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[Jsbml-svn] SF.net SVN: jsbml:[2410] trunk
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From: <nik...@us...> - 2015-11-27 14:54:29
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Revision: 2410
http://sourceforge.net/p/jsbml/code/2410
Author: niko-rodrigue
Date: 2015-11-27 14:54:26 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
corrected the last failing tests + improve few toString methods
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -327,10 +327,10 @@
@Override
public String toString() {
if (isSetName() && (getName().length() > 0)) {
- return name;
+ return getElementName() + ": name= " + name;
}
if (isSetId()) {
- return id;
+ return getElementName() + ": id= " + id;
}
return getElementName();
}
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -859,6 +859,7 @@
while (children.hasMoreElements()) {
TreeNode child = children.nextElement();
+
if (child instanceof AbstractSBase && ((AbstractSBase) child).getPackageName().equals(sbasePlugin.getPackageName()))
{
success &= ((AbstractSBase) child).setPackageNamespaceAndVersion(sbasePlugin.getPackageName(), packageNamespace, packageVersion);
@@ -1088,12 +1089,7 @@
SBasePlugin sbasePlugin = (SBasePlugin) newValue;
if (doc != null) {
- String packageNamespace = doc.getEnabledPackageNamespace(sbasePlugin.getPackageName());
- int packageVersion = PackageUtil.extractPackageVersion(packageNamespace);
-
- ((AbstractSBasePlugin) sbasePlugin).setNamespace(packageNamespace);
- sbasePlugin.setPackageVersion(packageVersion);
-
+ checkAndSetPackageNamespaceAndVersion(sbasePlugin, doc);
}
}
@@ -2050,6 +2046,7 @@
while (children.hasMoreElements()) {
TreeNode child = children.nextElement();
+
if (child instanceof AbstractSBase && ((AbstractSBase) child).getPackageName().equals(packageLabel)) {
success &= ((AbstractSBase) child).setPackageNamespaceAndVersion(packageLabel, namespace, packageVersion);
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -315,11 +315,12 @@
*/
@Override
public String toString() {
+
if (isSetName() && (getName().length() > 0)) {
- return name;
+ return getElementName() + ": name= " + name;
}
if (isSetId()) {
- return id;
+ return getElementName() + ": id= " + id;
}
return getElementName();
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -108,6 +108,8 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = CompConstants.shortLabel;
}
/* (non-Javadoc)
@@ -126,4 +128,18 @@
return new Port(this);
}
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ return "Port [id=" + getId() + ", name=" + getName()
+ + (isSetPortRef() ? ", portRef=" + getPortRef() : "")
+ + (isSetIdRef() ? ", idRef=" + getIdRef() : "")
+ + (isSetMetaIdRef() ? ", metaIdRef=" + getMetaIdRef() : "")
+ + "]";
+ }
+
+
+
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -547,8 +547,12 @@
*/
@Override
public String toString() {
- return "SBaseRef [portRef=" + portRef + ", idRef=" + idRef
- + ", unitRef=" + unitRef + ", metaIdRef=" + metaIdRef
+ return "SBaseRef ["
+ + (isSetPortRef() ? ", portRef=" + getPortRef() : "")
+ + (isSetIdRef() ? ", idRef=" + getIdRef() : "")
+ + (isSetMetaIdRef() ? ", metaIdRef=" + getMetaIdRef() : "")
+ + (isSetUnitRef() ? ", unitIdRef=" + getUnitRef() : "")
+ + (isSetSBaseRef() ? "SBaseRef child is set" : "")
+ "]";
}
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -686,7 +686,7 @@
public String toString() {
return "Group [id=" + getId() + ", name=" + getName()
+ (isSetKind()?", kind=" + getKind():"")
- + ", listOfMembers=" + listOfMembers + "]";
+ + ", memberCount=" + getMemberCount() + "]";
}
/* (non-Javadoc)
Modified: trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -160,7 +160,7 @@
g2.createMemberWithIdRef("G_M4", "S1");
g2.getMember(0).setIdRef("S2");
g2.getMember("G_M2").setIdRef(cell);
- g2.createMemberConstraint("G_MC1").setDistinctAttribute("test");
+// g2.createMemberConstraint("G_MC1").setDistinctAttribute("test");
QualModelPlugin qualModel = (QualModelPlugin) m.getPlugin(QualConstants.shortLabel);
qualModel.createQualitativeSpecies("Q_QS1");
Modified: trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -25,6 +25,8 @@
import javax.xml.stream.XMLStreamException;
+import junit.framework.Assert;
+
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -436,6 +438,8 @@
CompModelPlugin comp = new CompModelPlugin(model);
+ Assert.assertFalse(CompConstants.namespaceURI_L3V1V1.equals(comp.getElementNamespace()));
+
Port port = comp.createPort();
port.setId("c");
port.setIdRef("s");
@@ -446,12 +450,17 @@
SBaseRef sbaseRefRecursive = sbaseRef.createSBaseRef();
sbaseRefRecursive.setMetaId("CMeta2");
- model.addExtension(CompConstants.namespaceURI, comp);
+ model.addExtension(CompConstants.namespaceURI_L3V1V1, comp);
assertTrue(doc.findSBase("CPortMeta1").equals(port));
assertTrue(doc.findSBase("CMeta2").equals(sbaseRefRecursive));
assertTrue(doc.findSBase("CMeta1").equals(sbaseRef));
-
+
+ assertTrue(CompConstants.namespaceURI_L3V1V1.equals(comp.getElementNamespace()));
+ assertTrue(CompConstants.namespaceURI_L3V1V1.equals(port.getNamespace()));
+ assertTrue(CompConstants.namespaceURI_L3V1V1.equals(sbaseRef.getNamespace()));
+
+
String docString = null;
try {
@@ -601,7 +610,7 @@
/**
- * Create a SBasePlugin by hand without extenddeSBase set, add it to an element and check that the ids are registered.
+ * Create a SBasePlugin by hand without extendedSBase set, add it to an element and check that the ids are registered.
*
*/
@Test public void testQual() {
@@ -621,12 +630,14 @@
qualModel.createTransition("T1");
qualModel.createTransition("T2");
- model.addPlugin(QualConstants.shortLabel, qualModel);
+ model.addPlugin(QualConstants.namespaceURI_L3V1V1, qualModel);
assertTrue(model.findUniqueNamedSBase("QS1").equals(qs1));
assertTrue(model.findUniqueNamedSBase("QS3") != null);
assertTrue(model.findUniqueNamedSBase("T2") != null);
assertTrue(doc.findSBase("QS1") != null);
+ assertTrue(qs1.getPackageVersion() == 1);
+ assertTrue(qs1.getNamespace().equals(QualConstants.namespaceURI_L3V1V1));
// cloning the whole document
SBMLDocument clonedDoc = doc.clone();
@@ -673,11 +684,11 @@
group.createMemberWithIdRef("GM2", "S2");
Member member3 = group.createMemberWithIdRef("GM3", "S1");
member3.setMetaId("GM3");
- group.createMemberConstraint("GMC1");
+ // group.createMemberConstraint("GMC1");
assertTrue(groupsModel.getGroupCount() == 1);
assertTrue(group.getMemberCount() == 3);
- assertTrue(group.getMemberConstraintCount() == 1);
+ // assertTrue(group.getMemberConstraintCount() == 1);
try {
Group g2 = groupsModel.createGroup();
@@ -692,12 +703,12 @@
} catch (IllegalArgumentException e) {
assertTrue(true);
}
- try {
- groupsModel.createGroup("GMC1");
- assertTrue("We should not be allowed to have several element with the same id inside the same model", false);
- } catch (IllegalArgumentException e) {
- assertTrue(true);
- }
+// try {
+// groupsModel.createGroup("GMC1");
+// assertTrue("We should not be allowed to have several element with the same id inside the same model", false);
+// } catch (IllegalArgumentException e) {
+// assertTrue(true);
+// }
// try {
// groupsModel.createGroup("GLMC1");
// assertTrue("We should not be allowed to have several element with the same id inside the same model", false);
@@ -728,7 +739,7 @@
assertTrue(clonedDoc.findSBase("GM3") != null);
assertTrue(clonedModel.findUniqueNamedSBase("GM3") != null);
assertTrue(clonedModel.findUniqueNamedSBase("G1") != null);
- assertTrue(clonedModel.findUniqueNamedSBase("GMC1") != null);
+// assertTrue(clonedModel.findUniqueNamedSBase("GMC1") != null);
}
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