extra options

[diffany-admin]

Issue by svlandeg
Thu Nov 20 08:19:41 2014

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I am seeing the "extra options" menu twice in the diffany plugin?

[diffany-admin]

Comment by svlandeg
Thu Nov 20 08:29:01 2014

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This happened after uninstalling the plugin, and installing a new one from file. Then suddenly the old one was mentioned as "installed" again, too. Still, I wonder how the menu got duplicated then.

I just tried again by uninstalling, actually closing cytoscape, reopening and installing again. This time I see only one version, and the menu is OK as well...

[diffany-admin]

Comment by tvparys
Thu Nov 20 14:07:40 2014

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The is probably because the nature of the Extra Options menu (with the radio buttons) required a manual adding, instead of using the built-in app menu registration.
So, re-installing the App without closing Cytoscape, simply executes the menu initialization twice.
This might be solved by implementing an App destructor, which cleans up more nicely when the app is uninstalled.

[diffany-admin]

Comment by svlandeg
Thu Nov 20 14:13:50 2014

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Right. I guess if it's too much work for now, move to a future milestone?

[diffany-admin]

Comment by tvparys
Thu Nov 20 14:18:14 2014

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I can see how it should be done.
The annoying thing seems to be that it's simple to implement the bundle's start() method, but the stop() method has a final default implementation, so it can't be overridden.
The solution would be to not use the AbstractActivator, but to completely implement our own BundleActivator I guess...

[diffany-admin]

Comment by tvparys
Thu Nov 20 14:57:26 2014

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Simply copying the whole AbstractActivator to our own package in order to make a non-final stop() method, does not seem to work:

[ERROR] /home/thpar/git/diffnet/diffany/src/main/java/be/svlandeg/diffany/cytoscape/internal/AbstractDiffanyActivator.java:[33,19] cannot access org.osgi.util.tracker.ServiceTracker
[ERROR] class file for org.osgi.util.tracker.ServiceTracker not found

[diffany-admin]

Comment by tvparys
Thu Nov 20 15:26:01 2014

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Version 3.1.1 features a shutdown() method for App devs to override.
We are using the 3.0.1 libs. What was the reason for that again?
Let's NOT toy around with big version changes for this release though...

[diffany-admin]

Comment by tvparys
Thu Nov 20 15:28:21 2014

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From API 3.1.1:

        /**
         * Cleans up resources used by the app.  If the app creates threads, **adds
         * menu items via Swing**, or performs any other operation that modifies the
         * environment, this method this method should be overridden to
         * perform any necessary clean up.
         */

[diffany-admin]

Comment by svlandeg
Thu Nov 20 15:33:03 2014

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No idea why were are using the 3.0.1 libs ... :s

[diffany-admin]

Comment by tvparys
Thu Nov 20 15:33:46 2014

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I think that was the recommended stable version when we started out.

[diffany-admin]

Comment by tvparys
Thu Nov 20 15:39:09 2014

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Changing the pom.xml dependencies to 3.1.1 compiles and runs without problems and enables the shutdown() method. Implementing and testing.

[diffany-admin]

Comment by tvparys
Thu Nov 20 15:54:10 2014

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Too risky an operation for now. Menu's can be removed effectively, but don't appear anymore at all when the App is installed a second time.