Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-09

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Time Nick Message
05:32 egonw joined #bioclipse
06:39 egonw moin
06:39 zarah oh hai egonw
07:05 Gpox joined #bioclipse
07:07 olass joined #bioclipse
07:07 olass moin
07:07 zarah hello olass, you fantastic person you
07:07 olass egonw: I met Jörg
07:08 egonw good
07:08 egonw did you talk about JOELib?
07:08 olass he seems like a nice person
07:08 olass a bit
07:08 egonw yes, that's the impression I always had too :)
07:09 olass he said 2 guys working on it but under the umbrella of a commercial initiative.. at least I got that impression
07:11 egonw did you sell a lot of Bioclipse support licenses?
07:11 olass haha
07:11 egonw you should have, you know
07:11 olass I made good PR
07:13 olass that is the first step
07:14 olass got home at 02 tonight, sort of feeling dizzy
07:14 egonw no worries
07:14 egonw I have a (proceedings) paper deadline on Monday
07:14 egonw so really busy finishing that
07:15 olass I need to focus on my thesis until wednesday next week
07:15 * olass is entering thesis mode
07:25 egonw Gpox: are you going to this too: http://www.eclipseusers.se/forum/showthread.ph​p?s=e4d97852c3cb7ce669d97033adafd5b7&t=137 ?
07:25 zarah egonw's link is also http://tinyurl.com/yf9vlmd
07:25 * egonw hopes Gpox is...
07:40 egonw olass: short question:
07:40 egonw ./bioclipse.core/features/net.bio​clipse.core_feature/feature.xml:         id="org.eclipse.update.core.linux"
07:40 egonw does that make sense?
07:40 egonw to have that plugin part of the core feature??
07:40 olass hmm, mom, is that a fragment?
07:40 * olass is looking
07:41 egonw I see too: org.eclipse.swt.carbon.macosx
07:41 olass yes, think so
07:41 egonw and that is indeed a fragment
07:41 olass click on the fragment and you see that it is only installed if OS is Linux
07:42 olass and that is needed
07:42 egonw yes, indeed
07:42 egonw OK
07:42 egonw thanx
07:42 olass no prob
07:42 olass you can try removing it..
07:42 olass but update might fail then
07:43 egonw there only is an updated variant for linux and win32
07:43 egonw not fox osx
07:43 egonw for
07:43 egonw did you try 64bit win?
07:46 olass no
07:46 egonw I might see a pattern
07:46 egonw ok, thanx for now
07:48 jonalv joined #bioclipse
07:49 egonw olass: looks promising
07:49 jonalv oh hai
07:49 zarah saluton jonalv
07:49 olass egonw: you suspect that additional plugins are needed in feature efter 3.5?
07:49 egonw hi jonalv
07:49 olass hi jonalv
07:50 egonw olass: well, now just removed those two update plugins
07:50 egonw update.core.[linux|win32]
07:50 jonalv olass: how was your trip?
07:50 egonw 78% now
07:50 jonalv left #bioclipse
07:50 jonalv joined #bioclipse
07:50 olass bye jonalv
07:50 olass hi jonalv
07:51 jonalv wrong window...
07:51 olass jonalv: trip was OK, a bit tired now
07:51 olass boring to travel
07:52 olass got home at 02.00 tonight
07:53 jonalv olass: 0 that's a bit late.... :)
07:53 jonalv olass: how did your presentation go?
07:54 olass good
07:55 olass I am happy about the results
07:55 jonalv tell me more
07:55 olass no time, writing thesis
07:55 olass IRL next week :)
07:56 olass jonalv: you solved problems with update site?
07:56 jonalv olass: NO
07:56 olass jonalv: caps-lock?
07:58 jonalv it's really strange, but you are experienced with update sites so I hope you might be able to get it to work...
08:00 egonw wow, export worked
08:00 egonw olass: and it boots too!
08:00 jonalv w00t
08:00 olass egonw: what was the problem?
08:01 egonw olass: those two update plugins
08:01 olass added them?
08:01 egonw there was just one for win32 and one for linux
08:01 egonw not for osx
08:01 olass please commit them
08:01 olass hmm, we should make that branch now
08:01 egonw right
08:01 olass in core and cheminfo and all other plugins affected
08:01 egonw how shall we proceed?
08:01 olass 2.2.x
08:01 egonw we need to make branches
08:01 egonw clear
08:02 egonw but we need to get all developers to move to the branches too
08:02 olass we set up the branches then email on devel
08:02 olass hmm
08:03 CIA-51 bioclipse.core: Egon Willighagen master * r4e7f1f7 / features/net.bioclipse.core_feature/feature.xml :
08:03 CIA-51 bioclipse.core: Removed org.eclipse.update.core.[linux|win32] which no longer seem to
08:03 CIA-51 bioclipse.core: exist for Eclipse 3.5.1 and at least make it impossible to export
08:03 CIA-51 bioclipse.core: for Linux 64 bit. There was no variant for osx, argumenting that these
08:03 CIA-51 bioclipse.core: are remnants of an older Eclipse platform. - http://bit.ly/Qbulo
08:03 egonw ok, here's the commit
08:04 olass thx
08:04 olass egonw: it still works to export on 32 bit platforms?
08:05 egonw yes
08:05 olass great
08:05 egonw I exported:
08:05 egonw drwxr-xr-x  3 egonw egonw   4096 2009-10-09 09:20 linux.gtk.x86
08:05 egonw drwxr-xr-x  3 egonw egonw   4096 2009-10-09 09:21 linux.gtk.x86_64
08:05 egonw drwxr-xr-x  3 egonw egonw   4096 2009-10-09 09:49 win32.win32.x86
08:05 egonw drwxr-xr-x  3 egonw egonw   4096 2009-10-09 09:50 win32.win32.x86_64
08:06 egonw not osx
08:06 egonw but since that was working anyway
08:15 egonw I'll make branches now then
08:16 egonw olass: if you find time for a official 2.1.1 linux.gtk.x86_64 release, I would be indebted
08:16 egonw so that I can finish the PharmBio PDF for the Bioclipse exercises
08:16 olass can you not build it yourself?
08:17 olass and upload to pele?
08:17 egonw no, because I have not the same checkout you have for the other builds
08:17 olass ok
08:17 egonw and I need them to be identical
08:17 olass hmm, I have pulled cheminfo since I built
08:17 egonw Gpox: I really hope you are going to that meeting in Stkhm on Buckminster
08:17 olass and no tag
08:17 Gpox Yes I plan to
08:17 olass Gpox: sounds good
08:18 olass egonw: I can use my current build
08:18 egonw olass: yes, tagging would have allowed me to make an export
08:18 egonw please do
08:18 egonw thanx
08:18 olass but that is not 100% the 2.1.1 release
08:18 olass should be fine though
08:40 stain good morning!
08:41 egonw hi stain
08:41 jonalv hi stain
08:47 masak joined #bioclipse
09:15 egonw in case you missed it...
09:15 egonw #nobel #committee #fail
09:15 egonw nobel--
09:15 egonw nobel--
09:15 egonw nobel--
09:15 zarah nobel--
09:15 egonw nobel--
09:15 egonw nobel--
09:15 egonw nobel--
09:15 egonw nobel--
09:15 egonw giving Obama the nobel prize for Peace
09:15 masak o.O
09:15 egonw maybe when he actually acchieved something
09:15 egonw but now?!?!?!
09:15 egonw WTF?!?!?!?!
09:16 masak sounds like a publicity stunt or something.
09:16 masak like getting a price for "being better than the last president" :P
09:16 egonw strengthen
09:16 egonw http://bit.ly/3Kv1f
09:16 egonw that's the official news page
09:16 egonw masak: indeed
09:18 egonw I mean ... Al Gore was questionable...
09:18 egonw surely better environment == more stable world...
09:18 egonw all of a sudden Sweden drops in my respect...
09:18 masak sorry...
09:19 egonw it's the committee, I know
09:19 masak I'm not on that committee.
09:19 egonw makes you wonder who the other candidates were
09:19 egonw Osama perhaps?
09:25 olass egonw: blame the norwegians, they deliver the peace prize
09:25 egonw do they?
09:25 olass yup
09:25 egonw rich bastards
09:26 egonw I'm literally shocked by this news and furiated
09:26 egonw not that I don't think Obama is a good guy
09:26 egonw I am happy that he is in office
09:26 egonw but, but...
09:26 olass do you think Arafat deserved it more?
09:27 egonw there are plenty of people who have actually acchieved something in world piece
09:27 egonw and are putting in effort to acchieve world piece
09:27 egonw he is just a lefty like half the world population
09:27 egonw thank you very much
09:28 egonw question on the official page
09:28 olass Arafat a leftie?
09:28 egonw "Did you know about Obama's efort for a nuclear weapon-free world!?
09:28 egonw who cares?
09:28 egonw I demonstrated for that in the 80ties!
09:28 egonw as a 10 year old kid
09:28 egonw give me the Nobel prize then!
09:29 * olass was born in the 80ies
09:29 egonw or someone else of the millions that demonstrated against nuclear weapons then
09:29 olass egonw: it's all about impact, not your personal feelings
09:29 egonw yes, and what extraordinary impact has Obama had?
09:29 egonw so far...
09:29 olass let us hope this turns out to be proactive
09:30 egonw before he was in office
09:30 egonw as if he personally removed Bush
09:30 egonw from office
09:30 egonw I hope Obama will be wise and see, "thanx, but no thanx"
09:30 egonw really
09:30 * olass goes back into thesis mode
09:30 egonw if he has any decency
10:02 egonw yeah, rakudo entered Debian
10:13 mgerlich joined #bioclipse
10:39 masak about time. :)
10:39 masak there's only been 21 releases...
10:40 egonw :)
10:56 egonw @tell samuell: reasoning with SPARQL http://jeenbroekstra.blogspot.com/2009/10/s​imple-rules-using-construct-queries-in.html
10:56 zarah egonw's link is also http://tinyurl.com/yhl2vnh
10:56 zarah Consider it noted.
10:56 egonw @tell samuell I met Jeen last year in Wageningen, a first order FOAF
10:56 zarah Consider it noted.
10:58 stain egonw: how difficult was it to make your first Google Wave bot?
10:58 stain did you just go through the tutorial?
10:58 egonw about an afternoon
10:58 egonw yes
10:58 stain nice
10:58 egonw eclipse + google plugin
10:58 stain I think I'll try to make a bot that can execute workflows
10:58 egonw marvelous
10:58 stain yeah, I have the appengine plugin already
10:58 egonw cool
10:59 egonw I sure hope it will use remote data caches
10:59 egonw as promised by Tom's T2 slides two years ago :)
11:00 egonw but T2 is not that far, is it?
11:16 stain egonw: what formulas can I  use with the CDKitty?
11:16 egonw CH4 like
11:17 egonw mwOf:CH4
11:17 stain it does not do anything..
11:18 egonw be patient
11:18 egonw the VM seems to need a boot
11:19 stain so do you do everything in the appengine, or is it talking to a service you have elsewhere?
11:19 stain we obviously could not start running workflows in the quite restrited appengine
11:19 egonw CDKitty is all in appengine
11:19 egonw but I think you are free to do whatever in that engine
11:20 stain yeah, but I doubt the full Taverna code would just work.. for instance it times out after just a few seconds
11:21 egonw I guess you need a MyExperiment robot too
11:21 stain and we would have to rewrite the datamanager to store in the bigdata-thingie (which should be easy as we're using Hibernate for those)
11:21 egonw for pulling in workflows
11:21 stain yep.. you should also be able to just paste the link to the myExperiment workflow
11:21 egonw right :)
11:21 egonw just the number, I guess
11:22 stain the myXP bot could come in and you could ask it about what workflows he has for something.. and when you get one added to the wave, the taverna bot would provide you with the execution bit! hihi
11:22 egonw oh, yes... :)
11:24 stain if I only I had time for such funny stuff instead of writing boring.. reports!
11:43 olass stain: what is your opinion on caBIG?
11:51 samuell joined #bioclipse
12:25 samuell olass: May I suggest adding a links to the "Community portal" (or we could have a better name) for the wiki. There needs to be a place to tell others about efforts going on on the wiki, et.c.
12:25 zarah samuell: You have new messages. Write '/msg zarah @messages' to read them.
12:25 samuell For example if someone creates a new category, or template, that others are encouraged to use.
12:27 samuell olass: Other suggestions for page name: "How to edit this wikI" / "Editing help" etc.
12:32 olass samuell: you have good suggestions but I am sorry to say that I have little time to put on this
12:32 olass maybe you should write an email about your thoughts to bioclipse-devel to start a discussion?
12:33 samuell Yeah, well, that's one idea
12:35 samuell But having a page such as "Community portal" on the wiki, then the discussion can take place on the talk page of that
12:35 samuell and it will be stored, and readily available in the relevant context
12:36 samuell That is how they do on wikipedia projects et.c. and by experience it works rather well.
12:38 samuell But I can of course start with a mail on bioclipse-devel !
12:50 stain olass: opinion.. well.. that's what our robot is about
12:51 stain our REPORT
12:51 stain olass: what do you want to know?
12:51 * masak wants to write a song called "that's what our robot is about"
12:52 stain olass: they are quite big on cancer data services, and some analytical services, all indexed in a service catalogue - which forms their 'grid'. In addition they have security standards and authentication services for the more sensitive data, all based on Globus and WSRF
12:53 stain invoking WSRF services without Globus libraries can be a bit tricky.. we had to hack it into Taverna
12:53 stain luckily - one of the few advantages of our Raven - we were able to build service support using the globus libraries without it affecting the normal Axis-based WSDL-services (in a different classloader)
12:54 stain they spend lot of effort on describing the data formats and services in UML models - but unfortunately there is no straight one-to-one-mapping from the UML to the actual XML - in theory these services could interoperate, but that is still early days
13:03 olass stain: how mature is their framework? how much is it used?
13:03 olass They seem to have quite some resources
13:04 olass obviously quite bureaucratic too :)
13:29 masak` joined #bioclipse
13:49 stain olass: I was going to say that thing about bureucratic.. glad you mentioned that :)
13:49 stain so.. be careful
13:50 olass lol
13:50 olass I have no relations with the project
13:50 olass it sems advanced though
13:50 stain it's quite mature, but also quite specialized.. you could set up your own 'caGrid' - but I'm not sure what you want to achieve with that
13:50 olass sems
13:50 olass right
13:50 stain the grid stuff is just Globus.. so if you don't mind Globus then feel free..
13:50 stain but it tends to isolate you from anyone else
13:51 olass stain: how easy is it now to execute a T2 workflow from java code?
13:52 olass do you have a url for a tutorial?
13:52 olass Would be nice to execute a WF locally and via a WS on a remote server
13:52 stain olass: using the T2 platform, about 10 lines and a few files that a Maven archetype makes for you
13:52 stain we have a remote execution service with a simple REST interface
13:52 olass sounds quite doable
13:52 stain which is probably the easiest
13:53 stain and we're developing it further to also help with finding information about a workflow and for changing/building it
13:53 olass what is the footprint of the engine without GUI stuff?
13:53 olass to just run things?
13:53 stain it depends a bit on which type of services in your workflow.. let's say 100 megs? Not sure..
13:53 olass oh
13:54 olass that's a lot
13:54 olass is the engine that big?
13:54 olass or do you mean dragging down services on the local machine?
13:54 olass I meant just the engine
13:54 stain oh, without being able to invoke any services?
13:54 olass ?
13:54 olass no
13:55 olass that is quite required IMO :)
13:55 stain we have different service implementations that know how to talk to different types of services.. like WSDL services, BioMart, local scripts, etc
13:55 olass ah, I see
13:55 olass ok, 100 Mb, good to know
13:56 olass As you know I once wrote a Taverna plugin for Bioclipse, but Tav was not ready for that at that point
13:56 olass we never got that running
13:56 olass T2 seems much more mature in this respect
13:56 olass refactoring++
13:56 stain well, there's these issues of classloaders
13:57 stain that invites to do a more separation of concerns..
13:57 stain how tight would you like it to be integrated?
13:57 stain is it mainly just to run workflows, or also do some editing?
13:57 olass well, I can think of several options
13:57 stain say 150 to be safe
13:57 olass but first is jut to run
13:57 olass in the future, edit perhaps
13:57 stain ok, that should be simple enough.. perhaps we can show you some code used by the portlets that execute workflows
13:57 olass but would require an Eclipse Editor which we don't have resources to build now
13:58 stain yeah
13:58 olass would be nice :)
13:58 stain would the workflows be 'pre-canned' (provided by you) or loaded by the user?
13:58 olass I think both
13:58 olass extension points can contribute some
13:58 olass but then usres likely want to add their own
13:58 olass and look up on myXP
13:59 olass should be pretty easy to set up
13:59 stain because for the precanned ones it could be possible to do some kind of wrapping that specialises the inputs/outputs.. otherwise you would just get a general text field pr input port or something
13:59 olass right
13:59 olass yes, have not thought so far yet
13:59 olass first things first
13:59 olass running something simple must be the first step
14:00 olass then we need to bridge the Bioclipse object model in some way
14:00 olass but if you have a pointer to the portlets that'd be great
14:00 olass is it in SVN or have you moved to git?
14:25 stain we made this API called the T2 platform which should make it easier to run workflows.. the problem now is that our workbench is not using that API yet.. and we'll move towards OSGI and would have to change the API slightly then
14:25 stain we're still on SVN.. :)
14:26 stain I'll find the portlet thingie
14:27 stain see http://code.google.com/p/tavernaportal
14:27 zarah stain's link is also http://tinyurl.com/yzafbxp
14:27 stain it's using the REST api
14:28 stain http://code.google.com/p/tavernaportal/sour​ce/browse/#svn/jsfTest/src/java/tavernacon
14:28 zarah stain's link is also http://tinyurl.com/yj2z8o8
14:29 stain see http://www.mygrid.org.uk/dev/taverna-server/ for the server itself.. which unfortunately does not have much doc yet
14:29 zarah stain's link is also http://tinyurl.com/yjqc8a4
14:29 stain but it's mainly just a WAR file
14:37 olass stain: thanks for the pointers
14:37 olass so I can just deploy the WAR file?
14:38 olass any example REST invocation exists?
14:38 stain yes, see how the portlet does it
14:38 stain or you could just play around with curl.. but I don't have a trace of that laying around
14:39 stain jeah, just deploy the WAR and that should be it.. at first run it would initiate the taverna environment and download whatever is neccessary
14:40 jonalv hey guys, I have a set of commits in a git branch. I want to move them to another branch and add signoffs to them. How do I do that?
14:40 olass jonalv: sry, I am no git expert
14:40 olass stain: thanks for the pointers
14:40 olass will save your help and try it out next week
14:41 olass this week is almost over, save for thesis writing during the weekend :(
14:45 stain ouch.. no slouching for you in the weekend then!
14:50 olass stain: absolutely not :(
14:50 olass and proofing is sooo boooring
14:54 jonalv olass: nah that is the fun part
14:54 jonalv olass: that is when you go from good to perfect and that is always gun
14:54 jonalv |fun
14:55 * olass feels like he is going from crap to acceptable
14:55 olass brb
14:55 CIA-51 bioclipse.structuredb: Arvid Berg master * r0f57c91 / plugins/net.bioclipse.structuredb/src/net/b​ioclipse/structuredb/domain/DBMolecule.java :
14:55 CIA-51 bioclipse.structuredb: Fix for updated cdk.
14:55 CIA-51 bioclipse.structuredb: new version of inchi library - http://bit.ly/145J6q
14:55 CIA-51 bioclipse.structuredb: Arvid Berg master * r63ff1fb / plugins/net.bioclipse.structuredb/src/net/bioc​lipse/structuredb/DBMoleculesEditorModel.java : Added method for changing properties for molecules in molTable - http://bit.ly/KjFx2
15:11 CIA-51 bioclipse.core: jonalv master * rea28548 / plugins/net.bioclipse.core.tests/src​/net/bioclipse/managers/tests/Abstra​ctManagerMethodDispatcherTest.java : Cleaned up imports. - http://bit.ly/YMCco
15:19 CIA-51 bioclipse.core: Carl Masak 2.2-releng * r7b36036 / plugins/net.bioclipse.usermanager/src/net/bioclips​e/usermanager/dialogs/UserManagerLoginDialog.java :
15:19 CIA-51 bioclipse.core: [UserManagerLoginDialog] general cleanup
15:19 CIA-51 bioclipse.core: - removed unused imports
15:19 CIA-51 bioclipse.core: - removed unexplained commented-out code
15:19 CIA-51 bioclipse.core: - made static field accesses go through class, not through instances - http://bit.ly/7lsvI
15:19 CIA-51 bioclipse.core: Carl Masak 2.2-releng * rd25b182 / (3 files in 2 dirs):
15:19 CIA-51 bioclipse.core: [UserManagerLoginDialog -> LoginDialog]
15:19 CIA-51 bioclipse.core: None of the other dialog window class names feel the need to mention that
15:19 CIA-51 bioclipse.core: they are a part of the UserManager. - http://bit.ly/2TUrVa
15:21 CIA-51 bioclipse.core: jonalv master * rde41288 / plugins/net.bioclipse.core/src/net/bi​oclipse/core/util/TimeCalculater.java :
15:21 CIA-51 bioclipse.core: say "< 1s" remaining if less that 1 s is remaining
15:21 CIA-51 bioclipse.core: Fixes bug: #1528 - http://bit.ly/3nXscx
15:21 zarah bug #1528 | http://tinyurl.com/yzzsqps
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16:13 jonalv egonw: I think we are going to need a spring concentraing on jmol.
16:13 jonalv *sprint
16:13 masak phew.
16:14 jonalv but perhaps a spring is more realistic...
16:14 masak "Springtime for Jmol..."
16:28 jonalv -me gives up
16:29 jonalv gah
16:29 * jonalv gives up
16:29 jonalv have fun
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19:12 mgerlich joined #bioclipse
19:19 dsurdyk hey guys - quick question about the bioinformatics implementation - anyone working on implementing a PHYLIP plugin?
19:19 dsurdyk left #bioclipse
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