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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