Skip to content
Snippets Groups Projects
Commit 7811f845 authored by Jason Hough's avatar Jason Hough
Browse files

Removed ignored files

parent 7ac8abb5
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
Showing
with 8 additions and 1361 deletions
webapp/.gitignore 0 → 100644
+ 8
− 0
View file @ 7811f845
/.project/
/NuCLIAVault/.classpath/
/NuCLIAVault/.settings/
/NuCLIAVault/WebContent/WEB-INF/servlets.xml
/NuCLIAVault/src/utsw/bicf/nucliavault/security/ClarityDBConnection.java
webapp/NuCLIAVault/.settings/.jsdtscope deleted 100644 → 0
+ 0
− 12
View file @ 7ac8abb5
<?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>
webapp/NuCLIAVault/.settings/org.eclipse.jdt.core.prefs deleted 100644 → 0
+ 0
− 7
View file @ 7ac8abb5
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
webapp/NuCLIAVault/.settings/org.eclipse.wst.common.component deleted 100644 → 0
+ 0
− 8
View file @ 7ac8abb5
<?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>
webapp/NuCLIAVault/.settings/org.eclipse.wst.common.project.facet.core.xml deleted 100644 → 0
+ 0
− 7
View file @ 7ac8abb5
<?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>
webapp/NuCLIAVault/.settings/org.eclipse.wst.jsdt.ui.superType.container deleted 100644 → 0
+ 0
− 1
View file @ 7ac8abb5
org.eclipse.wst.jsdt.launching.baseBrowserLibrary
\ No newline at end of file
webapp/NuCLIAVault/.settings/org.eclipse.wst.jsdt.ui.superType.name deleted 100644 → 0
+ 0
− 1
View file @ 7ac8abb5
Window
\ No newline at end of file
webapp/NuCLIAVault/WebContent/WEB-INF/servlets.xml deleted 100644 → 0
+ 0
− 149
View file @ 7ac8abb5
<?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>
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment