Revert "First draft of a parser that loads EMBL MSA data files of the .dat and .aln format into MySQL"

Jonathan Bell [2012-01-10 19:17:00]
Revert "First draft of a parser that loads EMBL MSA data files of the .dat and .aln format into MySQL"

This reverts commit 5d121dc3256ab419151022b6f84598de5afd242e.

Conflicts:

	EmblAlignParser/.classpath
	EmblAlignParser/src/META-INF/persistence.xml
	EmblAlignParser/src/coms6901/fall2011/ReadEMBL.java
	EmblAlignParser/src/org/geworkbench/components/genspace/entity/msa/Alignment.java
	genspace-common/.classpath
	genspace-common/makeStubs.sh
	genspace-common/src/org/geworkbench/components/genspace/entity/msa/Alignment.java
	genspace-common/src/org/geworkbench/components/genspace/entity/msa/Reference.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/Alignment.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/LazyCycleBreaker.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/Reference.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/package-info.java
	genspace-ejb/.classpath
	genspace-ejb/build/classes/META-INF/persistence.xml
	genspace-ejb/build/classes/META-INF/sun-ejb-jar.xml
	genspace-ejb/ejbModule/META-INF/persistence.xml
	genspace-ejb/ejbModule/META-INF/sun-ejb-jar.xml
Filename
.gitignore
EmblAlignParser/.project
EmblAlignParser/bin/META-INF/persistence.xml
EmblAlignParser/lib/eclipselink.jar
EmblAlignParser/src/org/geworkbench/components/genspace/entity/msa/Reference.java
genspace-common/.classpath
genspace-common/.gitignore
genspace-common/.project
genspace-common/.settings/org.eclipse.jdt.core.prefs
genspace-common/.settings/org.eclipse.wst.common.component
genspace-common/.settings/org.eclipse.wst.common.project.facet.core.xml
genspace-common/bin/META-INF/MANIFEST.MF
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/all-wcprops
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/entries
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/xxxjaxb.properties
genspace-common/doc/entities.PNG
genspace-common/doc/entities.ucls
genspace-common/lib/javax.ejb.jar
genspace-common/lib/javax.persistence.jar
genspace-common/src/META-INF/MANIFEST.MF
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/all-wcprops
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/entries
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEventParameter.java
genspace-common/src/org/geworkbench/components/genspace/entity/Friend.java
genspace-common/src/org/geworkbench/components/genspace/entity/IncomingWorkflow.java
genspace-common/src/org/geworkbench/components/genspace/entity/LazyCycleBreaker.java
genspace-common/src/org/geworkbench/components/genspace/entity/LogAction.java
genspace-common/src/org/geworkbench/components/genspace/entity/Network.java
genspace-common/src/org/geworkbench/components/genspace/entity/Setting.java
genspace-common/src/org/geworkbench/components/genspace/entity/TasteUser.java
genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
genspace-common/src/org/geworkbench/components/genspace/entity/ToolComment.java
genspace-common/src/org/geworkbench/components/genspace/entity/ToolRating.java
genspace-common/src/org/geworkbench/components/genspace/entity/Transaction.java
genspace-common/src/org/geworkbench/components/genspace/entity/UsageEvent.java
genspace-common/src/org/geworkbench/components/genspace/entity/User.java
genspace-common/src/org/geworkbench/components/genspace/entity/UserNetwork.java
genspace-common/src/org/geworkbench/components/genspace/entity/UserWorkflow.java
genspace-common/src/org/geworkbench/components/genspace/entity/Workflow.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowComment.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowFolder.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowRating.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowTool.java
genspace-common/src/org/geworkbench/components/genspace/entity/xxxjaxb.properties
genspace-common/src/org/geworkbench/components/genspace/server/FriendFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/NetworkFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/PublicFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/ToolInformationProvider.java
genspace-common/src/org/geworkbench/components/genspace/server/UsageInformationRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/UserFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/WorkflowRepositoryRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/task/ManualRunnerRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/task/Test.java
genspace-common/src/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainerLocal.java
genspace-ejb/.classpath
genspace-ejb/.gitignore
genspace-ejb/.project
genspace-ejb/.settings/org.eclipse.jdt.core.prefs
genspace-ejb/.settings/org.eclipse.wst.common.component
genspace-ejb/.settings/org.eclipse.wst.common.project.facet.core.xml
genspace-ejb/INSTALL.txt
genspace-ejb/NOTES
genspace-ejb/bin/.classpath
genspace-ejb/bin/.project
genspace-ejb/bin/.settings/org.eclipse.jdt.core.prefs
genspace-ejb/bin/.settings/org.eclipse.jst.j2ee.ejb.annotations.xdoclet.prefs
genspace-ejb/bin/.settings/org.eclipse.ltk.core.refactoring.prefs
genspace-ejb/bin/.settings/org.eclipse.wst.common.component
genspace-ejb/bin/.settings/org.eclipse.wst.common.project.facet.core.xml
genspace-ejb/bin/.settings/org.eclipse.wst.ws.service.policy.prefs
genspace-ejb/bin/INSTALL.txt
genspace-ejb/bin/NOTES
genspace-ejb/bin/build/classes/META-INF/MANIFEST.MF
genspace-ejb/bin/build/classes/META-INF/ejb-jar.xml
genspace-ejb/bin/build/classes/META-INF/login.conf
genspace-ejb/bin/build/classes/META-INF/mysql-resource.xml
genspace-ejb/bin/build/classes/META-INF/persistence.xml
genspace-ejb/bin/build/classes/META-INF/sun-application.xml
genspace-ejb/bin/build/classes/META-INF/sun-ejb-jar.xml
genspace-ejb/bin/ejbModule/META-INF/MANIFEST.MF
genspace-ejb/bin/ejbModule/META-INF/ejb-jar.xml
genspace-ejb/bin/ejbModule/META-INF/login.conf
genspace-ejb/bin/ejbModule/META-INF/mysql-resource.xml
genspace-ejb/bin/ejbModule/META-INF/persistence.xml
genspace-ejb/bin/ejbModule/META-INF/sun-application.xml
genspace-ejb/bin/ejbModule/META-INF/sun-ejb-jar.xml
genspace-ejb/bin/lib/mahout-core-0.5-job.jar
genspace-ejb/bin/lib/mahout-core-0.5.jar
genspace-ejb/bin/lib/mahout-math-0.5.jar
genspace-ejb/bin/lib/mahout-utils-0.5.jar
genspace-ejb/build/classes/META-INF/MANIFEST.MF
genspace-ejb/build/classes/META-INF/ejb-jar.xml
genspace-ejb/build/classes/META-INF/login.conf
genspace-ejb/build/classes/META-INF/mysql-resource.xml
genspace-ejb/build/classes/META-INF/persistence.xml
genspace-ejb/build/classes/META-INF/sun-application.xml
genspace-ejb/build/classes/META-INF/sun-ejb-jar.xml
genspace-ejb/ejbModule/META-INF/MANIFEST.MF
genspace-ejb/ejbModule/META-INF/ejb-jar.xml
genspace-ejb/ejbModule/META-INF/login.conf
genspace-ejb/ejbModule/META-INF/mysql-resource.xml
genspace-ejb/ejbModule/META-INF/persistence.xml
genspace-ejb/ejbModule/META-INF/sun-application.xml
genspace-ejb/ejbModule/META-INF/sun-ejb-jar.xml
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/AbstractFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/FriendFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommenderLocal.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/NetworkFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/PublicFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UserFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemSimilarity.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceSimilarWorkflowRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/stubs/Tool.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/ManualRunner.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
genspace-ejb/lib/mahout-core-0.5-job.jar
genspace-ejb/lib/mahout-core-0.5.jar
genspace-ejb/lib/mahout-math-0.5.jar
genspace-ejb/lib/mahout-utils-0.5.jar
diff --git a/.gitignore b/.gitignore
index 3f3152a..73a6866 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,2 @@
 *.class
 .DS_Store
-geworkbench-core/classes
diff --git a/EmblAlignParser/.project b/EmblAlignParser/.project
deleted file mode 100755
index 8b5fddb..0000000
--- a/EmblAlignParser/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>EmblAlignParser</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.wst.common.project.facet.core.builder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
-	</natures>
-</projectDescription>
diff --git a/EmblAlignParser/bin/META-INF/persistence.xml b/EmblAlignParser/bin/META-INF/persistence.xml
deleted file mode 100755
index a3c9578..0000000
--- a/EmblAlignParser/bin/META-INF/persistence.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<persistence xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
-	version="2.0" xmlns="http://java.sun.com/xml/ns/persistence">
-	<persistence-unit name="genspace_persist"
-		transaction-type="RESOURCE_LOCAL">
-		<provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
-
-		<class>org.geworkbench.components.genspace.entity.msa.Alignment</class>
-		<class>org.geworkbench.components.genspace.entity.msa.Reference</class>
-		<class>org.geworkbench.components.genspace.entity.msa.Sequence</class>
-
-		<properties>
-			<property name="javax.persistence.jdbc.user" value="genspace" />
-			<property name="javax.persistence.jdbc.password" value="g3nsp4c3" />
-			<property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver" />
-			<property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost:3306/genspace" />
-			<property name="eclipselink.ddl-generation" value="create-tables" />
-			<property name="eclipselink.logging.level" value="INFO" />
-
-			<!--Use the java2db feature -->
-			<property name="eclipselink.ddl-generation.output-mode"
-				value="database" />
-			<property name="eclipselink.ddl-generation.table-creation-suffix"
-				value=" engine=InnoDB" />
-		</properties>
-	</persistence-unit>
-</persistence>
\ No newline at end of file
diff --git a/EmblAlignParser/lib/eclipselink.jar b/EmblAlignParser/lib/eclipselink.jar
deleted file mode 100755
index 1d975b7..0000000
Binary files a/EmblAlignParser/lib/eclipselink.jar and /dev/null differ
diff --git a/EmblAlignParser/src/org/geworkbench/components/genspace/entity/msa/Reference.java b/EmblAlignParser/src/org/geworkbench/components/genspace/entity/msa/Reference.java
deleted file mode 100755
index 46cb040..0000000
--- a/EmblAlignParser/src/org/geworkbench/components/genspace/entity/msa/Reference.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package org.geworkbench.components.genspace.entity.msa;
-
-import java.io.Serializable;
-
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-@Entity
-@XmlRootElement
-public class Reference implements Serializable {
-
-	private int id;
-
-	private String title;
-
-	private String authors;
-
-	private String locator;
-
-	private Alignment alignment;
-
-	@Id
-	@GeneratedValue(strategy=GenerationType.IDENTITY)
-	@XmlElement
-	public int getId() {
-		return id;
-	}
-	public void setId(int id) {
-		this.id = id;
-	}
-	public String getTitle() {
-		return title;
-	}
-	public void setTitle(String title) {
-		this.title = title;
-	}
-	public String getAuthors() {
-		return authors;
-	}
-	public void setAuthors(String authors) {
-		this.authors = authors;
-	}
-	public String getLocator() {
-		return locator;
-	}
-	public void setLocator(String locator) {
-		this.locator = locator;
-	}
-
-	@ManyToOne(cascade=CascadeType.ALL)
-	public Alignment getAlignment() {
-		return alignment;
-	}
-	public void setAlignment(Alignment alignment) {
-		this.alignment = alignment;
-	}
-
-}
diff --git a/genspace-common/.classpath b/genspace-common/.classpath
old mode 100755
new mode 100644
diff --git a/genspace-common/.gitignore b/genspace-common/.gitignore
old mode 100755
new mode 100644
diff --git a/genspace-common/.project b/genspace-common/.project
old mode 100755
new mode 100644
diff --git a/genspace-common/.settings/org.eclipse.jdt.core.prefs b/genspace-common/.settings/org.eclipse.jdt.core.prefs
new file mode 100644
index 0000000..1715cee
--- /dev/null
+++ b/genspace-common/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,12 @@
+#Wed Jun 22 14:17:58 EDT 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6
diff --git a/genspace-common/.settings/org.eclipse.wst.common.component b/genspace-common/.settings/org.eclipse.wst.common.component
new file mode 100644
index 0000000..3b8aeb0
--- /dev/null
+++ b/genspace-common/.settings/org.eclipse.wst.common.component
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="genspace-common">
+        <wb-resource deploy-path="/" source-path="/src"/>
+    </wb-module>
+</project-modules>
diff --git a/genspace-common/.settings/org.eclipse.wst.common.project.facet.core.xml b/genspace-common/.settings/org.eclipse.wst.common.project.facet.core.xml
new file mode 100644
index 0000000..124526e
--- /dev/null
+++ b/genspace-common/.settings/org.eclipse.wst.common.project.facet.core.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <runtime name="GlassFish v3 Java EE 6"/>
+  <fixed facet="jst.utility"/>
+  <fixed facet="java"/>
+  <installed facet="java" version="1.6"/>
+  <installed facet="jst.utility" version="1.0"/>
+  <installed facet="jst.java" version="6.0"/>
+</faceted-project>
diff --git a/genspace-common/bin/META-INF/MANIFEST.MF b/genspace-common/bin/META-INF/MANIFEST.MF
old mode 100755
new mode 100644
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/all-wcprops b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/all-wcprops
new file mode 100644
index 0000000..ddc947e
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/all-wcprops
@@ -0,0 +1,113 @@
+K 25
+svn:wc:ra_dav:version-url
+V 95
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+END
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+END
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+END
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diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
new file mode 100644
index 0000000..dd2e482
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
@@ -0,0 +1,93 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+
+@Entity
+public class AnalysisEvent implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -8668839464594843903L;
+	private int id;
+	private java.util.Date createdAt;
+	private Tool tool;
+	private Transaction transaction;
+	private Set<AnalysisEventParameter> parameters = new HashSet<AnalysisEventParameter>();
+	private String toolname;
+
+//	@Override
+//	protected Object clone() throws CloneNotSupportedException {
+//		AnalysisEvent ret = new AnalysisEvent();
+//
+//		ret.id = id;
+//		ret.createdAt = (Date) createdAt.clone();
+//		ret.transaction = (Transaction) transaction.clone();
+//		ret.parameters = parameters;
+//		ret.toolname = toolname.cl
+//		return ret;
+//	}
+	@Transient
+	public String getToolname() {
+		if(tool != null)
+			return tool.getName();
+		return toolname;
+	}
+	public void setToolname(String toolname) {
+		this.toolname = toolname;
+	}
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+	@ManyToOne
+	public Transaction getTransaction() {
+		return transaction;
+	}
+	public void setTransaction(Transaction transaction) {
+		this.transaction = transaction;
+	}
+
+	@OneToMany(mappedBy="event", cascade=CascadeType.PERSIST, fetch=FetchType.EAGER)
+	public Set<AnalysisEventParameter> getParameters() {
+		return parameters;
+	}
+	public void setParameters(Set<AnalysisEventParameter> parameters) {
+		this.parameters = parameters;
+	}
+
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
new file mode 100644
index 0000000..6beda26
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
@@ -0,0 +1,51 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+
+@Entity
+public class AnalysisEventParameter implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 1559558337334158046L;
+	private int id;
+	private AnalysisEvent event;
+	private String parameterKey;
+	private String parameterValue;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	@ManyToOne
+	public AnalysisEvent getEvent() {
+		return event;
+	}
+	public void setEvent(AnalysisEvent event) {
+		this.event = event;
+	}
+	public String getParameterKey() {
+		return parameterKey;
+	}
+	public void setParameterKey(String parameterKey) {
+		this.parameterKey = parameterKey;
+	}
+	public String getParameterValue() {
+		return parameterValue;
+	}
+	public void setParameterValue(String parameterValue) {
+		this.parameterValue = parameterValue;
+	}
+
+
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
new file mode 100644
index 0000000..b6b03e1
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
@@ -0,0 +1,65 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+@Entity
+@Table(name="Friend")
+public class Friend implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 7217903012674558469L;
+	private int id;
+	private User leftUser;
+	private User rightUser;
+	private boolean mutual;
+	private boolean visible;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public boolean isMutual() {
+		return mutual;
+	}
+	public void setMutual(boolean mutual) {
+		this.mutual = mutual;
+	}
+	public boolean isVisible() {
+		return visible;
+	}
+	public void setVisible(boolean visible) {
+		this.visible = visible;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="id_1")
+	public User getLeftUser() {
+		return leftUser;
+	}
+	public void setLeftUser(User leftUser) {
+		this.leftUser = leftUser;
+	}
+
+	@JoinColumn(name="id_2")
+	public User getRightUser() {
+		return rightUser;
+	}
+	public void setRightUser(User rightUser) {
+		this.rightUser = rightUser;
+	}
+
+
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
new file mode 100644
index 0000000..4836e05
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
@@ -0,0 +1,74 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class IncomingWorkflow implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -5712035910336297173L;
+	private int id;
+	private User sender;
+	private User receiver;
+	private Workflow workflow;
+	private java.util.Date createdAt;
+	private String name;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@ManyToOne
+	public User getSender() {
+		return sender;
+	}
+	public void setSender(User sender) {
+		this.sender = sender;
+	}
+
+	@ManyToOne
+	public User getReceiver() {
+		return receiver;
+	}
+	public void setReceiver(User receiver) {
+		this.receiver = receiver;
+	}
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	@Override
+	public String toString() {
+		return "WorkflowInbox - name: " + name + ", sender: " + sender
+				+ ", date: " + createdAt.toString() + ", " + workflow;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
new file mode 100644
index 0000000..09f2c01
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
@@ -0,0 +1,73 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+
+@Entity
+public class Network implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 330141032033420545L;
+	private int id;
+	private String name;
+	private User owner;
+
+
+	private List<UserNetwork> members = new ArrayList<UserNetwork>();
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="owner")
+	public User getOwner() {
+		return owner;
+	}
+	public void setOwner(User owner) {
+		this.owner = owner;
+	}
+
+	@OneToMany(mappedBy="network")
+	public List<UserNetwork> getMembers() {
+		return members;
+	}
+	public void setMembers(List<UserNetwork> members) {
+		this.members = members;
+	}
+
+	@Override
+	public String toString() {
+		return name;
+	}
+	@Override
+	public boolean equals(Object obj) {
+		if(obj instanceof Network)
+		{
+			Network o = (Network) obj;
+			return o.getId() == getId() && o.getName().equals(getName());
+		}
+		return false;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
new file mode 100644
index 0000000..5374b4d
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
@@ -0,0 +1,39 @@
+package org.geworkbench.components.genspace.entity;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+@Entity
+public class Setting {
+	private int id;
+	private String key;
+	private String value;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@Column(name="data_key")
+	public String getKey() {
+		return key;
+	}
+	public void setKey(String key) {
+		this.key = key;
+	}
+
+	@Column(name="data_value")
+	public String getValue() {
+		return value;
+	}
+	public void setValue(String value) {
+		this.value = value;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
new file mode 100644
index 0000000..a354208
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
@@ -0,0 +1,155 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.Transient;
+
+
+@Entity
+public class Tool implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -6971084517255287450L;
+	private int id;
+
+	private String name;
+	private String description;
+	private List<ToolComment> comments = new ArrayList<ToolComment>();
+	private List<ToolRating> ratings = new ArrayList<ToolRating>();
+	private String mostCommonParameters;
+	private int mostCommonParametersCount;
+	private int usageCount;
+	private int wfCountHead;
+	private int sumRating =0;
+	private int numRating =0;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	@OrderBy
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	public String getDescription() {
+		return description;
+	}
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	@OneToMany(mappedBy="tool")
+	public List<ToolComment> getComments() {
+		return comments;
+	}
+	public void setComments(List<ToolComment> comments) {
+		this.comments = comments;
+	}
+
+	@OneToMany(mappedBy="tool")
+	public List<ToolRating> getRatings() {
+		return ratings;
+	}
+	public void setRatings(List<ToolRating> ratings) {
+		this.ratings = ratings;
+	}
+
+	public String getMostCommonParameters() {
+		return mostCommonParameters;
+	}
+	public void setMostCommonParameters(String mostCommonParameters) {
+		this.mostCommonParameters = mostCommonParameters;
+	}
+	public int getMostCommonParametersCount() {
+		return mostCommonParametersCount;
+	}
+	public void setMostCommonParametersCount(int mostCommonParametersCount) {
+		this.mostCommonParametersCount = mostCommonParametersCount;
+	}
+
+	public int getUsageCount() {
+		return usageCount;
+	}
+	public void setUsageCount(int usageCount) {
+		this.usageCount = usageCount;
+	}
+	public int getWfCountHead() {
+		return wfCountHead;
+	}
+	public void setWfCountHead(int wfCountHead) {
+		this.wfCountHead = wfCountHead;
+	}
+	public void setSumRating(int sumRating) {
+		this.sumRating = sumRating;
+	}
+	public int getSumRating() {
+		return sumRating;
+	}
+	public void setNumRating(int numRating) {
+		this.numRating = numRating;
+	}
+	public int getNumRating() {
+		return numRating;
+	}
+	@Override
+	public boolean equals(Object o) {
+		if (o instanceof Tool) {
+			Tool t = (Tool) o;
+			return t.name.equals(this.name) && t.id == this.id;
+		}
+		return false;
+	}
+
+	@Override
+	public int hashCode() {
+		return name.hashCode();
+	}
+
+	@Override
+	public String toString() {
+		return getName();
+	}
+
+	@Transient
+	public void updateRatingCache()
+	{
+		//TODO make this called automatically on save of ratings?
+		int numRating =0;
+		int totalRating =0;
+		for(ToolRating tr : getRatings())
+		{
+			numRating++;
+			totalRating += tr.getRating();
+		}
+		setNumRating(numRating);
+		setSumRating(totalRating);
+	}
+	@Transient
+	public double getOverallRating() {
+		if(getNumRating() == 0)
+			return 0;
+		else
+			return (double) getSumRating() / (double) getNumRating();
+	}
+	@Transient
+	public void incrementUsageCount() {
+		setUsageCount(getUsageCount() + 1);
+	}
+
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
new file mode 100644
index 0000000..e9ee63f
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
@@ -0,0 +1,62 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class ToolComment implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -3122267726128323333L;
+	private int id;
+	private String comment;
+	private User creator;
+	private java.util.Date createdAt;
+	private Tool tool;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getComment() {
+		return comment;
+	}
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+
+	@ManyToOne
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+
+	@ManyToOne
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
new file mode 100644
index 0000000..f7a6011
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
@@ -0,0 +1,60 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class ToolRating implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 2013611574000236034L;
+	private int id;
+	private User creator;
+	private int rating;
+	private Tool tool;
+	private Date createdAt;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+	public int getRating() {
+		return rating;
+	}
+	public void setRating(int rating) {
+		this.rating = rating;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
new file mode 100644
index 0000000..e8458a3
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
@@ -0,0 +1,95 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+@Entity
+public class Transaction implements Serializable {
+
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -4341632811573425064L;
+	private int id;
+	private String clientID;
+	private String hostname;
+	private java.util.Date date;
+	private User user;
+	private List<AnalysisEvent> analysisEvents;
+	private String dataSetName;
+	private Workflow workflow;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getClientID() {
+		return clientID;
+	}
+	public void setClientID(String clientID) {
+		this.clientID = clientID;
+	}
+	public String getHostname() {
+		return hostname;
+	}
+	public void setHostname(String hostname) {
+		this.hostname = hostname;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getDate() {
+		return date;
+	}
+	public void setDate(java.util.Date date) {
+		this.date = date;
+	}
+	public User getUser() {
+		return user;
+	}
+	public void setUser(User user) {
+		this.user = user;
+	}
+
+	@OneToMany(mappedBy="transaction")
+	public List<AnalysisEvent> getAnalysisEvents() {
+		return analysisEvents;
+	}
+	public void setAnalysisEvents(List<AnalysisEvent> analysisEvents) {
+		this.analysisEvents = analysisEvents;
+	}
+
+	public String getDataSetName() {
+		return dataSetName;
+	}
+	public void setDataSetName(String dataSetName) {
+		this.dataSetName = dataSetName;
+	}
+
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+
+	private String userName;
+	@Transient
+	public String getUserName() {
+		return userName;
+	}
+	public void setUserName(String userName) {
+		this.userName = userName;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
new file mode 100644
index 0000000..236fa8d
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
@@ -0,0 +1,491 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Lob;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+
+import org.geworkbench.components.genspace.GenSpaceServerFactory;
+
+@Entity
+@Table(name="registration")
+public class User implements Serializable, Comparable<User>{
+
+	private static final long serialVersionUID = 2972043173442132575L;
+	private int id;
+	private String username;
+	private String password;
+	private String email;
+	private String firstName;
+	private String lastName;
+	private String workTitle;
+	private String phone;
+	private String labAffiliation;
+	private String addr1;
+	private String addr2;
+	private String city;
+	private String state;
+	private String zipcode;
+	private int onlineStatus;
+	private String interests;
+	private int logData;
+	private int dataVisibility;
+	private java.util.Date createdAt;
+	private WorkflowFolder rootFolder;
+
+	private List<Friend> friends = new ArrayList<Friend>();
+	private List<UserNetwork> networks = new ArrayList<UserNetwork>();
+
+	private Set<Workflow> workflows = new HashSet<Workflow>();
+	private List<WorkflowFolder> folders = new ArrayList<WorkflowFolder>();
+	private List<WorkflowComment> workflowComments = new ArrayList<WorkflowComment>();
+	private List<ToolComment> toolComments = new ArrayList<ToolComment>();
+	private List<Transaction> transactions = new ArrayList<Transaction>();
+	private List<IncomingWorkflow> incomingWorkflows = new ArrayList<IncomingWorkflow>();
+	private List<IncomingWorkflow> outgoingWorkflows = new ArrayList<IncomingWorkflow>();
+	private Set<Network> myOwnedNetworks = new HashSet<Network>();
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@Column(length=50, nullable = false)
+	public String getUsername() {
+		return username;
+	}
+	public void setUsername(String username) {
+		this.username = username;
+	}
+
+	@Column(length=50, nullable = false)
+	private String getPassword() {
+		return password;
+	}
+	private void setPassword(String password) {
+		this.password = password;
+	}
+
+	@Column(length=50)
+	public String getEmail() {
+		return email;
+	}
+	public void setEmail(String email) {
+		this.email = email;
+	}
+
+	@Column(name="first_name", length=50, nullable = false)
+	public String getFirstName() {
+		return firstName;
+	}
+	public void setFirstName(String firstName) {
+		this.firstName = firstName;
+	}
+
+	@Column(name="last_name", length=50, nullable = false)
+	public String getLastName() {
+		return lastName;
+	}
+	public void setLastName(String lastName) {
+		this.lastName = lastName;
+	}
+
+	@Column(name="work_title", length=50)
+	public String getWorkTitle() {
+		return workTitle;
+	}
+	public void setWorkTitle(String workTitle) {
+		this.workTitle = workTitle;
+	}
+
+	@Column(length=50)
+	public String getPhone() {
+		return phone;
+	}
+	public void setPhone(String phone) {
+		this.phone = phone;
+	}
+
+	@Column(name="lab_affiliation", length=100, nullable = false)
+	public String getLabAffiliation() {
+		return labAffiliation;
+	}
+	public void setLabAffiliation(String labAffiliation) {
+		this.labAffiliation = labAffiliation;
+	}
+
+	@Column(length=50)
+	public String getAddr1() {
+		return addr1;
+	}
+	public void setAddr1(String addr1) {
+		this.addr1 = addr1;
+	}
+
+	@Column(length=50)
+	public String getAddr2() {
+		return addr2;
+	}
+	public void setAddr2(String addr2) {
+		this.addr2 = addr2;
+	}
+
+	@Column(length=50)
+	public String getCity() {
+		return city;
+	}
+	public void setCity(String city) {
+		this.city = city;
+	}
+
+	@Column(length=50)
+	public String getState() {
+		return state;
+	}
+	public void setState(String state) {
+		this.state = state;
+	}
+
+	@Column(length=7)
+	public String getZipcode() {
+		return zipcode;
+	}
+	public void setZipcode(String zipcode) {
+		this.zipcode = zipcode;
+	}
+
+	@Column(name="online_status")
+	public int getOnlineStatus() {
+		return onlineStatus;
+	}
+	public void setOnlineStatus(int onlineStatus) {
+		this.onlineStatus = onlineStatus;
+	}
+
+	@Lob
+	public String getInterests() {
+		return interests;
+	}
+	public void setInterests(String interests) {
+		this.interests = interests;
+	}
+
+	public int getLogData() {
+		return logData;
+	}
+	public void setLogData(int logData) {
+		this.logData = logData;
+	}
+	public int getDataVisibility() {
+		return dataVisibility;
+	}
+	public void setDataVisibility(int dataVisibility) {
+		this.dataVisibility = dataVisibility;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+
+	@OneToMany(mappedBy="leftUser")
+	public List<Friend> getFriends() {
+		return friends;
+	}
+	public void setFriends(List<Friend> friends) {
+		this.friends = friends;
+	}
+	@OneToMany(mappedBy="user")
+	public List<UserNetwork> getNetworks() {
+		return networks;
+	}
+	public void setNetworks(List<UserNetwork> networks) {
+		this.networks = networks;
+	}
+
+	@OneToMany(mappedBy="creator")
+	public Set<Workflow> getWorkflows() {
+		return workflows;
+	}
+	public void setWorkflows(Set<Workflow> workflows) {
+		this.workflows = workflows;
+	}
+
+	@OneToMany(mappedBy="owner")
+	public List<WorkflowFolder> getFolders() {
+		return folders;
+	}
+	public void setFolders(List<WorkflowFolder> folders) {
+		this.folders = folders;
+	}
+
+	@OneToMany(mappedBy="creator")
+	public List<WorkflowComment> getWorkflowComments() {
+		return workflowComments;
+	}
+	public void setWorkflowComments(List<WorkflowComment> workflowComments) {
+		this.workflowComments = workflowComments;
+	}
+
+	@OneToMany(mappedBy="creator")
+	public List<ToolComment> getToolComments() {
+		return toolComments;
+	}
+	public void setToolComments(List<ToolComment> toolComments) {
+		this.toolComments = toolComments;
+	}
+
+	@OneToMany(mappedBy="user")
+	public List<Transaction> getTransactions() {
+		return transactions;
+	}
+	public void setTransactions(List<Transaction> transactions) {
+		this.transactions = transactions;
+	}
+
+	@OneToMany(mappedBy="receiver")
+	public List<IncomingWorkflow> getIncomingWorkflows() {
+		return incomingWorkflows;
+	}
+	public void setIncomingWorkflows(List<IncomingWorkflow> incomingWorkflows) {
+		this.incomingWorkflows = incomingWorkflows;
+	}
+
+	@OneToMany(mappedBy="sender")
+	public List<IncomingWorkflow> getOutgoingWorkflows() {
+		return outgoingWorkflows;
+	}
+	public void setOutgoingWorkflows(List<IncomingWorkflow> outgoingWorkflows) {
+		this.outgoingWorkflows = outgoingWorkflows;
+	}
+
+
+	@OneToMany(mappedBy="owner")
+	public Set<Network> getMyOwnedNetworks() {
+		return myOwnedNetworks;
+	}
+	public void setMyOwnedNetworks(Set<Network> myOwnedNetworks) {
+		this.myOwnedNetworks = myOwnedNetworks;
+	}
+
+	public WorkflowFolder getRootFolder() {
+		return rootFolder;
+	}
+	public void setRootFolder(WorkflowFolder rootFolder) {
+		this.rootFolder = rootFolder;
+	}
+
+	@Override
+	public String toString() {
+		String result = "User [" + username+"]";
+		return result;
+	}
+
+	public void setPasswordClearText(String password)
+	{
+		this.setPassword(this.getEncryptedPassword(password.toCharArray()));
+
+	}
+
+	public boolean passwordMatches(String password)
+	{
+		return this.getEncryptedPassword(password.toCharArray()).equals(this.getPassword());
+	}
+
+	@Override
+	public int hashCode() {
+		return this.getId();
+	}
+	@Override
+	public boolean equals(Object obj) {
+		if(obj instanceof User)
+		{
+			return ((User) obj).getId() == this.getId();
+		}
+		return false;
+	}
+
+	protected final static String HEX_DIGITS = "0123456789abcdef";
+
+	/**
+	 * This method is used to encrypt the password using SHA encryption.
+	 *
+	 * @param password
+	 *            represents the password to be encrypted
+	 * @return returns password in encrypted form
+	 */
+	private String getEncryptedPassword(char[] c_password) {
+		String plaintext = new String(c_password);
+
+		java.security.MessageDigest d =null;
+				try {
+					d = java.security.MessageDigest.getInstance("SHA-1");
+				} catch (NoSuchAlgorithmException e) {
+					GenSpaceServerFactory.logger.error("Error",e);
+				}
+				d.reset();
+				d.update(plaintext.getBytes());
+				byte[] hashedBytes =  d.digest();
+				StringBuffer sb = new StringBuffer(hashedBytes.length * 2);
+		        for (int i = 0; i < hashedBytes.length; i++) {
+		             int b = hashedBytes[i] & 0xFF;
+		             sb.append(HEX_DIGITS.charAt(b >>> 4)).append(HEX_DIGITS.charAt(b & 0xF));
+		        }
+		        return sb.toString();
+	}
+	@Transient
+	public String getFullName() {
+		return this.getFirstName() + " " + this.getLastName();
+	}
+	@Transient
+	public Friend isFriendsWith(User u) {
+		for(Friend f: getFriends())
+		{
+			if(f.getRightUser().equals(u))
+			{
+				setFriends(true);
+				return f;
+			}
+		}
+		setFriends(false);
+		return null;
+	}
+	@Transient
+	public UserNetwork isInNetwork(Network n) {
+		for(UserNetwork un : getNetworks())
+		{
+			if(un.getNetwork().equals(n))
+				return un;
+		}
+		return null;
+	}
+	@Transient
+	private boolean isVisibleTo(User other)
+	{
+		Friend f = isFriendsWith(other);
+		if(f != null && f.isVisible())
+		{
+			return true;
+		}
+		//Check the networks
+		for(UserNetwork u1 : this.getNetworks())
+		{
+			if(u1.isVisible())
+				for(UserNetwork u2 : other.getNetworks())
+				{
+					if(u2.getNetwork().equals(u1.getNetwork()))
+						return true;
+				}
+		}
+		return false;
+	}
+	@Transient
+	private String na(String s)
+	{
+		return (s == null || s.length() == 0 ? "N/A" : s);
+	}
+	@Transient
+	public String getFullNameWUsername()
+	{
+		if(getFirstName().length() == 0 && getLastName().length() ==0)
+			return getUsername();
+		else
+			return getFirstName() + " "
+			+ getLastName() + " (" + getUsername() + ")";
+	}
+
+	public String toHTML() {
+		String r = "<html><body><b>" +getFullNameWUsername() + "</b><br>";
+		if (GenSpaceServerFactory.isVisible(this)) {
+			r += "<i>"
+					+ (getWorkTitle() != null
+							&& getWorkTitle() != "" ? getWorkTitle() + " at " : "")
+					+ (getLabAffiliation() != null ? getLabAffiliation():  " (affiliation not disclosed)") + "</i><br><br>";
+			r += "<b>Research Interests:</b><br />"
+					+(getInterests() == null ? "(not disclosed)" : getInterests()) + "<br><br>";
+			r += "<b>Contact information:</b><br /><br>Phone: "
+					+ na(getPhone()) + "<br>Email: "
+					+ na(getEmail()) + "<br><br>Mailing Address:<br>"
+					+ (getAddr1().length() == 0 && getAddr2().length() == 00 && getCity().length() == 0 && getState().length() == 0 && getZipcode().length() == 0 ? "not provided" :
+						 na(getAddr1()) + "<br>" + na(getAddr2())
+					+ "<br>" + na(getCity()) + ", "
+					+ na(getState()) + ", " + na(getZipcode()));
+		} else {
+			r += "This user is not visible to you. Please add them as a friend or join one of their networks to see their profile.";
+		}
+		r += "</body>";
+		r += "</html>";
+		return r;
+	}
+	@Transient
+	public String getShortName() {
+		if(getFirstName() != null && !getFirstName().equals(""))
+			return getFirstName();
+		return getUsername();
+	}
+	@Transient
+	public List<User> getFriendsProfiles() {
+		ArrayList<User> ret = new ArrayList<User>();
+		for(Friend f: getFriends())
+			ret.add(f.getRightUser());
+		return ret;
+	}
+	@Transient
+	public boolean containsFolderByName(String folderName) {
+		for(WorkflowFolder f : getFolders())
+			if(f.getName().equals(folderName))
+				return true;
+		return false;
+	}
+	@Override
+	public int compareTo(User o) {
+		int r = this.getLastName().compareTo(o.getLastName());
+		if(r == 0)
+			return this.getFirstName().compareTo(o.getFirstName());
+		return r;
+	}
+	@Transient
+	public User loadVisibility(User from) {
+		setVisible(isVisibleTo(from));
+		return this;
+	}
+
+
+	private boolean isVisible;
+	@Transient
+	public boolean isVisible() {
+		return isVisible;
+	}
+	public void setVisible(boolean isVisible) {
+		this.isVisible = isVisible;
+	}
+	private boolean isFriends;
+	@Transient
+	public boolean isFriends() {
+		return isFriends;
+	}
+	public void setFriends(boolean isFriends) {
+		this.isFriends = isFriends;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
new file mode 100644
index 0000000..3f0ef41
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
@@ -0,0 +1,71 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+@Entity
+@Table(name="User_Network")
+public class UserNetwork implements Serializable {
+
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 2587552459317296299L;
+	private int id;
+	private User user;
+	private Network network;
+	private boolean verified;
+	private boolean visible;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="user_id")
+	public User getUser() {
+		return user;
+	}
+	public void setUser(User user) {
+		this.user = user;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="network_id")
+	public Network getNetwork() {
+		return network;
+	}
+	public void setNetwork(Network network) {
+		this.network = network;
+	}
+
+	public boolean isVerified() {
+		return verified;
+	}
+	public void setVerified(boolean verified) {
+		this.verified = verified;
+	}
+	public boolean isVisible() {
+		return visible;
+	}
+	public void setVisible(boolean visible) {
+		this.visible = visible;
+	}
+	@Override
+	public String toString() {
+		return "UserNetwork [user = {"+user.toString()+"}, network={"+network.toString()+"}, visible="+(isVisible() ? "true" : "false")+"]";
+	}
+
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
new file mode 100644
index 0000000..b062f90
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
@@ -0,0 +1,95 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+
+@Entity
+public class UserWorkflow implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -6313031043276205912L;
+	private int id;
+	private User owner;
+	private Workflow workflow;
+	private String name;
+	private Date createdAt;
+	private WorkflowFolder folder;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@ManyToOne
+	public User getOwner() {
+		return owner;
+	}
+	public void setOwner(User owner) {
+		this.owner = owner;
+	}
+
+	@ManyToOne(fetch = FetchType.EAGER)
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	@Temporal(TemporalType.TIMESTAMP)
+	public Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public WorkflowFolder getFolder() {
+		return folder;
+	}
+	public void setFolder(WorkflowFolder folder) {
+		this.folder = folder;
+	}
+	@Override
+	public String toString() {
+		return "UserWorkflow - name: " + name + ", " + owner.getUsername() + ", "
+				+ workflow;
+	}
+	@Override
+	public int hashCode() {
+		return this.getId();
+	}
+	@Override
+	public boolean equals(Object o) {
+		if(o == null)
+			return false;
+		try {
+			UserWorkflow uw = (UserWorkflow) o;
+			return owner.equals(uw.owner) && workflow.equals(uw.workflow);
+		} catch (ClassCastException e) {
+			e.printStackTrace();
+		}
+		return false;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
new file mode 100644
index 0000000..5e28dfb
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
@@ -0,0 +1,273 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+import org.geworkbench.components.genspace.RuntimeEnvironmentSettings;
+
+@Entity
+public class Workflow implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -344401848390541281L;
+	private int id;
+	private User creator;
+	private java.util.Date createdAt;
+	private Transaction creationTransaction;
+	private	List<WorkflowTool> tools = new ArrayList<WorkflowTool>();
+	private List<WorkflowComment> comments = new ArrayList<WorkflowComment>();
+	private List<WorkflowRating> ratings = new ArrayList<WorkflowRating>();
+	private int usageCount;
+	private Workflow parent;
+	private List<Workflow> children;
+
+	private int numRating = 0;
+	private int sumRating = 0;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+
+	@OneToOne(fetch=FetchType.LAZY)
+	public Transaction getCreationTransaction() {
+		return creationTransaction;
+	}
+	public void setCreationTransaction(Transaction creationTransaction) {
+		this.creationTransaction = creationTransaction;
+	}
+
+	@OneToMany(mappedBy="workflow")
+	@OrderBy("order ASC")
+	public List<WorkflowTool> getTools() {
+		return tools;
+	}
+	public void setTools(List<WorkflowTool> tools) {
+		this.tools = tools;
+	}
+
+	@OneToMany(mappedBy="parent")
+	public List<Workflow> getChildren() {
+		return children;
+	}
+	public void setChildren(List<Workflow> children) {
+		this.children = children;
+	}
+	@OneToMany(mappedBy="workflow")
+	public List<WorkflowComment> getComments() {
+		return comments;
+	}
+	public void setComments(List<WorkflowComment> comments) {
+		this.comments = comments;
+	}
+
+	@OneToMany(mappedBy="workflow")
+	public List<WorkflowRating> getRatings() {
+		return ratings;
+	}
+	public void setRatings(List<WorkflowRating> ratings) {
+		this.ratings = ratings;
+	}
+	public int getUsageCount() {
+		return usageCount;
+	}
+	public void setUsageCount(int usageCount) {
+		this.usageCount = usageCount;
+	}
+	@Transient
+	public double getAvgRating() {
+		double result = 0;
+		if (ratings.size() > 0) {
+			for (WorkflowRating r : ratings) {
+				result += r.getRating();
+			}
+			result /= ratings.size();
+		}
+		return result;
+	}
+
+	@Override
+	public String toString() {
+		String r = "";
+		for(WorkflowTool wt : getTools())
+		{
+			r += wt.getTool().getName() + ", ";
+		}
+		if(r.length() > 2)
+			r = r.substring(0,r.length()-2);
+		return r;
+	}
+
+	@OneToOne(fetch=FetchType.LAZY)
+	public Workflow getParent() {
+		return parent;
+	}
+	public void setParent(Workflow parent) {
+		this.parent = parent;
+	}
+	public int getNumRating() {
+		return numRating;
+	}
+	public void setNumRating(int numRating) {
+		this.numRating = numRating;
+	}
+	public int getSumRating() {
+		return sumRating;
+	}
+	public void setSumRating(int sumRating) {
+		this.sumRating = sumRating;
+	}
+
+	@Transient
+	public void updateRatingsCache()
+	{
+		//TODO make this called automatically
+		int numRating =0;
+		int totalRating =0;
+		for(WorkflowRating tr : getRatings())
+		{
+			numRating++;
+			totalRating += tr.getRating();
+		}
+		setNumRating(numRating);
+		setSumRating(totalRating);
+	}
+	@Transient
+	public Tool getLastTool()
+	{
+		return this.getTools().get(this.getTools().size() -1).getTool();
+	}
+	@Transient
+	public String getLastToolName()
+	{
+		return this.getLastTool().getName();
+	}
+	@Transient
+	public double getOverallRating() {
+		if(getNumRating() == 0)
+			return 0;
+		else
+			return (double) getSumRating() / (double) getNumRating();
+	}
+	@Transient
+	public void loadToolsFromCache()
+	{
+		if(getToolIds() != null && RuntimeEnvironmentSettings.tools != null)
+		{
+			ArrayList<WorkflowTool> ret = new ArrayList<WorkflowTool>();
+			int j = 1;
+			for(int i : getToolIds())
+			{
+				WorkflowTool t = new WorkflowTool();
+				t.setOrder(j);
+				t.setTool(RuntimeEnvironmentSettings.tools.get(i));
+				t.setWorkflow(this);
+				ret.add(t);
+				j++;
+			}
+			tools = ret;
+		}
+	}
+	private int[] toolIds = null;
+	@Transient
+	public int[] getToolIds() {
+		return toolIds;
+	}
+	public void setToolIds(int[] toolIds) {
+		this.toolIds = toolIds;
+	}
+
+	private int cachedParentId = -1;
+	@Transient
+	public int getCachedParentId() {
+		return cachedParentId;
+	}
+	public void setCachedParentId(int cachedParentId) {
+		this.cachedParentId = cachedParentId;
+	}
+
+	private int cachedChildrenCount;
+	@Transient
+	public int getCachedChildrenCount() {
+		return cachedChildrenCount;
+	}
+	public void setCachedChildrenCount(int cachedChildrenCount) {
+		this.cachedChildrenCount = cachedChildrenCount;
+	}
+	@Transient
+	public Workflow slimDown()
+	{
+		Workflow w = new Workflow();
+		w.setId(this.getId());
+		w.setRatings(this.getRatings());
+		int[] temp = new int[getTools().size()];
+    	for(WorkflowTool t : getTools())
+    	{
+    		temp[t.getOrder()-1] = t.getTool().getId();
+    	}
+    	getRatings().size();
+    	w.setRatings(getRatings());
+		w.setToolIds(temp);
+		w.setComments(getComments());
+		w.setUsageCount(getUsageCount());
+		w.setNumRating(getNumRating());
+		w.setSumRating(getSumRating());
+		w.setCreator(getCreator());
+		if(getCachedParentId() < 0 && getParent() != null)
+			w.setCachedParentId(getParent().getId());
+		return w;
+	}
+
+	@Transient
+	public Workflow slimDownTiny()
+	{
+		Workflow w = new Workflow();
+		w.setId(this.getId());
+		w.setRatings(this.getRatings());
+		int[] temp = new int[getTools().size()];
+    	for(WorkflowTool t : getTools())
+    	{
+    		temp[t.getOrder()-1] = t.getTool().getId();
+    	}
+		w.setToolIds(temp);
+		w.setUsageCount(getUsageCount());
+		w.setNumRating(getNumRating());
+		w.setSumRating(getSumRating());
+		if(getCachedParentId() < 0 && getParent() != null)
+			w.setCachedParentId(getParent().getId());
+		return w;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
new file mode 100644
index 0000000..3923dc3
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
@@ -0,0 +1,67 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class WorkflowComment implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 8507652685971547757L;
+	private int id;
+	private String comment;
+	private User creator;
+	private java.util.Date createdAt;
+	private Workflow workflow;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getComment() {
+		return comment;
+	}
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+
+	@ManyToOne
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+
+	@Override
+	public String toString() {
+		return "WorkflowComment - username: " + creator.getUsername() + ", postedOn: "
+				+ createdAt.toString() + ", comment: " + comment;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
new file mode 100644
index 0000000..f11b815
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
@@ -0,0 +1,87 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+
+@Entity
+public class WorkflowFolder implements Serializable, Comparable<WorkflowFolder>{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -1365608467302705177L;
+	private int id;
+	private User owner;
+	private String name;
+	private WorkflowFolder parent;
+	private List<UserWorkflow> workflows = new ArrayList<UserWorkflow>();
+
+	private List<WorkflowFolder> children = new ArrayList<WorkflowFolder>();
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public User getOwner() {
+		return owner;
+	}
+	public void setOwner(User ownerId) {
+		this.owner = ownerId;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	@OneToMany(mappedBy="parent")
+	public List<WorkflowFolder> getChildren(){
+		return children;
+	}
+	public void setChildren(List<WorkflowFolder> children) {
+		this.children = children;
+	}
+	@ManyToOne
+	public WorkflowFolder getParent() {
+		return parent;
+	}
+	public void setParent(WorkflowFolder parent) {
+		this.parent = parent;
+	}
+	@Override
+	public int compareTo(WorkflowFolder o) {
+		return this.getName().compareTo(o.getName());
+	}
+	@OneToMany(mappedBy="folder")
+	public List<UserWorkflow> getWorkflows() {
+		return workflows;
+	}
+	public void setWorkflows(List<UserWorkflow> workflows) {
+		this.workflows = workflows;
+	}
+	@Override
+	public String toString() {
+		return this.getName();
+	}
+	@Override
+	public boolean equals(Object obj) {
+		if(obj instanceof WorkflowFolder)
+			return ((WorkflowFolder) obj).getId() == getId();
+		return false;
+	}
+	@Override
+	public int hashCode() {
+		return new Integer(id).hashCode();
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
new file mode 100644
index 0000000..93cc6b4
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
@@ -0,0 +1,59 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class WorkflowRating implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 763395791318191799L;
+	private int id;
+	private User creator;
+	private int rating;
+	private Date createdAt;
+	private Workflow workflow;
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+	public int getRating() {
+		return rating;
+	}
+	public void setRating(int rating) {
+		this.rating = rating;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+}
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
new file mode 100644
index 0000000..974f328
--- /dev/null
+++ b/genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
@@ -0,0 +1,53 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+@Entity
+public class WorkflowTool implements Serializable{
+
+	private static final long serialVersionUID = 256557429649076135L;
+	private Workflow workflow;
+	private Tool tool;
+	private int id;
+	private int order;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+	@Column(name="CARDINALITY")
+	public int getOrder() {
+		return order;
+	}
+	public void setOrder(int order) {
+		this.order = order;
+	}
+	@Override
+	public String toString() {
+		return tool.toString();
+	}
+
+}
+
\ No newline at end of file
diff --git a/genspace-common/bin/org/geworkbench/components/genspace/entity/xxxjaxb.properties b/genspace-common/bin/org/geworkbench/components/genspace/entity/xxxjaxb.properties
old mode 100755
new mode 100644
diff --git a/genspace-common/doc/entities.PNG b/genspace-common/doc/entities.PNG
deleted file mode 100755
index bfeac24..0000000
Binary files a/genspace-common/doc/entities.PNG and /dev/null differ
diff --git a/genspace-common/doc/entities.ucls b/genspace-common/doc/entities.ucls
deleted file mode 100755
index 5609f81..0000000
--- a/genspace-common/doc/entities.ucls
+++ /dev/null
@@ -1,405 +0,0 @@
-<class-diagram version="1.0.4" icons="true" automaticImage="PNG" always-add-relationships="false" generalizations="true"
-  realizations="true" associations="true" dependencies="false" nesting-relationships="true">
-  <class id="1" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.User"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/User.java"
-    binary="false">
-    <position height="-1" width="-1" x="720" y="438"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="2" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.Friend"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/Friend.java"
-    binary="false">
-    <position height="-1" width="-1" x="314" y="67"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="3" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.IncomingWorkflow"
-    project="genspace-common"
-    file="/genspace-common/src/org/geworkbench/components/genspace/entity/IncomingWorkflow.java" binary="false">
-    <position height="-1" width="-1" x="1182" y="60"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="4" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.Network"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/Network.java"
-    binary="false">
-    <position height="-1" width="-1" x="595" y="50"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="5" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.UserNetwork"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/UserNetwork.java"
-    binary="false">
-    <position height="-1" width="-1" x="907" y="60"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="6" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.ToolComment"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/ToolComment.java"
-    binary="false">
-    <position height="-1" width="-1" x="277" y="229"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="7" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.Tool"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java"
-    binary="false">
-    <position height="-1" width="-1" x="278" y="511"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="8" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.Workflow"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/Workflow.java"
-    binary="false">
-    <position height="-1" width="-1" x="1182" y="363"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="9" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.Transaction"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/Transaction.java"
-    binary="false">
-    <position height="-1" width="-1" x="1028" y="730"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="10" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.ToolRating"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/ToolRating.java"
-    binary="false">
-    <position height="-1" width="-1" x="272" y="745"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="11" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.AnalysisEvent"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java"
-    binary="false">
-    <position height="-1" width="-1" x="536" y="752"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="12" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.UserWorkflow"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/UserWorkflow.java"
-    binary="false">
-    <position height="-1" width="-1" x="1258" y="700"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <class id="13" corner="BOTTOM_RIGHT" language="java" name="org.geworkbench.components.genspace.entity.WorkflowTool"
-    project="genspace-common" file="/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowTool.java"
-    binary="false">
-    <position height="-1" width="-1" x="1432" y="567"/>
-    <display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-      <attributes public="true" package="true" protected="true" private="true"/>
-      <operations public="false" package="false" protected="false" private="false"/>
-    </display>
-  </class>
-  <association>
-    <end type="SOURCE" nodeId="8" navigable="false">
-      <attribute name="creationTransaction"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="9" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="1" navigable="false">
-      <attribute name="workflows"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="8" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="7" navigable="false">
-      <attribute name="comments"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="6" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="4" navigable="false">
-      <attribute name="owner"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="9" navigable="false">
-      <attribute name="analysisEvents"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="11" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="receiver"/>
-      <multiplicity minimum="0" maximum="1"/>
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-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="5" navigable="false">
-      <attribute name="network"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="4" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="owner"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="13" navigable="false">
-      <attribute name="workflow"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="8" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="tools"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="13" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="6" navigable="false">
-      <attribute name="tool"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="7" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="1" navigable="false">
-      <attribute name="myOwnedNetworks"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="4" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="tool"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="7" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="1" navigable="false">
-      <attribute name="toolComments"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="6" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="1" navigable="false">
-      <attribute name="outgoingWorkflows"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="3" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="incomingWorkflows"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
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-    <end type="TARGET" nodeId="3" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
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-  <association>
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-      <attribute name="tool"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
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-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="workflow"/>
-      <multiplicity minimum="0" maximum="1"/>
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-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="transaction"/>
-      <multiplicity minimum="0" maximum="1"/>
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-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="user"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
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-    <display labels="true" multiplicity="true"/>
-  </association>
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-      <attribute name="friends"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
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-    <display labels="true" multiplicity="true"/>
-  </association>
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-      <attribute name="sender"/>
-      <multiplicity minimum="0" maximum="1"/>
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-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="workflow"/>
-      <multiplicity minimum="0" maximum="1"/>
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-    <display labels="true" multiplicity="true"/>
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-  <association>
-    <end type="SOURCE" nodeId="1" navigable="false">
-      <attribute name="transactions"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="9" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="7" navigable="false">
-      <attribute name="ratings"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="10" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="2" navigable="false">
-      <attribute name="leftUser"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
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-      <attribute name="rightUser"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="9" navigable="false">
-      <attribute name="workflow"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="8" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="6" navigable="false">
-      <attribute name="creator"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="10" navigable="false">
-      <attribute name="creator"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="1" navigable="false">
-      <attribute name="networks"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="5" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="4" navigable="false">
-      <attribute name="members"/>
-      <multiplicity minimum="0" maximum="2147483647"/>
-    </end>
-    <end type="TARGET" nodeId="5" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="9" navigable="false">
-      <attribute name="user"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="13" navigable="false">
-      <attribute name="tool"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="7" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <association>
-    <end type="SOURCE" nodeId="8" navigable="false">
-      <attribute name="creator"/>
-      <multiplicity minimum="0" maximum="1"/>
-    </end>
-    <end type="TARGET" nodeId="1" navigable="true"/>
-    <display labels="true" multiplicity="true"/>
-  </association>
-  <classifier-display autosize="true" package="true" initial-value="false" signature="false" visibility="true">
-    <attributes public="true" package="true" protected="true" private="true"/>
-    <operations public="false" package="false" protected="false" private="false"/>
-  </classifier-display>
-  <association-display labels="true" multiplicity="true"/>
-</class-diagram>
\ No newline at end of file
diff --git a/genspace-common/lib/javax.ejb.jar b/genspace-common/lib/javax.ejb.jar
old mode 100755
new mode 100644
diff --git a/genspace-common/lib/javax.persistence.jar b/genspace-common/lib/javax.persistence.jar
old mode 100755
new mode 100644
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old mode 100755
new mode 100644
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new file mode 100644
index 0000000..ddc947e
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/all-wcprops
@@ -0,0 +1,113 @@
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+END
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+END
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+K 25
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+V 112
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+END
+Network.java
+K 25
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+V 108
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+END
+WorkflowComment.java
+K 25
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+END
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+K 25
+svn:wc:ra_dav:version-url
+V 117
+/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/src/org/geworkbench/components/genspace/entity/IncomingWorkflow.java
+END
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new file mode 100644
index 0000000..2467c91
--- /dev/null
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diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
new file mode 100644
index 0000000..dd2e482
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
@@ -0,0 +1,93 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+
+@Entity
+public class AnalysisEvent implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -8668839464594843903L;
+	private int id;
+	private java.util.Date createdAt;
+	private Tool tool;
+	private Transaction transaction;
+	private Set<AnalysisEventParameter> parameters = new HashSet<AnalysisEventParameter>();
+	private String toolname;
+
+//	@Override
+//	protected Object clone() throws CloneNotSupportedException {
+//		AnalysisEvent ret = new AnalysisEvent();
+//
+//		ret.id = id;
+//		ret.createdAt = (Date) createdAt.clone();
+//		ret.transaction = (Transaction) transaction.clone();
+//		ret.parameters = parameters;
+//		ret.toolname = toolname.cl
+//		return ret;
+//	}
+	@Transient
+	public String getToolname() {
+		if(tool != null)
+			return tool.getName();
+		return toolname;
+	}
+	public void setToolname(String toolname) {
+		this.toolname = toolname;
+	}
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+	@ManyToOne
+	public Transaction getTransaction() {
+		return transaction;
+	}
+	public void setTransaction(Transaction transaction) {
+		this.transaction = transaction;
+	}
+
+	@OneToMany(mappedBy="event", cascade=CascadeType.PERSIST, fetch=FetchType.EAGER)
+	public Set<AnalysisEventParameter> getParameters() {
+		return parameters;
+	}
+	public void setParameters(Set<AnalysisEventParameter> parameters) {
+		this.parameters = parameters;
+	}
+
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
new file mode 100644
index 0000000..6beda26
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
@@ -0,0 +1,51 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+
+@Entity
+public class AnalysisEventParameter implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 1559558337334158046L;
+	private int id;
+	private AnalysisEvent event;
+	private String parameterKey;
+	private String parameterValue;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	@ManyToOne
+	public AnalysisEvent getEvent() {
+		return event;
+	}
+	public void setEvent(AnalysisEvent event) {
+		this.event = event;
+	}
+	public String getParameterKey() {
+		return parameterKey;
+	}
+	public void setParameterKey(String parameterKey) {
+		this.parameterKey = parameterKey;
+	}
+	public String getParameterValue() {
+		return parameterValue;
+	}
+	public void setParameterValue(String parameterValue) {
+		this.parameterValue = parameterValue;
+	}
+
+
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
new file mode 100644
index 0000000..b6b03e1
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
@@ -0,0 +1,65 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+@Entity
+@Table(name="Friend")
+public class Friend implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 7217903012674558469L;
+	private int id;
+	private User leftUser;
+	private User rightUser;
+	private boolean mutual;
+	private boolean visible;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public boolean isMutual() {
+		return mutual;
+	}
+	public void setMutual(boolean mutual) {
+		this.mutual = mutual;
+	}
+	public boolean isVisible() {
+		return visible;
+	}
+	public void setVisible(boolean visible) {
+		this.visible = visible;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="id_1")
+	public User getLeftUser() {
+		return leftUser;
+	}
+	public void setLeftUser(User leftUser) {
+		this.leftUser = leftUser;
+	}
+
+	@JoinColumn(name="id_2")
+	public User getRightUser() {
+		return rightUser;
+	}
+	public void setRightUser(User rightUser) {
+		this.rightUser = rightUser;
+	}
+
+
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
new file mode 100644
index 0000000..4836e05
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
@@ -0,0 +1,74 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class IncomingWorkflow implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -5712035910336297173L;
+	private int id;
+	private User sender;
+	private User receiver;
+	private Workflow workflow;
+	private java.util.Date createdAt;
+	private String name;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@ManyToOne
+	public User getSender() {
+		return sender;
+	}
+	public void setSender(User sender) {
+		this.sender = sender;
+	}
+
+	@ManyToOne
+	public User getReceiver() {
+		return receiver;
+	}
+	public void setReceiver(User receiver) {
+		this.receiver = receiver;
+	}
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	@Override
+	public String toString() {
+		return "WorkflowInbox - name: " + name + ", sender: " + sender
+				+ ", date: " + createdAt.toString() + ", " + workflow;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
new file mode 100644
index 0000000..09f2c01
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
@@ -0,0 +1,73 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+
+@Entity
+public class Network implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 330141032033420545L;
+	private int id;
+	private String name;
+	private User owner;
+
+
+	private List<UserNetwork> members = new ArrayList<UserNetwork>();
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="owner")
+	public User getOwner() {
+		return owner;
+	}
+	public void setOwner(User owner) {
+		this.owner = owner;
+	}
+
+	@OneToMany(mappedBy="network")
+	public List<UserNetwork> getMembers() {
+		return members;
+	}
+	public void setMembers(List<UserNetwork> members) {
+		this.members = members;
+	}
+
+	@Override
+	public String toString() {
+		return name;
+	}
+	@Override
+	public boolean equals(Object obj) {
+		if(obj instanceof Network)
+		{
+			Network o = (Network) obj;
+			return o.getId() == getId() && o.getName().equals(getName());
+		}
+		return false;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
new file mode 100644
index 0000000..5374b4d
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
@@ -0,0 +1,39 @@
+package org.geworkbench.components.genspace.entity;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+@Entity
+public class Setting {
+	private int id;
+	private String key;
+	private String value;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@Column(name="data_key")
+	public String getKey() {
+		return key;
+	}
+	public void setKey(String key) {
+		this.key = key;
+	}
+
+	@Column(name="data_value")
+	public String getValue() {
+		return value;
+	}
+	public void setValue(String value) {
+		this.value = value;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
new file mode 100644
index 0000000..a354208
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
@@ -0,0 +1,155 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.Transient;
+
+
+@Entity
+public class Tool implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -6971084517255287450L;
+	private int id;
+
+	private String name;
+	private String description;
+	private List<ToolComment> comments = new ArrayList<ToolComment>();
+	private List<ToolRating> ratings = new ArrayList<ToolRating>();
+	private String mostCommonParameters;
+	private int mostCommonParametersCount;
+	private int usageCount;
+	private int wfCountHead;
+	private int sumRating =0;
+	private int numRating =0;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	@OrderBy
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	public String getDescription() {
+		return description;
+	}
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	@OneToMany(mappedBy="tool")
+	public List<ToolComment> getComments() {
+		return comments;
+	}
+	public void setComments(List<ToolComment> comments) {
+		this.comments = comments;
+	}
+
+	@OneToMany(mappedBy="tool")
+	public List<ToolRating> getRatings() {
+		return ratings;
+	}
+	public void setRatings(List<ToolRating> ratings) {
+		this.ratings = ratings;
+	}
+
+	public String getMostCommonParameters() {
+		return mostCommonParameters;
+	}
+	public void setMostCommonParameters(String mostCommonParameters) {
+		this.mostCommonParameters = mostCommonParameters;
+	}
+	public int getMostCommonParametersCount() {
+		return mostCommonParametersCount;
+	}
+	public void setMostCommonParametersCount(int mostCommonParametersCount) {
+		this.mostCommonParametersCount = mostCommonParametersCount;
+	}
+
+	public int getUsageCount() {
+		return usageCount;
+	}
+	public void setUsageCount(int usageCount) {
+		this.usageCount = usageCount;
+	}
+	public int getWfCountHead() {
+		return wfCountHead;
+	}
+	public void setWfCountHead(int wfCountHead) {
+		this.wfCountHead = wfCountHead;
+	}
+	public void setSumRating(int sumRating) {
+		this.sumRating = sumRating;
+	}
+	public int getSumRating() {
+		return sumRating;
+	}
+	public void setNumRating(int numRating) {
+		this.numRating = numRating;
+	}
+	public int getNumRating() {
+		return numRating;
+	}
+	@Override
+	public boolean equals(Object o) {
+		if (o instanceof Tool) {
+			Tool t = (Tool) o;
+			return t.name.equals(this.name) && t.id == this.id;
+		}
+		return false;
+	}
+
+	@Override
+	public int hashCode() {
+		return name.hashCode();
+	}
+
+	@Override
+	public String toString() {
+		return getName();
+	}
+
+	@Transient
+	public void updateRatingCache()
+	{
+		//TODO make this called automatically on save of ratings?
+		int numRating =0;
+		int totalRating =0;
+		for(ToolRating tr : getRatings())
+		{
+			numRating++;
+			totalRating += tr.getRating();
+		}
+		setNumRating(numRating);
+		setSumRating(totalRating);
+	}
+	@Transient
+	public double getOverallRating() {
+		if(getNumRating() == 0)
+			return 0;
+		else
+			return (double) getSumRating() / (double) getNumRating();
+	}
+	@Transient
+	public void incrementUsageCount() {
+		setUsageCount(getUsageCount() + 1);
+	}
+
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
new file mode 100644
index 0000000..e9ee63f
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
@@ -0,0 +1,62 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class ToolComment implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -3122267726128323333L;
+	private int id;
+	private String comment;
+	private User creator;
+	private java.util.Date createdAt;
+	private Tool tool;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getComment() {
+		return comment;
+	}
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+
+	@ManyToOne
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+
+	@ManyToOne
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
new file mode 100644
index 0000000..f7a6011
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
@@ -0,0 +1,60 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class ToolRating implements Serializable{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 2013611574000236034L;
+	private int id;
+	private User creator;
+	private int rating;
+	private Tool tool;
+	private Date createdAt;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+	public int getRating() {
+		return rating;
+	}
+	public void setRating(int rating) {
+		this.rating = rating;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
new file mode 100644
index 0000000..e8458a3
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
@@ -0,0 +1,95 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+@Entity
+public class Transaction implements Serializable {
+
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -4341632811573425064L;
+	private int id;
+	private String clientID;
+	private String hostname;
+	private java.util.Date date;
+	private User user;
+	private List<AnalysisEvent> analysisEvents;
+	private String dataSetName;
+	private Workflow workflow;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getClientID() {
+		return clientID;
+	}
+	public void setClientID(String clientID) {
+		this.clientID = clientID;
+	}
+	public String getHostname() {
+		return hostname;
+	}
+	public void setHostname(String hostname) {
+		this.hostname = hostname;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getDate() {
+		return date;
+	}
+	public void setDate(java.util.Date date) {
+		this.date = date;
+	}
+	public User getUser() {
+		return user;
+	}
+	public void setUser(User user) {
+		this.user = user;
+	}
+
+	@OneToMany(mappedBy="transaction")
+	public List<AnalysisEvent> getAnalysisEvents() {
+		return analysisEvents;
+	}
+	public void setAnalysisEvents(List<AnalysisEvent> analysisEvents) {
+		this.analysisEvents = analysisEvents;
+	}
+
+	public String getDataSetName() {
+		return dataSetName;
+	}
+	public void setDataSetName(String dataSetName) {
+		this.dataSetName = dataSetName;
+	}
+
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+
+	private String userName;
+	@Transient
+	public String getUserName() {
+		return userName;
+	}
+	public void setUserName(String userName) {
+		this.userName = userName;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
new file mode 100644
index 0000000..236fa8d
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
@@ -0,0 +1,491 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Lob;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+
+import org.geworkbench.components.genspace.GenSpaceServerFactory;
+
+@Entity
+@Table(name="registration")
+public class User implements Serializable, Comparable<User>{
+
+	private static final long serialVersionUID = 2972043173442132575L;
+	private int id;
+	private String username;
+	private String password;
+	private String email;
+	private String firstName;
+	private String lastName;
+	private String workTitle;
+	private String phone;
+	private String labAffiliation;
+	private String addr1;
+	private String addr2;
+	private String city;
+	private String state;
+	private String zipcode;
+	private int onlineStatus;
+	private String interests;
+	private int logData;
+	private int dataVisibility;
+	private java.util.Date createdAt;
+	private WorkflowFolder rootFolder;
+
+	private List<Friend> friends = new ArrayList<Friend>();
+	private List<UserNetwork> networks = new ArrayList<UserNetwork>();
+
+	private Set<Workflow> workflows = new HashSet<Workflow>();
+	private List<WorkflowFolder> folders = new ArrayList<WorkflowFolder>();
+	private List<WorkflowComment> workflowComments = new ArrayList<WorkflowComment>();
+	private List<ToolComment> toolComments = new ArrayList<ToolComment>();
+	private List<Transaction> transactions = new ArrayList<Transaction>();
+	private List<IncomingWorkflow> incomingWorkflows = new ArrayList<IncomingWorkflow>();
+	private List<IncomingWorkflow> outgoingWorkflows = new ArrayList<IncomingWorkflow>();
+	private Set<Network> myOwnedNetworks = new HashSet<Network>();
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@Column(length=50, nullable = false)
+	public String getUsername() {
+		return username;
+	}
+	public void setUsername(String username) {
+		this.username = username;
+	}
+
+	@Column(length=50, nullable = false)
+	private String getPassword() {
+		return password;
+	}
+	private void setPassword(String password) {
+		this.password = password;
+	}
+
+	@Column(length=50)
+	public String getEmail() {
+		return email;
+	}
+	public void setEmail(String email) {
+		this.email = email;
+	}
+
+	@Column(name="first_name", length=50, nullable = false)
+	public String getFirstName() {
+		return firstName;
+	}
+	public void setFirstName(String firstName) {
+		this.firstName = firstName;
+	}
+
+	@Column(name="last_name", length=50, nullable = false)
+	public String getLastName() {
+		return lastName;
+	}
+	public void setLastName(String lastName) {
+		this.lastName = lastName;
+	}
+
+	@Column(name="work_title", length=50)
+	public String getWorkTitle() {
+		return workTitle;
+	}
+	public void setWorkTitle(String workTitle) {
+		this.workTitle = workTitle;
+	}
+
+	@Column(length=50)
+	public String getPhone() {
+		return phone;
+	}
+	public void setPhone(String phone) {
+		this.phone = phone;
+	}
+
+	@Column(name="lab_affiliation", length=100, nullable = false)
+	public String getLabAffiliation() {
+		return labAffiliation;
+	}
+	public void setLabAffiliation(String labAffiliation) {
+		this.labAffiliation = labAffiliation;
+	}
+
+	@Column(length=50)
+	public String getAddr1() {
+		return addr1;
+	}
+	public void setAddr1(String addr1) {
+		this.addr1 = addr1;
+	}
+
+	@Column(length=50)
+	public String getAddr2() {
+		return addr2;
+	}
+	public void setAddr2(String addr2) {
+		this.addr2 = addr2;
+	}
+
+	@Column(length=50)
+	public String getCity() {
+		return city;
+	}
+	public void setCity(String city) {
+		this.city = city;
+	}
+
+	@Column(length=50)
+	public String getState() {
+		return state;
+	}
+	public void setState(String state) {
+		this.state = state;
+	}
+
+	@Column(length=7)
+	public String getZipcode() {
+		return zipcode;
+	}
+	public void setZipcode(String zipcode) {
+		this.zipcode = zipcode;
+	}
+
+	@Column(name="online_status")
+	public int getOnlineStatus() {
+		return onlineStatus;
+	}
+	public void setOnlineStatus(int onlineStatus) {
+		this.onlineStatus = onlineStatus;
+	}
+
+	@Lob
+	public String getInterests() {
+		return interests;
+	}
+	public void setInterests(String interests) {
+		this.interests = interests;
+	}
+
+	public int getLogData() {
+		return logData;
+	}
+	public void setLogData(int logData) {
+		this.logData = logData;
+	}
+	public int getDataVisibility() {
+		return dataVisibility;
+	}
+	public void setDataVisibility(int dataVisibility) {
+		this.dataVisibility = dataVisibility;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+
+	@OneToMany(mappedBy="leftUser")
+	public List<Friend> getFriends() {
+		return friends;
+	}
+	public void setFriends(List<Friend> friends) {
+		this.friends = friends;
+	}
+	@OneToMany(mappedBy="user")
+	public List<UserNetwork> getNetworks() {
+		return networks;
+	}
+	public void setNetworks(List<UserNetwork> networks) {
+		this.networks = networks;
+	}
+
+	@OneToMany(mappedBy="creator")
+	public Set<Workflow> getWorkflows() {
+		return workflows;
+	}
+	public void setWorkflows(Set<Workflow> workflows) {
+		this.workflows = workflows;
+	}
+
+	@OneToMany(mappedBy="owner")
+	public List<WorkflowFolder> getFolders() {
+		return folders;
+	}
+	public void setFolders(List<WorkflowFolder> folders) {
+		this.folders = folders;
+	}
+
+	@OneToMany(mappedBy="creator")
+	public List<WorkflowComment> getWorkflowComments() {
+		return workflowComments;
+	}
+	public void setWorkflowComments(List<WorkflowComment> workflowComments) {
+		this.workflowComments = workflowComments;
+	}
+
+	@OneToMany(mappedBy="creator")
+	public List<ToolComment> getToolComments() {
+		return toolComments;
+	}
+	public void setToolComments(List<ToolComment> toolComments) {
+		this.toolComments = toolComments;
+	}
+
+	@OneToMany(mappedBy="user")
+	public List<Transaction> getTransactions() {
+		return transactions;
+	}
+	public void setTransactions(List<Transaction> transactions) {
+		this.transactions = transactions;
+	}
+
+	@OneToMany(mappedBy="receiver")
+	public List<IncomingWorkflow> getIncomingWorkflows() {
+		return incomingWorkflows;
+	}
+	public void setIncomingWorkflows(List<IncomingWorkflow> incomingWorkflows) {
+		this.incomingWorkflows = incomingWorkflows;
+	}
+
+	@OneToMany(mappedBy="sender")
+	public List<IncomingWorkflow> getOutgoingWorkflows() {
+		return outgoingWorkflows;
+	}
+	public void setOutgoingWorkflows(List<IncomingWorkflow> outgoingWorkflows) {
+		this.outgoingWorkflows = outgoingWorkflows;
+	}
+
+
+	@OneToMany(mappedBy="owner")
+	public Set<Network> getMyOwnedNetworks() {
+		return myOwnedNetworks;
+	}
+	public void setMyOwnedNetworks(Set<Network> myOwnedNetworks) {
+		this.myOwnedNetworks = myOwnedNetworks;
+	}
+
+	public WorkflowFolder getRootFolder() {
+		return rootFolder;
+	}
+	public void setRootFolder(WorkflowFolder rootFolder) {
+		this.rootFolder = rootFolder;
+	}
+
+	@Override
+	public String toString() {
+		String result = "User [" + username+"]";
+		return result;
+	}
+
+	public void setPasswordClearText(String password)
+	{
+		this.setPassword(this.getEncryptedPassword(password.toCharArray()));
+
+	}
+
+	public boolean passwordMatches(String password)
+	{
+		return this.getEncryptedPassword(password.toCharArray()).equals(this.getPassword());
+	}
+
+	@Override
+	public int hashCode() {
+		return this.getId();
+	}
+	@Override
+	public boolean equals(Object obj) {
+		if(obj instanceof User)
+		{
+			return ((User) obj).getId() == this.getId();
+		}
+		return false;
+	}
+
+	protected final static String HEX_DIGITS = "0123456789abcdef";
+
+	/**
+	 * This method is used to encrypt the password using SHA encryption.
+	 *
+	 * @param password
+	 *            represents the password to be encrypted
+	 * @return returns password in encrypted form
+	 */
+	private String getEncryptedPassword(char[] c_password) {
+		String plaintext = new String(c_password);
+
+		java.security.MessageDigest d =null;
+				try {
+					d = java.security.MessageDigest.getInstance("SHA-1");
+				} catch (NoSuchAlgorithmException e) {
+					GenSpaceServerFactory.logger.error("Error",e);
+				}
+				d.reset();
+				d.update(plaintext.getBytes());
+				byte[] hashedBytes =  d.digest();
+				StringBuffer sb = new StringBuffer(hashedBytes.length * 2);
+		        for (int i = 0; i < hashedBytes.length; i++) {
+		             int b = hashedBytes[i] & 0xFF;
+		             sb.append(HEX_DIGITS.charAt(b >>> 4)).append(HEX_DIGITS.charAt(b & 0xF));
+		        }
+		        return sb.toString();
+	}
+	@Transient
+	public String getFullName() {
+		return this.getFirstName() + " " + this.getLastName();
+	}
+	@Transient
+	public Friend isFriendsWith(User u) {
+		for(Friend f: getFriends())
+		{
+			if(f.getRightUser().equals(u))
+			{
+				setFriends(true);
+				return f;
+			}
+		}
+		setFriends(false);
+		return null;
+	}
+	@Transient
+	public UserNetwork isInNetwork(Network n) {
+		for(UserNetwork un : getNetworks())
+		{
+			if(un.getNetwork().equals(n))
+				return un;
+		}
+		return null;
+	}
+	@Transient
+	private boolean isVisibleTo(User other)
+	{
+		Friend f = isFriendsWith(other);
+		if(f != null && f.isVisible())
+		{
+			return true;
+		}
+		//Check the networks
+		for(UserNetwork u1 : this.getNetworks())
+		{
+			if(u1.isVisible())
+				for(UserNetwork u2 : other.getNetworks())
+				{
+					if(u2.getNetwork().equals(u1.getNetwork()))
+						return true;
+				}
+		}
+		return false;
+	}
+	@Transient
+	private String na(String s)
+	{
+		return (s == null || s.length() == 0 ? "N/A" : s);
+	}
+	@Transient
+	public String getFullNameWUsername()
+	{
+		if(getFirstName().length() == 0 && getLastName().length() ==0)
+			return getUsername();
+		else
+			return getFirstName() + " "
+			+ getLastName() + " (" + getUsername() + ")";
+	}
+
+	public String toHTML() {
+		String r = "<html><body><b>" +getFullNameWUsername() + "</b><br>";
+		if (GenSpaceServerFactory.isVisible(this)) {
+			r += "<i>"
+					+ (getWorkTitle() != null
+							&& getWorkTitle() != "" ? getWorkTitle() + " at " : "")
+					+ (getLabAffiliation() != null ? getLabAffiliation():  " (affiliation not disclosed)") + "</i><br><br>";
+			r += "<b>Research Interests:</b><br />"
+					+(getInterests() == null ? "(not disclosed)" : getInterests()) + "<br><br>";
+			r += "<b>Contact information:</b><br /><br>Phone: "
+					+ na(getPhone()) + "<br>Email: "
+					+ na(getEmail()) + "<br><br>Mailing Address:<br>"
+					+ (getAddr1().length() == 0 && getAddr2().length() == 00 && getCity().length() == 0 && getState().length() == 0 && getZipcode().length() == 0 ? "not provided" :
+						 na(getAddr1()) + "<br>" + na(getAddr2())
+					+ "<br>" + na(getCity()) + ", "
+					+ na(getState()) + ", " + na(getZipcode()));
+		} else {
+			r += "This user is not visible to you. Please add them as a friend or join one of their networks to see their profile.";
+		}
+		r += "</body>";
+		r += "</html>";
+		return r;
+	}
+	@Transient
+	public String getShortName() {
+		if(getFirstName() != null && !getFirstName().equals(""))
+			return getFirstName();
+		return getUsername();
+	}
+	@Transient
+	public List<User> getFriendsProfiles() {
+		ArrayList<User> ret = new ArrayList<User>();
+		for(Friend f: getFriends())
+			ret.add(f.getRightUser());
+		return ret;
+	}
+	@Transient
+	public boolean containsFolderByName(String folderName) {
+		for(WorkflowFolder f : getFolders())
+			if(f.getName().equals(folderName))
+				return true;
+		return false;
+	}
+	@Override
+	public int compareTo(User o) {
+		int r = this.getLastName().compareTo(o.getLastName());
+		if(r == 0)
+			return this.getFirstName().compareTo(o.getFirstName());
+		return r;
+	}
+	@Transient
+	public User loadVisibility(User from) {
+		setVisible(isVisibleTo(from));
+		return this;
+	}
+
+
+	private boolean isVisible;
+	@Transient
+	public boolean isVisible() {
+		return isVisible;
+	}
+	public void setVisible(boolean isVisible) {
+		this.isVisible = isVisible;
+	}
+	private boolean isFriends;
+	@Transient
+	public boolean isFriends() {
+		return isFriends;
+	}
+	public void setFriends(boolean isFriends) {
+		this.isFriends = isFriends;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
new file mode 100644
index 0000000..3f0ef41
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
@@ -0,0 +1,71 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+@Entity
+@Table(name="User_Network")
+public class UserNetwork implements Serializable {
+
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 2587552459317296299L;
+	private int id;
+	private User user;
+	private Network network;
+	private boolean verified;
+	private boolean visible;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="user_id")
+	public User getUser() {
+		return user;
+	}
+	public void setUser(User user) {
+		this.user = user;
+	}
+
+	@ManyToOne
+	@JoinColumn(name="network_id")
+	public Network getNetwork() {
+		return network;
+	}
+	public void setNetwork(Network network) {
+		this.network = network;
+	}
+
+	public boolean isVerified() {
+		return verified;
+	}
+	public void setVerified(boolean verified) {
+		this.verified = verified;
+	}
+	public boolean isVisible() {
+		return visible;
+	}
+	public void setVisible(boolean visible) {
+		this.visible = visible;
+	}
+	@Override
+	public String toString() {
+		return "UserNetwork [user = {"+user.toString()+"}, network={"+network.toString()+"}, visible="+(isVisible() ? "true" : "false")+"]";
+	}
+
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
new file mode 100644
index 0000000..b062f90
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
@@ -0,0 +1,95 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+
+@Entity
+public class UserWorkflow implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -6313031043276205912L;
+	private int id;
+	private User owner;
+	private Workflow workflow;
+	private String name;
+	private Date createdAt;
+	private WorkflowFolder folder;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	@ManyToOne
+	public User getOwner() {
+		return owner;
+	}
+	public void setOwner(User owner) {
+		this.owner = owner;
+	}
+
+	@ManyToOne(fetch = FetchType.EAGER)
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	@Temporal(TemporalType.TIMESTAMP)
+	public Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public WorkflowFolder getFolder() {
+		return folder;
+	}
+	public void setFolder(WorkflowFolder folder) {
+		this.folder = folder;
+	}
+	@Override
+	public String toString() {
+		return "UserWorkflow - name: " + name + ", " + owner.getUsername() + ", "
+				+ workflow;
+	}
+	@Override
+	public int hashCode() {
+		return this.getId();
+	}
+	@Override
+	public boolean equals(Object o) {
+		if(o == null)
+			return false;
+		try {
+			UserWorkflow uw = (UserWorkflow) o;
+			return owner.equals(uw.owner) && workflow.equals(uw.workflow);
+		} catch (ClassCastException e) {
+			e.printStackTrace();
+		}
+		return false;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
new file mode 100644
index 0000000..5e28dfb
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
@@ -0,0 +1,273 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import javax.persistence.Transient;
+
+import org.geworkbench.components.genspace.RuntimeEnvironmentSettings;
+
+@Entity
+public class Workflow implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -344401848390541281L;
+	private int id;
+	private User creator;
+	private java.util.Date createdAt;
+	private Transaction creationTransaction;
+	private	List<WorkflowTool> tools = new ArrayList<WorkflowTool>();
+	private List<WorkflowComment> comments = new ArrayList<WorkflowComment>();
+	private List<WorkflowRating> ratings = new ArrayList<WorkflowRating>();
+	private int usageCount;
+	private Workflow parent;
+	private List<Workflow> children;
+
+	private int numRating = 0;
+	private int sumRating = 0;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+
+	@OneToOne(fetch=FetchType.LAZY)
+	public Transaction getCreationTransaction() {
+		return creationTransaction;
+	}
+	public void setCreationTransaction(Transaction creationTransaction) {
+		this.creationTransaction = creationTransaction;
+	}
+
+	@OneToMany(mappedBy="workflow")
+	@OrderBy("order ASC")
+	public List<WorkflowTool> getTools() {
+		return tools;
+	}
+	public void setTools(List<WorkflowTool> tools) {
+		this.tools = tools;
+	}
+
+	@OneToMany(mappedBy="parent")
+	public List<Workflow> getChildren() {
+		return children;
+	}
+	public void setChildren(List<Workflow> children) {
+		this.children = children;
+	}
+	@OneToMany(mappedBy="workflow")
+	public List<WorkflowComment> getComments() {
+		return comments;
+	}
+	public void setComments(List<WorkflowComment> comments) {
+		this.comments = comments;
+	}
+
+	@OneToMany(mappedBy="workflow")
+	public List<WorkflowRating> getRatings() {
+		return ratings;
+	}
+	public void setRatings(List<WorkflowRating> ratings) {
+		this.ratings = ratings;
+	}
+	public int getUsageCount() {
+		return usageCount;
+	}
+	public void setUsageCount(int usageCount) {
+		this.usageCount = usageCount;
+	}
+	@Transient
+	public double getAvgRating() {
+		double result = 0;
+		if (ratings.size() > 0) {
+			for (WorkflowRating r : ratings) {
+				result += r.getRating();
+			}
+			result /= ratings.size();
+		}
+		return result;
+	}
+
+	@Override
+	public String toString() {
+		String r = "";
+		for(WorkflowTool wt : getTools())
+		{
+			r += wt.getTool().getName() + ", ";
+		}
+		if(r.length() > 2)
+			r = r.substring(0,r.length()-2);
+		return r;
+	}
+
+	@OneToOne(fetch=FetchType.LAZY)
+	public Workflow getParent() {
+		return parent;
+	}
+	public void setParent(Workflow parent) {
+		this.parent = parent;
+	}
+	public int getNumRating() {
+		return numRating;
+	}
+	public void setNumRating(int numRating) {
+		this.numRating = numRating;
+	}
+	public int getSumRating() {
+		return sumRating;
+	}
+	public void setSumRating(int sumRating) {
+		this.sumRating = sumRating;
+	}
+
+	@Transient
+	public void updateRatingsCache()
+	{
+		//TODO make this called automatically
+		int numRating =0;
+		int totalRating =0;
+		for(WorkflowRating tr : getRatings())
+		{
+			numRating++;
+			totalRating += tr.getRating();
+		}
+		setNumRating(numRating);
+		setSumRating(totalRating);
+	}
+	@Transient
+	public Tool getLastTool()
+	{
+		return this.getTools().get(this.getTools().size() -1).getTool();
+	}
+	@Transient
+	public String getLastToolName()
+	{
+		return this.getLastTool().getName();
+	}
+	@Transient
+	public double getOverallRating() {
+		if(getNumRating() == 0)
+			return 0;
+		else
+			return (double) getSumRating() / (double) getNumRating();
+	}
+	@Transient
+	public void loadToolsFromCache()
+	{
+		if(getToolIds() != null && RuntimeEnvironmentSettings.tools != null)
+		{
+			ArrayList<WorkflowTool> ret = new ArrayList<WorkflowTool>();
+			int j = 1;
+			for(int i : getToolIds())
+			{
+				WorkflowTool t = new WorkflowTool();
+				t.setOrder(j);
+				t.setTool(RuntimeEnvironmentSettings.tools.get(i));
+				t.setWorkflow(this);
+				ret.add(t);
+				j++;
+			}
+			tools = ret;
+		}
+	}
+	private int[] toolIds = null;
+	@Transient
+	public int[] getToolIds() {
+		return toolIds;
+	}
+	public void setToolIds(int[] toolIds) {
+		this.toolIds = toolIds;
+	}
+
+	private int cachedParentId = -1;
+	@Transient
+	public int getCachedParentId() {
+		return cachedParentId;
+	}
+	public void setCachedParentId(int cachedParentId) {
+		this.cachedParentId = cachedParentId;
+	}
+
+	private int cachedChildrenCount;
+	@Transient
+	public int getCachedChildrenCount() {
+		return cachedChildrenCount;
+	}
+	public void setCachedChildrenCount(int cachedChildrenCount) {
+		this.cachedChildrenCount = cachedChildrenCount;
+	}
+	@Transient
+	public Workflow slimDown()
+	{
+		Workflow w = new Workflow();
+		w.setId(this.getId());
+		w.setRatings(this.getRatings());
+		int[] temp = new int[getTools().size()];
+    	for(WorkflowTool t : getTools())
+    	{
+    		temp[t.getOrder()-1] = t.getTool().getId();
+    	}
+    	getRatings().size();
+    	w.setRatings(getRatings());
+		w.setToolIds(temp);
+		w.setComments(getComments());
+		w.setUsageCount(getUsageCount());
+		w.setNumRating(getNumRating());
+		w.setSumRating(getSumRating());
+		w.setCreator(getCreator());
+		if(getCachedParentId() < 0 && getParent() != null)
+			w.setCachedParentId(getParent().getId());
+		return w;
+	}
+
+	@Transient
+	public Workflow slimDownTiny()
+	{
+		Workflow w = new Workflow();
+		w.setId(this.getId());
+		w.setRatings(this.getRatings());
+		int[] temp = new int[getTools().size()];
+    	for(WorkflowTool t : getTools())
+    	{
+    		temp[t.getOrder()-1] = t.getTool().getId();
+    	}
+		w.setToolIds(temp);
+		w.setUsageCount(getUsageCount());
+		w.setNumRating(getNumRating());
+		w.setSumRating(getSumRating());
+		if(getCachedParentId() < 0 && getParent() != null)
+			w.setCachedParentId(getParent().getId());
+		return w;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
new file mode 100644
index 0000000..3923dc3
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
@@ -0,0 +1,67 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class WorkflowComment implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 8507652685971547757L;
+	private int id;
+	private String comment;
+	private User creator;
+	private java.util.Date createdAt;
+	private Workflow workflow;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public String getComment() {
+		return comment;
+	}
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+
+	@ManyToOne
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public java.util.Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(java.util.Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+
+	@Override
+	public String toString() {
+		return "WorkflowComment - username: " + creator.getUsername() + ", postedOn: "
+				+ createdAt.toString() + ", comment: " + comment;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
new file mode 100644
index 0000000..f11b815
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
@@ -0,0 +1,87 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+
+@Entity
+public class WorkflowFolder implements Serializable, Comparable<WorkflowFolder>{
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -1365608467302705177L;
+	private int id;
+	private User owner;
+	private String name;
+	private WorkflowFolder parent;
+	private List<UserWorkflow> workflows = new ArrayList<UserWorkflow>();
+
+	private List<WorkflowFolder> children = new ArrayList<WorkflowFolder>();
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public User getOwner() {
+		return owner;
+	}
+	public void setOwner(User ownerId) {
+		this.owner = ownerId;
+	}
+	public String getName() {
+		return name;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	@OneToMany(mappedBy="parent")
+	public List<WorkflowFolder> getChildren(){
+		return children;
+	}
+	public void setChildren(List<WorkflowFolder> children) {
+		this.children = children;
+	}
+	@ManyToOne
+	public WorkflowFolder getParent() {
+		return parent;
+	}
+	public void setParent(WorkflowFolder parent) {
+		this.parent = parent;
+	}
+	@Override
+	public int compareTo(WorkflowFolder o) {
+		return this.getName().compareTo(o.getName());
+	}
+	@OneToMany(mappedBy="folder")
+	public List<UserWorkflow> getWorkflows() {
+		return workflows;
+	}
+	public void setWorkflows(List<UserWorkflow> workflows) {
+		this.workflows = workflows;
+	}
+	@Override
+	public String toString() {
+		return this.getName();
+	}
+	@Override
+	public boolean equals(Object obj) {
+		if(obj instanceof WorkflowFolder)
+			return ((WorkflowFolder) obj).getId() == getId();
+		return false;
+	}
+	@Override
+	public int hashCode() {
+		return new Integer(id).hashCode();
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
new file mode 100644
index 0000000..93cc6b4
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
@@ -0,0 +1,59 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+@Entity
+public class WorkflowRating implements Serializable {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 763395791318191799L;
+	private int id;
+	private User creator;
+	private int rating;
+	private Date createdAt;
+	private Workflow workflow;
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public User getCreator() {
+		return creator;
+	}
+	public void setCreator(User creator) {
+		this.creator = creator;
+	}
+	public int getRating() {
+		return rating;
+	}
+	public void setRating(int rating) {
+		this.rating = rating;
+	}
+	@Temporal(TemporalType.TIMESTAMP)
+	public Date getCreatedAt() {
+		return createdAt;
+	}
+	public void setCreatedAt(Date createdAt) {
+		this.createdAt = createdAt;
+	}
+	@ManyToOne
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
new file mode 100644
index 0000000..974f328
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
@@ -0,0 +1,53 @@
+package org.geworkbench.components.genspace.entity;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+@Entity
+public class WorkflowTool implements Serializable{
+
+	private static final long serialVersionUID = 256557429649076135L;
+	private Workflow workflow;
+	private Tool tool;
+	private int id;
+	private int order;
+
+	@Id
+	@GeneratedValue(strategy=GenerationType.IDENTITY)
+	public int getId() {
+		return id;
+	}
+	public void setId(int id) {
+		this.id = id;
+	}
+	public Workflow getWorkflow() {
+		return workflow;
+	}
+	public void setWorkflow(Workflow workflow) {
+		this.workflow = workflow;
+	}
+	public Tool getTool() {
+		return tool;
+	}
+	public void setTool(Tool tool) {
+		this.tool = tool;
+	}
+	@Column(name="CARDINALITY")
+	public int getOrder() {
+		return order;
+	}
+	public void setOrder(int order) {
+		this.order = order;
+	}
+	@Override
+	public String toString() {
+		return tool.toString();
+	}
+
+}
+
\ No newline at end of file
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java b/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEventParameter.java b/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEventParameter.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Friend.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Friend.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/IncomingWorkflow.java b/genspace-common/src/org/geworkbench/components/genspace/entity/IncomingWorkflow.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/LazyCycleBreaker.java b/genspace-common/src/org/geworkbench/components/genspace/entity/LazyCycleBreaker.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/LogAction.java b/genspace-common/src/org/geworkbench/components/genspace/entity/LogAction.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Network.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Network.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Setting.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Setting.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/TasteUser.java b/genspace-common/src/org/geworkbench/components/genspace/entity/TasteUser.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/ToolComment.java b/genspace-common/src/org/geworkbench/components/genspace/entity/ToolComment.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/ToolRating.java b/genspace-common/src/org/geworkbench/components/genspace/entity/ToolRating.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Transaction.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Transaction.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/UsageEvent.java b/genspace-common/src/org/geworkbench/components/genspace/entity/UsageEvent.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/User.java b/genspace-common/src/org/geworkbench/components/genspace/entity/User.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/UserNetwork.java b/genspace-common/src/org/geworkbench/components/genspace/entity/UserNetwork.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/UserWorkflow.java b/genspace-common/src/org/geworkbench/components/genspace/entity/UserWorkflow.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Workflow.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Workflow.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowComment.java b/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowComment.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowFolder.java b/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowFolder.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowRating.java b/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowRating.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowTool.java b/genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowTool.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/xxxjaxb.properties b/genspace-common/src/org/geworkbench/components/genspace/entity/xxxjaxb.properties
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/FriendFacadeRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/FriendFacadeRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/NetworkFacadeRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/NetworkFacadeRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/PublicFacadeRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/PublicFacadeRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/ToolInformationProvider.java b/genspace-common/src/org/geworkbench/components/genspace/server/ToolInformationProvider.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/UsageInformationRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/UsageInformationRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/UserFacadeRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/UserFacadeRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/WorkflowRepositoryRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/WorkflowRepositoryRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/task/ManualRunnerRemote.java b/genspace-common/src/org/geworkbench/components/genspace/server/task/ManualRunnerRemote.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/task/Test.java b/genspace-common/src/org/geworkbench/components/genspace/server/task/Test.java
old mode 100755
new mode 100644
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainerLocal.java b/genspace-common/src/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainerLocal.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/.classpath b/genspace-ejb/.classpath
old mode 100755
new mode 100644
diff --git a/genspace-ejb/.gitignore b/genspace-ejb/.gitignore
old mode 100755
new mode 100644
diff --git a/genspace-ejb/.project b/genspace-ejb/.project
old mode 100755
new mode 100644
diff --git a/genspace-ejb/.settings/org.eclipse.jdt.core.prefs b/genspace-ejb/.settings/org.eclipse.jdt.core.prefs
new file mode 100644
index 0000000..75aac73
--- /dev/null
+++ b/genspace-ejb/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,8 @@
+#Tue Feb 01 11:50:13 EST 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6
diff --git a/genspace-ejb/.settings/org.eclipse.wst.common.component b/genspace-ejb/.settings/org.eclipse.wst.common.component
new file mode 100644
index 0000000..ad6d2f1
--- /dev/null
+++ b/genspace-ejb/.settings/org.eclipse.wst.common.component
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="genspace-ejb">
+        <wb-resource deploy-path="/" source-path="/ejbModule"/>
+        <property name="java-output-path" value="/genspace-ejb/build/classes"/>
+        <property name="ClientProject" value="genspace-ejbClient"/>
+        <property name="ClientJARURI" value="genspace-ejbClient.jar"/>
+    </wb-module>
+</project-modules>
diff --git a/genspace-ejb/.settings/org.eclipse.wst.common.project.facet.core.xml b/genspace-ejb/.settings/org.eclipse.wst.common.project.facet.core.xml
new file mode 100644
index 0000000..3e5b5da
--- /dev/null
+++ b/genspace-ejb/.settings/org.eclipse.wst.common.project.facet.core.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <runtime name="GlassFish v3 Java EE 6"/>
+  <fixed facet="java"/>
+  <fixed facet="jst.ejb"/>
+  <installed facet="java" version="1.6"/>
+  <installed facet="jst.ejb" version="3.1"/>
+  <installed facet="sun.facet" version="9"/>
+</faceted-project>
diff --git a/genspace-ejb/INSTALL.txt b/genspace-ejb/INSTALL.txt
old mode 100755
new mode 100644
diff --git a/genspace-ejb/NOTES b/genspace-ejb/NOTES
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/.classpath b/genspace-ejb/bin/.classpath
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/.project b/genspace-ejb/bin/.project
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/.settings/org.eclipse.jdt.core.prefs b/genspace-ejb/bin/.settings/org.eclipse.jdt.core.prefs
new file mode 100644
index 0000000..238557c
--- /dev/null
+++ b/genspace-ejb/bin/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,12 @@
+#Sat Jul 30 21:05:48 EDT 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6
diff --git a/genspace-ejb/bin/.settings/org.eclipse.jst.j2ee.ejb.annotations.xdoclet.prefs b/genspace-ejb/bin/.settings/org.eclipse.jst.j2ee.ejb.annotations.xdoclet.prefs
new file mode 100644
index 0000000..fe37bcd
--- /dev/null
+++ b/genspace-ejb/bin/.settings/org.eclipse.jst.j2ee.ejb.annotations.xdoclet.prefs
@@ -0,0 +1,6 @@
+#Sat Jul 30 21:38:24 EDT 2011
+XDOCLETBUILDERACTIVE=true
+XDOCLETHOME=
+XDOCLETUSEGLOBAL=true
+XDOCLETVERSION=1.2.1
+eclipse.preferences.version=1
diff --git a/genspace-ejb/bin/.settings/org.eclipse.ltk.core.refactoring.prefs b/genspace-ejb/bin/.settings/org.eclipse.ltk.core.refactoring.prefs
new file mode 100644
index 0000000..7b7f528
--- /dev/null
+++ b/genspace-ejb/bin/.settings/org.eclipse.ltk.core.refactoring.prefs
@@ -0,0 +1,3 @@
+#Sat Jul 30 21:38:24 EDT 2011
+eclipse.preferences.version=1
+org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false
diff --git a/genspace-ejb/bin/.settings/org.eclipse.wst.common.component b/genspace-ejb/bin/.settings/org.eclipse.wst.common.component
new file mode 100644
index 0000000..aa8e5af
--- /dev/null
+++ b/genspace-ejb/bin/.settings/org.eclipse.wst.common.component
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="genspace-ejb">
+        <wb-resource deploy-path="/" source-path="/"/>
+        <property name="java-output-path" value="/genspace-ejb/build/classes"/>
+        <property name="ClientProject" value="genspace-ejbClient"/>
+        <property name="ClientJARURI" value="genspace-ejbClient.jar"/>
+    </wb-module>
+</project-modules>
diff --git a/genspace-ejb/bin/.settings/org.eclipse.wst.common.project.facet.core.xml b/genspace-ejb/bin/.settings/org.eclipse.wst.common.project.facet.core.xml
new file mode 100644
index 0000000..d821ec7
--- /dev/null
+++ b/genspace-ejb/bin/.settings/org.eclipse.wst.common.project.facet.core.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <runtime name="GlassFish 3.1"/>
+  <fixed facet="java"/>
+  <fixed facet="jst.ejb"/>
+  <installed facet="java" version="1.6"/>
+  <installed facet="jst.ejb" version="3.1"/>
+  <installed facet="sun.facet" version="9"/>
+</faceted-project>
diff --git a/genspace-ejb/bin/.settings/org.eclipse.wst.ws.service.policy.prefs b/genspace-ejb/bin/.settings/org.eclipse.wst.ws.service.policy.prefs
new file mode 100644
index 0000000..a3f7d65
--- /dev/null
+++ b/genspace-ejb/bin/.settings/org.eclipse.wst.ws.service.policy.prefs
@@ -0,0 +1,3 @@
+#Sat Jul 30 21:38:24 EDT 2011
+eclipse.preferences.version=1
+org.eclipse.wst.ws.service.policy.projectEnabled=false
diff --git a/genspace-ejb/bin/INSTALL.txt b/genspace-ejb/bin/INSTALL.txt
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/NOTES b/genspace-ejb/bin/NOTES
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/MANIFEST.MF b/genspace-ejb/bin/build/classes/META-INF/MANIFEST.MF
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/ejb-jar.xml b/genspace-ejb/bin/build/classes/META-INF/ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/login.conf b/genspace-ejb/bin/build/classes/META-INF/login.conf
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/mysql-resource.xml b/genspace-ejb/bin/build/classes/META-INF/mysql-resource.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/persistence.xml b/genspace-ejb/bin/build/classes/META-INF/persistence.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/sun-application.xml b/genspace-ejb/bin/build/classes/META-INF/sun-application.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/build/classes/META-INF/sun-ejb-jar.xml b/genspace-ejb/bin/build/classes/META-INF/sun-ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/MANIFEST.MF b/genspace-ejb/bin/ejbModule/META-INF/MANIFEST.MF
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/ejb-jar.xml b/genspace-ejb/bin/ejbModule/META-INF/ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/login.conf b/genspace-ejb/bin/ejbModule/META-INF/login.conf
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/mysql-resource.xml b/genspace-ejb/bin/ejbModule/META-INF/mysql-resource.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/persistence.xml b/genspace-ejb/bin/ejbModule/META-INF/persistence.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/sun-application.xml b/genspace-ejb/bin/ejbModule/META-INF/sun-application.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/ejbModule/META-INF/sun-ejb-jar.xml b/genspace-ejb/bin/ejbModule/META-INF/sun-ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/lib/mahout-core-0.5-job.jar b/genspace-ejb/bin/lib/mahout-core-0.5-job.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/lib/mahout-core-0.5.jar b/genspace-ejb/bin/lib/mahout-core-0.5.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/lib/mahout-math-0.5.jar b/genspace-ejb/bin/lib/mahout-math-0.5.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/bin/lib/mahout-utils-0.5.jar b/genspace-ejb/bin/lib/mahout-utils-0.5.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/build/classes/META-INF/MANIFEST.MF b/genspace-ejb/build/classes/META-INF/MANIFEST.MF
old mode 100755
new mode 100644
diff --git a/genspace-ejb/build/classes/META-INF/ejb-jar.xml b/genspace-ejb/build/classes/META-INF/ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/build/classes/META-INF/login.conf b/genspace-ejb/build/classes/META-INF/login.conf
old mode 100755
new mode 100644
diff --git a/genspace-ejb/build/classes/META-INF/mysql-resource.xml b/genspace-ejb/build/classes/META-INF/mysql-resource.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/build/classes/META-INF/persistence.xml b/genspace-ejb/build/classes/META-INF/persistence.xml
new file mode 100644
index 0000000..e69de29
diff --git a/genspace-ejb/build/classes/META-INF/sun-application.xml b/genspace-ejb/build/classes/META-INF/sun-application.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/build/classes/META-INF/sun-ejb-jar.xml b/genspace-ejb/build/classes/META-INF/sun-ejb-jar.xml
new file mode 100644
index 0000000..e69de29
diff --git a/genspace-ejb/ejbModule/META-INF/MANIFEST.MF b/genspace-ejb/ejbModule/META-INF/MANIFEST.MF
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/META-INF/ejb-jar.xml b/genspace-ejb/ejbModule/META-INF/ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/META-INF/login.conf b/genspace-ejb/ejbModule/META-INF/login.conf
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/META-INF/mysql-resource.xml b/genspace-ejb/ejbModule/META-INF/mysql-resource.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/META-INF/persistence.xml b/genspace-ejb/ejbModule/META-INF/persistence.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/META-INF/sun-application.xml b/genspace-ejb/ejbModule/META-INF/sun-application.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/META-INF/sun-ejb-jar.xml b/genspace-ejb/ejbModule/META-INF/sun-ejb-jar.xml
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/AbstractFacade.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/AbstractFacade.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/FriendFacade.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/FriendFacade.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
old mode 100755
new mode 100644
index 5034e4f..712005e
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
@@ -60,7 +60,7 @@ import org.geworkbench.components.genspace.server.mahout.GenspaceUserSimilarity;
 public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 		implements ToolInformationProvider {

-//	@EJB MahoutRecommenderLocal mahoutBean;
+	@EJB MahoutRecommenderLocal mahoutBean;

 	/*
     @Schedule(minute="0/5",hour="*", persistent=false)
@@ -308,38 +308,35 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 	// Added by efedotov
 	@SuppressWarnings("unchecked")
 	public List<Workflow> getMahoutToolSuggestion(int userId, int filterMethod) {
-		return null;
-//		return mahoutBean.getToolSuggestions(userId, filterMethod);
+		return mahoutBean.getToolSuggestions(userId, filterMethod);
 	}

 	// Added by efedotov
 	@SuppressWarnings("unchecked")
 	public List<TasteUser> getMahoutUserSuggestion(int userId, int filterMethod) {
-		return null;
-//		return mahoutBean.getUserSuggestions(userId, filterMethod);
+		return mahoutBean.getUserSuggestions(userId, filterMethod);
 	}

 	// Added by efedotov
 	@SuppressWarnings("unchecked")
 	@Override
 	public List<Workflow> getMahoutSimilarWorkflowsSuggestion(List<Tool> tools) {
-		return null;
-//		return mahoutBean.getSimilarWorkflows(tools);
+
+		return mahoutBean.getSimilarWorkflows(tools);
 	}

 	// Added by efedotov
 	@SuppressWarnings("unchecked")
 	@Override
 	public List<Workflow> getMahoutUserWorkflowsSuggestion(int userID, int filterMethod) {
-		return null;
-//		return mahoutBean.getSimilarUserWorkflows(userID, filterMethod);
+		return mahoutBean.getSimilarUserWorkflows(userID, filterMethod);
 	}

 	// Added by efedotov
 	@SuppressWarnings("unchecked")
 	@Override
 	public void refreshMahoutRecommender() {
-//		mahoutBean.refresh();
+		mahoutBean.refresh();
 	}

 	@Override
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommenderLocal.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommenderLocal.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/NetworkFacade.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/NetworkFacade.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/PublicFacade.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/PublicFacade.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UserFacade.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UserFacade.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemRecommender.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemRecommender.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemSimilarity.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemSimilarity.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceSimilarWorkflowRecommender.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceSimilarWorkflowRecommender.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/stubs/Tool.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/stubs/Tool.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/ManualRunner.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/ManualRunner.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
old mode 100755
new mode 100644
diff --git a/genspace-ejb/lib/mahout-core-0.5-job.jar b/genspace-ejb/lib/mahout-core-0.5-job.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/lib/mahout-core-0.5.jar b/genspace-ejb/lib/mahout-core-0.5.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/lib/mahout-math-0.5.jar b/genspace-ejb/lib/mahout-math-0.5.jar
old mode 100755
new mode 100644
diff --git a/genspace-ejb/lib/mahout-utils-0.5.jar b/genspace-ejb/lib/mahout-utils-0.5.jar
old mode 100755
new mode 100644