Bug: cannot export downgraded OME-TIFFs from Linux or Windows

[mlinkert]

Using 4.4.1 or Insight built from the tip of develop, the downgrade schema selection is not available when exporting an image to OME-TIFF.

The exception thrown is:

java.lang.IllegalArgumentException: No Catalog found.
	at org.openmicroscopy.shoola.env.data.util.TransformsParser.parse(TransformsParser.java:168)
	at org.openmicroscopy.shoola.agents.util.ui.DowngradeChooser.parseData(DowngradeChooser.java:94)
	at org.openmicroscopy.shoola.agents.util.ui.DowngradeChooser.<init>(DowngradeChooser.java:132)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorControl.export(EditorControl.java:373)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorControl.actionPerformed(EditorControl.java:742)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
	at java.awt.Component.processMouseEvent(Component.java:6288)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
	at java.awt.Component.processEvent(Component.java:6053)
	at java.awt.Container.processEvent(Container.java:2041)
	at java.awt.Component.dispatchEventImpl(Component.java:4651)
	at java.awt.Container.dispatchEventImpl(Container.java:2099)
	at java.awt.Component.dispatchEvent(Component.java:4481)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
	at java.awt.Container.dispatchEventImpl(Container.java:2085)
	at java.awt.Window.dispatchEventImpl(Window.java:2478)
	at java.awt.Component.dispatchEvent(Component.java:4481)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643)
	at java.awt.EventQueue.access$000(EventQueue.java:84)
	at java.awt.EventQueue$1.run(EventQueue.java:602)
	at java.awt.EventQueue$1.run(EventQueue.java:600)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
	at java.awt.EventQueue$2.run(EventQueue.java:616)
	at java.awt.EventQueue$2.run(EventQueue.java:614)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:613)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

As far as I can tell, the problem is that the CLASSPATH on Linux and Windows is just 'omero.insight.jar', and 'libs/specification.jar' must be on the CLASSPATH in order for the schemas to be loaded. I would guess that this isn't an issue on Mac OS X as the CLASSPATH is set in the Info.plist.

[jburel]

I have used the latest merge-green build under Windows and do not notice the problem.
I am able

• read the catalog
• Select the schema I wish
• export a downgraded OME-TIFF w/o any problems

[jburel]

Looking closely at the code, the jar is loaded. The key ome-transforms.xml could not be found. Andrew did you modify the specification jar while I was away. Since I cannot reproduce the problem described in the ticket.

[jburel]

Any info on that one?
Gus could you test as well. I cannot reproduce it.

[jburel]

Investigating what's going on.

• Changing code so it is still possible to export even if an error occurred.

[mlinkert]

Screenshot attached of what I see when I do the following:

• download and unzip latest merge-green: OMERO.insight-4.4.1-74-aeb5eda-ice33-b127.zip
• run ./OMEROinsight_unix.sh
• log in to gretzky as user-3
• navigate to Image 11766
• click "Export as OME-TIFF" on the "General" tab

This is with Ubuntu 12.04 and Java 1.6.0_24-b07.

[jburel]

I modified the code to log the error if any. This will be available in tomorrow's build.
It could also be a UI problem when customizing the file chooser itself.

[jburel]

I managed to reproduce by building directly on Windows.
The problem only shows up when using directly the .sh or .bat files.

[jburel]

The problem occurs on all 3 platforms when running insight via the command java -jar omero.insight.jar
The commit 3426ca5cb65a6f8a56fcff3950c39a0f862d3e3b reads the manifest and determine the location of the specification.jar.

To test:

• run insight java -jar omero.insight.jar or use the .sh or .bat file depending on the platform.
• Make sure that the application works too

[jburel]

The solution in place does not work for webstart, imageJ. This will need a bit more work.

[jburel]

see #9472 for webstart

[jburel <j.burel@…>]

(In [6111e91032e98f329092b1b4a7d2bab81c1b710b/ome.git] on branch develop) Catch exception and allow to export if error (see #9407)

Log the exception. Allow to export as OME-TIFF when the catalog
cannot be read.

[jburel <j.burel@…>]

(In [3426ca5cb65a6f8a56fcff3950c39a0f862d3e3b/ome.git] on branch develop) Read Manifest to determine jars on the class path (see #9407)

Determine the location of the specification jar when
running insight via the command java -jar omero.insight.jar
The location is determined from the Manifest.

[jburel <j.burel@…>]

(In [8a13d6546cea4d7f9c7394545db042b394f5760a/ome.git] on branch develop) Modify reading of specification jar (see #9407)

This version now works for imageJ.

[jburel <j.burel@…>]

(In [49e67f631afbe754f783ce5d36b000a5df27b849/ome.git] on branch develop) Modify loader for webstart (see #9407)

[jburel <j.burel@…>]

(In [a5b6cecea5348059341324ced23a132bde1230c8/ome.git] on branch develop) Make sure the input streams are closed (see #9407)