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From: <yo...@us...> - 2009-10-23 15:47:17
|
Revision: 214
http://treebase.svn.sourceforge.net/treebase/?rev=214&view=rev
Author: youjun
Date: 2009-10-23 15:47:05 +0000 (Fri, 23 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/pom.xml
Modified: trunk/oai-pmh_data_provider/data_provider_core/pom.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/pom.xml 2009-10-23 15:20:23 UTC (rev 213)
+++ trunk/oai-pmh_data_provider/data_provider_core/pom.xml 2009-10-23 15:47:05 UTC (rev 214)
@@ -90,11 +90,7 @@
<version>2.1</version>
</dependency>
- <dependency>
- <groupId>ibm</groupId>
- <artifactId>db2jcc</artifactId>
- <version>2.6.80</version>
- </dependency>
+
@@ -159,6 +155,25 @@
<version>1.6.1</version>
</dependency>
+ <dependency>
+ <groupId>org.nexml.model</groupId>
+ <artifactId>nexml</artifactId>
+ <version>1.5-SNAPSHOT</version>
+ </dependency>
+
+ <dependency>
+ <groupId>mesquite</groupId>
+ <artifactId>mesquite</artifactId>
+ <version>2.01.tb</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.cipres</groupId>
+ <artifactId>framework</artifactId>
+ <version>1.0.1</version>
+ <scope>compile</scope>
+ </dependency>
+
</dependencies>
</project>
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-23 15:20:33
|
Revision: 213
http://treebase.svn.sourceforge.net/treebase/?rev=213&view=rev
Author: youjun
Date: 2009-10-23 15:20:23 +0000 (Fri, 23 Oct 2009)
Log Message:
-----------
Removed Paths:
-------------
trunk/treebase-core/src/main/perl/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-23 15:18:04
|
Revision: 212
http://treebase.svn.sourceforge.net/treebase/?rev=212&view=rev
Author: youjun
Date: 2009-10-23 15:17:51 +0000 (Fri, 23 Oct 2009)
Log Message:
-----------
Removed Paths:
-------------
trunk/oai-pmh_data_provider/data_provider_core/src/main/
trunk/oai-pmh_data_provider/data_provider_core/src/test/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-21 20:48:54
|
Revision: 211
http://treebase.svn.sourceforge.net/treebase/?rev=211&view=rev
Author: youjun
Date: 2009-10-21 20:48:42 +0000 (Wed, 21 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml
Modified: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml 2009-10-21 14:16:08 UTC (rev 210)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml 2009-10-21 20:48:42 UTC (rev 211)
@@ -17,7 +17,7 @@
<property name="locations">
<list>
<value>classpath:jdbc.properties</value>
- <value>classpath:treebase.properties</value>
+ <value>classpath:top.properties</value>
</list>
</property>
</bean>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-21 14:16:18
|
Revision: 210
http://treebase.svn.sourceforge.net/treebase/?rev=210&view=rev
Author: youjun
Date: 2009-10-21 14:16:08 +0000 (Wed, 21 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/target/classes/org/treebase/oai/App.class
trunk/oai-pmh_data_provider/data_provider_core/target/data_provider_core-0.0.1-SNAPSHOT.jar
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-service.xml
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/ehcache.xml
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/jdbc.properties
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/log4j.xml
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/matrices.lst
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/studies.lst
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/top.properties
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/top.sql
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/trees.lst
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,367 @@
+<?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"
+ default-autowire="no">
+
+
+
+ <bean id="propertyConfigurer"
+ class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
+ <property name="ignoreUnresolvablePlaceholders" value="true" />
+ <property name="locations">
+ <list>
+ <value>classpath:jdbc.properties</value>
+ <value>classpath:treebase.properties</value>
+ </list>
+ </property>
+ </bean>
+
+ <bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close">
+ <property name="driverClass" value="${jdbc.driverClassName}" />
+ <property name="jdbcUrl" value="${jdbc.url}" />
+ <property name="user" value="${jdbc.username}" />
+ <property name="password" value="${jdbc.password}" />
+ <property name="minPoolSize" value="5" />
+ <!-- reduce to expose connection leak problem, if any
+ property name="maxPoolSize" value="100" /-->
+ <property name="maxPoolSize" value="10" />
+ <property name="initialPoolSize" value="6" />
+ <property name="maxIdleTime" value="3600" />
+ <!--property name="maxIdleTime" value="9000" /-->
+ <property name="maxConnectionAge" value="18000" />
+ <property name="idleConnectionTestPeriod" value="300" />
+ <property name="maxIdleTimeExcessConnections" value="300" />
+ <property name="maxStatementsPerConnection" value="100" />
+ <property name="numHelperThreads" value="5" />
+ </bean>
+
+ <bean id="sessionFactory"
+ class="org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean">
+ <property name="dataSource" ref="dataSource" />
+ <property name="configurationClass" value="org.hibernate.cfg.AnnotationConfiguration" />
+ <property name="configLocation" value="classpath:hibernate.cfg.xml" />
+ <property name="hibernateProperties">
+ <props>
+ <prop key="hibernate.dialect">${hibernate.dialect}</prop>
+ <prop key="hibernate.show_sql">${hibernate.show_sql}</prop>
+ <prop key="hibernate.format_sql">${hibernate.format_sql}</prop>
+ <prop key="hibernate.generate_statistics">${hibernate.generate_statistics}</prop>
+ <prop key="hibernate.hbm2ddl.auto">${hibernate.hbm2ddl.auto}</prop>
+ <!-- Need this to update the schema, otherwise another schema might be used -->
+ <!-- prop key="hibernate.default_schema">TBASE2</prop-->
+ </props>
+ </property>
+ </bean>
+
+ <bean id="transactionManager"
+ class="org.springframework.orm.hibernate3.HibernateTransactionManager">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+
+ <!-- A parent bean definition which is a base definition for transaction proxies.
+ - The attributes can still be overridden in child bean definitions.
+ -->
+ <bean id="baseTransactionProxy"
+ class="org.springframework.transaction.interceptor.TransactionProxyFactoryBean" abstract="true">
+ <property name="transactionManager" ref="transactionManager" />
+ <property name="transactionAttributes">
+ <props>
+ <prop key="get*">PROPAGATION_REQUIRED,readOnly</prop>
+ <prop key="find*">PROPAGATION_REQUIRED,readOnly</prop>
+ <prop key="load*">PROPAGATION_REQUIRED,readOnly</prop>
+ <prop key="generate*">PROPAGATION_REQUIRED,readOnly</prop>
+ <prop key="store*">PROPAGATION_REQUIRED</prop>
+ <prop key="save*">PROPAGATION_REQUIRED</prop>
+ <prop key="create*">PROPAGATION_REQUIRED</prop>
+ <prop key="add*">PROPAGATION_REQUIRED</prop>
+ <prop key="update*">PROPAGATION_REQUIRED</prop>
+ <prop key="delete*">PROPAGATION_REQUIRED</prop>
+ <prop key="replace*">PROPAGATION_REQUIRED</prop>
+ <prop key="move*">PROPAGATION_REQUIRED</prop>
+
+ <!--prop key="*">PROPAGATION_REQUIRED,readOnly</prop-->
+ </props>
+ </property>
+ <!--
+ <property name="postInterceptors">
+ <list>
+ <ref bean="emailAdvisor"/>
+ </list>
+ </property>
+ -->
+ </bean>
+
+ <!-- DAO objects -->
+ <!-- DAO package: org.cipres.treebase.dao.admin -->
+ <bean id="personHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.admin.PersonHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.admin.PersonDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="helpHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.admin.HelpHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.admin.HelpDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="userHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.admin.UserHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.admin.UserDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <!-- DAO package: org.cipres.treebase.dao.matrix -->
+ <bean id="characterHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.CharacterHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.CharacterDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="itemDefinitionHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.ItemDefinitionHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.ItemDefinitionDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.MatrixDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ <property name="matrixColumnHome" ref="matrixColumnHome" />
+ <property name="matrixRowHome" ref="matrixRowHome" />
+ <property name="submissionHome" ref="submissionHome" />
+ <property name="analyzedDataHome" ref="analyzedDataHome" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixColumnHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixColumnHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.MatrixColumnDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixDataTypeHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixDataTypeHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.MatrixDataTypeDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixElementHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixElementHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.MatrixElementDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixRowHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixRowHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.MatrixRowDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="rowSegmentHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.RowSegmentHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.matrix.RowSegmentDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <!-- DAO package: org.cipres.treebase.dao.study -->
+ <bean id="algorithmHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AlgorithmHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.AlgorithmDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="analysisHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AnalysisHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.AnalysisDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="analysisStepHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AnalysisStepHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.AnalysisStepDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="analyzedDataHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AnalyzedDataHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.AnalyzedDataDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="citationHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.CitationHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.CitationDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="citationStatusHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.CitationStatusHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.CitationStatusDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="studyHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.StudyHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.StudyDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="studyStatusHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.StudyStatusHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.StudyStatusDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="submissionHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.SubmissionHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.study.SubmissionDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <!-- DAO package: org.cipres.treebase.dao.taxon -->
+ <bean id="taxonHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.taxon.TaxonHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.taxon.TaxonDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="taxonLabelHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.taxon.TaxonLabelHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.taxon.TaxonLabelDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ </bean>
+ </property>
+ </bean>
+
+ <!-- DAO package: org.cipres.treebase.dao.tree -->
+ <bean id="phyloTreeHome" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.tree.PhyloTreeHome</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.dao.tree.PhyloTreeDAO">
+ <property name="sessionFactory" ref="sessionFactory" />
+ <property name="submissionHome" ref="submissionHome" />
+ <property name="analyzedDataHome" ref="analyzedDataHome" />
+ <property name="taxonLabelHome" ref="taxonLabelHome" />
+ </bean>
+ </property>
+ </bean>
+
+
+</beans>
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-service.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-service.xml 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,300 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN 2.0//EN" "http://www.springframework.org/dtd/spring-beans-2.0.dtd">
+
+<beans default-autowire="no">
+
+
+ <!-- Service Objects -->
+ <!-- package: org.cipres.treebase.domain.admin -->
+ <bean id="personService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.admin.PersonService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.admin.PersonServiceImpl">
+ <property name="personHome" ref="personHome"/>
+ <property name="userHome" ref="userHome"/>
+ <property name="citationHome" ref="citationHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="helpService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.admin.HelpService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.admin.HelpServiceImpl">
+ <property name="helpHome" ref="helpHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="userService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.admin.UserService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.admin.UserServiceImpl">
+ <property name="userHome" ref="userHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <!-- package: org.cipres.treebase.domain.matrix -->
+ <bean id="characterService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.CharacterService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.matrix.CharacterServiceImpl">
+ <property name="characterHome" ref="characterHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.matrix.MatrixServiceImpl">
+ <property name="matrixHome" ref="matrixHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixColumnService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixColumnService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.matrix.MatrixColumnServiceImpl">
+ <property name="matrixColumnHome" ref="matrixColumnHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixElementService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixElementService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.matrix.MatrixElementServiceImpl">
+ <property name="matrixElementHome" ref="matrixElementHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="matrixRowService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.MatrixRowService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.matrix.MatrixRowServiceImpl">
+ <property name="matrixRowHome" ref="matrixRowHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="rowSegmentService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.matrix.RowSegmentService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.matrix.RowSegmentServiceImpl">
+ <property name="rowSegmentHome" ref="rowSegmentHome"/>
+ <property name="matrixElementHome" ref="matrixElementHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ </bean>
+ </property>
+ </bean>
+
+
+ <!-- package: org.cipres.treebase.domain.nexus -->
+ <!-- TODO: use a factory bean for nexus parser implementation. Wait for Spring 2.0
+ classproperties holder feature -->
+ <!--bean id="nexusService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.nexus.NexusService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.nexus.${nexus.parser.impl}">
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ </bean>
+ </property>
+ </bean-->
+
+ <!--bean id="nexusService" class = "org.cipres.treebase.domain.nexus.NexusParserFinder">
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ <property name="nexusParserStr" ref="${nexus.parser.impl}"/>
+ </bean-->
+
+ <!-- bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceNCL">
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ </bean-->
+
+ <bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+ <property name="mesquiteFolderDir" value="${mesquite.folder_dir}"/>
+ </bean>
+
+ <bean id="nexmlService" class = "org.cipres.treebase.service.nexus.NexusServiceNexml">
+ <!-- property name="domainHome" ref="domainHome"/ -->
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ </bean>
+
+ <bean id="rdfaService" class = "org.cipres.treebase.service.nexus.NexusServiceRDFa">
+ <!-- property name="domainHome" ref="domainHome"/ -->
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ </bean>
+
+ <!-- package: org.cipres.treebase.domain.study -->
+ <bean id="analysisService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AnalysisService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.study.AnalysisServiceImpl">
+ <property name="analysisStepService" ref="analysisStepService"/>
+ <property name="userHome" ref="userHome"/>
+ <property name="analysisHome" ref="analysisHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="analysisStepService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AnalysisStepService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.study.AnalysisStepServiceImpl">
+ <property name="analyzedDataService" ref="analyzedDataService"/>
+ <property name="algorithmHome" ref="algorithmHome"/>
+ <property name="analysisStepHome" ref="analysisStepHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="analyzedDataService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.AnalyzedDataService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.study.AnalyzedDataServiceImpl">
+ <property name="analyzedDataHome" ref="analyzedDataHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="citationService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.CitationService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.study.CitationServiceImpl">
+ <property name="citationHome" ref="citationHome"/>
+ <property name="citationStatusHome" ref="citationStatusHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="studyService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.StudyService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.study.StudyServiceImpl">
+ <property name="analysisService" ref="analysisService"/>
+ <property name="citationService" ref="citationService"/>
+ <property name="studyHome" ref="studyHome"/>
+ <property name="studyStatusHome" ref="studyStatusHome"/>
+ <property name="submissionHome" ref="submissionHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ <property name="phyloTreeHome" ref="phyloTreeHome"/>
+ <!--property name="taxonHome" ref="taxonHome"/-->
+ <property name="matrixHome" ref="matrixHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <bean id="submissionService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.study.SubmissionService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.study.SubmissionServiceImpl">
+ <property name="analysisService" ref="analysisService"/>
+ <property name="citationService" ref="citationService"/>
+ <property name="nexusService" ref="nexusService"/>
+ <property name="studyService" ref="studyService"/>
+ <property name="matrixHome" ref="matrixHome"/>
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="studyHome" ref="studyHome"/>
+ <property name="studyStatusHome" ref="studyStatusHome"/>
+ <property name="submissionHome" ref="submissionHome"/>
+ <property name="phyloTreeHome" ref="phyloTreeHome"/>
+ <property name="taxonHome" ref="taxonHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ <property name="userHome" ref="userHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <!-- package: org.cipres.treebase.domain.taxon -->
+ <bean id="taxonLabelService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.taxon.TaxonLabelService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.taxon.TaxonLabelServiceImpl">
+ <property name="phyloTreeHome" ref="phyloTreeHome"/>
+ <property name="taxonHome" ref="taxonHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ </bean>
+ </property>
+ </bean>
+
+
+ <!-- package: org.cipres.treebase.domain.tree -->
+ <bean id="phyloTreeService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.tree.PhyloTreeService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.tree.PhyloTreeServiceImpl">
+ <property name="phyloTreeHome" ref="phyloTreeHome"/>
+ </bean>
+ </property>
+ </bean>
+
+ <!-- package: org.cipres.treebase.domain.search -->
+ <bean id="searchService" parent="baseTransactionProxy">
+ <property name="proxyInterfaces">
+ <value>org.cipres.treebase.domain.search.SearchService</value>
+ </property>
+ <property name="target">
+ <bean class="org.cipres.treebase.service.search.SearchServiceImpl">
+ <property name="phyloTreeService" ref="phyloTreeService"/>
+ <property name="matrixService" ref="matrixService"/>
+ <property name="studyService" ref="studyService"/>
+ <property name="taxonLabelService" ref="taxonLabelService"/>
+ </bean>
+ </property>
+ </bean>
+
+ <!-- This is here to inject the searchService bean into the class member of SearchResults.
+ The choice of StudySearchResults as the target class is arbitrary. 20090313 MJD -->
+ <bean id="searchResultsDummy" class="org.cipres.treebase.domain.search.StudySearchResults">
+ <property name="searchService" ref="searchService"/>
+ </bean>
+
+
+
+</beans>
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/ehcache.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/ehcache.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/ehcache.xml 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,96 @@
+<ehcache>
+ <!-- On a standard Linux system this will be /tmp -->
+ <diskStore path="java.io.tmpdir"/>
+
+ <!--Default Cache configuration. These will applied to caches programmatically created through
+ the CacheManager.
+
+ The following attributes are required for defaultCache:
+
+ maxInMemory - Sets the maximum number of objects that will be created in memory
+ eternal - Sets whether elements are eternal. If eternal, timeouts are ignored and the element
+ is never expired.
+ timeToIdleSeconds - Sets the time to idle for an element before it expires. Is only used
+ if the element is not eternal. Idle time is now - last accessed time
+ timeToLiveSeconds - Sets the time to live for an element before it expires. Is only used
+ if the element is not eternal. TTL is now - creation time
+ overflowToDisk - Sets whether elements can overflow to disk when the in-memory cache
+ has reached the maxInMemory limit.
+
+ -->
+ <defaultCache
+ maxElementsInMemory="10000"
+ eternal="false"
+ timeToIdleSeconds="1200"
+ timeToLiveSeconds="1200"
+ overflowToDisk="true"
+ />
+
+ <!--Predefined caches. Add your cache configuration settings here.
+ If you do not have a configuration for your cache a WARNING will be issued when the
+ CacheManager starts
+
+ The following attributes are required for defaultCache:
+
+ name - Sets the name of the cache. This is used to identify the cache. It must be unique.
+ maxInMemory - Sets the maximum number of objects that will be created in memory
+ eternal - Sets whether elements are eternal. If eternal, timeouts are ignored and the element
+ is never expired.
+ timeToIdleSeconds - Sets the time to idle for an element before it expires. Is only used
+ if the element is not eternal. Idle time is now - last accessed time
+ timeToLiveSeconds - Sets the time to live for an element before it expires. Is only used
+ if the element is not eternal. TTL is now - creation time
+ overflowToDisk - Sets whether elements can overflow to disk when the in-memory cache
+ has reached the maxInMemory limit.
+
+ -->
+
+ <cache name="staticCache"
+ maxElementsInMemory="500"
+ eternal="true"
+ timeToIdleSeconds="0"
+ timeToLiveSeconds="0"
+ overflowToDisk="false"
+ />
+
+ <cache name="adminCache"
+ maxElementsInMemory="2000"
+ eternal="false"
+ timeToIdleSeconds="1200"
+ timeToLiveSeconds="2400"
+ overflowToDisk="true"
+ />
+
+ <cache name="studyCache"
+ maxElementsInMemory="10000"
+ eternal="false"
+ timeToIdleSeconds="1200"
+ timeToLiveSeconds="4800"
+ overflowToDisk="true"
+ />
+
+ <cache name="matrixCache"
+ maxElementsInMemory="30000"
+ eternal="false"
+ timeToIdleSeconds="1200"
+ timeToLiveSeconds="4800"
+ overflowToDisk="true"
+ />
+
+ <cache name="taxonCache"
+ maxElementsInMemory="5000"
+ eternal="false"
+ timeToIdleSeconds="1200"
+ timeToLiveSeconds="4800"
+ overflowToDisk="true"
+ />
+
+ <cache name="treeCache"
+ maxElementsInMemory="10000"
+ eternal="false"
+ timeToIdleSeconds="1200"
+ timeToLiveSeconds="4800"
+ overflowToDisk="true"
+ />
+
+</ehcache>
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,144 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-configuration PUBLIC
+ "-//Hibernate/Hibernate Configuration DTD 3.0//EN"
+ "http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">
+
+<hibernate-configuration>
+ <session-factory>
+
+ <!-- NOTE: only used for updating tables in TBASE2 schema during dev -->
+ <!--property name="hibernate.default_schema">TBASE2</property-->
+
+ <!-- cache -->
+ <property name="hibernate.cache.provider_class">
+ org.hibernate.cache.EhCacheProvider
+ </property>
+ <property name="hibernate.cache.provider_configuration_file_resource_path">/ehcache.xml</property>
+ <property name="hibernate.cache.use_query_cache">true</property>
+
+ <!-- Other settings -->
+ <property name="hibernate.jdbc.use_streams_for_binary">true</property>
+ <property name="hibernate.jdbc.batch_versioned_data">true</property>
+ <property name="hibernate.jdbc.batch_size">40</property>
+ <property name="hibernate.max_fetch_depth">3</property>
+ <property name="hibernate.default_batch_fetch_size">8</property>
+ <property name="hibernate.connection.autocommit">false</property>
+ <property name="hibernate.connection.release_mode">auto</property>
+ <property name="hibernate.query.substitutions">true 'T', false 'F'</property>
+
+ <!-- Mapping files -->
+ <!-- mapping package="org.cipres.treebase.domain" /-->
+ <mapping class="org.cipres.treebase.domain.AbstractPersistedObject" />
+
+ <!-- mapping package="org.cipres.treebase.domain.admin" /-->
+ <mapping class="org.cipres.treebase.domain.admin.Help" />
+ <mapping class="org.cipres.treebase.domain.admin.Person" />
+ <mapping class="org.cipres.treebase.domain.admin.User" />
+ <mapping class="org.cipres.treebase.domain.admin.UserRole" />
+ <mapping class="org.cipres.treebase.domain.admin.EmailAddress" />
+
+ <mapping class="org.cipres.treebase.domain.matrix.AncestralState" />
+ <mapping class="org.cipres.treebase.domain.matrix.AncStateSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.CharacterMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.CharGroup" />
+ <mapping class="org.cipres.treebase.domain.matrix.CharPartition" />
+ <mapping class="org.cipres.treebase.domain.matrix.CharSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.CharWeight" />
+ <mapping class="org.cipres.treebase.domain.matrix.CharWeightSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.ColumnRange" />
+ <mapping class="org.cipres.treebase.domain.matrix.CompoundMatrixElement" />
+ <mapping class="org.cipres.treebase.domain.matrix.CodonPositionSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.ContinuousAncState" />
+ <mapping class="org.cipres.treebase.domain.matrix.ContinuousChar" />
+ <mapping class="org.cipres.treebase.domain.matrix.ContinuousMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.ContinuousMatrixElement" />
+ <mapping class="org.cipres.treebase.domain.matrix.CSTree" />
+ <mapping class="org.cipres.treebase.domain.matrix.CSTreeNode" />
+ <mapping class="org.cipres.treebase.domain.matrix.DiscreteAncState" />
+ <mapping class="org.cipres.treebase.domain.matrix.DiscreteChar" />
+ <mapping class="org.cipres.treebase.domain.matrix.DiscreteCharState" />
+ <mapping class="org.cipres.treebase.domain.matrix.DiscreteMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.DiscreteMatrixElement" />
+ <mapping class="org.cipres.treebase.domain.matrix.DistanceMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.DistanceMatrixElement" />
+ <mapping class="org.cipres.treebase.domain.matrix.ExcludedCharSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.GapMode" />
+ <mapping class="org.cipres.treebase.domain.matrix.GeneticCode" />
+ <mapping class="org.cipres.treebase.domain.matrix.GeneticCodeRecord" />
+ <mapping class="org.cipres.treebase.domain.matrix.GeneticCodeSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.IntegerCharWeight" />
+ <mapping class="org.cipres.treebase.domain.matrix.ItemDefinition" />
+ <mapping class="org.cipres.treebase.domain.matrix.ItemValue" />
+ <mapping class="org.cipres.treebase.domain.matrix.Matrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.MatrixColumn" />
+ <mapping class="org.cipres.treebase.domain.matrix.MatrixDataType" />
+ <mapping class="org.cipres.treebase.domain.matrix.MatrixElement" />
+ <mapping class="org.cipres.treebase.domain.matrix.MatrixKind" />
+ <mapping class="org.cipres.treebase.domain.matrix.MatrixRow" />
+ <mapping class="org.cipres.treebase.domain.matrix.PhyloChar" />
+ <mapping class="org.cipres.treebase.domain.matrix.PolyTCount" />
+ <mapping class="org.cipres.treebase.domain.matrix.PredefinedCharSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.PredefinedCharType" />
+ <mapping class="org.cipres.treebase.domain.matrix.RealCharWeight" />
+ <mapping class="org.cipres.treebase.domain.matrix.RowSegment" />
+ <mapping class="org.cipres.treebase.domain.matrix.SequenceMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.StandardMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.StateChangeSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.StateFormat" />
+ <mapping class="org.cipres.treebase.domain.matrix.StateModifier" />
+ <mapping class="org.cipres.treebase.domain.matrix.StateSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.StepMatrix" />
+ <mapping class="org.cipres.treebase.domain.matrix.StepMatrixElement" />
+ <mapping class="org.cipres.treebase.domain.matrix.TypeSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.UserDefinedCharSet" />
+ <mapping class="org.cipres.treebase.domain.matrix.UserType" />
+ <mapping class="org.cipres.treebase.domain.matrix.UserTypeRecord" />
+
+ <mapping class="org.cipres.treebase.domain.study.Algorithm" />
+ <mapping class="org.cipres.treebase.domain.study.Analysis" />
+ <mapping class="org.cipres.treebase.domain.study.AnalysisStep" />
+ <mapping class="org.cipres.treebase.domain.study.AnalyzedData" />
+ <mapping class="org.cipres.treebase.domain.study.AnalyzedMatrix" />
+ <mapping class="org.cipres.treebase.domain.study.AnalyzedTree" />
+ <mapping class="org.cipres.treebase.domain.study.ArticleCitation" />
+ <mapping class="org.cipres.treebase.domain.study.BookCitation" />
+ <mapping class="org.cipres.treebase.domain.study.Citation" />
+ <mapping class="org.cipres.treebase.domain.study.CitationStatus" />
+ <mapping class="org.cipres.treebase.domain.study.DistanceAlgorithm" />
+ <mapping class="org.cipres.treebase.domain.study.InBookCitation" />
+ <mapping class="org.cipres.treebase.domain.study.LikelihoodAlgorithm" />
+ <mapping class="org.cipres.treebase.domain.study.OtherAlgorithm" />
+ <mapping class="org.cipres.treebase.domain.study.ParsimonyAlgorithm" />
+ <mapping class="org.cipres.treebase.domain.study.Software" />
+ <mapping class="org.cipres.treebase.domain.study.Study" />
+ <mapping class="org.cipres.treebase.domain.study.StudyStatus" />
+ <mapping class="org.cipres.treebase.domain.study.Submission" />
+
+ <mapping class="org.cipres.treebase.domain.taxon.LSIDTaxonLink" />
+ <mapping class="org.cipres.treebase.domain.taxon.SpecimenLabel" />
+ <mapping class="org.cipres.treebase.domain.taxon.Taxon" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonAuthority" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonLabel" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonLabelGroup" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonLabelPartition" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonLabelSet" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonLink" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonSet" />
+ <mapping class="org.cipres.treebase.domain.taxon.TaxonVariant" />
+ <mapping class="org.cipres.treebase.domain.taxon.TextTaxonLink" />
+
+ <mapping class="org.cipres.treebase.domain.tree.PhyloTreeNode" />
+ <mapping class="org.cipres.treebase.domain.tree.NodeAttribute" />
+ <mapping class="org.cipres.treebase.domain.tree.PhyloTree" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeAttribute" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeBlock" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeGroup" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeKind" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeNodeEdge" />
+ <mapping class="org.cipres.treebase.domain.tree.TreePartition" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeQuality" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeSet" />
+ <mapping class="org.cipres.treebase.domain.tree.TreeType" />
+
+ </session-factory>
+</hibernate-configuration>
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/jdbc.properties
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/jdbc.properties (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/jdbc.properties 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,21 @@
+# This is treebase-core jdbc.properties
+
+jdbc.driverClassName=org.postgresql.Driver
+jdbc.url=jdbc:postgresql://treebasedb-dev.nescent.org/treebasedev
+jdbc.username=treebase_app
+jdbc.password=tim5tema
+
+
+hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
+
+#for development only:
+#hibernate.show_sql=true
+#hibernate.format_sql=true
+#hibernate.generate_statistics=true
+#hibernate.use_sql_comments=true
+
+#options are: validate | update | create | create-drop
+hibernate.hbm2ddl.auto=
+
+#Mesquite installation directory
+mesquite.folder_dir=/home/mjd/Mesquite_Folder/
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/log4j.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/log4j.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/log4j.xml 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/">
+
+ <!-- BEGIN APPENDER: CONSOLE APPENDER (stdout) -->
+ <appender name="stdout" class="org.apache.log4j.ConsoleAppender">
+ <layout class="org.apache.log4j.TTCCLayout"/>
+ </appender>
+
+ <!-- BEGIN APPENDER: SOCKET APPENDER (socketLogger) -->
+ <appender name="socketLogger" class="org.apache.log4j.SocketAppender">
+ <param name="RemoteHost" value="localhost"/>
+ <param name="Port" value="4445"/>
+ <param name="LocationInfo" value="true"/>
+ </appender>
+
+ <!-- BEGIN APPENDER: ROLLING FILE APPENDER (rolling) -->
+ <appender name="rolling" class="org.apache.log4j.RollingFileAppender">
+ <param name="File" value="treebase.log"/>
+ <param name="MaxFileSize" value="900KB"/>
+ <param name="MaxBackupIndex" value="9"/>
+ <layout class="org.apache.log4j.PatternLayout">
+ <param name="ConversionPattern" value="%d %-5p %-17c{2} (%30F:%L) %3x - %m%n"/>
+ </layout>
+ </appender>
+
+ <!-- BEGIN APPENDER: LogFactor5 APPENDER (lf5) -->
+ <appender name="lf5" class="org.apache.log4j.lf5.LF5Appender">
+ <param name="MaxNumberOfRecords" value="1000"/>
+ </appender>
+
+ <!-- BEGIN APPENDER: xml file -->
+ <appender name="xml" class="org.apache.log4j.FileAppender">
+ <param name="File" value="treebase_xml.log"/>
+ <param name="Append" value="false"/>
+ <layout class="org.apache.log4j.xml.XMLLayout"/>
+ </appender>
+
+ <!-- BEGIN customized logger configurations -->
+ <!-- LEVELS: trace, debug, info, warn, error, fatal -->
+ <logger name="org.cipres.treebase">
+ <level value="debug"/>
+ <!--level value="info"/-->
+ </logger>
+
+ <logger name="org.springframework">
+ <level value="warn"/>
+ </logger>
+
+ <!-- show SQL statement -->
+ <!--logger name="org.hibernate.SQL">
+ <level value="debug"/>
+ </logger-->
+
+ <!-- show jdbc -->
+ <!--logger name="org.hibernate.jdbc">
+ <level value="debug"/>
+ </logger-->
+
+ <!-- show sessionImpl logging -->
+ <!--logger name="org.hibernate.impl.SessionImpl">
+ <level value="trace"/>
+ </logger-->
+
+ <!-- show parameter binding statement -->
+ <!--logger name="org.hibernate.type">
+ <level value="debug"/>
+ </logger-->
+
+ <!-- show entity state (max 20) when flushing -->
+ <!-- logger name="org.hibernate.pretty">
+ <level value="debug"/>
+ </logger-->
+
+ <!-- 2nd level cache activity -->
+ <logger name="org.hibernate.cache">
+ <level value="warn"/>
+ </logger>
+
+ <!--logger name="org.hibernate.tool.hbm2ddl">
+ <level value="debug"/>
+ </logger-->
+
+ <!--logger name="org.hibernate.transaction">
+ <level value="debug"/>
+ </logger-->
+
+ <!--logger name="org.hibernate">
+ <level value="info"/>
+ </logger-->
+
+ <logger name="org.cipres.treebase.web.controllers.ListSubmissionController">
+ <level value="info"/>
+ </logger>
+
+ <!-- unless specified otherwise, the level for all loggers is warn, and the following appenders are used. -->
+ <root>
+ <level value="warn"/>
+ <appender-ref ref="stdout"/>
+ <appender-ref ref="rolling"/>
+ <!--appender-ref ref="lf5"/-->
+ </root>
+</log4j:configuration>
Added: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/matrices.lst
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/matrices.lst (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/matrices.lst 2009-10-21 14:16:08 UTC (rev 210)
@@ -0,0 +1,3791 @@
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[truncated message content] |
|
From: <yo...@us...> - 2009-10-21 14:10:20
|
Revision: 209
http://treebase.svn.sourceforge.net/treebase/?rev=209&view=rev
Author: youjun
Date: 2009-10-21 14:10:09 +0000 (Wed, 21 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
Modified: 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 2009-10-21 13:56:26 UTC (rev 208)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml 2009-10-21 14:10:09 UTC (rev 209)
@@ -9,47 +9,5 @@
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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-21 13:56:36
|
Revision: 208
http://treebase.svn.sourceforge.net/treebase/?rev=208&view=rev
Author: youjun
Date: 2009-10-21 13:56:26 +0000 (Wed, 21 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
Removed Paths:
-------------
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
Deleted: 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 2009-10-20 21:46:44 UTC (rev 207)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/cxf-servlet.xml 2009-10-21 13:56:26 UTC (rev 208)
@@ -1,30 +0,0 @@
-
-
-<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
Deleted: 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 2009-10-20 21:46:44 UTC (rev 207)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/decorators.xml 2009-10-21 13:56:26 UTC (rev 208)
@@ -1,37 +0,0 @@
-<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>
Modified: 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/WEB-INF/web.xml 2009-10-20 21:46:44 UTC (rev 207)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml 2009-10-21 13:56:26 UTC (rev 208)
@@ -11,7 +11,6 @@
/WEB-INF/applicationContext.xml,
<!-- top is short for Treebase OAI-PMH Provider -->
/WEB-INF/top-security.xml,
- /WEB-INF/cxf-servlet.xml,
/WEB-INF/top-validation.xml
</param-value>
</context-param>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2009-10-20 21:48:19
|
Bugs item #2854613, was opened at 2009-09-08 20:11 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: Ryan Scherle (rscherle) >Assigned to: Rutger Vos (rvos) Summary: right-hand menu missing Initial Comment: When I try to create a new submission, or edit an existing submission, the menu on the right does not appear, and I cannot complete the submission. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-10-20 21:48 Message: Fixed as of revision 207: the "Associate Editor" was, erroneously, not added to the list of roles allowed to view the right-hand-side submission context menu. This has been corrected. ---------------------------------------------------------------------- Comment By: William Piel (sfrgpiel) Date: 2009-09-08 23:03 Message: Just to be clear: this is an issue that affects Associate Editors -- I think it's okay for normal users and Administrators. Definitely needs fixing, though. ---------------------------------------------------------------------- Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 20:14 Message: I tested this with several different browsers, and two different user accounts. ---------------------------------------------------------------------- Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 20:13 Message: (see attached screenshot) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 |
|
From: <rv...@us...> - 2009-10-20 21:46:51
|
Revision: 207
http://treebase.svn.sourceforge.net/treebase/?rev=207&view=rev
Author: rvos
Date: 2009-10-20 21:46:44 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Fix for bug 2854613 ("right-hand menu missing")
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/menu-config.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/menu-config.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/menu-config.xml 2009-10-20 21:25:56 UTC (rev 206)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/menu-config.xml 2009-10-20 21:46:44 UTC (rev 207)
@@ -24,17 +24,17 @@
</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"/>
+ <Menu name="SubmissionHome" title="nav.submission.home" description="SubmissionHome" page="/user/summary.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionNotes" title="nav.submission.notes" description="SubmissionNotes" page="/user/studyForm.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionCitation" title="nav.submission.citation" description="SubmissionCitation" page="/user/citationForm.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionAuthors" title="nav.submission.authors" description="SubmissionAuthors" page="/user/authorSearchForm.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionUploadFile" title="nav.submission.upload" description="SubmissionUploadFile" page="/user/uploadFile.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionNexusFiles" title="nav.submission.files" description="SubmissionNexusFiles" page="/user/nexusFiles.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionTaxa" title="nav.submission.taxa" description="SubmissionTaxa" page="/user/taxaList.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionMatrices" title="nav.submission.matrices" description="SubmissionMatrices" page="/user/matrixList.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionTrees" title="nav.submission.trees" description="SubmissionTrees" page="/user/treeBlockList.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionAnalyses" title="nav.submission.analyses" description="SubmissionAnalyses" page="/user/analyses.html" roles="Admin,User,Associate Editor"/>
+ <Menu name="SubmissionSubmissions" title="nav.submission.submissions" description="SubmissionSubmissions" page="/user/submissionList.html" roles="Admin,User,Associate Editor"/>
<!-- ==================== Submission metadata =========================== -->
<Menu name="AboutSubmission" title="nav.submission.about" description="About the submission">
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|
|
From: SourceForge.net <no...@so...> - 2009-10-20 21:31:09
|
Bugs item #2809158, was opened at 2009-06-19 17:19 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2809158&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Taxon Label validation too restrictive Initial Comment: Two problems: if a submission fails to validate all taxon labels, it cannot be toggled to "ready" state. This is too restrictive because some taxon labels can never be validated. Instead, when the user tries to toggle to "ready" he should be given a warning: "We notice that x of your y taxon labels have failed to be validated against an external taxonomy. Unless it is impossible to validate these labels, TreeBASE may refuse or delay the acceptance of your data." The other problem is that the user gets a very confusing message, saying on the one hand that the submission cannot be toggled to "Ready" (and the submit button is unavailable), while on the other hand including verbiage as though the "Submit" button is available: You cannot change the Status of the study because Taxon Labels for analyzed data in Analysis Step cannot be validated. Are you sure that you want to change the status of this particular study to 'Ready State'? It means, you are ready for the review process. If yes, then press the Submit button, else, choose the Cancel button. Please note, pressing the Submit button will disallow you to make any further changes to this study. However, it will be available in 'READ ONLY' mode. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-10-20 21:31 Message: Fixed as of revision 206: the suggested warning message is displayed, the surrounding verbiage is rewritten in English and the submit button is available. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2809158&group_id=248804 |
|
From: <rv...@us...> - 2009-10-20 21:26:04
|
Revision: 206
http://treebase.svn.sourceforge.net/treebase/?rev=206&view=rev
Author: rvos
Date: 2009-10-20 21:25:56 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Fixed bug 2809158 ("Taxon Label validation too restrictive")
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp 2009-10-20 21:20:03 UTC (rev 205)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp 2009-10-20 21:25:56 UTC (rev 206)
@@ -14,15 +14,15 @@
</c:if>
<p style="font-weight:bold">
Are you sure that you want to change the status of this study to 'Ready State'?
- This means that you are ready for the review process. If yes, press Submit,
- else, choose the Cancel button.
+ This means that you are ready for the review process. If yes press Submit,
+ else choose the Cancel button.
</p>
-<p style="font-weight:bold">
- Please note, pressing the Submit button will <strong>disallow you</strong> to make any further changes to this study.
+<p>
+ Please note: after you press the Submit button you will no longer be able to make any further changes to this study.
The study will be available in 'READ ONLY' mode.
</p>
-<input type="submit" name="Submit" value="Submit"/>
+<input type="submit" name="Submit" value="Submit"/>
<input type="submit" name="_cancel" value = "Cancel"/>
</form>
\ No newline at end of file
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|
|
From: <rv...@us...> - 2009-10-20 21:20:14
|
Revision: 205
http://treebase.svn.sourceforge.net/treebase/?rev=205&view=rev
Author: rvos
Date: 2009-10-20 21:20:03 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Fixed bug 2809158 ("Taxon Label validation too restrictive")
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp 2009-10-20 19:30:50 UTC (rev 204)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp 2009-10-20 21:20:03 UTC (rev 205)
@@ -7,15 +7,22 @@
<form method="post">
<c:if test="${AnalysesStatus eq false}">
- <p style="color: red;"><b>You cannot change the Status of the study because Taxon Labels for analyzed data in Analysis Step cannot be validated.</b></p>
-</c:if>
-<h3><strong>Are you sure that you want to change the status of this particular study to 'Ready State'?<br/>
- It means, you are ready for the review process. If yes, then press the Submit button,<br/>
- else, choose the Cancel button. </strong></h3>
- <p>
- Please note, pressing the Submit button will <strong>disallow you</strong> to make any further changes to this study.<br/>
-However, it will be available in 'READ ONLY' mode.</p>
+ <p style="color:red;font-weight:bold">
+ We notice that some of your taxon labels have failed to be validated against an external taxonomy.
+ Unless it is impossible to validate these labels, TreeBASE may refuse or delay the acceptance of your data.
+ </p>
+</c:if>
+<p style="font-weight:bold">
+ Are you sure that you want to change the status of this study to 'Ready State'?
+ This means that you are ready for the review process. If yes, press Submit,
+ else, choose the Cancel button.
+</p>
+<p style="font-weight:bold">
+ Please note, pressing the Submit button will <strong>disallow you</strong> to make any further changes to this study.
+ The study will be available in 'READ ONLY' mode.
+</p>
-<c:if test="${AnalysesStatus eq true}"> <input type="submit" name="Submit" value="Submit"></c:if> <input type="submit" name="_cancel" value = "Cancel">
+<input type="submit" name="Submit" value="Submit"/>
+<input type="submit" name="_cancel" value = "Cancel"/>
</form>
\ No newline at end of file
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|
|
From: SourceForge.net <no...@so...> - 2009-10-20 21:04:26
|
Bugs item #2870903, was opened at 2009-09-30 17:51 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2870903&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: Cannot get Matrix Row List to work Initial Comment: Requesting a Matrix Row List, e.g.: http://8ball.sdsc.edu:6666/treebase-web/user/matrixRowList.html?id=1495 generates an uncaught exception. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-10-20 21:04 Message: This works just fine on the new server. Perhaps there is a jar missing on 8ball? http://treebasedb-dev.nescent.org:6666/treebase-web/user/matrixRowList.html?id=1495 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2870903&group_id=248804 |
|
From: <yo...@us...> - 2009-10-20 19:31:08
|
Revision: 204
http://treebase.svn.sourceforge.net/treebase/?rev=204&view=rev
Author: youjun
Date: 2009-10-20 19:30:50 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
Modified: 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 2009-10-20 18:42:20 UTC (rev 203)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-10-20 19:30:50 UTC (rev 204)
@@ -35,9 +35,9 @@
<!-- ========================================================== -->
<!-- MESSAGE SOURCE DEFINITION -->
<!-- ========================================================== -->
- <bean id="messageSource" class="org.springframework.context.support.ResourceBundleMessageSource">
+ <!--bean id="messageSource" class="org.springframework.context.support.ResourceBundleMessageSource">
<property name="basename"><value>ApplicationResources</value></property>
- </bean>
+ </bean-->
<!-- ========================================================== -->
<!-- Spring View Resolvers for Templates -->
@@ -72,7 +72,7 @@
<!-- The default behavior of DispatcherServlet is to propagate all exceptions to the servlet container -->
<!-- This will happen here with all other types of exception -->
<!-- ==================================================================================================== -->
- <bean id="exceptionResolver" class="org.springframework.web.servlet.handler.SimpleMappingExceptionResolver">
+ <!--bean id="exceptionResolver" class="org.springframework.web.servlet.handler.SimpleMappingExceptionResolver">
<property name="exceptionMappings">
<props>
<prop key="org.springframework.dao.DataAccessException">/errors/dataAccessFailure</prop>
@@ -80,6 +80,6 @@
<prop key="org.cipres.treebase.web.exceptions.EmptyStudyException">/errors/studyAccessFailure</prop>
</props>
</property>
- </bean>
+ </bean-->
</beans>
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|
|
From: <yo...@us...> - 2009-10-20 18:42:30
|
Revision: 203
http://treebase.svn.sourceforge.net/treebase/?rev=203&view=rev
Author: youjun
Date: 2009-10-20 18:42:20 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
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/web.xml
Modified: 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 2009-10-20 14:39:22 UTC (rev 202)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-10-20 18:42:20 UTC (rev 203)
@@ -7,815 +7,31 @@
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">
-
+
+ <!-- ========================================================== -->
+ <!-- velocity configure -->
+ <!-- ========================================================== -->
+
+ <bean id="velocityConfigurer" class="org.springframework.web.servlet.view.velocity.VelocityConfigurer">
+ <property name="resourceLoaderPath">
+ <value>WEB-INF/vmFiles/</value>
+ </property>
+ </bean>
<!-- ========================================================== -->
- <!-- LIST OF CONTROLLERS FOR WEB-TIER -->
+ <!-- LIST OF CONTROLLERS FOR VERBS AND FORMATS -->
<!-- ========================================================== -->
- <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">
+ <!--bean id="appletInteractionController" class="org.cipres.treebase.web.controllers.AppletInteractionController">
<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- </bean>
+ </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>
- <!-- property name="successView"><value>redirect:/user/analysisStepList.html</value></property -->
- <property name="successView"><value>redirect:/user/analysisDisplay.html</value></property>
- <property name="cancelView"><value>redirect:/user/analysisDisplay.html</value></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="analysisService"><ref bean="analysisService"></ref></property>
- <property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
- <property name="analysisStepHome"><ref bean="analysisStepHome"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- </bean>
-
- <bean id="searchFormController" class="org.cipres.treebase.web.controllers.SearchFormController">
- <property name="commandName"><value>search</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
- <property name="formView"><value>searchForm</value></property>
- <property name="successView"><value>redirect:/searchResult.html</value></property>
- </bean>
- <bean id="updateStudyQueryController" class="org.cipres.treebase.web.controllers.UpdateStudyQueryController">
- <property name="commandName"><value>search</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
- <property name="formView"><value>study-query</value></property>
- <property name="successView"><value>redirect:/searchResult.html</value></property>
- </bean>
- <bean id="searchStudyController" class="org.cipres.treebase.web.controllers.SearchStudyController">
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="userService"><ref bean="userService"></ref></property>
- </bean>
- <bean id="listAnalyzedDataController" class="org.cipres.treebase.web.controllers.ListAnalyzedDataController">
- <property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
- </bean>
-
- <bean id="analyzedDataFormController" class="org.cipres.treebase.web.controllers.AnalyzedDataFormController">
- <property name="commandName"><value>data</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.AnalyzedDataCommand</value></property>
- <property name="analysisService"><ref bean="analysisService"></ref></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
- <property name="matrixService"><ref bean="matrixService"></ref></property>
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
- <property name="pages">
- <list>
- <value>analyzedDataForm</value>
- <value>analyzedDataForm-matrixSelection</value>
- <value>analyzedDataForm-treeSelection</value>
- <value>analyzedDataForm-treeBlockSelection</value>
- </list>
- </property>
- </bean>
-
- <bean id="updateAnalyzedDataListController" class="org.cipres.treebase.web.controllers.UpdateAnalyzedDataListController">
- <property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
- <property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
- </bean>
-
- <bean id="addAnalyzedDataController" class="org.cipres.treebase.web.controllers.AddAnalyzedDataController">
- <property name="analyzedDataService"><ref bean="analyzedDataService"></ref></property>
- <property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
- <property name="analysisService"><ref bean="analysisService"></ref></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="matrixService"><ref bean="matrixService"></ref></property>
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- </bean>
-
- <bean id="listMatrixController" class="org.cipres.treebase.web.controllers.ListMatrixController">
- <property name="commandName"><value>amatrixcollection</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="matrixService"><ref bean="matrixService"></ref></property>
- <property name="matrixHome"><ref bean="matrixHome"></ref></property>
- <property name="formView"><value>matrixList</value></property>
- <property name="successView"><value>redirect:/user/matrixList.html</value></property>
- <property name="cancelView"><value>redirect:/user/matrixList.html</value></property>
- </bean>
-
- <bean id="listMatrixRowController" class="org.cipres.treebase.web.controllers.ListMatrixRowController">
- <property name="matrixService"><ref bean="matrixService"></ref></property>
- </bean>
-
- <bean id="listMatrixRowSegmentController" class="org.cipres.treebase.web.controllers.ListMatrixRowSegmentController">
- <property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
- <property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
- </bean>
-
- <bean id="matrixRowSegmentFormController" class="org.cipres.treebase.web.controllers.SingleRowSegmentController">
- <property name="commandName"><value>arowsegment</value></property>
- <property name="commandClass"><value>org.cipres.treebase.domain.matrix.RowSegment</value></property>
- <property name="formView"><value>matrixRowSegmentForm</value></property>
- <property name="successView"><value>redirect:/user/matrixRowSegmentList.html</value></property>
- <property name="cancelView"><value>redirect:/user/matrixRowSegmentList.html</value></property>
- <property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
- <property name="matrixRowService"><ref bean="matrixRowService"></ref></property>
- </bean>
-
- <bean id="deleteAMatrixController" class="org.cipres.treebase.web.controllers.DeleteAMatrixController">
- <!--property name="commandName">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <!--property name="commandClass">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <property name="matrixService"><ref bean="matrixService"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
- <property name="formView"><value>generalDeletePage</value></property>
- <property name="successView"><value>redirect:/user/matrixList.html</value></property>
- <property name="cancelView"><value>redirect:/user/matrixList.html</value></property>
- </bean>
-
-
- <bean id="deleteARowSegmentController" class="org.cipres.treebase.web.controllers.DeleteARowSegmentController">
- <!--property name="commandName">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <!--property name="commandClass">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
- <property name="formView"><value>generalDeletePage</value></property>
- <property name="successView"><value>redirect:/user/viewAllRowSegmentData.html</value></property>
- <property name="cancelView"><value>redirect:/user/viewAllRowSegmentData.html</value></property>
- </bean>
-
- <bean id="listTreeController" class="org.cipres.treebase.web.controllers.ListTreeController">
- <property name="commandName"><value>atreecollection</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
- <property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
- <property name="formView"><value>treeList</value></property>
- <property name="successView"><value>redirect:/user/treeList.html</value></property>
- <property name="cancelView"><value>redirect:/user/treeList.html</value></property>
- <property name="sessionForm">
- <value>true</value>
- </property>
- <property name="synchronizeOnSession">
- <value>true</value>
- </property>
- </bean>
-
- <bean id="deleteATreeController" class="org.cipres.treebase.web.controllers.DeleteATreeController">
- <!--property name="commandName">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <!--property name="commandClass">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
- <property name="formView"><value>generalDeletePage</value></property>
- <property name="successView"><value>redirect:/user/treeList.html</value></property>
- <property name="cancelView"><value>redirect:/user/treeList.html</value></property>
- </bean>
-
- <bean id="directToPhyloWidgetController" class="org.cipres.treebase.web.controllers.DirectToPhyloWidgetController">
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="defaultView"><value>redirect:/test/newPhylowidget.html</value></property>
- </bean>
-
- <bean id="directMapToPhyloWidgetController" class="org.cipres.treebase.web.controllers.DirectMapToPhyloWidgetController">
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
- <property name="defaultView"><value>redirect:/test/newPhylowidget.html</value></property>
- </bean>
-
- <bean id="searchMapToPhyloWidgetController" class="org.cipres.treebase.web.controllers.SearchMapToPhyloWidgetController"
- parent="directMapToPhyloWidgetController">
- <property name="defaultView"><value>redirect:/test/newPhylowidget.html</value></property>
- </bean>
-
- <bean id="deleteATreeBlockController" class="org.cipres.treebase.web.controllers.DeleteATreeBlockController">
- <!--property name="commandName">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <!--property name="commandClass">NOT NEEDED, as we have no form and spring binding<value>dummy</value></property-->
- <property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
- <property name="formView"><value>generalDeletePage</value></property>
- <property name="successView"><value>redirect:/user/treeBlockList.html</value></property>
- <property name="cancelView"><value>redirect:/user/treeBlockList.html</value></property>
- </bean>
-
- <bean id="listTreeBlockController" class="org.cipres.treebase.web.controllers.ListTreeBlockController">
- <property name="commandName"><value>atreeblocklist</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- <property name="formView"><value>treeBlockList</value></property>
- <property name="successView"><value>redirect:/user/treeBlockList.html</value></property>
- <property name="cancelView"><value>redirect:/user/treeBlockList.html</value></property>
- </bean>
-
- <bean id="readOnlyListTreeController" class="org.cipres.treebase.web.controllers.ReadOnlyListTreeController">
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- </bean>
-
- <bean id="mailSender" class="org.springframework.mail.javamail.JavaMailSenderImpl">
- <property name="host" value="smtp.ucsd.edu"></property>
- </bean>
-
- <bean id="treeParserController" class="org.cipres.treebase.web.controllers.TreeParserController">
- <property name="commandClass"><value>org.cipres.treebase.web.model.MultiFileBean</value></property>
- <property name="formView"><value>treeParser</value></property>
- <property name="successView"><value>redirect:/user/treeParserResult.html</value></property>
- <property name="cancelView"><value>redirect:/user/treeParser.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="treeParserResultController" class="org.cipres.treebase.web.controllers.TreeParserResultController">
- <property name="commandName"><value>study</value></property>
- <property name="commandClass"><value>org.cipres.treebase.domain.study.Study</value></property>
- <property name="formView"><value>viewXML</value></property>
- <property name="successView"><value>redirect:/user/treeParser.html</value></property>
- <property name="cancelView"><value>redirect:/user/treeParser.html</value></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- </bean>
-
- <bean id="uploadRowSegmentDataController" class="org.cipres.treebase.web.controllers.UploadRowSegmentDataController">
-
- <property name="formView"><value>uploadRowSegmentData</value></property>
- <property name="successView"><value>redirect:/user/rowSegmentDataTable.html</value></property>
- <property name="cancelView"><value>redirect:/user/matrixList.html</value></property>
-
- </bean>
-
- <bean id="rowSegmentDataTableController" class="org.cipres.treebase.web.controllers.RowSegmentDataTableController">
- <property name="formView"><value>rowSegmentDataTable</value></property>
- <property name="successView"><value>redirect:/user/viewAllRowSegmentData.html</value></property>
- <property name="cancelView"><value>redirect:/user/matrixList.html</value></property>
- <property name ="rowSegmentService"><ref bean="rowSegmentService"/></property>
- <property name="matrixService"><ref bean="matrixService"/></property>
- <property name="studyService"><ref bean="studyService"/></property>
- </bean>
-
- <bean id="viewAllRowSegmentDataController" class="org.cipres.treebase.web.controllers.ViewAllRowSegmentDataController">
- <property name="commandName"><value>arowsegmentlist</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
- <property name="formView"><value>viewAllRowSegmentData</value></property>
- <property name="cancelView"><value>redirect:/user/matrixList.html</value></property>
- <property name ="rowSegmentService"><ref bean="rowSegmentService"/></property>
- </bean>
-
- <bean id="exportRowSegmentDataController" class="org.cipres.treebase.web.controllers.ExportRowSegmentDataController">
- <property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
- </bean>
-
- <bean id="exportRowSegmentTemplateController" class="org.cipres.treebase.web.controllers.ExportRowSegmentTemplateController">
- <property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
- </bean>
-
- <bean id="userManagementController" class="org.cipres.treebase.web.controllers.UserManagementController">
- <property name="successView"><value>redirect:/admin/changeStudyStatus.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>simpleUserManagement</value></property>
- <property name="userHome"><ref bean="userHome"></ref></property>
- <!--property name="submissionService"><ref bean="submissionService"></ref></property-->
- </bean>
-
- <bean id="selectStudiesController" class="org.cipres.treebase.web.controllers.SelectStudiesController">
- <property name="successView"><value>redirect:/admin/changeStudyStatus.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>selectStudies</value></property>
-
- <!--property name="submissionService"><ref bean="submissionService"></ref></property-->
- </bean>
-
- <bean id="adminSelectUsersController" class="org.cipres.treebase.web.controllers.AdminSelectUsersController">
- <property name="successView"><value>redirect:/admin/userList.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>adminSelectUsers</value></property>
- <property name="userHome"><ref bean="userHome"></ref></property>
- <!--property name="submissionService"><ref bean="submissionService"></ref></property-->
- </bean>
-
- <bean id="adminSelectPersonsController" class="org.cipres.treebase.web.controllers.AdminSelectPersonsController">
- <property name="successView"><value>redirect:/admin/personList.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>adminSelectPersons</value></property>
- <property name="personHome"><ref bean="personHome"></ref></property>
- <!--property name="submissionService"><ref bean="submissionService"></ref></property-->
- </bean>
-
- <bean id="changeStudyStatusController" class="org.cipres.treebase.web.controllers.ChangeStudyStatusController">
- <property name="commandName"><value>asubmissionlist</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.AGenericList</value></property>
- <property name="successView"><value>redirect:/admin/changeStudyStatus.html</value></property>
- <property name="cancelView"><value>redirect:/admin/changeStudyStatus.html</value></property>
- <property name="formView"><value>changeStudyStatus</value></property>
- <property name="userService"><ref bean="userService"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- </bean>
-
- <bean id="searchController" abstract="true" >
- <property name="commandName"><value>search</value></property>
- <property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
- <property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
- <property name="searchService"><ref bean="searchService"></ref></property>
- </bean>
-
- <bean id="studySearchController" parent="searchController" class="org.cipres.treebase.web.controllers.StudySearchController">
- <property name="formView"><value>search/studySearch</value></property>
- <property name="successView"><value>search/studySearch</value></property>
-
- </bean>
-
- <bean id="treeSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TreeSearchController">
- <property name="formView"><value>search/treeSearch</value></property>
- <property name="successView"><value>search/treeSearch</value></property>
- </bean>
-
- <bean id="treeTopSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TreeTopSearchController">
- <property name="formView"><value>search/treeTopSearch</value></property>
- <property name="successView"><value>search/treeTopSearch</value></property>
- </bean>
-
- <bean id="matrixSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.MatrixSearchController">
- <property name="formView"><value>search/matrixSearch</value></property>
- <property name="successView"><value>search/matrixSearch</value></property>
- </bean>
-
- <bean id="taxonSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.TaxonSearchController">
- <property name="formView"><value>search/taxonSearch</value></property>
- <property name="successView"><value>search/taxonSearch</value></property>
- <property name="taxonHome"><ref bean="taxonHome"></ref></property>
- <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>
- </bean>
-
- <bean id="searchBySubmissionIDController" class="org.cipres.treebase.web.controllers.SearchBySubmissionIDController">
- <property name="formView"><value>searchBySubmissionID</value></property>
- <property name="successView"><value>redirect:/admin/changeStudyStatus.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
- </bean>
-
- <bean id="adminUpdatingUserInfoController" class="org.cipres.treebase.web.controllers.AdminUpdatingUserInfoController">
- <property name="successView"><value>redirect:/admin/overrideUserProfile.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>adminUpdatingUserInfo</value></property>
- <property name="userService"><ref bean="userService"></ref></property>
- </bean>
-
- <bean id="adminOverridingUserFormController" class="org.cipres.treebase.web.controllers.AdminOverridingUserFormController">
- <property name="commandName"><value>user</value></property>
- <property name="commandClass"><value>org.cipres.treebase.domain.admin.User</value></property>
- <property name="formView"><value>overrideUserProfile</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</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 id="adminDeletingUserStepOneController" class="org.cipres.treebase.web.controllers.AdminDeletingUserStepOneController">
- <property name="successView"><value>redirect:/admin/adminDeletingUserStepTwo.html</value></property>
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>adminDeletingUserStepOne</value></property>
- <property name="userService"><ref bean="userService"></ref></property>
- </bean>
-
- <bean id="adminDeletingUserStepTwoController" class="org.cipres.treebase.web.controllers.AdminDeletingUserStepTwoController">
- <property name="cancelView"><value>redirect:/admin/administrationPage.html</value></property>
- <property name="formView"><value>adminDeletingUserStepTwo</value></property>
- <property name="userService"><ref bean="userService"></ref></property>
- <property name="userHome"><ref bean="userHome"></ref></property>
- <property name="submissionService"><ref bean="submissionService"></ref></property>
- </bean>
- <bean id="adminMergingUsersController" class="org.cipres.treebase.web.controllers.AdminMergingUsersController">
- <property name="userService"><ref bean="userService"></ref></property>
- <property name="pages">
- <list>
- <value>adminMergingUsers</value>
- <value>StepTwo</value>
- </list>
- </property>
- <!--property name="submissionService"><ref bean="submissionService"></ref></property-->
- </bean>
-
- <bean id="adminMergingPersonsController" class="org.cipres.treebase.web.controllers.AdminMergingPersonsController">
- <property name="personService"><ref bean="personService"></ref></property>
- <property name="pages">
- <list>
- <value>adminMergingPersons</value>
- <value>adminMergingPersonsStepTwo</value>
- </list>
- </property>
- <!--property name="submissionService"><ref bean="submissionService"></ref></property-->
- </bean>
-
- <!-- bean to supply help texts -->
- <bean id="helpController" class="org.cipres.treebase.web.controllers.HelpController">
- <property name="commandClass"><value>org.cipres.treebase.web.model.HelpControllerAction</value></property>
- <property name="formView"><value>help</value></property>
- <property name="successView"><value>help</value></property>
- <property name="failureView"><value>FAILfailFAIL</value></property>
- <property name="userService"><ref bean="userService"></ref></property>
- <property name="helpService"><ref bean="helpService"></ref></property>
- </bean>
-
<!-- ========================================================== -->
<!-- LIST OF VALIDATORS FOR CONTROLLER -->
<!-- ========================================================== -->
+
+
<!-- ========================================================== -->
<!-- MESSAGE SOURCE DEFINITION -->
<!-- ========================================================== -->
@@ -824,13 +40,18 @@
</bean>
<!-- ========================================================== -->
- <!-- Spring View Resolvers for JSPs -->
+ <!-- Spring View Resolvers for Templates -->
<!-- ========================================================== -->
- <bean id="viewResolver" class="org.springframework.web.servlet.view.InternalResourceViewResolver">
- <property name="requestContextAttribute" value="rc"/>
- <property name="viewClass" value="org.springframework.web.servlet.view.JstlView"/>
- <property name="prefix" value="/WEB-INF/pages/"/>
- <property name="suffix" value=".jsp"/>
+ <bean id="viewResolver" class="org.springframework.web.servlet.view.velocity.VelocityViewResolver">
+ <property name="suffix">
+ <value>.vm</value>
+ </property>
+ <property name="exposeRequestAttributes">
+ <value>true</value>
+ </property>
+ <property name="exposeSessionAttributes">
+ <value>true</value>
+ </property>
</bean>
<!-- ========================================================== -->
@@ -840,150 +61,8 @@
<property name="alwaysUseFullPath" value="true"/>
<property name="mappings">
- <props>
- <prop key="/phylows/**">phyloWSController</prop>
- <prop key="/home.html">filenameController</prop>
- <prop key="/login.html">filenameController</prop>
- <prop key="/user/viewXML.html">filenameController</prop>
- <prop key="/test/phylowidget.html">filenameController</prop>
- <prop key="/test/newPhylowidget.html">filenameController</prop>
- <prop key="/user/processUser.html">processUserController</prop>
- <prop key="/accessviolation.html">filenameController</prop>
-
- <prop key="/user/deleteStudy.html">deleteStudyController</prop>
- <prop key="/user/readyState.html">readyStateController</prop>
- <prop key="/user/downloadATree.html">downloadATreeController</prop>
- <prop key="/user/downloadATreeBlock.html">downloadATreeBlockController</prop>
- <prop key="/user/downloadAMatrix.html">downloadAMatrixController</prop>
- <prop key="/user/downloadANexusFile.html">downloadANexusFileController</prop>
- <prop key="/user/downloadANexusRCTFile.html">downloadANexusRCTFileController</prop>
- <prop key="/user/taxaList.html">listTaxaController</prop>
- <prop key="/user/editTaxonLabel.html">editTaxonLabelController</prop>
- <prop key="/user/editSetTaxonLabel.html">editSetTaxonLabelController</prop>
- <prop key="/user/summary.html">summaryController</prop>
- <prop key="/user/analyses.html">summaryController</prop>
-
- <prop key="/search/summary.html">summaryController</prop>
-
- <prop key="/user/deleteATree.html">deleteATreeController</prop>
- <prop key="/user/deleteATreeBlock.html">deleteATreeBlockController</prop>
- <prop key="/user/deleteAMatrix.html">deleteAMatrixController</prop>
- <prop key="/user/deleteARowSegment.html">deleteARowSegmentController</prop>
- <prop key="/user/readOnlyListTree.html">readOnlyListTreeController</prop>
- <prop key="/user/directToPhyloWidget.html">directToPhyloWidgetController</prop>
- <prop key="/user/directMapToPhyloWidget.html">directMapToPhyloWidgetController</prop>
- <prop key="/user/nexusFiles.html">nexusFilesController</prop>
- <prop key="/user/uploadRowSegmentData.html">uploadRowSegmentDataController</prop>
- <prop key="/user/rowSegmentDataTable.html">rowSegmentDataTableController</prop>
- <prop key="/user/viewAllRowSegmentData.html">viewAllRowSegmentDataController</prop>
- <prop key="/user/exportRowSegmentData.html">exportRowSegmentDataController</prop>
- <prop key="/user/exportRowSegmentTemplate.html">exportRowSegmentTemplateController</prop>
-
- <prop key="/appletInteraction.html">appletInteractionController</prop>
-
- <prop key="/test/testParser.html">treeParserController</prop>
-
- <prop key="/admin/userManagement.html">userManagementController</prop>
- <prop key="/admin/selectStudies.html">selectStudiesController</prop>
- <prop key="/admin/changeStudyStatus.html">changeStudyStatusController</prop>
- <prop key="/admin/readyStateStudies.html">changeStudyStatusController</prop>
- <!--prop key="/admin/readyStateStudies.html">readyStateStudiesController</prop-->
- <prop key="/admin/searchBySubmissionID.html">searchBySubmissionIDController</prop>
- <prop key="/admin/adminSelectUsers.html">adminSelectUsersController</prop>
- <prop key="/admin/adminUpdatingUserInfo.html">adminUpdatingUserInfoController</prop>
- <prop key="/admin/adminDeletingUserStepOne.html">adminDeletingUserStepOneController</prop>
- <prop key="/admin/adminDeletingUserStepTwo.html">adminDeletingUserStepTwoController</prop>
- <prop key="/admin/overrideUserProfile.html">adminOverridingUserFormController</prop>
- <prop key="/admin/adminMergingUsers.html">adminMergingUsersController</prop>
- <prop key="/admin/administrationPage.html">filenameController</prop>
- <prop key="/admin/messageToAdminAfterAction.html">filenameController</prop>
- <prop key="/admin/userList.html">filenameController</prop>
- <prop key="/admin/personList.html">filenameController</prop>
- <prop key="/admin/adminSelectPersons.html">adminSelectPersonsController</prop>
- <prop key="/admin/adminMergingPersons.html">adminMergingPersonsController</prop>
-
-
- <prop key="/register.html">registerUserController</prop>
- <prop key="/passwordForm.html">passwordFormController</prop>
- <prop key="/help.html">helpController</prop>
-
- <prop key="/searchForm.html">searchFormController</prop>
- <prop key="/searchResult.html">filenameController</prop>
- <prop key="/searchStudyList.html">listSearchStudyController</prop>
- <prop key="/searchStudy.html">searchStudyController</prop>
- <prop key="/study-query.html">updateStudyQueryController</prop>
- <prop key="/search/">studySearchController</prop>
- <prop key="/search/studySearch.html">studySearchController</prop>
- <prop key="/search/treeSearch.html">treeSearchController</prop>
- <prop key="/search/treeTopSearch.html">treeTopSearchController</prop>
- <prop key="/search/matrixSearch.html">matrixSearchController</prop>
- <prop key="/search/taxonSearch.html">taxonSearchController</prop>
- <prop key="/search/study/summary.html">searchSummaryController</prop>
- <prop key="/search/study/analyses.html">searchSummaryController</prop>
- <prop key="/search/study/matrices.html">searchSummaryController</prop>
- <prop key="/search/study/trees.html">searchSummaryController</prop>
- <prop key="/search/study/treeBlocks.html">searchSummaryController</prop>
- <prop key="/search/study/treeBlock.html">searchMapToPhyloWidgetController</prop>
- <prop key="/search/study/tree.html">searchMapToPhyloWidgetController</prop>
- <prop key="/search/study/matrix.html">searchSummaryController</prop>
- <prop key="/search/study/analysis.html">searchSummaryController</prop>
- <prop key="/search/study/taxa.html">searchSummaryController</prop>
- <prop key="/search/study/rowSegments.html">searchSummaryController</prop>
- <prop key="/search/study/anyObjectAsRDF.html">anyObjectAsRDFController</prop>
- <prop key="/search/searchResultsAsRDF.html">searchResultsAsRDFController</prop>
- <prop key="/search/matrixRowList.html">listMatrixRowController</prop>
- <prop key="/search/taxonList.html">listTaxaSearchController</prop>
- <prop key="/search/downloadAStudy.html">downloadAStudyController</prop>
- <prop key="/search/downloadATree.html">downloadATreeController</prop>
- <prop key="/search/downloadATreeBlock.html">downloadATreeBlockController</prop>
- <prop key="/search/downloadAMatrix.html">downloadAMatrixController</prop>
- <prop key="/search/downloadAnAnalysisStep.html">downl...
[truncated message content] |
|
From: <yo...@us...> - 2009-10-20 14:39:33
|
Revision: 202
http://treebase.svn.sourceforge.net/treebase/?rev=202&view=rev
Author: youjun
Date: 2009-10-20 14:39:22 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/uncaughtException.jsp
Removed Paths:
-------------
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
Modified: 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/WEB-INF/web.xml 2009-10-20 14:34:49 UTC (rev 201)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml 2009-10-20 14:39:22 UTC (rev 202)
@@ -82,7 +82,7 @@
<!-- ========================================================== -->
<error-page>
<exception-type>java.lang.Exception</exception-type>
- <location>/WEB-INF/pages/errors/uncaughtException.jsp</location>
+ <location>/uncaughtException.jsp</location>
</error-page>
<!-- Internal Server Error -->
<error-page>
Deleted: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/login.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/login.jsp 2009-10-20 14:34:49 UTC (rev 201)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/login.jsp 2009-10-20 14:39:22 UTC (rev 202)
@@ -1,14 +0,0 @@
-<%@ include file="/common/taglibs.jsp"%>
-
-<title><fmt:message key="login.title"/></title>
-<content tag="heading"><fmt:message key="login.title"/></content>
-
-<p>Please fill in following information to login<br/>
-<span class="required">* Required Fields</span></p>
-
-<body id="info"/>
-
-<!-- loginForm.jsp -->
-<c:import url="/WEB-INF/pages/loginForm.jsp"/>
-<!-- password -->
-<p>Forgot your password? Have your <a href="<c:url value="passwordForm.html"/>">password e-mailed to you</a></p>
Deleted: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/logout.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/logout.jsp 2009-10-20 14:34:49 UTC (rev 201)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/logout.jsp 2009-10-20 14:39:22 UTC (rev 202)
@@ -1 +0,0 @@
-<% session.invalidate(); response.sendRedirect("home.html");%>
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/uncaughtException.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/uncaughtException.jsp (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/uncaughtException.jsp 2009-10-20 14:39:22 UTC (rev 202)
@@ -0,0 +1,46 @@
+<%@ include file="/common/taglibs.jsp" %>
+
+<title>Java Uncaught Exception</title>
+<content tag="heading">Uncaught Exception Encountered</content>
+
+<p>
+
+<%
+try {
+ // The Servlet spec guarantees this attribute will be available
+ Throwable exception = (Throwable) request.getAttribute("javax.servlet.error.exception");
+
+ if (exception != null) {
+ if (exception instanceof ServletException) {
+ // It's a ServletException: we should extract the root cause
+ ServletException sex = (ServletException) exception;
+ Throwable rootCause = sex.getRootCause();
+ if (rootCause == null)
+ rootCause = sex;
+ out.println("** Root cause is: "+ rootCause.getMessage());
+ rootCause.printStackTrace(new java.io.PrintWriter(out));
+ }
+ else {
+ // It's not a ServletException, so we'll just show it
+ exception.printStackTrace(new java.io.PrintWriter(out));
+ }
+ }
+ else {
+ out.println("No error information available");
+ }
+
+ // Display cookies
+ out.println("\nCookies:\n");
+ Cookie[] cookies = request.getCookies();
+ if (cookies != null) {
+ for (int i = 0; i < cookies.length; i++) {
+ out.println(cookies[i].getName() + "=[" + cookies[i].getValue() + "]");
+ }
+ }
+
+} catch (Exception ex) {
+ ex.printStackTrace(new java.io.PrintWriter(out));
+}
+%>
+<p>
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-20 14:34:58
|
Revision: 201
http://treebase.svn.sourceforge.net/treebase/?rev=201&view=rev
Author: youjun
Date: 2009-10-20 14:34:49 +0000 (Tue, 20 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/
Removed Paths:
-------------
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/xfire-servlet.xml
Deleted: 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 2009-10-19 20:30:19 UTC (rev 200)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/dwr.xml 2009-10-20 14:34:49 UTC (rev 201)
@@ -1,12 +0,0 @@
-<!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
Deleted: 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 2009-10-19 20:30:19 UTC (rev 200)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/menu-config.xml 2009-10-20 14:34:49 UTC (rev 201)
@@ -1,79 +0,0 @@
-<?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${1+1}"/>
- <Item name="StudyAnalyses" title="search.study.menu.analyses" description="View study's analyses" page="/search/treeSearch.html"/>
- <Item name="StudyMatrices" title="search.study.menu.matrices" description="View study's matrices" page="/search/matrixSearch.html"/>
- <Item name="StudyTrees" title="search.study.menu.trees" description="View study's trees" page="/search/matrixSearch.html"/>
- <Item name="StudyTaxa" title="search.study.menu.taxa" description="View study's taxa" page="/search/matrixSearch.html"/>
- </Menu>
-
- </Menus>
-</MenuConfig>
Deleted: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml 2009-10-19 20:30:19 UTC (rev 200)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/sitemesh.xml 2009-10-20 14:34:49 UTC (rev 201)
@@ -1,17 +0,0 @@
-<sitemesh>
- <property name="decorators-file" value="/WEB-INF/decorators.xml" />
- <excludes file="${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
Modified: 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/WEB-INF/web.xml 2009-10-19 20:30:19 UTC (rev 200)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml 2009-10-20 14:34:49 UTC (rev 201)
@@ -30,84 +30,15 @@
<!-- ========================================================== -->
- <!-- List of Filters -->
- <!-- ========================================================== -->
- <filter>
- <filter-name>sitemesh</filter-name>
- <filter-class>com.opensymphony.module.sitemesh.filter.PageFilter</filter-class>
- </filter>
- <filter>
- <filter-name>securityFilter</filter-name>
- <filter-class>org.acegisecurity.util.FilterToBeanProxy</filter-class>
- <init-param>
- <param-name>targetClass</param-name>
- <param-value>org.acegisecurity.util.FilterChainProxy</param-value>
- </init-param>
- </filter>
- <filter>
- <filter-name>hibernateFilter</filter-name>
- <filter-class>org.springframework.orm.hibernate3.support.OpenSessionInViewFilter</filter-class>
- <init-param>
- <param-name>singleSession</param-name>
- <param-value>true</param-value>
- </init-param>
- </filter>
-
- <filter>
- <filter-name>ResponseOverrideFilter</filter-name>
- <filter-class>org.displaytag.filter.ResponseOverrideFilter</filter-class>
- </filter>
-
-
-
-
- <!-- ========================================================== -->
- <!-- Mappings for Filters defined aboved -->
- <!-- ========================================================== -->
- <filter-mapping>
- <filter-name>securityFilter</filter-name>
- <url-pattern>/*</url-pattern>
- </filter-mapping>
- <filter-mapping>
- <filter-name>sitemesh</filter-name>
- <url-pattern>/*</url-pattern>
- <dispatcher>REQUEST</dispatcher>
- <dispatcher>FORWARD</dispatcher>
- </filter-mapping>
- <filter-mapping>
- <filter-name>hibernateFilter</filter-name>
- <url-pattern>*.html</url-pattern>
- </filter-mapping>
-
- <filter-mapping>
- <filter-name>ResponseOverrideFilter</filter-name>
- <url-pattern>*.jsp</url-pattern>
- </filter-mapping>
- <filter-mapping>
- <filter-name>ResponseOverrideFilter</filter-name>
- <url-pattern>*.html</url-pattern>
- </filter-mapping>
-
-
- <!-- ========================================================== -->
<!-- Name of our servlet processed by Spring's front controller -->
<!-- DispatcherServlet -->
<!-- ========================================================== -->
<servlet>
- <servlet-name>treebase</servlet-name>
+ <servlet-name>TOPServlet</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
- <!-- ========================================================== -->
- <!-- Processed by XFireSpringServlet -->
- <!-- ========================================================== -->
- <!--servlet>
- <servlet-name>XFireServlet</servlet-name>
- <servlet-class>
- org.codehaus.xfire.spring.XFireSpringServlet
- </servlet-class>
- </servlet-->
<!-- ========================================================== -->
<!-- Processed by CXFServlet -->
@@ -125,27 +56,9 @@
<!-- url pattern that will be processed by DispatcherServlet -->
<!-- ========================================================== -->
<servlet-mapping>
- <servlet-name>treebase</servlet-name>
- <url-pattern>*.html</url-pattern>
+ <servlet-name>TOPServlet</servlet-name>
+ <url-pattern>/top/*</url-pattern>
</servlet-mapping>
- <servlet-mapping>
- <servlet-name>treebase</servlet-name>
- <url-pattern>/phylows/*</url-pattern>
- </servlet-mapping>
-
- <!-- ========================================================== -->
- <!-- url pattern that will be processed by XFireSpringServlet -->
- <!-- ========================================================== -->
-
- <!--servlet-mapping>
- <servlet-name>XFireServlet</servlet-name>
- <url-pattern>/servlet/XFireServlet/*</url-pattern>
- </servlet-mapping-->
-
- <!--servlet-mapping>
- <servlet-name>XFireServlet</servlet-name>
- <url-pattern>/services/*</url-pattern>
- </servlet-mapping-->
<!-- ========================================================== -->
<!-- url pattern that will be processed by CXFServlet -->
@@ -155,27 +68,7 @@
<url-pattern>/services/*</url-pattern>
</servlet-mapping>
- <!-- ========================================================== -->
- <!-- DWR Sruff -->
- <!-- ========================================================== -->
- <servlet>
- <servlet-name>dwr</servlet-name>
- <servlet-class>org.directwebremoting.spring.DwrSpringServlet</servlet-class>
- <init-param>
- <param-name>allowGetForSafariButMakeForgeryEasier</param-name>
- <param-value>true</param-value>
- </init-param>
- <init-param>
- <param-name>debug</param-name>
- <param-value>true</param-value>
- </init-param>
- </servlet>
-
- <servlet-mapping>
- <servlet-name>dwr</servlet-name>
- <url-pattern>/dwr/*</url-pattern>
- </servlet-mapping>
<!-- ========================================================== -->
<!-- define some default pages -->
@@ -183,6 +76,7 @@
<welcome-file-list>
<welcome-file>index.jsp</welcome-file>
</welcome-file-list>
+
<!-- ========================================================== -->
<!-- Error Pages -->
<!-- ========================================================== -->
Deleted: 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/WEB-INF/xfire-servlet.xml 2009-10-19 20:30:19 UTC (rev 200)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/xfire-servlet.xml 2009-10-20 14:34:49 UTC (rev 201)
@@ -1,52 +0,0 @@
-<?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 -->
- <!-- ========================================================== -->
-
- <import resource="classpath:org/codehaus/xfire/spring/xfire.xml"/>
-
-
- <bean id="searchStudiesByKeyword"
- class="org.cipres.treebase.web.webservices.StudyServiceByKeywordImp">
- <property name="studyService"><ref bean="studyService"></ref></property>
- </bean>
-
- <bean id="webAnnotations"
- class="org.codehaus.xfire.annotations.jsr181.Jsr181WebAnnotations"/>
- <bean id="handlerMapping"
- class="org.codehaus.xfire.spring.remoting.Jsr181HandlerMapping">
- <property name="typeMappingRegistry">
- <ref bean="xfire.typeMappingRegistry"/>
- </property>
- <property name="xfire">
- <ref bean="xfire"/>
- </property>
- <property name="webAnnotations">
- <ref bean="webAnnotations"/>
- </property>
- </bean>
-
- <bean class="org.springframework.web.servlet.handler.SimpleUrlHandlerMapping">
- <property name="urlMap">
- <map>
- <entry key="/">
- <ref bean="handlerMapping"/>
- </entry>
- </map>
- </property>
- </bean>
-
-
-
-</beans>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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>
+ <!--...
[truncated message content] |
|
From: <rsc...@us...> - 2009-10-16 13:26:18
|
Revision: 199
http://treebase.svn.sourceforge.net/treebase/?rev=199&view=rev
Author: rscherle
Date: 2009-10-16 13:26:10 +0000 (Fri, 16 Oct 2009)
Log Message:
-----------
updated citations from recent curation work
Modified Paths:
--------------
trunk/treebase-curation/studyCitations.enl
Modified: trunk/treebase-curation/studyCitations.enl
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-15 15:03:34
|
Revision: 198
http://treebase.svn.sourceforge.net/treebase/?rev=198&view=rev
Author: youjun
Date: 2009-10-15 15:03:26 +0000 (Thu, 15 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/pom.xml
Modified: trunk/oai-pmh_data_provider/data_provider_web/pom.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/pom.xml 2009-10-14 00:09:08 UTC (rev 197)
+++ trunk/oai-pmh_data_provider/data_provider_web/pom.xml 2009-10-15 15:03:26 UTC (rev 198)
@@ -8,7 +8,7 @@
<groupId>org.treebase.oai</groupId>
<artifactId>data_provider_web</artifactId>
<packaging>war</packaging>
- <name>data_provider_web Maven Webapp</name>
+ <name>data_provider_web</name>
<version>0.0.1-SNAPSHOT</version>
<url>http://maven.apache.org</url>
<build>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-14 00:09:14
|
Revision: 197
http://treebase.svn.sourceforge.net/treebase/?rev=197&view=rev
Author: youjun
Date: 2009-10-14 00:09:08 +0000 (Wed, 14 Oct 2009)
Log Message:
-----------
Added Paths:
-----------
trunk/oai-pmh_data_provider/
Removed Paths:
-------------
trunk/oai-pmh_data_provider/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-14 00:08:28
|
Revision: 196
http://treebase.svn.sourceforge.net/treebase/?rev=196&view=rev
Author: youjun
Date: 2009-10-14 00:08:19 +0000 (Wed, 14 Oct 2009)
Log Message:
-----------
Removed Paths:
-------------
trunk/data_provider/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-13 23:42:23
|
Revision: 195
http://treebase.svn.sourceforge.net/treebase/?rev=195&view=rev
Author: youjun
Date: 2009-10-13 23:42:14 +0000 (Tue, 13 Oct 2009)
Log Message:
-----------
Added Paths:
-----------
trunk/oai-pmh_data_provider/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-13 18:08:29
|
Revision: 194
http://treebase.svn.sourceforge.net/treebase/?rev=194&view=rev
Author: youjun
Date: 2009-10-13 18:08:17 +0000 (Tue, 13 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/data_provider/data_provider_web/pom.xml
Modified: trunk/data_provider/data_provider_web/pom.xml
===================================================================
--- trunk/data_provider/data_provider_web/pom.xml 2009-10-13 17:52:04 UTC (rev 193)
+++ trunk/data_provider/data_provider_web/pom.xml 2009-10-13 18:08:17 UTC (rev 194)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?><project>
<parent>
- <artifactId>data_provider</artifactId>
+ <artifactId>oai-pmh_data_provider</artifactId>
<groupId>org.treebase.oai</groupId>
<version>0.0.1-SNAPSHOT</version>
</parent>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-13 17:52:17
|
Revision: 193
http://treebase.svn.sourceforge.net/treebase/?rev=193&view=rev
Author: youjun
Date: 2009-10-13 17:52:04 +0000 (Tue, 13 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/data_provider/.classpath
trunk/data_provider/.project
trunk/data_provider/.settings/org.eclipse.jdt.core.prefs
trunk/data_provider/data_provider_core/.classpath
trunk/data_provider/data_provider_core/.project
trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs
trunk/data_provider/data_provider_core/pom.xml
trunk/data_provider/data_provider_web/.classpath
trunk/data_provider/data_provider_web/.project
trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs
trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml
trunk/data_provider/pom.xml
Added Paths:
-----------
trunk/data_provider/data_provider_core/src/test/resources/jdbc.properties
trunk/data_provider/data_provider_core/target/data_provider_core-0.0.1-SNAPSHOT.jar
trunk/data_provider/data_provider_core/target/maven-archiver/
trunk/data_provider/data_provider_core/target/maven-archiver/pom.properties
trunk/data_provider/data_provider_core/target/surefire-reports/
trunk/data_provider/data_provider_core/target/surefire-reports/TEST-org.treebase.oai.AppTest.xml
trunk/data_provider/data_provider_core/target/surefire-reports/org.treebase.oai.AppTest.txt
trunk/data_provider/data_provider_core/target/test-classes/jdbc.properties
trunk/data_provider/data_provider_web/target/data_provider_web/
trunk/data_provider/data_provider_web/target/data_provider_web/META-INF/
trunk/data_provider/data_provider_web/target/data_provider_web/META-INF/MANIFEST.MF
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/classes/
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/avalon-framework-4.1.3.jar
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-logging-1.1.jar
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/log4j-1.2.13.jar
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/logkit-1.0.1.jar
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/servlet-api-2.4.jar
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-2.0.7.jar
trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml
trunk/data_provider/data_provider_web/target/data_provider_web/index.jsp
Modified: trunk/data_provider/.classpath
===================================================================
--- trunk/data_provider/.classpath 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/.classpath 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <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"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
Modified: trunk/data_provider/.project
===================================================================
--- trunk/data_provider/.project 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/.project 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
- <name>data_provider</name>
+ <name>oai-pmh_data_provider</name>
<comment></comment>
<projects>
</projects>
Modified: trunk/data_provider/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/data_provider/.settings/org.eclipse.jdt.core.prefs 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/.settings/org.eclipse.jdt.core.prefs 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,5 +1,5 @@
-#Mon Oct 12 12:48:37 EDT 2009
+#Tue Oct 13 10:33:09 EDT 2009
eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
-org.eclipse.jdt.core.compiler.compliance=1.4
-org.eclipse.jdt.core.compiler.source=1.3
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.source=1.5
Modified: trunk/data_provider/data_provider_core/.classpath
===================================================================
--- trunk/data_provider/data_provider_core/.classpath 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_core/.classpath 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
- <classpathentry kind="src" path="src/main/resources"/>
- <classpathentry kind="src" path="src/test/resources"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <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.eclipse.jst.j2ee.internal.module.container"/>
<classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
- <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
Modified: trunk/data_provider/data_provider_core/.project
===================================================================
--- trunk/data_provider/data_provider_core/.project 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_core/.project 2009-10-13 17:52:04 UTC (rev 193)
@@ -16,12 +16,12 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>org.maven.ide.eclipse.maven2Builder</name>
+ <name>org.eclipse.wst.validation.validationbuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.wst.validation.validationbuilder</name>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
Modified: trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,7 +1,7 @@
-#Mon Oct 12 16:25:16 EDT 2009
+#Tue Oct 13 10:33:10 EDT 2009
eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
-org.eclipse.jdt.core.compiler.compliance=1.4
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
org.eclipse.jdt.core.compiler.problem.assertIdentifier=warning
org.eclipse.jdt.core.compiler.problem.enumIdentifier=warning
-org.eclipse.jdt.core.compiler.source=1.3
+org.eclipse.jdt.core.compiler.source=1.5
Modified: trunk/data_provider/data_provider_core/pom.xml
===================================================================
--- trunk/data_provider/data_provider_core/pom.xml 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_core/pom.xml 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?><project>
<parent>
- <artifactId>data_provider</artifactId>
+ <artifactId>oai-pmh_data_provider</artifactId>
<groupId>org.treebase.oai</groupId>
<version>0.0.1-SNAPSHOT</version>
</parent>
Added: trunk/data_provider/data_provider_core/src/test/resources/jdbc.properties
===================================================================
--- trunk/data_provider/data_provider_core/src/test/resources/jdbc.properties (rev 0)
+++ trunk/data_provider/data_provider_core/src/test/resources/jdbc.properties 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,21 @@
+# This is treebase-core jdbc.properties
+
+jdbc.driverClassName=org.postgresql.Driver
+jdbc.url=jdbc:postgresql://treebasedb-dev.nescent.org/treebasedev
+jdbc.username=treebase_app
+jdbc.password=tim5tema
+
+
+hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
+
+#for development only:
+#hibernate.show_sql=true
+#hibernate.format_sql=true
+#hibernate.generate_statistics=true
+#hibernate.use_sql_comments=true
+
+#options are: validate | update | create | create-drop
+hibernate.hbm2ddl.auto=
+
+#Mesquite installation directory
+mesquite.folder_dir=/home/mjd/Mesquite_Folder/
\ No newline at end of file
Added: trunk/data_provider/data_provider_core/target/data_provider_core-0.0.1-SNAPSHOT.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_core/target/data_provider_core-0.0.1-SNAPSHOT.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_core/target/maven-archiver/pom.properties
===================================================================
--- trunk/data_provider/data_provider_core/target/maven-archiver/pom.properties (rev 0)
+++ trunk/data_provider/data_provider_core/target/maven-archiver/pom.properties 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,5 @@
+#Generated by Maven
+#Tue Oct 13 10:46:39 EDT 2009
+version=0.0.1-SNAPSHOT
+groupId=org.treebase.oai
+artifactId=data_provider_core
Added: trunk/data_provider/data_provider_core/target/surefire-reports/TEST-org.treebase.oai.AppTest.xml
===================================================================
--- trunk/data_provider/data_provider_core/target/surefire-reports/TEST-org.treebase.oai.AppTest.xml (rev 0)
+++ trunk/data_provider/data_provider_core/target/surefire-reports/TEST-org.treebase.oai.AppTest.xml 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<testsuite failures="0" time="0.031" errors="0" skipped="0" tests="1" name="org.treebase.oai.AppTest">
+ <properties>
+ <property name="java.vendor" value="Sun Microsystems Inc."/>
+ <property name="localRepository" value="C:\Documents and Settings\youjun/.m2/repository"/>
+ <property name="sun.java.launcher" value="SUN_STANDARD"/>
+ <property name="sun.management.compiler" value="HotSpot Client Compiler"/>
+ <property name="env.PROMPT" value="$P$G"/>
+ <property name="os.name" value="Windows XP"/>
+ <property name="env.FP_NO_HOST_CHECK" value="NO"/>
+ <property name="sun.boot.class.path" value="C:\Java\sdk\jdk\jre\lib\resources.jar;C:\Java\sdk\jdk\jre\lib\rt.jar;C:\Java\sdk\jdk\jre\lib\sunrsasign.jar;C:\Java\sdk\jdk\jre\lib\jsse.jar;C:\Java\sdk\jdk\jre\lib\jce.jar;C:\Java\sdk\jdk\jre\lib\charsets.jar;C:\Java\sdk\jdk\jre\classes"/>
+ <property name="env.COMPUTERNAME" value="YALE-LD6ICZM0YC"/>
+ <property name="env.ALLUSERSPROFILE" value="C:\Documents and Settings\All Users"/>
+ <property name="sun.desktop" value="windows"/>
+ <property name="java.vm.specification.vendor" value="Sun Microsystems Inc."/>
+ <property name="java.runtime.version" value="1.6.0_16-b01"/>
+ <property name="env.HOMEPATH" value="\Documents and Settings\youjun"/>
+ <property name="user.name" value="youjun"/>
+ <property name="user.language" value="en"/>
+ <property name="sun.boot.library.path" value="C:\Java\sdk\jdk\jre\bin"/>
+ <property name="classworlds.conf" value="C:\eclipse\workspace\.metadata\.plugins\org.maven.ide.eclipse\launches\m2conf4321837184906225390.tmp"/>
+ <property name="java.version" value="1.6.0_16"/>
+ <property name="env.PROCESSOR_IDENTIFIER" value="x86 Family 15 Model 3 Stepping 4, GenuineIntel"/>
+ <property name="user.timezone" value=""/>
+ <property name="env.INCLUDE" value="C:\Program Files\Microsoft Visual Studio .NET 2003\SDK\v1.1\include\;C:\Program Files\Microsoft Visual Studio\VC98\atl\include;C:\Program Files\Microsoft Visual Studio\VC98\mfc\include;C:\Program Files\Microsoft Visual Studio\VC98\include"/>
+ <property name="env.CLIENTNAME" value="Console"/>
+ <property name="env.TEMP" value="C:\DOCUME~1\youjun\LOCALS~1\Temp"/>
+ <property name="sun.arch.data.model" value="32"/>
+ <property name="env.AXISCLASSPATH" value="C:\Java\axis-1_2RC2\lib\axis.jar;C:\Java\axis-1_2RC2\lib\commons-discovery.jar;C:\Java\axis-1_2RC2\lib\commons-logging.jar;C:\Java\axis-1_2RC2\lib\jaxrpc.jar;C:\Java\axis-1_2RC2\lib\saaj.jar;C:\Java\axis-1_2RC2\lib\log4j-1.2.8.jar;C:\Java\axis-1_2RC2\lib\xml-apis.jar;C:\Java\axis-1_2RC2\lib\xercesImpl.jar"/>
+ <property name="java.endorsed.dirs" value="C:\Java\sdk\jdk\jre\lib\endorsed"/>
+ <property name="sun.cpu.isalist" value=""/>
+ <property name="env.HOMEDRIVE" value="C:"/>
+ <property name="sun.jnu.encoding" value="Cp1252"/>
+ <property name="file.encoding.pkg" value="sun.io"/>
+ <property name="file.separator" value="\"/>
+ <property name="java.specification.name" value="Java Platform API Specification"/>
+ <property name="java.class.version" value="50.0"/>
+ <property name="user.country" value="US"/>
+ <property name="java.home" value="C:\Java\sdk\jdk\jre"/>
+ <property name="env.APPDATA" value="C:\Documents and Settings\youjun\Application Data"/>
+ <property name="java.vm.info" value="mixed mode"/>
+ <property name="env.ComSpec" value="C:\WINDOWS\system32\cmd.exe"/>
+ <property name="env.OS" value="Windows_NT"/>
+ <property name="env.CommonProgramFiles" value="C:\Program Files\Common Files"/>
+ <property name="os.version" value="5.1"/>
+ <property name="path.separator" value=";"/>
+ <property name="java.vm.version" value="14.2-b01"/>
+ <property name="user.variant" value=""/>
+ <property name="env.USERPROFILE" value="C:\Documents and Settings\youjun"/>
+ <property name="env.LIB" value="C:\Program Files\Microsoft Visual Studio .NET 2003\SDK\v1.1\Lib\;C:\Program Files\Microsoft Visual Studio\VC98\mfc\lib;C:\Program Files\Microsoft Visual Studio\VC98\lib"/>
+ <property name="env.JAVA_HOME" value="C:\Java\sdk\jdk\jre\bin"/>
+ <property name="java.awt.printerjob" value="sun.awt.windows.WPrinterJob"/>
+ <property name="env.TMP" value="C:\DOCUME~1\youjun\LOCALS~1\Temp"/>
+ <property name="sun.io.unicode.encoding" value="UnicodeLittle"/>
+ <property name="awt.toolkit" value="sun.awt.windows.WToolkit"/>
+ <property name="env.MSDevDir" value="C:\Program Files\Microsoft Visual Studio\Common\MSDev98"/>
+ <property name="user.home" value="C:\Documents and Settings\youjun"/>
+ <property name="env.SESSIONNAME" value="Console"/>
+ <property name="java.specification.vendor" value="Sun Microsystems Inc."/>
+ <property name="env.CLASSPATH" value=".;C:\Java\axis-1_2RC2\lib\axis.jar;C:\Java\axis-1_2RC2\lib\commons-discovery.jar;C:\Java\axis-1_2RC2\lib\commons-logging.jar;C:\Java\axis-1_2RC2\lib\jaxrpc.jar;C:\Java\axis-1_2RC2\lib\saaj.jar;C:\Java\axis-1_2RC2\lib\log4j-1.2.8.jar;C:\Java\axis-1_2RC2\lib\xml-apis.jar;C:\Java\axis-1_2RC2\lib\xercesImpl.jar"/>
+ <property name="env.NUMBER_OF_PROCESSORS" value="2"/>
+ <property name="java.library.path" value="C:\Java\sdk\jdk\jre\bin;.;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Java\jdk1.5.0_02\bin;C:\Program Files\Common Files\Adobe\AGL;"C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier";C:\Java\sdk5\bin;C:\Java\sdk\bin;C:\Program Files\Microsoft Visual Studio\Common\Tools\WinNT;C:\Program Files\Microsoft Visual Studio\Common\MSDev98\Bin;C:\Program Files\Microsoft Visual Studio\Common\Tools;C:\Program Files\Microsoft Visual Studio\VC98\bin"/>
+ <property name="java.vendor.url" value="http://java.sun.com/"/>
+ <property name="java.vm.vendor" value="Sun Microsystems Inc."/>
+ <property name="maven.home" value="EMBEDDED"/>
+ <property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/>
+ <property name="java.class.path" value="/C:/eclipse/jee/plugins/org.maven.ide.components.maven_embedder_2.1.0.20080530-2300/jars/plexus-classworlds-1.2-alpha-12.jar"/>
+ <property name="java.vm.specification.name" value="Java Virtual Machine Specification"/>
+ <property name="env.LOGONSERVER" value="\\YALE-LD6ICZM0YC"/>
+ <property name="env.windir" value="C:\WINDOWS"/>
+ <property name="java.vm.specification.version" value="1.0"/>
+ <property name="env.PROCESSOR_ARCHITECTURE" value="x86"/>
+ <property name="m2eclipse.workspace.state" value="C:\eclipse\workspace\.metadata\.plugins\org.maven.ide.eclipse\workspacestate.properties"/>
+ <property name="sun.os.patch.level" value="Service Pack 3"/>
+ <property name="sun.cpu.endian" value="little"/>
+ <property name="env.ProgramFiles" value="C:\Program Files"/>
+ <property name="surefire.test.class.path" value="C:\eclipse\workspace\data_provider\data_provider_core\target\test-classes;C:\eclipse\workspace\data_provider\data_provider_core\target\classes;C:\Documents and Settings\youjun\.m2\repository\org\springframework\spring\2.0.7\spring-2.0.7.jar;C:\Documents and Settings\youjun\.m2\repository\commons-logging\commons-logging\1.1\commons-logging-1.1.jar;C:\Documents and Settings\youjun\.m2\repository\log4j\log4j\1.2.13\log4j-1.2.13.jar;C:\Documents and Settings\youjun\.m2\repository\logkit\logkit\1.0.1\logkit-1.0.1.jar;C:\Documents and Settings\youjun\.m2\repository\avalon-framework\avalon-framework\4.1.3\avalon-framework-4.1.3.jar;C:\Documents and Settings\youjun\.m2\repository\javax\servlet\servlet-api\2.3\servlet-api-2.3.jar;C:\Documents and Settings\youjun\.m2\repository\org\springframework\spring-mock\2.0.7\spring-mock-2.0.7.jar;C:\Documents and Settings\youjun\.m2\repository\junit\junit\3.8.1\junit-3.8.1.jar;C:\Documents and Settings\youjun\.m2\repository\postgresql\postgresql\8.3-603.jdbc3\postgresql-8.3-603.jdbc3.jar;C:\Documents and Settings\youjun\.m2\repository\org\acegisecurity\acegi-security\1.0.1\acegi-security-1.0.1.jar;C:\Documents and Settings\youjun\.m2\repository\commons-codec\commons-codec\1.3\commons-codec-1.3.jar;C:\Documents and Settings\youjun\.m2\repository\oro\oro\2.0.8\oro-2.0.8.jar;C:\Documents and Settings\youjun\.m2\repository\commons-collections\commons-collections\3.1\commons-collections-3.1.jar;C:\Documents and Settings\youjun\.m2\repository\c3p0\c3p0\0.9.1.2\c3p0-0.9.1.2.jar;C:\Documents and Settings\youjun\.m2\repository\org\hibernate\hibernate-annotations\3.3.1.GA\hibernate-annotations-3.3.1.GA.jar;C:\Documents and Settings\youjun\.m2\repository\org\hibernate\hibernate\3.2.6.ga\hibernate-3.2.6.ga.jar;C:\Documents and Settings\youjun\.m2\repository\net\sf\ehcache\ehcache\1.2.3\ehcache-1.2.3.jar;C:\Documents and Settings\youjun\.m2\repository\javax\transaction\jta\1.0.1B\jta-1.0.1B.jar;C:\Documents and Settings\youjun\.m2\repository\dom4j\dom4j\1.6.1\dom4j-1.6.1.jar;C:\Documents and Settings\youjun\.m2\repository\antlr\antlr\2.7.6\antlr-2.7.6.jar;C:\Documents and Settings\youjun\.m2\repository\org\hibernate\hibernate-commons-annotations\3.0.0.ga\hibernate-commons-annotations-3.0.0.ga.jar;C:\Documents and Settings\youjun\.m2\repository\org\hibernate\ejb3-persistence\1.0.1.GA\ejb3-persistence-1.0.1.GA.jar;C:\Documents and Settings\youjun\.m2\repository\cglib\cglib-nodep\2.1_3\cglib-nodep-2.1_3.jar;C:\Documents and Settings\youjun\.m2\repository\commons-lang\commons-lang\2.1\commons-lang-2.1.jar;C:\Documents and Settings\youjun\.m2\repository\ibm\db2jcc\2.6.80\db2jcc-2.6.80.jar;C:\Documents and Settings\youjun\.m2\repository\ibm\db2jcc_license_cu\2.6.80\db2jcc_license_cu-2.6.80.jar;C:\Documents and Settings\youjun\.m2\repository\javax\sql\jdbc-stdext\2.0\jdbc-stdext-2.0.jar;C:\Documents and Settings\youjun\.m2\repository\jdom\jdom\1.1\jdom-1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-frontend-jaxws\2.1.1\cxf-rt-frontend-jaxws-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-jaxws_2.1_spec\1.0\geronimo-jaxws_2.1_spec-1.0.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-activation_1.1_spec\1.0.2\geronimo-activation_1.1_spec-1.0.2.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-api\2.1.1\cxf-api-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-common-utilities\2.1.1\cxf-common-utilities-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\springframework\spring-core\2.0.8\spring-core-2.0.8.jar;C:\Documents and Settings\youjun\.m2\repository\org\springframework\spring-beans\2.0.8\spring-beans-2.0.8.jar;C:\Documents and Settings\youjun\.m2\repository\org\springframework\spring-context\2.0.8\spring-context-2.0.8.jar;C:\Documents and Settings\youjun\.m2\repository\aopalliance\aopalliance\1.0\aopalliance-1.0.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-annotation_1.0_spec\1.1.1\geronimo-annotation_1.0_spec-1.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\javax\xml\bind\jaxb-api\2.1\jaxb-api-2.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-stax-api_1.0_spec\1.0.1\geronimo-stax-api_1.0_spec-1.0.1.jar;C:\Documents and Settings\youjun\.m2\repository\wsdl4j\wsdl4j\1.6.1\wsdl4j-1.6.1.jar;C:\Documents and Settings\youjun\.m2\repository\xml-resolver\xml-resolver\1.2\xml-resolver-1.2.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\ws\commons\schema\XmlSchema\1.4.2\XmlSchema-1.4.2.jar;C:\Documents and Settings\youjun\.m2\repository\org\codehaus\woodstox\wstx-asl\3.2.4\wstx-asl-3.2.4.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\neethi\neethi\2.0.4\neethi-2.0.4.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-common-schemas\2.1.1\cxf-common-schemas-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-core\2.1.1\cxf-rt-core-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\com\sun\xml\bind\jaxb-impl\2.1.6\jaxb-impl-2.1.6.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-javamail_1.4_spec\1.3\geronimo-javamail_1.4_spec-1.3.jar;C:\Documents and Settings\youjun\.m2\repository\com\sun\xml\fastinfoset\FastInfoset\1.2.2\FastInfoset-1.2.2.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-bindings-soap\2.1.1\cxf-rt-bindings-soap-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-tools-common\2.1.1\cxf-tools-common-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\velocity\velocity\1.4\velocity-1.4.jar;C:\Documents and Settings\youjun\.m2\repository\velocity\velocity-dep\1.4\velocity-dep-1.4.jar;C:\Documents and Settings\youjun\.m2\repository\com\sun\xml\bind\jaxb-xjc\2.1.6\jaxb-xjc-2.1.6.jar;C:\Documents and Settings\youjun\.m2\repository\javax\xml\soap\saaj-api\1.3\saaj-api-1.3.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-ws-metadata_2.0_spec\1.1.2\geronimo-ws-metadata_2.0_spec-1.1.2.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-databinding-jaxb\2.1.1\cxf-rt-databinding-jaxb-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-bindings-xml\2.1.1\cxf-rt-bindings-xml-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-frontend-simple\2.1.1\cxf-rt-frontend-simple-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-ws-addr\2.1.1\cxf-rt-ws-addr-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\com\sun\xml\messaging\saaj\saaj-impl\1.3\saaj-impl-1.3.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-transports-http\2.1.1\cxf-rt-transports-http-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\springframework\spring-web\2.0.8\spring-web-2.0.8.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\cxf\cxf-rt-transports-http-jetty\2.1.1\cxf-rt-transports-http-jetty-2.1.1.jar;C:\Documents and Settings\youjun\.m2\repository\org\mortbay\jetty\jetty\6.1.9\jetty-6.1.9.jar;C:\Documents and Settings\youjun\.m2\repository\org\mortbay\jetty\jetty-util\6.1.9\jetty-util-6.1.9.jar;C:\Documents and Settings\youjun\.m2\repository\org\apache\geronimo\specs\geronimo-servlet_2.5_spec\1.2\geronimo-servlet_2.5_spec-1.2.jar;C:\Documents and Settings\youjun\.m2\repository\xml-apis\xml-apis\1.0.b2\xml-apis-1.0.b2.jar;"/>
+ <property name="java.io.tmpdir" value="C:\DOCUME~1\youjun\LOCALS~1\Temp\"/>
+ <property name="env.PROCESSOR_REVISION" value="0304"/>
+ <property name="java.vendor.url.bug" value="http://java.sun.com/cgi-bin/bugreport.cgi"/>
+ <property name="env.SystemRoot" value="C:\WINDOWS"/>
+ <property name="java.awt.graphicsenv" value="sun.awt.Win32GraphicsEnvironment"/>
+ <property name="os.arch" value="x86"/>
+ <property name="java.ext.dirs" value="C:\Java\sdk\jdk\jre\lib\ext;C:\WINDOWS\Sun\Java\lib\ext"/>
+ <property name="env.tvdumpflags" value="8"/>
+ <property name="user.dir" value="C:\eclipse\workspace\data_provider\data_provider_core"/>
+ <property name="env.VS71COMNTOOLS" value="C:\Program Files\Microsoft Visual Studio .NET 2003\Common7\Tools\"/>
+ <property name="line.separator" value="
+"/>
+ <property name="java.vm.name" value="Java HotSpot(TM) Client VM"/>
+ <property name="env.PATHEXT" value=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH"/>
+ <property name="env.Path" value="C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Java\jdk1.5.0_02\bin;C:\Program Files\Common Files\Adobe\AGL;"C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier";C:\Java\sdk5\bin;C:\Java\sdk\bin;C:\Program Files\Microsoft Visual Studio\Common\Tools\WinNT;C:\Program Files\Microsoft Visual Studio\Common\MSDev98\Bin;C:\Program Files\Microsoft Visual Studio\Common\Tools;C:\Program Files\Microsoft Visual Studio\VC98\bin"/>
+ <property name="env.AXIS_LIB" value="C:\Java\axis-1_2RC2\lib"/>
+ <property name="basedir" value="C:\eclipse\workspace\data_provider\data_provider_core"/>
+ <property name="maven.mode.standalone" value="true"/>
+ <property name="env.USERNAME" value="youjun"/>
+ <property name="env.SystemDrive" value="C:"/>
+ <property name="file.encoding" value="Cp1252"/>
+ <property name="env.USERDOMAIN" value="YALE-LD6ICZM0YC"/>
+ <property name="java.specification.version" value="1.6"/>
+ <property name="env.PROCESSOR_LEVEL" value="15"/>
+ </properties>
+ <testcase time="0" classname="org.treebase.oai.AppTest" name="testApp"/>
+</testsuite>
\ No newline at end of file
Added: trunk/data_provider/data_provider_core/target/surefire-reports/org.treebase.oai.AppTest.txt
===================================================================
--- trunk/data_provider/data_provider_core/target/surefire-reports/org.treebase.oai.AppTest.txt (rev 0)
+++ trunk/data_provider/data_provider_core/target/surefire-reports/org.treebase.oai.AppTest.txt 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,4 @@
+-------------------------------------------------------------------------------
+Test set: org.treebase.oai.AppTest
+-------------------------------------------------------------------------------
+Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec
Added: trunk/data_provider/data_provider_core/target/test-classes/jdbc.properties
===================================================================
--- trunk/data_provider/data_provider_core/target/test-classes/jdbc.properties (rev 0)
+++ trunk/data_provider/data_provider_core/target/test-classes/jdbc.properties 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,21 @@
+# This is treebase-core jdbc.properties
+
+jdbc.driverClassName=org.postgresql.Driver
+jdbc.url=jdbc:postgresql://treebasedb-dev.nescent.org/treebasedev
+jdbc.username=treebase_app
+jdbc.password=tim5tema
+
+
+hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
+
+#for development only:
+#hibernate.show_sql=true
+#hibernate.format_sql=true
+#hibernate.generate_statistics=true
+#hibernate.use_sql_comments=true
+
+#options are: validate | update | create | create-drop
+hibernate.hbm2ddl.auto=
+
+#Mesquite installation directory
+mesquite.folder_dir=/home/mjd/Mesquite_Folder/
\ No newline at end of file
Modified: trunk/data_provider/data_provider_web/.classpath
===================================================================
--- trunk/data_provider/data_provider_web/.classpath 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_web/.classpath 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,15 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java"/>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
- <classpathentry kind="src" path="src/main/java"/>
- <classpathentry kind="src" path="src/test/java"/>
- <classpathentry kind="src" path="src/test/resources"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <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.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"/>
Modified: trunk/data_provider/data_provider_web/.project
===================================================================
--- trunk/data_provider/data_provider_web/.project 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_web/.project 2009-10-13 17:52:04 UTC (rev 193)
@@ -6,11 +6,6 @@
</projects>
<buildSpec>
<buildCommand>
- <name>org.eclipse.wst.jsdt.core.javascriptValidator</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
<name>org.eclipse.wst.common.project.facet.core.builder</name>
<arguments>
</arguments>
Modified: trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,7 +1,7 @@
-#Mon Oct 12 12:59:49 EDT 2009
+#Tue Oct 13 10:33:14 EDT 2009
eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
-org.eclipse.jdt.core.compiler.compliance=1.4
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=warning
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=warning
-org.eclipse.jdt.core.compiler.source=1.3
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.5
Modified: trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,11 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="data_provider_web">
- <wb-resource deploy-path="/" source-path="/src/main/webapp"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
- <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/test/java"/>
- <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/test/resources"/>
+ <wb-resource deploy-path="/" source-path="/src/main/webapp"/>
<dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/data_provider_core/data_provider_core">
<dependency-type>uses</dependency-type>
</dependent-module>
Modified: trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml 2009-10-13 17:52:04 UTC (rev 193)
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<faceted-project>
- <installed facet="jst.java" version="1.4"/>
+ <installed facet="jst.java" version="5.0"/>
<installed facet="jst.web" version="2.3"/>
</faceted-project>
Added: trunk/data_provider/data_provider_web/target/data_provider_web/META-INF/MANIFEST.MF
===================================================================
--- trunk/data_provider/data_provider_web/target/data_provider_web/META-INF/MANIFEST.MF (rev 0)
+++ trunk/data_provider/data_provider_web/target/data_provider_web/META-INF/MANIFEST.MF 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Class-Path:
+
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/avalon-framework-4.1.3.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/avalon-framework-4.1.3.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-logging-1.1.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/commons-logging-1.1.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/log4j-1.2.13.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/log4j-1.2.13.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/logkit-1.0.1.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/logkit-1.0.1.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/servlet-api-2.4.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/servlet-api-2.4.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-2.0.7.jar
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/spring-2.0.7.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml
===================================================================
--- trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml (rev 0)
+++ trunk/data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,7 @@
+<!DOCTYPE web-app PUBLIC
+ "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN"
+ "http://java.sun.com/dtd/web-app_2_3.dtd" >
+
+<web-app>
+ <display-name>Archetype Created Web Application</display-name>
+</web-app>
Added: trunk/data_provider/data_provider_web/target/data_provider_web/index.jsp
===================================================================
--- trunk/data_provider/data_provider_web/target/data_provider_web/index.jsp (rev 0)
+++ trunk/data_provider/data_provider_web/target/data_provider_web/index.jsp 2009-10-13 17:52:04 UTC (rev 193)
@@ -0,0 +1,5 @@
+<html>
+<body>
+<h2>Hello World!</h2>
+</body>
+</html>
Modified: trunk/data_provider/pom.xml
===================================================================
--- trunk/data_provider/pom.xml 2009-10-12 23:12:11 UTC (rev 192)
+++ trunk/data_provider/pom.xml 2009-10-13 17:52:04 UTC (rev 193)
@@ -2,10 +2,10 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.treebase.oai</groupId>
- <artifactId>data_provider</artifactId>
+ <artifactId>oai-pmh_data_provider</artifactId>
<packaging>pom</packaging>
<version>0.0.1-SNAPSHOT</version>
- <name>data_provider</name>
+ <name>oai-pmh_data_provider</name>
<url>http://maven.apache.org</url>
<!-- issueManagement>
<system>FogBugz</system>
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