Re-formatting files

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index dc5cee3..8c2fc89 100644 (file)
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -1,311 +1,321 @@
 <web-app xmlns="http://java.sun.com/xml/ns/j2ee"\r
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
-    xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"\r
-    version="2.4">\r
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
+ xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"\r
+ version="2.4">\r
 \r
-    <display-name>JABAWS</display-name>\r
-    <description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>\r
+<display-name>JABAWS</display-name>\r
+<description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>\r
 \r
+\r
+       <!-- JABAWS listeners -->\r
        <listener>\r
                <listener-class>compbio.ws.server.ShutdownEngines</listener-class>\r
        </listener>\r
-    <listener>\r
-        <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>\r
-     </listener>\r
-     <listener>\r
-        <listener-class>compbio.ws.server.SetExecutableFlag</listener-class>\r
-     </listener>\r
-     <listener>\r
-        <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>\r
-     </listener>\r
-    \r
-       <!-- Session timeout in minutes -->\r
+       <listener>\r
+               <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>\r
+       </listener>\r
+       <listener>\r
+               <listener-class>compbio.ws.server.SetExecutableFlag</listener-class>\r
+       </listener>\r
+       <listener>\r
+               <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>\r
+       </listener>\r
+\r
+\r
+       <!-- Session timeout in minutes -->\r
        <session-config>\r
-               <session-timeout>20</session-timeout>\r
-    </session-config>\r
- \r
-     <servlet>\r
-        <display-name>This is a standard tomcat 'default' servlet for making listings</display-name>\r
-        <servlet-name>listings</servlet-name>\r
-        <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>\r
-        <init-param>\r
-            <param-name>debug</param-name>\r
-            <param-value>0</param-value>\r
-        </init-param>\r
-        <init-param>\r
-            <param-name>readonly</param-name>\r
-            <param-value>true</param-value>\r
-        </init-param>\r
-        <init-param>\r
-            <param-name>listings</param-name>\r
-            <param-value>true</param-value>\r
-        </init-param>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-\r
-    <servlet>\r
-       <description>Display pre-calculated accounting info</description>\r
-       <servlet-name>DisplayStat</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>\r
-    </servlet>\r
-  \r
-   <servlet>\r
-       <description>WebServices Status</description>\r
-       <servlet-name>ServiceStatus</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>\r
-    </servlet>\r
-\r
-   <servlet>\r
-       <servlet-name>DownloadRedirector</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>\r
-    </servlet>\r
-   \r
-    <servlet>\r
-       <description>WebService Status with no UI. Accepts web service name as a parameter</description>\r
-       <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-       <description>Display job list</description>\r
-       <servlet-name>Joblist</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.Joblist</servlet-class>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-       <description>Display monthly summary statistics</description>\r
-       <servlet-name>AnnualStat</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
-    </servlet>\r
-    \r
-     <servlet>\r
-       <description>Display monthly summary statistics with no links to details</description>\r
-       <servlet-name>PublicAnnualStat</servlet-name>\r
-       <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>RegistryWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>ClustalWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>ClustalOWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>MuscleWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>MafftWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>TcoffeeWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-     \r
-    <servlet>\r
-        <servlet-name>ProbconsWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-     <servlet>\r
-        <servlet-name>AAConWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-   \r
-     <servlet>\r
-        <servlet-name>JronnWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-\r
-     <servlet>\r
-        <servlet-name>DisemblWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <session-timeout>20</session-timeout>\r
+       </session-config>\r
+\r
+\r
+       <servlet>\r
+               <display-name>This is a standard tomcat 'default' servlet for making listings</display-name>\r
+               <servlet-name>listings</servlet-name>\r
+               <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>\r
+               <init-param>\r
+                       <param-name>debug</param-name>\r
+                       <param-value>0</param-value>\r
+               </init-param>\r
+               <init-param>\r
+                       <param-name>readonly</param-name>\r
+                       <param-value>true</param-value>\r
+               </init-param>\r
+               <init-param>\r
+                       <param-name>listings</param-name>\r
+                       <param-value>true</param-value>\r
+               </init-param>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+\r
+       <!-- JABAWS servlets -->\r
+       <servlet>\r
+               <description>Display pre-calculated accounting info</description>\r
+               <servlet-name>DisplayStat</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <description>WebServices Status</description>\r
+               <servlet-name>ServiceStatus</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>DownloadRedirector</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <description>WebService Status with no UI. Accepts web service name as a parameter</description>\r
+               <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <description>Display job list</description>\r
+               <servlet-name>Joblist</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.Joblist</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <description>Display monthly summary statistics</description>\r
+               <servlet-name>AnnualStat</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <description>Display monthly summary statistics with no links to details</description>\r
+               <servlet-name>PublicAnnualStat</servlet-name>\r
+               <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>RegistryWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>ClustalWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>ClustalOWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>MuscleWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>MafftWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>TcoffeeWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>ProbconsWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>AAConWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>JronnWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
                <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-    <servlet>\r
-        <servlet-name>GlobPlotWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-    \r
-     <servlet>\r
-        <servlet-name>IUPredWS</servlet-name>\r
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-        <load-on-startup>1</load-on-startup>\r
-    </servlet>\r
-   \r
-    <servlet-mapping>\r
-       <servlet-name>listings</servlet-name>\r
-       <url-pattern>/</url-pattern>\r
-       </servlet-mapping>\r
-       \r
-            \r
-    <servlet-mapping>\r
-       <servlet-name>DownloadRedirector</servlet-name>\r
-       <url-pattern>/download</url-pattern>\r
-       </servlet-mapping>\r
-       \r
-    <servlet-mapping>\r
-       <servlet-name>DisplayStat</servlet-name>\r
-       <url-pattern>/DisplayStat</url-pattern>\r
-       </servlet-mapping>\r
-       \r
-       <servlet-mapping>\r
-       <servlet-name>ServiceStatus</servlet-name>\r
-       <url-pattern>/ServiceStatus</url-pattern>\r
-       </servlet-mapping>\r
-       \r
-       <servlet-mapping>\r
-       <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
-       <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
-       </servlet-mapping>\r
-       \r
-        <servlet-mapping>\r
-       <servlet-name>AnnualStat</servlet-name>\r
-       <url-pattern>/AnnualStat</url-pattern>\r
-       </servlet-mapping>  \r
-    \r
-     <servlet-mapping>\r
-       <servlet-name>PublicAnnualStat</servlet-name>\r
-       <url-pattern>/PublicAnnualStat</url-pattern>\r
-       </servlet-mapping>  \r
-    \r
-    \r
-    <servlet-mapping>\r
-       <servlet-name>Joblist</servlet-name>\r
-       <url-pattern>/Joblist</url-pattern>\r
-       </servlet-mapping> \r
-       \r
-    <servlet-mapping>\r
-       <servlet-name>RegistryWS</servlet-name>\r
-       <url-pattern>/RegistryWS</url-pattern>\r
-    </servlet-mapping>\r
-    \r
-    <servlet-mapping>\r
-       <servlet-name>ClustalWS</servlet-name>\r
-       <url-pattern>/ClustalWS</url-pattern>\r
-    </servlet-mapping>\r
-    \r
-     <servlet-mapping>\r
-       <servlet-name>ClustalOWS</servlet-name>\r
-       <url-pattern>/ClustalOWS</url-pattern>\r
-    </servlet-mapping>\r
-    \r
-    <servlet-mapping>\r
-       <servlet-name>MuscleWS</servlet-name>\r
-       <url-pattern>/MuscleWS</url-pattern>\r
-    </servlet-mapping>\r
-\r
-   <servlet-mapping>\r
-       <servlet-name>MafftWS</servlet-name>\r
-       <url-pattern>/MafftWS</url-pattern>\r
-    </servlet-mapping>\r
-    \r
-   <servlet-mapping>\r
-       <servlet-name>TcoffeeWS</servlet-name>\r
-       <url-pattern>/TcoffeeWS</url-pattern>\r
-   </servlet-mapping>\r
-\r
-   <servlet-mapping>\r
-       <servlet-name>ProbconsWS</servlet-name>\r
-       <url-pattern>/ProbconsWS</url-pattern>\r
-   </servlet-mapping>\r
- \r
-   <servlet-mapping>\r
-       <servlet-name>AAConWS</servlet-name>\r
-       <url-pattern>/AAConWS</url-pattern>\r
-   </servlet-mapping>\r
-   \r
-    <servlet-mapping>\r
-       <servlet-name>JronnWS</servlet-name>\r
-       <url-pattern>/JronnWS</url-pattern>\r
-   </servlet-mapping>\r
-   \r
-   <servlet-mapping>\r
-       <servlet-name>DisemblWS</servlet-name>\r
-       <url-pattern>/DisemblWS</url-pattern>\r
-   </servlet-mapping>\r
-   \r
-   <servlet-mapping>\r
-       <servlet-name>GlobPlotWS</servlet-name>\r
-       <url-pattern>/GlobPlotWS</url-pattern>\r
-   </servlet-mapping>\r
-   \r
-    <servlet-mapping>\r
-       <servlet-name>IUPredWS</servlet-name>\r
-       <url-pattern>/IUPredWS</url-pattern>\r
-   </servlet-mapping>\r
-   \r
-   <security-constraint>\r
-    <web-resource-collection>\r
-       <web-resource-name>Administrator pages</web-resource-name>\r
-               <!-- Prohibit access to any resources -->\r
-       <url-pattern>/DisplayStat</url-pattern>\r
-       <url-pattern>/Joblist</url-pattern>\r
-       <url-pattern>/AnnualStat</url-pattern>\r
-       <url-pattern>/conf/*</url-pattern>\r
-               <url-pattern>/binaries/*</url-pattern>\r
-               <url-pattern>/jobsout/*</url-pattern>\r
-               <url-pattern>/testsrc/*</url-pattern>\r
-               <url-pattern>/lib/*</url-pattern>\r
-               <url-pattern>/test-output/*</url-pattern>\r
-               <!-- Uncomment this to secure services status checker \r
-               <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
-               <url-pattern>/ServiceStatus</url-pattern>\r
-                -->\r
-       <!-- No http-method means all methods are constrained -->\r
-    </web-resource-collection>\r
-    <auth-constraint>\r
-      <role-name>admin</role-name>\r
-    </auth-constraint>\r
-   </security-constraint>\r
-\r
-  <!-- unsupported HTTP methods -->\r
-  <security-constraint>\r
-        <web-resource-collection>\r
-        <web-resource-name>unsupported HTTP methods</web-resource-name>\r
-        <url-pattern>/*</url-pattern>\r
-            <http-method>PUT</http-method>\r
-            <http-method>DELETE</http-method>\r
-            <http-method>TRACE</http-method>\r
-            <http-method>OPTIONS</http-method>\r
-        </web-resource-collection>\r
-        <auth-constraint/>\r
-  </security-constraint>\r
-      <!-- Define the Login Configuration for this Application -->\r
-  <login-config>\r
-        <auth-method>BASIC</auth-method>\r
-        <realm-name>JABAWS administrators</realm-name>\r
-  </login-config>\r
-  \r
-    <!-- Security roles referenced by this web application -->\r
-  <security-role>\r
-    <description>\r
-      The role that is required to log in and view JABAWS internals\r
-    </description>\r
-    <role-name>admin</role-name>\r
-  </security-role>\r
-  \r
-</web-app>
\ No newline at end of file
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>DisemblWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>GlobPlotWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <servlet>\r
+               <servlet-name>IUPredWS</servlet-name>\r
+               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+               <load-on-startup>1</load-on-startup>\r
+       </servlet>\r
+\r
+       <!-- JABAWS servlet mappings -->\r
+       <servlet-mapping>\r
+               <servlet-name>listings</servlet-name>\r
+               <url-pattern>/</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>DownloadRedirector</servlet-name>\r
+               <url-pattern>/download</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>DisplayStat</servlet-name>\r
+               <url-pattern>/DisplayStat</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>ServiceStatus</servlet-name>\r
+               <url-pattern>/ServiceStatus</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
+               <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>AnnualStat</servlet-name>\r
+               <url-pattern>/AnnualStat</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>PublicAnnualStat</servlet-name>\r
+               <url-pattern>/PublicAnnualStat</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>Joblist</servlet-name>\r
+               <url-pattern>/Joblist</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>RegistryWS</servlet-name>\r
+               <url-pattern>/RegistryWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>ClustalWS</servlet-name>\r
+               <url-pattern>/ClustalWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>ClustalOWS</servlet-name>\r
+               <url-pattern>/ClustalOWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>MuscleWS</servlet-name>\r
+               <url-pattern>/MuscleWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>MafftWS</servlet-name>\r
+               <url-pattern>/MafftWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>TcoffeeWS</servlet-name>\r
+               <url-pattern>/TcoffeeWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>ProbconsWS</servlet-name>\r
+               <url-pattern>/ProbconsWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>AAConWS</servlet-name>\r
+               <url-pattern>/AAConWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>JronnWS</servlet-name>\r
+               <url-pattern>/JronnWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>DisemblWS</servlet-name>\r
+               <url-pattern>/DisemblWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>GlobPlotWS</servlet-name>\r
+               <url-pattern>/GlobPlotWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+       <servlet-mapping>\r
+               <servlet-name>IUPredWS</servlet-name>\r
+               <url-pattern>/IUPredWS</url-pattern>\r
+       </servlet-mapping>\r
+\r
+\r
+\r
+       <!-- JABAWS security constraints -->\r
+       <security-constraint>\r
+               <web-resource-collection>\r
+               <web-resource-name>Administrator pages</web-resource-name>\r
+                       <!-- Prohibit access to any resources -->\r
+                       <url-pattern>/DisplayStat</url-pattern>\r
+                       <url-pattern>/Joblist</url-pattern>\r
+                       <url-pattern>/AnnualStat</url-pattern>\r
+                       <url-pattern>/conf/*</url-pattern>\r
+                       <url-pattern>/binaries/*</url-pattern>\r
+                       <url-pattern>/jobsout/*</url-pattern>\r
+                       <url-pattern>/testsrc/*</url-pattern>\r
+                       <url-pattern>/lib/*</url-pattern>\r
+                       <url-pattern>/test-output/*</url-pattern>\r
+                       <!-- Uncomment this to secure services status checker \r
+                       <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
+                       <url-pattern>/ServiceStatus</url-pattern>\r
+                       -->\r
+                       <!-- No http-method means all methods are constrained -->\r
+               </web-resource-collection>\r
+               <auth-constraint>\r
+                       <role-name>admin</role-name>\r
+               </auth-constraint>\r
+       </security-constraint>\r
+\r
+\r
+       <!-- unsupported HTTP methods -->\r
+       <security-constraint>\r
+               <web-resource-collection>\r
+                       <web-resource-name>unsupported HTTP methods</web-resource-name>\r
+                       <url-pattern>/*</url-pattern>\r
+                       <http-method>PUT</http-method>\r
+                       <http-method>DELETE</http-method>\r
+                       <http-method>TRACE</http-method>\r
+                       <http-method>OPTIONS</http-method>\r
+               </web-resource-collection>\r
+               <auth-constraint/>\r
+       </security-constraint>\r
+\r
+\r
+       <!-- Define the Login Configuration for this Application -->\r
+       <login-config>\r
+               <auth-method>BASIC</auth-method>\r
+               <realm-name>JABAWS administrators</realm-name>\r
+       </login-config>\r
+\r
+\r
+       <!-- Security roles referenced by this web application -->\r
+       <security-role>\r
+               <description>The role that is required to log in and view JABAWS internals</description>\r
+               <role-name>admin</role-name>\r
+       </security-role>\r
+\r
+</web-app>\r

diff --git a/wsbuild.xml b/wsbuild.xml
index bd9f15b..f61ffaf 100644 (file)
--- a/wsbuild.xml
+++ b/wsbuild.xml
@@ -52,120 +52,117 @@
                        <!-- resourcedestdir - Where to put generated source files -->\r
 \r
                <wsgen sei="compbio.ws.server.AAConWS" \r
-                                       sourcedestdir="${basedir}/webservices" \r
-                                       destdir="${classes}" \r
-                                       resourcedestdir="${wsdl.dir}" \r
-                                       keep="true" genwsdl="true" \r
-                                       extension="false" \r
-                                       xendorsed="true"                        \r
-                                       verbose="true">\r
-                                       <classpath refid="classes.path" />\r
-                                       <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
-\r
                <wsgen sei="compbio.ws.server.ClustalWS" \r
-                                       sourcedestdir="${basedir}/webservices" \r
-                                       destdir="${classes}" \r
-                                       resourcedestdir="${wsdl.dir}" \r
-                                       keep="true" genwsdl="true" \r
-                                       extension="false" \r
-                                       xendorsed="true"\r
-                                       verbose="true">\r
-                                       <classpath refid="classes.path" />\r
-                                       <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true"\r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
                <wsgen sei="compbio.ws.server.MuscleWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false"\r
-                                               xendorsed="true"\r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
-                       </wsgen>\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false"\r
+                               xendorsed="true"\r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
+               </wsgen>\r
                <wsgen sei="compbio.ws.server.MafftWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false"\r
-                                               xendorsed="true"\r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
-                       </wsgen>\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false"\r
+                               xendorsed="true"\r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
+               </wsgen>\r
                <wsgen sei="compbio.ws.server.TcoffeeWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false" \r
-                                               xendorsed="true"                        \r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
-               \r
                <wsgen sei="compbio.ws.server.DisemblWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false" \r
-                                               xendorsed="true"                        \r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
                <wsgen sei="compbio.ws.server.GlobPlotWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false" \r
-                                               xendorsed="true"                        \r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
                <wsgen sei="compbio.ws.server.JronnWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false" \r
-                                               xendorsed="true"                        \r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
                <wsgen sei="compbio.ws.server.IUPredWS" \r
-                                                               sourcedestdir="${basedir}/webservices" \r
-                                                               destdir="${classes}" \r
-                                                               resourcedestdir="${wsdl.dir}" \r
-                                                               keep="true" genwsdl="true" \r
-                                                               extension="false" \r
-                                                               xendorsed="true"                        \r
-                                                               verbose="true">\r
-                                                               <classpath refid="classes.path" />\r
-                                                               <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
                <wsgen sei="compbio.ws.server.RegistryWS" \r
-                                               sourcedestdir="${basedir}/webservices" \r
-                                               destdir="${classes}" \r
-                                               resourcedestdir="${wsdl.dir}" \r
-                                               keep="true" genwsdl="true" \r
-                                               extension="false" \r
-                                               xendorsed="true"                        \r
-                                               verbose="true">\r
-                                               <classpath refid="classes.path" />\r
-                                               <classpath refid="project.classpath" />\r
+                               sourcedestdir="${basedir}/webservices" \r
+                               destdir="${classes}" \r
+                               resourcedestdir="${wsdl.dir}" \r
+                               keep="true" genwsdl="true" \r
+                               extension="false" \r
+                               xendorsed="true" \r
+                               verbose="true">\r
+                               <classpath refid="classes.path" />\r
+                               <classpath refid="project.classpath" />\r
                </wsgen>\r
        </target>\r
 \r
-\r
        <taskdef name="wsimport" classname="com.sun.tools.ws.ant.WsImport">\r
                <classpath refid="project.classpath" />\r
        </taskdef>\r
@@ -182,54 +179,48 @@
                        <wsimport wsdl="${clustal.wsdl}" \r
                                sourcedestdir="${basedir}/webservices/" \r
                                keep="true" extension="false" \r
-                               verbose="true" xnocompile="true" xendorsed="true"
-                               package="compbio.ws.client.stub" target="2.1"
+                               verbose="true" xnocompile="true" xendorsed="true"\r
+                               package="compbio.ws.client.stub" target="2.1"\r
                                quiet="false">\r
                        </wsimport>\r
                        <wsimport wsdl="${muscle.wsdl}" \r
                                sourcedestdir="${basedir}/webservices/" \r
                                keep="true" extension="false" \r
-                               verbose="true" xnocompile="true" xendorsed="true"
-                               package="compbio.ws.client.stub" target="2.1"
+                               verbose="true" xnocompile="true" xendorsed="true"\r
+                               package="compbio.ws.client.stub" target="2.1"\r
                                quiet="false">\r
                        </wsimport>\r
                        <wsimport wsdl="${mafft.wsdl}" \r
                                sourcedestdir="${basedir}/webservices/" \r
                                keep="true" extension="false" \r
-                               verbose="true" xnocompile="true" xendorsed="true"
-                               package="compbio.ws.client.stub" target="2.1"
+                               verbose="true" xnocompile="true" xendorsed="true"\r
+                               package="compbio.ws.client.stub" target="2.1"\r
                                quiet="false">\r
                        </wsimport>\r
                        <wsimport wsdl="${tcoffee.wsdl}" \r
                                sourcedestdir="${basedir}/webservices/" \r
                                keep="true" extension="false" \r
-                               verbose="true" xnocompile="true" xendorsed="true"
-                               package="compbio.ws.client.stub" target="2.1"
+                               verbose="true" xnocompile="true" xendorsed="true"\r
+                               package="compbio.ws.client.stub" target="2.1"\r
                                quiet="false">\r
                        </wsimport>\r
                        <wsimport wsdl="${iupred.wsdl}" \r
-                                               sourcedestdir="${basedir}/webservices/" \r
-                                               keep="true" extension="false" \r
-                                               verbose="true" xnocompile="true" xendorsed="true"
-                                               package="compbio.ws.client.stub" target="2.1"
-                                               quiet="false">\r
+                               sourcedestdir="${basedir}/webservices/" \r
+                               keep="true" extension="false" \r
+                               verbose="true" xnocompile="true" xendorsed="true"\r
+                               package="compbio.ws.client.stub" target="2.1"\r
+                               quiet="false">\r
                        </wsimport>\r
-                   <wsimport wsdl="${registry.wsdl}" \r
-                                               sourcedestdir="${basedir}/webservices/" \r
-                                               keep="true" extension="false" \r
-                                               verbose="true" xnocompile="true" xendorsed="true"
-                                               package="compbio.ws.client.stub" target="2.1"
-                                               quiet="false">\r
+                       <wsimport wsdl="${registry.wsdl}" \r
+                               sourcedestdir="${basedir}/webservices/" \r
+                               keep="true" extension="false" \r
+                               verbose="true" xnocompile="true" xendorsed="true"\r
+                               package="compbio.ws.client.stub" target="2.1"\r
+                               quiet="false">\r
                        </wsimport>\r
-                       <!--            <xjcarg value="-cp" />\r
-                                               <xjcarg pathref="project.classpath" />\r
-                                               <xjcarg value="-Xcommons-lang" /> -->\r
-                               \r
                </target>\r
 \r
-       \r
        <!-- \r
-       \r
        <target name="Build artifacts from schema" description="Test task to generate JaxB commons annotated data classes DOES NOT REALLY WORK">\r
                <taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">\r
                        <classpath refid="project.classpath" />\r
@@ -259,10 +250,7 @@
                                        -XhashCode\r
                                        -Xcopyable\r
                                        -Xmergeable\r
-       \r
-       \r
-       \r
-       \r
+\r
        <target name="build-Clustal-client-from-live-server">\r
 \r
                <wsimport wsdl="http://localhost:7979/ClustalWS?wsdl" \r