[ome-devel] OMERO API Import: Exception on Pixels download inside Insight

[Chris Allan]

On 11 Mar 2008, at 16:52, Jost Gundelach wrote:

> Hello there,

Hi Jost.

>
> thanks for help Chris. But the top level build does not create the  
> 'target/generated/resources' :-|
>
> Still I try get the importer to run in the Eclipse environment, but  
> I needed up to now the following workarounds to solve some problems:
>
> 1.
> To get the 'target/generated/resources' I copied the ivy.xml from  
> base directory and cleared the dependencies. The build had then  
> some problems I ignored ;-)
>
> -----snip------snip------snip------
> /home/omero/devel/omero3.0-Beta2.3/components/bioformats-omero/src/ 
> ome/formats/importer/ImportFixture.java:24: package  
> ome.model.containers does not exist
> import ome.model.containers.Dataset;
> -----snip------snip------snip------
>
> 2.
> The loci.formats.ome.OMEXML2003FCMetadata missed the imports from  
> org.openmicroscopy.xml.*. To fix this, I downloaded the ome- 
> java.jar from http://www.loci.wisc.edu/ome/formats.html and put it  
> into the library path.
>
> 3.
> Also I had to download jgoodies forms
>
> 4.
> testNG I found in lib\repository\testng\testng\5.2-jdk15
>
> Now I am looking for fixes of unresolved types from the following  
> imports
> loci.formats.ome.OMEUtils.java misses the imports ij.gui (ImageJ  
> API) and loci.plugins
> omero.importer.engine.OMEROMetadataStore.java misses  
> loci.formats.MetadataStore and loci.formats.MetadataStoreException
> MetadataAutogen misses import org.apache.velocity.*.*
>
>
> I am getting the feeling, that Eclipse is not supported or used for  
> a long time ! Or what did I wrong?
> We are focused at omero3.0-Beta2.3 and can not change our  
> development to trunk now at this point!

There's nothing per say wrong with using Eclipse or  
the .classpath/.project files that are in the bioformats-omero  
component it's just that certain packages don't compile. You can  
basically ignore all the build failures from the all the above points  
(1), (2), (3) and (4).

You should be able to safely remove target/generated/resources from  
the .classpath that's likely an oversight, there's nothing the  
component specifically needs from that directory as far as I can recall.

>
> Again: I wish to get my files archived, which does not work with  
> the following code:
>
> File[] files2store = new File[] {myTiffFile};
> store.setOriginalFiles(files2store);
>
> // Code mostly copied from ImportFixture
>
> store.writeFilesToFileStore(files2store, pixId.get(0).getId());
>
> This do not produce any file in the servers /OMERO/Files directory.  
> I am not able to debug the JBoss, because I don't get the  
> breakpoint to work in the RawFileBean.write method. The remote  
> debugger does not halt on the breakpoint.

Unless you have written a Pixels object (with an OriginalFile linked)  
to the database this method will do a grand total of nothing and will  
spit errors to STDERR.

>
> howl........thanks a lot for help...... a kingdom for ....

No problem at all.

>
> Best Regards
> Jost

Ciao.

-Chris