Author: jm
Date: 2011-04-04 08:37:40 -0700 (Mon, 04 Apr 2011)
New Revision: 24649
Added:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/util/StaxHack.java
Modified:
core3/cpath2-impl/trunk/pom.xml
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/biopax/util/BioPaxUtil.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
Log:
Importing BioPAX format from cPath now works
Pulled StaxHack into a top-level class
Modified: core3/cpath2-impl/trunk/pom.xml
===================================================================
--- core3/cpath2-impl/trunk/pom.xml 2011-04-01 21:57:22 UTC (rev 24648)
+++ core3/cpath2-impl/trunk/pom.xml 2011-04-04 15:37:40 UTC (rev 24649)
@@ -65,6 +65,11 @@
<artifactId>commons-codec</artifactId>
<version>1.3</version>
</dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>collections-generic</artifactId>
+ <version>4.01</version>
+ </dependency>
<dependency>
<groupId>cytoscape-temp</groupId>
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/biopax/util/BioPaxUtil.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/biopax/util/BioPaxUtil.java
2011-04-01 21:57:22 UTC (rev 24648)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/biopax/util/BioPaxUtil.java
2011-04-04 15:37:40 UTC (rev 24649)
@@ -70,6 +70,7 @@
import org.biopax.paxtools.util.ClassFilterSet;
import org.cytoscape.cpath2.internal.biopax.ExternalLink;
import org.cytoscape.cpath2.internal.biopax.MapBioPaxToCytoscape;
+import org.cytoscape.cpath2.internal.util.StaxHack;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
import org.slf4j.Logger;
@@ -195,11 +196,15 @@
* @return BioPaxUtil new instance (containing the imported BioPAX data)
* @throws FileNotFoundException
*/
- public static Model read(InputStream in) throws FileNotFoundException {
+ public static Model read(final InputStream in) throws
FileNotFoundException {
Model model = null;
try {
- // TODO: Use StAXHack here
- model = (new SimpleReader()).convertFromOWL(in);
+ model = new StaxHack<Model>() {
+ @Override
+ public Model runWithHack() {
+ return new
SimpleReader().convertFromOWL(in);
+ }
+ }.runWithHack();
} catch (Exception e) {
log.warn("Import failed: " + e);
}
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2011-04-01 21:57:22 UTC (rev 24648)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2011-04-04 15:37:40 UTC (rev 24649)
@@ -28,6 +28,7 @@
import org.cytoscape.cpath2.internal.cytoscape.BinarySifVisualStyleUtil;
import org.cytoscape.cpath2.internal.util.AttributeUtil;
import org.cytoscape.cpath2.internal.util.SelectUtil;
+import org.cytoscape.cpath2.internal.util.StaxHack;
import org.cytoscape.cpath2.internal.web_service.CPathException;
import org.cytoscape.cpath2.internal.web_service.CPathProperties;
import org.cytoscape.cpath2.internal.web_service.CPathResponseFormat;
@@ -39,7 +40,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.session.CyNetworkNaming;
-import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.AbstractTask;
@@ -558,23 +558,3 @@
public void setTitle(String arg0) {
}
}
-
-/**
- * This class executes code using this bundle's ClassLoader as the current
- * thread's context ClassLoader. This enables the service discovery mechanism
- * used by some StAX implementations to function properly under OSGi.
- */
-abstract class StaxHack<T> {
- public abstract T runWithHack();
-
- public final T run() {
- Thread thread = Thread.currentThread();
- ClassLoader oldClassLoader = thread.getContextClassLoader();
- try {
-
thread.setContextClassLoader(getClass().getClassLoader());
- return runWithHack();
- } finally {
- thread.setContextClassLoader(oldClassLoader);
- }
- }
-}
Added:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/util/StaxHack.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/util/StaxHack.java
(rev 0)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/util/StaxHack.java
2011-04-04 15:37:40 UTC (rev 24649)
@@ -0,0 +1,21 @@
+package org.cytoscape.cpath2.internal.util;
+
+/**
+ * This class executes code using this bundle's ClassLoader as the current
+ * thread's context ClassLoader. This enables the service discovery mechanism
+ * used by some StAX implementations to function properly under OSGi.
+ */
+public abstract class StaxHack<T> {
+ public abstract T runWithHack();
+
+ public final T run() {
+ Thread thread = Thread.currentThread();
+ ClassLoader oldClassLoader = thread.getContextClassLoader();
+ try {
+
thread.setContextClassLoader(getClass().getClassLoader());
+ return runWithHack();
+ } finally {
+ thread.setContextClassLoader(oldClassLoader);
+ }
+ }
+}
\ No newline at end of file
Property changes on:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/util/StaxHack.java
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