Hi, 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. Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer ================================== > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Emil Lundberg > Sent: 05 September 2007 10:34 > To: BASE ML > Subject: [base] BatchDataImporter broken w/ 2.4? > > 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 > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
