X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=WEB-INF%2Fweb.xml;h=cec1884fca90d7e39753683f3860b1648839ac08;hb=9dc05c5beb667f2cc7dfc11bc0cb013325a92b88;hp=e9b1b394d1f6001b97e368fbc6d94b351b954834;hpb=eff7555f38a27ff33111f4ff1e83c4ae8186df16;p=jabaws.git

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index e9b1b39..cec1884 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -1,262 +1,363 @@
 <web-app xmlns="http://java.sun.com/xml/ns/j2ee"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
-    version="2.4">
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+ version="2.4">
 
-    <display-name>JABAWS</display-name>
-    <description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>
+<display-name>JABAWS</display-name>
+<description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>
 
+
+	<!-- JABAWS listeners -->
+	<listener>
+		<listener-class>compbio.ws.server.MainManager</listener-class>
+	</listener>
 	<listener>
-		<listener-class>compbio.ws.server.ShutdownEngines</listener-class>
+		<listener-class>compbio.stat.servlet.StatisticCollector</listener-class>
 	</listener>
-    <listener>
-        <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>
-     </listener>
-    <listener>
-        <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>
-    </listener>
-    
- 	<!-- Session timeout in minutes -->
+	<listener>
+		<listener-class>compbio.ws.server.SetExecutableFlag</listener-class>
+	</listener>
+	<listener>
+		<listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>
+	</listener>
+
+
+	<!-- Session timeout in minutes -->
 	<session-config>
-   		<session-timeout>20</session-timeout>
-    </session-config>
- 
-     <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>
-        <init-param>
-            <param-name>readonly</param-name>
-            <param-value>true</param-value>
-        </init-param>
-        <init-param>
-            <param-name>listings</param-name>
-            <param-value>true</param-value>
-        </init-param>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-
-    <servlet>
-    	<description>Display pre-calculated accounting info</description>
-    	<servlet-name>DisplayStat</servlet-name>
-    	<servlet-class>compbio.stat.servlet.DisplayStat</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>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>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>
+		<session-timeout>20</session-timeout>
+	</session-config>
+
+
+	<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>
+		<init-param>
+			<param-name>readonly</param-name>
+			<param-value>true</param-value>
+		</init-param>
+		<init-param>
+			<param-name>listings</param-name>
+			<param-value>true</param-value>
+		</init-param>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+
+	<!-- JABAWS 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>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-mapping>
-    	<servlet-name>listings</servlet-name>
-    	<url-pattern>/</url-pattern>
-  	</servlet-mapping>
-  	     
-    <servlet-mapping>
-    	<servlet-name>DisplayStat</servlet-name>
-    	<url-pattern>/DisplayStat</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>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>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>
-   
-   <security-constraint>
-    <web-resource-collection>
-    	<web-resource-name>Administrator pages</web-resource-name>
-   		<!-- Prohibit access to any resources -->
-    	<url-pattern>/</url-pattern>
-    	<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>/jobsout/*</url-pattern>
-   		<url-pattern>/testsrc/*</url-pattern>
-   		<url-pattern>/lib/*</url-pattern>
-   		<url-pattern>/test-output/*</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>HEAD</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>JABAWS administrators</realm-name>
-  </login-config>
-  
-    <!-- Security roles referenced by this web application -->
-  <security-role>
-    <description>
-      The role that is required to log in and view JABAWS internals
-    </description>
-    <role-name>admin</role-name>
-  </security-role>
-  
-</web-app>
\ No newline at end of file
+	</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>
+
+	<!-- JABAWS servlet mappings -->
+	<servlet-mapping>
+		<servlet-name>listings</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>
+
+
+	<!-- JABAWS 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>/jobsout/*</url-pattern>
+			<url-pattern>/testsrc/*</url-pattern>
+			<url-pattern>/lib/*</url-pattern>
+			<url-pattern>/test-output/*</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>JABAWS administrators</realm-name>
+	</login-config>
+
+
+	<!-- Security roles referenced by this web application -->
+	<security-role>
+		<description>The role that is required to log in and view JABAWS internals</description>
+		<role-name>admin</role-name>
+	</security-role>
+
+</web-app>