Hi Micha,
I did another test run with a non-root user, as you suggested and the
import failed (see the exception). I have stated what I noticed below.
Please check them out in addition to the suggestion by Nicklas
=====================================
===========NEW BATCH IMPORT =========
=====================================
zn =HG-U133A.cdf
experiment: Experiment[id=6; name=New experiment]
file selected: affyMicher.zip
user = Dominic
net.sf.basedb.core.ItemNotFoundException: Item not found:
Directory[path=/home/d
ominic/raw data]
at net.sf.basedb.core.Directory.getIdFromPath(Directory.java:236)
at net.sf.basedb.core.Directory.getByPath(Directory.java:179)
at sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:143)
at sbrn.base.BatchDataImport.importData(BatchDataImport.java:197)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)
1. raw data sub directory must be created before hand for the import to
work.
2. User Quota for files needs to be greater than the file size to be
imported. If this is not done the import fails.
These should either be specified in the documentation or better still
handled in the code with appropriate messages.
Also, despite creating an affy experiment with raw data type correctly
specified, I got the ff exception:
java.lang.Exception: Affymetrix data found but Experiment data type was
specified
as non-Affy
at sbrn.base.BatchDataImport.importData(BatchDataImport.java:294)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
t.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
a:420)
at java.lang.Thread.run(Thread.java:595)
Hope this helps. Thanks. Got to move on now.
¬Dominic
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