[Treebase-guts] SF.net SVN: treebase:[784] trunk/treebase-core/src/main

[<hs...@us...>]

Revision: 784
          http://treebase.svn.sourceforge.net/treebase/?rev=784&view=rev
Author:   hshyket
Date:     2011-04-14 21:09:54 +0000 (Thu, 14 Apr 2011)

Log Message:
-----------
Setting limit for the number of trees allowed in a block.  This is set in the treebase.properties file.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
    trunk/treebase-core/src/main/resources/applicationContext-service.xml
    trunk/treebase-core/src/main/resources/treebase.properties

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java	2011-04-12 20:16:48 UTC (rev 783)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java	2011-04-14 21:09:54 UTC (rev 784)
@@ -7,7 +7,10 @@
 import java.util.Collection;
 import java.util.Date;
 import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
 
+
 import org.apache.log4j.Logger;
 import org.cipres.treebase.dao.jdbc.MatrixJDBC;
 import org.cipres.treebase.dao.jdbc.NexusDataSetJDBC;
@@ -65,6 +68,8 @@
 	private CitationService mCitationService;
 	private StudyService mStudyService;
 	private NexusService mNexusService;
+	
+	private int mMaxTreeCount;
 
 	/**
 	 * Constructor.
@@ -297,8 +302,25 @@
 
 		return sub;
 	}
+	
+	/**
+	 * Return the MaxTreeCount field.
+	 * 
+	 * @return MatrixDataTypeHome mMatrixDataTypeHome
+	 */
+	private int getMaxTreeCount() {
+		return mMaxTreeCount;
+	}
 
 	/**
+	 * Set the MaxTreeCount field.
+	 */
+	public void setMaxTreeCount(int maxTreeCount) {
+		mMaxTreeCount = maxTreeCount;
+	}
+
+
+	/**
 	 * 
 	 * @see org.cipres.treebase.domain.study.SubmissionService#createSubmission(org.cipres.treebase.domain.admin.User,
 	 *      org.cipres.treebase.domain.study.Study)
@@ -680,8 +702,30 @@
 			// alltrees.addAll(block.getTreeList());
 			// }
 			// getPhyloTreeHome().storeAll(alltrees);
+			
+			
+			//If there are more than the number of trees in getMaxTreeCount trees in a TreeBlock we need to remove them
+			for (TreeBlock treeblock : data.getTreeBlocks()) {
+					if (treeblock.getTreeCount() > getMaxTreeCount()) {
+						Iterator tree = treeblock.getTreeListIterator();
+						int treecount = 1;
+						
+						while(tree.hasNext()) {
+							if (treecount > getMaxTreeCount()) {
+								tree.remove();
+							}
+							tree.next();
+							treecount++;
+						}
+					}
+			}
+			
 			getPhyloTreeHome().storeAll(data.getTreeBlocks());
 			sub.addPhyloTreeBlocks(data.getTreeBlocks());
+			
+			
+			
+		
 			getPhyloTreeHome().flush();
 			update(sub);
 

Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml	2011-04-12 20:16:48 UTC (rev 783)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml	2011-04-14 21:09:54 UTC (rev 784)
@@ -243,6 +243,7 @@
                 <property name="taxonHome" ref="taxonHome"/>
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>
                 <property name="userHome" ref="userHome"/>
+                <property name="maxTreeCount" value="${treeblock.trees.max_count}"/>
 			</bean>
 		</property>
 	</bean>

Modified: trunk/treebase-core/src/main/resources/treebase.properties
===================================================================
--- trunk/treebase-core/src/main/resources/treebase.properties	2011-04-12 20:16:48 UTC (rev 783)
+++ trunk/treebase-core/src/main/resources/treebase.properties	2011-04-14 21:09:54 UTC (rev 784)
@@ -1,6 +1,9 @@
 #options are: NexusServiceMesquite | NexusServiceNCL
 nexus.parser.impl=NexusServiceMesquite
 
+#The number of trees allowed in a treeblock
+treeblock.trees.max_count=30
+
 ########################################################################
 ###  Prior to 2010-04-29, these were in jdbc.properties, 
 ###  which now contains only properties not used by the web app
@@ -18,6 +21,8 @@
 hibernate.format_sql=true
 hibernate.generate_statistics=false
 
+
+
 # options are: validate | update | create | create-drop
 hibernate.hbm2ddl.auto=
 


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