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$JobRunner.run(InternalJobQueue.java:
428)
at java.lang.Thread.run(Thread.java:619)
Caused by: net.sf.basedb.core.BaseException: For input string: "NORMAL"
on line 2: 3xSLv1(-)3xSLv1 ...
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFile
Importer.java:581)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImpor
ter.java:432)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.
java:88)
at
net.sf.basedb.core.InternalJobQueue$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:17
9)
at
net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(RawDataFlatFile
Importer.java:536)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFile
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
==================================
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