Author: rodche
Date: 2012-06-13 16:57:47 -0700 (Wed, 13 Jun 2012)
New Revision: 29560
Removed:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/StaxHack.java
Modified:
core3/impl/trunk/biopax-impl/pom.xml
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
Log:
Fix (unencode html) for network/node/edge 'name' to show the actual latin
symbol instead e.g. "β", etc. Some polishing.
Modified: core3/impl/trunk/biopax-impl/pom.xml
===================================================================
--- core3/impl/trunk/biopax-impl/pom.xml 2012-06-13 23:37:36 UTC (rev
29559)
+++ core3/impl/trunk/biopax-impl/pom.xml 2012-06-13 23:57:47 UTC (rev
29560)
@@ -9,7 +9,7 @@
<properties>
<bundle.symbolicName>org.cytoscape.biopax-impl</bundle.symbolicName>
<bundle.namespace>org.cytoscape.biopax</bundle.namespace>
- <paxtools.version>4.1.1</paxtools.version>
+ <paxtools.version>4.1.5-SNAPSHOT</paxtools.version>
</properties>
<modelVersion>4.0.0</modelVersion>
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-06-13 23:37:36 UTC (rev 29559)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-06-13 23:57:47 UTC (rev 29560)
@@ -19,6 +19,7 @@
import org.biopax.paxtools.util.Filter;
import org.cytoscape.biopax.internal.util.AttributeUtil;
import org.cytoscape.biopax.internal.util.BioPaxUtil;
+import org.cytoscape.biopax.internal.util.BioPaxUtil.StaxHack;
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.biopax.internal.util.ExternalLink;
import org.cytoscape.biopax.internal.util.ExternalLinkUtil;
@@ -691,7 +692,7 @@
// add a piece of the BioPAX (RDF/XML without parent|child
elements)
String owl = BioPaxUtil.toOwl(element); // (requires
common-lang-2.4 bundle to be started)
- AttributeUtil.set(network, node,
CyNetwork.HIDDEN_ATTRS,BioPaxUtil.BIOPAX_DATA, owl, String.class);
+ AttributeUtil.set(network, node, CyNetwork.HIDDEN_ATTRS,
BioPaxUtil.BIOPAX_DATA, owl, String.class);
String name =
BioPaxUtil.truncateLongStr(BioPaxUtil.getNodeName(element) + "");
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
2012-06-13 23:37:36 UTC (rev 29559)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
2012-06-13 23:57:47 UTC (rev 29560)
@@ -2,6 +2,7 @@
import java.io.InputStream;
+import org.apache.commons.lang.StringEscapeUtils;
import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.model.Model;
import org.cytoscape.biopax.internal.util.BioPaxUtil;
@@ -89,10 +90,9 @@
//normalize/infer properties: displayName, cellularLocation,
organism, dartaSource
BioPaxUtil.fixDisplayName(model);
- ModelUtils mu = new ModelUtils(model);
- mu.inferPropertyFromParent("dataSource");
- mu.inferPropertyFromParent("organism");
- mu.inferPropertyFromParent("cellularLocation");
+ ModelUtils.inferPropertyFromParent(model, "dataSource");
+ ModelUtils.inferPropertyFromParent(model, "organism");
+ ModelUtils.inferPropertyFromParent(model, "cellularLocation");
// Map BioPAX Data to Cytoscape Nodes/Edges (run as task)
BioPaxMapper mapper = new BioPaxMapper(model, networkFactory,
taskMonitor);
@@ -121,7 +121,7 @@
}
// Take appropriate adjustments, if name already exists
- name = naming.getSuggestedNetworkTitle(name);
+ name =
naming.getSuggestedNetworkTitle(StringEscapeUtils.unescapeHtml(name));
if(log.isDebugEnabled())
log.debug("New BioPAX network name is: " + name);
Deleted:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/StaxHack.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/StaxHack.java
2012-06-13 23:37:36 UTC (rev 29559)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/StaxHack.java
2012-06-13 23:57:47 UTC (rev 29560)
@@ -1,16 +0,0 @@
-package org.cytoscape.biopax.internal;
-
-import com.ctc.wstx.stax.WstxInputFactory;
-
-public class StaxHack {
- public static final void runWithHack(Runnable runnable) {
- Thread thread = Thread.currentThread();
- ClassLoader loader = thread.getContextClassLoader();
- try {
-
thread.setContextClassLoader(WstxInputFactory.class.getClassLoader());
- runnable.run();
- } finally {
- thread.setContextClassLoader(loader);
- }
- }
-}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-06-13 23:37:36 UTC (rev 29559)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-06-13 23:57:47 UTC (rev 29560)
@@ -38,6 +38,7 @@
import java.util.Map;
import java.util.Set;
+import org.apache.commons.lang.StringEscapeUtils;
import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.converter.OneTwoThree;
@@ -58,11 +59,12 @@
import org.biopax.paxtools.model.level3.Xref;
import org.biopax.paxtools.util.ClassFilterSet;
import org.cytoscape.biopax.internal.BioPaxMapper;
-import org.cytoscape.biopax.internal.StaxHack;
import org.cytoscape.model.CyNetwork;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import com.ctc.wstx.stax.WstxInputFactory;
+
/**
* BioPax Utility Class - is a BioPAX Model Adapter
* that also defines additional constants.
@@ -86,6 +88,19 @@
* BioPAX Class: protein phosphorylated
*/
public static final String PROTEIN_PHOSPHORYLATED =
"Protein-phosphorylated";
+
+ public static class StaxHack {
+ public static final void runWithHack(Runnable runnable) {
+ Thread thread = Thread.currentThread();
+ ClassLoader loader = thread.getContextClassLoader();
+ try {
+
thread.setContextClassLoader(WstxInputFactory.class.getClassLoader());
+ runnable.run();
+ } finally {
+ thread.setContextClassLoader(loader);
+ }
+ }
+ }
// private Constructor
private BioPaxUtil() {}
@@ -164,22 +179,17 @@
}
String nodeName = getShortName(bpe);
-
- if ((nodeName != null) && (nodeName.length() > 0)) {
- return nodeName;
+ if (nodeName == null || nodeName.length()== 0) {
+ nodeName = getStandardName(bpe);
+ if (nodeName == null || nodeName.length() == 0) {
+ Collection<String> names = getSynonymList(bpe);
+ if (!names.isEmpty())
+ nodeName = getTheShortestString(names);
+ }
}
- nodeName = getStandardName(bpe);
- if ((nodeName != null) && (nodeName.length() > 0)) {
- return nodeName;
- }
-
- Collection<String> names = getSynonymList(bpe);
- if (names != null && !names.isEmpty()) {
- return getTheShortestString(names);
- }
-
- return bpe.getRDFId();
+ return (nodeName == null || nodeName.length() == 0)
+ ? bpe.getRDFId() :
StringEscapeUtils.unescapeHtml(nodeName);
}
@@ -445,15 +455,13 @@
public static String getName(Model model) {
StringBuffer modelName = new StringBuffer();
- ModelUtils mu = new ModelUtils(model);
-
- Collection<Pathway> pws = mu.getRootElements(Pathway.class);
+ Collection<Pathway> pws = ModelUtils.getRootElements(model,
Pathway.class);
for(Pathway pw: pws) {
modelName.append(" ").append(getNodeName(pw));
}
if(modelName.length()==0) {
- Collection<Interaction> itrs =
mu.getRootElements(Interaction.class);
+ Collection<Interaction> itrs =
ModelUtils.getRootElements(model, Interaction.class);
for(Interaction it: itrs) {
modelName.append(" ").append(getNodeName(it));
}
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
2012-06-13 23:37:36 UTC (rev 29559)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
2012-06-13 23:57:47 UTC (rev 29560)
@@ -39,9 +39,9 @@
import java.util.Set;
import java.util.Stack;
+import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.biopax.paxtools.controller.AbstractTraverser;
-import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.controller.ObjectPropertyEditor;
import org.biopax.paxtools.controller.PropertyEditor;
import org.biopax.paxtools.controller.SimpleEditorMap;
@@ -57,7 +57,6 @@
import org.biopax.paxtools.model.level3.Interaction;
import org.biopax.paxtools.model.level3.Level3Element;
import org.biopax.paxtools.model.level3.Named;
-import org.biopax.paxtools.model.level3.Pathway;
import org.biopax.paxtools.model.level3.PhysicalEntity;
import org.biopax.paxtools.model.level3.Provenance;
import org.biopax.paxtools.model.level3.PublicationXref;
@@ -177,22 +176,17 @@
}
String nodeName = getShortName(bpe);
-
- if ((nodeName != null) && (nodeName.length() > 0)) {
- return nodeName;
+ if (nodeName == null || nodeName.length()== 0) {
+ nodeName = getStandardName(bpe);
+ if (nodeName == null || nodeName.length() == 0) {
+ Collection<String> names = getSynonymList(bpe);
+ if (!names.isEmpty())
+ nodeName = getTheShortestString(names);
+ }
}
- nodeName = getStandardName(bpe);
- if ((nodeName != null) && (nodeName.length() > 0)) {
- return nodeName;
- }
-
- Collection<String> names = getSynonymList(bpe);
- if (names != null && !names.isEmpty()) {
- return getTheShortestString(names);
- }
-
- return bpe.getRDFId();
+ return (nodeName == null || nodeName.length() == 0)
+ ? bpe.getRDFId() :
StringEscapeUtils.unescapeHtml(nodeName);
}
@@ -446,41 +440,6 @@
return subclasses;
}
-
-
- /**
- * Creates a name for to the BioPAX model
- * using its top-level process name(s).
- *
- * @param model
- * @return
- */
- public static String getName(Model model) {
- StringBuffer modelName = new StringBuffer();
-
- ModelUtils mu = new ModelUtils(model);
-
- Collection<Pathway> pws = mu.getRootElements(Pathway.class);
- for(Pathway pw: pws) {
- modelName.append(" ").append(getNodeName(pw));
- }
-
- if(modelName.length()==0) {
- Collection<Interaction> itrs =
mu.getRootElements(Interaction.class);
- for(Interaction it: itrs) {
- modelName.append(" ").append(getNodeName(it));
- }
- }
-
- if(modelName.length()==0) {
- modelName.append(model.getXmlBase());
- }
-
- String name = modelName.toString().trim();
-
- return name;
- }
-
/**
* Gets all the objects of provided BioPAX types.
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