Import fixes insight

[ximenesuk]

This fixes the Insight ImageJ plug-in to work with slf4j logging and uses new bioformats_package.jar

--depends-on ome/bioformats#882

No longer valid rebase tag (was to gh-2097) now partially
--rebased-to #2122

[ximenesuk]

I can confirm that when run as an ImageJ plug-in Insight logs to the ImageJ log and the omeroinsight.log file is not touched.

There is a problem with opening images, when double-clicking a thumbnail this dialog was thrown up:

and the image failed to open. But this looks like a scifio problem, fom the log:

...
runPlugIn: loci.plugins.LociImporter
runUserPlugIn: loci.plugins.LociImporter
out> 11:18:31.710 [AWT-EventQueue-0] DEBUG ome.scifio.common.ReflectedUniverse - No such class: org.apache.log4j.Level
java.lang.ClassNotFoundException: org.apache.log4j.Level
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202) ~[na:1.6.0_65]
...

[melissalinkert]

The issue there is that Bio-Formats does have a hard dependency on log4j in some places. As discussed with @joshmoore, we're going to need to change that to logback and reduce the number of places in which it's hard-coded. A PR to do that is forthcoming.

[joshmoore]

Currently testing a (local) merge build with @melissalinkert's fixes to my ome/bioformats#889. Adding:

• bioformats_package.jar
• 2 logback jars
• the OMERO.insight-ij.zip to a vanilla IJ1
  produces this on "Connect to OMERO":

(ome1)jamoore@blue:/tmp/ImageJ$ sh run 
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/tmp/ImageJ/plugins/logback-classic-1.0.9.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/tmp/ImageJ/plugins/OMERO.insight-ij-5.0.0-rc1-DEV-ice35/libs/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
09:33:58.018 [Connect to OMERO] DEBUG n.s.e.config.ConfigurationFactory - Configuring ehcache from InputStream
09:33:58.057 [Connect to OMERO] DEBUG n.s.e.config.ConfigurationFactory - Did not find a system property for the ${multicastGroupPort} token specified in the configuration.Replacing with ""
09:33:58.057 [Connect to OMERO] DEBUG n.s.e.config.ConfigurationFactory - Did not find a system property for the ${token} token specified in the configuration.Replacing with ""
09:33:58.065 [Connect to OMERO] DEBUG net.sf.ehcache.config.BeanHandler - Ignoring ehcache attribute xmlns:xsi
...
All of the same output *also* goes to the Edit>Options>Debug menu.

TODOs:

• Strip logback jars (and possibly other BF jars) from the insight zip.
• Consider if there's a way to have insight use the IJ logging as BF does. (Quite possibly out of scope)

[joshmoore]

Propose merging as this is certainly functional today with the merge build. The rest of the TODOs will need to get addressed in a follow-up PR (along with possibly checking for either loci_tools.jar || bioformats_package.jar)