Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-07

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All times shown according to UTC.

Time Nick Message
05:19 masak joined #bioclipse
07:24 simard joined #bioclipse
07:40 Gpox joined #bioclipse
07:40 Gpox joined #bioclipse
07:42 Gpox joined #bioclipse
08:30 olass joined #bioclipse
08:30 olass hi
08:30 zarah hi olass
08:38 masak OH HAI
08:38 zarah hi masak
08:44 edrin joined #bioclipse
08:45 edrin hi
08:45 zarah hi edrin
08:45 masak hi edrin
08:45 edrin hi masak
08:54 stain hi.
08:54 stain edrin: I am now :-)
08:54 stain normally I leave work at 17..
08:55 edrin stain: egon and me were trying to find out how to write a plugin for taverna
08:55 stain what is the plugin to do?
08:57 stain and do you mean for Taverna 1 or 2..?
08:57 edrin the plugin should support a "activator?" menu item, similar to wsdl, where a dialog pops up and allows the user to specify the address of a service. the dialog should then create a "worker?", the thing i can drag&drop into the workflow as a node...
08:57 edrin Taverna 2
08:57 stain activity
08:58 stain there's a little selection of SPIs and interfaces you'll need to implement, because you'll need both the actual activity (that can do the work), the way to find the activities based on an address, and a menu item for popping up the question
08:59 edrin i think that's valuable :)
08:59 stain we are going to create some maven archetypes and developer documentation about how to do this, but I think it's not there until in about 2 months time
08:59 stain as a head start you can have a look at any of the existing activities
08:59 edrin oh, ok
08:59 stain check out the t2activities/ from our CVS
08:59 edrin i think egon tried but he could not compile it
08:59 stain you would find pairs (or really tripples) such as wsdl-activity, wsdl-activity-ui and wsdl-translator
09:00 stain you'll only need the translator-bit if you are going to support translation of similar Processors from Taverna 1 workflows
09:01 stain there's some issues with our snapshots at the moment as we have just bumped all the version numbers after the release.. check out using the tag t2activities-0-4 - that's the ones used for the 2.0 release
09:02 edrin stain: and question: the input of a wsdl/soap service can be quite "complex". however taverna seems to parse this complexity to String, String [], or even String[][] for input and output. how can the user finally know he is setting the right things in the xml input ?
09:05 stain you can use the xml splitters to create and parse the XML inputs and outputs
09:05 stain but at some points you'll have to insert the real strings, no? :)
09:06 * masak .oO( XML all the way down... )
09:06 olass stain: What do you think of the possibility to run the new Taverna GUI editor as an Eclipse/Bioclipse editor?
09:06 stain did you manage that with Taverna 1..?
09:07 olass no
09:07 stain to put say the diagram inside?
09:07 olass well, I exported the image from T1
09:07 olass just to look at
09:07 olass I guess my question is: How decoupled is the actual GUI editor from the underlying model?
09:09 jonalv joined #bioclipse
09:09 olass This is most out of curiosity, we do not have the m,anpower (yet) to write a graphical editor for Taverna in Bioclipse...
09:09 olass but we would like to :-)
09:09 jonalv oh hai
09:09 zarah hi jonalv
09:09 masak jonalv: OH HAI
09:10 stain the GUI editor is using Batik SVG, and generates the SVG from the Dataflow. It uses graphviz to do the layout (but not any more for SVG-generation). There's some kind of graph model used behind this all, with hooks for doing the interactions - but they all assume you have a Taverna 2 Dataflow
09:10 stain why would you want to use the editor without the Dataflow model?
09:13 stain I guess you'll have a few issues such as that you want to use Bioclipse's open files and undo/redo instead of the ones we made for Taverna
09:13 stain most of those things are done through interfaces, so you could in theory make your own implementations that just proxy through to Bioclipse/Eclipse instead
09:14 jonalv stain: that might be an option but it do sound like a lot of work to me...
09:14 stain you might have to patch it a bit, though..
09:14 stain yeah, it was not designed as a standalone component
09:15 stain as it's tying most of the workbench together it's quite integrated
09:15 stain for instance it has to be able to receive activities dragged in, selecting items, update when change happens elsewhere, etc
09:16 stain but it could be easier if you put a mini-workbench inside bioclipse
09:16 jonalv okey?
09:16 stain you'll have to figure out something clever with menues etc
09:17 olass stain: http://wiki.bioclipse.net/​images/ServiceViewFull.png
09:17 zarah olass's link is also http://tinyurl.com/746w2t
09:18 stain olass: so it's even discovering services now? :)
09:19 stain nice to see it working :)
09:21 stain jonalv: how are you thinking of interacting with the graphical editor (I think we call it the 'interactive diagram') within Bioclipse? How do you say add a service?
09:21 jonalv stain: uhm in general in Bioclipse or in some specifc case?
09:22 olass stain: we'd like to open, edit, and run T2 workflows inside Bioclipse with as minimum work as possible
09:22 olass easiest will be to just open and run
09:23 olass we (almost) had that in BC1
09:23 stain in general.. I mean you easily get the editor in there, but I assume you also want to do something with it..?
09:23 stain so you could for instance make it so that when you do File->Open in Bioclipse you open a workflow, then you do FileManager.getInstance().​openDataflow(theDataflow) as well - which should show it in the diagram
09:24 stain but I guess you would want to have multiple diagrams for multiple workflows
09:24 stain and not a single component that changes what it's viewing (which is how it is in Taverna workbench)
09:25 jonalv is it: 1 file <~> 1 workflow <~> 1 editor?
09:25 * jonalv is afk in meeting
09:26 stain the editor - or GraphViewComponent which is probably the class you're after - is connected to a Dataflow instance
09:27 stain you can change what that is (which is what happens when you change the active workflow in the Workflows menu)
09:27 stain or you can have multiple instances of the component - attached to different dataflows
09:27 stain which is what happens in the result-perspective when you see the little picture of the dataflow there
09:27 stain note that those are not interactive for obvious reasons
09:28 stain so that should work fine, the main problems would be the interactions.. for instance if you click on a beanshell script and you want to configure it
09:29 stain in the Taverna workbench we don't have (yet) a way to pop up the configure box from the diagram, but you'll have to click Configure in another component, the contextual view
09:29 stain that get's updated depending on the current selection
09:29 stain if you use the graph component standalone, there's no problem, the selection is done, but there's no other components listening to that selection
09:39 stain and most actions assume 'the current workflow' for the edit manager, but unless you want to support undo/redo you shouldn't need to care about that
09:39 stain I think it's doable, but it will be more work the heavier integration you want :-)
09:40 stain perhaps slightly exponentially
09:51 edrin stain: http://wiki.bioclipse.net/​images/ServiceViewFull.png
09:51 zarah edrin's link is also http://tinyurl.com/746w2t
09:52 edrin stain: the Right upper window shows the XMPP Services discovered in realtime on the xmpp servers. with the (+) button/green you can create a XML Binding for the service...
09:54 edrin zarah: tell egonw In your cdk xws service, please rename it in CDK XMPP Services
09:54 zarah Consider it noted.
09:56 edrin stain: and the editor window of the massXWS.js shows a script that is using such a service. it's using the autogenerated binding
09:57 stain but do yo have to know what the parameters are then..?
09:57 stain I didn't quite understand what is an ios, iof and smidoc
09:58 edrin the script is doing the following (right now it is independent from the Discovery view, it is an old script)
09:59 edrin stain: f.getIoSchemataSync(timeout); returns XML Schemata of input and output of the function f
10:00 edrin xws.getIoFactory(ios); auto-generates a binding for the function f and returns the factory object.
10:00 edrin the factory object can be used to generate an input object
10:01 edrin or parse output
10:02 edrin the iof.createSmilesDocument() is a service specific function that was autogenerated according to the XML Schema of input.
10:03 edrin the IoFactory is mainly interesting for the javascript console that supports tab-autocompletion of commands, this way you can "discover" the new autogenerated functions while you type...
10:04 edrin for plain Java programs this does not make much sense, but here you can use the Java classes for input and output that are also autogenerated and saved in teh workspace
10:06 edrin stain: was the explanation somehow helpful?
10:32 stain yeah.. I just wonder why it's exposed ;)
10:32 edrin stain: the function?
10:33 stain these factories
10:33 edrin ah
10:33 edrin well, the "api" of the function is generated And used in this script...
10:34 simard edrin, hello again
10:34 edrin hello simard
10:34 simard yes, I am studying for a master degree in EE at university
10:49 simard so edrin what do you use bioclipse for, professionnaly
10:52 edrin simard: its just a development projct
11:00 Gpox joined #bioclipse
11:04 gilleain joined #bioclipse
11:04 gilleain 'lo
12:08 edrin hi
12:08 zarah hi edrin
12:12 gilleain hi edrin
12:12 gilleain interesting discussion I saw earlier about bioclipse/taverna
12:13 edrin you saw? at stain's screen?
12:13 gilleain er.
12:13 edrin or chatlog?
12:14 gilleain no, I read the irc log.
12:14 edrin ah ok
12:14 edrin there is a log, right..
12:14 gilleain I think stain is in manchester?
12:14 edrin ah ok
12:14 edrin :)
12:15 gilleain http://irclog.perlgeek.de/​text.pl?channel=bioclipse
12:15 zarah gilleain's link is also http://tinyurl.com/8sak95
12:16 gilleain but anyway, I think that bioclipse and taverna could work well together, so long as they don't try to do the same thing as each other
12:16 stain gilleain: feel free to visit! ;)
12:16 gilleain (separation of concerns, that is)
12:16 gilleain :)
12:22 edrin stain: i modified a beanshell script in taverna. but it seems i cannot save it as a worker in the worker view
12:22 stain no, that's not  implemented yet
12:22 edrin ok
12:22 edrin but it will?
12:22 edrin :)
12:24 masak @tell olass http://developer.apple.com/technology/xcode.html
12:24 zarah masak's link is also http://tinyurl.com/6jrkh8
12:24 zarah Consider it noted.
12:26 gilleain I've never really used xcode. I understood it to be great for obj-c, though.
12:27 masak gilleain: it's mostly for getting MacPorts to work in this case.
12:27 gilleain ohhh.
12:27 masak but yes, I've also heard nice things about Obj-C.
12:27 gilleain port install bioclipse, eh?
12:28 masak not yet :)
12:35 CIA-54 bioclipse: carl_masak * r8143 /bioclipse2/trunk/keep-clean.pl:
12:35 CIA-54 bioclipse: [keep-clean] found and fixed the bug that removed all empty lines
12:36 CIA-54 bioclipse: in the last code cleanup
12:37 olass joined #bioclipse
12:38 olass hi again
12:38 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
12:38 olass @msg
12:38 zarah olass: 13 m 27 s ago, masak said http://developer.apple.com/technology/xcode.html
12:39 olass masak: 995.8 MB download...
12:39 masak olass: or just use the Mac OS X CD.
12:39 olass 8.7 MB per sec
12:40 olass so pretty fast
12:40 masak uni++
12:40 olass karma uni
12:40 zarah uni has a karma of 1
12:41 olass masak: and then?
12:44 masak install it :)
12:45 masak http://www.macports.org/install.php
12:45 zarah masak's link is also http://tinyurl.com/34hhb9
12:57 * masak reverse-merges r8084
12:59 masak svn is really slow at reverse-merges, by the way.
13:00 olass masak: ok, done port selfupdate
13:00 olass how do I search for ports?
13:01 olass like, git?
13:01 masak olass: everything works to satisfaction?
13:01 olass so far...
13:01 masak olass: the MacPorts webpage has long lists.
13:01 olass ok
13:01 masak olass: there's also some `port list` subcommand, IIRC.
13:01 olass what git should I install?
13:01 olass git-core?
13:01 masak olass: git-core
13:01 olass ok
13:02 masak http://github.com/guides/get-git-on-mac
13:02 zarah masak's link is also http://tinyurl.com/83wdow
13:03 olass I assume +svn is important?
13:04 olass should I cancel and rerun with + svn?
13:04 masak olass: if you plan to use git-svn, yes.
13:04 masak olass: perhaps :)
13:04 masak or just run it again when it's done.
13:04 * olass just cancelled
13:05 olass a nice git tutorial that you like? Want to print it out and read on train...
13:05 olass I could google myself :-)
13:05 masak olass: hold on.
13:05 olass thx
13:05 masak I have just what you wnat.
13:05 masak s/na/an/
13:06 masak first, this one for motivation: http://tomayko.com/writings/the-thing-about-git
13:06 zarah masak's link is also http://tinyurl.com/69xpm2
13:06 masak then, this one for the groundwork: http://www.newartisans.com/blo​g_files/git.from.bottom.up.php
13:06 zarah masak's link is also http://tinyurl.com/6lc3sa
13:06 masak pleasant reading.
13:07 masak for git-svn perhaps this one: http://tsunanet.blogspot.com/2007​/07/learning-git-svn-in-5min.html
13:07 zarah masak's link is also http://tinyurl.com/38brwe
13:08 masak oh, and this one for reference: http://git.or.cz/course/svn.html
13:08 zarah masak's link is also http://tinyurl.com/2coemo
13:08 masak I'll stop now.
13:09 masak er, the last one wasn't a git-svn crash course, as I thought, but rather a git crash course for svn users.
13:09 masak not too bad either, of course...
13:16 masak ok, when conflicts occur in a reverse-merge, the option that leaves the file alone is 'mf'. just so you know.
13:17 olass masak++ //for help with good GIT articles
13:17 gilleain so noted. now : what is a 'reverse-merge' :)
13:17 masak olass: glad you like them.
13:17 olass takes quite a while to install git
13:17 olass requires perl among others...
13:17 masak gilleain: it's something that a stupid person needs to do when he's screwed up a source tree.
13:18 gilleain ohh.
13:18 olass hmm, sounds like I might end up in such a situation at some point...
13:18 masak gilleain: say, removed all the empty lines from all the java files in plugins/
13:19 masak that's when a reverse-merge might come in handy.
13:19 gilleain ahhh. shk3 and I had noticed that...
13:19 olass masak: I get this error
13:19 olass Error: Target org.macports.activate returned: Image error: /opt/local/lib/perl5/5.8.9/darwi​n-2level/auto/List/Util/Util.bs is being used by the active perl5.8 port.  Please deactivate this port first, or use the -f flag to force the activation.
13:19 gilleain it was in the grand cleanup, eh?
13:19 olass masak: seems perl does something evil
13:19 masak gilleain: yes.
13:19 olass (as always?)
13:20 olass masak: any idea how to deactivate the perl5.8 port?
13:20 gilleain there's a deactivate command
13:20 masak olass: no, not offhand.
13:20 masak olass: what gilleain just said.
13:20 gilleain try "port help"
13:21 olass hrmmf
13:21 gilleain like svn, it has the great "port help {command}" syntax
13:23 olass seems port deactivate perl5.8 did the trick...
13:23 olass (no idea what it did though)
13:24 olass why download it if you don't use it?
13:24 gilleain maybe they forgot to change the list of dependencies
13:26 masak olass: you could always try reactivating it after installing git.
13:27 olass masak: true
13:29 olass masak: and latex, is that texlive?
13:30 masak olass: tetex, methinks.
13:30 olass ok
13:30 masak if such a beast exists.
13:32 olass it does indeed
13:32 olass and I am oh so greatful for that help
13:33 olass grateful
13:33 olass thankful
13:33 olass (what's the difference?)
13:33 edrin btw. how to run a .js file in bc2?
13:33 olass click the play icon in toolbar
13:33 masak olass: when you're thankful, you're full of thanks. when you're grateful, you're full of grates.
13:33 edrin ah
13:34 gilleain weird. that was exactly the reply I was going to give.
13:34 jonalv masak: uhm this forces me to ask>
13:34 masak gilleain: grate minds think alike :)
13:34 jonalv grace / thanks what\s the difference?
13:34 olass lol
13:34 gilleain *spangs*
13:34 jonalv |grates
13:34 masak jonalv: "By the grace of God go I" -- good line
13:35 * jonalv cant spell
13:35 gilleain grace is more religious
13:35 masak jonalv: "By the thanks of God go I" -- bad line
13:35 jonalv masak: "but you understand..."
13:35 olass masak: git has a lot of deps....
13:36 olass it's still downloading things here
13:39 jonalv git++
13:39 jonalv oh and c-- btw
13:39 olass jonalv: for being a large beast?
13:39 jonalv for being git++
13:39 masak me++
13:39 olass olass++
13:39 zarah shame on you, olass, giving yourself karma like that
13:39 gilleain c-- is a language
13:39 olass gilleain: suitable name in this channel
13:40 olass karma c
13:40 zarah c has a karma of -5
13:40 masak c--
13:40 gilleain http://www.cminusminus.org/
13:40 olass karma me
13:40 zarah me has a karma of 5349680
13:40 olass ?
13:40 masak *lol*
13:40 olass me--
13:40 olass karma me
13:40 zarah me has a karma of 5349679
13:40 masak :)
13:40 olass woops
13:40 jonalv me++ >(
13:40 jonalv btw, what does that smiley mean?
13:41 olass masak: I have an RFE for zarah
13:41 masak jonalv: looks like a guy with pointy eyebrows and no nose.
13:41 masak olass: shoot.
13:41 olass @loop me++;i<5000;i++
13:41 masak um.
13:41 masak was that the RFE?
13:41 olass well, you get the point
13:42 olass ability to loop commands
13:42 olass it would be easier for people who wants to do dirty tricks
13:42 masak olass: I'll put the RFE here among the 'dream on buddy' requests.
13:42 gilleain no implementing irc languages!
13:42 olass not that I am such a person but anyway
13:42 masak olass: not sure what you're trying to say here...
13:42 olass good
13:43 olass karma me
13:43 zarah me has a karma of 5349681
13:43 olass karma /me
13:43 zarah /me has a karma of 0
13:43 masak (/me)++
13:43 masak karma /me
13:43 zarah /me has a karma of 1
13:44 jonalv karma zarah
13:44 zarah zarah has a karma of 52
13:44 olass /me++
13:44 olass karma /me
13:44 zarah /me has a karma of 1
13:44 masak olass: needs the parens.
13:44 olass obviously
13:44 masak aye, read source, damnit!
13:44 olass arrgghhh, installing git from macports is SLOOOOOOW
13:44 masak olass: so is reverse-merging.
13:45 olass I need more coffee
13:45 masak I need more raw processing power.
13:45 jonalv olass: come in here nad I will show you something that didn\t work last time...
13:45 olass that does not sound like fun
13:45 masak :)
13:45 jonalv olass: not?
13:46 gilleain does it work this time?
13:46 gilleain (whatever it is)
13:46 masak gilleain: seems so.
13:47 gilleain good, good.
13:49 masak (git-svn)++
13:51 jonalv olass: I am getting  it to work here... why did you leave?
13:51 olass my git install broke again!
13:53 masak olass: what is it _now_?
13:54 olass masak: help!
13:54 olass could you come here?
13:54 masak allright...
13:54 olass always perl
13:54 * masak leaves his warm, comfy chair
13:54 olass perl--
13:54 masak hey!
13:54 olass karma perl
13:54 zarah perl has a karma of -1
13:54 jonalv olass: I have opened the molecule now. it works
13:54 masak do you want me to come over or not?
13:54 jonalv bioclipse++
13:54 olass perl++ :-)
13:54 * masak comes over
13:59 olass jonalv: could you come over here when you are finished? Want your eyes on the setller thingy
14:04 masak jonalv: you missed 'ta'!
14:07 CIA-54 bioclipse: carl_masak * r8144 /bot/trunk/zarah.pl: [zarah] private commands can now also be spelled @command
14:07 CIA-54 bioclipse: ospjuth * r8145 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Added setResource() to IBioObject and implemented BioObject. Also added several CDKManager methods saveMolecule(...).
14:29 Gpox joined #bioclipse
14:37 Gpoks joined #bioclipse
15:05 CIA-54 bioclipse: goglepox * r8146 /bioclipse2/trunk/plugins/net.​bioclipse.specmol/.classpath: Removed /org.eclipse.jdt.internal.debug.ui​.launcher.StandardVMType/J2SE-1.5 from JRE_CONTAINER classpath entry
15:09 jonalv joined #bioclipse
15:12 olass masak: is there a port that contains pdflatex?
15:12 * masak thought tetex did
15:12 olass hmm
15:12 * jonalv too
15:12 jonalv @pz
15:12 zarah jonalv: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
15:13 olass oh, it does
15:13 olass locate was not updated :-)
15:16 masak olass: `updatedb`
15:16 olass yup
15:27 jonalv @pz structuredb delete
15:27 zarah [206] Structuredb Editor actions - de... http://tinyurl.com/85c3z2
15:27 zarah Entire list at http://tinyurl.com/7v9mgr
15:27 * masak likes the @pz feature
15:27 * jonalv too
15:30 jonalv @pz molecules editor properties
15:30 zarah jonalv: Zarro boogs found.
15:31 * masak likes that too :)
15:31 jonalv @pz sdf editor properties
15:31 zarah [174] SDFEditor should display proper... http://tinyurl.com/79fbdp
15:31 zarah Entire list at http://tinyurl.com/8zttl7
15:32 jonalv @pz sdf editor select
15:32 zarah [205] Structuredb Editor actions - ex... http://tinyurl.com/a2k8hn
15:32 zarah [162] SDFeditor has same toolbar as JCP  http://tinyurl.com/5krqbm
15:32 zarah Entire list at http://tinyurl.com/8tndrc
15:34 egonw joined #bioclipse
15:35 jonalv egonw: o/
15:35 egonw hej
15:35 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
15:35 masak egonw: \o
15:35 egonw @msg
15:35 zarah egonw: 5 h 41 m 17 s ago, edrin said In your cdk xws service, please rename it in CDK XMPP Services
15:36 jonalv masak: don't wave with right arm it looks like a nazi salute...
15:36 egonw @tell edrin yes, can do, but please file a bug report at pele.farmbio.uu.se/cgi-bin/index.cgi
15:36 zarah Consider it noted.
15:36 masak jonalv: I think someone needs a hug.
15:37 gilleain hmmm. is \o is only right handed from your point of view
15:37 egonw hi all
15:37 zarah hi egonw
15:37 masak gilleain: right. in actualy fact, I'm sitting on the other side of the IRC window.
15:37 masak s/y//
15:37 gilleain masak : exactly.
15:38 gilleain hi egonw
15:38 jonalv gilleain: nope it\s from all our points of views in here actually
15:38 jonalv except maybe the writer...
15:39 masak jonalv: \o o/ /o o\
15:39 jonalv poor guy is upside down....
15:40 jonalv /o\
15:40 masak jonalv: not really. you see, Einstein discovered in 1905...
15:40 gilleain egonw : I tried out the CML tab-complete stuff, and it's pretty cool.
15:40 egonw gilleain: good :)
15:41 egonw saw the bug report on the new CML file wizard
15:41 egonw that will be removed
15:41 gilleain ok cool.
15:41 egonw I think...
15:41 egonw at least, I'll fix it
15:41 gilleain I hadn't actually used features before, so that was good to try.
15:42 masak (git stash)++
15:42 jonalv @pz changelistener
15:42 zarah [207] Changelistener for DBMolecule      http://tinyurl.com/7k6fkc
15:42 zarah [39] ChangeListeners of domainObjects    http://tinyurl.com/8fg5pb
15:42 zarah Entire list at http://tinyurl.com/9yv34x
15:44 olass jonalv: http://rcptoolbox.sourceforge.net/​RCPToolbox/Widgets%20Blog/B042E66E​-58BA-4FE9-AB65-77FE0F22A84F.html
15:44 zarah olass's link is also http://tinyurl.com/9n9xjk
15:45 jonalv olass: what am I looking at?
15:45 olass we talked about behavious on progress without knowing the number of steps...
15:45 jonalv aha
15:45 jonalv but where do you want me to show this widget?
15:46 olass wel..
15:46 olass if you DC a DB and before editor opens, for example?
15:46 * masak successfully git resets --hard, and feels like a real man
15:46 jonalv "I didn\t ask when \I asked where...
15:46 jonalv masak: w00t
15:47 masak real men reset --hard.
15:47 masak AFAIU, 'reset' in git means 'put the HEAD somewhere else'.
15:47 masak which is kinda scary, actually.
15:49 * gilleain abhors widgets with the word "cool" in their name
15:52 gilleain on the other hand, they do look quite cool.
15:52 masak today's bitter Perl lesson: "\n"=~/\s/
15:52 masak :/
15:54 masak olass: bless you.
15:54 gilleain "Bitter Perl Lessons" would be good name for a book. hmmm.
15:54 olass masak: dz
15:54 * egonw will try to set up a new IBioclipse resource thingy for RDF files
15:55 masak gilleain: I have a book named "Bitter Java" at home. unfortunately, it's not very good.
15:55 olass egonw: I'd vote for working with core Bioclipse 2.0 things
15:55 olass egonw: like load, save etc
15:55 egonw olass: shame for you I am on holiday :)
15:55 masak olass: why? :P
15:55 olass egonw: right :-)
15:56 CIA-54 bioclipse: carl_masak * r8147 /bioclipse2/trunk/ (1300 files in 304 dirs): reverted r8084, except for files that caused conflicts
15:57 masak yess! I restored (almost all of) your empty lines!
15:57 edrin egonw: got my mail? ->"stain was here"
15:57 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
15:57 masak you're a smart girl, zarah.
15:57 zarah masak: I bet you tell that to all the girls. Over.
15:58 egonw edrin: yes
15:58 masak zarah: yes
15:58 zarah masak: I see.
15:58 olass olass: yes
15:58 masak :)
15:58 olass (just to add to the confusion)
15:59 masak confusion++
16:14 CIA-54 bioclipse: carl_masak * r8148 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: [ScriptingConsoleView] added back empty lines
16:16 CIA-54 bioclipse: goglepox * r8149 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): Added manager method for opening IBioObjects with a given editor
16:27 Gpox joined #bioclipse
16:28 masak olass, jonalv: here's the GUI horribleness I was talking about: http://www.secretgeek.net/baby_robots.asp
16:28 zarah masak's link is also http://tinyurl.com/97ev6d
16:31 edrin egonw: what do you think? do you think this info will help you to compile the stuff?
16:31 egonw the IRC transcript?
16:32 egonw no, that will not help
16:32 egonw got a reply via the ML too now
16:32 egonw things are known to be broken right now
16:32 egonw nothing to fix, what I understood...
16:32 egonw stain: if you could resend me the zip with only the plugin stuff, I can try that again...
16:33 egonw stain: I seem to have lost that...
16:34 * olass successfully added a PDF viewer to Bioclipse
16:34 egonw excellent :)
16:34 olass it's not great
16:34 olass trying another now
16:34 egonw does it provide access tot he plain text content?
16:35 egonw oh, ok
16:35 olass but nice to highlight things in the pdf
16:35 olass search etc
16:35 egonw ic
16:35 olass it has an API, yes
16:35 olass hmm, the other one looks better
16:35 olass would be nice to extract things from the PDF
16:35 olass like the Rich Browser
16:35 olass but for PDFs
16:36 egonw ok, sounds not bad
16:36 egonw what's the problem with it?
16:36 olass But the least we need is a PDf viewer for Bioclipse
16:36 olass bugs
16:36 olass will let you know the progress of the other one
16:36 olass thought I'd try to get Subclipse into Bioclispe (again)
16:37 olass it is on my table...
16:37 egonw olass: can you chat with Gpox about the JCP state?
16:37 egonw assuming he is back from holidays
16:37 olass why chat?
16:37 olass he's in the room next to me
16:37 olass (or was)
16:37 olass and will be tomorrow
16:37 olass what do you want to know?
16:37 egonw chat is not restricted to IRC
16:37 egonw IRC is 'internet relay' chat
16:38 egonw not the normal chat, but chatting via the internet
16:38 egonw normal chat can be done in two separate rooms too
16:38 egonw just shout very loud
16:38 egonw please chat with him about JCP bug fixes to current functionality...
16:42 olass ok
16:55 jonalv @pz 71
16:55 zarah http://tinyurl.com/6gmsm5
16:55 masak dz
16:56 jonalv vote on bug 71!
16:56 jonalv zarah: tell all to vote for bug 71
16:56 zarah Consider it noted.
17:04 edrin ola, egon, do you like the Service Discovery View as it is?
17:05 edrin it can now create bindings
17:05 edrin and if there is already an older binding it asks to replace the existing binding
17:05 edrin in js console you can use the created binding by just doing
17:05 edrin iof = xmpp.getIoFactory();
17:05 gilleain jonalv : what is a Quality Assurance feature? I know what QA is, but..
17:06 jonalv it\s a Bioclipse plugin
17:06 masak gilleain: it's a "phone home" device that sends test results back to us from users.
17:07 gilleain ahh ok.
17:07 jonalv it let's our users run the tests suites
17:07 gilleain Automated Bug Reports.
17:11 gilleain huh. I thought that you were joking. You can actually vote on the bugs.
17:11 masak I didn't know that either.
18:52 edrin left #bioclipse
21:30 edrin joined #bioclipse
21:37 CIA-54 bioclipse: edrin_t * r8150 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/XwsConsole.java: changed window label

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