Commit cf5de25f authored by Piotr Gawron's avatar Piotr Gawron
Browse files

cleaning after moving to git

parent c216477d
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package lcsb.mapviewer.annotation.services.genome;
/**
* Thrown when there is aproblem with accessing reference genome database or
* there are problems with performing some operation on reference genome
* connection.
*
* @author Piotr Gawron
*
*/
public class ReferenceGenomeConnectorException extends Exception {
/**
*
*/
private static final long serialVersionUID = 1L;
/**
* Default constructor.
*
* @param message
* message associated with exception
* @param exception
* original exception
*/
public ReferenceGenomeConnectorException(String message, Exception exception) {
super(message, exception);
}
/**
* Default constructor.
*
* @param message
* message associated with exception
*/
public ReferenceGenomeConnectorException(String message) {
super(message);
}
public ReferenceGenomeConnectorException(Exception cause) {
super(cause);
}
}
package lcsb.mapviewer.annotation.services.genome;
/**
* Thrown when there is aproblem with accessing reference genome database or
* there are problems with performing some operation on reference genome
* connection.
*
* @author Piotr Gawron
*
*/
public class ReferenceGenomeConnectorException extends Exception {
/**
*
*/
private static final long serialVersionUID = 1L;
/**
* Default constructor.
*
* @param message
* message associated with exception
* @param exception
* original exception
*/
public ReferenceGenomeConnectorException(String message, Exception exception) {
super(message, exception);
}
/**
* Default constructor.
*
* @param message
* message associated with exception
*/
public ReferenceGenomeConnectorException(String message) {
super(message);
}
/**
* Default constructor.
*
* @param cause
* original exception
*/
public ReferenceGenomeConnectorException(Exception cause) {
super(cause);
}
}
<?xml version="1.0" encoding="UTF-8"?>
<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://java.sun.com/xml/ns/javaee" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd" version="2.5">
<display-name>MapViewer2</display-name>
<context-param>
<param-name>com.sun.faces.enableMissingResourceLibraryDetection</param-name>
<param-value>true</param-value>
</context-param>
<context-param>
<param-name>primefaces.THEME</param-name>
<param-value>home</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
/WEB-INF/applicationContext.xml
/WEB-INF/security-context.xml
classpath:applicationContext-annotation.xml
classpath:applicationContext-persist.xml
classpath:applicationContext-service.xml
</param-value>
</context-param>
<context-param>
<param-name>javax.faces.FACELETS_BUFFER_SIZE</param-name>
<param-value>65535</param-value>
</context-param>
<context-param>
<param-name>facelets.BUFFER_SIZE</param-name>
<param-value>65535</param-value>
</context-param>
<context-param>
<param-name>javax.faces.FACELETS_LIBRARIES</param-name>
<param-value>/WEB-INF/springsecurity.taglib.xml</param-value>
</context-param>
<context-param>
<param-name>javax.faces.CONFIG_FILES</param-name>
<param-value>/WEB-INF/faces-config.xml</param-value>
</context-param>
<context-param>
<param-name>javax.faces.DEFAULT_SUFFIX</param-name>
<param-value>.xhtml</param-value>
</context-param>
<context-param>
<param-name>javax.faces.FACELETS_SKIP_COMMENTS</param-name>
<param-value>true</param-value>
</context-param>
<listener>
<listener-class>
org.springframework.web.context.ContextLoaderListener
</listener-class>
</listener>
<listener>
<listener-class>
org.springframework.security.web.session.HttpSessionEventPublisher
</listener-class>
</listener>
<context-param>
<param-name>log4jConfigLocation</param-name>
<param-value>/WEB-INF/resources/log4j.properties</param-value>
</context-param>
<listener>
<listener-class>org.springframework.web.util.Log4jConfigListener</listener-class>
</listener>
<welcome-file-list>
<welcome-file>index.xhtml</welcome-file>
</welcome-file-list>
<servlet>
<servlet-name>appServlet</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value></param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet>
<servlet-name>Faces Servlet</servlet-name>
<servlet-class>javax.faces.webapp.FacesServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.css</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.js</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.gif</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.jpg</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.png</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.pdf</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.xhtml</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.jsf</url-pattern>
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<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.faces</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>/login</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>/j_spring_security_logout</url-pattern>
</servlet-mapping>
<servlet>
<servlet-name>rest-api-serlvet</servlet-name>
<servlet-class>com.sun.jersey.spi.container.servlet.ServletContainer</servlet-class>
<init-param>
<param-name>com.sun.jersey.config.property.packages</param-name>
<param-value>lcsb.mapviewer.api</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>rest-api-serlvet</servlet-name>
<url-pattern>/api/*</url-pattern>
</servlet-mapping>
<filter>
<filter-name>PrimeFaces FileUpload Filter</filter-name>
<filter-class>
org.primefaces.webapp.filter.FileUploadFilter
</filter-class>
<init-param>
<param-name>thresholdSize</param-name>
<param-value>51200</param-value>
</init-param>
</filter>
<filter-mapping>
<filter-name>PrimeFaces FileUpload Filter</filter-name>
<servlet-name>Faces Servlet</servlet-name>
</filter-mapping>
<session-config>
<session-timeout>120</session-timeout>
<tracking-mode>COOKIE</tracking-mode>
</session-config>
<!-- content type of css resources sometimes is not set (IE), this filter fix this issue -->
<filter>
<filter-name>cssContentTypeFix</filter-name>
<filter-class>lcsb.mapviewer.bean.utils.CssContentTypeFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>cssContentTypeFix</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<!-- custom x-frames configuration-->
<filter>
<filter-name>xFrameFilter</filter-name>
<filter-class>lcsb.mapviewer.bean.utils.XFrameAccessControlFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>xFrameFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<!-- ajax queries outside of the domain by default are blocked, this filter enable ajax queries for everybody -->
<filter>
<filter-name>allowAjaxCrossSiteQueries</filter-name>
<filter-class>lcsb.mapviewer.bean.utils.JsfAjaxAccessControlAllowFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>allowAjaxCrossSiteQueries</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<filter>
<filter-name>springSecurityFilterChain</filter-name>
<filter-class>org.springframework.web.filter.DelegatingFilterProxy</filter-class>
</filter>
<filter-mapping>
<filter-name>springSecurityFilterChain</filter-name>
<url-pattern>/*</url-pattern>
<dispatcher>FORWARD</dispatcher>
<dispatcher>REQUEST</dispatcher>
</filter-mapping>
<?xml version="1.0" encoding="UTF-8"?>
<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://java.sun.com/xml/ns/javaee" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd" version="2.5">
<display-name>MapViewer2</display-name>
<context-param>
<param-name>com.sun.faces.enableMissingResourceLibraryDetection</param-name>
<param-value>true</param-value>
</context-param>
<context-param>
<param-name>primefaces.THEME</param-name>
<param-value>home</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
/WEB-INF/applicationContext.xml
/WEB-INF/security-context.xml
classpath:applicationContext-annotation.xml
classpath:applicationContext-persist.xml
classpath:applicationContext-service.xml
</param-value>
</context-param>
<context-param>
<param-name>javax.faces.FACELETS_BUFFER_SIZE</param-name>
<param-value>65535</param-value>
</context-param>
<context-param>
<param-name>facelets.BUFFER_SIZE</param-name>
<param-value>65535</param-value>
</context-param>
<context-param>
<param-name>javax.faces.FACELETS_LIBRARIES</param-name>
<param-value>/WEB-INF/springsecurity.taglib.xml</param-value>
</context-param>
<context-param>
<param-name>javax.faces.CONFIG_FILES</param-name>
<param-value>/WEB-INF/faces-config.xml</param-value>
</context-param>
<context-param>
<param-name>javax.faces.DEFAULT_SUFFIX</param-name>
<param-value>.xhtml</param-value>
</context-param>
<context-param>
<param-name>javax.faces.FACELETS_SKIP_COMMENTS</param-name>
<param-value>true</param-value>
</context-param>
<listener>
<listener-class>
org.springframework.web.context.ContextLoaderListener
</listener-class>
</listener>
<listener>
<listener-class>
org.springframework.security.web.session.HttpSessionEventPublisher
</listener-class>
</listener>
<context-param>
<param-name>log4jConfigLocation</param-name>
<param-value>/WEB-INF/resources/log4j.properties</param-value>
</context-param>
<listener>
<listener-class>org.springframework.web.util.Log4jConfigListener</listener-class>
</listener>
<welcome-file-list>
<welcome-file>index.xhtml</welcome-file>
</welcome-file-list>
<servlet>
<servlet-name>appServlet</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value></param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet>
<servlet-name>Faces Servlet</servlet-name>
<servlet-class>javax.faces.webapp.FacesServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.css</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.js</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.gif</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.jpg</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.png</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>*.pdf</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.xhtml</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.jsf</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.faces</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>/login</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>default</servlet-name>
<url-pattern>/j_spring_security_logout</url-pattern>
</servlet-mapping>
<servlet>
<servlet-name>rest-api-serlvet</servlet-name>
<servlet-class>com.sun.jersey.spi.container.servlet.ServletContainer</servlet-class>
<init-param>
<param-name>com.sun.jersey.config.property.packages</param-name>
<param-value>lcsb.mapviewer.api</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>rest-api-serlvet</servlet-name>
<url-pattern>/api/*</url-pattern>
</servlet-mapping>
<filter>
<filter-name>PrimeFaces FileUpload Filter</filter-name>
<filter-class>
org.primefaces.webapp.filter.FileUploadFilter
</filter-class>
<init-param>
<param-name>thresholdSize</param-name>
<param-value>51200</param-value>
</init-param>
</filter>
<filter-mapping>
<filter-name>PrimeFaces FileUpload Filter</filter-name>
<servlet-name>Faces Servlet</servlet-name>
</filter-mapping>
<session-config>
<session-timeout>120</session-timeout>
<tracking-mode>COOKIE</tracking-mode>
</session-config>
<filter>
<filter-name>cssContentTypeFix</filter-name>
<filter-class>lcsb.mapviewer.bean.utils.CssContentTypeFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>cssContentTypeFix</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<filter>
<filter-name>xFrameFilter</filter-name>
<filter-class>lcsb.mapviewer.bean.utils.XFrameAccessControlFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>xFrameFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<filter>
<filter-name>allowAjaxCrossSiteQueries</filter-name>
<filter-class>lcsb.mapviewer.bean.utils.JsfAjaxAccessControlAllowFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>allowAjaxCrossSiteQueries</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<filter>
<filter-name>springSecurityFilterChain</filter-name>
<filter-class>org.springframework.web.filter.DelegatingFilterProxy</filter-class>
</filter>
<filter-mapping>
<filter-name>springSecurityFilterChain</filter-name>
<url-pattern>/*</url-pattern>
<dispatcher>FORWARD</dispatcher>
<dispatcher>REQUEST</dispatcher>
</filter-mapping>
</web-app>
\ No newline at end of file
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