treebase-guts

[Treebase-guts] SF.net SVN: treebase:[577] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/Taxon.java

[<rv...@us...>]

Revision: 577
          http://treebase.svn.sourceforge.net/treebase/?rev=577&view=rev
Author:   rvos
Date:     2010-03-15 01:13:21 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Added getLabel() for nexml and rdf serialization.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-03-15 01:12:42 UTC (rev 576)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-03-15 01:13:21 UTC (rev 577)
@@ -13,6 +13,7 @@
 import javax.persistence.JoinColumn;
 import javax.persistence.OneToMany;
 import javax.persistence.Table;
+import javax.persistence.Transient;
 
 import org.hibernate.annotations.BatchSize;
 import org.hibernate.annotations.Cache;
@@ -239,5 +240,10 @@
 	public void setForeignLinks(Collection<TaxonLink> pNewForeignLinks) {
 		mForeignLinks = pNewForeignLinks;
 	}
+	
+	@Transient
+	public String getLabel() {
+		return getName();
+	}
 
 }


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[Treebase-guts] SF.net SVN: treebase:[598] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/Taxon.java

[<rv...@us...>]

Revision: 598
          http://treebase.svn.sourceforge.net/treebase/?rev=598&view=rev
Author:   rvos
Date:     2010-03-16 16:47:24 +0000 (Tue, 16 Mar 2010)

Log Message:
-----------
Added getAnnotations() method, which returns skos: predicates to link to ubio and ncbi.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-03-16 16:46:12 UTC (rev 597)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-03-16 16:47:24 UTC (rev 598)
@@ -5,6 +5,7 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 import javax.persistence.AttributeOverride;
 import javax.persistence.CascadeType;
@@ -20,7 +21,9 @@
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.hibernate.annotations.Index;
 
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
 import org.cipres.treebase.domain.TBPersistable;
 
 /**
@@ -245,5 +248,23 @@
 	public String getLabel() {
 		return getName();
 	}
+	
+	@Transient
+	public List<Annotation> getAnnotations() {
+		List<Annotation> annotations = super.getAnnotations();
+		try {
+			if ( null != getNcbiTaxId() ) {
+				annotations.add(new Annotation(Constants.SKOSURI,"skos:exactMatch",Constants.NCBITaxonomyBase + getNcbiTaxId()));
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ncbi", getNcbiTaxId()));				
+			}
+			if ( null != getUBioNamebankId() ) {
+				annotations.add(new Annotation(Constants.SKOSURI,"skos:exactMatch",Constants.uBioBase + getUBioNamebankId()));
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ubio", getUBioNamebankId()));				
+			}
+		} catch ( Exception e ) {
+			e.printStackTrace();
+		}
+		return annotations;
+	}	
 
 }


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[Treebase-guts] SF.net SVN: treebase:[1031] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/Taxon.java

[<rv...@us...>]

Revision: 1031
          http://treebase.svn.sourceforge.net/treebase/?rev=1031&view=rev
Author:   rvos
Date:     2012-02-01 21:06:21 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Removed commented-out code and changed the NCBI taxonomy url prefix from the ugly NCBI URL to the pretty uniprot one, which is at least consistent with how we do it elsewhere.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2012-02-01 21:03:24 UTC (rev 1030)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2012-02-01 21:06:21 UTC (rev 1031)
@@ -1,8 +1,6 @@
 
 package org.cipres.treebase.domain.taxon;
 
-import org.apache.log4j.Logger;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -40,7 +38,6 @@
 @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "taxonCache")
 @BatchSize(size = 10)
 public class Taxon extends AbstractPersistedObject {
-	private static final Logger LOGGER = Logger.getLogger(Taxon.class);
 
 	private static final long serialVersionUID = 1L;
 
@@ -169,63 +166,6 @@
 		mTB1LegacyId = legacyId;
 	}
 
-	//	/**
-//	 * Return the TaxonVariants field.
-//	 * 
-//	 * @return Collection<TaxonVariant> mTaxonVariants
-//	 */
-//	@OneToMany(mappedBy = "taxon", cascade = {CascadeType.PERSIST, CascadeType.MERGE})
-//	// @Cascade(org.hibernate.annotations.CascadeType.DELETE_ORPHAN)
-//	@Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "taxonCache")
-//	protected Collection<TaxonVariant> getTaxonVariants() {
-//		return mTaxonVariants;
-//	}
-//
-//	/**
-//	 * Set the TaxonVariants field.
-//	 */
-//	public void setTaxonVariants(Collection<TaxonVariant> pNewTaxonVariants) {
-//		mTaxonVariants = pNewTaxonVariants;
-//	}
-//
-//	/**
-//	 * Append a new variant to the end of the list. Manage bi-directional relationship.
-//	 * 
-//	 * Creation date: Feb 22, 2006 12:06:25 PM
-//	 * 
-//	 * @param pVariant
-//	 */
-//	public void addTaxonVariant(TaxonVariant pVariant) {
-//		if (pVariant != null && !getTaxonVariants().contains(pVariant)) {
-//			getTaxonVariants().add(pVariant);
-//			pVariant.setTaxon(this);
-//		}
-//	}
-//
-//	/**
-//	 * Remove a new variant to the end of the list. Manage bi-directional relationship.
-//	 * 
-//	 * Creation date: Feb 22, 2006 12:06:25 PM
-//	 * 
-//	 * @param pVariant
-//	 */
-//	public void removeTaxonVariant(TaxonVariant pVariant) {
-//		if (pVariant != null && getTaxonVariants().contains(pVariant)) {
-//			getTaxonVariants().remove(pVariant);
-//			pVariant.setTaxon(null);
-//		}
-//	}
-//
-//	/**
-//	 * Return a read only list of taxon variants.
-//	 * 
-//	 * @return
-//	 */
-//	@Transient
-//	public Collection<TaxonVariant> getTaxonVariantsReadOnly() {
-//		return Collections.unmodifiableCollection(getTaxonVariants());
-//	}
-//
 	/**
 	 * Return the ForeignLinks field.
 	 * 
@@ -255,7 +195,7 @@
 		List<Annotation> annotations = super.getAnnotations();
 		try {
 			if ( null != getNcbiTaxId() ) {
-				annotations.add(new Annotation(Constants.SKOSURI,"skos:exactMatch",Constants.NCBITaxonomyBase + getNcbiTaxId()));
+				annotations.add(new Annotation(Constants.SKOSURI,"skos:exactMatch",String.format(Constants.NCBITaxonomyFormat, getNcbiTaxId())));
 				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ncbi", getNcbiTaxId()));				
 			}
 			if ( null != getUBioNamebankId() ) {

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[Treebase-guts] SF.net SVN: treebase:[714] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/Taxon.java

[<rv...@us...>]

Revision: 714
          http://treebase.svn.sourceforge.net/treebase/?rev=714&view=rev
Author:   rvos
Date:     2010-06-04 11:26:33 +0000 (Fri, 04 Jun 2010)

Log Message:
-----------
Adding annotation of tb:identifier.taxon.tb1

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-06-04 11:25:52 UTC (rev 713)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-06-04 11:26:33 UTC (rev 714)
@@ -261,6 +261,9 @@
 				annotations.add(new Annotation(Constants.SKOSURI,"skos:exactMatch",Constants.uBioBase + getUBioNamebankId()));
 				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ubio", getUBioNamebankId()));				
 			}
+			if ( null != getTB1LegacyId() ) {
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon.tb1", getTB1LegacyId()));
+			}
 		} catch ( Exception e ) {
 			e.printStackTrace();
 		}


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