Embedded jvnet.Equals/ToString interfaces and implementation in prov-…

…xml to avoid nasty artifact class. Fixed a bug with xsd namespace when parsing rdf. Fixed issue #61.
lucmoreau · Dec 20, 2013 · 4fc1c43 · 4fc1c43
1 parent 2b2139b
commit 4fc1c43
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Showing 58 changed files with 580 additions and 294 deletions.
diff --git a/prov-interop/src/main/java/org/openprovenance/prov/interop/InteropException.java b/prov-interop/src/main/java/org/openprovenance/prov/interop/InteropException.java
@@ -1,15 +1,20 @@
 package org.openprovenance.prov.interop;
 
 public class InteropException extends RuntimeException {
+    /**
+     * 
+     */
+    private static final long serialVersionUID = 341614640704209138L;
+
     public InteropException(Exception e) {
 	super(e);
     }
 
     public InteropException(Throwable e) {
-	// TODO Auto-generated constructor stub
+        super (e);
     }
 
     public InteropException(String string) {
-	// TODO Auto-generated constructor stub
+        super(string);
     }
 }
diff --git a/prov-model/src/main/java/org/openprovenance/prov/model/ValueConverter.java b/prov-model/src/main/java/org/openprovenance/prov/model/ValueConverter.java
@@ -143,7 +143,6 @@ public Object convertToJava(QualifiedName datatype, String value) {
             return pFactory.base64Decoding(value);
         }
 
-	//transform to qname!!
 	if (datatype.equals(name.RDF_LITERAL)) {
 	    return value;
 	}
@@ -156,29 +155,29 @@ public Object convertToJava(QualifiedName datatype, String value) {
 
     public QualifiedName getXsdType(Object o) {
 	if (o instanceof Integer)
-	    return name.XSD_INT; //"xsd:int";
+	    return name.XSD_INT; 
 	if (o instanceof String)
-	    return name.XSD_STRING; //"xsd:string";
+	    return name.XSD_STRING; 
 	if (o instanceof LangString)
-	    return name.XSD_STRING; //"xsd:string";
+	    return name.XSD_STRING;
 	if (o instanceof BigInteger)
 	    return name.XSD_INTEGER;
 	if (o instanceof Long)
-	    return name.XSD_LONG; //"xsd:long";
+	    return name.XSD_LONG; 
 	if (o instanceof Short)
-	    return name.XSD_SHORT; //"xsd:short";
+	    return name.XSD_SHORT; 
 	if (o instanceof Double)
-	    return name.XSD_DOUBLE; //"xsd:double";
+	    return name.XSD_DOUBLE; 
 	if (o instanceof Float)
-	    return name.XSD_FLOAT; //"xsd:float";
+	    return name.XSD_FLOAT; 
 	if (o instanceof java.math.BigDecimal)
-	    return name.XSD_DECIMAL; //"xsd:decimal";
+	    return name.XSD_DECIMAL; 
 	if (o instanceof Boolean)
-	    return name.XSD_BOOLEAN; //"xsd:boolean";
+	    return name.XSD_BOOLEAN; 
 	if (o instanceof Byte)
-	    return name.XSD_BYTE; //"xsd:byte";
+	    return name.XSD_BYTE;
 	if (o instanceof QName)
-	    return name.XSD_QNAME; //"xsd:QName";
+	    return name.XSD_QNAME; 
 	if (o instanceof XMLGregorianCalendar) {
 	    XMLGregorianCalendar cal=(XMLGregorianCalendar)o;
 	    QName t=cal.getXMLSchemaType();
@@ -188,8 +187,11 @@ public QualifiedName getXsdType(Object o) {
             // default, return xsd:datetime
             return name.XSD_DATETIME;
 	}
-	//FIXME: see issue #54, value can be an element, when xsi:type was unspecified.
+	//issue #54 flagged a concern: value can be an element, when xsi:type was unspecified.
-	System.out.println("getXsdType() " + o.getClass());
+	// this is no longer the case
+	//System.out.println("getXsdType() " + o.getClass());
+
+	// Let's be permissive, and return the unknown qualified name
 	return name.QNAME_UNKNOWN;
     }
 

diff --git a/prov-rdf/src/main/java/org/openprovenance/prov/rdf/Utility.java b/prov-rdf/src/main/java/org/openprovenance/prov/rdf/Utility.java
@@ -45,7 +45,11 @@ public Document parseRDF(String filename) throws RDFParseException,
 	RdfCollector rdfCollector = new QualifiedCollector(pFactory,onto);
 	rdfParser.setRDFHandler(rdfCollector);
 	rdfParser.parse(inputStream, documentURL.toString());
-	return rdfCollector.getDocument();
+	Document doc=rdfCollector.getDocument();
+	Namespace ns=doc.getNamespace();
+	ns.unregister("xsd", "http://www.w3.org/2001/XMLSchema#");
+	ns.register("xsd", "http://www.w3.org/2001/XMLSchema");
+	return doc;
     }
 
     public void dumpRDF(Document document,

diff --git a/prov-rdf/src/main/java/org/openprovenance/prov/rdf/collector/RdfCollector.java b/prov-rdf/src/main/java/org/openprovenance/prov/rdf/collector/RdfCollector.java
@@ -54,7 +54,7 @@ public class RdfCollector extends RDFHandlerBase {
     protected HashMap<QualifiedName, HashMap<QualifiedName, List<Statement>>> collators;
     private Hashtable<QualifiedName, BundleHolder> bundles;
     protected Document document;
-    private Hashtable<String, String> revnss;
+   // private Hashtable<String, String> revnss;
     private ValueConverter valueConverter;
     final protected Ontology onto;
     protected static String BNODE_NS = "http://openprovenance.org/provtoolbox/bnode/";
@@ -66,7 +66,7 @@ public RdfCollector(ProvFactory pFactory, Ontology onto) {
    	this.name=pFactory.getName();
    	this.onto=onto;
    	this.collators = new HashMap<QualifiedName, HashMap<QualifiedName, List<Statement>>>();
-   	this.revnss = new Hashtable<String, String>();
+   	//this.revnss = new Hashtable<String, String>();
    	this.document = pFactory.newDocument();
    	this.valueConverter = new ValueConverter(pFactory);
    	this.bundles = new Hashtable<QualifiedName, BundleHolder>();
@@ -375,14 +375,6 @@ protected Object decodeLiteral(Literal literal) {
 	}
     }
 
-    //FIXME make a map
-
-    public QualifiedName getTypeForLiteral(String uri) {
-	if (uri.equals(NamespacePrefixMapper.XSD_HASH_NS + "unsignedInt")) {
-	    return name.XSD_UNSIGNED_INT;
-	}
-	return name.QNAME_UNKNOWN;
-    }
 
 
     private void handleTypes(Types.ProvType[] types, QualifiedName context, QualifiedName subject) {
@@ -895,7 +887,7 @@ public void handleNamespace(String prefix, String namespace) {
 	}
 	this.document.getNamespace().register(prefix, namespace);
 	//pFactory.setNamespaces(this.document.getNss());
-	this.revnss.put(namespace, prefix);
+	//this.revnss.put(namespace, prefix);
     }
 
 

diff --git a/prov-xml/pom.xml b/prov-xml/pom.xml
@@ -27,22 +27,27 @@
       <version>${jaxb.api.version}</version>
     </dependency>
 
-<!--
+
     <dependency>
      <groupId>com.sun.xml.bind</groupId>
      <artifactId>jaxb-impl</artifactId>
      <version>${jaxb.impl.version}</version>
     </dependency>
--->
 
 
+   <dependency>
+    <groupId>commons-lang</groupId>
+    <artifactId>commons-lang</artifactId>
+    <version>2.6</version>
+  </dependency>
 
+<!-- Should no longer needed since we use our own copy of Tostring etdc,
+    owerver seems ot make com.sun.xml.bin.marshaller available 
     <dependency>
       <groupId>org.jvnet.jaxb2_commons</groupId>
       <artifactId>runtime</artifactId>
       <version>${jaxb.common.version}</version>
-    </dependency>
+    </dependency>...-->
-
 
 
 <!-- If we want to run moxy 

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/ActedOnBehalfOf.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/ActedOnBehalfOf.java
@@ -11,12 +11,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 import org.openprovenance.prov.model.Attribute;
 
 

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/Activity.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/Activity.java
@@ -15,12 +15,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 import org.openprovenance.prov.model.Attribute;
 
 

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/Agent.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/Agent.java
@@ -12,12 +12,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 import org.openprovenance.prov.model.Attribute;
 
 

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/AlternateOf.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/AlternateOf.java
@@ -15,12 +15,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 
 
 /**

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/Bundle.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/Bundle.java
@@ -14,12 +14,13 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
+
 
 
 /**

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/Collection.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/Collection.java
@@ -15,12 +15,13 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
+
 
 
 /**

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/DerivedByInsertionFrom.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/DerivedByInsertionFrom.java
@@ -11,12 +11,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 import org.openprovenance.prov.model.Attribute;
 
 

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/DerivedByRemovalFrom.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/DerivedByRemovalFrom.java
@@ -11,12 +11,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 import org.openprovenance.prov.model.Attribute;
 
 

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/Dictionary.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/Dictionary.java
@@ -15,12 +15,13 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
+
 
 
 /**

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/DictionaryMembership.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/DictionaryMembership.java
@@ -9,12 +9,13 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
+
 
 
 /**

diff --git a/prov-xml/src/main/java/org/openprovenance/prov/xml/Document.java b/prov-xml/src/main/java/org/openprovenance/prov/xml/Document.java
@@ -10,12 +10,12 @@
 import org.apache.commons.lang.builder.EqualsBuilder;
 import org.apache.commons.lang.builder.HashCodeBuilder;
 import org.apache.commons.lang.builder.ToStringBuilder;
-import org.jvnet.jaxb2_commons.lang.Equals;
+import org.openprovenance.prov.xml.builder.Equals;
-import org.jvnet.jaxb2_commons.lang.HashCode;
+import org.openprovenance.prov.xml.builder.HashCode;
-import org.jvnet.jaxb2_commons.lang.ToString;
+import org.openprovenance.prov.xml.builder.ToString;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBEqualsBuilder;
+import org.openprovenance.prov.xml.builder.JAXBEqualsBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBHashCodeBuilder;
+import org.openprovenance.prov.xml.builder.JAXBHashCodeBuilder;
-import org.jvnet.jaxb2_commons.lang.builder.JAXBToStringBuilder;
+import org.openprovenance.prov.xml.builder.JAXBToStringBuilder;
 import org.openprovenance.prov.model.Namespace;
 import org.openprovenance.prov.model.StatementOrBundle;