Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-30

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All times shown according to UTC.

Time Nick Message
05:52 sneumann__ joined #bioclipse
06:28 egonw_ joined #bioclipse
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06:40 stain joined #bioclipse
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07:58 egonw @tell jonalv http://usefulchem.blogspot.com/2009/10/​chemistry-in-second-life-paper-in.html
07:58 zarah egonw's link is also http://tinyurl.com/yk258ma
07:58 zarah Consider it noted.
08:03 Gpox joined #bioclipse
08:06 Gpoks joined #bioclipse
08:11 Gpox joined #bioclipse
08:36 jonalv joined #bioclipse
08:38 egonw jonalv: ping
08:38 egonw jonalv: did you work on the jmol manager?
08:39 jonalv egonw: yes
08:39 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
08:39 egonw perhaps fixing it to have JmolManager not extend IJmolManager ?
08:39 jonalv egonw: yes
08:39 egonw ok
08:39 jonalv zarah: just tell me
08:39 zarah jonalv: 40 m 38 s ago, egonw said http://usefulchem.blogspot.com/2009/10/​chemistry-in-second-life-paper-in.html
08:39 egonw you forgot to fix the jmol.test plugin
08:39 egonw will do so now
08:39 jonalv egonw: oh, sry
08:40 egonw you did run the unit tests when you patched the manager, right?
08:40 egonw right?
08:40 * jonalv tries to look innocent
08:40 egonw right
08:43 egonw but you did add a unit test for the new code, right?
08:43 CIA-54 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r5b01485 / plugins/net.bioclipse.jmol.test/src/net/​bioclipse/jmol/test/JmolManagerTest.java : Fixed a compile error introduced by 2f14a721b6252e2d3d07247b57e652fb777eafe6, which fixed the JmolManager not to extend IJmolManager - http://bit.ly/1mBH4K
08:46 jonalv egonw, reminf me again what the new code was?
08:46 egonw git show 2f14a721b6252e2d3d07247b57e652fb777eafe6
08:47 egonw (try to do that in subversion!)
08:47 jonalv fatal: bad object 2f14a721b6252e2d3d07247b57e652fb777eafe6
08:48 jonalv egonw: this is in chemoinformatics right?
08:48 jonalv ah I was missing a fetch call
08:49 jonalv egonw: no I did not. (trust the anarchy?) How would you write such a test?
08:55 olass joined #bioclipse
08:55 jonalv olass: hi
08:55 olass o/
08:56 egonw jonalv: you can test jmol scripting, by testing from the state of the model
08:57 egonw hi olass
08:57 olass hi egonw
08:57 egonw we'll likely have a guest in December
08:57 egonw working on CDK-Taverna
08:57 * jonalv would prefer to stay as far away from the Jmol model as possible. It is strange and undocumented
08:58 egonw a student
08:58 olass egonw: sounds interesting
08:58 egonw yes, should be
08:58 egonw he'll update the current CDK-Taverna work
08:59 egonw and we'll talk about Taverna2 plugins
09:09 egonw good for me to clean up the XMPP plugin
09:10 olass yup
09:16 * egonw is noticing lack of manpower to maintain bioclipse stuff
09:16 egonw and seriously gonna look at the GUI testing toolkit Stefan is using for JChemPaint
09:17 jonalv egonw: that sounds intresting and expensive
09:17 egonw (post 2.2)
09:17 egonw expensive?
09:17 egonw money or time?
09:17 jonalv yea, GUI testing usually is expensive
09:17 jonalv money
09:17 egonw how so?
09:18 jonalv egonw: the companies making the tools charge good for them
09:19 egonw how expensive is the toolkit that shk3 is using?
09:19 * jonalv has no idea
09:19 jonalv I don't know wht toolkit he is using
09:19 egonw then why do you think it is expensive then?
09:19 jonalv I am just referring to the ones I ahve heard about
09:19 egonw ah, interesting
09:19 jonalv I did some googling for GUI testing some time ago
09:26 egonw did you summarize that somewhere?
09:27 jonalv egonw: nope
09:27 jonalv egonw: how can we calcualte a tanimoto score for BitSets?
09:27 jonalv egonw: are these bitsets fingerprints?
09:28 egonw these refers to?
09:28 jonalv egonw: (is that the definition for tanimoto score btw?)
09:28 egonw that refers to?
09:28 egonw tanimoto is defined for bit sets
09:28 jonalv egonw: I am looking at tanimoto methods in cdkmanager and I am trying to uderstand when the different ones are used
09:28 egonw basically the same as the jaccard distance measure
09:57 egonw mmm... wondering if the kabsch alignment is now operational...
09:57 egonw (manager level)
10:12 mgerlich joined #bioclipse
10:33 * egonw finds himself copy/pasting jonalv's append(IFile) code
10:34 jonalv egonw: intresting, what did I do wrong?
10:34 egonw where did I say you did something wrong?
10:35 egonw if there was something wrong, I would not be copy/pasting ... :)
10:35 jonalv egonw: okey you lsot me
10:35 egonw well, we do have some coding style differences...
10:35 jonalv egonw: copy pasting is wrong, no?
10:35 egonw your code hurts my eyes
10:35 egonw yes, I should file a bug report to clean up this code after submission of the reviewer comments
10:35 jonalv egonw: oh? that's sad. Many peoples code hurts my eyes though...
10:36 jonalv egonw: what about it hurts?
10:36 egonw redundant whitespace
10:36 egonw short meaningless variable names
10:38 egonw append( "\n" )
10:39 egonw creating a String for just a single char
10:41 jonalv egonw: this is intresting
10:43 egonw http://www.swat4ls.org/2009/progr.php
10:43 zarah egonw's link is also http://tinyurl.com/ylsc59o
10:44 jonalv 1995 called, they want their light blue web page background color back
10:45 egonw :)
10:45 egonw wondering how to open a JmolEditor with an IMolecule
10:46 jonalv egonw: save it as a temp file
10:46 jonalv egonw: that's what olass told me when I asked the same question
10:46 egonw but then I need to save it in /Virtual, not?
10:46 egonw to allow. ui.open("/Virtual/foo.bla", "foo.bar.JmolEditor")
10:50 jonalv egonw: uhm well I meant after that.
10:50 egonw ah, right
10:50 egonw but that's not what I want
10:50 jonalv ui.open(IMolecule m, "foo.bar.JmolEditor") does something liek that I think
10:50 egonw I have a List<IMolecule> and want to visualize that in Jmol
10:51 egonw ok, that would be good enough for me...
10:51 egonw I'll test if that works here too
10:51 jonalv egonw: so save all of them as a temp files and then open the first and load append the rest I think
10:51 egonw yes, perhaps
10:51 jonalv it's not ideal but I think it is what we must do
10:51 egonw but then I still need to open the editor...
10:51 egonw I need something like:
10:51 egonw jmol.load(IMolecule)
10:52 egonw and jmol.load(List<IMolecule>)
10:52 egonw and jmol.append(IMolecule)
10:52 jonalv egonw: I think you should do:
10:52 jonalv jmol.open(file1)
10:52 egonw define file1
10:52 egonw I don't have an IFile
10:52 egonw I have a IMolecule
10:52 jonalv for ( f : files) { jmol.append(f)};
10:53 egonw and don't want to save it in /Virtual
10:53 jonalv files here would be tempfiles
10:53 egonw no, there's that IFile again...
10:53 jonalv no not IFile
10:53 jonalv real files
10:53 jonalv "real"
10:53 jonalv :)
10:53 egonw can we handle 'real' files in JavaScript then?
10:53 jonalv egonw: hm
10:53 samuell joined #bioclipse
10:53 jonalv egonw: do we need to? Don't we jsut hadnle IMolecuels in JS?
10:54 egonw jonalv: that's where I am going
10:54 egonw you started about files
10:54 egonw :)
10:54 egonw hi samuell
10:54 egonw jonalv: hence, I need jmol.load(IMolecule)
10:54 jonalv and then when jmol are about to open the IMolecule you save it to a tempfile and let jmol open that temp file
10:54 egonw but we do not have that yet
10:54 egonw ok, will try that with ui.open(, "jmolEditor")
10:55 egonw ah, crap
10:55 jonalv egonw: I think that method is always going to have to be implemented using temp files
10:55 egonw no, that won't work
10:55 egonw then we still need a tmp file in /Foo
10:56 jonalv egonw: as far as I know jmol need a file to read from
10:57 samuell egonw: Hi egon
10:58 masak joined #bioclipse
11:00 * samuell had a hard time getting to sleep at all :(, and decided to rest out...
11:01 * masak mumbles inaudibly
11:01 masak '...someone keeps putting good literature by my bedside...'
11:02 egonw "Load jmoo with a file" ?????
11:02 masak jmoo? :)
11:03 jonalv jmol!
11:03 egonw someone felt rather cowish
11:04 jonalv sometimes I feel that IRC is not the best way to communicate
11:04 jonalv ...quite often actually
11:05 jonalv egonw: but did you solve it now?
11:06 egonw the jmoo ?
11:06 egonw no
11:06 egonw I leave it there for people to enjoy running 'git blame' :)
11:07 egonw http://scratch.mit.edu/projects/danpengo/712779
11:07 zarah egonw's link is also http://tinyurl.com/ygs8xon
11:07 egonw mmm... I wish Java was working on my laptop :)
11:08 masak Java's not working on your laptop?
11:08 egonw not in the browser
11:08 egonw and I am too lazy to fix it
11:08 egonw who knows...
11:08 egonw maybe the kubuntu upgrade does
11:08 egonw it's something trivial...
11:08 egonw but not depending on it, so no priority
11:09 egonw oh... wow
11:09 egonw just discovered a new EP
11:09 egonw editorShortname ??
11:09 egonw @wiki editorShortname
11:09 egonw zarah: @wiki editorShortname
11:09 zarah egonw: you've just exceeded my capabilities :/
11:10 egonw yes, it seems so
11:10 egonw @tell masak feature request: @wiki so search the bioclipse wiki
11:10 zarah Consider it noted.
11:10 masak @msg
11:10 zarah masak: 13 s ago, egonw said feature request: @wiki so search the bioclipse wiki
11:10 egonw s/so/to/
11:11 masak egonw: problem: MediaWiki's built-in search is crappy.
11:11 * egonw thinks we should have a wiki template for extension point too
11:11 masak hm, meant to say "unbelievably crappy".
11:11 egonw samuell: can you please (at your next convenient time) look at the Feature template and let me know why the URL for Update Site is not working?
11:12 jonalv google site:wiki.bioclipse.net editorShortname
11:12 zarah jonalv: No hits.
11:12 jonalv google site:wiki.bioclipse.net editor
11:12 zarah jonalv: http://wiki.bioclipse.net/index.php%3Ft​itle%3DHow_to_write_a_Multi_Page_Editor
11:12 egonw jonalv++ (very good thinking!)
11:12 * jonalv heads out hunting for food
11:12 samuell egonw: Ok, in the wiki?
11:13 egonw @msg masak please make @bcwiki shortcut for "@google site:wiki.bioclipse.net"
11:13 zarah egonw: You have no new messages.
11:13 egonw samuell: yes
11:13 egonw @tell masak please make @bcwiki shortcut for "@google site:wiki.bioclipse.net"
11:13 zarah Consider it noted.
11:13 masak egonw: why are you sending messages to me instead of addressing me directly?
11:13 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
11:13 masak @clear
11:13 zarah masak: Messages cleared.
11:13 egonw @tell masak I have no clue
11:13 zarah Consider it noted.
11:13 masak @clear
11:13 zarah masak: Messages cleared.
11:14 samuell egonw: On the speclipse, and Bioclipse SDK articles, you're not giving that variable any value, in the template call
11:14 egonw sure
11:14 egonw did not update those, indeed
11:15 egonw check one of the two cheminfo's
11:15 egonw I added it to one of those two
11:15 egonw but yes...
11:15 egonw how do I make the template have the field optional...
11:15 samuell Ok
11:16 samuell egonw: Yeah, that's something we should do. I'll look into how to do that
11:16 samuell egonw: Ohterwise, if you're just giving an url, you don't need to enclose it in [ ]
11:16 samuell egonw: It will be recognized as a link anyway
11:16 egonw ah, ic
11:16 egonw ok, thanx
11:17 egonw all: please update your feature pages to use the feature template
11:18 egonw samuell: btw, the link to the Features index page
11:18 egonw always says:
11:18 egonw this page has not been created yet...
11:18 egonw do you know why that is?
11:18 samuell Yeah, because it isn't :)
11:18 samuell You have to edit it and put some content there.
11:19 samuell On the other similar pages I put a short info message + a link to the template
11:19 samuell ...used to categorize into that category.
11:19 egonw ah, ic
11:19 egonw it said 'this is a preview'
11:19 egonw after which I saved
11:19 egonw but that did not help
11:19 egonw I'll try adding some manual content
11:20 samuell Ah, ok. Well, it's indeed a bit confusing
11:20 CIA-54 bioclipse: carl_masak * r11736 /bot/trunk/zarah.pl: [zarah] now has a new command @bcwiki
11:20 masak zarah: reboot
11:20 zarah joined #bioclipse
11:20 egonw @bcwiki cheminformatics
11:20 zarah egonw: http://wiki.bioclipse.net/index.php%3F​title%3DBioclipse_2.0_Cheminformatics
11:20 egonw nice :)
11:20 egonw masak++
11:20 egonw thanx!
11:20 masak np :)
11:21 * masak likes adding features to zarah
11:21 masak take a look at that patch and see how easy it was. :)
11:21 egonw wow that was easy
11:22 * egonw lives up to masak's expectations :)
11:22 masak zarah++
11:22 masak Smart Girl is more or less in the sweet spot of refactoring right now.
11:22 masak I sometimes wish she had state, but it's also kinda good that she doesn't...
11:23 egonw sometimes it's good not to know what you did last nite
11:27 masak I'll take your word for it.
11:28 egonw no worries
11:28 egonw it's just heresay
11:28 egonw I'd say, smart girls know do know the state of there sweet spots
11:28 egonw even the morning after
11:29 masak nod.
11:29 egonw damn... stupid Jmol manager
11:29 egonw stupid Bioclipse2 for not having IJmolMolecule
11:29 egonw stupid JmolEditor... :(
11:32 egonw olass: ping
11:32 egonw olass: urgently need your advice
11:37 samuell egonw: Conditional output of template variables is done like so:
11:37 samuell {{#if: {{{Conditional variable|}}} | Show this if variable is set to sth | Show this if variable is empty }}
11:37 samuell So for example:
11:37 samuell {{#if: {{{Conditional variable|}}} | '''Nice label:''' {{{Conditional variable|}}} | }}
11:38 samuell or, more correctly:
11:39 samuell {{#if: {{{Conditional variable|}}} | '''Nice label:''' {{{Conditional variable}}} | }}
11:39 egonw ok, thanx
11:40 egonw jonalv: http://gist.github.com/222280
11:41 egonw or as one-liner:
11:41 egonw jmol.load(cdk.generate3dCoord​inates(cdk.fromSMILES("CCC"))
11:49 egonw olass: when you are back from lunch... please ping
11:56 stain why not a few more {{{{s ? :)
11:57 egonw please file a feature request at bugs.bioclipse.net :)
11:57 egonw stain: you saw the KNIME/GPLv3 news?
12:02 stain yeah
12:03 stain good news, I guess
12:03 egonw for the Open Source (bio|chemo)informatics scene at least
12:03 egonw more competition is good for users
12:04 egonw I hope this will not result in a bio- and chemoinformatics divide
12:04 egonw (but don't really expect that)
12:05 egonw now operational: http://wiki.bioclipse.net/inde​x.php?title=Category:Features
12:05 zarah egonw's link is also http://tinyurl.com/yfbpgjd
12:14 egonw oh, f**k it...
12:14 egonw while waiting for olas to return
12:14 egonw why not implement JmolMolecule
12:14 egonw and be done with it'
12:32 egonw ok, first full draft for Kabsh: http://gist.github.com/222305
12:34 egonw no GUI
12:34 egonw yet, at least
12:34 egonw but first need to talk to Ola
12:36 jonalv egonw: does that kabsh code work?
12:36 egonw almost
12:36 egonw there is a problem with proper rotation of the first compound
12:36 egonw but the rest is nicely aligned it seems
12:37 egonw the first is special, because it is both a reference and needs rotation
12:37 jonalv cool
12:37 jonalv egonw++
12:37 egonw no tmp files
12:37 egonw but, there is one tricky commit
12:37 egonw which I need olas for
12:39 egonw samuell: can you have a look at http://wiki.bioclipse.net/​index.php?title=CDK_plugin
12:39 zarah egonw's link is also http://tinyurl.com/yz2v7cy
12:39 egonw the whole page is in the box now :)
12:40 samuell Oh... I know... I't a bug that I made, which i obviously haven't fixed in all templates
12:40 samuell It's an unclosed div tag
12:40 egonw no, apparently not :)
12:40 samuell Check now
12:41 samuell refresh, I  mean
12:41 egonw ok, good!
12:41 jonalv samuell: I am a bout to add some stuff to a "How to make a manager 2" om the wiki. I jsut noticed some template stuff on that page and there is a "Last updated" field. Do I ahve to update that manually?
12:42 samuell jonalv: Yeah, right now you have.
12:42 samuell jonalv: Though I will look at some way to fix that
12:42 jonalv oki
12:42 egonw samuell++ (for his great mediawiki contributions!)
12:42 samuell thx
12:43 jonalv oh, yea samuell++
12:43 egonw @karma samuell
12:43 zarah samuell has a karma of 13
12:43 samuell It makes me access all the great content there more easily
12:43 egonw @karma
12:43 zarah egonw has a karma of 140
12:43 egonw ummm...
12:43 egonw no, that's not what I wanted...
12:43 jonalv @karma
12:43 zarah jonalv has a karma of 168
12:44 egonw masak: would be nice if there was a way to get a hall of fame of karma...
12:44 egonw @karmahof or so
12:44 masak egonw: nope.
12:44 masak not doing that one.
12:44 egonw which lists all known karmas
12:44 egonw why not?
12:44 jonalv egonw: that's not how karma works
12:44 masak because it's not a competition.
12:44 egonw oh...
12:44 egonw hahahahhaa
12:44 masak jonalv++ # groks it
12:44 egonw no, indeed not
12:44 egonw hahahahhaa
12:44 egonw hahahahhaa
12:44 egonw hahahahhaa
12:44 zarah hahahahhaa
12:44 egonw ROFL
12:44 masak /ignore egonw
12:45 egonw swedes are so funny
12:45 * egonw is still recovering from the cultural shock
12:45 jonalv oh I am not sure it's a swedish thing.
12:45 jonalv or is it?
12:45 egonw yes, it is
12:45 egonw or
12:45 jonalv hm...
12:45 masak no, karma works this way all over IRC.
12:45 egonw perhaps the Dutch are overly competitive :)
12:46 egonw masak: please elaborate
12:46 egonw what's the point of @karma being numerical and not boolean than?
12:46 egonw I'd vote for:
12:46 egonw @karma
12:46 zarah egonw has a karma of 140
12:47 egonw zarah: "egonw has karma"
12:47 masak egonw: karma is part of a system wherein you tie accomplishments to your online avatar.
12:47 masak that's a good thing.
12:47 egonw it's like temparature?
12:47 masak it's bordering another type of system wherein the objective is getting more points than others.
12:47 egonw you're not supposed to compare it?
12:48 masak well, it's not meaningful to do so.
12:48 samuell jonalv: I fixed it now... it was too easy
12:48 masak except in the sense that new users tend to have karma near 0.
12:48 egonw yeah, why then?
12:48 masak a well-functioning individual will tend to get more karma as time goes by.
12:48 jonalv samuell: but what happend when I try to save my page now?
12:48 samuell all: So, now you don't have to update the dates anymore (The date you set will not be shown anyway)
12:48 masak the actual number is more of an indication of how long the bot has been online.
12:49 egonw masak: why not @karma random() to start with ?
12:49 samuell jonalv: ?
12:49 jonalv samuell: nm
12:49 samuell 2009-10-10 .. hmm...
12:49 samuell Ic the problem
12:50 samuell Date settings of server doesn't seem ok?
12:50 masak egonw: I'm wondering whether you don't understand, or don't want to understand.
12:51 egonw no, I literally do not understand...
12:51 egonw in a world where there are so many things we can't measure
12:51 egonw and still compare
12:51 egonw we have something numerical but are not allowed to compare...??
12:51 egonw yeah, that breaks my logic
12:51 masak it's very easy to make a top-10.
12:51 samuell jonalv: Ok... no problem with the date.... but what happened?
12:52 masak it's technologically a no-brainer.
12:52 masak I mean, come on, it's Perl.
12:52 samuell jonalv: You had some problem to save the article?
12:52 masak I just don't think socially it's a good idea.
12:52 egonw true
12:52 jonalv samuell: nope I ahven't tried to save yet
12:52 masak I want to discourage the competition part of karma.
12:52 egonw we already have 'git blame' for that
12:52 masak at least at the level of top-10s.
12:52 samuell jonalv: Ok
12:53 masak egonw: the nifty thing about karma is that you can basically only increase it by being a productive member (or by cheating, like olass)
12:56 samuell egonw: By the way... what was "last updated" supposed to mean, for a feature e.g.? It is when the software was last updated, or the wiki page? (If the former, I guess it should not have automatic date stamping of the article on save)
12:57 samuell egonw: I went too fast and added it...
12:57 egonw samuell: not sure
12:57 samuell egonw: Maybe the last updated date of the wiki page is not that relevant
12:58 egonw well, it says something about how old the info on that page it...
12:58 egonw it's good that that is visible, I guess
12:58 samuell egonw: Ok... well, maybe we should change the label
12:58 samuell "Wiki page last  updated" ?
13:00 egonw yes, perhaps
13:00 samuell egonw: Ok, then I'll change it to that for now.
13:23 egonw 4 new H1N1 deaths in NL
13:23 egonw all young people, 3 with other health problems, 1 yet unknown
13:24 egonw flu season very early in NL too...
13:31 samuell egonw: What about conventions for predicates. Is "Has Author" or simply "Author" better? (See: http://wiki.bioclipse.net/index.​php?title=Bioclipse_on_Mac_OS_X )
13:32 zarah samuell's link is also http://tinyurl.com/yzc6o52
13:32 samuell egonw: I tend to like "HasAuthor" better, since it is very explicit
13:32 samuell egonw: But are there other aspects to think about?
13:33 samuell egonw: (See fact box of that page)
13:33 egonw hasAuthor tends to be prefered in the ontology community, I think
13:33 samuell egonw: Ok!
13:34 samuell egonw: Good then. (First letter capitalized by MW though)
13:34 egonw ack
13:45 egonw olass: ping
13:45 egonw olass: still not around?
13:47 olass egonw: pong
13:47 egonw I need your advice...
13:47 egonw in CDKMolecule there is getAdapter()
13:48 olass yes
13:48 egonw is there any harm in implementing CDKMolecule.getAdapter(String.class) to return a CML String?
13:48 olass hmm
13:48 olass I don't think so...
13:49 Gpox It is for conversion to JMolMolecule?
13:49 egonw I need it for this kabsch script: http://gist.github.com/222305
13:49 egonw Gpox: was just looking at that...
13:49 egonw it seems Jmol 11.8 is not able to 'save' files ...
13:50 olass egonw: why not use getCML()?
13:50 egonw Gpox: so, no step forward with JmolMolecule yet
13:50 egonw olass: because this is because of the JmolEditor
13:50 egonw and IEditor does not know about getCML()
13:50 olass I see
13:50 egonw so, when I tried:
13:50 egonw ui.open(IMolecule, "jmol")
13:50 olass you want no dep to cdk
13:51 egonw it said: don't recognize this format
13:51 egonw correct
13:51 olass egonw: yes, that is why we have no JmolMolecule
13:51 olass because
13:51 egonw and apparently the JmolEditor is calling getAdapter(String.class) on the CDKMolecule
13:51 egonw hence my request
13:51 olass egonw: I don't see any problems but Gpox is teh master of the Adapter pattern.
13:52 egonw Gpox: what do you think?
13:52 egonw Gpox: about CDKMolecule.getAdapter(String.class) returning a CML String serialization ?
13:55 egonw olass: btw, there are rather intruisive patches...
13:56 egonw perhaps slip the 2.2 release to get all this properly tested?
13:56 egonw we're breaking the freeze very much anyway
13:56 Gpox egonw: it sounds bad, and the JmolEditor dose no such thing as far as i can see
13:59 egonw it's actually UIManager
13:59 egonw line 176
13:59 egonw which relays a getAdapter(String.class) call
14:03 samuell egonw: Try adding this to your user page (when you have time):
14:03 samuell {{#ask: [[Category:Development tutorials]] [[has author::User:Egon Willighagen]]
14:03 samuell | ?applies to bioclipse version
14:03 samuell }}
14:03 samuell ("applies to bioclipse version" is the only property that gets semantically tagged right now)
14:04 Gpox if I understand correctly you want to open an IMolecule with jmol using ui.open(IMolecule, "jmol")
14:04 egonw Gpox: yes
14:04 egonw Gpox: for jmol.load(IMolecule)
14:05 egonw which opens a new editor
14:05 Gpox and why cant you use toCML() ?
14:06 egonw because there is no toCML() in IEditorInput
14:07 egonw this is magic in UIManager
14:07 egonw line 134ff
14:07 egonw 152 onwards in particular
14:07 egonw and relies on IBioObject
14:08 egonw which does not have toCML()
14:09 egonw of course we could add UIManager.open(IFoo, "editor") methods...
14:09 egonw but that does not sound right
14:09 egonw at least not better
14:10 egonw samuell: nice!
14:11 Gpox so you cant do ui.open(IMolecule, "jmol") right now?
14:11 egonw no
14:11 egonw not in the current 2.2.x branch
14:12 samuell egonw: So I skipped the "Articles maintained by {{{author}}}" category, since you can now combine things with queries instead.
14:12 egonw indeed
14:12 egonw samuell++
14:12 egonw which templates are so far semantically enriched?
14:12 egonw what did you do to make them such?
14:12 Gpox added fix for that in JmolEditor
14:12 samuell Only the development articles template so far
14:13 egonw Gpox: can you send me the patch?
14:13 egonw then I can rework my own patches
14:13 samuell egonw: I added [[has author::User:{{{Author}}}]] and [[applies to bioclipse version::{{{bioclipse version}}}]]
14:13 egonw ok
14:13 egonw easy enough
14:13 egonw :: has the special semantics, I assume ? :)
14:14 samuell egonw: Or [[has author::User:{{{Author}}}|]] and [[applies to bioclipse version::{{{bioclipse version}}}|]] so that they became invisible (pipes at the end).
14:14 samuell egonw: Yes, that divides the predicate (called "property" in SMW) and the object
14:14 Gpox can it go into 2.2.x going to push the drag to MolTable patches
14:15 egonw Gpox: can you repeat that?
14:15 egonw you're DnD patches are done too?
14:15 egonw so I can pull them right now?
14:15 * samuell going for lunch now
14:15 egonw I'm sort of stuck with the kabsch, until opening in Jmol is resolved
14:15 Gpox well drag to MolTable works, no internal drag in the MolTable itself
14:16 egonw ok, that sounds fair to me :)
14:16 Gpox I just need to pull in the latest and then push
14:16 egonw ok
14:28 * olass is in tel too much
14:35 Gpox egonw: sent pull request
14:35 egonw ok, thanx
14:38 * Gpox closes 151 firefox-tabs
14:40 egonw :)
14:41 * olass is trying to push net.bc.webservices into NWO
14:41 olass squeeze
14:42 jonalv olass: any problems or just much work?
14:42 olass mainly work
14:42 olass things just are not smooth, many places that can fail
14:43 CIA-54 bioclipse.core: jonalv master * rabff5d7 / (2 files in 2 dirs):
14:43 CIA-54 bioclipse.core: Added silentAfter timeout to @SilentNotification
14:43 CIA-54 bioclipse.core: Now the SilentNotification will start after a certain "silentAfter" amount of
14:43 CIA-54 bioclipse.core: time has passed. This value can be set using the annotation and the default
14:43 CIA-54 bioclipse.core: value is 500ms. That is if the job is finnished within half a second after it is
14:43 CIA-54 bioclipse.core: started it will opo up the result at once and if it takes longer the user will
14:43 CIA-54 bioclipse.core: have to click in the progress view to see the result. - http://bit.ly/u8T9P
14:45 egonw wow...
14:46 egonw eclipse autocomplete hides API from superclasses in plugins that are not imported
14:46 egonw that's something you need to be aware off... :(
14:55 * egonw finds himself writing a CML writer for Jmol
14:55 egonw bloody reviewers
14:55 egonw always rushing things
14:55 egonw bioclipse--
14:56 egonw for making all these fancy things so within reach
14:56 jonalv egonw: are you fixing save from jmol now?
14:56 egonw yes
14:56 * jonalv is trying to grasp what that means
14:56 egonw something broken in the Jmol we are using
14:56 egonw need *some* way of debuggin
14:57 * jonalv has a feeling that will reveal som ugly hack somewhere. He jsut can't wuite remember where it was..
14:57 egonw no worries
14:57 egonw I don't wuite either
14:58 jonalv |quite
15:07 * egonw is testing jmol.getMolecules()
15:10 * olass is reworking WebservicesManager with proper testing
15:10 olass grr, this was indeed badly written
15:10 olass mostly by me though :)
15:18 egonw jmol.getMolecules().get(0).toCML() works now
15:18 egonw well... partly
15:18 egonw need to serialize much more than atom number of course :)
15:21 * jonalv is considering taking weekend. Wasn't today a half-day?
15:29 stain calfday
15:43 egonw something seriously broken with the model index in the Jmol we are using
15:43 egonw I think that also explains the Outline problems
15:45 jonalv egonw: hm that sounds bad, what more symptoms have you found?
15:45 * egonw will try updating the Jmol version to the latest bug fix release
15:45 egonw serialization
15:45 egonw some bonds are in model 2 while all atoms are in model 0
15:46 jonalv strange
16:18 egonw it seems a bug in Jmol...
16:21 jonalv mhm
16:24 egonw I might have found the cause
16:24 egonw building an updated Jmol.jar as we speak
16:24 jonalv w00t
16:26 * jonalv gives up
16:26 jonalv I am off
16:26 jonalv cya
16:36 CIA-54 bioclipse.core: Ola Spjuth 2.2.x * raec42f5 / (9 files in 5 dirs): Upgraded webservices plugin to NWO. - http://bit.ly/15Ur2j
16:36 CIA-54 bioclipse.core: Ola Spjuth 2.2.x * r5a3c8dd / (2 files):
16:36 CIA-54 bioclipse.core: Implemented querying of PDB files from wsdbfetch.
16:36 CIA-54 bioclipse.core: This allows for splitting up multiple results into several files and replaces old functionality. - http://bit.ly/2NCzxE
16:36 CIA-54 bioclipse.core: Ola Spjuth 2.2.x * r518d9d1 / (4 files in 3 dirs): Implemented a wizard to query for multiple PDBs. - http://bit.ly/1xLt45
16:36 CIA-54 bioclipse.core: Ola Spjuth 2.2.x * r1071538 / (7 files): Updated webservices.tests to NWO and test DL PDB. - http://bit.ly/2jUwmD
16:45 samuell egonw: Is there a "decided upon" internal semantic format in Bioclipse
16:45 samuell egonw: That is, a format to use for passing around semantic data between plugins
16:46 samuell egonw: I'm thinking of what format I will have to accept in the bilpkit plugin when using the rdf plugin to get external data etc.
16:46 egonw IRDFStore
16:46 samuell egonw: Ah ok
16:53 samuell egonw: Where can I find information about it?
16:53 samuell egonw: Is it a Bioclipse specific format, or used elsewhere?
17:04 egonw it's a bioclipse specific API
17:04 samuell egonw: Ok
17:04 egonw use the rdf manager to get common formats
17:05 samuell Ok
17:05 samuell egonw: So I could use any typical format, in the blipkit module?
17:05 samuell egonw: N3?
17:05 egonw yes, for example
17:05 samuell egonw: Ok
17:06 samuell egonw: BTW... starting to think about how nice it would be to use MediaWiki as an RDF Store :)
17:06 samuell egonw: You could quickly export a lot of data and make it available for community editing, and then get it back
17:07 egonw indeed
17:07 samuell egonw: MW has superfine import/export functionality, both batch-wise via commandline, and via REST API.
17:08 egonw that's what I meant yesterday when I talked about a HIV knowledge base
17:08 samuell egonw: Yep, that's gonna be interesting!
17:08 * egonw is happy you like that idea
17:08 samuell Yes... the more I'm thinking about it ... :)
17:08 egonw should be trivial and a nice topic for the report for your intern at our department
17:09 egonw good thing is...
17:09 egonw we could ask Maris and Martin to help with the knowledge base
17:09 samuell egonw: Yes
17:11 samuell Ok... have to go for a while for a student group meeting. bbl.
17:11 egonw ok, bye
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19:56 CIA-54 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r66167c7 / (2 files in 2 dirs):
19:56 CIA-54 bioclipse.cheminformatics: Fix for inconsistent atom typing from CML files created the FromSMILES wizard (closes #1434).
19:56 CIA-54 bioclipse.cheminformatics: * wizards now performs atom type perception
19:56 CIA-54 bioclipse.cheminformatics: * CDKMolecule.toCML() now saves atom type information, just like the CDKManager equivalent
19:56 CIA-54 bioclipse.cheminformatics: * atom types are correctly perceived from the SMILES (see upstream CDK patch #2826961),
19:56 CIA-54 bioclipse.cheminformatics:  and the problem is with atom typing starting from the CML (to be explored) - http://bit.ly/14uers
22:07 egonw bloody fucking idiot
22:18 CIA-54 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r34d82a9 / (2 files): Added kabsch alignment - http://bit.ly/1EknuI
22:18 CIA-54 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r22d16fe / (2 files): Added a method to load a IMolecule in a new JmolEditor - http://bit.ly/159eE4
22:18 CIA-54 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rab4b4f1 / (3 files in 2 dirs): Added a method to append a IMolecule in the current JmolEditor - http://bit.ly/2YY5tW
23:11 samuell joined #bioclipse

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