Camelia, the Perl 6 bug

IRC log for #bioclipse, 2013-02-20

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All times shown according to UTC.

Time Nick Message
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10:03 hybridivy egonw : hi
10:04 hybridivy i have gone through how to make an editor , and could redo wats asked
10:10 hybridivy seems like there is already a plugin for wikipathways and pathvisio in bioclipse , and  someone working on it
10:12 hybridivy olass: hi i was going through your module , for bioclipse (ie) pathvisio and wikipathways ,wat are the usecases of the module?
10:13 olass hi hybridivy
10:14 olass let me see...
10:14 olass from Bioclipse we commonly start with a question concerning chemistry
10:14 olass so looking up and visualizing pathways is indeed one
10:15 olass hold on, need to do a mental context switch
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10:20 olass hybridivy: I did some initial work on this but did not get too far
10:20 olass I am not so experienced with wikipathways and pathvisio
10:20 olass but the API was straightforward
10:21 olass I would however be interested in learning what more can be done
10:21 olass do you have more expertise in these tools?
10:21 olass egonw: perhaps you can add in on use cases here?
10:21 olass one thing that would be great would be to query based on chemistry and not only name
10:22 olass also, to highlight e.g. a target or ligand in a pathway
10:22 hybridivy i have been working on with pathvisio modules and have experince with how things work in pathvisio
10:23 hybridivy so i am intrerested in one of gsoc idea to integrate pathvisio visualisation with bioclipse
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10:23 olass where are you from?
10:24 olass I would say egonw is the key person to ask about use cases
10:24 olass but exposing the api of pathvisio in Bioclipse would be really great
10:24 olass it can be a very valuable tool
10:24 olass and we have merely scratched the surface so far
10:25 hybridivy i was interested in what the present plugin (pathvisio and wikipathways) do
10:25 hybridivy ok so its a basic one
10:25 olass yes, a very basic one I hacked up in 2 days
10:25 olass as a proof of concept
10:25 hybridivy i just forked it from github and trying out this
10:26 olass works?
10:26 hybridivy im not sure, as right now im checking wat it does
10:26 hybridivy :)
10:27 hybridivy i mean the module which you created
10:28 hybridivy as in the picture @ http://www.wiki.bioclipse.net/in​dex.php?title=File:Wp-script.png shows its working
10:29 hybridivy but could not reproduce the same thing
10:32 olass hmm, I will check again
10:32 olass it seems their API has been in flux
10:32 olass so it might need some tweaking to get up to speed
10:32 olass maybe that is something you are familiar with?
10:32 olass ok, be back later
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13:13 commitbot [bioclipse.opentox01] goglepox pushed 3 new commits to develop: http://git.io/yIPGxQ
13:13 commitbot bioclipse.opentox/develop a45e21c Egon Willighagen: Made the inner class public, because it caused a ClassNotFoundException as soon as I add another prefs page, which does not even use that class... yes, really weird; really Eclipse
13:13 commitbot bioclipse.opentox/develop 32aefbf Egon Willighagen: Adds preferences and matching page for some network properties....
13:13 commitbot bioclipse.opentox/develop 35af67e Arvid Berg: Merge pull request #8 from egonw/2-networkPrefs...
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13:32 egonw Gpox: so, what is AbstractUIPlugin actually being replaced with?
13:38 egonw konditorn: I think this may be a regression from your login work?
13:39 egonw Caused by: java.lang.IllegalStateException: not logged in
13:39 egonw at net.bioclipse.usermanager.UserContain​er.getAccount(UserContainer.java:488)
13:39 egonw at net.bioclipse.usermanager.UserContaine​r.getProperty(UserContainer.java:292)
13:39 egonw at net.bioclipse.usermanager.business.UserM​anager.getProperty(UserManager.java:104)
13:39 egonw at sun.reflect.NativeMethodAc​cessorImpl.invoke0(Native Method)
13:39 egonw at sun.reflect.NativeMethodAccessorImpl.in​voke(NativeMethodAccessorImpl.java:57)
13:39 egonw at sun.reflect.DelegatingMethodAccessorImpl.in​voke(DelegatingMethodAccessorImpl.java:43)
13:39 egonw at java.lang.reflect.Method.invoke(Method.java:616)
13:39 egonw at org.springframework.aop.support.AopUtils.invo​keJoinpointUsingReflection(AopUtils.java:301)
13:39 egonw at org.springframework.aop.framework.Refl​ectiveMethodInvocation.invokeJoinpoint​(ReflectiveMethodInvocation.java:182)
13:39 egonw at org.springframework.aop.framework.R​eflectiveMethodInvocation.proceed(R​eflectiveMethodInvocation.java:149)
13:39 egonw at org.springframework.aop.framework.adapter​.AfterReturningAdviceInterceptor.invoke(A​fterReturningAdviceInterceptor.java:50)
13:39 egonw at org.springframework.aop.framework.R​eflectiveMethodInvocation.proceed(R​eflectiveMethodInvocation.java:171)
13:39 egonw at org.springframework.aop.framework.JdkDynamic​AopProxy.invoke(JdkDynamicAopProxy.java:204)
13:39 egonw at sun.proxy.$Proxy12.getProperty(Unknown Source)
13:39 egonw at net.bioclipse.opentox.business.Opentox​Manager.login(OpentoxManager.java:136)
13:39 egonw see Hudson
13:44 konditorn egonw: it might be… But I need more info about it then the stack trace… What did you (tried) do/ to get it?
13:44 egonw see http://pele.farmbio.uu.se/jenki​ns/job/Bioclipse.test.opentox/
13:49 Gpox egonw: BundleActivator if an activator is needed most of the time they are not.
13:49 egonw so, plugins should extend BundleActivator?
13:50 egonw is the Bioclipse SDK already updated for that?
13:50 Gpox no
13:50 egonw plugins with managers always need an activitor, right?
13:50 egonw so, when is an activitator is needed other than that?
13:50 Gpox as it is now but most of it is just for an easy access singleton
13:53 Gpox when you use the start/stop method to do stuff that belongs there
14:02 konditorn egonw: The reason is probably that you need to be logged in on a bioclipse user account for loving in that way… In that case a solution would be to login via the openTox manager instead..
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18:56 hybridivy hi egonw
18:56 egonw hi hybridivy
18:57 hybridivy i think we can use the rpc plugin created by anwesha for the idea :integrating pathvisio visulaisation in bioclipse
18:57 hybridivy egonw :right?
18:57 egonw yes and no
18:58 egonw that's the route that olas took in Paris
18:58 egonw at SWAT4LS
18:58 egonw but that does not allow editing
18:58 egonw so, yes, for viz it works, but we want editing
18:58 hybridivy ok
18:59 hybridivy i guess editing can be done too, as the functions mentioned here http://pathvisiorpc.wordpress.com/functions/ says we can add elements
19:00 egonw I rather just embed the existing editor, than completely rewriting one from scratch on top of RPC
19:01 hybridivy existing editor? do you mean the module done by olass
19:02 egonw no, the PathVisio editor
19:04 hybridivy Pathvisio editor exists?
19:04 hybridivy or you mean we have to create one?
19:12 egonw no, PathVisio == is the editor
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19:28 hybridivy egonw_: so i have to use the pathvisio as library and build an editor ,right?
19:28 egonw_ right
19:29 hybridivy where visualaisation and editing both can be done
19:29 hybridivy egonw :ok, got it :)
19:30 hybridivy egonw_: one correction has to be made here http://www.wiki.bioclipse.net/in​dex.php?title=Swat4ls-paris2012
19:31 egonw_ I'm in a telcon
19:31 egonw_ can you please file a bug report, at bugs.bioclipse.net ?
19:31 hybridivy ok sure :)
19:32 egonw_ hybridivy++
19:41 hybridivy filed :Bug 3491
19:41 zarah bug #3491 | http://pele.farmbio.uu.se/bu​gzilla/show_bug.cgi?id=3491
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