Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-20

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All times shown according to UTC.

Time Nick Message
07:00 egonw joined #bioclipse
07:36 Gpox joined #bioclipse
07:42 rojasm joined #bioclipse
07:54 olas joined #bioclipse
07:54 olas moin
07:54 zarah hi olas
07:55 egonw hi olas
07:55 olas hi egonw
07:58 egonw Gpox: https://apps.sourceforge.net/mediawiki/cdk/i​ndex.php?title=JChemPaint_Rendering_Modules
07:59 egonw Gpox: it's work in progress...
07:59 egonw will add more bits during the next day(s)
08:01 Gpox looks nice
08:11 jonalv joined #bioclipse
08:26 maclean joined #bioclipse
08:27 * olas will make coffee
08:27 * maclean continues to drink his coffee
08:28 * olas is jealous at maclean
08:31 egonw hi maclean
08:31 maclean hola.
08:31 egonw maclean: https://apps.sourceforge.net/mediawiki/cdk/i​ndex.php?title=JChemPaint_Rendering_Modules
08:31 egonw work in progress
08:32 maclean will take a butchers.
08:32 edrin joined #bioclipse
08:32 maclean does sf mediawiki always ask for password?
08:32 edrin hi
08:32 zarah hi edrin
08:32 egonw only in https mode, I think
08:33 maclean ahhh.
08:33 maclean nice looking page, egon.
08:33 edrin egonw: hey, yesterday I even got the generated xsd schemata Java source files compiled with the eclipse compile at runtime...
08:34 egonw edrin: cool!
08:35 edrin now i will need to also load them to the runtime's classpath. still very complicated...
08:35 maclean Don't forget quadruple bonds, btw. :)
08:35 edrin however. the concept might work
08:36 maclean Oh, and I was going to ask : in what situations do bonds have more than 2 atoms? 3-center hbonds?
08:36 olas egonw: does XOM always give elements with capitalized first letter?
08:36 olas result -> Result ?
08:36 egonw huh?
08:37 olas seems to do so here...
08:37 egonw maclean: can be lot's of things...
08:37 egonw hydrogen bonding, I guess :)
08:37 egonw B2H4
08:37 egonw the latter is a nice example
08:37 egonw olas: explain
08:37 maclean hmmm. ta.
08:37 egonw <result> versus <Result>
08:37 egonw element Result ?
08:38 egonw umm: Element Result ?
08:38 olas result is my own element
08:38 egonw oh, and a bio example: porpherin
08:38 olas XOM writes it out as result
08:38 olas with capital R
08:39 olas so Result
08:39 egonw where the two hydrogens in the middle are delocalized...
08:39 egonw olas: no, not good
08:39 egonw and it does not do that by default
08:39 egonw have never seen that in CMLDOM
08:39 olas ok
08:39 egonw nor in any custom XOM code I wrote
08:40 egonw mmm... inkscape has a bit of a learning curve...
08:40 egonw but amazingly cool
08:42 maclean joined #bioclipse
08:43 maclean I quite like inkscape. the tutorials are nice.
08:43 egonw there are tutorials?!??!
08:43 maclean Yup.
08:43 maclean they come as inkscape documents.
08:44 maclean http://www.inkscape.org/doc​/basic/tutorial-basic.html
08:44 zarah maclean's link is also http://tinyurl.com/yvzc2e
09:01 edrin olas: hi
09:01 * egonw is getting some coffee
09:01 olas hi edrin
09:01 * olas forgot the coffee, must make new
09:01 edrin olas: I slightly modified the xws4j lib, mainly for client site now...
09:02 edrin olas: there are no severe changes, just that several things are now done with interfaces, to hide functions from the user that are not intended to be used by him...
09:02 olas sounds good
09:02 olas will up�date
09:02 olas finally managed to read in model in EMF again
09:03 olas been working hard on it
09:03 olas XML namespaces are not trivial things
09:03 edrin like client.getXmppItem() returns now IXmppItem and not XmppItem
09:03 olas edrin++ # use interfaces
09:04 edrin olas: i got a schema translated in java source files and compiled to .class at runtime for the xws-binding lib
09:04 edrin (using XML Beans and eclipse compiler lib...
09:05 olas edrin: why is that important?
09:05 olas for writing on console?
09:05 edrin yes
09:05 olas I see
09:06 edrin for two things: 1. to autogenerate a client stub java library to be used in a project (similar to the tools of soap libs, for example something like wsdl2clientstub)
09:06 edrin 2. for console...
09:06 edrin or scripting in general
09:07 edrin user could then GUI-browse through xmpp with service discovery, click a servic function, select "create binding" and add this binding .jar to the local binding library to be used within scripts...
09:07 edrin same could be done in console...
09:08 edrin with refelction
09:08 olas yes
09:08 edrin like
09:08 olas Question for all: I can't get my main() to output exceptions to console, i.e. not in a plugin but a standalone class with main. How to solve this?
09:09 olas it just dies silently...
09:09 olas ideas anyone?
09:09 olas Gpox?
09:09 jonalv olas: I don't think I understand the situation
09:09 olas I have a class
09:09 olas with a main
09:10 jonalv okey
09:10 olas and it just dies, without writing excetions to stdout
09:10 olas -consolelog missing
09:10 olas but this is not a plugin
09:10 jonalv hm
09:10 olas hence -consolelog does not solve it
09:10 jonalv what are you doing? :)
09:11 jonalv I don't thionk I have been in that situation
09:11 edrin f = xws.getFunction(...); ios = f.getIoSchemata(); fac = xws.getIoFactory(ios); in = fac.createInputObject(); in.setProteinSequence("ccsaallhh"); r = f.invokeSync(in); out = fac.getOutputObject(r); out.getCalculationResult();
09:11 jonalv at least not in a long time...
09:12 jonalv edrin: very "wordy"...
09:12 jonalv as in many words
09:14 edrin jonalv: huh? you don't like it?
09:14 olas I like it a lot!
09:15 jonalv edrin: I don't know. What lvl is this on?
09:15 olas console
09:15 jonalv and what did that do?
09:16 jonalv since I know nothing of how the xws technique works I am somewhat confused. is xws the manager btw?
09:16 edrin olas: it's still some way to it, it's a lot of work. especially because many things have to be passed to the binding lib, like locations where to put the source files, where to put the .jar what jars are required for compiling... very complex. we should not fix on it
09:16 edrin we should ready up without it
09:17 edrin jonalv: yes, xws is the manager...
09:18 olas edrin: can input schema be same as output schema?
09:18 olas for me it is...
09:18 edrin olas: sure
09:18 jonalv I was sort of expecting something like: result = xws.run("serviceName", "input")... :)
09:18 jonalv perhaps I am just naive...
09:18 olas jonalv: you must discover the service first
09:19 edrin jonalv:  in = fac.createInputObject() creates an object for the input on-the-fly according to the function's input XML Schema; this is cool because your eclipse instance "imports" a new Class at runtime!
09:19 jonalv :)
09:20 jonalv that sort of requires JavaScript :)
09:20 edrin jonalv: complicated i know, example: what if result = xws.run( very_complicated_input_object_w​ith_many_arrays_and_sub_objects )
09:21 jonalv yea well I have obviously not thought about this problem I am just suprised that it is so complicated...
09:30 olas edrin: explain this:
09:30 olas when does the xws use the schema?
09:30 olas or need I do it manually in my run() ?
09:32 edrin olas: the "input" schema is used by the component to validated function invocations. if input is valid, the function will be called. however i am not sure if the validation code in the component is fully correct. it might be that it returns valid always...
09:33 edrin input and output schemata are in general used to be pass to the clients if they ask for it...
09:35 edrin olas: does this answer the question?
09:35 olas ok
09:36 olas I guess so
09:43 CIA-52 bioclipse: jonalv * r7325 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (8 files in 4 dirs): [structuredb] a few more persistence tests passes
10:05 edrin do you have access to the following article: http://www.landesbioscience.com/​journals/autophagy/article/7075 ?
10:05 edrin left #bioclipse
10:05 zarah edrin's link is also http://tinyurl.com/5tqm2y
10:07 edrin joined #bioclipse
10:07 edrin sorry
10:07 edrin do you have access to the following article: http://www.landesbioscience.com/​journals/autophagy/article/7075 ?
10:07 zarah edrin's link is also http://tinyurl.com/5tqm2y
10:13 olas ask jonalv
10:13 olas he's in Uppsala
10:14 jonalv edrin: no it doesn't seem so :(
10:15 egonw Gpox, maclean:
10:15 maclean yarss?
10:16 egonw http://chem-bla-ics.blogspot.co​m/2008/10/chemical-editing.html
10:16 zarah egonw's link is also http://tinyurl.com/5dvoeu
10:16 egonw sorry, had a fight with my FF
10:16 maclean your firefox?
10:16 maclean your female friend?
10:16 egonw right
10:17 egonw friendfeed?
10:17 maclean :)
10:17 egonw well, does it matter?
10:17 maclean Er, no, I just wondered what you meant.
10:17 olas edrin: what is the difference between net.bioclipse.xws.client.adhoc.ProcessStatus and net.bioclipse.xws.component​.xmpp.process.ProcessStatus ?
10:18 olas use which one when?
10:26 thomasku joined #bioclipse
10:30 * jonalv -> lunch
10:32 edrin olas: use client.adhoc.ProcessStatus for Client and component.xmpp.process.ProcessStatus for component
10:32 olas ok
10:32 olas found that already :-)
10:32 * olas is trying to run his first service against ayena
10:33 edrin olas: afaik except you wont need to instantiate any of them yourself, do you?
10:33 olas in client from java, yes
10:33 olas not all use javascript
10:33 edrin oh?
10:33 olas hmm, no
10:33 olas just from my junit test
10:33 olas using ProcessStatusMock
10:33 edrin ah ok
10:34 edrin ProcessStatusMock is only for component
10:34 * olas is wrestling with java classpath
10:34 olas I know
10:34 olas thx anyway
10:34 edrin ok
10:36 egonw plug: http://chem-bla-ics.blogspot.com/2008/10/g​ittodo-support-for-freemind-graphical.html
10:36 zarah egonw's link is also http://tinyurl.com/6hhn6g
10:38 olas edrin: help
10:39 olas I want to run the Component for my new service Jar
10:39 olas but the service jar (hivpred.jar) complains it cannot find net.bioclipse.xws.component.functions.Functions
10:39 olas classnotfoundexception
10:39 olas clearly a classpath problem
10:39 olas how do I set which jars are on classpath in config file?
10:40 olas add them as FUNCTION_JARS seems not to be the correct place...
10:40 olas edrin?
10:43 olas hmm it seems my JAR does not include all required jars
10:43 olas so I need to add them to the classpath
10:43 olas edrin: could you add a line in config "CLASSPATH" ?
10:46 olas hmm, jar in a jar seems to be problematic...
10:47 egonw anyone here on LinkedIn to which I am not connected yet?
11:00 olas edrin: let me know when you're back
11:00 * olas will have lunch now
11:02 egonw jag ockso
11:21 * maclean lunch
11:24 * jonalv is back
11:28 Gpoks joined #bioclipse
11:34 shk3 joined #bioclipse
11:40 edrin shk3: do you have access to the following article: http://www.landesbioscience.com/​journals/autophagy/article/7075 ??
11:40 zarah edrin's link is also http://tinyurl.com/5tqm2y
11:44 * olas is back from lunch
11:44 olas edrin: did you read my problems with classpath?
11:48 edrin sorry, olas: yes
11:48 olas what do you think?
11:48 edrin i think it is not possible to put a .jar in a .jar
11:48 olas ok
11:48 edrin as far as I remember
11:48 olas can we add a line "CLASSPATH" in config file?
11:49 olas or is that not good?
11:49 edrin olas: i think this is not required, is it?
11:49 olas no
11:49 olas it is not
11:49 olas but would be convenient
11:49 edrin ah...
11:50 olas at least I think it would
11:50 olas not sure actually
11:51 egonw Gpox: did you get my email this morning on the JCP paper?
11:51 egonw sent it to your SF account...
11:52 Gpox yes i got it
11:53 edrin olas: from what I read in xws4j code I already load the .jars set as function jars in the config to the classpath
11:53 olas yes
11:53 olas that is not the problem
11:53 olas if my function jar requires a third party jar
11:54 olas like commons.logging.jar
11:54 edrin ah, ic
11:54 olas it CAN be picked up if I include it in the java classpath when executing the jar
11:54 olas it's just problematic
11:54 edrin sure, I can add this
11:54 olas and leads to looong command line args if you have many jars
11:55 olas would really simplify for me
11:55 edrin can you write me a mail, then i can add this later/this week
11:55 olas can you do it now?
11:55 olas oh
11:55 olas :-(
11:55 olas I need it quite now...
11:55 edrin olas: no, i am in the lab, no eclipse, no admin account, no internet ...
11:55 olas else I will not have time to build my service until I leave for holidays
11:55 olas ok
11:55 olas will email you AND try to resolve this anyway
11:56 egonw Gpox: did you reply?
11:56 edrin olas: for now you could just run your service with a long command line, no?
11:56 olas maybe
11:56 olas will try
11:57 Gpox egonw: no not yet
11:57 edrin olas: when will you leave for holidays ?
11:57 olas Nov 2.
11:58 olas back on Doc 8
11:58 olas Dec
11:58 edrin Gpox: do you have access to this article: http://www.ncbi.nlm.nih.gov/pub​med/18927489?dopt=AbstractPlus
11:58 zarah edrin's link is also http://tinyurl.com/6fcz7r
11:58 edrin olas: ok, where are you going?
11:58 olas Caribbean
11:58 olas puerto rico, cuba, jamaica etc
11:59 edrin oh
11:59 edrin nice
11:59 olas yes, will be nice
12:01 maclean joined #bioclipse
12:02 edrin maclean: do you have access to the following article: http://www.ncbi.nlm.nih.gov/pub​med/18927489?dopt=AbstractPlus  ??
12:02 zarah edrin's link is also http://tinyurl.com/6fcz7r
12:02 maclean I'll check
12:03 edrin thx
12:03 maclean hmmm. doesn't seem like it - unless I want to pay $19!
12:04 edrin ok
12:04 edrin thanks anyway
12:05 olas edrin: is it not possible to use ayena today?
12:05 olas xws.ayena.de
12:05 olas I get a Connection refused
12:07 olas edrin?
12:11 shk3 edrin: sorry, we have been to lunch
12:11 shk3 doesn't look like we have that journal
12:13 edrin olas: oh, it seems so... probably server is down?
12:13 olas :-(
12:13 olas not good
12:13 edrin i cant browse to it via PSI's XMPP discovery, too
12:14 edrin shk3: thank you
12:14 edrin olas: ah
12:14 edrin olas: wait, now its on again
12:14 olas ?
12:14 olas how do I connect to it in psi?
12:14 edrin olas: i think it was just restarted
12:14 edrin olas: server is there again:
12:15 olas server: ayena.de
12:15 olas port 5222
12:15 olas in psi
12:15 olas right?
12:15 olas edrin?
12:15 edrin olas: from your PSI jabber.org account -> goto menu ->  Service Discovery ->
12:15 edrin enter ayena.de
12:16 olas I need not connect to ayena?
12:16 olas ok
12:16 edrin no
12:16 edrin olas: just go online with your jabber.org account
12:16 olas xws.ayena.de ai guess?
12:17 olas ok
12:17 olas found it
12:17 olas hmm, I get connection refused from java
12:17 edrin did the Service Discovery window popup?
12:17 edrin hm...
12:18 edrin the port is not 5222!
12:18 olas there's a red cross on xws.ayena.de
12:18 olas 8765
12:18 olas I know
12:18 edrin olas: yes, the red cross means: error. error because component is not running ;)
12:18 olas yes
12:18 olas but I can't run component
12:18 edrin if error would be running you could see all supported functions ;)
12:19 olas indeed
12:19 edrin ah
12:19 olas when I try to run component I get connection refused error
12:19 edrin for the component try xws.ayena.de as server
12:19 olas that's what I did
12:19 edrin and if it does not work, try ayena.de
12:19 olas ok
12:20 olas ah
12:20 olas server=xws.ayena.de worked!
12:20 olas WORKS!
12:21 olas great
12:21 edrin olas: yes, this guy runs his server at another subdomain and actually just forwards the 5222 port from ayena.de something
12:21 olas brb
12:21 edrin i can see your service :)
12:26 olas where does all the test functions come from?
12:53 malick left #bioclipse
12:57 CIA-52 bioclipse: jonalv * r7326 /bioclipse2/trunk/plugins/ (10 files in 4 dirs): [structuredb] a few more persistence tests passes
13:00 olas edrin: if you write the wrond function_JARS xws4j does not complain
13:00 olas it should
13:04 olas edrin: I get error validating my input!
13:04 olas hence it is actually doing something
13:07 olas edrin: I need help
13:08 olas edrin: I get the following log in my component: http://paste2.org/p/89511
13:10 olas @tell edrin: ping me when you get back
13:10 zarah Consider it noted.
13:50 edrin1 joined #bioclipse
13:50 edrin1 hi
13:50 zarah hi edrin1
13:50 edrin1 stupid jabber.org server crashed, probably too high user load...
13:50 edrin1 olas:
13:50 olas yes
13:50 edrin1 olas: ah, it might be that the Exception you see is because you did not pass a proper input schema string! maybe therefore input validation fails and returns an exception
13:50 olas ok
13:51 olas will test to pass your empty schema
13:51 edrin1 yes...
13:51 olas jabber.org seems to be down
13:51 olas buggy
13:51 olas do you have an alternative?
13:52 olas can you connect to jabber.org?
13:53 edrin1 olas: try kdetalk.net
13:54 edrin1 http://www.jabber.org/web/Services
13:54 zarah edrin1's link is also http://tinyurl.com/69jfgk
13:55 olas host unknown
13:55 edrin1 maybe jabber.ccc.de
13:55 edrin1 swissjabber.ch
13:55 edrin1 ok, jabber.org is online again
13:56 edrin joined #bioclipse
13:56 edrin1 left #bioclipse
14:08 olas edrin, edrin1: around?
14:11 rojasm joined #bioclipse
14:22 egonw OK, I thikn I got Mylyn working with Pele :)
14:22 olas sounds good
14:23 egonw cool
14:24 egonw http://pele.farmbio.uu.se/cgi-​bin/bugzilla/show_bug.cgi?id=1
14:24 zarah egonw's link is also http://tinyurl.com/55k8wf
14:24 egonw comment added with Mylyn :)
14:24 egonw common guys... doesn't this deserver a 'egonw++' ??
14:25 zarah shame on you, egonw, giving yourself karma like that
14:25 egonw com'on ?
14:25 egonw come on guyes
14:25 egonw shk3: you're good at UK spelling...
14:25 egonw which one is it?
14:27 CIA-52 bioclipse: jonalv * r7327 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/persistency/dao/DBMoleculeDao.java: Whitespace...
14:30 maclean it's "come on". and egonw++
14:31 maclean also Gpox++ for the new generators.
14:31 jonalv egonw++
14:32 egonw tack :)
14:33 CIA-52 bioclipse: jonalv * r7328 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
14:33 CIA-52 bioclipse: [Structuredb] All (now created) persistence tests now passes. It was a bit of
14:33 CIA-52 bioclipse: permutation programming regarding such strange sql stuff as LEFT OUTER JOINS
14:33 CIA-52 bioclipse: (and don't ask me why it works) but now it seems to be working! :)
14:42 maclean Hmmm. jonalv, there seem to be some errors in structuredb plugin.
14:42 jonalv maclean: You think so? ;)
14:42 maclean oh, you know. n/m. :)
14:42 maclean Only 7 though!
14:43 shk3 eclipse thinks so
14:43 * jonalv should have used a branch a few weeks ago. That was sort of what inspired this git for Bioclispe hype...
14:43 jonalv maclean: 7 things that doesn't compile perhaps... Many more errors
14:43 maclean Yes, there may be hidden errors, I suppose.
14:44 jonalv the new annotations structure means that the database suddenly more than doubled in size and things works differently...
14:44 maclean :(
14:44 * jonalv is refactoring from bottom up
14:44 jonalv the domain object tests and the persistence tests are passing now
14:45 jonalv remains internal business and public business and then the gui parts... :)
14:45 jonalv then it's time to start hunting bugs again... :)
14:46 maclean good luck!
14:46 jonalv luck is only a small part of it :)
14:47 shk3 I am trying to run the qsar plugin
14:47 shk3 it needs emf, it seems
14:48 shk3 I installed emf sdk 2.4.1, but still missing plugins
14:48 shk3 does somebody know what I need to install?
14:49 jonalv olas should know...
14:49 olas see qsar feature
14:49 jonalv I think it sort of just worked for me... I don't know why though... :)
14:49 shk3 hm, there are org.eclipse.emf plugins in my eclipse install
14:49 shk3 but somehow not found
15:34 egonw http://wiki.bioclipse.net/index.php?title=Git
15:34 zarah egonw's link is also http://tinyurl.com/6d23sy
15:34 maclean joined #bioclipse
15:44 shk3 how can I use the qsar plugin?
15:45 shk3 i. e. what does it add to the ui?
15:46 jonalv shk3: you create a project
15:47 shk3 special type?
15:47 egonw dinner time
15:47 egonw bye all!
15:49 shk3 jonalv: just a project?
15:54 jonalv shk3: "just"?
15:54 jonalv shk3: isn\t hat enough?
15:54 shk3 but what then?
15:54 shk3 I have an empty project
15:54 jonalv an empty qsar project?
15:54 jonalv you should have an xml file in it I think
15:55 shk3 there is no qwar project for me
15:55 jonalv shk3: then you haven't got all htat's needed...
15:56 shk3 ah, there is a qsar.ui project as well
15:56 shk3 ok, need to get more plugins
15:57 shk3 sorry
15:58 shk3 another question: Is it possible to open several mol files or a whole directory with structure files (perhaps even different types)
15:58 shk3 in the structure tabel?
15:58 shk3 i. e. the sdf editor?
15:59 shk3 I think that's a usefull feature
16:01 CIA-52 bioclipse: jonalv * r7329 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): [Structuredb] Started work on updating internal-business-tests to new world order
16:02 jonalv shk3: no but have a word with Gpox about that...
16:02 olas I too think that is an important feature
16:03 shk3 essential, i would say
16:03 olas shk3: please file a bug for Gpox
16:04 shk3 it's a pleasure
16:09 shk3 where can i get org.eclipse.core.databinding plugin from?
16:10 olas ganymede
16:10 olas in software update
16:10 edrin left #bioclipse
16:10 shk3 where exactly?
16:10 shk3 ganymed has lots of subsections for em
16:10 * jonalv is off to swim. You have fun now! :)
16:10 olas software update
16:10 olas bye jonalv
16:11 olas type databinding in box
16:13 shk3 hm, there is only emf databinding
16:21 maclean left #bioclipse
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16:58 edrin joined #bioclipse
19:29 CIA-52 bioclipse: edrin_t * r7330 /xws/trunk/xws4j/src/net/bioclipse/xws/ (6 files in 5 dirs): fixed some sever bugs, added support for optional enabling/disabling input validation.
19:33 CIA-52 bioclipse: edrin_t * r7331 /xws/trunk/xws4j-coffee-machine-sample/src/ (2 files in 2 dirs): added suppress warnings, makeNewCoffe now returns the amount of coffe in the can (100 % full can :! )
19:39 CIA-52 bioclipse: edrin_t * r7332 /xws/trunk/xws4j-sample-client/: Initial import.
19:41 CIA-52 bioclipse: edrin_t * r7333 /xws/trunk/xws4j-sample-client/ (6 files in 4 dirs):
21:22 CIA-52 bioclipse: edrin_t * r7334 /xws/trunk/xws4j-sample-client/src​/sample/client/SampleClient.java: added several test
22:37 malic1 joined #bioclipse

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