Dear BASErs,
I'm having problems configuring the raw data importer to import data from a
ScanArray CSV file into a new raw data table that I created by modifying
raw-data-types.xml. Every plugin configuration I try returns a
NullPointerException error. Can you give me some clues on how I might fix this?
The plugin automatically identifies the correct file type, but it freturns the
error whether I have all of the error checking options set to "fail" or "skip".
I am able to import GPR raw data files into the RawDataGenePix table using a
GenePix configuration without any problems.
Error message, plugin job parameters, db schema, and new edits to
raw-data-types.xml are below.
Thanks,
Jim Collett
James R. Collett, Ph.D.
Systems Biology Fellow
Battelle Memorial Institute
Biological Sciences Division
Pacific Northwest National Laboratory
PO Box 999
MS P7-58
Richland, WA 99354
------------------------------------------------------------------------------------------------------
java.lang.NullPointerException
at net.sf.basedb.util.parser.ConstantMapper.<init>(ConstantMapper.java:70)
at net.sf.basedb.util.parser.FlatFileParser.getMapper(FlatFileParser.java:865)
at net.sf.basedb.util.parser.FlatFileParser.getMapper(FlatFileParser.java:789)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.getMapper(AbstractFlatFileImporter.java:870)
at
net.sf.basedb.plugins.RawDataFlatFileImporter.beginData(RawDataFlatFileImporter.java:489)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:562)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:442)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
at java.lang.Thread.run(Thread.java:619)
---------------------------------
Job parameters
Character set ISO-8859-1
Decimal separator dot
Default error handling skip
featureMismatchError
File /home/jim/raw data/exp091806_slide1_LP65_nameIDblock2.csv
Missing a required value skip
Reporter not found skip
Invalid numeric value skip
Numeric value out of range skip
Raw bioassay exp091806_slide1_LP65_nameIDblock.csv.rba
String too long skip
Plugin configuration parameters
Parameter version 4 (4)
Block \Block\
Character set ISO-8859-1
Column \Spot Column\
Data footer ^END\sDATA
Data header \QIndex,Block,Array Row,Array Column,Spot Row,Spot
Column,Name,ID,X,Y,Diameter,F Pixels,B Pixels,Footprint,Flags,Ch1 Median,Ch1
Mean,Ch1 SD,Ch1 B Median,Ch1 B Mean,Ch1 B SD,Ch1 % > B + 1 SD,Ch1 % > B + 2
SD,Ch1 F % Sat.,Ch1 Median - B,Ch1 Mean - B,Ch1 SignalNoiseRatio\E
Data splitter ,
Decimal separator dot
Header
Ignore
Max data columns
MetaGridX \Array Row\
MetaGridY \Array Column\
Min data columns
B Pixels \B Pixels\
Ch1 B Mean \Ch1 B Mean\
Ch1 B Median \Ch1 B Median\
Ch1 B SD \Ch1 B SD\
Ch1 F % Sat. \Ch1 F % Sat.\
Ch1 Mean \Ch1 Mean\
Ch1 Mean - B \Ch1 Mean - B\
Ch1 Median \Ch1 Median\
Ch1 Median - B \Ch1 Median - B\
Ch1 % > B + 1 SD \Ch1 % > B + 1 SD\
Ch1 % > B + 2 SD \Ch1 % > B + 2 SD\
Ch1 SD \Ch1 SD\
Ch1 SignalNoiseRatio \Ch1 SignalNoiseRatio\
Diameter \Diameter\
F Pixels \F Pixels\
Flags \Flags\
Footprint \Footprint\
Raw data type scanarray1chCSV
Reporter ID \ID\
Row \Spot Row\
Remove quotes true
X \X\
Y \Y\
-----------------------------------
mysql> describe RawDataScanArray1chCSV;
+------------------------+---------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+------------------------+---------+------+-----+---------+----------------+
| id | int(11) | NO | PRI | NULL | auto_increment |
| version | int(11) | NO | | | |
| rawbioassay_id | int(11) | NO | MUL | | |
| feature_id | int(11) | YES | MUL | NULL | |
| reporter_id | int(11) | YES | MUL | NULL | |
| position | int(11) | NO | | | |
| x | float | YES | | NULL | |
| y | float | YES | | NULL | |
| block | int(11) | YES | | NULL | |
| metagrid_x | int(11) | YES | | NULL | |
| metagrid_y | int(11) | YES | | NULL | |
| row | int(11) | YES | | NULL | |
| column | int(11) | YES | | NULL | |
| diameter | int(11) | YES | | NULL | |
| fgPixels | int(11) | YES | | NULL | |
| bgPixels | int(11) | YES | | NULL | |
| footprint | int(11) | YES | | NULL | |
| flags | int(11) | YES | | NULL | |
| ch1Median | int(11) | YES | | NULL | |
| ch1Mean | int(11) | YES | | NULL | |
| ch1SD | float | YES | | NULL | |
| ch1BgMedian | int(11) | YES | | NULL | |
| ch1BgMean | int(11) | YES | | NULL | |
| ch1BgSD | float | YES | | NULL | |
| ch1PercGrThanBgPlus1SD | int(11) | YES | | NULL | |
| ch1PercGrThanBgPlus2SD | int(11) | YES | | NULL | |
| ch1FgPercSat. | int(11) | YES | | NULL | |
| ch1MedianMinusBg | int(11) | YES | | NULL | |
| ch1MeanMinusBg | int(11) | YES | | NULL | |
| ch1SignalNoiseRatio | float | YES | | NULL | |
+------------------------+---------+------+-----+---------+----------------+
30 rows in set (0.01 sec)
--------------------------------------------------------------------------------------------------------------------------------------------
[EMAIL PROTECTED] classes]# cat raw-data-types.xml
<?xml version="1.0" ?>
<?xml-stylesheet type="text/xsl" href="raw-data-types.xsl"?>
<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" >
<!--
$Id: raw-data-types.xml 2959 2006-11-27 11:36:37Z nicklas $
Copyright (C) 2005-2006 Jari Häkkinen, Nicklas Nordborg
This file is part of BASE - BioArray Software Environment.
Available at http://base.thep.lu.se/
BASE is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published
by
the Free Software Foundation; either version 2 of the License,
or
(at your option) any later version.
BASE is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU
General Public License for more details.
You should have received a copy of the GNU General Public
License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
02111-1307, USA.
-->
<raw-data-types>
<raw-data-type
id="scanarray1chCSV"
channels="1"
name="ScanArray1chCSV"
table="RawDataScanArray1chCSV"
>
<property
name="diameter"
title="Diameter"
description=""
column="diameter"
type="int"
/>
<property
name="fgPixels"
title="F Pixels"
description=""
column="fgPixels"
type="int"
/>
<property
name="bgPixels"
title="B Pixels"
description=""
column="bgPixels"
type="int"
/>
<property
name="footprint"
title="Footprint"
description=""
column="footprint"
type="int"
/>
<property
name="flags"
title="Flags"
description=""
column="flags"
type="int"
/>
<property
name="ch1Median"
title="Ch1 Median"
description=""
column="ch1Median"
type="int"
/>
<property
name="ch1Mean"
title="Ch1 Mean"
description=""
column="ch1Mean"
type="int"
/>
<property
name="ch1SD"
title="Ch1 SD"
description=""
column="ch1SD"
type="float"
/>
<property
name="ch1BgMedian"
title="Ch1 B Median"
description=""
column="ch1BgMedian"
type="int"
/>
<property
name="ch1BgMean"
title="Ch1 B Mean"
description=""
column="ch1BgMean"
type="int"
/>
<property
name="ch1BgSD"
title="Ch1 B SD"
description=""
column="ch1BgSD"
type="float"
/>
<property
name="ch1PercGrThanBgPlus1SD"
title="Ch1 % > B + 1 SD"
description=""
column="ch1PercGrThanBgPlus1SD"
type="int"
/>
<property
name="ch1PercGrThanBgPlus2SD"
title="Ch1 % > B + 2 SD"
description=""
column="ch1PercGrThanBgPlus2SD"
type="int"
/>
<property
name="ch1FgPercSat."
title="Ch1 F % Sat."
description=""
column="ch1FgPercSat."
type="int"
/>
<property
name="ch1MedianMinusBg"
title="Ch1 Median - B"
description=""
column="ch1MedianMinusBg"
type="int"
/>
<property
name="ch1MeanMinusBg"
title="Ch1 Mean - B"
description=""
column="ch1MeanMinusBg"
type="int"
/>
<property
name="ch1SignalNoiseRatio"
title="Ch1 SignalNoiseRatio"
description=""
column="ch1SignalNoiseRatio"
type="float"
/>
</raw-data-type>
<raw-data-type
id="genepix"
channels="2"
name="GenePix"
table="RawDataGenePix"
>
-------------------------------------------------------------------------
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