Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-15

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All times shown according to UTC.

Time Nick Message
03:42 ilogger2_ joined #bioclipse
05:46 Gpox joined #bioclipse
05:49 Gpox hi
05:49 zarah hi Gpox
06:35 olas joined #bioclipse
06:37 olas hi
06:37 zarah hi olas
07:43 jonalv joined #bioclipse
07:43 jonalv moin
07:43 zarah hi jonalv
07:44 olas jo jonalv
07:45 jonalv olas: skype?
07:45 olas mom
07:45 olas 3 mins
07:56 maclean joined #bioclipse
08:04 ilogger2 joined #bioclipse
08:15 olas hi maclean
08:16 maclean hi olas
09:04 maclean joined #bioclipse
09:04 CIA-49 bioclipse: ospjuth * r6600 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/ (MoleculeType.java impl/MoleculeTypeImpl.java): Removed renamed type.
09:05 CIA-49 bioclipse: ospjuth * r6601 /bioclipse2/trunk/plugins/net.bioclip​se.qsar/src/net/bioclipse/qsar/util/: Removed unused package.
09:10 CIA-49 bioclipse: ospjuth * r6602 /bioclipse2/trunk/plugins/net.bioclipse.qsar.edit/ (13 files in 6 dirs): Updated edit, and test code.
09:12 * olas is battling with subclipse
09:12 CIA-49 bioclipse: ospjuth * r6603 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (21 files in 5 dirs): Updated xsd and model mode.
09:13 CIA-49 bioclipse: ospjuth * r6604 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (MoleculesPage.java QSARFormEditor.java): Use new model. Dirty state is properly shown on add/remove.
09:15 thomas_ku joined #bioclipse
09:52 CIA-49 bioclipse: ospjuth * r6605 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (MoleculesPage.java QSARFormEditor.java QsarXMLEditor.java): Used XMLEditor instead of Texteditor. Also fixed Save in XMLEditor to clear dirty state for molpage.
10:13 edrin joined #bioclipse
10:15 olas hi edrin
10:15 olas glad we got it working yesterday
10:15 edrin hi olas
10:15 olas barely made the train as well :-)
10:15 edrin cool :)
10:16 olas edrin: so, how do I create my own service?
10:16 olas and how do I call it from Java?
10:16 edrin that's quite simple
10:16 olas I guess you have written convenience methods to produce accurate xml
10:16 edrin what do you mean by call it from Java?
10:17 olas well
10:17 olas not by hardcoding xml via PSI
10:17 olas call my service from a main() in a java prog
10:17 edrin is this an holiday at your place, too?
10:17 olas no
10:17 edrin ah
10:18 olas so I'm working :-)
10:18 olas are you free?
10:18 edrin well, in general yes, although I just cam back from diagnostics this morning, i have weekend service this week and next week
10:18 olas oh :-(
10:19 edrin and "emergeny" service as well, so they can call me back to the lab
10:19 olas so no time to assist me?
10:19 edrin yes, emergencies are not predictable
10:19 edrin well, i mean "yes, i can assist"
10:19 olas :-)
10:20 edrin i was about to program anyway
10:20 olas ok, first I'd like to write a java client that calls the coffe-machine service I set up yesterday
10:20 olas second, I'd like to discover available services
10:20 edrin later i will have to go to the lab to do some diagnostics stuff there... but only for 1 h i hope
10:20 olas third, I'd like to write my own service
10:20 olas great, then we can hack some
10:21 olas let's work together extending the wiki as we go
10:21 edrin olas: third you can already do. first and second is not ready yet. I am currently working on this...
10:21 olas ok
10:21 olas let's start wth third then
10:21 olas what do I need to check out?
10:21 edrin i will upload the lgpled coffee machine sample
10:22 edrin pls wait
10:22 olas ok
10:22 * olas is making coffee meanwhile
10:25 edrin I reneamed xws to xws4j to have the possibility to use XMPP Web Services as general term
10:28 CIA-49 bioclipse: edrin_t * r6606 /xws/trunk/xws4j-coffee-machine-sample/: Initial import.
10:30 CIA-49 bioclipse: edrin_t * r6607 /xws/trunk/xws4j-coffee-machine-sample/ (14 files in 9 dirs): Initial import.
10:31 edrin sample uploaded.
10:31 olas ok
10:31 olas I need to DL all in trunk/xws?
10:31 olas xws/runk I mean
10:31 edrin btw. yesterday some xmpp guy, who supported my XEP mentioned to me that he will write a plugin for the XEP for python...
10:31 olas cool :-)
10:31 edrin no
10:32 olas just that?
10:32 olas component?
10:32 olas backend?
10:32 edrin he is doing it for comercial purposes
10:32 olas oh :-)
10:32 edrin he did not tell me what exactly he is doimg with it
10:32 edrin just communication and not scientific
10:32 olas right
10:32 edrin communication related
10:33 olas what do I need to download?
10:33 edrin whatever this means
10:33 olas what you uploaded, anything else?
10:33 edrin you just need /xws/trunk/xws4j-coffee-machine-sample/ for now
10:33 olas ok
10:33 olas done
10:33 olas hmm
10:33 olas does not compile
10:33 edrin why not?
10:33 edrin ah
10:34 edrin of course
10:34 olas xws4j missing
10:34 olas you need to commit that too
10:34 edrin well, you will have to add the xws4j-alpha1_ola.jar to your project
10:35 edrin and the jso-full.jar
10:35 edrin just link the project with these two jars
10:35 edrin (in my own eclipse workspace i linked the sample to the other xws project...)
10:36 olas ok
10:37 edrin do you want to write a long lasting service or a fast responding service?
10:37 olas both :-)
10:38 olas ok, compiles now
10:38 olas hmm
10:38 olas just thought about one thing
10:38 olas working from home today
10:38 olas which means I might not be able to access ws1.bmc.uu.se
10:38 olas testing...
10:38 olas no :-(
10:39 edrin GetCoffeeCanStatus.java is a fast responding service and MakeNewCoffee.java needs some seconds to finish and notifies the client about completion
10:39 olas ok
10:39 edrin ;)
10:39 olas can't log in
10:39 olas damn
10:39 edrin i guess the server is firewalled
10:39 edrin or missconfigured
10:39 olas can fix this on tuesday earliest
10:39 olas yes
10:39 edrin ah
10:39 olas I think there is a port issue
10:39 edrin however
10:40 edrin my test server is online ;)
10:40 olas can I use that?
10:40 olas that's the info you sent me yestarday?
10:40 edrin i think so
10:40 edrin yes
10:40 olas how do I connect to it?
10:40 edrin i will ask the owner, pls wait
10:40 olas with PSI I mean?
10:41 CIA-49 bioclipse: jonalv * r6608 /bioclipse2/trunk/_playground_/LazyTreeExample/: Initial import.
10:43 CIA-49 bioclipse: jonalv * r6609 /bioclipse2/trunk/_playground_/LazyTreeExample/ (15 files in 7 dirs): A little sample example for a lazy tree. Something like this will be used when expanding for example an sdf file.
10:44 edrin olas: you may try to create ayena.de or
10:44 olas how?
10:44 olas modify account Z connection > manually specify server?
10:44 jonalv voila a first stupid example for lazy trees. Now food. Will start trying to make this for an sdf file after lunch.
10:47 olas jonalv++
11:09 shk3 joined #bioclipse
11:10 CIA-49 bioclipse: shk3 * r6610 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/ValidateCMLManager.java: made a method public which will be used somewhere else as well
11:20 olas edrin++ #xws seems very nice!
11:43 CIA-49 bioclipse: jonalv * r6611 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/ (3 files in 2 dirs): Lightweight SDF parsing
12:55 shk3 just worked on the spectrum editor to handle cml
12:56 shk3 need the xpp library for that
12:56 shk3 added it to the plugin
12:56 shk3 so it should be in three places now?
12:56 shk3 what do we do with it?
12:58 CIA-49 bioclipse: shk3 * r6612 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (7 files in 5 dirs): spectrum editor works on cml files
13:02 olas shk3: could we not place in core?
13:02 CIA-49 bioclipse: shk3 * r6613 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/src/net/bioclipse/spe​ctrum/editor/PeakTableViewer.java: cleaned up some things
13:02 olas jonalv: what do you think?
13:02 olas seems to be used regularly enough for that
13:02 jonalv mom, backloggging
13:03 jonalv so just so that I understand what we are talking about, which plugins use this thing?
13:33 shk3 spectrum
13:33 shk3 ui
13:34 shk3 and I think there was a third one
13:42 edrin joined #bioclipse
13:50 jonalv how do I make an iterator over a file? When do I close the file? I can never be sure the file get's closed can I?
13:51 olas I have no idea
13:52 maclean It sounds risky.
13:52 jonalv brb
13:55 jonalv :(
13:56 jonalv It's just a pile of problems right now... :(
13:57 maclean In some languages (python for example) you do iterate over file contents.
13:58 maclean like "for line in open(filename): print line"
13:58 maclean but, usually, you have a handle to the file, and then close it outside the loop
13:59 maclean like: "fp = open(filename); for line in fp: ...; fp.close()
14:01 maclean hmmm. maybe you want java.util.Scanner. That isa Iterator.
14:03 olas jonalv: you can always ask on ##java
14:05 jonalv I want to read molecules from a file and present them in the ui on by one when I find them...
14:05 jonalv I'll mocj it for now
14:06 jonalv *mock
14:13 olas jonalv: Subclipse only displays them when they have found all
14:13 jonalv I wanna do better than that :)
14:13 CIA-49 bioclipse: ospjuth * r6614 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (10 files in 2 dirs): Updated MoleculesPage to two sections with molecular resources and preprocessingSteps. Fully working regarding molecular resources.
14:14 CIA-49 bioclipse: ospjuth * r6615 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (MoleculesPage.java MoleculesPage2.java QSARFormEditor.java): Renamed new moleculespage.
14:56 olas have a nice weekend all
14:56 olas bye
14:56 olas left #bioclipse
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19:58 edrin joined #bioclipse

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