Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-29

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All times shown according to UTC.

Time Nick Message
07:55 olass joined #bioclipse
08:25 egonw joined #bioclipse
08:26 egonw hi olass
08:26 olass hi
08:26 zarah hi olass
08:27 olass egonw: did you see http://www.kva.se/KVA_Root/eng/award​s/scholarships/researchservices.asp ?
08:27 zarah olass's link is also http://tinyurl.com/8ttz39
08:28 olass ask Jarl if this is applicable for you
08:28 olass hmm
08:29 olass seems you need to run a group...
08:29 olass maybe not suitable (yet) for you
08:30 egonw oncology, right?
08:30 egonw just saw it...
08:31 egonw I don't even know what oncology is...
08:31 egonw well, I should have know...
08:32 egonw it's cancer research
08:32 egonw I don't think I qualify
08:32 olass there are general positions too
08:32 olass oncology is just one
08:32 olass but anyway
08:32 olass egonw: you got my mail regarding tag in cdk?
08:32 olass read your post on cdk .2.0
08:32 egonw yes, sent 2 replies
08:33 olass oh, got it now
08:33 olass sry
08:33 egonw the problem basically is the use of code that depends on aromaticity detection...
08:33 olass which is a lot...
08:33 egonw if perceived aromaticty changes, then the FPs change
08:33 egonw so, the most important thing is, not a CDK tag...
08:34 egonw but being sure atom types are correctly percieved for the database
08:34 egonw in natural language: CDK understand the chemistry read from the files
08:34 olass how much do you have left until this?
08:34 egonw no idea
08:34 egonw not unless I have access to the data
08:35 egonw or a list of atoms for which the type is misconceived
08:35 olass database is commercial
08:35 olass so that is not possible
08:35 egonw depends...
08:36 egonw I can work confidential too :)
08:36 olass but... missconceived atom types compared to what?
08:36 egonw correctly perceived atom types
08:36 olass define correct
08:36 olass we compared to openbabel last time...
08:36 egonw no, you'll have to do this manually...
08:36 olass and comparison were good enough
08:36 egonw but a good start is just detection NULLs
08:37 olass so, just run large SDFiles and detect NULLs?
08:37 egonw yes, that would be the primary thing to do...
08:37 olass you got some Nulls in the unit test I wrote...
08:37 olass some 10-20, right?
08:37 egonw did not count
08:37 egonw possible
08:37 egonw have not looked at it, actually...
08:38 egonw they are now converted into 'X's
08:38 olass egonw: to sum up, what is the attack plan for this and timefraqme?
08:38 olass 1.2.0 will not be released until this is fixed, right?
08:39 egonw no idea...
08:39 egonw I don't want to wait with 1.2.0 for just Polymer.clone
08:39 olass egonw: please help me here, I have problems understanding the implications of all this
08:39 egonw but will talk with Chris and Rajarshi what they think
08:40 egonw your work is unaffected by that...
08:40 olass atom typing is really affecting me
08:40 egonw so, you/BC can settle with a beta release...
08:40 egonw 1.1.x
08:40 edrin joined #bioclipse
08:40 olass hi edrin
08:40 egonw the atom type perception is a different story...
08:40 egonw that will get fixed anyway...
08:40 edrin hi olass
08:40 edrin hi egonw
08:40 egonw now that testing the data classes is finished, I can focus on that again
08:41 egonw hi edrin
08:41 olass egonw: and you wanted to fix some AT before the tag and bc plugins upgrade?
08:41 egonw right
08:42 olass and that will be before you leave?
08:42 egonw yes, will release 1.1.5 before I leave
08:42 olass great
08:42 egonw and I think we can release BC2.0.0 with that version
08:42 olass ok
08:43 egonw olass: and your plugins will just have to depend on exactly that CDK version
08:43 olass yup
08:43 olass I know it's hard but you don't have time to fix CDK all by yourself
08:43 egonw right
08:43 egonw I can fix my own code
08:43 egonw but fixing other peoples code is really difficult
08:43 olass you need to focus on the parts of CDK that you need to do new science and publish
08:44 olass it is important that you get the new projects going this spring
08:44 olass fragments etc
08:44 olass after JCP and BC2 of course
08:44 olass :-)
08:45 olass I know, time time time...
08:45 egonw yes, yes ...
08:45 olass it's good that we have several good people working on BC with us
08:45 egonw yes indeed
08:45 olass we divide and conquer
08:46 egonw but first we write papers now :)
08:46 olass you and I really need focus on science this year
08:46 egonw yes
08:46 olass edrin: I very much liked how the XWS paper is getting along
08:47 olass will you be able to put more work into it?
08:48 edrin it's stuck right now
08:49 olass edrin: why?
08:50 edrin completing the manuscript is one thing, finishing the demo apps is the other thing...
08:50 olass edrin: if I and egon finished ours, would that improve things?
08:50 edrin sadly it will be difficult to complete the manuscript how exactly the plugins/sample services...
08:50 edrin yes, i think sp
08:50 edrin so
08:50 olass ok, I am really close actually
08:51 edrin i must finish it...
08:51 olass finish the library?
08:51 olass or the manuscript?
08:51 olass (or both)?
08:51 edrin manuscript
08:51 edrin both
08:52 edrin well, i think the lib is complete
08:52 olass but the lib is kinda finished, right?
08:52 olass right
08:52 edrin yes
08:52 olass egonw,edrin: could we decide on a title?
08:52 edrin that's the good thing
08:53 edrin i liked the first one you gave a +2
08:53 olass and teh second +2, comments there?
08:54 olass #2: Next generation Web services in Bioinformatics: Discovery and invocation of truly asynchronous services based on XMPP
08:54 olass #1:  XMPP as protocol for cloud computing in bioinformatics supporting discovery and invocation of truly asynchronous Web services
08:54 egonw both too long
08:54 olass hmm, maybe wrong channel
08:54 edrin heh
08:54 olass but anyway
08:54 olass egonw: I disagree
08:54 egonw #xws
08:54 edrin ok... new channel
08:54 edrin ok
09:56 olass joined #bioclipse
09:59 egonw he, who deleted the text I just wrote on the CDK services?!?
10:00 edrin i think something straneg happened when clsing the window
10:01 edrin maybe it was accidentally
10:01 edrin ,e
10:01 edrin me
10:02 olass egonw: I commented there
10:02 edrin i am sorry for this
10:02 olass Should we not call it XWS service?
10:02 olass or XMPP service?
10:02 edrin XMPP service
10:02 edrin XMPP Web Service service
10:02 edrin hm
10:02 edrin will be around, cu later
10:03 olass egonw: what's your opinion?
10:03 olass egonw: sorry for writing in your section
10:03 olass see it as a comment
10:03 egonw no worries...
10:03 egonw adding bits is fine...
10:03 egonw but gdocs should not loose the text
10:03 olass cloud service is larger than just XWS and XMPP IMO
10:04 egonw true...
10:04 egonw but if we say XWS == cloud, the we did implement cloud services
10:04 egonw anyway... it's just a draft to get things to sat together
10:04 egonw anyway... it's just a draft to get things to say together
10:05 egonw and refs...
10:05 olass right
10:05 olass but the sooner we agree on terminology
10:05 olass the better
10:08 olass egonw: would it be interesting to benchmark SOAP against XWS?
10:08 egonw no
10:08 olass maybe not...
10:08 egonw because that would require us to be experts in SOAP...
10:08 egonw which we are not...
10:08 egonw so the comparison would alwasy be flawed...
10:10 olass right
10:10 egonw but a SOAP services does not allow plugging in of a second 'component'...
10:10 egonw which XWS does :)
10:11 egonw so, we do not have to do that to show XWS is better performance wise
13:19 CIA-55 joined #bioclipse
14:26 egonw edrin: ping
14:27 jonalv joined #bioclipse
14:28 egonw hi jonalv
14:29 jonalv hi egonw
15:11 edrin hi egonw
15:11 edrin hi jonalv
15:12 egonw hi edrin
15:12 egonw edrin: can you please check ws1.bmc.uu.se?
15:12 egonw and see if the services are working for you?
15:12 edrin im not home, cant access internet in lab from my laptop
15:12 egonw ack
15:15 masak joined #bioclipse
16:01 olass joined #bioclipse
16:01 olass hi
16:01 zarah hi olass
16:03 egonw olass: ping
16:03 olass pong
16:04 egonw how did you tie the TextEditor to net.bioclipse.contenttypes.cml ?
16:04 olass eonw: pong
16:04 egonw in which plugin.xml is that done?
16:04 olass mom
16:05 masak we need more 'your mom' jokes here on #bioclipse
16:05 olass not really
16:05 olass egonw: is that really done?
16:05 masak perhaps not.
16:06 egonw not sure...
16:06 egonw trying to get the WST XML editor online in BC2
16:06 olass I think the cml content type extends xml which extends text, and hence the texteditor picks it up
16:07 olass it's called base-type in the contenttype
16:07 egonw right, so how do I get it to show the XML editor (not the BC2 one, but the WST) in Open With...
16:07 egonw yes, figured that out, by now...
16:07 egonw I really like this system...
16:07 olass me too
16:07 egonw and will actually look into the matchers...
16:07 olass it's very flexible
16:07 olass yup :-)
16:08 olass you need to associate the editor with the content type
16:08 egonw so, that is a learning experience for me...
16:08 masak egonw, olass: svn+ssh://pele.farmbio.uu.se/o​pt/svnroot/Extending_Bioclipse
16:08 masak that's where we're having fun right now.
16:08 olass zarah: give me a short URL
16:08 zarah olass: please rephrase or stop trying to be witty :)
16:08 masak olass: it's not a http URL
16:08 olass zarah: sorry
16:08 zarah olass: excuse me?
16:09 olass zarah: that's my line!
16:09 zarah olass: eh... wha'?
16:09 olass zarah: I missed you during christmas...
16:09 zarah olass: are you making fun of me?
16:09 egonw masak: ack
16:09 * masak missed zarah too
16:09 olass egonw: when you define an editor you associate it with a contenttype
16:09 olass donät know how to add a contenttype to an existing editor
16:10 egonw masak: OK, if I 'convert' it into a TexClipse project? for those who like it...
16:10 egonw olass: right
16:10 egonw ok, me continues his search
16:10 olass you can just override the editor
16:10 masak egonw: what does that entail?
16:10 olass mom, will give you a pointer
16:10 masak egonw: as long as it's non-destructive, it's fine by me.
16:10 egonw masak: it's not... and optional too
16:10 egonw brb
16:10 masak hm.
16:11 masak egonw: it's just that we have this workflow...
16:11 masak a really, really good one.
16:11 olass egonw: like is done in plugin.xml of net.bc.cdk.jchempaint. Create a new editor ID but same class and vary the contenttype.
16:14 olass brb
16:20 masak olass: you missed Santa this year.
16:22 egonw masak: what workflow?
16:22 egonw that broken make.sh?
16:23 masak egonw: yes, among other things.
16:23 masak egonw: what's broken about it?
16:23 egonw OK :)
16:24 egonw well, for once... you need to run tex thrice, not twice, to get the tocs etc right
16:24 masak egonw: oh?
16:24 egonw also rm will fail if there is no toc...
16:24 masak egonw: fixing.
16:24 egonw no use of bibtex yet
16:24 egonw this is much better done with a Makefile
16:25 masak egonw: aye, agreed
16:25 masak egonw: feel free to turn it into one.
16:25 jonalv egonw: uhm we are doing as little as possible for the moment. Porting part by part from our other project...
16:25 jonalv +we started today...
16:25 egonw masak: ack
16:25 * masak is insufficiently skilled in the Makefile arts
16:26 jonalv egonw: but if you have a better way to do things...
16:26 egonw btw, no git??
16:26 masak egonw: we considered it.
16:26 masak egonw: however, we thought that even svn might be a big step for Jarl
16:26 masak so we kept back.
16:26 egonw then again...
16:27 masak s/kept/held/
16:27 egonw he has to learn something anyway...
16:27 masak egonw: he's on Windows.
16:27 egonw and to him 'git pull' and 'svn update' is all the same
16:27 jonalv + masak said something about not knowing how to set up git without github...
16:27 masak egonw: there are GUI svn clients on Windows.
16:27 egonw which comes with git GUIs
16:28 egonw jonalv: yeah... that's a good point... I've never done that yet either :)
16:28 masak right. we wanted to get to the writing stage quickly, not fiddle around a lot with infrastructure.
16:28 egonw but plenty of readmes online
16:28 masak aye.
16:28 masak it's probably not that difficult.
16:28 masak jonalv: let's make next project a git project. :)
16:28 jonalv masak: haha oki
16:29 jonalv Anyway, I think svn is a better solution than google docs
16:29 masak indubitably.
16:30 egonw 100% agreed
16:30 masak that said, Google Docs is cool technology.
16:30 masak pretty neat for muggles.
16:31 jonalv I guess I should have said: svn + LaTeX
16:32 masak knuth++
19:32 CIA-55 bioclipse: carl_masak * r8099 /bioclipse2/trunk/plugins/net.biocli​pse.scripting.ui/src/net/bioclipse/s​cripting/ui/views/VirtualView.java:
19:32 CIA-55 bioclipse: [VirtualView.java] made some inner classes static, by the rule "if you can make
19:32 CIA-55 bioclipse: inner classes static, do"
19:44 masak to anyone who notices a strange lack of empty lines in their .java files: sorry :/
19:44 masak I'll fix that, promise.
20:45 masak @pz console
20:45 zarah [78] CR/LF problems on windows           http://tinyurl.com/6eznsa
20:45 zarah [76] Bioclipse crashes when text is d... http://tinyurl.com/5eaofv
20:45 zarah [113] The js console says "unexpected... http://tinyurl.com/5hey86
20:45 zarah [123] scripting hangs the UI             http://tinyurl.com/67c3my
20:45 zarah [139] Exception upon added a first atom  http://tinyurl.com/54rkap
20:45 zarah Entire list (11) at http://tinyurl.com/6pke5y
20:45 masak you're a smart girl, zarah.
20:45 zarah masak: If I'm so smart, how come you're shacked up with that other chick?
20:45 masak you tell me.
20:47 CIA-55 bioclipse: carl_masak * r8100 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (JsConsoleView.java ScriptingConsoleView.java): [scripting.ui] fixed locking-up behavior after 'help' and 'man' commands (bug #193)
20:47 zarah bug #193 | http://tinyurl.com/9wqyj9
21:08 CIA-55 bioclipse: egonw * r8101 /bioclipse2/trunk/plugins/ne​t.bioclipse.cml/plugin.xml: Registered the CML XML Schema
21:08 CIA-55 bioclipse: egonw * r8102 /bioclipse2/trunk/features/​net.bioclipse.cml_feature/ (. .project build.properties feature.properties feature.xml):
21:08 CIA-55 bioclipse: Added feature for allowing CML editing using the WTP XML editor, with CML XML
21:08 CIA-55 bioclipse: Schema back up for autocomplete for elements and attributes; it's a long list of
21:08 CIA-55 bioclipse: included features and plugins, so not directly material for the cheminformatics
21:08 CIA-55 bioclipse: feature
21:14 masak egonw++ # Makefile
21:14 masak @tell egonw thanks for the Makefile -- egonw++
21:14 zarah Consider it noted.
21:15 jonalv @tell egonw The makefile doesn't do the same things as the shell script did... :(
21:15 zarah Consider it noted.
21:18 masak @tell egonw that's right. what you may not have realized is that the chapters sit in separate .tex files. so the Makefile thinks nothing needs to be done in situations when something actually needs to be done.
21:18 zarah Consider it noted.
21:19 masak jonalv: hehe. two-person @tell is almost like having a real conversation. :)
21:49 CIA-55 joined #bioclipse
21:49 ilogger2 joined #bioclipse
21:49 zarah joined #bioclipse
21:49 stain joined #bioclipse

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