Author: Christian Lopes
Date: 2011-06-30 08:49:34 -0700 (Thu, 30 Jun 2011)
New Revision: 25981
Modified:
core3/io-impl/trunk/
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.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/xgmml/XGMMLNetworkReaderTest.java
Log:
closes #299 (Equations are not being parsed from XGMML files)
Property changes on: core3/io-impl/trunk
___________________________________________________________________
Modified: svn:ignore
- .settings
target
.classpath
.project
+ .settings
target
.classpath
.project
itextTest.pdf
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-06-30 00:35:38 UTC (rev 25980)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-06-30 15:49:34 UTC (rev 25981)
@@ -131,6 +131,9 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
+ // any existing equations should be parsed first
+ readDataMgr.parseAllEquations();
+
netView = cyNetworkViewFactory.getNetworkView(network);
if (netView != null) {
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-06-30 00:35:38 UTC (rev 25980)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-06-30 15:49:34 UTC (rev 25981)
@@ -126,48 +126,55 @@
}
public ParseState handleAttribute(Attributes atts, CyRow row) throws
SAXParseException {
- String name = atts.getValue("name");
+ ParseState parseState = ParseState.NONE;
+
+ String name = atts.getValue("name");
String type = atts.getValue("type");
String equationStr = atts.getValue("cy:equation");
+ boolean isEquation = equationStr != null ?
Boolean.parseBoolean(equationStr) : false;
ObjectType objType = typeMap.getType(type);
CyColumn column = row.getTable().getColumn(name);
+ Object value = null;
- if (equationStr == null) {
- // Regular attribute value (NOT an equation)...
- Object obj = getTypedAttributeValue(objType, atts);
-
- switch (objType) {
- case BOOLEAN:
- if (obj != null && name != null) setAttribute(row, name,
(Boolean) obj);
- break;
- case REAL:
- if (obj != null && name != null) setAttribute(row, name,
(Double) obj);
- break;
- case INTEGER:
- if (obj != null && name != null) setAttribute(row, name,
(Integer) obj);
- break;
- case STRING:
- if (obj != null && name != null) setAttribute(row, name,
(String) obj);
- break;
- // We need to be *very* careful. Because we duplicate
attributes for
- // each network we write out, we wind up reading and
processing each
- // attribute multiple times, once for each network. This isn't
a problem
- // for "base" attributes, but is a significant problem for
attributes
- // like LIST and MAP where we add to the attribute as we
parse. So, we
- // must make sure to clear out any existing values before we
parse.
- case LIST:
- manager.currentAttributeID = name;
- if (column != null &&
List.class.isAssignableFrom(column.getType())) row.set(name, null);
- return ParseState.LISTATT;
+ if (isEquation) {
+ // It is an equation...
+ String formula = atts.getValue("value");
+
+ if (name != null && formula != null) {
+ manager.addEquationString(row, name, formula);
}
} else {
- // It is an equation...
- if (name != null) manager.addEquation(name, row, equationStr);
- if (objType.equals(ObjectType.LIST)) return ParseState.LISTATT;
+ // Regular attribute value...
+ value = getTypedAttributeValue(objType, atts);
}
- return ParseState.NONE;
+ switch (objType) {
+ case BOOLEAN:
+ if (name != null) setAttribute(row, name,
Boolean.class, (Boolean) value);
+ break;
+ case REAL:
+ if (name != null) setAttribute(row, name,
Double.class, (Double) value);
+ break;
+ case INTEGER:
+ if (name != null) setAttribute(row, name,
Integer.class, (Integer) value);
+ break;
+ case STRING:
+ if (name != null) setAttribute(row, name,
String.class, (String) value);
+ break;
+ // We need to be *very* careful. Because we duplicate
attributes for
+ // each network we write out, we wind up reading and
processing each
+ // attribute multiple times, once for each network.
This isn't a problem
+ // for "base" attributes, but is a significant problem
for attributes
+ // like LIST and MAP where we add to the attribute as
we parse. So, we
+ // must make sure to clear out any existing values
before we parse.
+ case LIST:
+ manager.currentAttributeID = name;
+ if (column != null &&
List.class.isAssignableFrom(column.getType())) row.set(name, null);
+ return ParseState.LISTATT;
+ }
+
+ return parseState;
}
public CyNode createNode(String id, String label) {
@@ -223,18 +230,24 @@
try {
Long id = new Long(strId);
- setAttribute(row,
XGMMLNetworkReader.ORIGINAL_ID_COLUMN, id);
+ setAttribute(row,
XGMMLNetworkReader.ORIGINAL_ID_COLUMN, Long.class, id);
} catch (Exception e) {
logger.warn("Cannot convert node or edge id from string
to long: " + strId);
}
}
}
- private <T> void setAttribute(CyRow row, String name, T value) {
- if (name != null && value != null) {
+ private <T> void setAttribute(CyRow row, String name, Class<T> type, T
value) {
+ if (name != null) {
CyTable table = row.getTable();
- if (table.getColumn(name) == null) table.createColumn(name,
value.getClass(), false);
- row.set(name, value);
+
+ if (table.getColumn(name) == null) {
+ table.createColumn(name, type, false);
+ }
+
+ if (value != null) {
+ row.set(name, value);
+ }
}
}
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-06-30 00:35:38 UTC (rev 25980)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-06-30 15:49:34 UTC (rev 25981)
@@ -1,19 +1,26 @@
package org.cytoscape.io.internal.read.xgmml.handler;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
+import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.Stack;
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.io.internal.read.xgmml.ParseState;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTableEntry;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.xml.sax.Attributes;
public class ReadDataManager {
@@ -72,19 +79,22 @@
private Map<CyNode, Map<String/*att name*/, String/*att value*/>>
nodeGraphics;
private Map<CyEdge, Map<String/*att name*/, String/*att value*/>>
edgeGraphics;
+
+ private Map<CyRow, Map<String/*column name*/, String/*equation*/>>
equations;
protected Map<CyNode, List<CyNode>> groupMap;
private boolean sessionFormat;
+
+ private final EquationCompiler equationCompiler;
+
+ private static final Logger logger =
LoggerFactory.getLogger(ReadDataManager.class);
- public boolean isSessionFormat() {
- return sessionFormat;
+ public ReadDataManager(final EquationCompiler equationCompiler) {
+ this.equationCompiler = equationCompiler;
+ initAllData();
}
- public void setSessionFormat(boolean sessionFormat) {
- this.sessionFormat = sessionFormat;
- }
-
public void initAllData() {
networkName = null;
@@ -110,6 +120,8 @@
nodeGraphics = new LinkedHashMap<CyNode, Map<String, String>>();
edgeGraphics = new LinkedHashMap<CyEdge, Map<String, String>>();
+ equations = new Hashtable<CyRow, Map<String,String>>();
+
currentNode = null;
currentEdge = null;
currentGroupNode = null;
@@ -132,10 +144,14 @@
sessionFormat = false;
}
- public ReadDataManager() {
- initAllData();
+ public boolean isSessionFormat() {
+ return sessionFormat;
}
-
+
+ public void setSessionFormat(boolean sessionFormat) {
+ this.sessionFormat = sessionFormat;
+ }
+
public String getNetworkName() {
return networkName;
}
@@ -220,15 +236,57 @@
return this.network;
}
- public void addEquation(String columnName, CyRow row, String
equationStr) {
- // TODO: should just store all the equation strings per
columnName/row?
- // TODO: create all equations after all CyTables/CyColumns are
loaded?
+ /**
+ * Just stores all the equation strings per CyTableEntry and column
name.
+ * It does not create the real Equation objects yet.
+ * @param row The network/node/edge row
+ * @param columnName The name of the column
+ * @param formula The equation formula
+ */
+ public void addEquationString(CyRow row, String columnName, String
formula) {
+ Map<String, String> colEquationMap = equations.get(row);
+
+ if (colEquationMap == null) {
+ colEquationMap = new HashMap<String, String>();
+ equations.put(row, colEquationMap);
+ }
+
+ colEquationMap.put(columnName, formula);
}
/**
+ * Should be called only after all XGMML attributes have been read.
+ */
+ public void parseAllEquations() {
+ for (Map.Entry<CyRow, Map<String, String>> entry :
equations.entrySet()) {
+ CyRow row = entry.getKey();
+ Map<String, String> colEquationMap = entry.getValue();
+
+ Map<String, Class<?>> colNameTypeMap = new
Hashtable<String, Class<?>>();
+ Collection<CyColumn> columns =
row.getTable().getColumns();
+
+ for (CyColumn col : columns) {
+ colNameTypeMap.put(col.getName(),
col.getType());
+ }
+
+ for (Map.Entry<String, String> colEqEntry :
colEquationMap.entrySet()) {
+ String columnName = colEqEntry.getKey();
+ String formula = colEqEntry.getValue();
+
+ if (equationCompiler.compile(formula,
colNameTypeMap)) {
+ Equation equation =
equationCompiler.getEquation();
+ row.set(columnName, equation);
+ } else {
+ logger.error("Error parsing equation
\"" + formula + "\": " + equationCompiler.getLastErrorMsg());
+ }
+ }
+ }
+ }
+
+ /**
* It controls which graphics attributes should be parsed.
- * @param element
- * @param attName
+ * @param element The network, node or edge
+ * @param attName The name of the XGMML attribute
* @return
*/
protected boolean ignoreGraphicsAttribute(final CyTableEntry element,
String attName) {
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-06-30 00:35:38 UTC (rev 25980)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-06-30 15:49:34 UTC (rev 25981)
@@ -623,6 +623,7 @@
if (attType == Double.class) {
if (equation != null) {
+ // TODO: Should Cy3 still save equations when exporting to
XGMML?
writeEquationAttributeXML(attName, ObjectType.REAL,
equation.toString(), true);
} else {
Double dAttr = row.get(attName, Double.class);
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
2011-06-30 00:35:38 UTC (rev 25980)
+++
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-06-30 15:49:34 UTC (rev 25981)
@@ -51,6 +51,9 @@
<osgi:reference id="passthroughMappingFactoryServiceRef"
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
filter="(mapping.type=passthrough)" />
+
+ <osgi:reference id="equationCompilerServiceRef"
+ interface="org.cytoscape.equations.EquationCompiler" />
<!-- Export services -->
<osgi:service id="cyNetworkReaderManagerService"
ref="cyNetworkReaderManager"
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
2011-06-30 00:35:38 UTC (rev 25980)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-06-30 15:49:34 UTC (rev 25981)
@@ -548,9 +548,10 @@
<bean id="objectTypeMap"
class="org.cytoscape.io.internal.read.xgmml.ObjectTypeMap" />
<bean id="readDataManager"
-
class="org.cytoscape.io.internal.read.xgmml.handler.ReadDataManager" />
+
class="org.cytoscape.io.internal.read.xgmml.handler.ReadDataManager">
+ <constructor-arg ref="equationCompilerServiceRef" />
+ </bean>
-
<bean id="attributeValueUtil"
class="org.cytoscape.io.internal.read.xgmml.handler.AttributeValueUtil">
<constructor-arg ref="objectTypeMap" />
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReaderTest.java
2011-06-30 00:35:38 UTC (rev 25980)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReaderTest.java
2011-06-30 15:49:34 UTC (rev 25981)
@@ -7,6 +7,7 @@
import java.io.File;
import java.io.FileInputStream;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderTester;
import org.cytoscape.io.internal.read.xgmml.handler.AttributeValueUtil;
import org.cytoscape.io.internal.read.xgmml.handler.ReadDataManager;
@@ -46,7 +47,7 @@
.thenReturn(new MinimalVisualLexicon(new
NullVisualProperty("MINIMAL_ROOT",
"Minimal Root Visual Property")));
- readDataMgr = new ReadDataManager();
+ readDataMgr = new ReadDataManager(mock(EquationCompiler.class));
ObjectTypeMap objectTypeMap = new ObjectTypeMap();
attributeValueUtil = new AttributeValueUtil(objectTypeMap,
readDataMgr);
HandlerFactory handlerFactory = new HandlerFactory(readDataMgr,
attributeValueUtil);
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