around here
14:48 CIA-52 bioclipse: carl_masak * r7340 /bot/trunk/zarah.pl: [zarah] extracted method "pick" which picks a random alternative out of a list
14:48 egonw nice script:
14:48 egonw mom
14:48 egonw git://gist.github.com/18315.git
14:49 egonw http://gist.github.com/18315
14:49 masak :)
14:49 masak at least one step too many, by me
14:49 masak but yeah, nice
14:50 masak egonw++
14:50 egonw it's a shame gist doesn't do commit messages :)
14:50 masak why?
14:50 egonw I like commit messages :)
14:50 * jonalv is so happy to see a Bioclipse 2 script using managers written by someone but himself
14:51 * masak is happy to see a Bioclipse 2 script
14:51 masak egonw: oh, and I advice you to use semicolons, even though you don't have to. at least in files.
14:52 egonw was going to ask about that
14:52 masak "advice"? "advise"?
14:52 masak English is difficult...
14:52 egonw it actually gives errors about that, when I leave them out
14:52 masak egonw: they're not required, no matter what the editor says
14:52 edrin masak: what about the '\n" bug?
14:52 egonw I think the Action History should automatically add them
14:52 masak but I'd say they're highly encouraged
14:52 egonw well, the script fails without them...
14:53 egonw another remark: comment support would be nice
14:53 masak edrin: thank you for reminding me. still haven't really looked into it. maybe I should bug jonalv++ about it a bit, he has Windows
14:53 masak egonw: comment support? in what way?
14:53 egonw # some remakr
14:53 egonw / some remark
14:53 egonw // some remark
14:53 egonw would that be the syntax I should use...
14:53 egonw mm... testing
14:53 masak egonw: see ECMAScript standard.
14:54 edrin // should comment stuff out...
14:54 masak aye
14:54 egonw // ah, ok
14:54 masak ISTR /* */ works too
14:54 egonw tack
14:54 edrin hm...
14:54 masak np
14:54 edrin is a script file not pushed into rhino at once as in bc1?
14:55 masak "pushed into rhino"?
14:55 masak please explain.
14:55 edrin i mean as one a complete string?
14:55 masak edrin: it is.
14:55 edrin one big string containing the whole scipt ...
14:55 edrin ah
14:55 masak for better or worse.
14:56 masak the alternative would involve parsing, and I'd prefer not to do that.
14:56 edrin ok, so my old scripts should still work, right?
14:56 masak edrin: apart from the vastly different bc architecture, yes :)
14:56 edrin ok
14:57 masak edrin: are your old scripts dependent on being sent in as entire strings?
14:57 edrin masak: is there auto completion in the script editor available now?
14:57 edrin masak: i dont know
14:57 masak edrin: dunno, haven't used the editor much. I just plugged it in.
14:57 edrin masak: but they depend on other thing not in bc2
14:57 masak I really should use it a bit.
14:57 masak edrin: ok. then they have a greater chance of working.
14:58 edrin masak: it would be worth it to have the java reflection thing in the script editor. this would be really appreciated !
14:58 masak edrin: noted.
14:59 masak thing is, it consists of three hacks glued together.
14:59 edrin masak: because for xws you could just desicover the input output objects and then just start coding...
14:59 masak it feels a bit irresponsible to reduplicate it in the editor.
14:59 masak edrin: you're aware that tab completion only works for managers, right?
14:59 * masak grins
15:00 jonalv masak: uhm that's not entierely correct...
15:00 edrin like fac = new IoFactory(ioschemata); input = fac.createInputObject;
15:00 masak jonalv: sssh!
15:01 edrin input.setChemicalFormular("H2O");
15:01 masak edrin: uhm.
15:01 edrin jonalv: i think
15:01 masak edrin: I see what you want. I'd have to ask permission for such an undertaking.
15:01 * jonalv is lost...
15:01 edrin problem is:
15:01 masak edrin: it, too, requires parsing.
15:02 masak parsing is difficult.
15:02 edrin stuff would have to be evaluated when typing...
15:02 masak edrin: yes.
15:02 masak and it's the "evaluated" part that's the challenge
15:03 masak it's a task I would love to do, but I fear it's not very high-priority right now
15:03 masak nevertheless, I will ask
15:03 CIA-52 bioclipse: egonw * r7341 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added cdk.debug plugin
15:03 edrin masak: its too complicated right. better forget about ir
15:03 edrin t
15:04 masak edrin: I didn't say "too complicated". I said "challenging" :)
15:04 CIA-52 bioclipse: egonw * r7342 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added methods to write CML and MDL molfiles
15:04 masak edrin: but yes, it's not exactly a one-day hack.
15:04 masak (and Java is not exactly a perfect fit for this kind of task)
15:07 CIA-52 bioclipse: egonw * r7343 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Added missing annotation so that tab complete shows them
15:14 egonw minimize: forcefield = org.jmol.minimize.forcefield.ForceFieldUFF@2b1495
15:15 egonw Exception no content-type in getResource UFF.prm0 force field parameters read
15:15 egonw :(
15:41 CIA-52 bioclipse: egonw * r7344 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: Added the final Jmol 11.6.0 release
15:47 * egonw is adding a new bug report to pele via Mylyn
15:47 egonw and it worked :)
15:48 egonw http://pele.farmbio.uu.se/bugs/show_bug.cgi?id=2
15:48 zarah egonw's link is also http://tinyurl.com/6csgrk
15:48 egonw OK, enough for today
15:48 egonw bye all!
15:52 jonalv zarah: ask egonw is our bugzilla totally open or do I have to get a log in?
15:52 zarah Consider it noted.
15:53 masak hm, and here I thought @ask wasn't implemented :)
15:53 jonalv masak: huh?
15:53 jonalv zarah: ask masak but it is isn't it?
15:53 zarah Consider it noted.
15:53 masak @clear
15:53 zarah masak: Messages cleared.
15:53 masak apparently
15:54 jonalv masak: How can you be sure since you just cleared taht?
15:54 masak but not in the way I thought
15:54 masak jonalv: I'm sure. if Smart Girl says "Consider it noted." then she stored it
16:15 CIA-52 bioclipse: jonalv * r7345 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): [Structuredb] Added a domain test which I thought I had written already... ...it was not related to my problems at dao level :(
16:16 edrin olas: got the validation thing solved?
16:16 olas I know the reason
16:16 olas have not had time to fix it though
16:16 edrin oh
16:17 olas working on a ne wexport of Bioclipse :-(
16:17 edrin ok, so the schema did not match the input/output?
16:17 olas boooring
16:17 olas nope
16:17 edrin ah ok
16:17 * olas is hungry
16:17 edrin olas: so maybe the valdation code of xws could work :)
16:18 olas I'm sure it dies
16:18 * jonalv gives up now and heads home :(
16:18 edrin but anyway, there is now the option for disabeling it in cfg
16:18 maclean left #bioclipse
16:19 edrin and beside this I added a better error message for the case the schema is null. thus user will not get this strange exception anymore...
16:20 edrin XwsLogger.error("ProcessFactory.validateRunInput: could not create validator; function schemata correct?");
16:20 edrin 71 return false;
16:26 CIA-52 bioclipse: ospjuth * r7346 /bioclipse2/trunk/plugins/net.bioc​lipse.logger/META-INF/MANIFEST.MF: Updated manifest info, set ID for new release 2.0.0.A20081022
16:45 CIA-52 bioclipse: ospjuth * r7347 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Set version for new release to 2.0.0.A20081022
16:47 CIA-52 bioclipse: ospjuth * r7348 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated manifest info, set version for new release to 2.0.0.A20081022
16:48 CIA-52 bioclipse: ospjuth * r7349 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (.settings/org.eclipse.jdt.core.prefs META-INF/MANIFEST.MF): Set version for new release to 2.0.0.A20081022
16:50 thomasku joined #bioclipse
18:15 edrin left #bioclipse
18:39 CIA-52 bioclipse: ospjuth * r7350 /bioclipse2/trunk/features/ (3 files in 3 dirs): Updated feature versions to 2.0.0.A20081022. Also added net.bioclipse.chemoinformatics to chemoinformatics_feature.
21:31 edrin joined #bioclipse
23:42 olas joined #bioclipse
23:43 olas hi
23:43 zarah hi olas
23:43 jonalv left #bioclipse
23:46 zarah joined #bioclipse
23:47 zarah joined #bioclipse

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