Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-23

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All times shown according to UTC.

Time Nick Message
00:56 yangming edrin: hi! I am a biologist.
05:34 masak joined #bioclipse
06:20 egonw_ joined #bioclipse
07:32 miguelrojasc1 moin
07:52 masak hi miguelrojasc1
08:32 olas joined #bioclipse
08:35 egonw_ OK, I got a project now
08:35 egonw_ with an empty PDB file...
08:36 * egonw_ assumes the PDB retrievel webservice is not functional in BC2 yet
08:36 egonw_ sneumann: does the mzdata plugin work with the default eclipse resource system?
08:37 EskilA joined #bioclipse
08:38 olas egonw_: correct
08:38 olas egonw_: just copy in a PDB file in the runtime-bioclipse workspace
08:38 egonw_ using BC2?
08:38 olas using cp
08:38 egonw_ that is... does import or so work?
08:39 olas no
08:39 olas use command line cp
08:39 olas import does not work due to some unresolved dependency...
08:39 olas I tried to fix but need more time on that
08:39 olas don't make things more complex than they are
08:39 olas just copy in a file
08:39 olas then hit refresh
08:41 egonw_ :)
08:42 masak olas: there's also a renameTo(File) method in java.io.File
08:42 masak so importing could technically be done from the consoles :)
08:42 masak hardly practical, but would be fun to try
08:42 egonw_ masak: likely not so easy
08:42 masak egonw_: perhaps not
08:42 egonw_ because eclipse also sort of mirrors things
08:43 masak oh?
08:43 egonw_ which is why one needs to 'refresh' your SVN checkout...
08:43 egonw_ when you updated from the command line
08:43 masak yes, sure
08:43 masak one would need to update the navigator afterwards
08:43 masak but that can be done from the console too :)
08:44 * masak realizes we need file scripting in bc2 too
08:44 egonw_ suggesting that is is just the tree that needs updating?
08:44 olas masak: yes
08:44 masak egonw_: yes, did I misunderstand you?
08:44 egonw_ no
08:44 egonw_ did not realize it was that stupid...
08:44 olas stupid?
08:44 egonw_ I though Eclipse had a data model that mirrored the disk
08:44 olas it has
08:45 olas that's why you need to refresh
08:45 egonw_ so, it's more than just the tree that is refreshed?
08:45 olas in memory only
08:45 olas (I think)
08:45 olas Eclipse stores last used editor for all files etc
08:46 olas which means it needs a model for it, right?
08:46 * olas could be wrong
08:46 masak olas: seems about right
08:46 olas we are learning as we go
08:46 olas /me's car has a flat tire
08:46 masak but the refresh is needed because Eclipse does not automatically sense changes outside of Eclipse
08:47 * olas 's car
08:47 olas yes
08:47 olas and no
08:47 masak olas: I thought you used the train
08:47 olas it senses changes, but does not automatically reload them
08:47 olas as that could be expensive
08:47 masak right
08:48 olas that's why you get "resource out of sync" msg
08:48 masak we like to avoid constant polling
08:48 olas which is resolved with refresh
08:48 olas I see no problem here, what am I missing?
08:48 masak yes, and the out-of-sync message is only triggered my user actions
08:48 masak olas: I don't think we're really disagreeing on anything
08:49 masak just agreeing differently :)
08:49 olas are you afraid that console scripts modifying the file system wil require manual refresh?
08:49 masak no
08:49 masak they will require a refresh
08:50 masak but that can be done easily in a single line from the script
08:50 olas exactly
08:50 * olas has to fix the flat tire
08:50 olas egonw: yes, train to Uppsala. Car within/around Stockholm
08:51 masak ah
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08:58 masak file copying isn't a primitive
08:58 masak in Java
08:58 masak I see examples where people implement it using ~50 lines of code
08:59 masak (the copying loop itself is rather small, but there's a lot of error handling before that)
09:03 CIA-18 joined #bioclipse
09:06 olas yes
09:06 olas masak: can you not use Eclipse IFile and IFolder?
09:06 olas or IFileBuffer
09:07 olas And there is an import feature in Eclipse
09:07 olas These kinds of tasks are exactly what Eclipse try to solve by its framework
09:07 olas simplify things for users, avoid all the gory plumbing
09:08 * olas is away to see to his car
09:13 masak joined #bioclipse
09:18 jonalv joined #bioclipse
10:17 CIA-18 bioclipse: jonalv * r4321 /trunk/playground/plugins/net.bioclipse.expres​sion.tests/src/net/bioclipse/expression/tests/ (CalculatorBaseTest.java FunctionsTest.java): Added tests for a bug found while doing live demo. (Never do live demo...)
10:18 masak jonalv: :)
10:18 masak don't do that then!
10:21 CIA-18 bioclipse: carl_masak * r4322 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
10:21 CIA-18 bioclipse: [FunctionsTest.java]
10:21 CIA-18 bioclipse: * removed nasty @Overrides attribute
10:23 masak for some reason, even though it's perfectly legal Java, my version of Eclipse disallows it
10:24 * jonalv thinks it's funny (not actually rather broken) that masak will hunt down all @Overrides and remove them
10:24 jonalv hm s/not/nop
10:24 jonalv lol no
10:24 jonalv My fingers are not awake today..
10:25 masak stuck in an infinite loop of auto-correction...
10:25 masak what cruel a fate
10:25 jonalv heh?
10:25 masak :)
10:26 * jonalv feels that masak avoided the real issue here..
10:27 masak fixing Eclipse?
10:27 masak yeah, I know, I should
10:27 masak it's just that, with time and all being a bit short lately...
10:47 CIA-18 bioclipse: carl_masak * r4323 /trunk/plugins/net.bioclips​e.rhino/src/net/bioclipse/ (8 files in 3 dirs):
10:47 CIA-18 bioclipse: [net.bioclipse.rhino]
10:47 CIA-18 bioclipse: * renamed IScriptProvider -> INamespaceProvider
10:47 CIA-18 bioclipse: * (because that's what it provides)
10:47 CIA-18 bioclipse: * this change is a backport form bc2
10:47 jonalv backports... cool masak++
10:47 masak :)
10:47 masak see, we're already benefitting from bc2
10:48 masak speaking of which, download the latest perl version, 5.10
10:48 masak it's much influenced by perl 6
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12:49 edrin joined #bioclipse
13:15 masak joined #bioclipse
13:24 CIA-18 bioclipse: ospjuth * r4324 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (6 files in 4 dirs): JmolEditor now populates Outline with Model/BioPolymer/Monomer. It also listens to selections of 1-N Monomers and highlights them in JmolEditor, JmolView.
13:24 egonw_ olas: cool!
13:24 * egonw_ boots BC2
13:25 jonalv not as in "boot to the head" I hope
13:27 egonw_ nor like boot in the fork :)
13:29 * olas is away for a break
13:29 egonw_ yeah, r4324 is worth a sauna trip
13:30 jonalv :)
13:30 jonalv have I missed somehting cool?
13:30 egonw_ yes... the Outline is working now for PDB files
13:30 masak cool indeed
13:31 jonalv sounds great
13:31 jonalv which plugin?
13:31 egonw_ [14:24] <CIA-18> bioclipse: ospjuth * r4324 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (6 files in 4 dirs): JmolEditor now populates Outline with Model/BioPolymer/Monomer. It also listens to selections of 1-N Monomers and highlights them in JmolEditor, JmolView.
13:31 * jonalv takes a look
13:32 edrin hi
13:32 masak hi edrin
13:32 edrin hello masak
13:32 jonalv y0 edrin :)
13:33 edrin hax0r
13:35 * egonw_ sees only an empty outline...
13:35 edrin outline? where?
13:35 egonw_ in BC2
13:38 edrin i will start with BC2 this weekend
13:39 edrin masak: would you mind to have a bc2 plugin with rhino script files functionality? you could move the conosole there later if you want
13:39 masak edrin: I'm fine with that
13:40 edrin to
13:40 masak I agree that we need file scripting somehow
13:40 jonalv I get a strange error in my log when starting bc2. Am I the only one? <http://pastebin.com/m3a43cff5>
13:40 masak edrin: in turn, I hopy you don't mind if I occasionally reorder things to better fit the data model of the day?
13:41 jonalv null of course... :)
13:41 edrin "fit the data model of the day" what is this?
13:41 masak bc2 is under construction
13:41 masak hence, the data model is not fix
13:42 masak our current strategy is to take pride in that, and adapt to it :)
13:42 masak ...at least, that's my strategy...
13:43 edrin why not have the naming conventions egon did on bioclipse1?
13:43 masak which ones are that?
13:43 masak (I'm new here)
13:46 edrin ask egonw
13:46 masak egonw_: did you have naming conventions for bc1?
13:47 thomas_ku joined #bioclipse
13:47 egonw_ yes
13:47 edrin egon, didn't you change most names in bioclipse to a certain naming convention?
13:47 egonw_ yes...
13:47 egonw_ net.bioclipse.<plugin>
13:47 jonalv I guess there is a blog post about this somewhere or?
13:47 egonw_ but that's what is now used too, not?
13:47 edrin i will do them in bc2, too
13:47 masak egonw_: yes
13:47 masak edrin: yes, please
13:48 edrin egonw: why is bioclipse2 in branch and not in trunk?
13:49 edrin i am a little bit confused with bioclipse2 now
13:49 * jonalv thinks that the Jmol editor in bioclipse 2 feels very much as things should be
13:49 egonw_ edrin: ummm... I did not set that up...
13:50 egonw_ jonalv: yes, that is very much going in the right direction :)
13:50 egonw_ brb
13:50 masak edrin: why don't you think bc2 should be in branches?
13:50 edrin it should but there is no release yet
13:51 edrin i thought development should happen in trunk
13:51 masak edrin: so what's branches for, then?
13:51 edrin and at a certain timepoint a compilation is copied to branch as a release, but maybe I am wrong?
13:51 masak edrin: yes, you are
13:52 masak trunk: one main release
13:52 masak branches: experiments and projects which "branch" out
13:52 masak tags: specific versions
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13:53 CIA-18 bioclipse: carl_masak * r4325 /trunk/plugins/net.bioclipse.rhino/src/net/​bioclipse/views/ScriptingConsoleView.java:
13:53 CIA-18 bioclipse: [ScriptingConsoleView.java]
13:53 CIA-18 bioclipse: * fixed backspace bug
13:56 masak I don't understand why the same bug does not occur in bc2, though
13:56 masak but who ever really understood software?
13:58 egonw_ edrin: you confuse tags with branches
13:58 egonw_ tags/ is for releases
13:58 edrin and branches for bug fixes of releases, no?
13:58 edrin or plugins for certain versions
13:59 * edrin checks wikipedia
14:04 edrin egonw: http://en.wikipedia.org/wiki/Subversio​n_%28software%29#Branching_and_tagging
14:04 edrin that means there should be:
14:05 egonw_ yes, there can be branches based on a particular version, to be used for applying bug fixes
14:05 egonw_ meaning that branches/ is for development, just like trunk/
14:06 egonw_ or, trunk/ is just a special version of some dir in branches/
14:06 edrin but if i understand it correct, trunk (the main trunk is the folder where current development should happen
14:06 egonw_ unlike tags/
14:06 egonw_ which basically are not suppose to change once put there
14:06 egonw_ yes
14:06 egonw_ BC2 is in experimental mode
14:07 edrin so maybe we should move all stuff in /trunk to /branch/bc1/trunk
14:07 edrin and move the bc2 code to /trunk and when a release is ready create a /branch/bc2 ?
14:08 edrin or at least create a /branch/bc2/trunk folder and move all the plugins of bc2 there as there was no release yet?
14:09 edrin how experimental is bc2?
14:09 edrin egonw: did you already write a plugin for it?
14:09 jonalv wow bc2 remembers which editors whre open when exiting
14:10 edrin ah
14:10 jonalv but the explorer soesn't get updated until I right cklick in it.
14:10 edrin maybe there should be no trunk in the project root at all
14:12 egonw_ b2 is very experimental, I think
14:12 egonw_ and no, I have not written any plugin yet
14:12 edrin example: from wikipedia:
14:12 edrin * branches/
14:12 edrin o 1.2/
14:12 edrin + trunk/
14:12 edrin + tags/
14:12 egonw_ no idea how to do that...
14:12 edrin # 1.2.3/
14:12 jonalv is it really worth all the work to move everything around?
14:12 edrin + branches/
14:12 edrin o 2.0/
14:12 edrin + trunk/
14:12 edrin + tags/
14:12 edrin + branches/
14:12 edrin # 2.0.1/
14:12 edrin * trunk/
14:12 edrin * tags/
14:12 edrin * branches/
14:12 egonw_ that's one big advanced versioned development :)
14:13 edrin jonalv: if you dont want international people to be confused i would suggest keeping naming conventions
14:13 egonw_ looks good, though
14:13 jonalv what will be in trunk then?
14:14 jonalv edrin, I guess you do have a point...
14:14 edrin jonalv: maybe we should move current /trunk to /branch/bc1/trunk
14:14 jonalv maybe we shuold have bc1 and bc2 in the root and then have trunk brancches tags in each of those since they are really separate projects...
14:14 edrin and also not have a /trunk in projects root folder
14:15 edrin jonalv: but that's the reason for branches
14:15 edrin never mind, don't have time now
14:15 jonalv ?
14:15 egonw_ no, a trunk/ is fine...
14:16 edrin /ne is gone
14:16 edrin /me!
14:16 egonw_ it's not until you decide, OK, this trunk/ will now be the base of a new release...
14:16 egonw_ by edrin
14:16 jonalv bye
14:17 jonalv egonw, bc1 and bc2 are really two separate projects and thus it wouldn't really be wrong the separate them at the root level of the repo right?
14:22 egonw_ nothing is really wrong
14:22 jonalv true...
14:22 egonw_ I like edrins suggestion though...
14:22 egonw_ but then again...
14:22 egonw_ we don't have the resources for very formal release cycles...
14:23 jonalv I don't really think I understood edrins suggestion
14:23 jonalv Would there be no trunk in the root?
14:23 jonalv only branches?
14:24 egonw_ no, not really...
14:25 jonalv egonw, was that meant for me?
14:25 jonalv not really what?
14:26 * jonalv is lost again...
14:27 jonalv It's not so easy for a bear of very little brain...
14:27 egonw_ yes, that was for you...
14:27 egonw_ jonalv: never mind...
14:27 egonw_ it's really not important...
14:28 egonw_ but I would be happy to support edrins suggestion... if he brings it up as proposed change
14:31 sneumann_ Hi egonw, you asked for our updateSite
14:31 sneumann_ http://msbi.ipb-halle.de/updateSite
14:32 sneumann_ I just learned more about eclipse than I ever wanted to know.
14:32 sneumann_ It's nice, though ;-)
14:32 sneumann_ Editor plugins et al are not yet tested, provider et al are www.example.org all over etc.
14:33 sneumann_ That'll come next. Plugins are already prepared for Teneo/JPOX persistence, though not tested, either.
14:36 egonw_ oh, very cool
14:36 egonw_ mom, I'll try and see if I can get it installed in BC2
14:38 egonw_ ah, it does not work here...
14:38 egonw_ sneumann_: it seems to require eclipse.rcp_r20070802
14:38 egonw_ and I have a plugin version _r20071002
14:38 egonw_ two months newer...
14:39 sneumann_ Hm. where and how to change that ?
14:39 egonw_ mom
14:39 egonw_ if you go to the plugin.xml
14:39 egonw_ and then the Dependencies tab
14:40 egonw_ and right click on the plugin...
14:40 egonw_ and then pick Properties...
14:40 egonw_ then you should see the plugin version requirements...
14:40 egonw_ however, that's only for explicit version deps
14:40 sneumann_ My stuff is completely auto-generated (That's why I was able to produce it in first place;-)
14:40 egonw_ if you would upload to SVN, I got have a further look at it...
14:40 egonw_ right...
14:41 sneumann_ Is it save to relac versions ?
14:41 egonw_ was afraid it would :)
14:41 egonw_ should be safe to relax to 3.3.1_any
14:42 sneumann_ still can't find the eclipse.rcp dependency. Could it be recursive ?
14:43 sneumann_ find . -type f -exec grep -H r20070802 \{\} \; | grep -v .history
14:43 sneumann_ ./.metadata/.plugins/org.eclipse.pde.core/Eclipse Application/org.eclipse.update/platform.xml
14:44 egonw_ no idea
14:44 sneumann_ Ah sorry, there is only org.eclipse.cvs version="1.0.1.R33x_r20070802
14:44 egonw_ eclipse can be a pain
14:44 sneumann_ Yzo!
14:45 sneumann_ Yup!
14:45 egonw_ maybe olas got a tip... he does the bioclipse update site
14:45 egonw_ olas: ping...
14:46 egonw_ ha, our manuscript "Userscripts for the Life Sciences" has been accepted 'in principle' for BMC Bioinformatics
14:50 sneumann_ For "org.eclipse.rcp" the "Show dependent plug-ins and fragments" is empty ...
14:52 egonw_ :(
14:52 egonw_ you could try running a grep on the files created for the update site..
14:53 egonw_ sneumann_: OK stop
14:54 egonw_ I tried it in the Eclipse I am running... instead of the BC2 I was starting with it...
14:54 egonw_ in Eclipse it does not complain...
14:54 egonw_ so, it's either something in the BC2 settings...
14:54 egonw_ or something to do with BC2 not running standalone, ... ?
14:55 edrin sneumann_: what kind of plugin do you provide?
14:55 egonw_ mass spectral data
14:56 edrin :)
15:05 egonw_ sneumann_: it seems the update site does have a patch plugin for org.eclipse.rcp, but not the plugin itself...
15:06 egonw_ and bioclipse itself does not have that plugin, but Eclipse does, of course...
15:10 sneumann_ "update site does have a patch plugin for org.eclipse.rcp" refers to the BC updateSite or mine ?
15:10 egonw_ yours
15:10 egonw_ BC2 does not have an update site yet
15:11 egonw_ don't think it will work with BC1, as the editor setup is custom, not RCP specific
15:11 sneumann_ My site.xml looks completely unspectacular, only my plugins are mentioned.
15:11 egonw_ yeah. something in the config should trigger that the update site also has the org.eclipse.rcp plugin...
15:12 sneumann_ Hm. Waiting for advice, I don't really want to host eclipse.rcp
15:13 egonw_ yeah, I understand :)
15:19 egonw_ I'm trying to figure out which Eclipse update site to include, so that it can pick up the rcp plugins from there...
15:36 egonw_ can't find an update site which provides that org.eclipse.rcp plugin :(
15:39 sneumann_ if I check the org.eclipse.rcp feature.xml I get http://update.eclipse.org/updates/3.3
15:43 egonw_ ah, thanx
15:43 egonw_ testing...
15:47 egonw_ no, that site does not help either :(
15:52 masak joined #bioclipse
15:54 jonalv masak, check: <http://download.eclipse.org/birt/downloads/​examples/misc/BIRT2.1Demo/EclipseDemo.html>
15:54 masak oki
16:04 egonw_ jonalv:  nice screencast
16:04 egonw_ you did that nicely...
16:04 egonw_ cool stuff
16:05 jonalv egonw, I am not quite sure I know what you are talking about..
16:07 egonw_ never mind :)
16:17 jonalv viklund, have you tested  TreeViewJ <treeviewj.sourceforge.net>?
16:32 CIA-18 bioclipse: carl_masak * r4326 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (model/Assay.java model/Experiment.java views/TreeView.java):
16:32 CIA-18 bioclipse: [net.bioclipse.base2.model]
16:32 CIA-18 bioclipse: * added Experiment and Assay
16:32 CIA-18 bioclipse: [net.bioclipse.base2.views.TreeView]
16:32 CIA-18 bioclipse: * new, better mockup
16:33 CIA-18 bioclipse: * shiny new icons
16:34 * olas is back from coffee break
16:34 olas hi
16:34 jonalv hi
16:34 olas much activity here :-)
16:36 CIA-18 bioclipse: carl_masak * r4327 /trunk/plugins/net.bioclipse.webservic​es/src/net/bioclipse/plugins/bc_webser​vices/scripts/WebservicesTools.java:
16:36 CIA-18 bioclipse: [WebservicesTools.java]
16:36 CIA-18 bioclipse: * chased name refactoring from net.bioclipse.rhino
16:36 masak olas: yup :)
16:36 * masak opens the next box of toffifees
16:37 olas it's friday!
16:37 jonalv yep
16:37 olas toffifee is a friday-treat
16:37 * jonalv thinks it is very much friday afternoon
16:38 olas egonw: did you have any questions for me?
16:38 olas hi edrin
16:38 masak jonalv: you're right, it really is
16:43 edrin hi olas
17:01 edrin i'm doing a southern blot in parallel, that's why i am delayed...
17:03 CIA-18 bioclipse: carl_masak * r4328 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java:
17:03 CIA-18 bioclipse: [Calculator.java]
17:03 CIA-18 bioclipse: * fixed illegal characters bug
17:03 CIA-18 bioclipse: * all tests now pass
17:04 jonalv najs masak++
17:04 masak thx
18:21 edrin joined #bioclipse
18:50 egonw_ joined #bioclipse
19:30 edrin left #bioclipse
20:24 viklund jonalv: no
20:30 edrin joined #bioclipse

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