Commit 7811f845 authored by Jason Hough's avatar Jason Hough
Browse files

Removed ignored files

parent 7ac8abb5
/.project/
/NuCLIAVault/.classpath/
/NuCLIAVault/.settings/
/NuCLIAVault/WebContent/WEB-INF/servlets.xml
/NuCLIAVault/src/utsw/bicf/nucliavault/security/ClarityDBConnection.java
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry excluding="**/bower_components/*|**/node_modules/*|**/*.min.js" kind="src" path="WebContent"/>
<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.WebProject">
<attributes>
<attribute name="hide" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.baseBrowserLibrary"/>
<classpathentry kind="output" path=""/>
</classpath>
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.source=1.8
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="NuCLIAVault">
<wb-resource deploy-path="/" source-path="/WebContent" tag="defaultRootSource"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src"/>
<property name="context-root" value="NuCLIAVault"/>
<property name="java-output-path" value="/NuCLIAVault/build/classes"/>
</wb-module>
</project-modules>
<?xml version="1.0" encoding="UTF-8"?>
<faceted-project>
<runtime name="Apache Tomcat v8.5 (2)"/>
<installed facet="java" version="1.8"/>
<installed facet="jst.web" version="3.0"/>
<installed facet="wst.jsdt.web" version="1.0"/>
</faceted-project>
org.eclipse.wst.jsdt.launching.baseBrowserLibrary
\ No newline at end of file
<?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:beans="http://www.springframework.org/schema/beans"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:mvc="http://www.springframework.org/schema/mvc"
xmlns:aop="http://www.springframework.org/schema/aop"
xmlns:util="http://www.springframework.org/schema/util"
xmlns:tx="http://www.springframework.org/schema/tx"
xmlns:security="http://www.springframework.org/schema/security"
xsi:schemaLocation="
http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context.xsd
http://www.springframework.org/schema/mvc
http://www.springframework.org/schema/mvc/spring-mvc.xsd
http://www.springframework.org/schema/aop
http://www.springframework.org/schema/aop/spring-aop.xsd
http://www.springframework.org/schema/util
http://www.springframework.org/schema/util/spring-util.xsd
http://www.springframework.org/schema/tx
http://www.springframework.org/schema/tx/spring-tx.xsd
http://www.springframework.org/schema/security
http://www.springframework.org/schema/security/spring-security.xsd">
<aop:aspectj-autoproxy></aop:aspectj-autoproxy>
<!-- Add support for component scanning -->
<context:component-scan base-package="utsw.bicf.nucliavault" />
<!-- Add support for conversion, formatting and nucliavault support -->
<mvc:annotation-driven />
<!-- Add support for reading web resources: css, images, js, etc... -->
<mvc:resources location="/resources/" mapping="/resources/**" />
<mvc:resources location="file:/opt/nuclia-jason/nuclia_clean/links/tdfs/" mapping="/tdfs/**" />
<mvc:resources location="file:/opt/nuclia-jason/nuclia_clean/files/beds/" mapping="/beds/**" />
<!-- Define Spring MVC view resolver -->
<bean id="internalResourceViewResolver" class="org.springframework.web.servlet.view.InternalResourceViewResolver">
<property name="prefix" value="/WEB-INF/view/templates/" />
<property name="suffix" value=".jsp" />
</bean>
<!-- Define Database DataSource / connection pool -->
<bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource"
destroy-method="close">
<property name="driverClass" value="com.mysql.jdbc.Driver" />
<property name="jdbcUrl" value="jdbc:mysql://localhost:3306/${db.name}?useSSL=false" />
<property name="user" value="${db.user}" />
<property name="password" value="${db.password}" />
<!-- these are connection pool properties for C3P0 -->
<property name="initialPoolSize" value="5" />
<property name="minPoolSize" value="5" />
<property name="maxPoolSize" value="20" />
<property name="maxIdleTime" value="30000" />
</bean>
<bean id="ldapAuthentication" class="utsw.bicf.nucliavault.security.LDAPAuthentication">
<property name="username" value="${ldap.username}" />
<property name="password" value="${ldap.password}" />
<property name="url" value="${ldap.url}" />
</bean>
<bean id="clarityAPIAuthentication" class="utsw.bicf.nucliavault.security.ClarityAPIAuthentication">
<property name="username" value="${clarity.api.username}" />
<property name="password" value="${clarity.api.password}" />
<property name="url" value="${clarity.api.url}" />
<property name="dataOutputDirPath" value="${clarity.data.output.dir}" />
</bean>
<bean id="clarityDBAuthentication" class="utsw.bicf.nucliavault.security.ClarityDBAuthentication">
<property name="username" value="${clarity.db.username}" />
<property name="password" value="${clarity.db.password}" />
<property name="hostname" value="${clarity.db.hostname}" />
<property name="dbName" value="${clarity.db.name}" />
<property name="useSSL" value="${clarity.db.ssl}" />
</bean>
<bean id="pipelineProperties" class="utsw.bicf.nucliavault.security.PipelineProperties">
<property name="rootDirPath" value="${pipeline.root.dir}" />
<property name="outputDirPaths" value="${pipeline.output.dirs}" />
<property name="runSubDir" value="${pipeline.sub.run.dir}" />
<property name="outputValidationRootDirPath" value="${pipeline.output.validation.root.dir}" />
<property name="outputValidationDirPaths" value="${pipeline.output.validation.dirs}" />
<property name="alignmentSuffix" value="${pipeline.file.alignment.suffix}" />
<property name="exonCoverageSuffix" value="${pipeline.file.exoncoverage.suffix}" />
<property name="exonCoverageUniqSuffix" value="${pipeline.file.exoncoverage.uniq.suffix}" />
<property name="seqRunRootPaths" value="${pipeline.seqrun.roots}" />
<property name="dmuxFileName" value="${pipeline.dmux.name}" />
<property name="statsDirName" value="${pipeline.dmux.stats.dir}" />
<property name="conversionStatsName" value="${pipeline.dmux.stats.conversion.name}" />
<property name="fusionFileSuffix" value="${pipeline.file.fusion.suffix}" />
<property name="snspFileSuffix" value="${pipeline.file.snsp.suffix}" />
<property name="somaticDirName" value="${pipeline.file.somatic.root.dir}" />
<property name="somaticFileSuffix" value="${pipeline.file.somatic.suffix}" />
<property name="tdfRawSuffix" value="${pipeline.file.tdf.raw.suffix}" />
<property name="tdfUniqSuffix" value="${pipeline.file.tdf.uniq.suffix}" />
</bean>
<bean id="requestUtils" class="utsw.bicf.nucliavault.clarity.api.utils.RequestUtils">
</bean>
<bean id="fileProps" class="utsw.bicf.nucliavault.security.FileProperties">
<property name="tdfLinksPath" value="${tdf.link.location}" />
<property name="tdfFilesPath" value="${tdf.file.location}" />
<property name="tmpFilesPath" value="${tmp.file.location}" />
</bean>
<!-- Setup Hibernate session factory -->
<bean id="sessionFactory"
class="org.springframework.orm.hibernate5.LocalSessionFactoryBean">
<property name="dataSource" ref="dataSource" />
<property name="packagesToScan" value="utsw.bicf.nucliavault.model" />
<property name="hibernateProperties">
<props>
<prop key="hibernate.dialect">org.hibernate.dialect.MySQLDialect</prop>
<prop key="hibernate.show_sql">false</prop>
</props>
</property>
</bean>
<!-- Setup Hibernate transaction manager -->
<bean id="transactionManager"
class="org.springframework.orm.hibernate5.HibernateTransactionManager">
<property name="sessionFactory" ref="sessionFactory" />
</bean>
<!-- Enable configuration of transactional behavior based on annotations -->
<tx:annotation-driven transaction-manager="transactionManager" />
<!-- <context:property-placeholder location="/WEB-INF/application.properties"/> -->
<!-- <context:property-placeholder location="file:///C:/nuclia.properties"/> -->
<context:property-placeholder location="file:///opt/nuclia-jason/nuclia_clean/conf/nuclia.properties"/>
</beans>
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