X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=WEB-INF%2Fweb.xml;h=9f2caa576805fbbbceec97ecc1cd8c20459f846e;hb=6094cb1ef55124629c1862daf9ef9e9b05433a60;hp=b8436c2bbb3b7e2789bd8a21fb416e8fa00ad76a;hpb=d4eea7f5a8fea637ab742ce69c84a0f835266567;p=proteocache.git

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index b8436c2..9f2caa5 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -4,368 +4,73 @@
  version="2.4">
 
 <display-name>ProteoCache</display-name>
-<description>ProteoCache - Results repository for the Dundee Resource</description>
+	<description>ProteoCache - caching framework for Jpred and other program in Dundee Resource</description>
 
 	<welcome-file-list>
-		<welcome-file>Index.jsp</welcome-file>
+		<welcome-file>index.jsp</welcome-file>
 	</welcome-file-list>
 
-	<!-- ProteoCache listeners -->
+	<!-- ############################################################################################################ -->
+	<!-- Spring Security -->
+
 	<listener>
-		<listener-class>compbio.listeners.ContextListener</listener-class>
+		<listener-class>org.springframework.web.util.Log4jConfigListener</listener-class>
 	</listener>
-	<servlet-mapping>
-		<servlet-name>ServletDeleteRecord</servlet-name>
-		<url-pattern>/ServletDeleteRecord</url-pattern>
-	</servlet-mapping>
-
-
-	<!-- Session timeout in minutes -->
-	<session-config>
-		<session-timeout>20</session-timeout>
-	</session-config>
 
+	<listener>
+		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
+	</listener>
 
-	<servlet>
-		<display-name>This is a standard tomcat 'default' servlet for making listings</display-name>
-		<servlet-name>listings</servlet-name>
-		<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
-		<init-param>
-			<param-name>debug</param-name>
-			<param-value>0</param-value>
-		</init-param>
+	<context-param>
+		<param-name>contextConfigLocation</param-name>
+		<param-value>
+			/WEB-INF/spring-security.xml
+		</param-value>
+	</context-param>
+	
+	<context-param>
+		<param-name>log4jConfigLocation</param-name>
+		<param-value>/WEB-INF/classes/log4j.properties</param-value>
+	</context-param>
+
+	<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>
+	</filter-mapping>
+
+	<!-- Main Spring Servlet: annotation based configuration -->
+	<servlet>
+		<servlet-name>proteocache</servlet-name>
+		<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
 		<init-param>
-			<param-name>readonly</param-name>
-			<param-value>true</param-value>
+			<param-name>contextClass</param-name>
+			<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
 		</init-param>
 		<init-param>
-			<param-name>listings</param-name>
-			<param-value>true</param-value>
+			<param-name>contextConfigLocation</param-name>
+			<param-value>compbio.spring</param-value>
 		</init-param>
 		<load-on-startup>1</load-on-startup>
 	</servlet>
-	<servlet>
-		<description>
-		</description>
-		<display-name>ServletDeleteRecord</display-name>
-		<servlet-name>ServletDeleteRecord</servlet-name>
-		<servlet-class>compbio.listeners.ServletDeleteRecord</servlet-class>
-	</servlet>
-
-
-	<!-- ProteoCache servlets -->
-<!--
-	<servlet>
-		<description>Display pre-calculated accounting info</description>
-		<servlet-name>DisplayStat</servlet-name>
-		<servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>
-	</servlet>
-
-	<servlet>
-		<description>WebServices Status</description>
-		<servlet-name>ServiceStatus</servlet-name>
-		<servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>
-	</servlet>
-
-	<servlet>
-		<servlet-name>DownloadRedirector</servlet-name>
-		<servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>
-	</servlet>
-
-	<servlet>
-		<description>WebService Status with no UI. Accepts web service name as a parameter</description>
-		<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
-		<servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>
-	</servlet>
-
-	<servlet>
-		<description>Display job list</description>
-		<servlet-name>Joblist</servlet-name>
-		<servlet-class>compbio.stat.servlet.Joblist</servlet-class>
-	</servlet>
-
-	<servlet>
-		<description>Display monthly summary statistics</description>
-		<servlet-name>AnnualStat</servlet-name>
-		<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
-	</servlet>
-
-	<servlet>
-		<description>Display monthly summary statistics with no links to details</description>
-		<servlet-name>PublicAnnualStat</servlet-name>
-		<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
-	</servlet>
-
-	<servlet>
-		<servlet-name>RegistryWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>ClustalWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>ClustalOWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>MuscleWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>MafftWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>TcoffeeWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>ProbconsWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
 
-	<servlet>
-		<servlet-name>MSAprobsWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>GLprobsWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>AAConWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>JronnWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>DisemblWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>GlobPlotWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>IUPredWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>JpredWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-	<servlet>
-		<servlet-name>RNAalifoldWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
--->
-
-
-
-	<!-- ProteoCache servlet mappings -->
-<!--
 	<servlet-mapping>
-		<servlet-name>listings</servlet-name>
+		<servlet-name>proteocache</servlet-name>
 		<url-pattern>/</url-pattern>
 	</servlet-mapping>
 
-	<servlet-mapping>
-		<servlet-name>DownloadRedirector</servlet-name>
-		<url-pattern>/download</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>DisplayStat</servlet-name>
-		<url-pattern>/DisplayStat</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>ServiceStatus</servlet-name>
-		<url-pattern>/ServiceStatus</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
-		<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>AnnualStat</servlet-name>
-		<url-pattern>/AnnualStat</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>PublicAnnualStat</servlet-name>
-		<url-pattern>/PublicAnnualStat</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>Joblist</servlet-name>
-		<url-pattern>/Joblist</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>RegistryWS</servlet-name>
-		<url-pattern>/RegistryWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>ClustalWS</servlet-name>
-		<url-pattern>/ClustalWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>ClustalOWS</servlet-name>
-		<url-pattern>/ClustalOWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>MuscleWS</servlet-name>
-		<url-pattern>/MuscleWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>MafftWS</servlet-name>
-		<url-pattern>/MafftWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>TcoffeeWS</servlet-name>
-		<url-pattern>/TcoffeeWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>ProbconsWS</servlet-name>
-		<url-pattern>/ProbconsWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>MSAprobsWS</servlet-name>
-		<url-pattern>/MSAprobsWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>GLprobsWS</servlet-name>
-		<url-pattern>/GLprobsWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>AAConWS</servlet-name>
-		<url-pattern>/AAConWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>JronnWS</servlet-name>
-		<url-pattern>/JronnWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>DisemblWS</servlet-name>
-		<url-pattern>/DisemblWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>GlobPlotWS</servlet-name>
-		<url-pattern>/GlobPlotWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>IUPredWS</servlet-name>
-		<url-pattern>/IUPredWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>JpredWS</servlet-name>
-		<url-pattern>/JpredWS</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>RNAalifoldWS</servlet-name>
-		<url-pattern>/RNAalifoldWS</url-pattern>
-	</servlet-mapping>
--->
-
-
-	<!-- ProteoCache security constraints -->
-	<security-constraint>
-		<web-resource-collection>
-		<web-resource-name>Administrator pages</web-resource-name>
-			<!-- Prohibit access to any resources -->
-			<url-pattern>/DisplayStat</url-pattern>
-			<url-pattern>/Joblist</url-pattern>
-			<url-pattern>/AnnualStat</url-pattern>
-			<url-pattern>/conf/*</url-pattern>
-			<url-pattern>/binaries/*</url-pattern>
-			<url-pattern>/testsrc/*</url-pattern>
-			<url-pattern>/lib/*</url-pattern>
-			<!-- Uncomment this to secure services status checker 
-			<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
-			<url-pattern>/ServiceStatus</url-pattern>
-			-->
-			<!-- No http-method means all methods are constrained -->
-		</web-resource-collection>
-		<auth-constraint>
-			<role-name>admin</role-name>
-		</auth-constraint>
-	</security-constraint>
-
-
-	<!-- unsupported HTTP methods -->
-	<security-constraint>
-		<web-resource-collection>
-			<web-resource-name>unsupported HTTP methods</web-resource-name>
-			<url-pattern>/*</url-pattern>
-			<http-method>PUT</http-method>
-			<http-method>DELETE</http-method>
-			<http-method>TRACE</http-method>
-			<http-method>OPTIONS</http-method>
-		</web-resource-collection>
-		<auth-constraint/>
-	</security-constraint>
-
-	<!-- Define the Login Configuration for this Application -->
-	<login-config>
-		<auth-method>BASIC</auth-method>
-		<realm-name>ProteCache administrators</realm-name>
-	</login-config>
-
+	<!-- ProteoCache listeners -->
+	<listener>
+		<listener-class>compbio.listeners.ContextListener</listener-class>
+	</listener>
 
-	<!-- Security roles referenced by this web application -->
-	<security-role>
-		<description>The role that is required to log in and view ProteCache internals</description>
-		<role-name>admin</role-name>
-	</security-role>
+	<!-- Session timeout in minutes -->
+	<session-config>
+		<session-timeout>20</session-timeout>
+	</session-config>
 
 </web-app>