Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-09

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All times shown according to UTC.

Time Nick Message
00:08 stain joined #bioclipse
05:39 sneumann joined #bioclipse
06:44 egonw joined #bioclipse
06:48 egonw moin
06:48 zarah hello egonw, you fantastic person you
06:48 olass joined #bioclipse
06:48 olass moin
06:48 zarah hello olass, you fantastic person you
06:55 egonw @pz git
06:55 zarah Cannot detect feed type
06:56 egonw oh...
06:57 egonw @pz git
06:57 zarah Cannot detect feed type
06:58 egonw @pz 782
06:58 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=782
06:58 egonw weird
07:24 egonw mmm... basement is being flooded again
07:24 egonw heavy rain, strong winter...
07:24 egonw mm... autumn
07:24 egonw early this year
07:28 mgerlich joined #bioclipse
07:28 olass egonw: lovely swedish weather, don't you think?
07:36 mgerlich joined #bioclipse
07:38 olass egonw: about git
07:38 olass should we email to bc-devel?
07:47 mgerlich joined #bioclipse
08:04 sneumann joined #bioclipse
08:06 edrin joined #bioclipse
08:06 edrin hi
08:06 zarah hello edrin, you fantastic person you
08:09 shk3 joined #bioclipse
08:18 edrin egonw: available?
08:23 mgerlich joined #bioclipse
08:34 egonw_ joined #bioclipse
08:34 shk3 hi sneumann
08:44 shk3 olass: did you decide on the doc plugin?
08:44 olass decide?
08:44 shk3 what is the strategy for 2.0 with this
08:44 shk3 ?
08:44 shk3 well, what do we do?
08:44 shk3 one per feature?
08:45 shk3 leave as it is?
08:45 shk3 or something else?
08:45 olass one per feature or one per site
08:45 olass doc plugin is for the release
08:45 shk3 ok, what do I need to do?
08:45 olass it does only include what you get in teh SF download
08:45 shk3 is there documentation?
08:46 olass shk3: add documentation to any of speclipse features
08:46 shk3 but that's autogenerated, right?
08:46 shk3 so where do I get the scripts from?
08:46 shk3 how do I run them?
08:46 olass all are in the doc plugin
08:46 olass ask masak if you have problems
08:47 shk3 so I copy the scripts to one of my plugins and run them?
08:47 olass if you want to
08:48 olass it's your choice
08:48 shk3 well, I don't want to, but I need to
08:48 olass but I'd recommend that
08:48 shk3 will masak be round later?
08:48 olass no idea
08:49 shk3 ok
08:54 shk3 olass: could you announce such stuff on the mailing list, please?
08:54 shk3 or did I miss it there?
09:00 CIA-54 bioclipse: shk3 * r11654 /bioclipse2/trunk/ (10 files in 10 dirs): preparing speclipse 2.0
09:06 shk3 olass: I think i will do a net.bioclipse.doc.speclipse plugin.
09:06 shk3 is that ok?
09:07 olass shk3: in speclipse, you can do what plugins you like
09:07 olass why do you ask me?
09:07 olass I am not in charge of speclipse
09:07 shk3 well, I thought you might have some plan
09:07 olass if you need help with the docs plugin, please ask masak who wrote it
09:07 shk3 or it might conflict with something
09:08 shk3 just wanted to make sure
09:08 shk3 sorry for asking
09:08 olass shk3: I think it sounds like a good idea if you want my opinion
09:08 olass but I can only recommend
09:08 olass in fact, having a separate documentation plugin for all features is not desirable IMO
09:09 olass some features are small, only one plugin
09:09 olass so I'd say: a separate doc plugin for large features
09:09 olass but then again, this is just a matter of taste
09:09 shk3 that was my reasoning as well
09:09 shk3 I thought speclipse is large enough
09:09 egonw_ the current net.bioclipse.doc
09:09 egonw_ is actually not..
09:10 shk3 to justify it
09:10 egonw_ for just one feature
09:10 egonw_ it's wrapped around the product_feature
09:10 shk3 it isn't?
09:10 olass that is your decision
09:10 shk3 umm, that was my understanding of what alass said
09:10 egonw_ shk3: if you set up a speclipse product_feature too
09:10 egonw_ you can base your net.bioclipse.doc.speclipse on that feature.xml
09:10 olass egonw_: I thought it was wrapped around the platform_feature
09:10 egonw_ and the scripts will recurse to featuers one level lower
09:11 egonw_ olass: sorry...
09:11 egonw_ yes, that's the correct name
09:11 olass ok good
09:11 olass teh product file is something different
09:11 shk3 ok, I will try
09:44 egonw__ joined #bioclipse
10:02 egonw olass: linux 32 bit is fine
10:02 egonw now downloading 64 bit
10:02 egonw basement flooded... roof leaking...
10:02 egonw and wireless going up and down today :(
10:02 egonw bad day in enköping kommun
10:03 egonw but at least I did not have to cycle to the bus stop
10:12 olass joined #bioclipse
10:12 stain joined #bioclipse
10:13 egonw joined #bioclipse
10:13 mgerlich joined #bioclipse
10:14 ChanServ joined #bioclipse
10:19 egonw linux 32 bit looks fine too
10:19 egonw olass: linux is fine for release
10:23 olass egonw: have you tried all scripts in sample data?
10:23 olass please do
10:23 olass I see some problems here
10:23 egonw ok
10:24 olass they must all work
10:27 egonw the two seems to work for me
10:27 egonw did you make sure to reinstall the data?
10:28 olass two?
10:28 olass I have 9 scripts
10:28 olass buildmol.js seems to be the problematic
10:28 olass all others seem to work nicely
10:30 ChanServ joined #bioclipse
10:30 masak joined #bioclipse
10:31 olass egonw: can you confirm?
10:31 egonw mom
10:32 masak pop!
10:32 egonw buildMol.js works for me
10:32 olass without stacktrace?
10:34 olass egonw?
10:34 egonw ah, Invalid thread access
10:34 egonw did not see that
10:34 olass any idea what's causing it?
10:34 * olass is puzzled
10:35 egonw something with the outline
10:35 egonw but the outline is updated...
10:35 egonw file a bug report
10:35 egonw this is minor
10:35 egonw as the functionality seems working
10:35 olass it looks terrible on windows
10:35 olass a lot of exceptions to console
10:35 olass they do not go to file :(
10:38 masak egonw: heh, thanks for the tip about 'git svn fetch' :)
10:38 egonw not here either
10:40 olass egonw: I really don't like this logging behaviour
10:40 olass but no idea how to turn it off
10:41 egonw neither do I
10:42 egonw most people will not see it anyway
10:42 egonw since they do not a console
10:43 olass AAARGH
10:43 olass I forgot to remove -consolelog
10:43 olass GRRR
10:43 olass that's why
10:43 olass :(
10:43 olass will be a new export
10:43 masak olass++
10:44 * olass is glad we didn't upload this to SF
10:44 masak aye.
10:45 * olass has started a rebuild
10:47 olass seems inchi docu is also missing
10:49 olass damn, help system is crappy
10:49 olass egonw: I am going to remove some useless docu from the Bioclipse help that just confuses people
10:51 olass if help just adds noise, I consider it not so good
10:52 egonw ack
10:54 masak nod
11:07 CIA-54 bioclipse: ospjuth * r11655 /bioclipse2/trunk/ (12 files in 11 dirs): Cleanup of the Help system for various plugins before the Bioclipse 2.0 release.
11:08 * olass is building 2.0 (again)
11:09 olass I think we can safely upload to SF this time
11:09 olass egonw: you agree?
11:09 egonw agreed
11:09 egonw linux boots, windows boots
11:09 egonw mac boots
11:09 olass yes
11:09 olass but this is a new build
11:09 olass but should boot :)
11:10 olass The Bioclipse Help can really use soem improvement for all plugins
11:10 olass but that can be added later
11:10 olass at least we have SOMETHING there now
11:10 olass better than nothing
11:12 masak olass: I forgot my umbrella at your place yesterday.
11:12 masak it's black and kinda crappy-looking.
11:12 olass masak: ok
11:13 olass egonw: you forgit a T-shirt too, right?
11:13 olass masak: can't find any umbrella... what did it look like?
11:14 masak olass: black and kinda crappy.
11:14 masak though I might have forgotten it on the train too.
11:14 * olass will look again
11:15 * masak hopes he forgot it on the train
11:18 olass sorry, no umbrella here
11:18 olass at least I don't find any
11:18 masak ok. good.
11:18 olass why is that good?
11:18 masak because now I won't have to get rid of it.
11:19 olass lol
11:19 masak and maybe even someone else got an umrella for free.
11:22 egonw olass: yes
11:22 olass will bring it to BMC
11:22 egonw olass: or this weekend?
11:22 olass yea
11:22 olass that can be arranged
11:26 * olass is uploading 2.0 to SF
11:26 masak \o/
11:37 masak lunch &
11:57 stain olass: good luck.. when we did our Taverna release last week the whole download/upload system of SF broke!
11:57 olass stain: nice ;)
11:57 olass seems to work now
11:57 olass but SF is a bit unreliable...
12:42 egonw first round of bioclipse-git removal of non-feature stuff at 66%
12:42 egonw not going to finish this today, I think
13:06 masak joined #bioclipse
13:08 shk3 hi masak
13:08 masak hej shk3
13:08 shk3 do you have a few minutes?
13:08 masak yes, sure.
13:08 shk3 I try to run the doc stuff for speclipse
13:08 masak ok.
13:09 shk3 I changed the feature to run for
13:09 olass http://bioclipse.blogspot.com/20​09/07/biocipse-20-released.html
13:09 zarah olass's link is also http://tinyurl.com/lqlc89
13:09 masak olass++
13:09 shk3 what I get on console is a html output titled Manager documentation
13:09 shk3 but with no content
13:10 shk3 my suspicion was the recursion in find-released-bioclipse-features is not working
13:10 olass masak: please proofread and comment
13:10 masak shk3: the run-the-whole-thing script indeed outputs HTML.
13:10 shk3 I try to do stuff like print $feature there, but I get nothing
13:10 shk3 is print somehow redirected or so?
13:10 masak shk3: it is.
13:10 shk3 even print "jhkljk" does not show up
13:10 shk3 ah
13:10 masak shk3: try 'warn' instead of 'print'
13:10 shk3 where?
13:10 shk3 ok, thanks
13:11 shk3 I will come back to you if I have more problems
13:11 shk3 thanks for the time being
13:11 masak olass: you also need to update the "Latest news" column at the left on bioclipse.net
13:11 olass yes
13:11 olass I'm working on it
13:11 olass also updating the update sites
13:11 olass had almost forgotten that :)
13:12 masak olass: I think we can have bioinformatics in 2.1, even if we adopt a monthly release cycle.
13:12 shk3 masak: @features seems to be empty
13:12 olass yes
13:12 shk3 can I output this?
13:13 shk3 warn @features gives an error
13:13 masak shk3: please be more specific.
13:13 masak warn outputs on STDERR, that's what it does.
13:13 masak that's why it's better to use it when STDOUT is redirected.
13:14 masak olass: it's now the second Thursday of the month. shall we try to release 2.1 on the second Thursday of August?
13:14 shk3 ah, found something which could be the reason
13:14 masak 2009-08-13
13:15 shk3 hang on
13:15 masak egonw: how's the git migration going?
13:15 olass masak: I think that is in the middle of holidays
13:15 egonw masak: 5538/6050
13:15 masak olass: ok, so maybe some later date in August?
13:15 masak egonw: \o/
13:15 egonw masak: and only of the first itereation
13:15 egonw git filter-branch --tree-filter 'rm -rf _playground_ outdated' HEAD
13:16 masak olass: I think we need some fixed rule like that, "the nth x-day of every month"
13:16 egonw so, I got a long way to go before bioclipse.core.git is done
13:16 masak egonw: ok
13:16 masak still, nice to know it's ongoing.
13:18 masak olass: 'provides means'. I'd write 'provides the means', for some reason.
13:18 masak makes 'means' look less like a verb.
13:18 olass ok
13:19 masak nice jsconsole screenshot! \o/
13:20 masak (though I note that the editor has no title, maybe it should...)
13:20 olass masak++ //din förtjänst
13:20 masak olass: I didn't do anything, I just resisted a lot of detrimental feature additions. :)
13:21 olass masak: that is sometimes hard
13:21 masak saying no? yes.
13:24 egonw joined #bioclipse
13:24 edrin ok...
13:24 edrin regarding the sentence:
13:31 egonw ok, first iteration finished
13:34 shk3 masak: I now get the correct html outputted
13:34 masak shk3: nice!
13:34 shk3 but I need the index.html to be written, don't I?
13:35 masak shk3: . run-the-whole-thing > index.html
13:35 shk3 ok
13:36 shk3 very good
13:36 shk3 thanks for your help
13:39 masak no problem.
13:41 CIA-54 bioclipse: shk3 * r11656 /bioclipse2/trunk/plugins/ne​t.bioclipse.doc.speclipse/: Initial import.
13:42 CIA-54 bioclipse: shk3 * r11657 /bioclipse2/trunk/plugins/n​et.bioclipse.doc.speclipse/ (14 files in 3 dirs): Initial import.
13:43 olass shk3: which is the main Speclipse URL?
13:43 olass if you would send a link to someone, which URL would you give?
13:44 shk3 hm
13:44 shk3 good question
13:44 CIA-54 bioclipse: shk3 * r11658 /bioclipse2/trunk/plugins/n​et.bioclipse.doc.speclipse/ (.project META-INF/MANIFEST.MF toc.xml): changed some references to bioclipse
13:45 shk3 the only one I can think of right now is http://wiki.bioclipse.net/​index.php?title=Speclipse
13:45 shk3 I would rework that
13:45 shk3 but I think this is the best
13:45 zarah shk3's link is also http://tinyurl.com/5vumof
13:45 shk3 is it ok if we have stuff in the Bioclipse wiki?
13:46 olass you should consider having a wiki for speclipse IMO
13:46 olass but sure
13:46 olass feel free
13:47 shk3 let me ask Christoph
13:47 shk3 Politics are his matter
13:47 shk3 ok?
13:47 shk3 I will tell you asap
13:48 olass sure
13:48 olass just wanted to link to it in the blog announcement
13:49 shk3 you can use http://wiki.bioclipse.net/​index.php?title=Speclipse
13:49 zarah shk3's link is also http://tinyurl.com/5vumof
13:49 shk3 i think
13:49 shk3 either we will use this or I will link there
13:49 olass will do
13:50 olass let me know if you set up a speclipse page at EBI
13:50 olass (IMO you should)
13:51 CIA-54 bioclipse: shk3 * r11659 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: added doc to speclipse feature
13:52 CIA-54 bioclipse: ospjuth * r11660 /bioclipse2/trunk/experime​ntal-updatesite/site.xml: Removed XML feature from experimental update site since it did not work.
13:52 egonw so, where should experimental features go then?
13:52 egonw the experimental update site was for stuff in developement
13:52 egonw where something broken should be acceptable
13:53 egonw this was the whole point of the experiment update site, IIRC
13:54 olass egonw: you can't even download it
13:54 olass so quite useless
13:54 olass I agree that things donät need to work there
13:54 olass but at least it should not give error when selecting it for download
13:55 egonw ah, ok... one could not even download it...
13:55 olass filed bug 1410
13:55 egonw ok, thanx
13:55 egonw olass++
13:55 olass no¨
13:55 olass @pz xml-feature
13:55 zarah [1411] XML-feature is not operational    http://tinyurl.com/nlswk5
13:55 zarah [1395] XML-feature not working in RC5    http://tinyurl.com/nu95vv
13:55 zarah Entire list at http://tinyurl.com/ndfq8c
13:56 olass 1411 :)
13:57 masak look like duplicates.
14:00 * olass will celebrate the release announcement with a coffee
14:02 masak very fitting.
14:05 * shk3 will celebrate speclipse update site being ready with a coke
14:05 shk3 once it's done
14:16 shk3 does somebody know how to link to help pages of other plugins in help
14:16 shk3 ?
14:16 shk3 bioclipse help, this is
14:18 olass nope
14:20 olass but I'm sure it's possible
14:20 olass search eclipse help
14:23 olass egonw: need help with 1410
14:23 olass does not work
14:24 egonw yeah, seems a OS/X thing...
14:24 egonw problem is... this is deep inside the RDF stuff :(
14:24 egonw it's Jena reading of the RDF/XML, I think
14:25 egonw all I can do about that is upgrade to the latest release and pray to $DEITY
14:25 egonw S. Jobs in this case
14:26 masak he's not a deity, he just has his own Reality Distortion Field.
14:26 egonw well, fortunately he lost a kidney, so less heave, less distortion ?
14:26 masak yes, I think so.
14:27 edrin olass, any provisos ?
14:27 edrin or objections?
14:27 egonw OK, this is painful
14:27 egonw cleaning up all stuff not in a feature :(
14:28 edrin who lost a kidney?
14:29 shk3 ok, the syntax for linking help to other plugins help is /help/topic/other.plugin.id/path/to/file.html
14:29 shk3 in case somebody is interested
14:30 egonw masak, olass: maybe we can reconsider, and just loose history?
14:31 olass egonw: how much history?
14:31 egonw and start from 2.0.0 with the feature git repositories?
14:31 egonw I mean, it will stay in SVN...
14:31 CIA-54 bioclipse: shk3 * r11661 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/html/firststeps.html: added scripting to getting started with speclipse
14:33 olass egonw: do you mean that git can't handle history?
14:34 egonw no, this is about me not being able to split up histories...
14:34 egonw it takes soo long to rewrite history for every feature git repository we want to create
14:35 olass sad to loose history
14:35 olass how di you do it in CDK?
14:37 egonw no need to split up there
14:40 shk3 olass: I just downloaded bioclipse2.0.linux.gtk.x86.zip and it seems to contain an MACOSX folder as well
14:40 shk3 empty, but still not too great
14:45 egonw olass: OK to loose history?
14:57 egonw ok, never mind
14:57 egonw will do it the hard way...
14:57 egonw let's hope it is done by tomorrow
15:01 CIA-54 bioclipse: shk3 * r11662 /bioclipse2/trunk/ (11 files in 11 dirs): this was speclipse 2.0, it's on the update site now
15:04 * shk3 is getting a coke
15:18 egonw OK, I found a faster alternative for the git filter-branch stuff....
15:18 egonw considerably faster
15:19 olass egonw: any ida how I can assist with bug 1410?
15:20 olass idea
15:20 egonw take your laptop this weekend
15:20 olass no
15:20 olass will not work
15:20 egonw :)
15:20 olass and neither can you
15:20 olass laptops are not allowed on that island
15:20 egonw still no battery
15:20 olass *phew*
15:20 egonw so my laptop would not be an option anyway
15:20 olass good
15:21 olass still, any idea?
15:21 olass I am using jena now in the QSAR feature
15:21 olass so it is possible to get going
15:21 olass onviously
15:21 olass obviously
15:24 olass Caused by: java.lang.NoClassDefFoundError
15:24 olass at com.hp.hpl.jena.ontology.OntDocumentManager.setDe​faultPrefixMappings(OntDocumentManager.java:1232)
15:24 olass not good
15:26 * egonw is googling
15:26 * olass too
15:27 egonw can you try removing xercesImpl and xml-apis from the classpath for the externals/com.hp.hpl.jena plugin?
15:27 egonw (possibly adding a dep on Xerces from an Eclipse plugin...)
15:27 olass hmm
15:27 olass read this:
15:28 olass I’ve seen the error:
15:28 olass org.apache.xerces.impl.dv.dtd.DTDDVFactoryImpl does not extend from DTDDVFactory in another context. It occurs when the version of Xerces shipped with the JDK is inadvertently used instead of the version shipped with JRules.
15:28 olass The solution was to make sure that the plugin in question had a dependency on the plugin ilog.rules.shared (which packages Xerces).
15:28 olass hmm
15:28 olass hmm
15:29 olass testing
15:30 olass yes!
15:30 olass worked
15:30 olass I removed the xercesimpl.jar and added dep to plugin org.apache.zerces
15:31 olass should I commit or are we in middle of git transition?
15:32 egonw please commit
15:34 CIA-54 bioclipse: ospjuth * r11663 /bioclipse2/trunk/externals/com.hp.hpl.jena/ (.classpath META-INF/MANIFEST.MF build.properties): Removed dep to the file xercesimpl.jar and added dep to plugin org.apache.xerces. Solves 1410.
15:39 egonw who is downloading from Pele ?
15:40 egonw mmm... maybe some heavy xmpp computation?
15:40 egonw or are the bioclipse-xmpp downloads also served from there?
15:42 olass oh no
15:42 olass hmm, maybe
15:42 edrin that was me
15:43 egonw :)
15:43 edrin egonw: i downloaded them to upload the for submission
15:43 edrin is it forbidden to download stuff from pele?
15:43 egonw oh, no excuse needed :)
15:43 olass oh no
15:43 egonw no, was just wondering...
15:43 egonw noticed heavy eth0 load :)
15:43 egonw does not happen too often
15:44 egonw oh no?
15:44 olass it is not forbidden to dl from pele
15:44 olass in fact, we encourage it ;)
15:44 egonw ah, "oh no"
15:44 edrin ok
15:45 edrin but the submission portal did not eat the big uploads anyway, so i did w/o the big bundles
15:46 masak egonw: http://en.wiktionary.org/wiki/octothorpe
15:46 zarah masak's link is also http://tinyurl.com/3dn5x7
15:46 edrin olass: got my mail?
15:47 edrin more specific forward mail
15:48 egonw masak: :)
15:49 masak egonw: the Esperanto term appears to be 'dieso' or 'krado'.
15:56 CIA-54 bioclipse: ospjuth * r11664 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Added org.apache.xerces to rdf feature too
15:58 olass egonw: what was the descriptor gist again?
15:58 olass nvm, found it
16:01 olass egonw: where is the latest version of the descriptor ontology?
16:01 olass can you give me a url?
16:02 egonw that's in the gist
16:02 egonw mom
16:02 egonw http://gist.github.com/95946
16:05 olass do you keep the giost updated?
16:05 olass gist
16:05 olass ?
16:05 egonw yes
16:05 olass ack
16:05 egonw each time I use it again, that is
16:05 olass so, every day?
16:05 olass :)
16:07 CIA-54 bioclipse: ospjuth * r11665 /bioclipse2/trunk/plugins/net.bioclipse.​qsar/ontology/descriptor-algorithms.owl: Updated to latest descriptor ontology.
16:16 edrin while you are always talking about gist, is the bioclipse2 svn repository also available via gist!?
16:18 masak what would that mean?
16:18 masak edrin: do you mean git, not gist?
16:18 edrin git
16:18 edrin always mixing them up
16:18 masak gist is a pastebin service.
16:18 edrin yes
16:19 edrin we use it for javascripts
16:19 masak edrin: well yes, it will be. but it won't be an svn repository then.
16:19 edrin and git?
16:19 edrin so we move to git?
16:19 masak aye.
16:19 edrin what is the advantage?
16:19 masak edrin: it's easier to branch and merge with git than with svn.
16:20 masak that's perhaps the main advantage.
16:20 edrin ok
16:20 edrin does sourceforge support a git repo already?
16:20 masak yes, but not in the way we want.
16:20 masak since the Bioclipse repo is so large, we're splitting it up into features.
16:20 masak one feature, one git repo.
16:21 masak that'll have the extra advantage that we can assign responsibilities more precisely.
16:22 masak so only those who are working on a feature will have write access to it.
16:22 edrin ah right
16:22 edrin ok
16:22 masak still, with git, anyone can make a clone on a repo and make commits to the clone.
16:23 masak that's the beauty of distributed systems like git, as opposed to SVN.
16:23 edrin ic
16:23 edrin its next generation svn
16:23 masak you could say that.
16:23 masak distributed systems have been brewing for a few years now, but git marks some sort of tipping point.
16:24 masak it's the one thing that has made me feel the pain of using SVN more acutely. :)
16:24 masak next to git, SVN feels like a crude tool.
16:25 edrin is it commercial?
16:26 egonw yes, just like the linux kernel
16:26 edrin meaning it is opensource ?
16:26 edrin GPL?
16:26 egonw not sure about GPL
16:26 egonw but opensource, yes
16:27 edrin while we are talking about disrtibutes archiving systems...
16:27 egonw dinner
16:27 egonw bbl
16:27 edrin Google wants to bring a Google OS
16:27 edrin Chrome OS
16:28 edrin Google is developing and becoming evil
16:28 edrin Its now associates with the name "Datenkrake"
16:29 edrin http://de.wikipedia.org/wiki/Datenkrake
16:29 zarah edrin's link is also http://tinyurl.com/mawcab
16:29 edrin masak: isn't this something you like?
16:29 edrin I mean these kind of special words
16:30 edrin in foreign languages
16:30 edrin the translation in english would be
16:30 edrin data octopus
16:30 edrin something like this
16:35 edrin olass: what are you doing right now?
17:23 * edrin 's going home
17:23 edrin left #bioclipse
17:46 * olass is back from runnig and has a lasagne in the oven
17:46 olass running
17:53 olass @pz rajarshi
17:53 zarah [1107] Use SPARQL to set up descripto... http://tinyurl.com/n55t8e
17:53 zarah Entire list at http://tinyurl.com/mptyd7
18:08 * egonw is making some progress with feature repositories
18:08 egonw or something close to it...
18:08 egonw it will not actually be one feature for every repository
18:08 egonw e.g. the 'core' repository will have platform + core feature
18:08 egonw cheminformatics: cheminformatics + cdk (maybe a bit more)
18:16 olass sounds logical
18:18 egonw slowly making progress...
18:18 egonw lots of stuff to remove...
18:18 egonw and split up
18:18 egonw each iteration takes 15 minutes at least...
18:19 egonw but getting there...
18:19 egonw problem is... there is so much history :)
18:20 shk3 joined #bioclipse
18:27 olass egonw: I need you help
18:27 olass starting from the gist
18:28 olass how do I extract the name and id of each returned descriptor?
18:28 olass and how do I get the name of a descriptor category?
18:29 olass since now we query by id
18:29 olass egonw: ping
18:39 egonw ok, please file me a bug report
18:47 olass can you not show me now?
18:47 olass is it not easy?
18:47 olass if difficult, I'll file a bug
18:47 olass sure
18:47 olass just thought that was a 10 second thing
18:48 olass for an experienced RDF wizard like you ;)
19:03 olass egonw: updated bug 1107 for this
19:06 sneumann joined #bioclipse
19:44 egonw no, it's not difficult
19:44 egonw but had to read Harry Potter to my son
19:46 egonw and tired and want to finish this git stuff for bioclipse.core first
21:23 sneumann joined #bioclipse
21:23 egonw sneumann: thanx for the mail... sounds good!
21:25 sneumann Evening!
21:26 sneumann Also had a talk with shk3 on the possible combination of MetFrag with his NMR prediction
21:29 rojasm joined #bioclipse
21:31 egonw mmm...
21:31 egonw please explain...
21:32 egonw NMR on the fragments will not give good prediction
21:32 egonw as I expect the charges to have a serious effect on the shifts
21:32 egonw and the nmrshiftdb has not data on that
21:32 egonw so you're stuck with the nmr of the full compound...
21:32 egonw or am I missing something?
21:33 egonw hi rojasm!
21:33 rojasm hi egonw
21:33 egonw rojasm: really around, or just your client silently going online?
21:33 egonw btw
21:33 egonw sneumann, rojasm:
21:33 egonw bioclipse 2 is moving to the git world
21:34 rojasm ooo sound good. So all project already to git
21:34 egonw nope
21:34 egonw because we are splitting up things...
21:34 egonw to make it easier to maintain
21:34 egonw so, several git repositories
21:35 egonw one for the core bioclipse
21:35 egonw one for the cheminfo feature
21:35 egonw etc
21:35 egonw one for speclipse
21:35 egonw so, we need to think how to set up the metabolomics related stuff...
21:35 egonw each of these git repositories will have a benevolent dictator
21:35 egonw who decides what patches he puts in,
21:36 egonw possible using trusted luitanents
21:36 egonw it seems we are moving to GitHub for this, as SF only allows 1 git repository (at this moment, at least)
21:36 egonw so, there is plenty of opportunity to become a benevolent dictator now
21:37 egonw or luitanent...
21:39 sneumann I'm not pushing to be one ...
21:40 egonw at least we need to decide on a 'unit' here
21:41 egonw but I'll get back on this next week
21:50 stain why does it have to be different repositories..?
21:51 egonw various advantages...
21:51 egonw 1. git tar makes sense now
21:52 egonw e.g. a run on the bioclipse.core repos will give a nice source distrib for all the core stuff
21:52 egonw so that people can easily start developing for bioclipse
21:52 egonw same if they like specific extensions
21:52 egonw 2. maintainance: we'll have one person in control over a well defined set of plugins
21:53 egonw 3. it's git
21:54 egonw 4. smaller repositories, easier to clone (the full svn repos has become pretty large)
22:07 egonw http://github.com/egonw/bioclipse.core/tree/master
22:07 zarah egonw's link is also http://tinyurl.com/kn37tf
22:08 egonw let's hope I did not removed something I should not have
22:08 egonw sleep well, cu tomorrow
22:08 egonw stain: that bioclipse.core alone is about 90MB
22:08 egonw bye

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