> I haven't installed BASE 2.4 as yet -- will give it a go this
> afternoon
> and try out the batch importer with it.
>
> I have to admit to not having done any of the fixes/feature
> enhancements
> to the batch importer that were requested, quite simply because I was
> waiting for the Tab2MageImporter to materialize. This is now part of
> BASE 2.4 and my assumption was that most people would then want to use
> this instead(which includes part of the batch importer code anyway)
> because it does so much more than the batch importer.
>
> So this is perhaps a good time for a little straw poll - is there
> anyone
> out there who will want to continue using the plain vanilla batch
> importer even though they could be using the all singing, all dancing
> Tab2MageImporter ?
>
> If yes, I am happy to continue supporting the original batch importer,
> but I guess it will be slightly awkward because that would potentially
> also mean Dominic having to apply any fixes etc to the
> Tab2MageImporter
> because it uses batch importer code.
Hi Micha and others,
Thanks for the info. We had (amazingly) not realized the Tab2Mage
importer was an all-out replacement for the batch importer, but now
that you mention it...
Having just started to try out the latter, we are happy to go with
Tab2Mage (bells, whistles, etc) if that's where it's at. We'll get
right on it.
regards,
Emil
P.S. Got B.M. and M.B. mixed up in the original message. My bad :-)
>> Hi again,
>>
>> We've recently started to try the BatchDataImporter plugin
>> contributed by Bob/SCRI. Under BASE 2.4 (release), this invariably
>> fails, apparently due to the sucessfully unzipped files not being
>> found. Has anyone else seen this or is it just us?
>>
>> * For 2-ch data, we get the following in catalina.out:
>>
>> experiment: Experiment[id=2; name=Batch test]
>> file selected: DEMO_2_channel.zip
>> zipFile is located in dir Directory[id=50; name=demo]
>> new subDir = DEMO_2_channel030907_135900
>> quotaValue for user User[id=8; name=Demo User] = 1073741824
>> currentDiskUsage = 146562032
>> remainingSpace = 927179792
>> zipFileSize = 39238108
>> unpacking
>> numUnpackedFiles = 8
>> BatchDataImport importData
>> dir = DEMO_2_channel030907_135900
>> rawDataType = GenePix
>> instantiating dataFiles array of length 0
>> data files:
>> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
>> at java.util.ArrayList.RangeCheck(ArrayList.java:546)
>> at java.util.ArrayList.get(ArrayList.java:321)
>> at net.sf.basedb.core.ItemResultList.get
>> (ItemResultList.java:
>> 99)
>> at sbrn.base.BatchDataImport.importData
>> (BatchDataImport.java:
>> 339)
>> at
> sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
>> at net.sf.basedb.core.PluginExecutionRequest.invoke
>> (PluginExecutionRequest.java:89)
>> at net.sf.basedb.core.InternalJobQueue$JobRunner.run
>> (InternalJobQueue.java:421)
>> at java.lang.Thread.run(Thread.java:613)
>>
>>
>> * For Affy, the message is slightly different:
>>
>> zn =DEMO_AffyExpression/
>> experiment: Experiment[id=3; name=DEMO, Affy Expression]
>> file selected: DEMO_AffyExpression.zip
>> zipFile is located in dir Directory[id=33; name=Expression_1ch]
>> new subDir = DEMO_AffyExpression030907_172000
>> quotaValue for user User[id=50; name=demo = 1073741824
>> currentDiskUsage = 564826891
>> remainingSpace = 508914933
>> zipFileSize = 153247255
>> unpacking
>> numUnpackedFiles = 5
>> BatchDataImport importData
>> dir = DEMO_AffyExpression030907_172000
>> rawDataType = Affymetrix
>> java.lang.NegativeArraySizeException
>> at sbrn.base.BatchDataImport.importData
>> (BatchDataImport.java:
>> 271)
>> at
> sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
>> at net.sf.basedb.core.PluginExecutionRequest.invoke
>> (PluginExecutionRequest.java:89)
>> at net.sf.basedb.core.InternalJobQueue$JobRunner.run
>> (InternalJobQueue.java:421)
>> at java.lang.Thread.run(Thread.java:613)
>>
>>
>> * Looking at the code (BatchDataImport.java), lines 252-253 for some
>> reason returns an empty list of files:
>>
>> try
>> {
>> // list all files in dir -- this should be what we
>> // unzipped from the zip file
>> fileQuery = dir.getFiles();
>> fileList = fileQuery.list(dc);
>>
>> File[] dataFiles = null;
>> if (fileQuery != null)
>> {
>> [...]
>>
>> As fileQuery is not null but fileList is empty, it's downhill from
>> there...
>>
>>
>> We could certainly start hacking/debugging, but I thought I'd ask
>> those in the know first.
>>
>>
>> TIA,
>>
>> /Emil
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