<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.MainManager</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>compbio.ws.server.ShutdownEngines</listener-class>\r
+ <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</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
+\r
+ <!-- Session timeout in minutes -->\r
<session-config>\r
- <session-timeout>20</session-timeout>\r
- </session-config>\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/>\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/>\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/>\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/>\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/>\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/>\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/>\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
- <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/>\r
- </servlet>\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>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
- <security-constraint>\r
- <web-resource-collection>\r
- <web-resource-name>Administrator pages</web-resource-name>\r
- <!-- Prohibit access to any resources -->\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
- <!-- 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>HEAD</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
+ <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>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
+ <servlet>\r
+ <servlet-name>RNAalifoldWS</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
+ <servlet>\r
+ <display-name>Apache-Axis Servlet</display-name>\r
+ <servlet-name>AxisServlet</servlet-name>\r
+ <servlet-class>org.apache.axis.transport.http.AxisServlet</servlet-class>\r
+ </servlet>\r
+ <servlet>\r
+ <display-name>Axis Admin Servlet</display-name>\r
+ <servlet-name>AdminServlet</servlet-name>\r
+ <servlet-class>org.apache.axis.transport.http.AdminServlet</servlet-class>\r
+ <load-on-startup>100</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
+ <servlet-mapping>\r
+ <servlet-name>RNAalifoldWS</servlet-name>\r
+ <url-pattern>/RNAalifoldWS</url-pattern>\r
+ </servlet-mapping>\r
+ <servlet-mapping>\r
+ <servlet-name>AxisServlet</servlet-name>\r
+ <url-pattern>/servlet/AxisServlet</url-pattern>\r
+ </servlet-mapping>\r
+ <servlet-mapping>\r
+ <servlet-name>AxisServlet</servlet-name>\r
+ <url-pattern>*.jws</url-pattern>\r
+ </servlet-mapping>\r
+ <servlet-mapping>\r
+ <servlet-name>AxisServlet</servlet-name>\r
+ <url-pattern>/services/*</url-pattern>\r
+ </servlet-mapping>\r
+ <servlet-mapping>\r
+ <servlet-name>AdminServlet</servlet-name>\r
+ <url-pattern>/servlet/AdminServlet</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