Author: jm
Date: 2011-05-13 12:41:41 -0700 (Fri, 13 May 2011)
New Revision: 25052
Added:
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/ColumnInfo.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TableInfo.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
Log:
Added preliminary support for reading CSV files with CyTable/CyColumn schema
details
Added:
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
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2011-05-13 19:41:41 UTC (rev 25052)
@@ -0,0 +1,150 @@
+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.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.cytoscape.io.read.CyTableReader;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.work.TaskMonitor;
+
+import au.com.bytecode.opencsv.CSVReader;
+
+public class CSVCyReader implements CyTableReader {
+
+ private Pattern classPattern = Pattern.compile("([^<>]+)(<(.*?)>)?");
+
+ private final InputStream stream;
+ private final boolean readSchema;
+ private final CyTableFactory tableFactory;
+
+ private boolean isCanceled;
+ private CyTable table;
+
+
+ public CSVCyReader(InputStream stream, boolean readSchema,
CyTableFactory tableFactory) {
+ this.stream = stream;
+ this.readSchema = readSchema;
+ this.tableFactory = tableFactory;
+ }
+
+ @Override
+ public void cancel() {
+ isCanceled = true;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ CSVReader reader = new CSVReader(new InputStreamReader(stream));
+ TableInfo info = readHeader(reader);
+ table = createTable(reader, info);
+ }
+
+ 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());
+
+ for (int i = 1; i < columns.length; i++) {
+ ColumnInfo column = columns[i];
+ Class<?> type = column.getType();
+ if (type.equals(List.class)) {
+ table.createListColumn(column.getName(),
column.getListElementType(), !column.isMutable());
+ } else {
+ table.createColumn(column.getName(), type,
!column.isMutable());
+ }
+ }
+ String[] values = reader.readNext();
+ while (values != null) {
+ 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);
+ }
+ }
+ values = reader.readNext();
+ }
+ return table;
+ }
+
+ Object parseValue(Class<?> type, Class<?> listElementType, String
value) {
+ if (type.equals(List.class)) {
+ List<Object> list = new ArrayList<Object>();
+ String[] values = value.split("\n");
+ for (String item : values) {
+ list.add(parseValue(listElementType, null,
item));
+ }
+ return list;
+ } else if (type.equals(String.class)) {
+ return value;
+ } else {
+ try {
+ Method method = type.getMethod("valueOf",
String.class);
+ return method.invoke(null, value);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+ }
+
+ TableInfo readHeader(CSVReader reader) throws IOException,
ClassNotFoundException {
+ String[] values = reader.readNext();
+ TableInfo table = new TableInfo();
+ ColumnInfo[] columns = new ColumnInfo[values.length];
+ for (int i = 0; i < values.length; i++) {
+ ColumnInfo column = new ColumnInfo();
+ column.setName(values[i]);
+ columns[i] = column;
+ }
+ table.setColumns(columns);
+ if (!readSchema) {
+ return table;
+ }
+ values = reader.readNext();
+ for (int i = 0; i < values.length; i++) {
+ Matcher matcher = classPattern.matcher(values[i]);
+ matcher.matches();
+ String typeName = matcher.group(1);
+ Class<?> type = Class.forName(typeName);
+ if (type.equals(List.class)) {
+ String elementName = matcher.group(3);
+ Class<?> elementType =
Class.forName(elementName);
+ columns[i].setListElementType(elementType);
+ } else {
+ columns[i].setType(type);
+ }
+ }
+ values = reader.readNext();
+ table.setTitle(values[0]);
+ for (String option : values[1].split(",")) {
+ if ("public".equals(option)) {
+ table.setPublic(true);
+ } else if ("mutable".equals(option)) {
+ table.setMutable(true);
+ }
+ }
+ return table;
+ }
+
+ @Override
+ public CyTable[] getCyTables() {
+ if (table == null) {
+ return null;
+ }
+ return new CyTable[] { table };
+ }
+
+}
Property changes on:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/ColumnInfo.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/ColumnInfo.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/ColumnInfo.java
2011-05-13 19:41:41 UTC (rev 25052)
@@ -0,0 +1,44 @@
+package org.cytoscape.io.internal.read.datatable;
+
+import java.util.List;
+
+public class ColumnInfo {
+
+ private String name;
+ private Class<?> type;
+ private Class<?> elementType;
+ private boolean isMutable;
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String newName) {
+ name = newName;
+ }
+
+ public Class<?> getType() {
+ return type;
+ }
+
+ public void setType(Class<?> type) {
+ this.type = type;
+ }
+
+ public Class<?> getListElementType() {
+ return elementType;
+ }
+
+ public void setListElementType(Class<?> type) {
+ this.type = List.class;
+ elementType = type;
+ }
+
+ public boolean isMutable() {
+ return isMutable;
+ }
+
+ public void setMutable(boolean mutable) {
+ isMutable = mutable;
+ }
+}
Property changes on:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/ColumnInfo.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TableInfo.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TableInfo.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TableInfo.java
2011-05-13 19:41:41 UTC (rev 25052)
@@ -0,0 +1,41 @@
+package org.cytoscape.io.internal.read.datatable;
+
+public class TableInfo {
+
+ private String title;
+ private ColumnInfo[] columns;
+ private boolean isPublic;
+ private boolean isMutable;
+
+ public String getTitle() {
+ return title;
+ }
+
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ public boolean isPublic() {
+ return isPublic;
+ }
+
+ public void setPublic(boolean isPublic) {
+ this.isPublic = isPublic;
+ }
+
+ public boolean isMutable() {
+ return isMutable;
+ }
+
+ public void setMutable(boolean isMutable) {
+ this.isMutable = isMutable;
+ }
+
+ public ColumnInfo[] getColumns() {
+ return columns;
+ }
+
+ public void setColumns(ColumnInfo[] columns) {
+ this.columns = columns;
+ }
+}
Property changes on:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TableInfo.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added:
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
(rev 0)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2011-05-13 19:41:41 UTC (rev 25052)
@@ -0,0 +1,103 @@
+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;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.util.List;
+
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTable.Mutability;
+import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.test.support.DataTableTestSupport;
+import org.cytoscape.work.TaskMonitor;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mock;
+import org.mockito.MockitoAnnotations;
+
+public class CSVCyReaderTest {
+ @Mock TaskMonitor taskMonitor;
+
+ private CyTableFactory tableFactory;
+
+ @Before
+ public void setUp() {
+ DataTableTestSupport tableTestSupport = new
DataTableTestSupport();
+ 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);
+ reader.run(taskMonitor);
+ CyTable[] tables = reader.getCyTables();
+ assertNotNull(tables);
+ assertEquals(1, tables.length);
+ CyTable table = tables[0];
+ assertNotNull(table);
+ assertEquals(2, table.getRowCount());
+ CyRow row = table.getRow(5L);
+ assertNotNull(row);
+ Long value = row.get("SUID", Long.class);
+ assertEquals((Long) 5L, value);
+ assertTrue(table.isPublic());
+ 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);
+ 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);
+ 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);
+ reader.run(taskMonitor);
+ CyTable[] tables = reader.getCyTables();
+ CyTable table = tables[0];
+ CyRow row = table.getRow(50L);
+ assertEquals(Boolean.TRUE, row.get("hidden", Boolean.class));
+ }
+
+ @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);
+ reader.run(taskMonitor);
+ CyTable[] tables = reader.getCyTables();
+ CyTable table = tables[0];
+ CyRow row = table.getRow(1L);
+ List<String> list = row.getList("list", String.class);
+ assertEquals("c", list.get(2));
+ }
+}
Property changes on:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
