Open Microscopy Environment

Under Ubuntu 12.04 (kernel ver. 3.2.0-26, 64b, Java7-32b) I get the following error when I try to start OMERO.importer GUI (4.4.0, ice34):

Code: Select all

Starting OMERO.importer...
Suitable java version found [java = 1.7.0_05]
Configuring environment...
Java exec found in PATH. Verifying...
Loading OMERO.importer:
java -Xmx512m -cp "./OmeroImporter.jar:./omero.insight.jar:./libs/asm-1.5.3.jar:./libs/asm-attrs-1.5.3.jar:./libs/bio-formats-4.4.0-ice34-b3033.jar:./libs/bufr-1.1.00.jar:./libs/cglib-nodep-2.2.jar:./libs/common-4.4.0-ice34-b3033.jar:./libs/commons-codec-1.3.jar:./libs/commons-collections-3.2.jar:./libs/commons-httpclient-3.1.jar:./libs/commons-io-1.4.jar:./libs/commons-logging-1.1.1.jar:./libs/dsl-4.4.0-ice34-b3033.jar:./libs/grib-5.1.03.jar:./libs/gtkjfilechooser-1.4.8.jar:./libs/hibernate-3.5.6-4510.jar:./libs/ini4j-0.3.2.jar:./libs/jai_imageio-4.4.0-ice34-b3033.jar:./libs/java-getopt-1.0.13.jar:./libs/jul-to-slf4j-1.5.8.jar:./libs/loci-common-4.4.0-ice34-b3033.jar:./libs/log4j-1.2.14.jar:./libs/mdbtools-java-4.4.0-ice34-b3033.jar:./libs/metakit-4.4.0-ice34-b3033.jar:./libs/model-psql-4.4.0-ice34-b3033.jar:./libs/netcdf-4.0.jar:./libs/ome-io-4.4.0-ice34-b3033.jar:./libs/omero_client-4.4.0-ice34-b3033.jar:./libs/omero-clients-util-r7223-b1483.jar:./libs/ome-xml-4.4.0-ice34-b3033.jar:./libs/org.springframework.asm-3.0.1.RELEASE-A.jar:./libs/org.springframework.beans-3.0.1.RELEASE-A.jar:./libs/org.springframework.context-3.0.1.RELEASE-A.jar:./libs/org.springframework.core-3.0.1.RELEASE-A.jar:./libs/org.springframework.expression-3.0.1.RELEASE-A.jar:./libs/org.springframework.jdbc-3.0.1.RELEASE-A.jar:./libs/org.springframework.orm-3.0.1.RELEASE-A.jar:./libs/org.springframework.transaction-3.0.1.RELEASE-A.jar:./libs/perf4j-0.9.10.jar:./libs/poi-loci-4.4.0-ice34-b3033.jar:./libs/romio-4.4.0-ice34-b3033.jar:./libs/scifio-4.4.0-ice34-b3033.jar:./libs/serializer-2.7.1.jar:./libs/slf4j-api-1.5.8.jar:./libs/slf4j-log4j12-1.5.8.jar:./libs/specification-4.4.0-ice34-b3033.jar:./libs/swingx-0.9.4.jar:./libs/TableLayout-bin-jdk1.5-2009-08-26.jar:./libs/xalan-2.7.1.jar" -Djava.library.path="/home/jciach/opt/OMERO.importer"  ome.formats.importer.gui.GuiImporter
Exception in thread "main" java.lang.NullPointerException
   at ome.formats.importer.gui.GuiImporter.<init>(GuiImporter.java:199)
   at ome.formats.importer.gui.GuiImporter.main(GuiImporter.java:1238)
Exit from OMERO.importer complete
OMERO.importer TERMINATED.

CLI version of the importer (as well as other OMERO software) works without any problems.

The OMERO.importer GUI as you know it is deprecated, you'll want to use the OMEROimporter_unix.sh startup script. All imports from 4.3.0 forward can also be done via OMERO.insight. That being said though, how did you produce your OMERO.importer folder? Just download the Linux clients from the website and renamed the folder OMERO.importer?

(To be honest I must admit, that I didn't know that OMERO.importer GUI was deprecated.)
I've just tried OMEROimporter_unix.sh and it works.

cxallan wrote:how did you produce your OMERO.importer folder? Just download the Linux clients from the website and renamed the folder OMERO.importer?

Yes, I simply renamed the folder from OMERO.importer-4.4.0-ice34-b3033 to OMERO.importer

And now a question arised in my head: why is OMERO.imported GUI included in 'OMERO.importer-4.4.0-ice34-b3033.zip', though it's deprecated and does not work?

jacek.ciach wrote:And now a question arised in my head: why is OMERO.imported GUI included in 'OMERO.importer-4.4.0-ice34-b3033.zip', though it's deprecated and does not work?

Completely an oversight on our parts. Apologies. We'll remove it in the next version.

Sorry again for any confusion.
~Josh