Added a fat jar distribution of imagej for fiji

[rgozim]

Adds a fat jar distribution for FIJI

• run gradle installFijiDist to build the Fiji distribution
• test with fiji

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#138. See the console output for more details.
Possible conflicts:

• PR class path fix for imagej plugin #65 rgozim 'class path fix for imagej plugin'
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#138. See the console output for more details.
Possible conflicts:

• Upstream changes
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#59. See the console output for more details.
Possible conflicts:

• PR class path fix for imagej plugin #65 rgozim 'class path fix for imagej plugin'
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#59. See the console output for more details.
Possible conflicts:

• Upstream changes
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[pwalczysko]

built locally being on this branch using gradle build.
Then unzipped and transferred to Win7 machine, into the freshly downloaded Fiji from yesterday.
Fiji started, connect to OMERO, splashscreen appeared. Put creds in, then:

[Thu Aug 22 11:45:25 BST 2019] [ERROR] [] null
java.lang.NoSuchMethodException: Could not find method com.sun.jna.Native.load(Ljava/lang/String;Ljava/lang/Class;Ljava/util/Map;)Lcom/sun/jna/Library;
There was a problem with the class com.sun.jna.Native which can be found here:
/C:/Users/petr/DOWNLO~1/FIJI-W~1/Fiji.app/jars/jna-4.5.2.jar
/C:/Users/petr/DOWNLO~1/FIJI-W~1/Fiji.app/plugins/OMERO.fiji-5.5.4-SNAPSHOT/omero_fiji-5.5.4-SNAPSHOT-all.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: com.sun.jna.Native.load(Ljava/lang/String;Ljava/lang/Class;Ljava/util/Map;)Lcom/sun/jna/Library;
	at com.sun.jna.platform.win32.Version.<clinit>(Version.java:37)
	at org.openmicroscopy.shoola.env.data.model.appdata.WindowsApplicationDataExtractor.extractAppData(WindowsApplicationDataExtractor.java:236)
	at org.openmicroscopy.shoola.env.data.model.ApplicationData.<init>(ApplicationData.java:112)
	at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.readExternalApplications(TreeViewerFactory.java:477)
	at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:427)
	at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:193)
	at org.openmicroscopy.shoola.agents.treeviewer.TreeViewerAgent.activate(TreeViewerAgent.java:661)
	at org.openmicroscopy.shoola.env.Container.activateAgents(Container.java:327)
	at org.openmicroscopy.shoola.env.Container.startService(Container.java:360)
	at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:197)
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:488)
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:412)
	at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:272)
	at ij.IJ.runUserPlugIn(IJ.java:230)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)

	at com.sun.jna.platform.win32.Version.<clinit>(Version.java:37)
	at org.openmicroscopy.shoola.env.data.model.appdata.WindowsApplicationDataExtractor.extractAppData(WindowsApplicationDataExtractor.java:236)
	at org.openmicroscopy.shoola.env.data.model.ApplicationData.<init>(ApplicationData.java:112)
	at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.readExternalApplications(TreeViewerFactory.java:477)
	at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:427)
	at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:193)
	at org.openmicroscopy.shoola.agents.treeviewer.TreeViewerAgent.activate(TreeViewerAgent.java:661)
	at org.openmicroscopy.shoola.env.Container.activateAgents(Container.java:327)
	at org.openmicroscopy.shoola.env.Container.startService(Container.java:360)
	at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:197)
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:488)
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:412)
	at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:272)
	at ij.IJ.runUserPlugIn(IJ.java:230)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#140. See the console output for more details.
Possible conflicts:

• PR class path fix for imagej plugin #65 rgozim 'class path fix for imagej plugin'
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[rgozim]

Regardless of the above error discovered by @pwalczysko still persisting, this PR should probably still be included into insight.

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#141. See the console output for more details.
Possible conflicts:

• PR class path fix for imagej plugin #65 rgozim 'class path fix for imagej plugin'
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[jburel]

The fat jar did not solve the problem. We can revisit when we have a bit more time.
Also from feedback, it will be good to include the config dir in the jar since that was the source of several problems during training sessions.

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-insight-push#147. See the console output for more details.
Possible conflicts:

• Upstream changes
  • buildSrc/src/main/groovy/org/openmicroscopy/InsightBasePlugin.groovy

--conflicts

[jburel]

Closing in favour of #72