Hi Dominic,
Thanks for trying this out.
> I tested the batch import today, on an affy experiment and I got the
ff
> exception:
> ------------
> =====================================
> ===========NEW BATCH IMPORT =========
> =====================================
> zn =HG-U133A.cdf
> experiment: Experiment[id=5; name=Batch Importer Test]
> file selected: affyMicher.zip
> java.lang.NullPointerException
> at
> sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:135)
> 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$JobRunner.run(InternalJobQueue.ja
> va:420)
> at java.lang.Thread.run(Thread.java:595)
>
> -----------------
> Is this happeneing because of the file format you mentioned in your
read
> me note? The zippped file is in affy format and containes 4 cel file
and
> a cdf file. (5 files in total)
This looks like you are running this as user root. For some reason, user
root does not seem to have a home directory but the code needs to find
the user's home directory so that it can unzip the file there. If you
are logged in as root, then
homeDir = user.getHomeDirectory();
returns null and this is where the NullPointerException is thrown. I
guess I can catch that and set an appropriate error message.
Try rerunning this as a non-root user, and if that doesn't work, can you
send me the zip file please so I can try to reproduce the error here.
I'll also put a note in to the documentation to that extent.
> Also
>
> ------------------
> 7:59:52,287 WARN DbControl:1046 - Found unclosed DbControl during
> finalize; is
> LoggedIn = true; clientId = 0; userId = 1
> java.lang.Throwable: Please check the code to make sure that
> DbControl.close() i
> s always called. Stacktrace of code that created this DbControl:
> at net.sf.basedb.core.DbControl.<init>(DbControl.java:140)
> at
> net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
> 0)
> at sbrn.base.BatchDataImport.<init>(BatchDataImport.java:109)
> at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
> st.java:88)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
> va:420)
> at java.lang.Thread.run(Thread.java:595)
> ---------------
>
> About the above warning, I suggest you close the dbcontrol object in
> your code:
> i.e. finally
> {
> if (dc != null)
> dc.close();
> }
Well spotted -- thanks. I'll get that sorted.
Cheers
Micha
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