Author: jm
Date: 2012-08-07 13:02:52 -0700 (Tue, 07 Aug 2012)
New Revision: 30112
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
Log:
References #1288: Session tables default to using UTF-8 for reading/writing.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2012-08-07 19:23:23 UTC (rev 30111)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2012-08-07 20:02:52 UTC (rev 30112)
@@ -31,19 +31,21 @@
private final boolean handleEquations;
private final CyTableFactory tableFactory;
private final EquationCompiler compiler;
+ private final String encoding;
private boolean isCanceled;
private CyTable table;
public CSVCyReader(final InputStream stream, final boolean readSchema,
final boolean handleEquations, final CyTableFactory
tableFactory,
- final EquationCompiler compiler)
+ final EquationCompiler compiler, final String
encoding)
{
this.stream = stream;
this.readSchema = readSchema;
this.handleEquations = handleEquations;
this.tableFactory = tableFactory;
this.compiler = compiler;
+ this.encoding = encoding;
}
@Override
@@ -55,7 +57,7 @@
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setProgress(0.0);
- CSVReader reader = new CSVReader(new InputStreamReader(stream));
+ CSVReader reader = new CSVReader(new InputStreamReader(stream,
encoding));
taskMonitor.setProgress(0.2);
TableInfo info = readHeader(reader);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2012-08-07 19:23:23 UTC (rev 30111)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2012-08-07 20:02:52 UTC (rev 30112)
@@ -29,6 +29,6 @@
@Override
public TaskIterator createTaskIterator(InputStream stream, String
inputName) {
- return new TaskIterator(new CSVCyReader(stream, readSchema,
handleEquations, tableFactory, compiler));
+ return new TaskIterator(new CSVCyReader(stream, readSchema,
handleEquations, tableFactory, compiler, "UTF-8"));
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
2012-08-07 19:23:23 UTC (rev 30111)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
2012-08-07 20:02:52 UTC (rev 30112)
@@ -26,15 +26,17 @@
private boolean isCanceled;
private final boolean handleEquations;
private final boolean includeVirtualColumns;
+ private String encoding;
public CSVCyWriter(final OutputStream outputStream, final CyTable table,
- final boolean writeSchema, final boolean
handleEquations, final boolean includeVirtualColumns)
+ final boolean writeSchema, final boolean
handleEquations, final boolean includeVirtualColumns, final String encoding)
{
this.outputStream = outputStream;
this.table = table;
this.writeSchema = writeSchema;
this.handleEquations = handleEquations;
this.includeVirtualColumns = includeVirtualColumns;
+ this.encoding = encoding;
}
@Override
@@ -45,7 +47,7 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setProgress(0.0);
- CSVWriter writer = new CSVWriter(new
OutputStreamWriter(outputStream), ',', '"', "\r\n");
+ CSVWriter writer = new CSVWriter(new
OutputStreamWriter(outputStream, encoding), ',', '"', "\r\n");
try {
List<CyColumn> columns = new ArrayList<CyColumn>();
for (CyColumn column : table.getColumns()) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
2012-08-07 19:23:23 UTC (rev 30111)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
2012-08-07 20:02:52 UTC (rev 30112)
@@ -1,12 +1,13 @@
package org.cytoscape.io.internal.write.datatable.csv;
+import java.io.OutputStream;
+
import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.internal.write.AbstractCyWriterFactory;
import org.cytoscape.io.write.CyTableWriterFactory;
-import org.cytoscape.io.internal.write.AbstractCyWriterFactory;
import org.cytoscape.io.write.CyWriter;
import org.cytoscape.model.CyTable;
-import java.io.OutputStream;
public class CSVTableWriterFactory extends AbstractCyWriterFactory implements
CyTableWriterFactory {
@@ -25,6 +26,6 @@
@Override
public CyWriter createWriter(OutputStream outputStream, CyTable table) {
- return new CSVCyWriter(outputStream, table, writeSchema,
handleEquations, includeVirtualColumns);
+ return new CSVCyWriter(outputStream, table, writeSchema,
handleEquations, includeVirtualColumns, "UTF-8");
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2012-08-07 19:23:23 UTC (rev 30111)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2012-08-07 20:02:52 UTC (rev 30112)
@@ -43,7 +43,7 @@
public void testReadSimple() throws Exception {
String data = "SUID\r\njava.lang.Long\r\ntest
table,\"public\\,mutable\"\r\n5\r\n6";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory, null);
+ /* handleEquations = */
false, tableFactory, null, "UTF-8");
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
assertNotNull(tables);
@@ -64,7 +64,7 @@
public void testReadString() throws Exception {
String data =
"SUID,name\r\njava.lang.Long,java.lang.String\r\ntest
table,\"public\\,mutable\"\r\n1,Alice\r\n2,Bob\r\n3,Carol";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory, null);
+ /* handleEquations = */
false, tableFactory, null, "UTF-8");
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
@@ -76,7 +76,7 @@
public void testReadDouble() throws Exception {
String data =
"SUID,weight\r\njava.lang.Long,java.lang.Double\r\ntest
table,\"public\\,mutable\"\r\n0,0.56\r\n-5,-1.234";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory, null);
+ /* handleEquations = */
false, tableFactory, null, "UTF-8");
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
@@ -88,7 +88,7 @@
public void testReadBoolean() throws Exception {
String data =
"SUID,hidden\r\njava.lang.Long,java.lang.Boolean\r\ntest
table,\"public\\,mutable\"\r\n30,true\r\n40,false\r\n50,true";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory, null);
+ /* handleEquations = */
false, tableFactory, null, "UTF-8");
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
@@ -100,7 +100,7 @@
public void testReadList() throws Exception {
String data =
"SUID,list\r\njava.lang.Long,java.util.List<java.lang.String>\r\ntest
table,\"public\\,mutable\"\r\n1,\"a\rb\rc\"";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory, null);
+ /* handleEquations = */
false, tableFactory, null, "UTF-8");
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
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