Modify servlet configuration

diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml
deleted file mode 100644 (file)
index 13d6fac..0000000
--- a/WEB-INF/sun-jaxws.xml
+++ /dev/null
@@ -1,51 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>\r
-<endpoints xmlns='http://java.sun.com/xml/ns/jax-ws/ri/runtime' version='2.0'>\r
-       <endpoint name='RegistryWS'\r
-               implementation='compbio.ws.server.RegistryWS'\r
-               url-pattern='/RegistryWS'/>\r
-       <endpoint name='ClustalWS'\r
-               implementation='compbio.ws.server.ClustalWS'\r
-               url-pattern='/ClustalWS'/>\r
-       <endpoint name='ClustalOWS'\r
-               implementation='compbio.ws.server.ClustalOWS'\r
-               url-pattern='/ClustalOWS'/>\r
-       <endpoint name='MuscleWS'\r
-               implementation='compbio.ws.server.MuscleWS'\r
-               url-pattern='/MuscleWS'/>\r
-       <endpoint name='TcoffeeWS'\r
-               implementation='compbio.ws.server.TcoffeeWS'\r
-               url-pattern='/TcoffeeWS'/>\r
-       <endpoint name='MafftWS'\r
-               implementation='compbio.ws.server.MafftWS'\r
-               url-pattern='/MafftWS'/>\r
-       <endpoint name='ProbconsWS'\r
-               implementation='compbio.ws.server.ProbconsWS'\r
-               url-pattern='/ProbconsWS'/>\r
-       <endpoint name='MSAprobsWS'\r
-               implementation='compbio.ws.server.MSAprobsWS'\r
-               url-pattern='/MSAprobsWS'/>\r
-       <endpoint name='GLprobsWS'\r
-               implementation='compbio.ws.server.GLprobsWS'\r
-               url-pattern='/GLprobsWS'/>\r
-       <endpoint name='AAConWS'\r
-               implementation='compbio.ws.server.AAConWS'\r
-               url-pattern='/AAConWS'/>\r
-       <endpoint name='JronnWS'\r
-               implementation='compbio.ws.server.JronnWS'\r
-               url-pattern='/JronnWS'/>\r
-       <endpoint name='DisemblWS'\r
-               implementation='compbio.ws.server.DisemblWS'\r
-               url-pattern='/DisemblWS'/>\r
-       <endpoint name='GlobPlotWS'\r
-               implementation='compbio.ws.server.GlobPlotWS'\r
-               url-pattern='/GlobPlotWS'/>\r
-       <endpoint name='IUPredWS'\r
-               implementation='compbio.ws.server.IUPredWS'\r
-               url-pattern='/IUPredWS'/>\r
-       <endpoint name='JpredWS'\r
-               implementation='compbio.ws.server.JpredWS'\r
-               url-pattern='/JpredWS'/>\r
-       <endpoint name='RNAalifoldWS'\r
-               implementation='compbio.ws.server.RNAalifoldWS'\r
-               url-pattern='/RNAalifoldWS'/>\r
-</endpoints>\r

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index cec1884..242a900 100644 (file)
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -3,22 +3,16 @@
  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>ProteoCache</display-name>\r
+<description>ProteoCache - Results repository for the Dundee Resource</description>\r
 \r
+       <welcome-file-list>\r
+               <welcome-file>Index.jsp</welcome-file>\r
+       </welcome-file-list>\r
 \r
-       <!-- JABAWS listeners -->\r
+       <!-- ProteoCache 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>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>\r
+               <listener-class>compbio.listeners.ContextListener</listener-class>\r
        </listener>\r
 \r
 \r
@@ -48,7 +42,8 @@
        </servlet>\r
 \r
 \r
-       <!-- JABAWS servlets -->\r
+       <!-- ProteoCache servlets -->\r
+<!--\r
        <servlet>\r
                <description>Display pre-calculated accounting info</description>\r
                <servlet-name>DisplayStat</servlet-name>\r
@@ -184,8 +179,12 @@
                <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
                <load-on-startup>1</load-on-startup>\r
        </servlet>\r
+-->\r
+\r
 \r
-       <!-- JABAWS servlet mappings -->\r
+\r
+       <!-- ProteoCache servlet mappings -->\r
+<!--\r
        <servlet-mapping>\r
                <servlet-name>listings</servlet-name>\r
                <url-pattern>/</url-pattern>\r
@@ -305,9 +304,10 @@
                <servlet-name>RNAalifoldWS</servlet-name>\r
                <url-pattern>/RNAalifoldWS</url-pattern>\r
        </servlet-mapping>\r
+-->\r
 \r
 \r
-       <!-- JABAWS security constraints -->\r
+       <!-- ProteoCache security constraints -->\r
        <security-constraint>\r
                <web-resource-collection>\r
                <web-resource-name>Administrator pages</web-resource-name>\r
@@ -317,10 +317,8 @@
                        <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
@@ -346,17 +344,16 @@
                <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
+               <realm-name>ProteCache 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
+               <description>The role that is required to log in and view ProteCache internals</description>\r
                <role-name>admin</role-name>\r
        </security-role>\r
 \r