jackson update (to v 2.2). come code cleaning

VarioML · May 9, 2013 · 373a3b9 · 373a3b9
1 parent 02856ae
commit 373a3b9
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Showing 83 changed files with 510 additions and 129,644 deletions.
diff --git a/src/java/varioml/.classpath b/src/java/varioml/.classpath
@@ -7,12 +7,14 @@
 	<classpathentry kind="lib" path="lib/joda-time-1.6.2.jar"/>
 	<classpathentry kind="lib" path="lib/junit-dep-4.9b4.jar"/>
 	<classpathentry kind="lib" path="lib/exificient.jar"/>
-	<classpathentry kind="lib" path="lib/xercesImpl.jar"/>
-	<classpathentry kind="lib" path="lib/bson4jackson-1.3.0.jar"/>
-	<classpathentry kind="lib" path="lib/jackson-all-1.9.9.jar"/>
 	<classpathentry kind="lib" path="lib/simple-xml-2.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/xml-apis-1.4.01.jar"/>
 	<classpathentry kind="lib" path="lib/xml-writer.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="lib/bson4jackson-2.1.0.jar"/>
+	<classpathentry kind="lib" path="lib/jackson-annotations-2.2.0.jar"/>
+	<classpathentry kind="lib" path="lib/jackson-core-2.2.0.jar"/>
+	<classpathentry kind="lib" path="lib/jackson-databind-2.2.0.jar"/>
+	<classpathentry kind="lib" path="lib/jackson-module-jaxb-annotations-2.2.1.jar"/>
+	<classpathentry kind="lib" path="lib/xercesImpl-2.11.0.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/src/java/varioml/ORIG_build.xml b/src/java/varioml/ORIG_build.xml
diff --git a/src/java/varioml/example0.xml b/src/java/varioml/example0.xml
diff --git a/src/java/varioml/example1.xml b/src/java/varioml/example1.xml
diff --git a/src/java/varioml/example11.xml b/src/java/varioml/example11.xml
diff --git a/src/java/varioml/lib/bson4jackson-1.3.0.jar b/src/java/varioml/lib/bson4jackson-1.3.0.jar
diff --git a/src/java/varioml/lib/bson4jackson-2.1.0.jar b/src/java/varioml/lib/bson4jackson-2.1.0.jar
diff --git a/src/java/varioml/lib/jackson-all-1.9.9.jar b/src/java/varioml/lib/jackson-all-1.9.9.jar
diff --git a/src/java/varioml/lib/jackson-annotations-2.2.0.jar b/src/java/varioml/lib/jackson-annotations-2.2.0.jar
diff --git a/src/java/varioml/lib/jackson-core-2.2.0.jar b/src/java/varioml/lib/jackson-core-2.2.0.jar
diff --git a/src/java/varioml/lib/jackson-databind-2.2.0.jar b/src/java/varioml/lib/jackson-databind-2.2.0.jar
diff --git a/src/java/varioml/lib/jackson-module-jaxb-annotations-2.2.1.jar b/src/java/varioml/lib/jackson-module-jaxb-annotations-2.2.1.jar
diff --git a/src/java/varioml/lib/xercesImpl.jar → src/java/varioml/lib/xercesImpl-2.11.0.jar b/src/java/varioml/lib/xercesImpl.jar → src/java/varioml/lib/xercesImpl-2.11.0.jar
diff --git a/src/java/varioml/lib/xml-apis-1.4.01.jar b/src/java/varioml/lib/xml-apis-1.4.01.jar
diff --git a/src/java/varioml/lsdb_test1.xml b/src/java/varioml/lsdb_test1.xml
diff --git a/src/java/varioml/src/org/varioml/generator/GenerateJAXBCode.java b/src/java/varioml/src/org/varioml/generator/GenerateJAXBCode.java
@@ -14,9 +14,6 @@
 import javax.xml.xpath.XPathFactory;
 
 
-import org.codehaus.jackson.annotate.JsonAutoDetect;
-import org.codehaus.jackson.annotate.JsonAutoDetect.Visibility;
-import org.codehaus.jackson.annotate.JsonPropertyOrder;
 import org.simpleframework.xml.stream.CamelCaseStyle;
 import org.varioml.generator.GenerateSimpleXMLCode.Counter;
 import org.varioml.util.Util;

diff --git a/src/java/varioml/src/org/varioml/generator/patch-jackson b/src/java/varioml/src/org/varioml/generator/patch-jackson
@@ -0,0 +1,4 @@
+perl -pi.bak -e "s/org.codehaus.jackson.annotate/com.fasterxml.jackson.annotation/g" *.java
+perl -pi.bak -e "s/org.codehaus.jackson.map.annotate/com.fasterxml.jackson.databind.annotation/g" *.java
+
+
diff --git a/src/java/varioml/src/org/varioml/jaxb/Acknowledgement.java b/src/java/varioml/src/org/varioml/jaxb/Acknowledgement.java
@@ -2,12 +2,16 @@
 import java.util.ArrayList;
 import java.util.List;
 
-@org.codehaus.jackson.annotate.JsonAutoDetect( fieldVisibility =  org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE, getterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE,setterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE)
-@org.codehaus.jackson.map.annotate.JsonSerialize(include = org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion.NON_NULL)
+import com.fasterxml.jackson.annotation.JsonAutoDetect;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+@JsonAutoDetect( fieldVisibility =  JsonAutoDetect.Visibility.NONE, getterVisibility= JsonAutoDetect.Visibility.NONE,setterVisibility= JsonAutoDetect.Visibility.NONE)
+@JsonSerialize(include = JsonSerialize.Inclusion.NON_NULL)
 @javax.xml.bind.annotation.XmlAccessorType(javax.xml.bind.annotation.XmlAccessType.FIELD)
 @javax.xml.bind.annotation.XmlRootElement(namespace="http://varioml.org/xml/1.0",name="acknowledgement")
 @javax.xml.bind.annotation.XmlType(propOrder = {  "_name","_grantNumber","_dbXref","_comment"})
-@org.codehaus.jackson.annotate.JsonPropertyOrder(value={  "_name","_grantNumber","_dbXref","_comment"})
+@JsonPropertyOrder(value={  "_name","_grantNumber","_dbXref","_comment"})
 
 
 public class Acknowledgement /**/implements VmlAnnotatable /**/ {
@@ -37,7 +41,7 @@ public GrantNumber getGrantNumber() {
 	}
 
 	// ===========-- db_xref --===========
-   @org.codehaus.jackson.annotate.JsonProperty("db_xrefs")
+   @JsonProperty("db_xrefs")
    @javax.xml.bind.annotation.XmlElement(required=false,name="db_xref",type=DbXref.class,namespace="http://varioml.org/xml/1.0")
 	private List<DbXref> _dbXref ;
 	public void setDbXrefList( List<DbXref> dbXref) { 
@@ -54,7 +58,7 @@ public void addDbXref(DbXref item ) {
 	}
 
 	// ===========-- comment --===========
-   @org.codehaus.jackson.annotate.JsonProperty("comments")
+   @JsonProperty("comments")
    @javax.xml.bind.annotation.XmlElement(required=false,name="comment",type=Comment.class,namespace="http://varioml.org/xml/1.0")
 	private List<Comment> _comment ;
 	public void setCommentList( List<Comment> comment) { 

diff --git a/src/java/varioml/src/org/varioml/jaxb/Age.java b/src/java/varioml/src/org/varioml/jaxb/Age.java
@@ -1,12 +1,13 @@
 package org.varioml.jaxb;
-import java.util.ArrayList;
-import java.util.List;
 
-@org.codehaus.jackson.annotate.JsonAutoDetect( fieldVisibility =  org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE, getterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE,setterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE)
-@org.codehaus.jackson.map.annotate.JsonSerialize(include = org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion.NON_NULL)
+import com.fasterxml.jackson.annotation.JsonAutoDetect;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+@JsonAutoDetect( fieldVisibility =  com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE, getterVisibility= com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE,setterVisibility= com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE)
+@JsonSerialize(include = com.fasterxml.jackson.databind.annotation.JsonSerialize.Inclusion.NON_NULL)
 @javax.xml.bind.annotation.XmlAccessorType(javax.xml.bind.annotation.XmlAccessType.FIELD)
 @javax.xml.bind.annotation.XmlRootElement(namespace="http://varioml.org/xml/1.0",name="age")
-@org.codehaus.jackson.annotate.JsonPropertyOrder(value={  "_attr_coded","__float"})
+@com.fasterxml.jackson.annotation.JsonPropertyOrder(value={  "_attr_coded","__float"})
 
 
 public class Age /**/ /**/ {
@@ -25,7 +26,7 @@ public Boolean isCoded() {
 		return this._attr_coded;
 	}
 	// =========-- TEXT NODE --=========
-	@org.codehaus.jackson.annotate.JsonProperty("float")
+	@com.fasterxml.jackson.annotation.JsonProperty("float")
    @javax.xml.bind.annotation.XmlValue
 	private Float __float ;
 	public Age( Float v ) {

diff --git a/src/java/varioml/src/org/varioml/jaxb/Aliases.java b/src/java/varioml/src/org/varioml/jaxb/Aliases.java
@@ -2,12 +2,12 @@
 import java.util.ArrayList;
 import java.util.List;
 
-@org.codehaus.jackson.annotate.JsonAutoDetect( fieldVisibility =  org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE, getterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE,setterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE)
-@org.codehaus.jackson.map.annotate.JsonSerialize(include = org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion.NON_NULL)
+@com.fasterxml.jackson.annotation.JsonAutoDetect( fieldVisibility =  com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE, getterVisibility= com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE,setterVisibility= com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE)
+@com.fasterxml.jackson.databind.annotation.JsonSerialize(include = com.fasterxml.jackson.databind.annotation.JsonSerialize.Inclusion.NON_NULL)
 @javax.xml.bind.annotation.XmlAccessorType(javax.xml.bind.annotation.XmlAccessType.FIELD)
 @javax.xml.bind.annotation.XmlRootElement(namespace="http://varioml.org/xml/1.0",name="aliases")
 @javax.xml.bind.annotation.XmlType(propOrder = {  "_variant","_value","_evidenceCode","_protocolId","_observationDate","_dbXref","_comment"})
-@org.codehaus.jackson.annotate.JsonPropertyOrder(value={  "_variant","_value","_evidenceCode","_protocolId","_observationDate","_dbXref","_comment"})
+@com.fasterxml.jackson.annotation.JsonPropertyOrder(value={  "_variant","_value","_evidenceCode","_protocolId","_observationDate","_dbXref","_comment"})
 
 
 public class Aliases /**/implements VmlAnnotatable /**/ {
@@ -17,7 +17,7 @@ public Aliases(  ) {
 	}
 
 	// ===========-- variant --===========
-   @org.codehaus.jackson.annotate.JsonProperty("variants")
+   @com.fasterxml.jackson.annotation.JsonProperty("variants")
    @javax.xml.bind.annotation.XmlElement(required=false,name="variant",type=Variant.class,namespace="http://varioml.org/xml/1.0")
 	private List<Variant> _variant ;
 	public void setVariantList( List<Variant> variant) { 
@@ -34,7 +34,7 @@ public void addVariant(Variant item ) {
 	}
 
 	// ===========-- value --===========
-   @org.codehaus.jackson.annotate.JsonProperty("values")
+   @com.fasterxml.jackson.annotation.JsonProperty("values")
    @javax.xml.bind.annotation.XmlElement(required=false,name="value",type=Value.class,namespace="http://varioml.org/xml/1.0")
 	private List<Value> _value ;
 	public void setValueList( List<Value> value) { 
@@ -51,7 +51,7 @@ public void addValue(Value item ) {
 	}
 
 	// ===========-- evidence_code --===========
-   @org.codehaus.jackson.annotate.JsonProperty("evidence_codes")
+   @com.fasterxml.jackson.annotation.JsonProperty("evidence_codes")
    @javax.xml.bind.annotation.XmlElement(required=false,name="evidence_code",type=EvidenceCode.class,namespace="http://varioml.org/xml/1.0")
 	private List<EvidenceCode> _evidenceCode ;
 	public void setEvidenceCodeList( List<EvidenceCode> evidenceCode) { 
@@ -68,7 +68,7 @@ public void addEvidenceCode(EvidenceCode item ) {
 	}
 
 	// ===========-- protocol_id --===========
-   @org.codehaus.jackson.annotate.JsonProperty("protocol_ids")
+   @com.fasterxml.jackson.annotation.JsonProperty("protocol_ids")
    @javax.xml.bind.annotation.XmlElement(required=false,name="protocol_id",type=ProtocolId.class,namespace="http://varioml.org/xml/1.0")
 	private List<ProtocolId> _protocolId ;
 	public void setProtocolIdList( List<ProtocolId> protocolId) { 
@@ -95,7 +95,7 @@ public ObservationDate getObservationDate() {
 	}
 
 	// ===========-- db_xref --===========
-   @org.codehaus.jackson.annotate.JsonProperty("db_xrefs")
+   @com.fasterxml.jackson.annotation.JsonProperty("db_xrefs")
    @javax.xml.bind.annotation.XmlElement(required=false,name="db_xref",type=DbXref.class,namespace="http://varioml.org/xml/1.0")
 	private List<DbXref> _dbXref ;
 	public void setDbXrefList( List<DbXref> dbXref) { 
@@ -112,7 +112,7 @@ public void addDbXref(DbXref item ) {
 	}
 
 	// ===========-- comment --===========
-   @org.codehaus.jackson.annotate.JsonProperty("comments")
+   @com.fasterxml.jackson.annotation.JsonProperty("comments")
    @javax.xml.bind.annotation.XmlElement(required=false,name="comment",type=Comment.class,namespace="http://varioml.org/xml/1.0")
 	private List<Comment> _comment ;
 	public void setCommentList( List<Comment> comment) { 

diff --git a/src/java/varioml/src/org/varioml/jaxb/CafeVariome.java b/src/java/varioml/src/org/varioml/jaxb/CafeVariome.java
@@ -2,12 +2,12 @@
 import java.util.ArrayList;
 import java.util.List;
 
-@org.codehaus.jackson.annotate.JsonAutoDetect( fieldVisibility =  org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE, getterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE,setterVisibility= org.codehaus.jackson.annotate.JsonAutoDetect.Visibility.NONE)
-@org.codehaus.jackson.map.annotate.JsonSerialize(include = org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion.NON_NULL)
+@com.fasterxml.jackson.annotation.JsonAutoDetect( fieldVisibility =  com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE, getterVisibility= com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE,setterVisibility= com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.NONE)
+@com.fasterxml.jackson.databind.annotation.JsonSerialize(include = com.fasterxml.jackson.databind.annotation.JsonSerialize.Inclusion.NON_NULL)
 @javax.xml.bind.annotation.XmlRootElement(namespace="http://varioml.org/xml/1.0",name="cafe_variome")
 @javax.xml.bind.annotation.XmlAccessorType(javax.xml.bind.annotation.XmlAccessType.FIELD)
 @javax.xml.bind.annotation.XmlType(propOrder = {  "_created","_source","_variant","_dbXref","_comment"})
-@org.codehaus.jackson.annotate.JsonPropertyOrder(value={  "_attr_id","_attr_schemaVersion","_attr_submissionidType","_attr_uri","_attr_xmlns","_attr_xmlnsXsi","_attr_xsiSchemaLocation","_created","_source","_variant","_dbXref","_comment"})
+@com.fasterxml.jackson.annotation.JsonPropertyOrder(value={  "_attr_id","_attr_schemaVersion","_attr_submissionidType","_attr_uri","_attr_xmlns","_attr_xmlnsXsi","_attr_xsiSchemaLocation","_created","_source","_variant","_dbXref","_comment"})
 
 
 public class CafeVariome /**/implements VmlAnnotatable /**/ {
@@ -97,7 +97,7 @@ public org.varioml.util.VMLDateTime getCreated() {
 	}
 
 	// ===========-- source --===========
-   @org.codehaus.jackson.annotate.JsonProperty("sources")
+   @com.fasterxml.jackson.annotation.JsonProperty("sources")
    @javax.xml.bind.annotation.XmlElement(required=false,name="source",type=Source.class,namespace="http://varioml.org/xml/1.0")
 	private List<Source> _source ;
 	public void setSourceList( List<Source> source) { 
@@ -114,7 +114,7 @@ public void addSource(Source item ) {
 	}
 
 	// ===========-- variant --===========
-   @org.codehaus.jackson.annotate.JsonProperty("variants")
+   @com.fasterxml.jackson.annotation.JsonProperty("variants")
    @javax.xml.bind.annotation.XmlElement(required=false,name="variant",type=Variant.class,namespace="http://varioml.org/xml/1.0")
 	private List<Variant> _variant ;
 	public void setVariantList( List<Variant> variant) { 
@@ -131,7 +131,7 @@ public void addVariant(Variant item ) {
 	}
 
 	// ===========-- db_xref --===========
-   @org.codehaus.jackson.annotate.JsonProperty("db_xrefs")
+   @com.fasterxml.jackson.annotation.JsonProperty("db_xrefs")
    @javax.xml.bind.annotation.XmlElement(required=false,name="db_xref",type=DbXref.class,namespace="http://varioml.org/xml/1.0")
 	private List<DbXref> _dbXref ;
 	public void setDbXrefList( List<DbXref> dbXref) { 
@@ -148,7 +148,7 @@ public void addDbXref(DbXref item ) {
 	}
 
 	// ===========-- comment --===========
-   @org.codehaus.jackson.annotate.JsonProperty("comments")
+   @com.fasterxml.jackson.annotation.JsonProperty("comments")
    @javax.xml.bind.annotation.XmlElement(required=false,name="comment",type=Comment.class,namespace="http://varioml.org/xml/1.0")
 	private List<Comment> _comment ;
 	public void setCommentList( List<Comment> comment) {