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treebase-guts
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From: <rv...@us...> - 2009-06-25 02:43:45
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Revision: 108
http://treebase.svn.sourceforge.net/treebase/?rev=108&view=rev
Author: rvos
Date: 2009-06-25 02:43:44 +0000 (Thu, 25 Jun 2009)
Log Message:
-----------
Added getTreebaseIDString() and getNamespacedGUID() transient methods
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2009-06-25 02:41:29 UTC (rev 107)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2009-06-25 02:43:44 UTC (rev 108)
@@ -28,8 +28,12 @@
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.MappedSuperclass;
+import javax.persistence.Transient;
import javax.persistence.Version;
+import org.cipres.treebase.NamespacedGUID;
+import org.cipres.treebase.TreebaseIDString;
+
/**
* The abstract super class for all persisted domain objects.
*
@@ -97,5 +101,15 @@
private void setVersion(int pNewVersion) {
mVersion = pNewVersion;
}
+
+ @Transient
+ public TreebaseIDString getTreebaseIDString () {
+ return new TreebaseIDString(this);
+ }
+
+ @Transient
+ public NamespacedGUID getNamespacedGUID () {
+ return getTreebaseIDString().getNamespacedGUID();
+ }
}
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From: <rv...@us...> - 2009-06-28 10:14:11
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Revision: 137
http://treebase.svn.sourceforge.net/treebase/?rev=137&view=rev
Author: rvos
Date: 2009-06-28 10:11:30 +0000 (Sun, 28 Jun 2009)
Log Message:
-----------
Implemented interface methods
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2009-06-28 10:11:14 UTC (rev 136)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2009-06-28 10:11:30 UTC (rev 137)
@@ -32,6 +32,7 @@
import javax.persistence.Version;
import org.cipres.treebase.NamespacedGUID;
+import org.cipres.treebase.PhyloWSPath;
import org.cipres.treebase.TreebaseIDString;
/**
@@ -111,5 +112,10 @@
public NamespacedGUID getNamespacedGUID () {
return getTreebaseIDString().getNamespacedGUID();
}
+
+ @Transient
+ public PhyloWSPath getPhyloWSPath() {
+ return new PhyloWSPath(this);
+ }
}
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From: <rv...@us...> - 2009-11-18 17:51:32
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Revision: 282
http://treebase.svn.sourceforge.net/treebase/?rev=282&view=rev
Author: rvos
Date: 2009-11-18 17:51:00 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
Changed GenerationType for IDs from AUTO to SEQUENCE
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2009-11-18 17:02:31 UTC (rev 281)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2009-11-18 17:51:00 UTC (rev 282)
@@ -53,7 +53,7 @@
* @see org.cipres.treebase.domain.TBPersistable#getId()
*/
@Id
- @GeneratedValue(strategy = GenerationType.AUTO)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE)
public Long getId() {
return mId;
}
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From: <rv...@us...> - 2010-03-15 01:25:54
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Revision: 584
http://treebase.svn.sourceforge.net/treebase/?rev=584&view=rev
Author: rvos
Date: 2010-03-15 01:25:48 +0000 (Mon, 15 Mar 2010)
Log Message:
-----------
Added getAnnotations() and getLabel() for nexml and rdf serialization.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-03-15 01:20:38 UTC (rev 583)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-03-15 01:25:48 UTC (rev 584)
@@ -2,19 +2,22 @@
package org.cipres.treebase.domain;
import java.io.Serializable;
+import java.net.URI;
+import java.util.ArrayList;
import java.util.Comparator;
-
+import java.util.List;
import javax.persistence.Column;
import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.MappedSuperclass;
import javax.persistence.Transient;
import javax.persistence.Version;
+import org.cipres.treebase.Constants;
import org.cipres.treebase.NamespacedGUID;
import org.cipres.treebase.PhyloWSPath;
import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.TreebaseUtil;
import org.hibernate.annotations.GenericGenerator;
/**
@@ -100,5 +103,30 @@
public PhyloWSPath getPhyloWSPath() {
return new PhyloWSPath(this);
}
+
+ /*
+ * (non-Javadoc)
+ * @see org.cipres.treebase.domain.Annotatable#getAnnotations()
+ */
+ @Transient
+ public List<Annotation> getAnnotations() {
+ // This is called by child classes using super.getAnnotations()
+ // to get the common annotations out of the way
+ List<Annotation> annotations = new ArrayList<Annotation>();
+ URI uri = URI.create(TreebaseUtil.getPurlDomain()+getPhyloWSPath());
+ annotations.add(new Annotation(Constants.OWLURI,"owl:sameAs",uri));
+ return annotations;
+ }
+ /*
+ * (non-Javadoc)
+ * @see org.cipres.treebase.domain.NexmlWritable#getLabel()
+ */
+ @Transient
+ public String getLabel() {
+ // This is overridden by child classes that want a name/title/label
+ // to be serialized in nexml or rdf
+ return null;
+ }
+
}
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From: <rv...@us...> - 2010-03-16 16:53:54
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Revision: 604
http://treebase.svn.sourceforge.net/treebase/?rev=604&view=rev
Author: rvos
Date: 2010-03-16 16:53:37 +0000 (Tue, 16 Mar 2010)
Log Message:
-----------
Added dummy implementation for getContext, which just returns null.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-03-16 16:52:28 UTC (rev 603)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-03-16 16:53:37 UTC (rev 604)
@@ -128,5 +128,16 @@
// to be serialized in nexml or rdf
return null;
}
+
+ /*
+ * (non-Javadoc)
+ * @see org.cipres.treebase.domain.TBPersistable#getContext()
+ */
+ @Transient
+ public TBPersistable getContext() {
+ // This is overridden by child classes to indicate which other object
+ // provides the invocant's context. E.g. for a node this would be a tree.
+ return null;
+ }
}
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From: <rv...@us...> - 2010-06-03 17:16:17
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Revision: 711
http://treebase.svn.sourceforge.net/treebase/?rev=711&view=rev
Author: rvos
Date: 2010-06-03 17:16:11 +0000 (Thu, 03 Jun 2010)
Log Message:
-----------
Where available, now adds rdfs:isDefinedBy annotations that point to the containing context (e.g. for a tree, the study in which it is published). This is on the recommendation of the SADI bunch, and at @rdmpage's request.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-06-03 17:14:46 UTC (rev 710)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2010-06-03 17:16:11 UTC (rev 711)
@@ -115,6 +115,11 @@
List<Annotation> annotations = new ArrayList<Annotation>();
URI uri = URI.create(TreebaseUtil.getPurlBase()+getPhyloWSPath());
annotations.add(new Annotation(Constants.OWLURI,"owl:sameAs",uri));
+ TBPersistable context = getContext();
+ if ( null != context ) {
+ URI contextUri = URI.create(TreebaseUtil.getPurlBase()+context.getPhyloWSPath());
+ annotations.add(new Annotation(Constants.RDFSURI, "rdfs:isDefinedBy",contextUri));
+ }
return annotations;
}
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From: <rv...@us...> - 2011-04-19 11:22:38
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Revision: 793
http://treebase.svn.sourceforge.net/treebase/?rev=793&view=rev
Author: rvos
Date: 2011-04-19 11:22:32 +0000 (Tue, 19 Apr 2011)
Log Message:
-----------
No longer returning owl:sameAs annotations because we are using the TreebaseIDString values as xml id's directly.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2011-04-19 11:20:14 UTC (rev 792)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2011-04-19 11:22:32 UTC (rev 793)
@@ -111,10 +111,9 @@
@Transient
public List<Annotation> getAnnotations() {
// This is called by child classes using super.getAnnotations()
- // to get the common annotations out of the way
+ // to get the common annotations out of the way. We no longer need
+ // to do owl:sameAs because we use TreeBASE ID strings as XML IDs.
List<Annotation> annotations = new ArrayList<Annotation>();
- URI uri = URI.create(TreebaseUtil.getPurlBase()+getPhyloWSPath());
- annotations.add(new Annotation(Constants.OWLURI,"owl:sameAs",uri));
TBPersistable context = getContext();
if ( null != context ) {
URI contextUri = URI.create(TreebaseUtil.getPurlBase()+context.getPhyloWSPath());
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From: <rv...@us...> - 2011-06-11 22:20:38
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Revision: 912
http://treebase.svn.sourceforge.net/treebase/?rev=912&view=rev
Author: rvos
Date: 2011-06-11 22:20:32 +0000 (Sat, 11 Jun 2011)
Log Message:
-----------
Added javadoc
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2011-06-11 22:19:57 UTC (rev 911)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java 2011-06-11 22:20:32 UTC (rev 912)
@@ -89,16 +89,28 @@
mVersion = pNewVersion;
}
+ /**
+ * Returns an object whose string representation is of the format
+ * S1787
+ */
@Transient
public TreebaseIDString getTreebaseIDString () {
return new TreebaseIDString(this);
}
+ /**
+ * Returns an object whose string representation is of the format
+ * TB2:S1787
+ */
@Transient
public NamespacedGUID getNamespacedGUID () {
return getTreebaseIDString().getNamespacedGUID();
}
+ /**
+ * Returns an object whose string representation is of the format
+ * study/TB2:1787
+ */
@Transient
public PhyloWSPath getPhyloWSPath() {
return new PhyloWSPath(this);
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