ImageJ plugin testing

[jamoore]

From Harri's recent email:

I tried to use ImageJ plugin I downloaded from ​http://hudson.openmicroscopy.org.uk/job/OMERO-trunk/3016/artifact/src/target/, and a newly installed Fiji (ImageJ 1.46j). The plugin appears as a 'OMERO' menu item under plugins, but when I select this, nothing happens. There is no error message or anything. How could I debug this?

[jmoore]

Actually, moving to blocker since this may require last minute commits.

[jmoore]

Note: with the OMERO.imagej zip I saw no plugin created. With OMERO.insight-ij I got the following on trying OMERO > Connect to OMERO...:

java.lang.RuntimeException: Failed to intialize the Container in test mode.
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:412)
	at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:160)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.Executer.runCommand(Executer.java:147)
	at ij.Executer.run(Executer.java:78)
	at java.lang.Thread.run(Thread.java:680)
Caused by: org.openmicroscopy.shoola.env.init.StartupException: Unable to load Container configuration
	at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(ContainerConfigInit.java:100)
	at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:255)
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:407)
	... 6 more
Caused by: org.openmicroscopy.shoola.env.config.ConfigException: An error occurred while attempting to process config/container.xml. (config/container.xml (No such file or directory))
	at org.openmicroscopy.shoola.env.config.Parser.rethrow(Parser.java:105)
	at org.openmicroscopy.shoola.env.config.Parser.parse(Parser.java:173)
	at org.openmicroscopy.shoola.env.config.RegistryFactory.fillFromFile(RegistryFactory.java:102)
	at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(ContainerConfigInit.java:84)
	... 8 more
Caused by: java.io.FileNotFoundException: config/container.xml (No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:120)
	at java.io.FileInputStream.<init>(FileInputStream.java:79)
	at org.openmicroscopy.shoola.util.file.IOUtil.readConfigFile(IOUtil.java:262)
	at org.openmicroscopy.shoola.env.config.Parser.parse(Parser.java:156)
	... 10 more

[mlinkert]

PR opened: ​https://github.com/openmicroscopy/openmicroscopy/pull/225

I don't know that code very well, so maybe there is a better way to do it. At the very least, though, that should allow the plugin to work if OMERO.insight-ij....zip is unpacked into the $IMAGEJ/plugins directory. I didn't test with OMERO.imagej....zip, as I couldn't find a way to build it and Jenkins is 502 at the moment.

[jmoore]

J-M mentioned in the PR that he will have a fix ready for this. Assigning.

[jburel]

see ​https://github.com/melissalinkert/openmicroscopy/pull/2

[Melissa Linkert <melissa@…>]

(In [aea531b28e8da16c0b57f36de30a6ff4ed0eaecc/ome.git] on branch develop) Use absolute paths when referring to config files

This prevents exceptions due to the configuration files not being found
when running Insight as an ImageJ plugin.

See #9308.

[jburel <j.burel@…>]

(In [6678bb404ec86d0df96f0d0236464cadf4655c93/ome.git] on branch develop) Review reading of configuration files (see #9308)

Change reading of config files so insight can be used as
an ImageJ plugin, using webstart, and a standalone application.