[MOBY-guts] biomoby commit
Paul Gordon
gordonp at dev.open-bio.org
Fri Nov 30 17:23:17 UTC 2007
gordonp
Fri Nov 30 12:23:16 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv2857/src/main/org/biomoby/shared/data
Modified Files:
MobyDataBoolean.java MobyDataComposite.java
MobyDataDateTime.java MobyDataFloat.java MobyDataInt.java
MobyDataObject.java MobyDataString.java
Log Message:
Fixed missing passing of the registry to c-tors, which caused incorrect use of default registry for DOM-based object building
moby-live/Java/src/main/org/biomoby/shared/data MobyDataBoolean.java,1.5,1.6 MobyDataComposite.java,1.19,1.20 MobyDataDateTime.java,1.10,1.11 MobyDataFloat.java,1.8,1.9 MobyDataInt.java,1.7,1.8 MobyDataObject.java,1.20,1.21 MobyDataString.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataBoolean.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataBoolean.java 2007/06/09 18:14:33 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataBoolean.java 2007/11/30 17:23:16 1.6
@@ -30,7 +30,7 @@
public MobyDataBoolean(org.w3c.dom.Element element, Registry registry) throws IllegalArgumentException{
this(getName(element), getTextContents(element), registry);
setId(getId(element));
- addNamespace(getNamespace(element));
+ addNamespace(getNamespace(element, registry));
}
/**
@@ -43,7 +43,7 @@
/** Every c-tor eventually winds up here */
public MobyDataBoolean(String articleName, Boolean b, Registry registry){
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYBOOLEAN, registry));
value = b;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2007/10/31 15:35:55 1.19
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2007/11/30 17:23:16 1.20
@@ -40,7 +40,7 @@
public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{
this(MobyDataType.getDataType(element.getLocalName(), registry),
getName(element),
- getNamespace(element),
+ getNamespace(element, registry),
getId(element));
if(getDataType() == null){
throw new MobyException("Attempted to build a composite MOBY object from XML, " +
@@ -75,7 +75,7 @@
" does not have an article " +
"name, which is required (tag "+element.getNodeName()+")");
}
- MobyDataObject childObject = (MobyDataObject) createInstanceFromDOM(child);
+ MobyDataObject childObject = (MobyDataObject) createInstanceFromDOM(child, registry);
if(childObject == null){
throw new MobyException("The object member '" + fieldName + "' for object '"+ getName() +
" could not be properly parsed into a MOBY object");
@@ -86,7 +86,7 @@
}
public MobyDataComposite(MobyDataType type, String name, MobyNamespace namespace, String id){
- super(namespace.getName(), id);
+ super(namespace.getName(), id, type.getRegistry());
setName(name);
setDataType(type);
members = new ConcurrentHashMap<String, MobyDataObject>();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataDateTime.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataDateTime.java 2007/06/09 18:14:33 1.10
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataDateTime.java 2007/11/30 17:23:16 1.11
@@ -41,7 +41,7 @@
public MobyDataDateTime(org.w3c.dom.Element element, Registry registry) throws IllegalArgumentException{
this(getName(element), getTextContents(element), registry);
setId(getId(element));
- addNamespace(getNamespace(element));
+ addNamespace(getNamespace(element, registry));
}
/**
@@ -53,7 +53,7 @@
}
public MobyDataDateTime(String articleName, String stringISO8601, Registry registry) throws IllegalArgumentException{
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYDATETIME, registry));
value = parseISO8601(stringISO8601.trim());
}
@@ -67,7 +67,7 @@
}
public MobyDataDateTime(String articleName, GregorianCalendar cal, Registry registry){
- super(articleName, "");
+ super(articleName, "", registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYDATETIME, registry));
value = cal;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataFloat.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataFloat.java 2007/06/09 18:14:33 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataFloat.java 2007/11/30 17:23:16 1.9
@@ -34,7 +34,7 @@
public MobyDataFloat(org.w3c.dom.Element element, Registry registry) throws IllegalArgumentException{
this(getName(element), getTextContents(element), registry);
setId(getId(element));
- addNamespace(getNamespace(element));
+ addNamespace(getNamespace(element, registry));
}
/**
@@ -46,7 +46,7 @@
}
public MobyDataFloat(String articleName, Number n, Registry r){
- super(articleName);
+ super(articleName, r);
setDataType(MobyDataType.getDataType(MobyTags.MOBYFLOAT, r));
if(n instanceof BigDecimal){
value = (BigDecimal) n;
@@ -100,7 +100,7 @@
}
public MobyDataFloat(String articleName, String stringNumber, Registry registry) throws NumberFormatException{
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYFLOAT, registry));
value = new BigDecimal(stringNumber.trim());
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataInt.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataInt.java 2007/06/09 18:14:33 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataInt.java 2007/11/30 17:23:16 1.8
@@ -33,7 +33,7 @@
public MobyDataInt(org.w3c.dom.Element element, Registry registry) throws IllegalArgumentException{
this(getName(element), getTextContents(element), registry);
setId(getId(element));
- addNamespace(getNamespace(element));
+ addNamespace(getNamespace(element, registry));
}
/**
@@ -46,7 +46,7 @@
}
public MobyDataInt(String articleName, Number n, Registry registry){
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYINTEGER, registry));
if(n instanceof BigInteger){
value = (BigInteger) n;
@@ -76,7 +76,7 @@
}
public MobyDataInt(String articleName, int i, Registry registry){
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYINTEGER, registry));
value = new BigInteger(""+i);
}
@@ -95,7 +95,7 @@
}
public MobyDataInt(String articleName, String stringNumber, Registry registry) throws NumberFormatException{
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYINTEGER, registry));
value = new BigInteger(stringNumber.trim());
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java 2007/10/31 15:35:55 1.20
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java 2007/11/30 17:23:16 1.21
@@ -175,7 +175,7 @@
"instance to create");
}
- return createInstanceFromDOM(elementChild);
+ return createInstanceFromDOM(elementChild, registry);
}
// There are six types of objects we can populate with data directly
@@ -208,7 +208,7 @@
else{
MobyDataType type = MobyDataType.getDataType(objectClass, registry);
// Treat base64-encoded binary data as a special case, as we have a convenience class for it
- if(type != null && type.inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE))){
+ if(type != null && type.inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, registry))){
return new MobyDataBytes(objectTag, registry);
}
else{
@@ -238,11 +238,16 @@
}
protected static MobyNamespace getNamespace(Element e){
+ return getNamespace(e, null);
+ }
+
+ protected static MobyNamespace getNamespace(Element e, Registry registry){
String namespace = MobyPrefixResolver.getAttr(e, "namespace");
- MobyNamespace nsObj = MobyNamespace.getNamespace(namespace);
+ MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, registry);
if(nsObj == null){
// Not in the ontology, so create a token namespace
nsObj = new MobyNamespace(namespace == null ? "" : namespace);
+ nsObj.setRegistry(registry);
}
return nsObj;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataString.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataString.java 2007/07/23 21:32:58 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataString.java 2007/11/30 17:23:16 1.8
@@ -29,7 +29,7 @@
public MobyDataString(org.w3c.dom.Element element, Registry registry) throws IllegalArgumentException{
this(getName(element), getTextContents(element), registry);
setId(getId(element));
- addNamespace(getNamespace(element));
+ addNamespace(getNamespace(element, registry));
}
/**
@@ -41,7 +41,7 @@
}
public MobyDataString(String articleName, CharSequence stringValue, Registry registry){
- super(articleName);
+ super(articleName, registry);
setDataType(MobyDataType.getDataType(MobyTags.MOBYSTRING, registry));
value = stringValue == null ? null : new StringBuffer(stringValue.toString());
}
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