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[Treebase-guts] SF.net SVN: treebase:[210] trunk/oai-pmh_data_provider/data_provider_core
|
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 @@
+M1000
+M1001
+M1002
+M1003
+M1004
+M1005
+M1006
+M1007
+M1008
+M1009
+M1010
+M1011
+M1012
+M1013
+M1014
+M1015
+M1016
+M1017
+M1018
+M1019
+M101c2x3x96c12c55c08
+M101c2x3x96c13c11c04
+M1020
+M1021
+M1022
+M1023
+M1024
+M1025
+M1026
+M1027
+M1028
+M1029
+M102c2x3x96c13c14c20
+M1030
+M1031
+M1032
+M1033
+M1034
+M1035
+M1036
+M1037
+M1038
+M1039
+M103c2x3x96c13c22c21
+M1040
+M1041
+M1042
+M1043
+M1044
+M1045
+M1046
+M1047
+M1048
+M1049
+M104c2x3x96c13c27c15
+M1050
+M1051
+M1052
+M1053
+M1054
+M1055
+M1056
+M1057
+M1058
+M1059
+M105c2x3x96c13c36c53
+M1060
+M1061
+M1062
+M1063
+M1064
+M1065
+M1066
+M1067
+M1068
+M106c2x3x96c13c42c44
+M1075
+M1076
+M1077
+M1078
+M1079
+M107c2x3x96c13c47c16
+M1080
+M1081
+M1082
+M1083
+M1084
+M1085
+M1086
+M1087
+M1088
+M1089
+M108c2x3x96c13c54c35
+M1090
+M1091
+M1092
+M1093
+M1094
+M1095
+M1096
+M1097
+M1098
+M1099
+M109c2x3x96c13c55c52
+M10c11x4x95c21c26c07
+M1100
+M1101
+M1102
+M1105
+M1106
+M1107
+M1108
+M1109
+M110c2x3x96c16c42c29
+M1110
+M1111
+M1112
+M1113
+M1114
+M1115
+M1116
+M1117
+M1118
+M1119
+M111c2x3x96c16c46c54
+M1120
+M1121
+M1122
+M1123
+M1124
+M1125
+M1126
+M1128
+M112c2x3x96c16c50c04
+M1130
+M1131
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