Author: rodche
Date: 2012-10-16 11:14:05 -0700 (Tue, 16 Oct 2012)
New Revision: 30676
Modified:
cytoscape/trunk/coreplugins/BioPAX/pom.xml
cytoscape/trunk/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
cytoscape/trunk/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
Log:
bug fixed, related to getLocalRdfId method (also - renamed, made private); this
was also related to proper using of BioPAX model's xml:base (URI prefix)...
Modified: cytoscape/trunk/coreplugins/BioPAX/pom.xml
===================================================================
--- cytoscape/trunk/coreplugins/BioPAX/pom.xml 2012-10-16 09:55:03 UTC (rev
30675)
+++ cytoscape/trunk/coreplugins/BioPAX/pom.xml 2012-10-16 18:14:05 UTC (rev
30676)
@@ -67,7 +67,7 @@
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
- <version>4.1.1</version>
+ <version>4.1.5b</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
Modified:
cytoscape/trunk/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
===================================================================
---
cytoscape/trunk/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
2012-10-16 09:55:03 UTC (rev 30675)
+++
cytoscape/trunk/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
2012-10-16 18:14:05 UTC (rev 30676)
@@ -33,6 +33,7 @@
import cytoscape.logger.CyLogger;
import org.biopax.paxtools.controller.EditorMap;
+import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXElement;
@@ -245,21 +246,20 @@
return getTheShortestString(names);
}
- return getLocalPartRdfId(bpe);
+ return fixPepRdfId(bpe);
}
+ /**
+ * Generates a unique CyNode identifier
+ */
public static String generateId(BioPAXElement bpe) {
- String id = (bpe instanceof physicalEntityParticipant
- &&
((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()!=null)
- ?
((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY().getRDFId()
- : bpe.getRDFId();
- return Cytoscape.getCurrentNetwork().getIdentifier().hashCode()
+
- "" + id.hashCode() + "-" +
getLocalPartRdfId(bpe);
+ String id = fixPepRdfId(bpe);
+ return
ModelUtils.md5hex(Cytoscape.getCurrentNetwork().getIdentifier() + id);
}
- public static String getLocalPartRdfId(BioPAXElement bpe) {
+ private static String fixPepRdfId(BioPAXElement bpe) {
if(bpe == null) return "";
// also fix pEPs
@@ -268,7 +268,7 @@
?
((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY().getRDFId()
: bpe.getRDFId();
- return id.replaceFirst("^.+#", "");
+ return id;
}
// get the shortest string
Modified:
cytoscape/trunk/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
===================================================================
---
cytoscape/trunk/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
2012-10-16 09:55:03 UTC (rev 30675)
+++
cytoscape/trunk/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
2012-10-16 18:14:05 UTC (rev 30676)
@@ -117,8 +117,9 @@
while (nodeIterator.hasNext()) {
CyNode node = (CyNode) nodeIterator.next();
-
- if (node.getIdentifier().endsWith("CPATH-126")) {
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(),
MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.endsWith("CPATH-126")) {
targetNodeIndex = node.getRootGraphIndex();
}
}
@@ -181,8 +182,9 @@
while (nodeIterator.hasNext()) {
CyNode node = (CyNode) nodeIterator.next();
-
- if
(node.getIdentifier().endsWith("physicalInteraction1")) {
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(),
MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.endsWith("physicalInteraction1")) {
targetNodeIndex = node.getRootGraphIndex();
}
}
@@ -215,8 +217,9 @@
int nodeCount = cyNetwork.getNodeCount();
assertEquals(12, nodeCount);
- // This HashMap contains a list of expected node identifiers.
- // correction: these are identifier's part (real id now begins
with hash code)
+ // This HashMap contains all expected nodes.
+ // But node identifier is now a auto-generated md5hex digest;
+ // so it's easier to test here by using biopax.rdfid values
instead)
Map<String, Integer> nodeMap = new HashMap<String, Integer>();
nodeMap.put("protein45", new Integer(0));
nodeMap.put("protein32", new Integer(0));
@@ -226,7 +229,6 @@
nodeMap.put("smallMolecule27", new Integer(0));
nodeMap.put("smallMolecule39", new Integer(0));
nodeMap.put("smallMolecule99", new Integer(0));
-
// These represent interaction nodes
nodeMap.put("catalysis43", new Integer(0));
nodeMap.put("biochemicalReaction6", new Integer(0));
@@ -239,9 +241,10 @@
while (nodeIterator.hasNext()) {
CyNode node = (CyNode) nodeIterator.next();
String id = node.getIdentifier();
-
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(id,
MapBioPaxToCytoscape.BIOPAX_RDF_ID);
// Test a specific node label
- if (id.endsWith("smallMolecule99")) {
+ if (uri.endsWith("smallMolecule99")) {
String label = Cytoscape.getNodeAttributes()
.getStringAttribute(id,
BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
assertEquals("Mg2+", label);
@@ -249,7 +252,9 @@
String found = null;
for(String key : nodeMap.keySet()) {
- if(id.endsWith(key)) {
+ uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(id,
MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if(uri.endsWith(key)) {
found = key;
break;
}
@@ -287,8 +292,9 @@
while (nodeIterator.hasNext()) {
CyNode node = (CyNode) nodeIterator.next();
-
- if
(node.getIdentifier().endsWith("biochemicalReaction37")) {
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(),
MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.endsWith("biochemicalReaction37")) {
targetNodeIndex = node.getRootGraphIndex();
}
}
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