Hi,
I had a session today explaining our lab users how to use batch
import/annotate plugins and we came across a bug (maybe). It seems like
the batch import plugin disregards some of these options (I would expect
the 3rd one):
In current project
Owned by me
Owned by others
Shared to me
To reproduce it, you have to log in as a user who has access to many
items (like administrator). First import some biosources and then the
problem occurs while importing samples linked to these biosources. If
there is more than one biosource (owned by other users) with the same
name which administrator is trying to create, plugin fails. The
identification method is 'name' of course and the plugin fails
irrespective of what combination of options above is used (dry-run log
at the end). So it looks like it doesn't filter the items to link (in
this case biosources) on permission level.
In this case natural for me would be that combination:
In current project - true
Owned by me - true
Owned by others - false
Shared to me - false
would do the job. Surprisingly when I set all the options to 'false',
the result was the same. It is Friday evening and I might be missing
something, but I thought it is better to post it before the weekend.
Cheers,
Pawel
Parsing file: batchimport_sample_my_samples.csv
Failed
Found 6 Biosource [Name, external ID or internal ID=Mouse_01] on line
2: "Treated_01" 424...
net.sf.basedb.core.BaseException: Found 6 Biosource [Name, external ID
or internal ID=Mouse_01] on line 2: "Treated_01" 424...
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:638)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:443)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:108)
at
net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.executeJob(ThreadJobExecutor.java:111)
at
net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.main(ThreadJobExecutor.java:204)
Caused by: net.sf.basedb.core.BaseException: Found 6 Biosource [Name,
external ID or internal ID=Mouse_01]
at
net.sf.basedb.plugins.batchimport.AbstractItemImporter.findReferencedItem(AbstractItemImporter.java:1472)
at
net.sf.basedb.plugins.batchimport.AbstractItemImporter.findBioSource(AbstractItemImporter.java:1213)
at
net.sf.basedb.plugins.batchimport.SampleImporter.updateItem(SampleImporter.java:274)
at
net.sf.basedb.plugins.batchimport.SampleImporter.createItem(SampleImporter.java:246)
at
net.sf.basedb.plugins.batchimport.SampleImporter.createItem(SampleImporter.java:54)
at
net.sf.basedb.plugins.batchimport.AbstractItemImporter.handleData(AbstractItemImporter.java:625)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:608)
... 4 more
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