From 3921ff16e30d7886f6122a110871a13c9ce08a88 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 1 Dec 2010 08:17:07 +0000
Subject: [PATCH] LMS-1883 bug fixed
SVN: 18944
---
.../CsvFeatureVectorMigrator.java | 3 +--
.../CsvToCanonicalFeatureVector.java | 24 +++++++++++++++----
.../FeatureVectorStorageProcessor.java | 3 +--
...reVectorStorageProcessorConfiguration.java | 14 +++++++++++
4 files changed, 36 insertions(+), 8 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
index a7dd36f72da..1ebcb450341 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
@@ -49,8 +49,7 @@ public class CsvFeatureVectorMigrator extends AbstractFeatureVectorMigrator
this.configuration = new FeatureVectorStorageProcessorConfiguration(properties);
convertorConfig =
- new CsvToCanonicalFeatureVectorConfiguration(configuration.getWellRow(),
- configuration.getWellColumn());
+ new CsvToCanonicalFeatureVectorConfiguration(configuration);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
index fff41bff674..e79cb1d878d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
@@ -52,10 +52,23 @@ public class CsvToCanonicalFeatureVector
private final boolean isSplit;
+ private final Set<String> columnsToBeIgnored;
+
+ public CsvToCanonicalFeatureVectorConfiguration(FeatureVectorStorageProcessorConfiguration config)
+ {
+ this(config.getWellRow(), config.getWellColumn(), config.getColumnsToBeIgnored());
+ }
+
public CsvToCanonicalFeatureVectorConfiguration(String wellRow, String wellColumn)
+ {
+ this(wellRow, wellColumn, Collections.<String> emptySet());
+ }
+
+ public CsvToCanonicalFeatureVectorConfiguration(String wellRow, String wellColumn, Set<String> columnsToBeIgnored)
{
this.wellRowColumn = wellRow;
this.wellColumnColumn = wellColumn;
+ this.columnsToBeIgnored = columnsToBeIgnored;
isSplit = (false == wellRow.equals(wellColumn));
}
@@ -74,6 +87,11 @@ public class CsvToCanonicalFeatureVector
{
return isSplit;
}
+
+ public boolean shouldColumnBeIgnored(String column)
+ {
+ return columnsToBeIgnored.contains(column);
+ }
}
private final CsvToCanonicalFeatureVectorConfiguration configuration;
@@ -257,16 +275,14 @@ public class CsvToCanonicalFeatureVector
for (int i = 0; i < header.length; ++i)
{
String headerName = header[i];
- boolean isWellName;
+ boolean isWellName = true;
if (configuration.getWellRowColumn().equals(headerName))
{
xColumn = i;
- isWellName = true;
} else if (configuration.getWellColumnColumn().equals(headerName))
{
yColumn = i;
- isWellName = true;
- } else
+ } else if (configuration.shouldColumnBeIgnored(headerName) == false)
{
isWellName = false;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
index f4506727b96..326cd5db600 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
@@ -67,8 +67,7 @@ public class FeatureVectorStorageProcessor extends AbstractDelegatingStorageProc
super(properties);
this.configuration = new FeatureVectorStorageProcessorConfiguration(properties);
convertorConfig =
- new CsvToCanonicalFeatureVectorConfiguration(configuration.getWellRow(),
- configuration.getWellColumn());
+ new CsvToCanonicalFeatureVectorConfiguration(configuration);
this.dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
this.openBisService = ServiceProvider.getOpenBISService();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessorConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessorConfiguration.java
index 1c443f6c6a3..d6780668f84 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessorConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessorConfiguration.java
@@ -16,7 +16,10 @@
package ch.systemsx.cisd.openbis.dss.etl.featurevector;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.Properties;
+import java.util.Set;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration;
@@ -48,6 +51,8 @@ class FeatureVectorStorageProcessorConfiguration implements
private final String wellColumn;
+ private final Set<String> columnsToBeIgnored;
+
FeatureVectorStorageProcessorConfiguration(Properties properties)
{
comment = '#';
@@ -60,6 +65,10 @@ class FeatureVectorStorageProcessorConfiguration implements
this.wellRow = properties.getProperty(WELL_NAME_ROW_PROPERTY_KEY, DEFAULT_WELL_ROW);
this.wellColumn = properties.getProperty(WELL_NAME_COL_PROPERTY_KEY, DEFAULT_WELL_COL);
+
+ columnsToBeIgnored =
+ new HashSet<String>(Arrays.asList(properties.getProperty("columns-to-be-ignored",
+ "barcode").split(", *")));
}
public char getColumnDelimiter()
@@ -91,4 +100,9 @@ class FeatureVectorStorageProcessorConfiguration implements
{
return wellColumn;
}
+
+ public final Set<String> getColumnsToBeIgnored()
+ {
+ return columnsToBeIgnored;
+ }
}
\ No newline at end of file
--
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