[ome-devel] Customising OMERO client software

[josh.moore at gmx.de]

Hi Mark.

Woodbridge, Mark R writes:
 > > Did setting ICE_HOME in your environment not work?
 > 
 > Thanks. I didn't know about that one! I actually tried to avoid building
 > the ICE stuff completely (by having no.ice=true in etc/local.properties)
 > but that didn't work. It doesn't matter though, because the full build
 > was successful (if a bit slow) and I won't be running it again.

If you happen to still know, what was the problem you had with the
with the no.ice build? I just tested:

ant clean cleantools quick build dist

with no.ice=true.

 > > The newly built jar should be under build/jar/bio-formats.jar. Note:
 > > if you need a version other than 3935, let us know. OMERO 
 > > won't work with all version of bio-formats.
 > 
 > I noticed that the importer won't compile with the latest bio-formats.

Exactly.

 > However, I can easily modify and build 3935 and put it in
 > lib/repository(?). 

Yes. Overwrite the jar that's present in the clean checkout.

 > I was concerned that I would be missing any
 > OMERO-specific patches though. 

Possibly. I'm attaching a patch here, which should work. Brian, do you
see any problems with this? Would Mark also need a patch for the importer?

 > The filename
 > (bio-formats-r3935-patched.jar) and the existence of the
 > components/bioformats-omero implies that you've made some changes? Will
 > the importer run ok with a vanilla bio-formats library?

bioformats-omero is the component which will be removed. But
nevertheless, no, OMERO will not necessarily work with a vanilla
bio-formats library, since Brian makes changes which eventually get
sent back upstream.

 > Finally, I'm not sure whether this is significant, but whenever I do
 > upload an image using the importer it appears to complete successfully
 > but I get the following error logged to the console:
 > 
 > java.sql.SQLException: Column not found: FILEPATH in statement [INSERT
 > INTO file_table(importID, experimenterID, rowNum, filename, projectID,
 > datasetID, date, status, filepath)]
 > 	at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
 > 	at org.hsqldb.jdbc.jdbcStatement.fetchResult(Unknown Source)
 > 	at org.hsqldb.jdbc.jdbcStatement.executeUpdate(Unknown Source)
 > 	at ome.formats.importer.HistoryDB.update(HistoryDB.java:350)
 > 	at
 > ome.formats.importer.HistoryDB.insertFileHistory(HistoryDB.java:311)
 > 	at
 > ome.formats.importer.ImportHandler.importImages(ImportHandler.java:145)
 > 	at
 > ome.formats.importer.ImportHandler.access$000(ImportHandler.java:36)
 > 	at
 > ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)

That means that your system is not configured for HSQLDB, but the
importer will work regardless.

 > Mark.
~Josh.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: bioformats-r3935.patch
Type: application/octet-stream
Size: 9155 bytes
Desc: not available
Url : http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20080611/a48e3c96/attachment-0001.obj