This is expected. When looking for referenced items, all items are included in the search. The options you are referring to are only valid for the main type of item. Eg. in this case the samples.
/Nicklas Pawel Sztromwasser wrote: > 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 > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
