Author: clopes
Date: 2012-08-01 12:26:25 -0700 (Wed, 01 Aug 2012)
New Revision: 30066
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriter.java
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriterTest.java
Log:
Fixes #1332 (XGMML Export: Long type attributes are not exported).
Fixes #1333 (XGMML Export: boolean attributes saved as [true|false], not [1|0]).
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriter.java
2012-08-01 18:54:23 UTC (rev 30065)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriter.java
2012-08-01 19:26:25 UTC (rev 30066)
@@ -652,13 +652,15 @@
return new String[]{};
}
- protected void writeAttributes(CyRow row) throws IOException {
+ protected void writeAttributes(final CyRow row) throws IOException {
// If it is a Cy Session XGMML, writing the CyRows would be
redundant,
// because they are already serialized in .cytable files.
- CyTable table = row.getTable();
+ final CyTable table = row.getTable();
- for (final CyColumn column : table.getColumns())
- writeAttribute(row, column.getName());
+ for (final CyColumn column : table.getColumns()) {
+ if (!CyIdentifiable.SUID.equals(column.getName()))
+ writeAttribute(row, column.getName());
+ }
}
/**
@@ -681,43 +683,51 @@
if (attType == Double.class) {
Double dAttr = row.get(attName, Double.class);
writeAttributeXML(attName, ObjectType.REAL, dAttr,
true);
- } else {
- if (attType == Integer.class) {
- Integer iAttr = row.get(attName, Integer.class);
- writeAttributeXML(attName, ObjectType.INTEGER,
iAttr, true);
- } else if (attType == String.class) {
- String sAttr = row.get(attName, String.class);
- // Protect tabs and returns
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
- }
+ } else if (attType == Integer.class) {
+ Integer iAttr = row.get(attName, Integer.class);
+ writeAttributeXML(attName, ObjectType.INTEGER, iAttr,
true);
+ } else if (attType == Long.class) {
+ Long lAttr = row.get(attName, Long.class);
+ writeAttributeXML(attName, ObjectType.REAL, lAttr,
true);
+ } else if (attType == String.class) {
+ String sAttr = row.get(attName, String.class);
+ // Protect tabs and returns
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
- writeAttributeXML(attName, ObjectType.STRING,
sAttr, true);
- } else if (attType == Boolean.class) {
- Boolean bAttr = row.get(attName, Boolean.class);
- writeAttributeXML(attName, ObjectType.BOOLEAN,
bAttr, true);
- } else if (attType == List.class) {
- final List<?> listAttr = row.getList(attName,
column.getListElementType());
- writeAttributeXML(attName, ObjectType.LIST,
null, false);
+ writeAttributeXML(attName, ObjectType.STRING, sAttr,
true);
+ } else if (attType == Boolean.class) {
+ Boolean bAttr = row.get(attName, Boolean.class);
+ writeAttributeXML(attName, ObjectType.BOOLEAN,
ObjectTypeMap.toXGMMLBoolean(bAttr), true);
+ } else if (attType == List.class) {
+ final List<?> listAttr = row.getList(attName,
column.getListElementType());
+ writeAttributeXML(attName, ObjectType.LIST, null,
false);
- if (listAttr != null) {
- depth++;
- // iterate through the list
- for (Object obj : listAttr) {
+ if (listAttr != null) {
+ depth++;
+ // iterate through the list
+ for (Object obj : listAttr) {
+ String sAttr = null;
+
+ if (obj instanceof Boolean) {
+ sAttr =
ObjectTypeMap.toXGMMLBoolean((Boolean) obj);
+ } else {
// Protect tabs and returns (if
necessary)
- String sAttr = obj.toString();
+ sAttr = obj.toString();
if (sAttr != null) {
sAttr =
sAttr.replace("\n", "\\n");
sAttr =
sAttr.replace("\t", "\\t");
}
- // set child attribute value &
label
- writeAttributeXML(attName,
checkType(obj), sAttr, true);
}
- depth--;
+ // set child attribute value & label
+ writeAttributeXML(attName,
checkType(obj), sAttr, true);
}
- writeAttributeXML(null, null, null, true);
+ depth--;
}
+
+ writeAttributeXML(null, null, null, true);
}
}
@@ -790,18 +800,19 @@
* @param obj
* @return Attribute type in string.
*/
- private ObjectType checkType(final Object obj) {
- if (obj.getClass() == String.class) {
+ private ObjectType checkType(final Object obj) {
+ final Class<?> type = obj.getClass();
+
+ if (type == String.class)
return ObjectType.STRING;
- } else if (obj.getClass() == Integer.class) {
+ else if (type == Integer.class)
return ObjectType.INTEGER;
- } else if ((obj.getClass() == Double.class) || (obj.getClass() ==
Float.class)) {
+ else if (type == Double.class || type == Float.class || type ==
Long.class)
return ObjectType.REAL;
- } else if (obj.getClass() == Boolean.class) {
+ else if (type == Boolean.class)
return ObjectType.BOOLEAN;
- } else {
- return null;
- }
+
+ return null;
}
protected String getLabel(CyNetwork network, CyIdentifiable entry) {
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriterTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriterTest.java
2012-08-01 18:54:23 UTC (rev 30065)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/GenericXGMMLWriterTest.java
2012-08-01 19:26:25 UTC (rev 30066)
@@ -5,6 +5,7 @@
import java.awt.Color;
import java.io.UnsupportedEncodingException;
+import java.util.Arrays;
import javax.xml.xpath.XPathConstants;
@@ -48,6 +49,83 @@
}
@Test
+ public void testIntegerAttributeSavedAsInteger() {
+ net.getRow(net).getTable().createColumn("test_int",
Integer.class, false);
+ net.getRow(net).set("test_int", Integer.MAX_VALUE);
+ net.getRow(net).getTable().createListColumn("test_list_int",
Integer.class, false);
+ net.getRow(net).set("test_list_int", Arrays.asList(new
Integer[]{ 1 }));
+ write(net);
+ assertEquals("integer",
evalString("/x:graph/x:att[@name=\"test_int\"]/@type"));
+ assertEquals(Integer.MAX_VALUE,
evalNumber("/x:graph/x:att[@name=\"test_int\"]/@value"));
+ assertEquals("list",
evalString("/x:graph/x:att[@name=\"test_list_int\"]/@type"));
+ assertEquals("integer",
evalString("/x:graph/x:att[@name=\"test_list_int\"]/x:att[@value=\"1\"]/@type"));
+ }
+
+ @Test
+ public void testLongAttributeSavedAsReal() {
+ net.getRow(net).getTable().createColumn("test_long",
Long.class, false);
+ net.getRow(net).set("test_long", Long.MAX_VALUE);
+ net.getRow(net).getTable().createListColumn("test_list_long",
Long.class, false);
+ net.getRow(net).set("test_list_long", Arrays.asList(new Long[]{
1L }));
+ write(net);
+ assertEquals("real",
evalString("/x:graph/x:att[@name=\"test_long\"]/@type"));
+ assertEquals(Long.MAX_VALUE,
evalNumber("/x:graph/x:att[@name=\"test_long\"]/@value"));
+ assertEquals("list",
evalString("/x:graph/x:att[@name=\"test_list_long\"]/@type"));
+ assertEquals("real",
evalString("/x:graph/x:att[@name=\"test_list_long\"]/x:att[@value=\"1\"]/@type"));
+ }
+
+ @Test
+ public void testDoubleAttributeSavedAsReal() {
+ net.getRow(net).getTable().createColumn("test_double",
Double.class, false);
+ net.getRow(net).set("test_double", Double.MAX_VALUE);
+ net.getRow(net).getTable().createListColumn("test_list_double",
Double.class, false);
+ net.getRow(net).set("test_list_double", Arrays.asList(new
Double[]{ 1.2D }));
+ write(net);
+ assertEquals("real",
evalString("/x:graph/x:att[@name=\"test_double\"]/@type"));
+ assertEquals(Double.MAX_VALUE, new
Double(evalString("/x:graph/x:att[@name=\"test_double\"]/@value")), 0.0);
+ assertEquals("list",
evalString("/x:graph/x:att[@name=\"test_list_double\"]/@type"));
+ assertEquals("real",
evalString("/x:graph/x:att[@name=\"test_list_double\"]/x:att[@value=\"1.2\"]/@type"));
+ }
+
+ @Test
+ public void testStringAttributeSavedAsString() {
+ net.getRow(net).getTable().createColumn("test_str",
String.class, false);
+ net.getRow(net).set("test_str", "My String");
+ net.getRow(net).getTable().createListColumn("test_list_str",
String.class, false);
+ net.getRow(net).set("test_list_str", Arrays.asList(new
String[]{ "A", "B" }));
+ write(net);
+ assertEquals("string",
evalString("/x:graph/x:att[@name=\"test_str\"]/@type"));
+ assertEquals("My String",
evalString("/x:graph/x:att[@name=\"test_str\"]/@value"));
+ assertEquals("list",
evalString("/x:graph/x:att[@name=\"test_list_str\"]/@type"));
+ assertEquals("string",
evalString("/x:graph/x:att[@name=\"test_list_str\"]/x:att[@value=\"B\"]/@type"));
+ }
+
+ @Test
+ public void testBooleanAttributeSavedAsBoolean() {
+ net.getRow(net).getTable().createColumn("test_bool",
Boolean.class, false);
+ net.getRow(net).set("test_bool", true);
+ net.getRow(net).getTable().createListColumn("test_list_bool",
Boolean.class, false);
+ net.getRow(net).set("test_list_bool", Arrays.asList(new
Boolean[]{ true, false }));
+ write(net);
+ // see
http://www.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/draft-xgmml-20010628.html#BT
+ assertEquals("boolean",
evalString("/x:graph/x:att[@name=\"test_bool\"]/@type"));
+ assertEquals("1",
evalString("/x:graph/x:att[@name=\"test_bool\"]/@value")); // XGMML boolean
[0|1]
+ assertEquals("list",
evalString("/x:graph/x:att[@name=\"test_list_bool\"]/@type"));
+ assertEquals("boolean",
evalString("/x:graph/x:att[@name=\"test_list_bool\"]/x:att[1]/@type"));
+ assertEquals("1",
evalString("/x:graph/x:att[@name=\"test_list_bool\"]/x:att[1]/@value"));
+ assertEquals("0",
evalString("/x:graph/x:att[@name=\"test_list_bool\"]/x:att[last()]/@value"));
+ }
+
+ @Test
+ public void testSUIDAttNotSaved() throws UnsupportedEncodingException {
+ // The SUID should NEVER be saved as an att tag
+ CyNetwork newNet =
netFactory.createNetwork(SavePolicy.DO_NOT_SAVE);
+ setRegistered(newNet, false); // It shouldn't make any
difference either
+ write(newNet);
+ assertEquals(0, evalNumber("count(//x:att[@name=\"SUID\"])"));
+ }
+
+ @Test
public void testTopNetworkSavedEvenIfDoNotSavePolicy() throws
UnsupportedEncodingException {
// The network that is passed to the writer should always be
saved, even if its save policy is DO_NOT_SAVE,
// because it doesn't make sense to prevent an app from
exporting it if the app explicitly wants to do so.
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