Hi again, Just occurred to me that perhaps I might be barking up the wrong tree here altogether and that the flags should in fact be e.g. 0 and 1 instead of actual Strings like "NORMAL"?
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 Micha Bayer > Sent: 05 October 2007 10:21 > To: BASE ML > Subject: [base] BASE2: problem parsing flag strings to floats > > Hi, > > I am trying to import some raw data with flags such as "NORMAL" and > "ABNORMAL" into raw bioassays. I have mapped this column to the 'Flags' > field in the raw data importer config for Genepix format (this is on > BASE 2.3.0). For some reason the importer chokes on the values for the > flags though and throws a NumberFormatException. It looks to me as > though it is trying to parse the String to a float -- see stack trace > below. > In the raw-data-types.xml config file the Flags field for the Genepix > data format is listed as being an integer type. Could that be the > problem? Is this a problem with my setup or potentially a bug, and has > anyone else seen this behaviour? > > Cheers > > Micha > > ===================first 2 lines from the data > file:================================= > > Name Clone ID F595 median F685 median B595 median > B685 median Flagged As Block Column Row > 3xSLv1 (-)3xSLv1 323 461.5 137.5 190 NORMAL 1 > 3 1 > > ==============stack trace:============ > > 09:28:40,961 ERROR jobqueue:434 - Exception while executing job: > Job[id=336; name=Run plugin: Raw data importer] > net.sf.basedb.core.BaseException: For input string: "NORMAL" on line 2: > 3xSLv1 (-)3xSLv1... > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java > : > 428) > at java.lang.Thread.run(Thread.java:619) > Caused by: net.sf.basedb.core.BaseException: For input string: "NORMAL" > on line 2: 3xSLv1(-)3xSLv1 ... > at > net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFil > e > Importer.java:581) > at > net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImpo > r > ter.java:432) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest > . > java:88) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java > : > 420) > ... 1 more > Caused by: java.lang.NumberFormatException: For input string: "NORMAL" > at > sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224 > ) > at java.lang.Float.valueOf(Float.java:388) > at net.sf.basedb.core.Type$1.parseString(Type.java:72) > at > net.sf.basedb.core.ExtendedProperty.parseString(ExtendedProperty.java:1 > 7 > 9) > at > net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(RawDataFlatFil > e > Importer.java:536) > at > net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFil > e > Importer.java:559) > ... 4 more > > ================================== > 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 > ================================== > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ _ > > 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. 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