Yes, that is 'true' by default.  (Wipes brow, glad I didn't miss that one!)

When I set the "item not found" response to "fail"
I get the following stack trace:


net.sf.basedb.core.BaseException: Item not found: 
Sample[name=gcfk_anotis_carcass_g1] on line 2: gcfk_anotis_carca...
at 
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:626)
at 
net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:441)
at 
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:108)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:487)
at java.lang.Thread.run(Thread.java:619)
Caused by: net.sf.basedb.core.ItemNotFoundException: Item not found: 
Sample[name=gcfk_anotis_carcass_g1]
at 
net.sf.basedb.plugins.AnnotationFlatFileImporter.handleData(AnnotationFlatFileImporter.java:705)
at 
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:597)
... 4 more


and, yes, the item really is there.  If I run the same plugin on the same text
file while impersonating the item's owner it works fine.  (I did this for
around 5 users as a workaround.  Note/tip: if you need to provide a "shared"
directory for all users to read it has to be under /home/ and of course have
Everyone read/use permissions.)


I'm running 2.6.2pre (==2.6.1) on a pretty standard system.

cheers,
Bob


Nicklas Nordborg writes:
 > Bob MacCallum wrote:
 > > Hi all,
 > > 
 > > I'm having difficulty getting my head around plugin permissions or perhaps
 > > there's a bug here.
 > > 
 > > I want to annotate samples or biosources while logged in as Administrator.
 > > Some of the items belong to Administrator and these get annotated OK,
 > > while the items belonging to other users are not annotated.  There's
 > > a warning like this in the Job output:
 > > 
 > > Done: 12 item(s) annotated with 12 annotation(s) (12 was replaced); 139 
 > > row(s) skipped because no item was found
 > 
 > 
 > > any ideas, other than to take ownership of these items?
 > 
 > Have you selected the "Owned by others" option in the last step of of 
 > importer wizard?
 > 
 > /Nicklas
 > 
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-- 
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]

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