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[Treebase-guts] SF.net SVN: treebase:[200] trunk/oai-pmh_data_provider/data_provider_web
|
From: <yo...@us...> - 2009-10-19 20:30:30
|
Revision: 200
http://treebase.svn.sourceforge.net/treebase/?rev=200&view=rev
Author: youjun
Date: 2009-10-19 20:30:19 +0000 (Mon, 19 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/.classpath
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/index.jsp
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/cxf-servlet.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/decorators.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/dwr.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/menu-config.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/mvs/
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-security.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-validation.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validation.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validator-rules.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/xfire-servlet.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/error-403.jsp
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/error-404.jsp
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/error-500.jsp
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/error.jsp
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/login.jsp
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/logout.jsp
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/FastInfoset-1.2.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/XmlSchema-1.4.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/acegi-security-1.0.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/activation-1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/antlr-2.7.6.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/aopalliance-1.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/c3p0-0.9.1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cglib-nodep-2.1_3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-beanutils-1.7.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-codec-1.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-collections-3.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-digester-1.5.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-fileupload-1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-io-1.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-lang-2.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-validator-1.1.4.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cql-java-1.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-api-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-common-schemas-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-common-utilities-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-bindings-soap-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-bindings-xml-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-core-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-databinding-jaxb-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-frontend-jaxws-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-frontend-simple-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-transports-http-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-transports-http-jetty-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-rt-ws-addr-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/cxf-tools-common-2.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/data_provider_core-0.0.1-SNAPSHOT.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/db2jcc-2.6.80.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/db2jcc_license_cu-2.6.80.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/displaytag-1.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/dom4j-1.6.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/dwr-2.0.rc2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/ehcache-1.2.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/ejb3-persistence-1.0.1.GA.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-activation_1.1_spec-1.0.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-annotation_1.0_spec-1.1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-javamail_1.4_spec-1.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-jaxws_2.1_spec-1.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-servlet_2.5_spec-1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-stax-api_1.0_spec-1.0.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/geronimo-ws-metadata_2.0_spec-1.1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/hibernate-3.2.6.ga.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/hibernate-annotations-3.3.1.GA.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/hibernate-commons-annotations-3.0.0.ga.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/hsqldb-1.7.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/itext-1.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jaxb-api-2.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jaxb-impl-2.1.6.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jaxb-xjc-2.1.6.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jcl104-over-slf4j-1.4.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jdbc-stdext-2.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jdom-1.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jetty-6.1.9.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jetty-util-6.1.9.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jmock-1.0.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jstl-1.1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/jta-1.0.1B.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/mail-1.4.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/neethi-2.0.4.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/oro-2.0.8.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/postgresql-8.3-603.jdbc3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/saaj-api-1.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/saaj-impl-1.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/sitemesh-2.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/slf4j-api-1.4.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/slf4j-log4j12-1.4.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-beans-2.0.8.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-context-2.0.8.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-core-2.0.8.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-web-2.0.8.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/springmodules-validator-0.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/standard-1.1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/string-1.1.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/struts-1.2.9.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/struts-menu-2.3.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/velocity-1.4.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/velocity-dep-1.4.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/wsdl4j-1.6.1.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/wstx-asl-3.2.4.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/xalan-2.7.0.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/xml-apis-1.0.b2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/xml-resolver-1.2.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web.war
trunk/oai-pmh_data_provider/data_provider_web/target/war/
trunk/oai-pmh_data_provider/data_provider_web/target/war/work/
trunk/oai-pmh_data_provider/data_provider_web/target/war/work/webapp-cache.xml
Modified: trunk/oai-pmh_data_provider/data_provider_web/.classpath
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.classpath 2009-10-16 13:26:10 UTC (rev 199)
+++ trunk/oai-pmh_data_provider/data_provider_web/.classpath 2009-10-19 20:30:19 UTC (rev 200)
@@ -4,16 +4,12 @@
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
<classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
</attributes>
</classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk">
- <attributes>
- <attribute name="owner.project.facets" value="jst.java"/>
- </attributes>
- </classpathentry>
<classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.web.container"/>
<classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
<classpathentry kind="output" path="target/classes"/>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<beans default-autowire="no"
+ xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.0.xsd
+ http://www.directwebremoting.org/schema/spring-dwr
+ http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd">
+
+
+ <!-- ========================================================== -->
+ <!-- LIST OF DWR beans/methods -->
+ <!-- ========================================================== -->
+
+
+ <bean id="remoteSoftwareNameService" class="org.cipres.treebase.dao.study.AnalysisStepDAO">
+ <dwr:remote javascript="RemoteSoftwareNameService">
+ <dwr:include method="findCompleteSoftwareName" />
+ </dwr:remote>
+ <property name="sessionFactory"><ref bean="sessionFactory"></ref></property>
+ </bean>
+
+ <bean id="remotePersonService" class="org.cipres.treebase.dao.admin.PersonDAO">
+ <dwr:remote javascript="RemotePersonService">
+ <dwr:include method="findCompleteEmailAddress" />
+ </dwr:remote>
+ <property name="sessionFactory"><ref bean="sessionFactory"></ref></property>
+ </bean>
+
+ <bean id="remoteJournalNameService" class="org.cipres.treebase.dao.study.CitationDAO">
+ <dwr:remote javascript="RemoteJournalNameService">
+ <dwr:include method="findCompleteJournalName" />
+ </dwr:remote>
+ <property name="sessionFactory"><ref bean="sessionFactory"></ref></property>
+ </bean>
+
+ <bean id="remoteUniqueOtherAlgorithmService" class="org.cipres.treebase.dao.study.AlgorithmDAO">
+ <dwr:remote javascript="RemoteUniqueOtherAlgorithmService">
+ <dwr:include method="findAllUniqueOtherAlgorithmDescriptions" />
+ </dwr:remote>
+ <property name="sessionFactory"><ref bean="sessionFactory"></ref></property>
+ </bean>
+
+ <bean id="remoteAjaxProgressListener" class="org.cipres.treebase.web.controllers.AjaxProgressListener">
+ <dwr:remote javascript="RemoteAjaxProgressListener">
+ <dwr:include method="getStatus"/>
+ </dwr:remote>
+ </bean>
+ <dwr:configuration>
+ <dwr:convert type="bean" class="org.cipres.treebase.web.model.UploadInfoBean"/>
+ </dwr:configuration>
+
+</beans>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/cxf-servlet.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/cxf-servlet.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/cxf-servlet.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,30 @@
+
+
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:jaxws="http://cxf.apache.org/jaxws"
+ xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
+http://cxf.apache.org/jaxws http://cxf.apache.org/schemas/jaxws.xsd">
+
+ <import resource="classpath:META-INF/cxf/cxf.xml" />
+ <import resource="classpath:META-INF/cxf/cxf-extension-soap.xml" />
+ <import resource="classpath:META-INF/cxf/cxf-servlet.xml" />
+
+<!--
+ <jaxws:endpoint
+ id="searchStudiesByKeyword"
+ implementor="org.cipres.treebase.web.webservices.StudyServiceByKeywordImp"
+ address="/SearchStudiesByKeyword" />
+ -->
+
+ <jaxws:endpoint id="searchStudiesByKeyword" address="/SearchStudiesByKeyword">
+ <jaxws:implementor>
+ <bean id="studyServiceByKeywordImp" class="org.cipres.treebase.web.webservices.StudyServiceByKeywordImp">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+ </jaxws:implementor>
+ </jaxws:endpoint>
+
+
+</beans>
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/decorators.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/decorators.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,37 @@
+<decorators defaultdir="/decorators">
+
+ <excludes>
+ <pattern>/help/*.htm</pattern>
+ </excludes>
+
+ <!-- decoration page for the main opening page -->
+ <decorator name="main" page="mainTemplate.jsp">
+ <pattern>/home.html</pattern>
+ </decorator>
+
+ <!-- decoration page for search pages -->
+ <decorator name="search" page="defaultSearchTemplate.jsp">
+ <pattern>/search/*</pattern>
+ <pattern>/search/study/*</pattern>
+ </decorator>
+
+ <!-- decoration page for test pages -->
+ <decorator name="test" page="testTemplate.jsp">
+ <pattern>/test/*</pattern>
+ </decorator>
+
+ <!-- decoration page for everything else -->
+ <decorator name="default" page="defaultTemplate.jsp">
+ <pattern>/*</pattern>
+ </decorator>
+
+ <decorator name="administration" page="adminTemplate.jsp">
+ <pattern>/admin/*</pattern>
+ </decorator>
+
+ <decorator name="services" page="testTemplate.jsp">
+ <pattern>/services/*</pattern>
+ <pattern>/services</pattern>
+ </decorator>
+
+</decorators>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/dwr.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/dwr.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/dwr.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,12 @@
+<!DOCTYPE dwr PUBLIC
+ "-//GetAhead Limited//DTD Direct Web Remoting 1.0//EN"
+ "http://www.getahead.ltd.uk/dwr/dwr10.dtd">
+<dwr>
+ <allow>
+ <!--create creator="spring" javascript="UserManager">
+ <param name="beanName" value="userManager"/>
+ <include method="getUsers"/>
+ </create>
+ <convert converter="bean" match="org.appfuse.model.User"/-->
+ </allow>
+</dwr>
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/menu-config.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/menu-config.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/menu-config.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<MenuConfig>
+ <Displayers>
+ <Displayer name="ListMenu" type="net.sf.navigator.displayer.ListMenuDisplayer"/>
+ <Displayer name="SimpleMenu"
+ type="net.sf.navigator.displayer.SimpleMenuDisplayer"/>
+
+ </Displayers>
+ <Menus>
+ <!-- ==================== Administrator Menus =========================== -->
+ <Menu name="StudyManagementMenu" title="Study Management" description="Study Management" roles="Admin,Associate Editor">
+ <Item name="UserManagement" title="For a User" page="/admin/userManagement.html"/>
+ <Item name="ReadyStudies" title="studies.ready.state" page="/admin/readyStateStudies.html"/>
+ <Item name="SearchBySubmissionId" title="search.by.submission.id" page="/admin/searchBySubmissionID.html"/>
+ <Item name="SelectStudies" title="select.studies" page="/admin/selectStudies.html"/>
+ </Menu>
+ <Menu name="UserManagementMenu" title="User Management" description="User Management" roles="Admin,Associate Editor">
+ <Item name="SelectUsers" title="Select Users" page="/admin/adminSelectUsers.html"/>
+ <Item name="UpdateUserInfo" title="Update User Info" page="/admin/adminUpdatingUserInfo.html"/>
+ <Item name="DeleteUser" title="Delete User" page="/admin/adminDeletingUserStepOne.html"/>
+ <Item name="MergeUsers" title="Merge Users" page="/admin/adminMergingUsers.html"/>
+ <Item name="SelectPersons" title="Select Persons" page="/admin/adminSelectPersons.html"/>
+ <Item name="MergePersons" title="Merge Persons" page="/admin/adminMergingPersons.html"/>
+ </Menu>
+
+ <!-- ==================== User Menu =========================== -->
+ <Menu name="SubmissionHome" title="nav.submission.home" description="SubmissionHome" page="/user/summary.html" roles="Admin,User"/>
+ <Menu name="SubmissionNotes" title="nav.submission.notes" description="SubmissionNotes" page="/user/studyForm.html" roles="Admin,User"/>
+ <Menu name="SubmissionCitation" title="nav.submission.citation" description="SubmissionCitation" page="/user/citationForm.html" roles="Admin,User"/>
+ <Menu name="SubmissionAuthors" title="nav.submission.authors" description="SubmissionAuthors" page="/user/authorSearchForm.html" roles="Admin,User"/>
+ <Menu name="SubmissionUploadFile" title="nav.submission.upload" description="SubmissionUploadFile" page="/user/uploadFile.html" roles="Admin,User"/>
+ <Menu name="SubmissionNexusFiles" title="nav.submission.files" description="SubmissionNexusFiles" page="/user/nexusFiles.html" roles="Admin,User"/>
+ <Menu name="SubmissionTaxa" title="nav.submission.taxa" description="SubmissionTaxa" page="/user/taxaList.html" roles="Admin,User"/>
+ <Menu name="SubmissionMatrices" title="nav.submission.matrices" description="SubmissionMatrices" page="/user/matrixList.html" roles="Admin,User"/>
+ <Menu name="SubmissionTrees" title="nav.submission.trees" description="SubmissionTrees" page="/user/treeBlockList.html" roles="Admin,User"/>
+ <Menu name="SubmissionAnalyses" title="nav.submission.analyses" description="SubmissionAnalyses" page="/user/analyses.html" roles="Admin,User"/>
+ <Menu name="SubmissionSubmissions" title="nav.submission.submissions" description="SubmissionSubmissions" page="/user/submissionList.html" roles="Admin,User"/>
+
+ <!-- ==================== Submission metadata =========================== -->
+ <Menu name="AboutSubmission" title="nav.submission.about" description="About the submission">
+ <Item name="Summary" title="nav.summary" description="Summary Section" page="/user/summary.html"/>
+ <Item name="SubmissionInfo" title="nav.submission.info" description="Submission Name" page="/user/studyForm.html"/>
+ <Item name="Citation" title="nav.citation" description="Citation Menu" roles="Admin,User">
+ <Item name="Publication" title="nav.citation.publication" page="/user/citationForm.html"/>
+ <Item name="Authors" title="nav.citation.authors" page="/user/authorSearchForm.html"/>
+ </Item>
+ </Menu>
+
+ <!-- ==================== Raw Data =========================== -->
+ <Menu name="RawData" title="nav.rawdata" description="Raw Data Menu" roles="Admin,User">
+ <Item name="UploadFile" title="nav.uploadfile" description="Upload File" page="/user/uploadFile.html"/>
+ <Item name="NexusFiles" title="nav.nexusfiles" description="Nexus Files Section" page="/user/nexusFiles.html"/>
+ </Menu>
+ <!-- ==================== PhyloData Sections =========================== -->
+ <Menu name="ProcessedData" title="nav.processed" description="Processed Data Menu" roles="Admin,User">
+ <Item name="Taxa" title="nav.taxa" description="Taxa Section" page="/user/taxaList.html"/>
+ <Item name="Matrices" title="nav.matrix" description="Data Matrices" page="/user/matrixList.html"/>
+ <Item name="Trees" title="nav.trees" description="Trees Section" page="/user/treeBlockList.html"/>
+ </Menu>
+ <!-- ==================== Analysis Menu =========================== -->
+ <Menu name="Analyses" title="nav.analyses" description="Analyses Section" page="/user/analysisDisplay.html"/>
+
+ <!-- ==================== Searching =========================== -->
+ <Menu name="Searches" title="search.menu.title" >
+ <Item name="SearchStudies" title="search.menu.studies" description="Search for studies" page="/search/studySearch.html?action=discard"/>
+ <Item name="SearchTrees" title="search.menu.trees" description="Search for trees" page="/search/treeSearch.html?action=discard"/>
+ <Item name="SearchMatrices" title="search.menu.matrices" description="Search for matrices" page="/search/matrixSearch.html?action=discard"/>
+ </Menu>
+
+ <Menu name="Study" title="search.study.menu.title" >
+ <Item name="StudySummary" title="search.study.menu.summary" description="View study citation and summary" page="/search/studySearch.html${1+1}"/>
+ <Item name="StudyAnalyses" title="search.study.menu.analyses" description="View study's analyses" page="/search/treeSearch.html"/>
+ <Item name="StudyMatrices" title="search.study.menu.matrices" description="View study's matrices" page="/search/matrixSearch.html"/>
+ <Item name="StudyTrees" title="search.study.menu.trees" description="View study's trees" page="/search/matrixSearch.html"/>
+ <Item name="StudyTaxa" title="search.study.menu.taxa" description="View study's taxa" page="/search/matrixSearch.html"/>
+ </Menu>
+
+ </Menus>
+</MenuConfig>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,17 @@
+<sitemesh>
+ <property name="decorators-file" value="/WEB-INF/decorators.xml" />
+ <excludes file="${decorators-file}" />
+
+ <page-parsers>
+ <parser content-type="text/html"
+ class="com.opensymphony.module.sitemesh.parser.FastPageParser" />
+ <parser content-type="text/html;charset=ISO-8859-1"
+ class="com.opensymphony.module.sitemesh.parser.FastPageParser" />
+ </page-parsers>
+
+ <decorator-mappers>
+ <mapper class="com.opensymphony.module.sitemesh.mapper.ConfigDecoratorMapper">
+ <param name="config" value="${decorators-file}" />
+ </mapper>
+ </decorator-mappers>
+</sitemesh>
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-security.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-security.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-security.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,109 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN"
+ "http://www.springframework.org/dtd/spring-beans.dtd">
+
+<beans default-autowire="no">
+
+ <!-- ======================== FILTER CHAIN ======================= -->
+ <!-- if you wish to use channel security, add "channelProcessingFilter,"
+ in front of "httpSessionContextIntegrationFilter" in the list below -->
+ <bean id="filterChainProxy" class="org.acegisecurity.util.FilterChainProxy">
+ <property name="filterInvocationDefinitionSource">
+ <value>
+ CONVERT_URL_TO_LOWERCASE_BEFORE_COMPARISON
+ PATTERN_TYPE_APACHE_ANT
+ /**=httpSessionContextIntegrationFilter,authenticationProcessingFilter,requestMethodsFilter,exceptionTranslationFilter,filterInvocationInterceptor
+ </value>
+ </property>
+ </bean>
+
+ <!-- ======================== AUTHENTICATION MANAGER AND ITS DEPENDENTS ======================= -->
+ <bean id="authenticationManager" class="org.acegisecurity.providers.ProviderManager">
+ <property name="providers">
+ <list>
+ <ref local="daoAuthenticationProvider"/>
+ </list>
+ </property>
+ </bean>
+
+ <bean id="daoAuthenticationProvider" class="org.acegisecurity.providers.dao.DaoAuthenticationProvider">
+ <property name="userDetailsService"><ref bean ="userService"/></property>
+ <!-- encrypt password instead of storing in clear text in DB -->
+ <!-- property name="passwordEncoder" ref="passwordEncoder"/ -->
+ <!-- the next 2 lines are for debugging purpose -->
+ <!-- property name="userDetailsService" ref="jdbcDaoImpl"/ -->
+ <!-- property name="userDetailsService" ref="myUserServices"/ -->
+ </bean>
+ <!-- bean id="passwordEncoder" class="org.acegisecurity.providers.encoding.ShaPasswordEncoder"/ -->
+
+ <!-- bean id="myUserServices" class="org.cipres.treebase.web.controllers.UserDAOImpl"/ -->
+ <!-- use JDBC for authentication: only for debugging -->
+ <!-- bean id="jdbcDaoImpl" class="org.acegisecurity.userdetails.jdbc.JdbcDaoImpl">
+ <property name="dataSource"><ref bean="securityDataSource"/></property>
+ <property name="usersByUsernameQuery">
+ <value>SELECT username, password, 'true' as enabled FROM user WHERE username=?</value>
+ </property>
+ <property name="authoritiesByUsernameQuery">
+ <value>SELECT 'lcchan' as username, 'user' as rolename FROM user WHERE username=? </value>
+ </property>
+ </bean -->
+ <!-- =========================== HTTP REQUEST SECURITY ======================================== -->
+ <!-- Filter to propagate the established Authentication object through all requests -->
+ <bean id="httpSessionContextIntegrationFilter" class="org.acegisecurity.context.HttpSessionContextIntegrationFilter"/>
+
+ <!-- Filter to handle FORM authentication -->
+ <bean id="authenticationProcessingFilter" class="org.acegisecurity.ui.webapp.AuthenticationProcessingFilter">
+ <property name="authenticationManager" ref="authenticationManager"/>
+ <property name="authenticationFailureUrl" value="/login.jsp?error=true"/>
+ <property name="defaultTargetUrl" value="/user/processUser.html"/>
+ <property name="filterProcessesUrl" value="/j_security_check"/>
+ <property name="alwaysUseDefaultTargetUrl" value="true"/>
+ </bean>
+
+ <!-- Filter to link defintions of secured resources with the appropriate access control mechanism -->
+ <bean id="exceptionTranslationFilter" class="org.acegisecurity.ui.ExceptionTranslationFilter">
+ <property name="authenticationEntryPoint" ref="authenticationProcessingFilterEntryPoint"/>
+ </bean>
+
+ <bean id="requestMethodsFilter" class="org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter"/>
+
+ <!-- ======================== FILTER SECURITY INTERCEPTOR ======================= -->
+ <!-- Note the order that entries are placed against the objectDefinitionSource is critical.
+ The FilterSecurityInterceptor will work from the top of the list down to the FIRST pattern
+ that matches the request URL. Accordingly, you should place MOST SPECIFIC (ie a/b/c/d.*)
+ expressions first, with LEAST SPECIFIC (ie a/.*) expressions last -->
+ <bean id="filterInvocationInterceptor" class="org.acegisecurity.intercept.web.FilterSecurityInterceptor">
+ <property name="authenticationManager"><ref local ="authenticationManager"/></property>
+ <property name="accessDecisionManager"><ref local ="accessDecisionManager"/></property>
+ <property name="objectDefinitionSource">
+ <value>
+ CONVERT_URL_TO_LOWERCASE_BEFORE_COMPARISON
+ PATTERN_TYPE_APACHE_ANT
+ /submit.html=User,Admin, Associate Editor
+ /user/*=User,Admin, Associate Editor
+ /admin/*=Admin, Associate Editor
+ </value>
+ </property>
+ </bean>
+
+ <!-- ======================== ACCESSDECISION MANAGER AND ITS DEPENDENTS ======================= -->
+ <bean id="accessDecisionManager" class="org.acegisecurity.vote.AffirmativeBased">
+ <property name="allowIfAllAbstainDecisions" value="false"/>
+ <property name="decisionVoters">
+ <list>
+ <ref local ="roleVoter"/>
+ </list>
+ </property>
+ </bean>
+
+ <bean id="roleVoter" class="org.acegisecurity.vote.RoleVoter">
+ <property name="rolePrefix" value=""/>
+ </bean>
+
+ <!-- ======================== AUTHENTICATION ENTRY POINT ======================= -->
+ <bean id="authenticationProcessingFilterEntryPoint" class="org.acegisecurity.ui.webapp.AuthenticationProcessingFilterEntryPoint">
+ <property name="loginFormUrl"><value>/login.jsp</value></property>
+ <property name="forceHttps"><value>false</value></property>
+ </bean>
+
+</beans>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-10-19 20:30:19 UTC (rev 200)
@@ -0,0 +1,1006 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.0.xsd
+ http://www.directwebremoting.org/schema/spring-dwr
+ http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd">
+
+
+ <!-- ========================================================== -->
+ <!-- LIST OF CONTROLLERS FOR WEB-TIER -->
+ <!-- ========================================================== -->
+
+ <bean id="processUserController" class="org.cipres.treebase.web.controllers.ProcessUserController"/>
+
+ <bean id="anyObjectAsRDFController" class="org.cipres.treebase.web.controllers.AnyObjectAsRDFController"/>
+ <bean id="searchResultsAsRDFController" class="org.cipres.treebase.web.controllers.SearchResultsAsRDFController"/>
+
+ <bean id="appletInteractionController" class="org.cipres.treebase.web.controllers.AppletInteractionController">
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ </bean>
+
+ <bean id="readyStateStudiesController" class="org.cipres.treebase.web.controllers.ReadyStateStudiesController">
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ </bean>
+
+ <bean id="nexusFilesController" class="org.cipres.treebase.web.controllers.NexusFilesController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <bean id="phyloWSController" class="org.cipres.treebase.web.controllers.PhyloWSController">
+ <property name="matrixService"><ref bean="matrixService"></ref></property>
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <bean id="filenameController" class="org.cipres.treebase.web.controllers.ShortPathUrlFilenameViewController"/>
+ <!--bean id="filenameController" class="org.springframework.web.servlet.mvc.UrlFilenameViewController"/ -->
+
+ <!-- for parsing file uploads. Implementation for Commons FileUpload -->
+ <!--bean id="multipartResolver" class="org.springframework.web.multipart.commons.CommonsMultipartResolver"-->
+ <bean id="multipartResolver" class="org.cipres.treebase.web.controllers.AjaxMultipartResolver">
+ <!--property name="uploadTempDir"><value></value></property-->
+ <property name="maxUploadSize"><value>250000000</value></property>
+ </bean>
+
+ <!-- bean to register a new user -->
+ <bean id="registerUserController" class="org.cipres.treebase.web.controllers.RegisterUserController">
+ <property name="commandName"><value>user</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.User</value></property>
+ <property name="formView"><value>userForm</value></property>
+ <property name="successView"><value>redirect:login.jsp</value></property>
+ <property name="cancelView"><value>redirect:login.jsp</value></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ <property name="userHome"><ref bean="userHome"></ref></property>
+ <property name="validators">
+ <list>
+ <ref bean="beanValidator"/> <!--Commons Server-side validation -->
+ </list>
+ </property>
+
+ </bean>
+ <!-- bean to update a user -->
+ <bean id="userFormController" class="org.cipres.treebase.web.controllers.UserFormController">
+ <property name="commandName"><value>user</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.User</value></property>
+ <property name="formView"><value>userForm</value></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ <property name="userHome"><ref bean="userHome"></ref></property>
+ <property name="validators">
+ <list>
+ <ref bean="beanValidator"/> <!--Commons Server-side validation -->
+ </list>
+ </property>
+ </bean>
+
+ <!-- bean to update a user -->
+ <bean id="passwordFormController" class="org.cipres.treebase.web.controllers.PasswordFormController">
+ <property name="commandName"><value>user</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.User</value></property>
+ <property name="formView"><value>passwordForm</value></property>
+ <!-- property name="successView"><value>redirect:home.html</value></property -->
+ <property name="userService"><ref bean="userService"></ref></property>
+ <property name="mailSender"><ref bean="mailSender"></ref></property>
+ </bean>
+
+ <!-- Delete Study Controller to delete a particular study -->
+ <bean id="deleteStudyController" class="org.cipres.treebase.web.controllers.DeleteStudyController">
+ <property name="commandName"><value>submissionid</value></property>
+ <property name="commandClass"><value>java.lang.Long</value></property>
+ <property name="successView"><value>redirect:/user/submissionList.html</value></property>
+ <property name="cancelView"><value>redirect:/user/submissionList.html</value></property>
+ <property name="formView"><value>deleteStudy</value></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ </bean>
+
+ <!-- Change the status of the Study Controller to delete a particular study -->
+ <bean id="readyStateController" class="org.cipres.treebase.web.controllers.ReadyStateController">
+ <property name="successView"><value>redirect:/user/submissionList.html</value></property>
+ <property name="cancelView"><value>redirect:/user/submissionList.html</value></property>
+ <property name="formView"><value>readyState</value></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <!-- Download A Study -->
+ <bean id="downloadAStudyController" class="org.cipres.treebase.web.controllers.DownloadAStudyController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <!-- Download A Tree -->
+ <bean id="downloadATreeController" class="org.cipres.treebase.web.controllers.DownloadATreeController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <bean id="downloadATreeBlockController" class="org.cipres.treebase.web.controllers.DownloadATreeBlockController">
+ <property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <!-- Download A Matrix -->
+ <bean id="downloadAMatrixController" class="org.cipres.treebase.web.controllers.DownloadAMatrixController">
+ <property name="matrixService"><ref bean="matrixService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <!-- Download A NexusFile -->
+ <bean id="downloadANexusFileController" class="org.cipres.treebase.web.controllers.DownloadANexusFileController">
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="matrixService"><ref bean="matrixService"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <!-- Download An AnalysisStep's input and output as a NexusFile -->
+ <bean id="downloadAnAnalysisStepController" class="org.cipres.treebase.web.controllers.DownloadAnAnalysisStepController">
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ <property name="matrixService"><ref bean="matrixService"></ref></property>
+ <property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <!-- Download A NexusFile -->
+ <bean id="downloadANexusRCTFileController" class="org.cipres.treebase.web.controllers.DownloadANexusRCTFileController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="nexmlService"><ref bean="nexmlService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ </bean>
+
+ <!-- View Taxa -->
+ <bean id="listTaxaController" class="org.cipres.treebase.web.controllers.ListTaxaController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+ <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>
+ <property name="commandName"><value>txnlabelset</value></property>
+ <!--property name="commandClass"><value>org.cipres.treebase.web.model.ATaxonLabelSet</value></property-->
+ <property name="commandClass"><value>java.util.ArrayList</value></property>
+ <property name="successView"><value>redirect:/user/editSetTaxonLabel.html</value></property>
+ <property name="formView"><value>taxonLabels</value></property>
+ </bean>
+ <bean id="listTaxaSearchController" class="org.cipres.treebase.web.controllers.ListTaxaSearchController">
+ <property name="formView"><value>search/taxonList</value></property>
+ <property name="commandName"><value>taxonLabelStatus</value></property>
+ </bean>
+
+ <!-- Edit Taxon Label -->
+ <bean id="editTaxonLabelController" class="org.cipres.treebase.web.controllers.EditTaxonLabelController">
+ <property name="commandName"><value>txnlabel</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.taxon.TaxonLabel</value></property>
+ <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+ <property name="taxonHome"><ref bean="taxonHome"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="successView"><value>redirect:/user/taxaList.html</value></property>
+ <property name="cancelView"><value>redirect:/user/taxaList.html</value></property>
+ <property name="formView"><value>editTaxonLabel</value></property>
+ <!--property name="validator"><ref bean="taxonLabelValidator"></ref></property-->
+ <property name="validator">
+ <bean class="org.cipres.treebase.web.validators.TaxonLabelValidator"/>
+ </property>
+ </bean>
+
+ <!-- Edit A Set of Taxon Labels -->
+ <bean id="editSetTaxonLabelController" class="org.cipres.treebase.web.controllers.EditSetTaxonLabelController">
+ <property name="commandName"><value>atxnlabellist</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+ <property name="successView"><value>redirect:/user/taxaList.html</value></property>
+ <property name="cancelView"><value>redirect:/user/taxaList.html</value></property>
+ <property name="formView"><value>editSetTaxonLabel</value></property>
+ <property name="sessionForm"><value>true</value></property>
+ </bean>
+
+ <!-- View study -->
+ <bean id="summaryController" class="org.cipres.treebase.web.controllers.SummaryController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="commandName"><value>citationsummary</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.study.Citation</value></property>
+ <property name="formView"><value>submissionSummaryView</value></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ </bean>
+
+ <bean id="searchSummaryController" class="org.cipres.treebase.web.controllers.SearchSummaryController">
+ <property name="sessionForm"><value>true</value></property>
+ <property name="commandName"><value>study</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
+ <property name="defaultPage"><value>search/summary</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="matrixService"><ref bean="matrixService"></ref></property>
+ <property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ <property name="analysisService"><ref bean="analysisService"></ref></property>
+ <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+ </bean>
+
+ <!-- MultiActionController to display sumbissions by different criteria -->
+ <bean id="listSubmissionController" class="org.cipres.treebase.web.controllers.ListSubmissionController">
+ <property name="methodNameResolver"><ref bean="methodNameResolver"/></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ </bean>
+
+ <bean id="methodNameResolver" class="org.springframework.web.servlet.mvc.multiaction.ParameterMethodNameResolver">
+ <property name="paramName"><value>method</value></property>
+ <property name="defaultMethodName"><value>submissionsByUser</value></property>
+ </bean>
+
+ <bean id="citationFormController" class="org.cipres.treebase.web.controllers.CitationFormController">
+ <property name="commandName"><value>citation</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.study.Citation</value></property>
+ <!-- property name="commandClass"><value>org.cipres.treebase.web.model.CitationCommand</value></property-->
+ <property name="formView"><value>citationForm</value></property>
+ <!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="successView"><value>redirect:/user/summary.html</value></property>
+ <!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="citationService"><ref bean="citationService"></ref></property>
+ </bean>
+
+ <bean id="studyFormController" class="org.cipres.treebase.web.controllers.StudyFormController">
+ <property name="commandName"><value>study</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
+ <property name="formView"><value>studyForm</value></property>
+ <!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="successView"><value>redirect:/user/summary.html</value></property>
+ <property name="cancelView"><value>redirect:/user/submissionList.html</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ </bean>
+
+ <bean id="displaySubmissionMenuController" class="org.cipres.treebase.web.controllers.DisplaySubmissionMenuController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <bean id="submissionToJsonController" class="org.cipres.treebase.web.controllers.SubmissionToJsonController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <!-- bean id="displaySubmissionController" class="org.cipres.treebase.web.controllers.DisplaySubmissionController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ </bean-->
+
+ <bean id="listSearchStudyController" class="org.cipres.treebase.web.controllers.ListSearchStudyController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <!-- authorFormController IS REDUNDAND FOR NOW -->
+ <bean id="authorFormController" class="org.cipres.treebase.web.controllers.AuthorFormController">
+ <property name="commandName"><value>person</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.Person</value></property>
+ <property name="formView"><value>peopleForm</value></property>
+ <!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="successView"><value>redirect:/user/summary.html</value></property>
+ <!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="citationService"><ref bean="citationService"></ref></property>
+ <property name="personService"><ref bean="personService"></ref></property>
+ <property name="validators">
+ <list>
+ <ref bean="beanValidator"/>
+ </list>
+ </property>
+ <property name="sessionForm">
+ <value>true</value>
+ </property>
+ <property name="synchronizeOnSession">
+ <value>true</value>
+ </property>
+ </bean>
+
+ <bean id="authorSearchFormController" class="org.cipres.treebase.web.controllers.AuthorFormController">
+ <property name="commandName"><value>person</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.Person</value></property>
+ <property name="formView"><value>peopleSearchForm</value></property>
+ <!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="successView"><value>redirect:/user/addAuthor.html</value></property>
+ <!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="citationService"><ref bean="citationService"></ref></property>
+ <property name="personService"><ref bean="personService"></ref></property>
+ </bean>
+
+ <bean id="addAuthorController" class="org.cipres.treebase.web.controllers.AddAuthorController">
+ <property name="commandName"><value>person</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.Person</value></property>
+ <property name="formView"><value>addPersonForm</value></property>
+ <!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="successView"><value>redirect:/user/authorSearchForm.html</value></property>
+ <!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="citationService"><ref bean="citationService"></ref></property>
+ <property name="personService"><ref bean="personService"></ref></property>
+ <property name="personHome"><ref bean="personHome"></ref></property>
+ <property name="validators">
+ <list>
+ <ref bean="beanValidator"/>
+ </list>
+ </property>
+ <!--property name="sessionForm">
+ <value>true</value>
+ </property-->
+ <!--property name="synchronizeOnSession">
+ <value>true</value>
+ </property-->
+ </bean>
+
+ <bean id="editorFormController" class="org.cipres.treebase.web.controllers.EditorFormController">
+ <property name="commandName"><value>person</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.admin.Person</value></property>
+ <property name="formView"><value>peopleForm</value></property>
+ <!--property name="successView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="successView"><value>redirect:/user/summary.html</value></property>
+ <!--property name="cancelView"><value>redirect:/user/submissionMain.html</value></property-->
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="citationService"><ref bean="citationService"></ref></property>
+ <property name="personService"><ref bean="personService"></ref></property>
+ <property name="validators">
+ <list>
+ <ref bean="beanValidator"/> <!--Commons Server-side validation -->
+ </list>
+ </property>
+ </bean>
+
+ <bean id="uploadFileController" class="org.cipres.treebase.web.controllers.UploadFileController">
+ <property name="commandClass"><value>org.cipres.treebase.web.model.MultiFileBean</value></property>
+ <property name="formView"><value>uploadFile</value></property>
+ <property name="successView"><value>redirect:/user/uploadFileSummary.html</value></property>
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ <property name="userService"><ref bean="userService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="nexusService"><ref bean="nexusService"></ref></property>
+ </bean>
+
+ <bean id="uploadFileSummaryController" class="org.cipres.treebase.web.controllers.UploadFileSummaryController">
+ <!--property name="commandClass">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
+ <!--property name="commandName">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
+ <property name="commandClass"><value>java.lang.String</value></property>
+ <property name="formView"><value>uploadFileSummary</value></property>
+ <property name="successView"><value>redirect:/user/summary.html</value></property>
+ <property name="cancelView"><value>redirect:/user/summary.html</value></property>
+ </bean>
+
+
+ <bean id="listAnalysisController" class="org.cipres.treebase.web.controllers.ListAnalysisController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <bean id="displayAnalysisController" class="org.cipres.treebase.web.controllers.DisplayAnalysisController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ </bean>
+
+ <bean id="analysisFormController" class="org.cipres.treebase.web.controllers.AnalysisFormController">
+ <property name="commandName"><value>analysis</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.domain.study.Analysis</value></property>
+ <property name="formView"><value>analysisForm</value></property>
+ <property name="successView"><value>redirect:/user/analysisDisplay.html</value></property>
+ <property name="cancelView"><value>redirect:/user/analysisDisplay.html</value></property>
+ <property name="sessionForm"><value>true</value></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="analysisService"><ref bean="analysisService"></ref></property>
+ </bean>
+
+ <bean id="listAnalysisStepController" class="org.cipres.treebase.web.controllers.ListAnalysisStepController">
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="analysisService"><ref bean="analysisService"></ref></property>
+ </bean>
+
+ <bean id="analysisStepFormController" class="org.cipres.treebase.web.controllers.AnalysisStepFormController">
+ <property name="commandName"><value>step</value></property>
+ <property name="commandClass"><value>org.cipres.treebase.web.model.AnalysisStepCommand</value></property>
+ <property name="formView"><value>analysisStepForm</value></property>
+ <property name="sessionForm"><value>true</value></property>
+ <!--...
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