Open Microscopy Environment

I cannot find the Insight client application in the trunk. Has it been renamed omero_client.jar? If so, how do you run it. There is no helper script to launch it like the importer has and "java -jar omero_client.jar" cannot find the necessary classes.

cd ~/omero/trunk/components/tools/OmeroJava/target
java -jar omero_client.jar

Steve wrote:I cannot find the Insight client application in the trunk. Has it been renamed omero_client.jar? If so, how do you run it. There is no helper script to launch it like the importer has and "java -jar omero_client.jar" cannot find the necessary classes.

cd ~/omero/trunk/components/tools/OmeroJava/target
java -jar omero_client.jar

OMERO.insight is in its own Subversion repository:

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svn co http://svn.openmicroscopy.org.uk/svn/shoola/trunk INSIGHT-TRUNK

Hi Steve,

Insight has its own source code repository:http://svn.openmicroscopy.org.uk/svn/shoola/trunk and development trac http://trac.openmicroscopy.org.uk/shoola/wiki

You can launch it by changing to the "build" directory, and running:

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java build compile run


or you can download the latest builds from: http://hudson.openmicroscopy.org.uk/job/INSIGHT

Cheers,
~Josh

Thanks, I was able to follow the Hutson link, download the Linux zip file, extract and run the latest Insight.

I also downloaded the trunk source to Insight but I was unable to build. Am I missing some components? Here is the error I get.

$ java build
Buildfile: build.xml

BUILD FAILED
java.lang.NoSuchMethodError: org.mozilla.javascript.Context.getDebuggableEngine()Lorg/mozilla/javascript/debug/DebuggableEngine;
at org.apache.bsf.engines.javascript.JavaScriptEngine.eval(Unknown Source)
at org.apache.bsf.util.BSFEngineImpl.exec(Unknown Source)
at org.apache.bsf.BSFManager$6.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at org.apache.bsf.BSFManager.exec(Unknown Source)
at org.apache.tools.ant.util.ScriptRunner.executeScript(ScriptRunner.java:128)
at org.apache.tools.ant.taskdefs.optional.script.ScriptDef.executeScript(ScriptDef.java:317)
at org.apache.tools.ant.taskdefs.optional.script.ScriptDefBase.execute(ScriptDefBase.java:47)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275)
at org.apache.tools.ant.Task.perform(Task.java:364)
at org.apache.tools.ant.Target.execute(Target.java:341)
at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:125)
at org.apache.tools.ant.taskdefs.ImportTask.execute(ImportTask.java:142)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275)
at org.apache.tools.ant.Task.perform(Task.java:364)
at org.apache.tools.ant.Target.execute(Target.java:341)
at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:133)
at org.apache.tools.ant.ProjectHelper.configureProject(ProjectHelper.java:91)
at org.apache.tools.ant.Main.runBuild(Main.java:658)
at org.apache.tools.ant.Main.startAnt(Main.java:188)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at build.startAnt(build.java:304)
at build.main(build.java:332)

Total time: 0 seconds
java.lang.NoSuchMethodError: org.mozilla.javascript.Context.getDebuggableEngine()Lorg/mozilla/javascript/debug/DebuggableEngine;
at org.apache.bsf.engines.javascript.JavaScriptEngine.eval(Unknown Source)
at org.apache.bsf.util.BSFEngineImpl.exec(Unknown Source)
at org.apache.bsf.BSFManager$6.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at org.apache.bsf.BSFManager.exec(Unknown Source)
at org.apache.tools.ant.util.ScriptRunner.executeScript(ScriptRunner.java:128)
at org.apache.tools.ant.taskdefs.optional.script.ScriptDef.executeScript(ScriptDef.java:317)
at org.apache.tools.ant.taskdefs.optional.script.ScriptDefBase.execute(ScriptDefBase.java:47)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275)
at org.apache.tools.ant.Task.perform(Task.java:364)
at org.apache.tools.ant.Target.execute(Target.java:341)
at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:125)
at org.apache.tools.ant.taskdefs.ImportTask.execute(ImportTask.java:142)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275)
at org.apache.tools.ant.Task.perform(Task.java:364)
at org.apache.tools.ant.Target.execute(Target.java:341)
at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:133)
at org.apache.tools.ant.ProjectHelper.configureProject(ProjectHelper.java:91)
at org.apache.tools.ant.Main.runBuild(Main.java:658)
at org.apache.tools.ant.Main.startAnt(Main.java:188)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at build.startAnt(build.java:304)
at build.main(build.java:332)
org.mozilla.javascript.Context.getDebuggableEngine()Lorg/mozilla/javascript/debug/DebuggableEngine;

Hmmm... that sounds quite odd. Is it possible that the zip was corrupted during download? I just tried the following which completed normally.

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jmoore@necromancer ~/tmp $ wget -q http://hudson.openmicroscopy.org.uk/job/INSIGHT/lastSuccessfulBuild/artifact/trunk/OUT/dist/OMERO.insight-source-r6709.zip/lastSuccessfulBuild/artifact/trunk/OUT/dist/OMERO.insight-source-r6709.zip
jmoore@necromancer ~/tmp $ unzip -q OMERO.insight-source-r6709.zip
jmoore@necromancer ~/tmp $ cd build
jmoore@necromancer ~/tmp/build $ java build compile run
Buildfile: build.xml

init:
    [mkdir] Created dir: /home/jmoore/tmp/OUT

app-init:
    [mkdir] Created dir: /home/jmoore/tmp/OUT/app
    [mkdir] Created dir: /home/jmoore/tmp/OUT/app/compiled
    [mkdir] Created dir: /home/jmoore/tmp/OUT/app/config
    [mkdir] Created dir: /home/jmoore/tmp/OUT/app/lib
     [copy] Copying 613 files to /home/jmoore/tmp/OUT/app/compiled
...


I downloaded OMERO.insight-r6706-b1114.zip (no source code) and that ran.

However, for the source I didn't download the zip file but used subversion.

$ cd ~/omero/insighttrunk
$ svn co http://svn.openmicroscopy.org.uk/svn/shoola .
$ svn update
At revision 6710.
$ cd build
$ java build compile run
Buildfile: build.xml

BUILD FAILED
java.lang.NoSuchMethodError: org.mozilla.javascript.Context.getDebuggableEngine()Lorg/mozilla/javascript/debug/DebuggableEngine;
...

What Java version are you using?

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josh@mac:~$ java -version
java version "1.5.0_19"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_19-b02-306)
Java HotSpot(TM) Client VM (build 1.5.0_19-138, mixed mode, sharing)


I was using OpenJDK that comes with Ubuntu as my default. I changed to use Sun's version and the problem went away! Thanks.

For reference you can see your Java alternatives with
$ update-java-alternatives -l
java-6-openjdk 1061 /usr/lib/jvm/java-6-openjdk
java-6-sun 63 /usr/lib/jvm/java-6-sun

To change your default to Sun.
$ sudo update-java-alternatives -s java-6-sun

To verify your default.
$ java -version
java version "1.6.0_16"
Java(TM) SE Runtime Environment (build 1.6.0_16-b01)
Java HotSpot(TM) Client VM (build 14.2-b01, mixed mode, sharing)

Thanks for tracking that down, Steve. It's unfortunate that OpenJDK doesn't currently work. Moving forward we'll try to get that working. But for the 4.1 release, I'll make a mention of your instructions. Cheers, ~J.