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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