[Treebase-guts] SF.net SVN: treebase:[660] trunk/treebase-core/src/main/java/org/cipres/ treebase

[<yo...@us...>]

Revision: 660
          http://treebase.svn.sourceforge.net/treebase/?rev=660&view=rev
Author:   youjun
Date:     2010-03-30 15:54:49 +0000 (Tue, 30 Mar 2010)

Log Message:
-----------
clean taxonlabels after delete a tree

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java	2010-03-29 19:34:59 UTC (rev 659)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java	2010-03-30 15:54:49 UTC (rev 660)
@@ -18,6 +18,7 @@
 import org.cipres.treebase.domain.study.SubmissionHome;
 import org.cipres.treebase.domain.taxon.TaxonLabel;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+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.PhyloTreeHome;
@@ -124,7 +125,9 @@
 				block.removePhyloTree(pTree);
 
 				if (block.isEmpty()) {
+					TaxonLabelSet tSet=block.getTaxonLabelSet();
 					deleteTreeBlock(block);
+					getTaxonLabelHome().clean(tSet);
 				}
 			}
 
@@ -149,16 +152,18 @@
 
 			// getHibernateTemplate().delete(data);
 		}
-
+        
+		Set<TaxonLabel> tSet=pTree.getAllTaxonLabels();
 		// Delete by direct JDBC:
 		// * Tree nodes
 		// ** for each tree node, node attribute.
 		// ** (TODO) NodeEdge
-		PhyloTreeJDBC.deletePhyloTreeNodeSQL(pTree, getSession());
+		//PhyloTreeJDBC.deletePhyloTreeNodeSQL(pTree, getSession());
 
 		// cascade delete by hibernate:
 		// * tree atrribute
 		getHibernateTemplate().delete(pTree);
+		getTaxonLabelHome().clean(new ArrayList<TaxonLabel>(tSet));
 	}
 
 	/**

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java	2010-03-29 19:34:59 UTC (rev 659)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java	2010-03-30 15:54:49 UTC (rev 660)
@@ -1,6 +1,7 @@
 package org.cipres.treebase.domain.taxon;
 
 import java.net.URI;
+import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 
@@ -30,6 +31,7 @@
 import org.hibernate.annotations.Fetch;
 import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.Index;
+import org.hibernate.annotations.IndexColumn;
 
 /**
  * TaxonLabel usually associates with one Taxon. If it does not, it usually means the referred
@@ -57,7 +59,7 @@
 	private TaxonVariant mTaxonVariant;
 	private Study mStudy;
 	private Submission mSubmission;
-
+    private Set<TaxonLabelSet> mTaxonLabelSet;  
 	/**
 	 * Constructor.
 	 */
@@ -207,8 +209,28 @@
 		}
 		return null;
 	}
+	
+	/**
+	 * Return the TaxonLabelSet field.
+	 * 
+	 * @return List<PhyloTaxonLabel>
+	 */
+	@ManyToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
+	@JoinTable(name = "TaxonLabelSET_TaxonLabel", joinColumns = {@JoinColumn(name = "TaxonLabel_ID")}, inverseJoinColumns = @JoinColumn(name = "TaxonLabelSet_ID"))
+	protected Set<TaxonLabelSet> getTaxonLabelSet() {
+		return mTaxonLabelSet;
+	}
 
+
 	/**
+	 * Set the TaxonLabelSet field.
+	 */
+	protected void setTaxonLabelSet(Set<TaxonLabelSet> pTaxonLabelSet) {
+		mTaxonLabelSet = pTaxonLabelSet;
+	}
+
+
+	/**
 	 * Return the taxon name if it available.
 	 */
 	@Transient

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java	2010-03-29 19:34:59 UTC (rev 659)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java	2010-03-30 15:54:49 UTC (rev 660)
@@ -407,7 +407,7 @@
 	 * @return Set<TreeNode> 
 	 */
 	//@OneToMany(mappedBy = "tree", cascade = {CascadeType.MERGE, CascadeType.PERSIST}, fetch = FetchType.LAZY)
-	@OneToMany(mappedBy = "tree", cascade = {CascadeType.MERGE, CascadeType.PERSIST})
+	@OneToMany(mappedBy = "tree", cascade = {CascadeType.ALL})
 	//@Fetch(FetchMode.SUBSELECT)
 	@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "treeCache")
 	//@Loader(namedQuery="loadNodes")


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