Hi Bob, > I had a problem (stack trace) with the Tab2MageImporter on my first attempt > and am awaiting a reply from Dominic - but assume he is on vacation.
Could you please remind me of what the stack trace was about as I could not find an email about it. Thanks. ¬Dominic Bob MacCallum wrote: > Hi Micha, > > I vote for singing and dancing. > > > cheers, > Bob > > PS. The following attribution to "Bob" may be incorrect - it's certainly not > me. > > > > We've recently started to try the BatchDataImporter plugin > > > contributed by Bob/SCRI. Under BASE 2.4 (release), this invariably > > > Micha Bayer writes: > > 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] > -- Dominic Oyeniran ******************************* NET Project - Software Engineer European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: +44 (0)1223 492 561 Fax: +44 (0)1223 494 468 Url: http://www.ebi.ac.uk/~oyeniran Project page: www.ebi.ac.uk/net-project ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. 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