Author: rodche
Date: 2010-01-27 19:34:55 -0800 (Wed, 27 Jan 2010)
New Revision: 19059
Modified:
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java
Log:
tests fixed
Modified:
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
===================================================================
---
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
2010-01-28 03:03:58 UTC (rev 19058)
+++
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/mapper/TestBioPaxToCytoscapeMapper.java
2010-01-28 03:34:55 UTC (rev 19059)
@@ -31,6 +31,8 @@
**/
package cytoscape.coreplugins.biopax.mapper;
+import java.util.*;
+
import cytoscape.CyNetwork;
import cytoscape.CyNode;
import cytoscape.Cytoscape;
@@ -48,13 +50,6 @@
import org.biopax.paxtools.model.Model;
-import java.io.FileReader;
-
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Set;
-
-
/**
* Tests the MapBioPaxToCytoscape Mapper Class.
*
@@ -87,7 +82,7 @@
* @throws Exception All Exceptions.
*/
public void testMapper1() throws Exception {
- Model model =BioPaxUtil.readFile("biopax_sample1.owl");
+ Model model =
BioPaxUtil.readFile("test-resources/biopax_sample1.owl");
MapBioPaxToCytoscape mapper = new MapBioPaxToCytoscape();
mapper.doMapping(model);
@@ -137,9 +132,9 @@
Node target = edge.getTarget();
if (i == 0) {
- assertEquals("CPATH-125(PM)-CPATH-126",
target.getIdentifier());
+ assertEquals("CPATH-125-CPATH-126",
target.getIdentifier());
} else if (i == 1) {
- assertEquals("CPATH-124(PM)-CPATH-126",
target.getIdentifier());
+ assertEquals("CPATH-124-CPATH-126",
target.getIdentifier());
}
}
}
@@ -199,9 +194,9 @@
Node target = edge.getTarget();
if (i == 0) {
- assertEquals("protein2",
target.getIdentifier());
- } else if (i == 1) {
assertEquals("protein1",
target.getIdentifier());
+ } else if (i == 1) {
+ assertEquals("protein2",
target.getIdentifier());
}
}
}
@@ -220,8 +215,8 @@
nodeMap.put("protein45", new Integer(0));
nodeMap.put("protein32", new Integer(0));
nodeMap.put("smallMolecule10", new Integer(0));
- nodeMap.put("smallMolecule18(CY)", new Integer(0));
- nodeMap.put("smallMolecule23(CY)", new Integer(0));
+ nodeMap.put("smallMolecule18", new Integer(0));
+ nodeMap.put("smallMolecule23", new Integer(0));
nodeMap.put("smallMolecule27", new Integer(0));
nodeMap.put("smallMolecule39", new Integer(0));
nodeMap.put("smallMolecule99", new Integer(0));
@@ -250,7 +245,7 @@
if (nodeMap.containsKey(id)) {
nodeMap.put(id, new Integer(1));
} else {
- fail("Network contains an Node that we were not
expecting: " + "\"" + id + "\"");
+ fail("Network contains a Node that we were not
expecting: " + "\"" + id + "\"");
}
}
@@ -316,7 +311,7 @@
String edgeType = Cytoscape.getEdgeAttributes()
.getStringAttribute(edge.getIdentifier(),
MapBioPaxToCytoscape.BIOPAX_EDGE_TYPE);
- assertEquals("ACTIVATION-NONALLOSTERIC",
edgeType);
+ assertEquals("ACTIVATION_NONALLOSTERIC",
edgeType);
} else if (i == 2) {
// Validate the Left Side of the Reaction
// smallMolecule27 --> (LEFT) -->
biochemicalReaction37
Modified:
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java
===================================================================
---
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java
2010-01-28 03:03:58 UTC (rev 19058)
+++
csplugins/trunk/toronto/rodche/BioPAX/test/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java
2010-01-28 03:34:55 UTC (rev 19059)
@@ -50,7 +50,7 @@
*/
public void testFileConnect() throws Exception {
String str = WebFileConnect.retrieveDocument(new
File("test-resources/biopax_sample1.owl"));
- assertTrue(str.startsWith("<?xml version=\"1.0\" " +
"encoding=\"UTF-8\" ?>"));
+ assertTrue(str.startsWith("<?xml version=\"1.0\""));
}
/**
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