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 IDF595 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
==
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