Author: ruschein
Date: 2011-07-05 09:10:08 -0700 (Tue, 05 Jul 2011)
New Revision: 26017
Modified:
core3/io-impl/trunk/pom.xml
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
Log:
Added equation support for CSV files.
Modified: core3/io-impl/trunk/pom.xml
===================================================================
--- core3/io-impl/trunk/pom.xml 2011-07-04 21:32:50 UTC (rev 26016)
+++ core3/io-impl/trunk/pom.xml 2011-07-05 16:10:08 UTC (rev 26017)
@@ -117,6 +117,11 @@
<dependencies>
<dependency>
<groupId>org.cytoscape</groupId>
+ <artifactId>equations-api</artifactId>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
<version>3.0.0-alpha5-SNAPSHOT</version>
</dependency>
@@ -137,11 +142,6 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
- <artifactId>presentation-api</artifactId>
- <version>3.0.0-alpha4-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
<artifactId>core-task-api</artifactId>
<version>3.0.0-alpha4-SNAPSHOT</version>
</dependency>
@@ -155,11 +155,6 @@
<artifactId>default-mappings</artifactId>
<version>3.0.0-alpha4-SNAPSHOT</version>
</dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>equations-api</artifactId>
- <version>3.0.0-alpha2</version>
- </dependency>
<!-- 3rd party libraries -->
<!-- <dependency>
@@ -174,12 +169,13 @@
<artifactId>com.springsource.com.lowagie.text</artifactId>
<version>2.0.8</version>
</dependency>
-
+<!--
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.2.1</version>
</dependency>
+-->
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>opencsv</artifactId>
@@ -207,16 +203,20 @@
<artifactId>freehep-graphicsio-ps</artifactId>
<version>2.1.1</version>
</dependency>
+<!--
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>freehep-graphics-base</artifactId>
<version>2.1.3</version>
</dependency>
+-->
+<!--
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>freehep-io</artifactId>
<version>2.1</version>
</dependency>
+-->
<!-- For Testing -->
<dependency>
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2011-07-04 21:32:50 UTC (rev 26016)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2011-07-05 16:10:08 UTC (rev 26017)
@@ -1,14 +1,19 @@
package org.cytoscape.io.internal.read.datatable;
+
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.lang.reflect.Method;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.io.read.CyTableReader;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
@@ -17,24 +22,30 @@
import au.com.bytecode.opencsv.CSVReader;
+
public class CSVCyReader implements CyTableReader {
+ private final static Pattern classPattern =
Pattern.compile("([^<>]+)(<(.*?)>)?");
- private Pattern classPattern = Pattern.compile("([^<>]+)(<(.*?)>)?");
-
private final InputStream stream;
private final boolean readSchema;
+ private final boolean handleEquations;
private final CyTableFactory tableFactory;
-
+ private final EquationCompiler compiler;
+
private boolean isCanceled;
private CyTable table;
+ public CSVCyReader(final InputStream stream, final boolean readSchema,
+ final boolean handleEquations, final CyTableFactory
tableFactory,
+ final EquationCompiler compiler)
+ {
+ this.stream = stream;
+ this.readSchema = readSchema;
+ this.handleEquations = handleEquations;
+ this.tableFactory = tableFactory;
+ this.compiler = compiler;
+ }
- public CSVCyReader(InputStream stream, boolean readSchema,
CyTableFactory tableFactory) {
- this.stream = stream;
- this.readSchema = readSchema;
- this.tableFactory = tableFactory;
- }
-
@Override
public void cancel() {
isCanceled = true;
@@ -48,9 +59,15 @@
}
CyTable createTable(CSVReader reader, TableInfo info) throws
IOException, SecurityException {
- ColumnInfo[] columns = info.getColumns();
- CyTable table = tableFactory.createTable(info.getTitle(),
columns[0].getName(), columns[0].getType(), info.isPublic(), info.isMutable());
-
+ final ColumnInfo[] columns = info.getColumns();
+ final CyTable table = tableFactory.createTable(info.getTitle(),
columns[0].getName(),
+
columns[0].getType(), info.isPublic(),
+
info.isMutable());
+
+ final Map<String, Class<?>> variableNameToTypeMap = new
HashMap<String, Class<?>>();
+ for (final ColumnInfo colInfo : columns)
+ variableNameToTypeMap.put(colInfo.getName(),
colInfo.getType());
+
for (int i = 1; i < columns.length; i++) {
ColumnInfo column = columns[i];
Class<?> type = column.getType();
@@ -62,17 +79,33 @@
}
String[] values = reader.readNext();
while (values != null) {
- if (isCanceled) {
+ if (isCanceled)
return null;
- }
+
Object key = parseValue(columns[0].getType(), null,
values[0]);
CyRow row = table.getRow(key);
for (int i = 1; i < values.length; i++) {
ColumnInfo column = columns[i];
String name = column.getName();
- Object value = parseValue(column.getType(),
column.getListElementType(), values[i]);
- if (value != null) {
- row.set(name, value);
+ if (handleEquations &&
values[i].startsWith("=")) {
+ final Class<?> type =
variableNameToTypeMap.remove(name);
+ try {
+ if (!compiler.compile(values[i],
+
variableNameToTypeMap))
+ throw new
IOException("Error while reading \""
+ +
info.getTitle()
+ +
"\" cant compile equation because: "
+ +
compiler.getLastErrorMsg());
+ final Equation equation =
compiler.getEquation();
+ row.set(name, equation);
+ } catch (final Exception e) {
+ throw new
IOException(e.getMessage(), e.getCause());
+ }
+ variableNameToTypeMap.put(name, type);
+ } else {
+ Object value =
parseValue(column.getType(), column.getListElementType(), values[i]);
+ if (value != null)
+ row.set(name, value);
}
}
values = reader.readNext();
@@ -88,9 +121,9 @@
list.add(parseValue(listElementType, null,
item));
}
return list;
- } else if (type.equals(String.class)) {
+ } else if (type.equals(String.class))
return value;
- } else {
+ else {
try {
Method method = type.getMethod("valueOf",
String.class);
return method.invoke(null, value);
@@ -99,7 +132,7 @@
}
}
}
-
+
TableInfo readHeader(CSVReader reader) throws IOException,
ClassNotFoundException {
String[] values = reader.readNext();
TableInfo table = new TableInfo();
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2011-07-04 21:32:50 UTC (rev 26016)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2011-07-05 16:10:08 UTC (rev 26017)
@@ -1,28 +1,38 @@
package org.cytoscape.io.internal.read.datatable;
+
import java.io.InputStream;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.work.TaskIterator;
+
public class CSVCyReaderFactory implements InputStreamTaskFactory {
-
private final CyFileFilter filter;
private InputStream stream;
- private boolean readSchema;
- private CyTableFactory tableFactory;
+ private final boolean readSchema;
+ private final boolean handleEquations;
+ private final CyTableFactory tableFactory;
+ private final EquationCompiler compiler;
- public CSVCyReaderFactory(CyFileFilter filter, boolean readSchema,
CyTableFactory tableFactory) {
- this.filter = filter;
- this.readSchema = readSchema;
- this.tableFactory = tableFactory;
+ public CSVCyReaderFactory(final CyFileFilter filter, final boolean
readSchema,
+ final boolean handleEquations, final
CyTableFactory tableFactory,
+ final EquationCompiler compiler)
+ {
+ this.filter = filter;
+ this.readSchema = readSchema;
+ this.handleEquations = handleEquations;
+ this.tableFactory = tableFactory;
+ this.compiler = compiler;
}
@Override
public TaskIterator getTaskIterator() {
- return new TaskIterator(new CSVCyReader(stream, readSchema,
tableFactory));
+ return new TaskIterator(new CSVCyReader(stream, readSchema,
handleEquations,
+ tableFactory,
compiler));
}
@Override
@@ -34,5 +44,4 @@
public void setInputStream(InputStream stream, String inputName) {
this.stream = stream;
}
-
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
2011-07-04 21:32:50 UTC (rev 26016)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
2011-07-05 16:10:08 UTC (rev 26017)
@@ -1,5 +1,6 @@
package org.cytoscape.io.internal.write.datatable.csv;
+
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
@@ -17,17 +18,21 @@
import au.com.bytecode.opencsv.CSVWriter;
+
public class CSVCyWriter implements CyWriter {
-
private final OutputStream outputStream;
private final CyTable table;
private final boolean writeSchema;
private boolean isCanceled;
+ private final boolean handleEquations;
- public CSVCyWriter(OutputStream outputStream, CyTable table, boolean
writeSchema) {
- this.outputStream = outputStream;
- this.table = table;
- this.writeSchema = writeSchema;
+ public CSVCyWriter(final OutputStream outputStream, final CyTable table,
+ final boolean writeSchema, final boolean
handleEquations)
+ {
+ this.outputStream = outputStream;
+ this.table = table;
+ this.writeSchema = writeSchema;
+ this.handleEquations = handleEquations;
}
@Override
@@ -62,7 +67,7 @@
writer.flush();
}
}
-
+
private void writeSchema(CSVWriter writer, List<CyColumn> columns) {
String[] values = new String[columns.size()];
for (int i = 0; i < columns.size(); i++) {
@@ -77,7 +82,7 @@
writer.writeNext(values);
values = new String[2];
values[0] = table.getTitle();
-
+
StringBuilder builder = new StringBuilder();
if (table.isPublic()) {
builder.append("public");
@@ -94,12 +99,22 @@
private void writeValues(CSVWriter writer, Collection<CyColumn>
columns) {
for (CyRow row : table.getAllRows()) {
- if (isCanceled) {
+ if (isCanceled)
return;
- }
+
String[] values = new String[columns.size()];
int index = 0;
for (CyColumn column : columns) {
+ if (handleEquations) {
+ final Object rawValue =
row.getRaw(column.getName());
+ if (rawValue instanceof String
+ &&
((String)rawValue).startsWith("="))
+ {
+ values[index++] =
(String)rawValue;
+ continue;
+ }
+ }
+
Class<?> type = column.getType();
if (type.equals(List.class)) {
StringBuilder builder = new
StringBuilder();
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
2011-07-04 21:32:50 UTC (rev 26016)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVTableWriterFactory.java
2011-07-05 16:10:08 UTC (rev 26017)
@@ -1,20 +1,25 @@
package org.cytoscape.io.internal.write.datatable.csv;
+
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.write.datatable.AbstractCyTableWriterFactory;
import org.cytoscape.io.write.CyWriter;
+
public class CSVTableWriterFactory extends AbstractCyTableWriterFactory {
-
private final boolean writeSchema;
+ private final boolean handleEquations;
- public CSVTableWriterFactory(CyFileFilter fileFilter, boolean
writeSchema) {
+ public CSVTableWriterFactory(final CyFileFilter fileFilter, final
boolean writeSchema,
+ final boolean handleEquations)
+ {
super(fileFilter);
- this.writeSchema = writeSchema;
+ this.writeSchema = writeSchema;
+ this.handleEquations = handleEquations;
}
@Override
public CyWriter getWriterTask() {
- return new CSVCyWriter(outputStream, table, writeSchema);
+ return new CSVCyWriter(outputStream, table, writeSchema,
handleEquations);
}
}
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-07-04 21:32:50 UTC (rev 26016)
+++
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-07-05 16:10:08 UTC (rev 26017)
@@ -7,6 +7,8 @@
<!-- Import services -->
+ <osgi:reference id="compilerServiceRef"
interface="org.cytoscape.equations.EquationCompiler" />
+
<osgi:reference id="cyEventHelperRef"
interface="org.cytoscape.event.CyEventHelper" />
<osgi:reference id="cyLayoutsServiceRef"
interface="org.cytoscape.view.layout.CyLayoutAlgorithmManager" />
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
--- core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-07-04 21:32:50 UTC (rev 26016)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-07-05 16:10:08 UTC (rev 26017)
@@ -514,12 +514,14 @@
class="org.cytoscape.io.internal.write.datatable.csv.CSVTableWriterFactory">
<constructor-arg ref="csvFilter" />
<constructor-arg value="false" type="boolean" />
+ <constructor-arg value="false" type="boolean" />
</bean>
<bean id="sessionTableWriterFactory"
class="org.cytoscape.io.internal.write.datatable.csv.CSVTableWriterFactory">
<constructor-arg ref="sessionTableFilter" />
<constructor-arg value="true" type="boolean" />
+ <constructor-arg value="true" type="boolean" />
</bean>
<bean id="vizmapWriterFactory"
@@ -576,7 +578,9 @@
<bean id="sessionTableReaderFactory"
class="org.cytoscape.io.internal.read.datatable.CSVCyReaderFactory">
<constructor-arg ref="sessionTableFilter"/>
<constructor-arg value="true"/>
+ <constructor-arg value="true"/>
<constructor-arg ref="cyTableFactoryServiceRef"/>
+ <constructor-arg ref="compilerServiceRef"/>
</bean>
<!-- All Reader Managers -->
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2011-07-04 21:32:50 UTC (rev 26016)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2011-07-05 16:10:08 UTC (rev 26017)
@@ -1,5 +1,6 @@
package org.cytoscape.io.internal.read.datatable;
+
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
@@ -20,9 +21,10 @@
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
+
public class CSVCyReaderTest {
@Mock TaskMonitor taskMonitor;
-
+
private CyTableFactory tableFactory;
@Before
@@ -31,15 +33,17 @@
tableFactory = tableTestSupport.getDataTableFactory();
MockitoAnnotations.initMocks(this);
}
-
+
InputStream createStream(String data) throws
UnsupportedEncodingException {
return new ByteArrayInputStream(data.getBytes("UTF-8"));
}
-
+
@Test
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,
tableFactory);
+ CSVCyReader reader = new CSVCyReader(createStream(data), true,
+ /* handleEquations = */
false, tableFactory,
+ null);
reader.run(taskMonitor);
CyTable[] tables = reader.getCyTables();
assertNotNull(tables);
@@ -55,33 +59,39 @@
assertEquals(Mutability.MUTABLE, table.getMutability());
assertEquals("test table", table.getTitle());
}
-
+
@Test
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,
tableFactory);
+ CSVCyReader reader = new CSVCyReader(createStream(data), true,
+ /* handleEquations = */
false, tableFactory,
+ null);
reader.run(taskMonitor);
CyTable[] tables = reader.getCyTables();
CyTable table = tables[0];
CyRow row = table.getRow(3L);
assertEquals("Carol", row.get("name", String.class));
}
-
+
@Test
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,
tableFactory);
+ CSVCyReader reader = new CSVCyReader(createStream(data), true,
+ /* handleEquations = */
false, tableFactory,
+ null);
reader.run(taskMonitor);
CyTable[] tables = reader.getCyTables();
CyTable table = tables[0];
CyRow row = table.getRow(-5L);
assertEquals((Double) (-1.234), row.get("weight",
Double.class));
}
-
+
@Test
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,
tableFactory);
+ CSVCyReader reader = new CSVCyReader(createStream(data), true,
+ /* handleEquations = */
false, tableFactory,
+ null);
reader.run(taskMonitor);
CyTable[] tables = reader.getCyTables();
CyTable table = tables[0];
@@ -92,7 +102,9 @@
@Test
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,
tableFactory);
+ CSVCyReader reader = new CSVCyReader(createStream(data), true,
+ /* handleEquations = */
false, tableFactory,
+ null);
reader.run(taskMonitor);
CyTable[] tables = reader.getCyTables();
CyTable table = tables[0];
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