Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-18

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All times shown according to UTC.

Time Nick Message
00:16 Trev_ joined #bioclipse
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05:36 Gpox joined #bioclipse
07:03 thomas_ku joined #bioclipse
07:05 masak joined #bioclipse
07:06 masak zarah: you survived my vacation!
07:06 zarah masak: you've just exceeded my capabilities :/
07:06 zarah masak: You have new messages. Write '@messages' to read them.
07:06 masak zarah: massages
07:06 zarah masak: olas said Very nice work with icons. However, bond_aromatic seems to be missing. A missing commit?
07:06 zarah masak: jonalv said Please don't import sun.text.CompactShortArray.Iterator and hardcode java.util.Iterator in the code. Better to import java.util.Iterator from the beginning. :)
07:08 masak tell olas re icons: correct. fixed.
07:09 CIA-50 bioclipse: carl_masak * r6619 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/icons/bond_aromatic.png: [n.b.cdk10.jcp/icons] added bond_aromatic.png
07:09 masak tell jonalv: re sun.text.CompactShortArray.Iterator: gotcha. :)
07:34 CIA-50 bioclipse: carl_masak * r6620 /bot/trunk/zarah.pl: [zarah] less specific "you are the <something> one" matcher
07:34 zarah joined #bioclipse
07:49 olas joined #bioclipse
07:49 olas hi all
07:49 zarah hi olas
07:51 masak hi olas
07:59 jonalv joined #bioclipse
08:04 maclean joined #bioclipse
08:40 CIA-50 bioclipse: ospjuth * r6621 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/dialogs/WSFileDialog.java: Renamed a set operation from add to set.
08:55 CIA-50 bioclipse: carl_masak * r6622 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/BioclipseStore.java: [BioclipseStore.java] removed unused imports
09:06 egonw joined #bioclipse
09:08 edrin joined #bioclipse
09:08 edrin hi all
09:08 zarah hi edrin
09:10 egonw hi all
09:10 zarah hi egonw
09:10 zarah egonw: You have new messages. Write '@messages' to read them.
09:10 egonw @msg
09:10 zarah egonw: malick said chance installer java //location.setLocation("/faah/" + installer + ".CDF"); to location.setLocation("/faah/" + identifier+".CDF"); in the previous situation with installer.java I had SQL update: INSERT INTO metraw_datafile_location (metraw_datafile_location_id, location) VALUES ('6', '/faah/MetmetaUserBean: metmeta_user_id: 1  lastname: null firstname: null  metmeta_institute_id: null   email: me
09:10 zarah egonw: malick said I encounter when using navigation.xhtml from your platform version when clicking on Users MetmetaUserQueryBean is called which doesn't exist needs to be replaced by MetmetaUserBean.jsf btw very bad richfaces form
09:10 masak hi egonw
09:10 egonw hi masak
09:10 malick great zarah is working at more places
09:11 egonw yeah, it's being useful at #metware too
09:11 masak zarah: you're the useful one!
09:11 zarah masak: oh, shut up :)
09:11 masak :)
09:13 edrin ola, egon, i imported the newest version of xcd into svn (component+client).
09:13 edrin It's now almost complete. Still missing is getIoSchemata() from the client site (component is ok).
09:15 edrin but Discovery, invoke function (in both, blocking and listener based way) is already working
09:15 egonw edrin++
09:15 egonw edrin: I won't have time for it until I start in Uppsala
09:15 egonw sorry about that
09:15 edrin sure
09:15 edrin at what date will you start?
09:16 egonw Oct 1
09:17 edrin i also wanted to discuss a certain part of the implementation of the protocol, because there is an issue regarding implementation level... maybe at some time this afternoon?
09:18 egonw bbl
09:19 edrin egonw: did ola tell you that he already set up a service at Uppsala?
09:51 egonw edrin: no, but I already guessed so
10:02 * olas is back from lunch
10:02 olas hi edrin, hi egonw
10:03 olas edrin++ #for xws4j
10:03 olas edrin: what are the current capabilities? Can I write my vlient in Java now?
10:03 olas client that is...
10:03 olas egonw: I'd like to discuss QSAR with you this afternoon
10:03 olas do you have time for that?
10:05 egonw yes, think so
10:11 olas writing up an email to get the disc started
10:11 olas I know you will not agree with me on some things but that's ok :-)
10:11 olas I hope we can come to some sort of understanding
10:13 egonw hehehehe
10:13 egonw there are shades of correct approaches
10:13 olas always
10:13 olas egonw: is inchi a hash?
10:13 egonw I'm sure we'll find a good balance between Utopia and the finish of your thesis :)
10:14 egonw yes, and more
10:14 olas what more?
10:14 egonw I don't think a hash can typically be backconverted into the original
10:14 olas can inchi?
10:14 egonw well, the important bits
10:14 egonw the connectivity at least..
10:14 egonw but not 3D coords
10:14 olas so if I have a SMILES, get the inchi, can I get back my SMILES from it?
10:14 egonw or 2D, or fractional
10:14 egonw yes
10:15 olas good
10:15 egonw but are line notations for chemical connectivity tables
10:15 egonw but -> both
10:15 olas ok
10:16 olas egonw: can we get inchi into Bioclipse?
10:16 olas is that a hard problem?
10:16 olas with support for win, lin, mac?
10:17 egonw win/linux 32 bit, yes
10:17 olas yes as in hard problem?
10:17 egonw any other not without getting InChI libs compiled for that
10:17 egonw but no idea how to do that
10:18 olas is it open source?
10:18 egonw yes
10:18 olas java?
10:18 egonw no
10:18 olas will we use command line to create inchi?
10:18 egonw that's an option
10:18 olas can CDK parse inchi into an AtomContainer?
10:20 egonw yes
10:20 olas how good? 100%?
10:20 egonw never tested it myself
10:20 olas but relatively good?
10:20 egonw never tested it myself
10:21 olas so you have no clue?
10:21 olas and still answer yes?
10:21 olas :-)
10:21 egonw it's not difficult, so I guess it does >98%
10:21 olas that's relatively good IMO
10:21 egonw it's done by Sam Adams
10:21 olas he does that besides brewing beer?
10:22 egonw the only thing he brews is code, AFAIK
10:22 olas or is that his brother, Samuel?
10:22 egonw what are you talking about ?!?!
10:22 olas right... :-)
10:22 olas nevermind
10:22 egonw what's nevermind in Swedish?
10:22 olas hmm
10:23 egonw sounds as useful as Fiskpinne
10:23 egonw Fysk?
10:23 olas no, fiskpinne
10:23 olas I'd say Fiskpinne is much more useful
10:23 egonw ah, right... no German capticals :)
10:23 olas true
10:23 olas much easier
10:24 olas just lowercase everywhere expect starting sentences
10:24 olas masak, jonalv: nevermind in swedish?
10:24 masak olas: "det var inget"
10:25 olas ja, kanske
10:25 olas egonw: a useful link for you: http://lexin2.nada.kth.se/swe-eng.html
10:25 zarah olas's link is also http://tinyurl.com/2spfjr
10:25 masak olas: "glöm det"
10:26 olas mm
10:26 masak egonw: http://download.slayradio.org/m​astering_swedish_-_lesson_1.mp3
10:26 zarah masak's link is also http://tinyurl.com/b5s4c
10:26 masak there are corresponding 2, 3, 4 parts if you like the first one
10:32 masak @tell shk3 please don't use tab characters in bc2 source. you could reconfigure Eclipse to never insert tabs in your code. see my bioclipse-devel mail from 2008-05-07 for instructions.
10:32 zarah Consider it noted.
10:41 edrin olas: yes, you can
10:41 edrin olas: and
10:42 edrin i think it should be even possible to use xws services directly from the javascript console
10:42 edrin similar to this:
10:42 edrin s = new Service("xws.yourserv.com");
10:43 edrin f = s.getFunction("doSomething");
10:43 edrin f.invokeSync(input);
10:43 edrin err
10:43 edrin r = f.invokeSync(input);
10:44 edrin do something with r
10:45 edrin the thing that is still missing in the client is: getSchemata()
10:45 edrin but i will add this soon, will not be too much work
10:47 edrin and for example to write a xmpp service browser (with a tree view) for eclipse/bioclipse someone should use the discoverAsync() functions that are listener based
10:58 olas edrin: yes, we should
10:59 olas masak: in bioclispe1 we could make use of regular java code as well, by hust including Package.blh.bla before
10:59 olas can we do this in bc2 javascript as well?
11:00 edrin yes
11:00 olas oh, you tested?
11:00 edrin it's part of the rhino api
11:00 olas edrin: can you confirm it works?
11:00 shk3 joined #bioclipse
11:01 edrin no, it mainly depends on the settings of the rhino plugin
11:01 edrin if it imports all *
11:01 olas masak: do you hear this?
11:02 olas @tell masak please backlog conversation regarding scripting in #bioclipse
11:02 zarah Consider it noted.
11:02 edrin i am currently testing the lib in bc1
11:02 olas I see
11:02 olas should be easy to run in bc2 as well
11:02 edrin because i have certain function in the rhin plugin to use lib
11:02 edrin yes
11:02 edrin it should be really easy
11:02 olas edrin: do you have sample code for clients?
11:03 edrin yes
11:03 edrin in javascript though
11:03 edrin but it's the same in java anyway
11:03 olas should be ok
11:03 olas in svn?
11:04 edrin it contains samples for everything, sync and async/listener usage... how to discover, blah...
11:04 edrin no
11:04 edrin not in svn yet
11:04 olas let me know when you have comitted
11:05 olas then I can not only create the server but also test it from bioclipse2 :-)
11:05 edrin and there is still this protocol issue i wanted to discuss... because this makes the "usage" of the lib inconsistent for people that do not know the details
11:06 edrin but it is complicated to explain
11:13 olas edrin: protocol issue?
11:13 olas can you write up an email?
11:13 olas or should we have a skype conf with egonw?
11:13 edrin i will write an email
11:13 edrin later today
11:13 edrin and explain it
11:14 edrin it's not that the protocol has an issue itself. it's that it is a bit complicated to write a simple api for the protocol
11:15 olas understandable
11:15 olas proper documentation should resolve that
11:15 edrin sure
11:17 olas edrin: will you commit your javascript examples today so I can test them with bioclipse2?
11:18 edrin i cant because i am at work and our computer access is limited
11:18 CIA-50 bioclipse: ospjuth * r6623 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (17 files in 4 dirs): Added preprocessing steps and redesigned moleculerResource.
11:19 edrin i am not allowed to connect my laptop or install software
11:19 olas :-(
11:19 CIA-50 bioclipse: ospjuth * r6624 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/ (MoleculeResourceType.java impl/MoleculeResourceTypeImpl.java): Removed unused classes.
11:20 olas stupid subclipse.
11:20 olas 3 commits needed instead of one
11:20 olas karma
11:20 zarah olas has a karma of 19
11:20 olas :-(
11:20 CIA-50 bioclipse: ospjuth * r6625 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/ (MoleculeResourceType.java impl/MoleculeResourceTypeImpl.java): Re-added redesigned classes.
11:20 olas should be over 80
11:20 egonw karma olas
11:20 zarah olas has a karma of 19
11:20 edrin karma
11:20 zarah edrin has a karma of 7
11:20 egonw karma
11:20 zarah egonw has a karma of 2
11:20 edrin ?
11:20 edrin aha
11:21 * edrin stressed
11:21 olas karma jonalv
11:21 zarah jonalv has a karma of 24
11:21 olas karma masak
11:21 zarah masak has a karma of 19
11:22 olas @tell masak we should have a top list available on a URL ranking people by karma
11:22 zarah Consider it noted.
11:31 CIA-50 bioclipse: ospjuth * r6626 /bioclipse2/trunk/plugins/net.bioclipse.qsar.edit/ (16 files in 5 dirs): Updated edit code for new QSAR model with preprocessing steps.
11:35 edrin karma
11:35 zarah edrin has a karma of 7
11:35 masak olas: with all due respect, I think that a top list of karma goes against the intended use of karma, which is motivation for social good, not motivation to get karma
11:36 olas ok
11:36 edrin hm
11:36 olas just a proposal :-)
11:36 masak olas: re scripting and import *: I'm not sure what that means
11:36 masak but I remember that bc1 had it
11:36 olas to be able to run all java classes in javascript
11:36 masak I think it's a good idea if it does not cause chaos :)
11:36 edrin it does not
11:36 olas it certainly is very important
11:37 masak then I think it's a good idea
11:37 olas or was in bc1
11:37 masak edrin: would you be able to guide me through how to add this to bc2?
11:37 masak or maybe just point me to the relevant bc1 classes?
11:37 olas but it could also be replaced by the use of managers
11:37 olas I am not sure
11:37 edrin masak: did you add the scriptingTools to bioclipse2 code?
11:38 olas edrin: no, we use managers in bc2
11:38 masak edrin: no. completely redesigned.
11:38 edrin ?
11:38 * jonalv looks innocent...
11:38 masak edrin: what olas said.
11:38 olas jonalv: please explain to edrin how we inject code in bc2
11:38 olas as you are guilty of this
11:39 masak :)
11:39 olas (which, btw, works very good!
11:39 masak Bioclipse: where blame is always on target
11:39 jonalv hm, edrin we only have objects in the js environemnt
11:39 olas a good slogan
11:39 masak jonalv++ # doing magick in our code
11:39 jonalv so we don't have any (masak, right?) static imprts att all...
11:40 masak right.
11:40 olas I see an XWSManager coming along
11:40 jonalv Off course we could just do it but do we wan't too?
11:40 jonalv I don't know...
11:40 olas with methods to discover and run services
11:40 masak jonalv: neither do I
11:40 masak that's what I meant by "if it does not cause chaos"
11:40 olas we have a situation here
11:41 masak yay!
11:41 olas edrin wanät low-level scripting
11:41 olas want's
11:41 edrin yes
11:41 masak low-level?
11:41 jonalv We have an extension point where manger objects get's into js
11:41 olas not just manager + javascript
11:41 masak why?
11:42 olas he want's to call java classes directly in javascript
11:42 masak what's wrong with the perfect lie we're providing as-is in bc2?
11:42 masak :)
11:42 olas that means you have to wrap java code in manager calls
11:42 edrin what is the advantage of a manager? what is a manager? wikipage?
11:42 masak edrin: hold on, I'll get it for you
11:42 olas jonalv: Where did you write docu?
11:43 jonalv a manager is an object containing business code.
11:43 jonalv I think masak is fining it now
11:43 masak http://wiki.bioclipse.net/index.php?tit​le=General_design_model_for_Bioclipse2
11:43 zarah masak's link is also http://tinyurl.com/6byknp
11:43 masak it's the first diagram that's important
11:44 masak sorry about the size of it -- the server doesn't have thumbnail software installed
11:44 masak that green part is where all the actions take place in Bioclipse
11:44 edrin ok
11:44 masak for that to work, code that manipulates things has to reside in managers
11:45 CIA-50 bioclipse: ospjuth * r6627 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar.ui/src/net/bioclipse/qs​ar/ui/editors/MoleculesPage.java: updated for new moleculeresource syntax.
11:45 edrin i have nothing against these managers, it makes handling data much more easy
11:45 jonalv edrin: Do you feel that that answered your question?
11:45 masak edrin++
11:45 edrin sure
11:45 masak one advantage is, that you can then call your methods both from the GUI and from scripts
11:45 jonalv these managers get's set up by Spring and can be AOP empowered
11:46 masak magick
11:46 edrin AOP?
11:46 masak Aspect-Oriented Programming
11:46 jonalv Right now masak++ is working on a way to wrap manager calls into Eclipse jobs by simply annotating them with @job
11:46 masak edrin: it basically means that you don't mess up your code with orthogonal concerns
11:46 masak for example, logging is an orthogonal concern
11:46 masak AOP enables you to put logging code all in one place
11:47 jonalv (we don't do that for logging though...)
11:47 edrin but how to generate GUI fr a manager? I mean, a manager can hold *whatever* functionality. how do you automatically parse a manager to GUI?
11:47 edrin ,
11:47 jonalv you don't
11:47 masak edrin: that's handled elsewhere, in GUI code
11:47 edrin ah ok
11:47 masak the manager just acts out instructions
11:48 masak actually, there are some unresolved design issues there, I think
11:48 masak for example, how to handle wizards
11:48 jonalv you push as much as possible from the gui down to the manager because that maeks it easy to run the code from the JS. But you still write everything by hand :)
11:48 masak yay!
11:49 edrin how do the managers get documented? i guess the aim is to (and the advantage of the managers to the users) write scripting docu for the managers and make them uniform
11:49 jonalv there is an annotation for each manager method that should document the method a little
11:49 jonalv so when you write: help cdk.loadmolecules
11:49 jonalv you get that help text
11:50 jonalv that's what we have yet
11:50 masak jonalv: theoretically, we could have AOP code that throws an exception unless the manager methods are not properly documented :P
11:50 masak s/not//
11:51 jonalv we sure could but...
11:51 masak yes.
11:51 edrin sounds good
11:51 edrin this help command
11:51 masak yes?
11:53 edrin why not import everything to the project? thus an advanced user may take advantage of all eclipse classes!?
11:53 masak edrin: I'm itrigued by your ideas, but I don't quite see the implications yet.
11:53 jonalv tab completions would get a bit wacky...
11:54 masak hehe
11:54 masak actually, I'm not sure it would
11:54 masak would the modules really end up in the js namespace?
11:54 jonalv besides, olas always tells us to design for the biologist and not the poweruser. That's probably why we haven't thought about it so far...
11:55 jonalv but try it out and see what happends :)
11:55 masak I'm not too worried that it would be too powerful. but I do worry about other sanity issues.
11:55 masak for example, what does it _mean_ to import eveything into a plugin?
11:55 masak is it frowned upon in some way?
11:56 masak will we lose the ability to do something else once we do that?
11:56 * olas likes to follow this discussion
11:57 jonalv masak: I think it's frowned upon yea. But on the other hand this sounds like a situation that calls for it...
11:57 jonalv As for loss of functionality I can't see what that would be...
11:57 masak that's because the consequences are difficult to foresee
11:58 masak ok, so why is it frowned upon, and why would this situation be one that calls for it enough to break the convention?
11:58 edrin in principle the result is that everything of bc is added to the classpath used by rhino.
11:58 jonalv but will all these things be imported into the rhino environemnt too? Is there a heavy weght issue there?
11:58 edrin no
11:59 masak not to mention possible collisions
11:59 edrin btw. it took me ages to find out how to do this ;)
11:59 masak edrin: I remember.
11:59 masak it was just when I started out on bc that this was discussed
11:59 edrin masak: collisions are possible, indeed
12:00 jonalv I am sorry I feel like someone stopping edrin++ from doing cool things. I don't want that
12:00 jonalv I want cool things
12:00 masak edrin: by all means, try it out on your local setup
12:01 masak if everything seems to work, commit it and we here in Uppsala will try it out too
12:01 masak if we think it's sane, we might keep it :)
12:03 edrin sure
12:06 masak this is basically just to make sure that changes in those parts of the code are not inconsistent with the already-made plans for scripting. basically, everything you commit will be accepted if it doesn't clash.
12:06 edrin sure
12:18 CIA-50 bioclipse: ospjuth * r6628 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (4 files): Added a stub to a descriptors page. Nothing populated yet.
12:19 CIA-50 bioclipse: ospjuth * r6629 /bioclipse2/trunk/plugins/net.bioclipse.​qsar.edit/src/net/bioclipse/qsar/provide​r/MoleculeResourceTypeItemProvider.java: Missing commit from edit code generation.
12:32 CIA-50 bioclipse: carl_masak * r6630 /bioclipse2/trunk/plugins/ (3 files in 3 dirs):
12:32 CIA-50 bioclipse: [Job.java] created new annotation
12:32 CIA-50 bioclipse: [CreateJobAdvice.java] now wraps only those methods
12:32 CIA-50 bioclipse:  annotated by @Job
12:32 CIA-50 bioclipse: [CDKManager.java] added @Job annotations
12:49 CIA-50 bioclipse: jonalv * r6631 /bioclipse2/trunk/plugins/ (7 files in 4 dirs): Lazy loading of children from sdf files. Next step is that we want them to be organized in folders. This might be trickier perhaps...
13:07 CIA-50 bioclipse: jonalv * r6632 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.ui/src/net/bioclipse/cdk/ui/​views/MoleculeContentProvider.java: Fixes problem with sdf files sometimes seeming to not contain any children
13:20 masak egonw: I'm thinking how best to portray the aromatic bond in the outline of the JCP editor.
13:20 masak first I made an aromatic ring, but it didn't come out right, so then I started trying to depict the bond itself (which is what the icon should do, after all)
13:21 masak so I did a sort of mix between a single and double bond, making part of the bond transparent
13:21 masak is this chemically acceptable? or is there a better way?
13:28 egonw a ring is common
13:29 egonw i.e. normal six ring + a round ring in the middle
13:29 masak egonw: even for a single bond?
13:29 egonw huh?
13:29 egonw yes
13:29 masak the icons are depicting the individual bonds
13:29 egonw an aromatic system is always a ring
13:30 masak I've now arrived at this: it looks like the single-bond icon with a ring on top
13:30 masak acceptable?
13:30 egonw so you do all single + central ring for the isolated rings
13:30 egonw http://en.wikipedia.org/wiki​/Image:Benzene_structure.png
13:30 masak not sure I understand that.
13:30 zarah egonw's link is also http://tinyurl.com/5uhx8q
13:30 egonw third image
13:30 egonw that's the one you need
13:31 masak hm -- it's tough to fit that kind of detail into an icon
13:31 masak but I'll try
13:31 masak if I fail, I'm pretty happy with my current compromise
13:31 masak egonw: I'll commit so you can have a look at it
13:33 CIA-50 bioclipse: carl_masak * r6633 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk10.jchempaint/icons/ (17 files):
13:33 CIA-50 bioclipse: [jcp icons]
13:33 CIA-50 bioclipse: * moved all icons one pixel down
13:33 CIA-50 bioclipse: * tried out a new aromatic icon
13:34 maclean What about a straight line, with a curve below?
13:35 egonw for a single bond, a single solid line, with a dashed line is not uncommon
13:36 masak huh? solid+dashed for a single bond?
13:36 masak ah, you mean a single aromatic bond :)
13:36 masak yes, I tried that too
13:36 masak it didn't stand out enough from the double bond version
13:38 egonw ack
13:38 olas egonw: ok
13:39 olas egonw: ok to 15 mins
13:48 jonalv Would anyone have an idea of how I can hook up a comparator to the CNF?
13:48 olas to sort?
13:49 jonalv yea
13:49 olas you can in treeviewer use setSorter
13:49 olas I suspect you can do that in CNF too
13:49 jonalv yea but how...
13:49 olas no idea
13:51 olas jonalv: have you seen this?
13:51 olas http://scribbledideas.blogspot.com/2006/0​7/response-to-comments-and-status-on.html
13:51 zarah olas's link is also http://tinyurl.com/6akfs7
13:51 olas "At what point should I starting doing the work of building my nodes for my common navigator? I wanted to tie in the IProgress monitor and jobs to prevent blocking."
13:53 olas it seems possible to add sorters
13:53 olas I just donät know how
13:54 olas jonalv: get the source of the CNF and look at the EP
13:54 jonalv what EP?
13:54 olas dunno
13:54 olas check all in CNF
13:55 jonalv I don't know how to get the source for things...
13:55 olas do it again, shall we?
13:55 olas show view > plugins
13:55 olas right-click CNF plugin, shoose import as.. > source
13:57 jonalv okey gonna try that
13:57 jonalv but how do I know which plugin?
13:58 olas starts with org.eclipse.ui
13:58 jonalv k
14:01 * jonalv didn't find anythig
14:01 olas ?
14:01 olas mom
14:04 CIA-50 bioclipse: carl_masak * r6634 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/icons/bond_aromatic.png: [icons] new bond_aromatic.png
14:04 masak egonw: actually, that one turned out quite nice. thanks for the tip :)
14:05 olas jonalv: it's called commmonsorter
14:05 olas commonSorter
14:05 jonalv huh?
14:05 jonalv what the package?
14:05 olas child of navigatorContent
14:05 jonalv what does that mean?
14:05 olas org.eclipse.ui.internal.navigator.sorters
14:06 jonalv is that an extestion point?
14:06 olas no, a package
14:06 olas (you asked for a package)
14:06 jonalv I thought I asked how to do it...
14:07 olas jonalv (4:09:17 PM): what the package?
14:07 olas in your navigatorContent extension, add a commonSorter
14:07 olas ok?
14:08 olas in your plugin.xml you have navigatorContent, right?
14:08 jonalv okey
14:08 jonalv I see now
14:08 jonalv thanks
14:08 olas nop
14:24 CIA-50 bioclipse: jonalv * r6635 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Added number on sdfelements and made sorting of them correct
14:36 jonalv Could someone test the new way sdf files are extended and see if that is similar to what we want?
14:39 olas I can
14:39 * olas is updating and downloading a large sdfile
14:40 olas egonw: what xml format is pubchem using?
14:40 olas CML?
14:42 egonw no
14:43 egonw custom format
14:43 egonw based on there ASN.1 representation
14:43 olas why?
14:43 egonw CDK has readers
14:43 olas ok
14:43 egonw ask them
14:47 olas jonalv: I get wrong number of arguments
14:48 jonalv olas: update everything
14:48 olas will do
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15:23 malick left #bioclipse
15:31 CIA-50 bioclipse: jonalv * r6636 /bioclipse2/trunk/plugins/net.bioclipse.struct​uredb/src/net/bioclipse/structuredb/business/ (2 files): removed consoledecorated structuredbmanager. No more console progressmonitor
15:53 jonalv egonw: Can you help me?
15:54 egonw I can try
15:54 jonalv I have cdk error when running structuredb tests
15:54 jonalv I also have problems getting the path to a file...
15:55 jonalv Do you have structuredb and structuredb.tests in your eclipse?
15:57 egonw nope
15:57 egonw and I don't have time to install that at this moment...
15:57 egonw what error do you get?
15:58 jonalv mom
15:59 jonalv http://pastebin.com/d1ff5e844
15:59 edrin egonw: what are you doing?
15:59 egonw in general?
16:00 egonw or triggered by some event?
16:00 egonw edrin: see #metware
16:00 jonalv I have it on a bunch of tests
16:00 egonw jonalv: sounds like a missing class
16:01 egonw I'd guess the jumbo libs are not visible
16:01 jonalv okey
16:01 jonalv what can I do about that?
16:02 egonw import them?
16:02 jonalv uhm import what where?
16:02 jonalv is this in cdk there is something wrong?
16:05 egonw no, I think net.bioclipse.structuredb should import it
16:06 egonw is net.bioclipse.structuredb importing nb.cdk?
16:06 egonw or what's it called again
16:06 egonw depending on the plugin?
16:06 jonalv yes
16:06 egonw ok, then nb.cdk does not export the jumbo classes, maybe?
16:06 jonalv net.biocklispe.strucutedb depends on org.openscience.cdk
16:06 egonw how's that working again...
16:07 egonw jonalv: not sure
16:07 jonalv do you know the name of those jumbo things?
16:07 jonalv the package names
16:07 maclean org.xmlcml...
16:08 egonw org.xmlcml.cml
16:08 egonw ah :)
16:08 maclean I am also fighting with jumbo.
16:10 jonalv I tried exporting them  but that didn't have any effect
16:10 egonw jonalv: sorry, no idea
16:10 egonw the jar/ folder is in the bin.includes
16:10 egonw anyway...
16:10 egonw the problem occurs inside the cdk plugin
16:11 egonw CMLMolecule cmlMolecule = new CMLMolecule();
16:11 jonalv yes
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16:11 egonw jonalv: is structuredb doing any spring stuff?
16:12 jonalv egonw: ALOT
16:12 egonw could that be causing the problem?
16:12 jonalv :)
16:12 jonalv I have no idea
16:12 jonalv for he moment
16:12 jonalv I don't think oit should though
16:12 jonalv it worked before
16:12 egonw right
16:12 jonalv And I ahven't changed anything since
16:12 egonw so, check the diffs for the .classpath etc
16:12 egonw olas has
16:12 jonalv actually I ahven't touched structeedb since it worked  :)
16:13 egonw which revision was that?
16:13 jonalv cdk changes all the time though...
16:13 jonalv revision of cdk or bioclipse?
16:13 egonw both :)
16:13 egonw date is fine too
16:14 jonalv beginning of July I think
16:15 edrin what will you work on in uppsala, egon?
16:15 egonw chemoinformatics in bioclipse
16:16 edrin anyone knows when ola will finish his phd ?
16:16 egonw next year
16:16 edrin and then?
16:21 jonalv I tried exporting everything from cdk but that didn't help...
16:23 egonw no clue
16:23 egonw I've got void knowledge of spring things
16:25 jonalv egonw: I doubt it's a Spring thing
16:26 jonalv it seems reasonable it could be an OSGI classloeder issue though...
16:27 jonalv but since cdk has switched jumbo version since then I guess something must be different now...
16:27 jonalv with that
16:27 egonw yeah
16:27 egonw sounds logical
16:28 egonw therefore, check the 'svn log's
16:28 jonalv for cdk?
16:28 egonw yeah, guess so
16:29 jonalv I don't really know what to look for more than that...
16:30 egonw svn diff -r 11474:HEAD .classpath
16:30 jonalv huh?
16:30 jonalv .classpath in cdk?
16:31 egonw right
16:32 jonalv is that at the root?
16:32 egonw yeah, but don't see anything that might cause the problem
16:32 egonw because I don't think @sourcepath can cause this problem
16:34 jonalv it would be intresting to know if it's mac realated
16:34 jonalv I have had xml problems with mac before...
16:44 jonalv WEll I am headning homw. Will have to look more at that some other day...
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