Cytoscape 3.0 Developer's Beta

[Mike Smoot]

Hi Everyone,

The Cytoscape team is excited to announce the first developer's beta release of the Cytoscape 3.0 API.

This release is intended to provide App writers a solid foundation against which to port 2.X plugins or to build new apps.  By declaring the API in “beta” status the Cytoscape team is agreeing not to change the API beyond making simple additions and fixing bugs.  Specifically, this means that no methods that we expect App writers to use will change or go away.  Nor will any interface that we expect App writers to implement change.  This means that App writers should now feel confident that any 2.X plugin can now be ported to 3.0 without requiring significant changes for the actual 3.0 release.

This release will be followed by a full 3.0 Beta Release, which will be a feature-complete version ready for all users (not just developers) to transition from using Cytoscape 2.x. The final beta is scheduled to be released in the coming months.

To learn more, find the actual code, and get started porting your plugins go to:  http://www.cytoscape.org/documentation_cy3_dev.html

Don't hesitate to post questions to the cytoscape-discuss or cytoscape-helpdesk mailing list!

--  The Cytoscape Team

[Igor Rodchenkov]

Which is correct maven version for this release? (http://chianti.ucsd.edu/cytoscape-3.0.0-M4/API/ shows 3.0.0-beta1 javadoc; is this ok?)

IR.

[Michael Heuer]

Hello,

I started work on a cytoscape3 app version of a 2.x plugin by cobbling
together some bits from trunk/samples/sample02 and think there might
be a missing transitive dependency somewhere with api version
3.0.0-beta1, since all of my unit tests fail with

testConstructor(org.dishevelled.venn.cytoscape3.internal.CyActivatorTest)
 Time elapsed: 0.18 sec  <<< ERROR!
java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
       at org.cytoscape.service.util.AbstractCyActivator.<clinit>(AbstractCyActivator.java:30)
       at org.dishevelled.venn.cytoscape3.internal.CyActivatorTest.setUp(CyActivatorTest.java:53)
...
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
       at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
...


Checked into svn at

https://dishevelled.svn.sf.net/svnroot/dishevelled/trunk/venn-cytoscape3-app

  michael

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[Jing Lu]

I have exactly the same error:

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

SLF4J: Defaulting to no-operation (NOP) logger implementation

SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

My developing environment is eclipse with maven. Is there any solution to this error? I searched, but didn't find anything. I have my java updated with jdk1.7.0_21.

Thanks,

Jing 

[Jason Montojo]

Hi Jing,

If you're seeing this error in your build output, it's safe to ignore:

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

SLF4J: Defaulting to no-operation (NOP) logger implementation

SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

However, if your unit tests are failing like in Michael's case, you need to add an SLF4J implementation, such as pax-logging, as a test dependency to your pom.xml:

<dependency>

    <groupId>org.ops4j.pax.logging</groupId>

    <artifactId>pax-logging-api</artifactId>

    <version>1.5.2</version>

    <scope>test</scope>

</dependency>

Hope this helps,

Jason

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