Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-05-04

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All times shown according to UTC.

Time Nick Message
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06:01 CIA-70 bioclipse.opentox: Ola Spjuth master * r8f366d5 / (3 files in 3 dirs): Some small branding for features and provider - http://bit.ly/ixN6t8
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06:27 egonw http://logic.pdmi.ras.ru/aptu/node/211
06:31 egonw nice :)
06:31 egonw project page: http://osll.spb.ru/projects/genecode/wiki
07:08 olass fattar inget, vad är det egentligen?
07:08 olass sorry
07:08 olass I don't get it, what's it about?
07:08 egonw that's the project from the Russians
07:08 olass ah, of course
07:08 olass have not heard from them lately, have you?
07:08 olass are they making progress?
07:09 egonw they come online every now and then...
07:09 egonw I think it would help if we had that split of IMolecule and IProtein done for Jmol
07:11 egonw but I haven't gotten around to that yet
07:11 Gpox joined #bioclipse
07:11 egonw Gpox: ping
07:11 Gpox egonw: pong
07:12 egonw Gpox: I got opentox and ons working on Hudson
07:12 egonw but opentox broke again because:
07:12 egonw I had to patch the BioclipsePlatformManager
07:12 egonw in bioclispe.core if not mistaken
07:12 egonw that recompiled fine
07:12 egonw but bioclipse.opentox does not see the new method, it seems...
07:20 olass egonw: what is the URL for referencing BODO?
07:20 olass @ping
07:20 zarah olass: pong
07:20 egonw pong
07:20 egonw namespace?
07:20 olass no, the URL
07:20 olass web link
07:43 CIA-70 bioclipse.opentox: Ola Spjuth master * r5a373e8 / (10 files in 6 dirs): Added plugin net.bioclipse.opentox.ui - http://bit.ly/ju0kof
07:43 CIA-70 bioclipse.opentox: Ola Spjuth master * r3c8bf41 / plugins/net.bioclipse.opentox.ui/src/net/bioc​lipse/opentox/ui/handlers/CreateDataset.java : Stub for creating OT datasets - http://bit.ly/lLAASQ
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10:39 CIA-70 bioclipse.opentox: Egon Willighagen master * r4079f04 / plugins/net.bioclipse.opentox/src/net/biocl​ipse/opentox/business/IOpentoxManager.java : Fixed outdated API description - http://bit.ly/j6CmF2
10:39 CIA-70 bioclipse.opentox: Egon Willighagen master * r4e6faef / (5 files): Factored out parameterization of the *Method, adding AA on the fly - http://bit.ly/mtg69S
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12:04 jonalv o/
12:20 egonw oh hai jonalv
12:21 jonalv hi egonw, how are things?
12:21 egonw jonalv: please talk me into the bioclipse user login framework
12:21 jonalv ohh
12:21 egonw going ok... stressed about flying to finland tomorrow
12:21 jonalv finland?
12:21 jonalv yiekes
12:21 jonalv well what do you want to know?
12:21 egonw how to extend it for OpenTox
12:22 jonalv okey, what do you need for OpenTox?
12:22 * jonalv is profiling his fingerprint script
12:22 jonalv it takes 8 hours to createa diagram
12:22 jonalv seems Tanimnoto calculations are expensive
12:24 jonalv egonw: what do you need it to do for OpenTox?
12:27 egonw tanimoto is cheap... FPs are expensive
12:27 egonw simple login account keeping
12:27 egonw single account
12:27 jonalv egonw: it does that...
12:27 egonw + ability to click 'log in', see if 'online', and click 'logout'
12:28 jonalv egonw: you create an extension defining what you want to save for the account
12:28 jonalv web adress
12:28 jonalv password
12:28 jonalv username
12:28 jonalv perhapos?
12:28 egonw username + pwd
12:29 jonalv is there only one OpenTox server?
12:29 egonw multiple, but currently all with the same accounting
12:29 egonw so, just 1 AA server
12:29 jonalv okey but maybe you want to add more servers?
12:29 jonalv and sign in on all of them at once?
12:29 jonalv That's what the Keyring is designed for...
12:30 egonw no, sorry, there is just one server at this moment
12:30 jonalv no problem there is just one Brunn server too :)
12:30 jonalv it works
12:31 jonalv :)
12:31 egonw btw, is this keyring thing first published in the Brunn paper?
12:31 egonw if so, please send me a preprint
12:31 jonalv egonw: it's not mentioned really
12:31 egonw because I would have to cite it
12:31 jonalv actually not at all
12:31 egonw oh, too bad :(
12:32 jonalv it's technicalities
12:32 jonalv everyone tells me that publications are not about technicialties
12:33 jonalv acutally it's an unpublished Bioclipse feature...
12:34 egonw so, how do I use it?
12:34 egonw I have my net.bioclipse.opentox plugin
12:34 egonw with an opentox manager
12:34 egonw which has the API: login(user,pwd), logout(), and getToken()
12:34 jonalv there is an example plugin somewhere
12:34 egonw the last is needed for the AA when using OT services
12:35 egonw and the plugin's Activator has the logic, and holds that token
12:35 egonw how do I hook that up with your code?
12:35 olass jonalv: can the keyring handle the login part?
12:35 jonalv you need to implement an account extenstion
12:35 jonalv olass: yea I don't see why not
12:36 olass excellent
12:37 jonalv hm it's called usermanager now...
12:37 jonalv I wonder where that example plugin has gone
12:38 jonalv is it stuck in SVN?
12:40 jonalv yup
12:40 jonalv egonw: http://bioclipse.svn.sourceforge.net/vi​ewvc/bioclipse/bioclipse2/trunk/_playgr​ound_/net.bioclipse.usermanager.demo/
12:40 zarah jonalv's link is also http://tinyurl.com/64ojfou
12:40 jonalv yiekes this stuff is old...
12:41 egonw olass: I'm tempted to go for a quick hack then...
12:41 jonalv this works
12:41 jonalv Brunn is using it
12:41 egonw e.g. a simple OpenTox menu or so
12:41 jonalv it has not changed
12:41 egonw is the usermanager autocompiled on Jenkins?
12:42 jonalv you need to add an extension like row 29 here: http://bioclipse.svn.sourceforge.net/vi​ewvc/bioclipse/bioclipse2/trunk/_playgr​ound_/net.bioclipse.usermanager.demo/pl​ugin.xml?revision=11760&view=markup
12:42 zarah jonalv's link is also http://tinyurl.com/6934c8g
12:42 olass I think use the usermanager
12:42 olass if possible
12:42 egonw OK...
12:42 jonalv egonw: it ships with Bioclipse core
12:42 egonw jonalv: so, I'd define a new AccountType, something like:
12:42 olass yes, part of core
12:43 egonw <AccountType id="opentox.opensso" name="OpenTox OpenSSO Account">
12:43 egonw <property name="username" required="true"/>
12:43 egonw <property name="password" required="true"/>
12:43 egonw </AccountType>
12:43 jonalv yea
12:43 egonw then what?
12:43 egonw is that it?
12:43 jonalv then the usermanager will know about that account type and you can use the manager api or the gui to acccess it
12:43 egonw how do I tell the usermanager how it should use that account?
12:44 jonalv there is a call back
12:44 jonalv you can add a login listener
12:45 jonalv egonw: http://bioclipse.svn.sourceforge.net/viewvc/bioc​lipse/bioclipse2/trunk/_playground_/net.bioclips​e.usermanager.demo/src/net/bioclipse/views/Userm​anagerDemo.java?revision=11760&amp;view=markup
12:45 zarah jonalv's link is also http://tinyurl.com/6czu22k
12:45 jonalv egonw: row 91
12:46 egonw OK, how is UPDATE defined?
12:46 egonw LOGIN and LOGOUT are clear :)
12:46 jonalv If I recall correctly that is if one of the properties are changed
12:46 jonalv yea that must be it
12:48 jonalv egonw: also don't forget row 30 :)
12:53 egonw ack
12:53 egonw jonalv: I can do without the ViewPart bits, right?
12:54 jonalv egonw: yea this is an example view
12:54 egonw what does the usermanager plugin provide?
12:54 jonalv which shows the features of the UserMaanager
12:54 jonalv egonw: what do you mean?
12:54 egonw does it provide a 'login' button/menu somewhere which people press?
12:54 jonalv egonw: yea in the menu
12:55 jonalv file -> login
12:55 jonalv it's only visible if there is at least one user created
12:55 egonw and a GUI to change that values, I guess?
12:55 jonalv yea a property dialog
12:55 jonalv it is always there
12:56 jonalv fire up Bioclipse and check the usermanager properties :)
12:56 egonw which feature is this plugin part of?
12:57 egonw bioclipse.core_feature?
12:57 jonalv yea I think so
13:16 jonalv egonw: do you remember mentionining a weekend CDK hacksession earlier?
13:17 egonw yes, I did
13:17 egonw are you up for it?
13:17 jonalv egonw: yea it sounds like a good idea
13:17 jonalv I mean I can take a weekday of to compensate... This will be stuff that I need in that case...
13:18 jonalv egonw: or did you have something special in mind?
13:18 egonw no, not yet... but I'll email about a date
13:19 jonalv oki cool
13:28 egonw jonalv: how do I get the properties of an AccountThingy from an UserManagerEvent?
13:29 jonalv you get what you need thorugh the UserManager api
13:29 egonw oh...
13:30 egonw I see: userManager.getLoggedInUserName()
13:30 jonalv the event just tells you that _now_ someone has logged in
13:30 egonw but how does the manager know *which* account to get?
13:30 egonw that is, the OT one in my case...
13:30 jonalv so there are two levles of accoutns here
13:30 jonalv first level is which user logged in
13:30 jonalv second level is what accounts does that user have
13:31 jonalv did that make any sense?
13:31 egonw no
13:32 jonalv so you create a user on your computer
13:32 jonalv you then add accounts for that user
13:32 jonalv mayeb a Brun nacount and one OpenTox account
13:32 jonalv that user then logs in
13:33 jonalv you need to check whether the loged in user has an OpenTox account
13:33 jonalv if not, then you probably don't want to do anything. Or perhaps you want to show some message about not having set up an OpenTox account
13:33 jonalv on some label or so
13:33 jonalv depends on what you are doing...
13:34 jonalv I mean if you have something like an OpenTox view?
13:34 jonalv then when logged out it should probably just say not logged in
13:34 jonalv and when logged in if the logged in user has an OpenTox account I guess you should show relevant content in the viewe
13:35 jonalv but if the logged in user does not have an OpenTox account you probably want to explain that such an account needs to be created...
13:35 jonalv egonw: are you with me now?
13:35 egonw I think so...
13:36 jonalv cool
13:39 egonw mmm
13:39 egonw need help
13:39 jonalv oki?
13:39 egonw created a local Bioclipse keyring account
13:40 egonw + a OpenTox account
13:40 egonw code registers listener... but no login :(
13:40 jonalv a local Biolicpse keyring account?
13:40 egonw whatever the thing is called
13:41 egonw File -> Log in -> Create account
13:41 jonalv ah
13:41 jonalv okey
13:41 jonalv let's call it a User
13:41 egonw ok, I can live with that :)
13:41 jonalv so you found the accounttype?
13:42 jonalv and added username and fingerprint?
13:42 jonalv gah password
13:42 jonalv guess you know what I am working with here now.. :)
13:44 egonw :)
13:44 egonw yeah, the EP is in the net.bioclipse.opentox plugin.xml
13:45 jonalv and UserManager properties dialog picked it up?
13:47 egonw yes yes
13:47 egonw making progress, I think
13:48 jonalv okey?
13:48 jonalv that sounds good
13:48 egonw cool, it works!
13:48 egonw jonalv++
13:48 * jonalv is having a bit of trouble with Eclispe workspaces for the moment but firing up the Eclipse version I used for building 2.4 so I can look at code when you asks questions
13:48 jonalv oh awesome!
13:48 egonw I know Barry will not like this two account approach though :)
13:49 jonalv so the idea is tho collect all different accounts you want to access from Bioclipse under one login
13:49 egonw rigth, got that now
13:49 jonalv all those properties are saved in an encryoted file
13:50 jonalv using the password you enter for the Bioclipse user for the encryption
13:50 egonw good good
13:50 egonw now I only need to get it to use that OT AccountType...
13:51 jonalv hehe okey
13:51 egonw userManager.getProperty("net​.bioclipse.opentox.opensso", "username")
13:51 egonw something like that?
13:52 egonw <AccountType
13:52 egonw id="net.bioclipse.opentox.OpenSSOAccount"
13:52 egonw name="OpenTox OpenSSO Account">
13:52 egonw <property
13:52 egonw name="username"
13:52 egonw required="true">
13:52 egonw </property>
13:52 egonw <property
13:52 egonw name="password"
13:52 egonw required="true">
13:52 egonw </property>
13:52 egonw </AccountType>
13:52 egonw so:
13:52 egonw userManager.getProperty("net.bi​oclipse.opentox.OpenSSOAccount ?", "username")
13:52 egonw userManager.getProperty("net.bio​clipse.opentox.OpenSSOAccount", "username") ?
13:52 jonalv It's been almost three years since I wrote that and you expect me to remember details of the api? :)
13:52 egonw sure!
13:52 egonw :)
13:52 egonw anyways... this sounds OK... gonna try it
13:53 jonalv yea please
13:54 egonw crap
13:54 egonw user account info is *not* saved between sessions
13:54 jonalv it should be
13:54 egonw "Could not sign in egonw. Unrecognized username or password"
13:55 egonw and, no, I did not make a typo
13:55 jonalv oh dman
13:55 jonalv I just
13:55 jonalv fuck isn't that bug fixed yet
13:55 jonalv so I seem to remember that if yo ucreate you user from the login window it did not work
13:56 jonalv I thought that was fixed
13:56 jonalv create you user from the properties dialogue
13:56 jonalv jonalv--
13:56 egonw no, from login dialog
13:56 jonalv but I could have sworn we fixed that
13:56 jonalv yea you did create it from the login dialog
13:57 jonalv try from the properties dialog instead
13:57 egonw ok, there it is saved after BC reboot
13:58 jonalv if that works, can you do me a favour and grey out the create new user in that dialog?
13:58 jonalv it's sucks to have a button that doesn't work...
13:58 egonw file a RC bug report
13:58 jonalv RC?
13:58 egonw ok, accountID != AccountType id
13:58 egonw release critical
13:58 egonw ummm...
13:58 egonw blocker in Bugzilla terms
13:59 jonalv more trouble?
13:59 egonw blocker in Bugzilla terminology
13:59 jonalv ah
13:59 jonalv yea please, you found it...
14:00 egonw well, tied up with deadlines already...
14:00 egonw and you know the proper keywords
14:00 jonalv oki
14:01 jonalv I think threre should be a bug report there but I will make it a 2.5 release bleocker somehwer
14:01 * jonalv can't hardly remember how that works, Gpox?
14:03 jonalv where was the old bugzilla again?
14:03 egonw install Mylyn?
14:03 egonw need to do that too, actually :)
14:03 jonalv I am not running the correct Eclipse workspace anyways so I need to go through the web...
14:04 jonalv hm or hang on
14:04 jonalv maybe that old Eclipse can be of help... :)
14:05 * jonalv gives up and fiels a new Bug in the new Bugzilla
14:08 jonalv Gpox: is there are a container bug for 2.5 or 2.6 release?
14:09 Gpox dunno
14:09 jonalv Gpox: you are release manager, how do you want to do to keep track of things? Will there be one or do you have another way of keeping track of release blockers?
14:09 egonw jonalv: can I just hack in UserContainer?
14:10 egonw or is that autogenerated?
14:10 egonw olass is keen on autogenerated bean classes
14:10 olass hehe
14:10 jonalv egonw: there shouldn't be any autogenerated stuff there, does it look autogenerated?
14:10 egonw no
14:10 egonw good
14:10 egonw making a patch
14:10 jonalv cool
14:11 olass ice-cool
14:11 egonw jonalv-- (for not having the EP id in the AccountType class!)
14:12 * jonalv has a feeling that he is loosing more karma then he is earning for this USerManager code...
14:12 jonalv olass: did you get a mail about bugs now?
14:13 * jonalv wants to make sure it works
14:16 olass yes
14:16 olass egonw: ping
14:16 olass jonalv: this concerns you too...
14:16 egonw jonalv:
14:16 egonw userManager.getAccountIdsByAccountTypeId(
14:16 egonw "net.bioclipse.opentox.OpenSSOAccount"
14:16 egonw );
14:17 egonw wassup?
14:17 olass can we change:
14:17 egonw tim talking, rigth ?
14:17 jonalv olass: that's good, at least our bugzilla works now then :)
14:17 olass public List<ICDKMolecule> loadMolecules(...) to     public List<? extends IMolecule> loadMolecules(...) ?
14:17 olass else I cannot send that list into createDataset, which only accepts a List<IMolecule>
14:18 jonalv olass: sounds about right to me
14:18 olass egonw: what you say?
14:19 olass can I push this change to ICDKManager?
14:19 egonw olass: sure... IIRC you urged me to make it return ICDKMolecule :)
14:19 egonw because that was stronger typed
14:19 olass oh... I do not recall that... if so I take it back
14:19 egonw it was a long time ago
14:19 egonw it might have been jonalv, but I doubt that
14:20 jonalv I feel confused now
14:20 jonalv maybe change the other method?
14:20 olass which one?
14:20 olass createDataset should really accept List<IMolecule>
14:20 jonalv the on taking a List<Molecule>
14:20 egonw I think we need Gpox, our generic(s) wizard
14:20 jonalv why not having it accept List<? extends IMolecule>?
14:20 olass in general, we should accept IMolecule as input
14:21 olass ah, I see..
14:21 egonw jonalv: yeah, why not?
14:21 egonw Gpox: what do you think about that?
14:21 olass ok, so we have two ways...
14:21 olass Gpox: help!
14:21 jonalv be strict with what you return but accept a lot...
14:21 egonw I think jonalv's solution is the best, in fact
14:21 olass yes, I did not think of this
14:21 egonw jonalv: right, so maybe it was you!
14:21 egonw Gpox: help!
14:21 olass touché
14:22 jonalv egonw: I have no idea. Can't remember daying it but that doesn't mean I did not...
14:22 olass if Gpox agrees, I vote for jonalv's proposal
14:22 * egonw is testing his net.bioclipse.usermanager patch
14:22 olass egonw: I will update the OpenTox manager then
14:22 olass to accept ? extends IMolecule
14:22 egonw yes, please try that
14:23 egonw if Gpox agrees, we have a lot of patching to do...
14:23 * egonw is thinking of the future IJmolMolecule
14:24 Gpox returning List<ICDKMolecule> is right because that is what it generates but there is a lot to consider with generics
14:24 egonw Gpox: what about what methods should eat?
14:25 egonw foo(List<IMolecule>) or foo(List<? extends IMolecule>) ?
14:25 Gpox <? exntends IMolecule> should be good as it can use any IMolecule instance to do the job
14:25 egonw and the oracle has spoken
14:26 egonw Gpox++ (thanx!)
14:26 egonw damn... that means a lot of patching...
14:26 egonw can someone file a bug report please?
14:26 egonw nice junior job, btw
14:27 Gpox but you don't want to do if(! instanceOf ICDKMolecule) convertToCDKMolecule() all over the place either
14:28 Gpox lets discuss it in the bug report
14:28 egonw cdk.asCDKMolecule(someIMolecule)?
14:28 egonw Gpox: the context is in fact replacing eating List<IMolecule>
14:28 egonw so, that check is needed already
14:34 egonw ok, patch is not gonna work...
14:36 egonw jonalv-- (for caching account types by human readable name, rather than unique ID)
14:38 egonw jonalv++ (for an otherwise fine platform)
14:39 jonalv egonw: ah... Good point. I gues we should fix that some day...
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14:46 CIA-70 bioclipse.opentox: Egon Willighagen master * rf42b882 / (4 files in 3 dirs): OpenTox AA is now using the Bioclipse UserManager framework - http://bit.ly/kY01O4
14:51 jonalv yey egonw++
15:09 olass egonw: ok, implemented the wizard now. Seems to work fine.
15:09 olass will commit so you can test
15:10 olass have not tested with A&A, just confirmed that it fails with TUM server
15:10 olass "Forbidden"
15:10 olass hmm, need to catch that...
15:10 olass egonw: ping
15:11 olass should not createDataset throw an exception if it is not allowed (forbidden)?
15:11 olass damn, he's away...
15:11 olass egonw: let me know
15:14 CIA-70 bioclipse.opentox: Ola Spjuth master * r02b5022 / (7 files in 4 dirs):
15:14 CIA-70 bioclipse.opentox: Implemented wizard to create and upload dataset.
15:14 CIA-70 bioclipse.opentox: * Popup menu for SD-files
15:14 CIA-70 bioclipse.opentox: * Opens Browser with results
15:14 CIA-70 bioclipse.opentox: * Error reporting for A&A is not yet fully implemented - http://bit.ly/kag3Pv
15:14 CIA-70 bioclipse.opentox: Ola Spjuth master * ra0bb2f4 / plugins/net.bioclipse.opentox/src/net/biocl​ipse/opentox/business/IOpentoxManager.java : Updated API to accept List<? extends IMolecule> - http://bit.ly/mqo15U
15:14 olass it's actually pretty nice
15:14 olass olass++
15:14 zarah shame on you, olass, giving yourself karma like that
15:15 olass ;)
15:27 * olass enjoyed writing bioclipse code again
15:32 egonw yes, it should catch that
15:32 egonw unfortunately, you get a general IOException
15:32 egonw and have to check the exc message and hope there is something like 403 in it :(
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15:33 egonw ws1 server still doing fine :) http://labs.mondeca.com/sparqlEndpoin​tsStatus/details/farmbio-chembl.html
15:33 zarah egonw's link is also http://tinyurl.com/6frz879
15:33 olass egonw: can you catch that and turn it into e.g. a NotPermittedException?
15:34 olass egonw: please try my wizard!
15:34 * olass is a bit proud
15:34 egonw yeah, looks good!
15:35 egonw I was hoping to name it 'Social Share' or so...
15:35 egonw but current names will do fine for now :)
15:36 egonw olass: is the rich browser part of the OT feature?
15:36 egonw if not, let's make it like that
15:36 jonalv sounds like you guys are doing cool stuff now again :)
15:36 olass egonw: it's in core
15:36 egonw we always do cool stuff...
15:36 egonw we are cool
15:36 egonw olass: excellent :)
15:37 olass damn, running out of power on my laptop
15:37 egonw :(
15:37 olass well, it's been running since 13
15:37 egonw but you got the adapter in you rroom, right?
15:37 olass yes, but in training room now
15:38 egonw right
15:39 egonw Nina: "Where is the "Like"  button for your Bioclipse GUI progress :)"
15:39 olass :)
15:40 egonw olass: yeah, you should blog your screenshots !
15:42 olass I guess
15:42 olass yes
15:42 olass could be done
15:43 egonw yeah, got my very first spam on @ki.se !
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16:15 CIA-70 bioclipse.core: Egon Willighagen master * rb1a2622 / (2 files): Added a manager method for opening the wiki - http://bit.ly/iB4FTG
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