Where is Insight and how do you launch it?

[Steve]

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

[cxallan]

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:

Code: Select all

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

[jmoore]

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:

Code: Select all

java build compile run


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

Cheers,
~Josh

[Steve]

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;

[jmoore]

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
...


[Steve]

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;
...

[jmoore]

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)


[Steve]

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)

[jmoore]

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.