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treebase-guts
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From: <rv...@us...> - 2009-06-19 02:15:51
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Revision: 60
http://treebase.svn.sourceforge.net/treebase/?rev=60&view=rev
Author: rvos
Date: 2009-06-19 02:10:56 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added @Transient getTreeBlocks() method
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2009-06-18 09:40:42 UTC (rev 59)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2009-06-19 02:10:56 UTC (rev 60)
@@ -59,6 +59,7 @@
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.TreeBlock;
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -690,4 +691,20 @@
}
return trees;
}
+
+ /**
+ * @return all the treeblocks for all the trees from getTrees();
+ * @author rvosa
+ */
+ @Transient
+ public Set<TreeBlock> getTreeBlocks() {
+ Set<TreeBlock> treeBlocks = new HashSet<TreeBlock>();
+ for ( PhyloTree tree : getTrees() ) {
+ TreeBlock treeBlock = tree.getTreeBlock();
+ if ( ! treeBlocks.contains(treeBlock) ) {
+ treeBlocks.add(treeBlock);
+ }
+ }
+ return treeBlocks;
+ }
}
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From: <rv...@us...> - 2010-03-15 01:12:48
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Revision: 576
http://treebase.svn.sourceforge.net/treebase/?rev=576&view=rev
Author: rvos
Date: 2010-03-15 01:12:42 +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/study/Study.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2010-03-15 01:11:43 UTC (rev 575)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2010-03-15 01:12:42 UTC (rev 576)
@@ -26,8 +26,11 @@
import javax.persistence.Transient;
import org.apache.log4j.Logger;
+import org.cipres.treebase.Constants;
+import org.cipres.treebase.ContextManager;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
import org.cipres.treebase.domain.TBPersistable;
import org.cipres.treebase.domain.admin.Person;
import org.cipres.treebase.domain.admin.User;
@@ -38,6 +41,8 @@
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.TreeBlock;
+import org.hibernate.Session;
+import org.hibernate.SessionFactory;
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -46,6 +51,7 @@
import org.hibernate.annotations.Index;
import org.hibernate.annotations.IndexColumn;
import org.jdom.Element;
+import org.nexml.model.Document;
@Entity
@Table(name = "STUDY")
@@ -685,4 +691,54 @@
}
return treeBlocks;
}
+
+ @Override
+ @Transient
+ public String getLabel() {
+ if ( null != getCitation() ) {
+ return getCitation().getTitle();
+ }
+ return getName();
+ }
+
+ @Transient
+ public List<Annotation> getAnnotations() {
+ List<Annotation> annotations = super.getAnnotations();
+ annotations.add(new Annotation(Constants.PrismURI,"prism:section","Study"));
+ annotations.add(new Annotation(Constants.TBTermsURI,"tb:identifier.study",getId().toString()));
+ annotations.add(new Annotation(Constants.TBTermsURI,"tb:identifier.study.tb1",getTB1StudyID()));
+ if ( null != getName() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI,"tb:title.study",getName()));
+ }
+ if ( null != getReleaseDate() ) {
+ annotations.add(new Annotation(Constants.DCURI,"dc:date",getReleaseDate().toString()));
+ }
+ if ( null != getSubmission() ) {
+ if ( null != getSubmission().getSubmitter() ) {
+// annotations.add(new Annotation(Constants.DCURI,"dc:creator",getSubmission().getSubmitter().getPerson().getFullNameCitationStyle()));
+ }
+ if ( null != getSubmission().getCreateDate() ) {
+ annotations.add(new Annotation(Constants.PrismURI,"prism:creationDate",getSubmission().getCreateDate().toString()));
+ }
+ }
+ if ( null != getCitation() ) {
+ try {
+ List<Annotation> citationAnnotations = getCitation().getAnnotations();
+ Annotation deleteme = null;
+ for ( Annotation anno : citationAnnotations ) {
+ if ( anno.getProperty().equals("owl:sameAs") ) {
+ deleteme = anno;
+ }
+ }
+ if ( null != deleteme ) {
+ citationAnnotations.remove(deleteme);
+ }
+ annotations.addAll(citationAnnotations);
+ } catch ( Exception e ) {
+ e.printStackTrace();
+ }
+ }
+ return annotations;
+ }
+
}
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From: <rv...@us...> - 2011-05-12 12:05:25
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Revision: 838
http://treebase.svn.sourceforge.net/treebase/?rev=838&view=rev
Author: rvos
Date: 2011-05-12 12:05:19 +0000 (Thu, 12 May 2011)
Log Message:
-----------
tb:lastModifiedDate is now inserted as a study annotation in the NeXML output
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2011-05-12 12:04:32 UTC (rev 837)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2011-05-12 12:05:19 UTC (rev 838)
@@ -27,7 +27,6 @@
import org.apache.log4j.Logger;
import org.cipres.treebase.Constants;
-import org.cipres.treebase.ContextManager;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.Annotation;
@@ -41,8 +40,6 @@
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.TreeBlock;
-import org.hibernate.Session;
-import org.hibernate.SessionFactory;
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -51,7 +48,6 @@
import org.hibernate.annotations.Index;
import org.hibernate.annotations.IndexColumn;
import org.jdom.Element;
-import org.nexml.model.Document;
@Entity
@Table(name = "STUDY")
@@ -722,6 +718,9 @@
if ( null != getReleaseDate() ) {
annotations.add(new Annotation(Constants.DCURI,"dc:date",getReleaseDate().toString()));
}
+ if ( null != getLastModifiedDate() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:lastModifiedDate", getLastModifiedDate().toString()));
+ }
if ( null != getSubmission() ) {
if ( null != getSubmission().getSubmitter() ) {
// annotations.add(new Annotation(Constants.DCURI,"dc:creator",getSubmission().getSubmitter().getPerson().getFullNameCitationStyle()));
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From: <rv...@us...> - 2011-05-12 12:37:40
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Revision: 845
http://treebase.svn.sourceforge.net/treebase/?rev=845&view=rev
Author: rvos
Date: 2011-05-12 12:37:33 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Now using prism:modificationDate instead of tb:lastModifiedDate as study annotation predicate to indicate when a study record was last modified.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2011-05-12 12:13:55 UTC (rev 844)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2011-05-12 12:37:33 UTC (rev 845)
@@ -719,7 +719,7 @@
annotations.add(new Annotation(Constants.DCURI,"dc:date",getReleaseDate().toString()));
}
if ( null != getLastModifiedDate() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:lastModifiedDate", getLastModifiedDate().toString()));
+ annotations.add(new Annotation(Constants.PrismURI, "prism:modificationDate", getLastModifiedDate().toString()));
}
if ( null != getSubmission() ) {
if ( null != getSubmission().getSubmitter() ) {
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