<commit_before><!--  $Id$ -->
<andromda>
	<properties>
		<property name="modelValidation">${modelValidation}</property>
		<property name="cartridgeFilter">${filter}</property>
		<property name="loggingConfigurationUri">
			file:${project.basedir}/src/main/conf/log4j.xml
		</property>
	</properties>
	<server>
		<host>localhost</host>
		<port>4445</port>
	</server>
	<repositories>
		<repository name="netBeansMDR">
			<models>
				<model>
					<uri>
						jar:file:${project.basedir}/src/main/uml/gemma-om.xml.zip!/gemma-om.xml
					</uri>
					<moduleSearchLocations>
						<location patterns="**/*.xml.zip, **/*.uml2">
							${settings.localRepository}/org/andromda/profiles
						</location>
					</moduleSearchLocations>
				</model>
			</models>
		</repository>
	</repositories>
	<mappingsSearchLocations>
		<location patterns="*.xml">${project.basedir}/src/main/conf/</location>
	</mappingsSearchLocations>
	<namespaces>
		<namespace name="default">
			<properties>
				<property name="languageMappingsUri">Java</property>
				<property name="wrapperMappingsUri">JavaWrapper</property>
				<property name="sqlMappingsUri">file:${project.basedir}/src/main/conf/MySQLMappings.xml</property>
				<property name="jdbcMappingsUri">JDBC</property>
				<property name="maxSqlNameLength">60</property>
				<property name="hibernateVersion">3</property>
				<property name="enableTemplating">true</property>
				<property name="enumerations">${maven.andromda.core.generated.dir}</property>
			</properties>
		</namespace>
		<namespace name="bpm4struts">
			<!--  Note that we are not using this now -->
			<properties>
				<property name="forms">${maven.andromda.core.generated.dir}</property>
				<property name="pages">${maven.andromda.web.generated.pages.dir}/pages</property>
				<property name="actions">${maven.andromda.core.generated.dir}</property>
				<property name="controllers">${maven.andromda.core.generated.dir}</property>
				<property name="controller-impls">${maven.andromda.core.manual.dir}</property>
				<property name="decorators">${maven.andromda.core.manual.dir}</property>
				<property name="messages">${maven.andromda.web.messages.dir}</property>
				<property name="configuration">
					${maven.andromda.web.conf.generated.dir}/WEB-INF
				</property>
				<property name="securityRealm"></property>
				<property name="serviceAccessorPattern">
					${application.package}.ServiceLocator.instance().get{1}()
				</property>
				<property name="manageableServiceAccessorPattern">
					${application.package}.spring.ManageableServiceLocator.instance().get{1}()
				</property>
			</properties>
		</namespace>
		<namespace name="spring">
			<properties>
				<property name="hibernateDialect">
					org.hibernate.dialect.MySQLMyISAMDialect
				</property>
				<property name="hibernateShowSql">false</property>
				<property name="hibernateUseQueryCache">false</property>
				<property name="hibernateQueryUseNamedParameters">true</property>
				<property name="hibernateQueryCacheFactory">
					org.hibernate.cache.StandardQueryCacheFactory
				</property>
				<property name="hibernateCacheProvider">
					org.hibernate.cache.EhCacheProvider
				</property>
				<property name="hibernateInheritanceStrategy">subclass</property>
				<property name="springTypesPackage">ubic.gemma.spring</property>
				<property name="springPresentationTypesPackage">
					ubic.gemma.spring.presentation
				</property>
				<property name="mergeLocation">${maven.andromda.spring.merge.custom}</property>
				<property name="mergeMappingsUri">file:${maven.andromda.merge.mappings}</property>
				<property name="driver">com.mysql.jdbc.Driver</property>
				<property name="username">pavlidis</property>
				<property name="password"><PASSWORD></property>
				<property name="connectionUrl">jdbc:mysql://localhost:3306/gemd</property>
				<property name="serviceLocator">
					${maven.andromda.spring.service.locator.dir}
				</property>
				<property name="applicationContext">applicationContext-hibernate.xml</property>
				<property name="applicationContextLocalDataSource">localDataSource.xml</property>
				<property name="jdbcDataSourceClass">
					org.apache.commons.dbcp.BasicDataSource
				</property>
				<property name="localTransactionManager">
					org.springframework.orm.hibernate3.HibernateTransactionManager
				</property>
				<property name="sessionFactory">
					org.springframework.orm.hibernate3.LocalSessionFactoryBean
				</property>
				<property name="value-objects">${maven.andromda.core.generated.dir}</property>
				<property name="daos">${maven.andromda.core.generated.dir}</property>
				<property name="dao-impls">${maven.andromda.core.manual.dir}</property>
				<property name="services">${maven.andromda.core.generated.dir}</property>
				<property name="service-impls">${maven.andromda.core.manual.dir}</property>
				<property name="service-interfaces">${maven.andromda.core.generated.dir}</property>
				<property name="spring-configuration">
					${maven.andromda.spring.configuration.dir}
				</property>
				<property name="open-session-in-view">
					${maven.andromda.core.generated.dir}
				</property>
				<property name="parameterRequiredCheck">false</property>
				<!--  	
					<property name="acegiServiceSecurity">
					true
					</property>
					<property name="acegiServiceSecurityInterceptor">
					org.acegisecurity.intercept.method.aopalliance.MethodSecurityInterceptor
					</property>
					<property name="acegiAuthenticationManager">
					authenticationManager
					</property>
					<property name="acegiServiceAccessDecisionManager">
					org.acegisecurity.vote.AffirmativeBased
					</property>
					<property name="acegiServiceDecisionVoter">
					org.acegisecurity.vote.RoleVoter
					</property>
				-->
			</properties>
		</namespace>
		<namespace name="hibernate">
			<properties>
				<property name="hibernateDialect">
					org.hibernate.dialect.MySQLMyISAMDialect
				</property>
				<property name="hibernateTypeMappingsUri">file:${project.basedir}/src/main/conf/HibernateTypeMappings.xml</property>
				<property name="hibernateInheritanceStrategy">
					${hibernate.inheritance.strategy}
				</property>
				<property name="entities">${maven.andromda.core.generated.dir}</property>
				<property name="entity-impls">${maven.andromda.core.manual.dir}</property>
				<property name="entity-mappings">
					${maven.andromda.hibernate.configuration.dir}
				</property>
				<property name="enumerations">${maven.andromda.core.generated.dir}</property>
				<property name="user-types">${maven.andromda.core.generated.dir}</property>
				<property name="customTypesPackage">${application.package}</property>
				<property name="userTypesPackage">
					${application.package}.persistence.hibernate.usertypes
				</property>
				<property name="compositionDefinesEagerLoading">true</property>
				<property name="mergeLocation">${maven.andromda.hibernate.merge.custom}</property>
				<property name="mergeMappingsUri">file:${maven.andromda.merge.mappings}</property>
				<property name="hibernateCompositionCascade">all</property>
				<property name="hibernateAggregationCascade">none</property>
				<property name="hibernateDefaultCascade">none</property>
				<property name="specificCollectionInterfaces">false</property>
				<property name="associationEndCollectionIndexName">orderedCollectionIndex</property>
				<property name="configuration">
					${maven.andromda.hibernate.configuration.dir}
				</property>
				<property name="hibernateJdbcBatchSize">50</property>
				<property name="hibernateMaxFetchDepth">2</property>
				<property name="hibernateJdbcFetchSize">8</property>
				<property name="hibernateEnableCache">true</property>
				<property name="cache">${maven.andromda.hibernate.configuration.dir}</property>
				<property name="hibernateEnableAssociationsCache">true</property>
				<property name="ehCacheTimeToIdleSeconds">200</property>
				<property name="ehCacheTimeToLiveSeconds">200</property>
				<property name="hibernateTransactionFactoryClass">
					org.hibernate.transaction.JTATransactionFactory
				</property>
			</properties>
		</namespace>
		<namespace name="java">
			<properties>
				<property name="enumerations">${maven.andromda.core.generated.dir}</property>
				<property name="exceptions">${maven.andromda.core.generated.dir}</property>
				<property name="value-objects">${maven.andromda.core.generated.dir}</property>
			</properties>
		</namespace>
	</namespaces>
</andromda>

<commit_msg>change mappings search path so andromda.xml isn't included.<commit_after><?xml version="1.0" encoding="ISO-8859-1"?>
<andromda>
<!--  $Id$ -->
	<properties>
		<property name="modelValidation">${modelValidation}</property>
		<property name="cartridgeFilter">${filter}</property>
		<property name="loggingConfigurationUri">
			file:${project.basedir}/src/main/conf/log4j.xml
		</property>
	</properties>
	<server>
		<host>localhost</host>
		<port>4445</port>
	</server>
	<repositories>
		<repository name="netBeansMDR">
			<models>
				<model>
					<uri>
						jar:file:${project.basedir}/src/main/uml/gemma-om.xml.zip!/gemma-om.xml
					</uri>
					<moduleSearchLocations>
						<location patterns="**/*.xml.zip, **/*.uml2">
							${settings.localRepository}/org/andromda/profiles
						</location>
					</moduleSearchLocations>
				</model>
			</models>
		</repository>
	</repositories>
	<mappingsSearchLocations>
		<location patterns="*Mappings.xml">${project.basedir}/src/main/conf/</location>
	</mappingsSearchLocations>
	<namespaces>
		<namespace name="default">
			<properties>
				<property name="languageMappingsUri">Java</property>
				<property name="wrapperMappingsUri">JavaWrapper</property>
				<property name="sqlMappingsUri">file:${project.basedir}/src/main/conf/MySQLMappings.xml</property>
				<property name="jdbcMappingsUri">JDBC</property>
				<property name="maxSqlNameLength">60</property>
				<property name="hibernateVersion">3</property>
				<property name="enableTemplating">true</property>
				<property name="enumerations">${maven.andromda.core.generated.dir}</property>
			</properties>
		</namespace>
		<namespace name="bpm4struts">
			<!--  Note that we are not using this now -->
			<properties>
				<property name="forms">${maven.andromda.core.generated.dir}</property>
				<property name="pages">${maven.andromda.web.generated.pages.dir}/pages</property>
				<property name="actions">${maven.andromda.core.generated.dir}</property>
				<property name="controllers">${maven.andromda.core.generated.dir}</property>
				<property name="controller-impls">${maven.andromda.core.manual.dir}</property>
				<property name="decorators">${maven.andromda.core.manual.dir}</property>
				<property name="messages">${maven.andromda.web.messages.dir}</property>
				<property name="configuration">
					${maven.andromda.web.conf.generated.dir}/WEB-INF
				</property>
				<property name="securityRealm"></property>
				<property name="serviceAccessorPattern">
					${application.package}.ServiceLocator.instance().get{1}()
				</property>
				<property name="manageableServiceAccessorPattern">
					${application.package}.spring.ManageableServiceLocator.instance().get{1}()
				</property>
			</properties>
		</namespace>
		<namespace name="spring">
			<properties>
				<property name="hibernateDialect">
					org.hibernate.dialect.MySQLMyISAMDialect
				</property>
				<property name="hibernateShowSql">false</property>
				<property name="hibernateUseQueryCache">false</property>
				<property name="hibernateQueryUseNamedParameters">true</property>
				<property name="hibernateQueryCacheFactory">
					org.hibernate.cache.StandardQueryCacheFactory
				</property>
				<property name="hibernateCacheProvider">
					org.hibernate.cache.EhCacheProvider
				</property>
				<property name="hibernateInheritanceStrategy">subclass</property>
				<property name="springTypesPackage">ubic.gemma.spring</property>
				<property name="springPresentationTypesPackage">
					ubic.gemma.spring.presentation
				</property>
				<property name="mergeLocation">${maven.andromda.spring.merge.custom}</property>
				<property name="mergeMappingsUri">file:${maven.andromda.merge.mappings}</property>
				<property name="driver">com.mysql.jdbc.Driver</property>
				<property name="username">pavlidis</property>
				<property name="password"><PASSWORD></property>
				<property name="connectionUrl">jdbc:mysql://localhost:3306/gemd</property>
				<property name="serviceLocator">
					${maven.andromda.spring.service.locator.dir}
				</property>
				<property name="applicationContext">applicationContext-hibernate.xml</property>
				<property name="applicationContextLocalDataSource">localDataSource.xml</property>
				<property name="jdbcDataSourceClass">
					org.apache.commons.dbcp.BasicDataSource
				</property>
				<property name="localTransactionManager">
					org.springframework.orm.hibernate3.HibernateTransactionManager
				</property>
				<property name="sessionFactory">
					org.springframework.orm.hibernate3.LocalSessionFactoryBean
				</property>
				<property name="value-objects">${maven.andromda.core.generated.dir}</property>
				<property name="daos">${maven.andromda.core.generated.dir}</property>
				<property name="dao-impls">${maven.andromda.core.manual.dir}</property>
				<property name="services">${maven.andromda.core.generated.dir}</property>
				<property name="service-impls">${maven.andromda.core.manual.dir}</property>
				<property name="service-interfaces">${maven.andromda.core.generated.dir}</property>
				<property name="spring-configuration">
					${maven.andromda.spring.configuration.dir}
				</property>
				<property name="open-session-in-view">
					${maven.andromda.core.generated.dir}
				</property>
				<property name="parameterRequiredCheck">false</property>
				<!--  	
					<property name="acegiServiceSecurity">
					true
					</property>
					<property name="acegiServiceSecurityInterceptor">
					org.acegisecurity.intercept.method.aopalliance.MethodSecurityInterceptor
					</property>
					<property name="acegiAuthenticationManager">
					authenticationManager
					</property>
					<property name="acegiServiceAccessDecisionManager">
					org.acegisecurity.vote.AffirmativeBased
					</property>
					<property name="acegiServiceDecisionVoter">
					org.acegisecurity.vote.RoleVoter
					</property>
				-->
			</properties>
		</namespace>
		<namespace name="hibernate">
			<properties>
				<property name="hibernateDialect">
					org.hibernate.dialect.MySQLMyISAMDialect
				</property>
				<property name="hibernateTypeMappingsUri">file:${project.basedir}/src/main/conf/HibernateTypeMappings.xml</property>
				<property name="hibernateInheritanceStrategy">
					${hibernate.inheritance.strategy}
				</property>
				<property name="entities">${maven.andromda.core.generated.dir}</property>
				<property name="entity-impls">${maven.andromda.core.manual.dir}</property>
				<property name="entity-mappings">
					${maven.andromda.hibernate.configuration.dir}
				</property>
				<property name="enumerations">${maven.andromda.core.generated.dir}</property>
				<property name="user-types">${maven.andromda.core.generated.dir}</property>
				<property name="customTypesPackage">${application.package}</property>
				<property name="userTypesPackage">
					${application.package}.persistence.hibernate.usertypes
				</property>
				<property name="compositionDefinesEagerLoading">true</property>
				<property name="mergeLocation">${maven.andromda.hibernate.merge.custom}</property>
				<property name="mergeMappingsUri">file:${maven.andromda.merge.mappings}</property>
				<property name="hibernateCompositionCascade">all</property>
				<property name="hibernateAggregationCascade">none</property>
				<property name="hibernateDefaultCascade">none</property>
				<property name="specificCollectionInterfaces">false</property>
				<property name="associationEndCollectionIndexName">orderedCollectionIndex</property>
				<property name="configuration">
					${maven.andromda.hibernate.configuration.dir}
				</property>
				<property name="hibernateJdbcBatchSize">50</property>
				<property name="hibernateMaxFetchDepth">2</property>
				<property name="hibernateJdbcFetchSize">8</property>
				<property name="hibernateEnableCache">true</property>
				<property name="cache">${maven.andromda.hibernate.configuration.dir}</property>
				<property name="hibernateEnableAssociationsCache">true</property>
				<property name="ehCacheTimeToIdleSeconds">200</property>
				<property name="ehCacheTimeToLiveSeconds">200</property>
				<property name="hibernateTransactionFactoryClass">
					org.hibernate.transaction.JTATransactionFactory
				</property>
			</properties>
		</namespace>
		<namespace name="java">
			<properties>
				<property name="enumerations">${maven.andromda.core.generated.dir}</property>
				<property name="exceptions">${maven.andromda.core.generated.dir}</property>
				<property name="value-objects">${maven.andromda.core.generated.dir}</property>
			</properties>
		</namespace>
	</namespaces>
</andromda>


{'fraction_non_alphanumeric': 0.1534682418996374, 'fraction_numerical': 0.0036846414785355014, 'mean_word_length': 5.0548866855524075, 'pattern_counts': {'":': 0, '<': 464, '<?xml version=': 1, '>': 464, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 20}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3814271', 'n_tokens_mistral': 6284, 'n_tokens_neox': 4943, 'n_words': 597}