| Time |
Nick |
Message |
| 05:08 |
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| 05:52 |
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| 07:20 |
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| 08:00 |
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| 09:36 |
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| 09:40 |
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| 09:57 |
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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 |
| 10:18 |
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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 |
| 10:23 |
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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/index.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 |
| 10:49 |
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| 11:04 |
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| 11:21 |
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| 11:54 |
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| 12:55 |
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| 13:13 |
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commitbot joined #bioclipse |
| 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... |
| 13:13 |
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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.UserContainer.getAccount(UserContainer.java:488) |
| 13:39 |
egonw |
at net.bioclipse.usermanager.UserContainer.getProperty(UserContainer.java:292) |
| 13:39 |
egonw |
at net.bioclipse.usermanager.business.UserManager.getProperty(UserManager.java:104) |
| 13:39 |
egonw |
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) |
| 13:39 |
egonw |
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) |
| 13:39 |
egonw |
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) |
| 13:39 |
egonw |
at java.lang.reflect.Method.invoke(Method.java:616) |
| 13:39 |
egonw |
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:301) |
| 13:39 |
egonw |
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) |
| 13:39 |
egonw |
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) |
| 13:39 |
egonw |
at org.springframework.aop.framework.adapter.AfterReturningAdviceInterceptor.invoke(AfterReturningAdviceInterceptor.java:50) |
| 13:39 |
egonw |
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) |
| 13:39 |
egonw |
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) |
| 13:39 |
egonw |
at sun.proxy.$Proxy12.getProperty(Unknown Source) |
| 13:39 |
egonw |
at net.bioclipse.opentox.business.OpentoxManager.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/jenkins/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.. |
| 14:04 |
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| 14:42 |
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konditorn_ joined #bioclipse |
| 16:45 |
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egonw joined #bioclipse |
| 17:09 |
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| 17:14 |
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| 18:06 |
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hybridivy joined #bioclipse |
| 18:28 |
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egonw joined #bioclipse |
| 18:42 |
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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 |
| 19:18 |
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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/index.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/bugzilla/show_bug.cgi?id=3491 |
| 21:01 |
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| 21:11 |
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