Nicklas Nordborg wrote:
> Micha Bayer wrote:
>
>> 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$JobRunner.run(InternalJobQueue.ja
>>> va:420)
>>> at java.lang.Thread.run(Thread.java:595)
>>>
>>> -----------------
>>> Is this happeneing because of the file format you mentioned in your
>>>
>> read
>>
>>> me note? The zippped file is in affy format and containes 4 cel file
>>>
>> and
>>
>>> a cdf file. (5 files in total)
>>>
>> This looks like you are running this as user root. For some reason, user
>> root does not seem to have a home directory but the code needs to find
>> the user's home directory so that it can unzip the file there.
>>
>
> A user is not required to have a home directory. The home directory may
> be null for any user. To solve this the plugin could for example ask for
> a directory where the file should be unzipped (use a PathParameterType
> object for this). The default value of this directory could then be set
> to the user's home directory or maybe even better, the same directory
> where the zipped file is located.
>
> /Nicklas
>
>
Thanks for your response Micha. I agree with Nicklas on how to resolve
the directory issue.
Cheers,
¬Dominic
> > If youectory
>> o I can try to reproduce the error here.
>>
>> I'll also put a note in to the documentation to that extent.
>>
>>
>>
>>> Also
>>>
>>> ------------------
>>> 7:59:52,287 WARN DbControl:1046 - Found unclosed DbControl during
>>> finalize; is
>>> LoggedIn = true; clientId = 0; userId = 1
>>> java.lang.Throwable: Please check the code to make sure that
>>> DbControl.close() i
>>> s always called. Stacktrace of code that created this DbControl:
>>> at net.sf.basedb.core.DbControl.<init>(DbControl.java:140)
>>> at
>>> net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
>>> 0)
>>> at sbrn.base.BatchDataImport.<init>(BatchDataImport.java:109)
>>> at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
>>> at
>>> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
>>> st.java:88)
>>> at
>>> net.sf.basedb.core.InternalJobQueue$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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