WEB-INF/web.xml

   1 <web-app xmlns="http://java.sun.com/xml/ns/j2ee"\r
   2  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
   3  xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"\r
   4  version="2.4">\r
   5 \r
   6 <display-name>JABAWS</display-name>\r
   7 <description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>\r
   8 \r
   9 \r
  10         <!-- JABAWS listeners -->\r
  11         <listener>\r
  12                 <listener-class>compbio.ws.server.MainManager</listener-class>\r
  13         </listener>\r
  14         <listener>\r
  15                 <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>\r
  16         </listener>\r
  17         <listener>\r
  18                 <listener-class>compbio.ws.server.SetExecutableFlag</listener-class>\r
  19         </listener>\r
  20         <listener>\r
  21                 <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>\r
  22         </listener>\r
  23 \r
  24         <!-- Session timeout in minutes -->\r
  25         <session-config>\r
  26                 <session-timeout>20</session-timeout>\r
  27         </session-config>\r
  28 \r
  29 \r
  30         <servlet>\r
  31                 <display-name>This is a standard tomcat 'default' servlet for making listings</display-name>\r
  32                 <servlet-name>listings</servlet-name>\r
  33                 <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>\r
  34                 <init-param>\r
  35                         <param-name>debug</param-name>\r
  36                         <param-value>0</param-value>\r
  37                 </init-param>\r
  38                 <init-param>\r
  39                         <param-name>readonly</param-name>\r
  40                         <param-value>true</param-value>\r
  41                 </init-param>\r
  42                 <init-param>\r
  43                         <param-name>listings</param-name>\r
  44                         <param-value>true</param-value>\r
  45                 </init-param>\r
  46                 <load-on-startup>1</load-on-startup>\r
  47         </servlet>\r
  48 \r
  49 \r
  50         <!-- JABAWS servlets -->\r
  51         <servlet>\r
  52                 <description>Display pre-calculated accounting info</description>\r
  53                 <servlet-name>DisplayStat</servlet-name>\r
  54                 <servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>\r
  55         </servlet>\r
  56 \r
  57         <servlet>\r
  58                 <description>WebServices Status</description>\r
  59                 <servlet-name>ServiceStatus</servlet-name>\r
  60                 <servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>\r
  61         </servlet>\r
  62 \r
  63         <servlet>\r
  64                 <servlet-name>DownloadRedirector</servlet-name>\r
  65                 <servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>\r
  66         </servlet>\r
  67 \r
  68         <servlet>\r
  69                 <description>WebService Status with no UI. Accepts web service name as a parameter</description>\r
  70                 <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
  71                 <servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>\r
  72         </servlet>\r
  73 \r
  74         <servlet>\r
  75                 <description>Display job list</description>\r
  76                 <servlet-name>Joblist</servlet-name>\r
  77                 <servlet-class>compbio.stat.servlet.Joblist</servlet-class>\r
  78         </servlet>\r
  79 \r
  80         <servlet>\r
  81                 <description>Display monthly summary statistics</description>\r
  82                 <servlet-name>AnnualStat</servlet-name>\r
  83                 <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
  84         </servlet>\r
  85 \r
  86         <servlet>\r
  87                 <description>Display monthly summary statistics with no links to details</description>\r
  88                 <servlet-name>PublicAnnualStat</servlet-name>\r
  89                 <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
  90         </servlet>\r
  91 \r
  92         <servlet>\r
  93                 <servlet-name>RegistryWS</servlet-name>\r
  94                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
  95                 <load-on-startup>1</load-on-startup>\r
  96         </servlet>\r
  97 \r
  98         <servlet>\r
  99                 <servlet-name>ClustalWS</servlet-name>\r
 100                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 101                 <load-on-startup>1</load-on-startup>\r
 102         </servlet>\r
 103 \r
 104         <servlet>\r
 105                 <servlet-name>ClustalOWS</servlet-name>\r
 106                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 107                 <load-on-startup>1</load-on-startup>\r
 108         </servlet>\r
 109 \r
 110         <servlet>\r
 111                 <servlet-name>MuscleWS</servlet-name>\r
 112                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 113                 <load-on-startup>1</load-on-startup>\r
 114         </servlet>\r
 115 \r
 116         <servlet>\r
 117                 <servlet-name>MafftWS</servlet-name>\r
 118                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 119                 <load-on-startup>1</load-on-startup>\r
 120         </servlet>\r
 121 \r
 122         <servlet>\r
 123                 <servlet-name>TcoffeeWS</servlet-name>\r
 124                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 125                 <load-on-startup>1</load-on-startup>\r
 126         </servlet>\r
 127 \r
 128         <servlet>\r
 129                 <servlet-name>ProbconsWS</servlet-name>\r
 130                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 131                 <load-on-startup>1</load-on-startup>\r
 132         </servlet>\r
 133 \r
 134         <servlet>\r
 135                 <servlet-name>AAConWS</servlet-name>\r
 136                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 137                 <load-on-startup>1</load-on-startup>\r
 138         </servlet>\r
 139 \r
 140         <servlet>\r
 141                 <servlet-name>JronnWS</servlet-name>\r
 142                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 143                 <load-on-startup>1</load-on-startup>\r
 144         </servlet>\r
 145 \r
 146         <servlet>\r
 147                 <servlet-name>DisemblWS</servlet-name>\r
 148                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 149                 <load-on-startup>1</load-on-startup>\r
 150         </servlet>\r
 151 \r
 152         <servlet>\r
 153                 <servlet-name>GlobPlotWS</servlet-name>\r
 154                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 155                 <load-on-startup>1</load-on-startup>\r
 156         </servlet>\r
 157 \r
 158         <servlet>\r
 159                 <servlet-name>IUPredWS</servlet-name>\r
 160                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 161                 <load-on-startup>1</load-on-startup>\r
 162         </servlet>\r
 163         \r
 164         <servlet>\r
 165                 <servlet-name>RNAalifoldWS</servlet-name>\r
 166                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 167                 <load-on-startup>1</load-on-startup>\r
 168         </servlet>\r
 169         <servlet>\r
 170                 <display-name>Apache-Axis Servlet</display-name>\r
 171                 <servlet-name>AxisServlet</servlet-name>\r
 172                 <servlet-class>org.apache.axis.transport.http.AxisServlet</servlet-class>\r
 173         </servlet>\r
 174         <servlet>\r
 175                 <display-name>Axis Admin Servlet</display-name>\r
 176                 <servlet-name>AdminServlet</servlet-name>\r
 177                 <servlet-class>org.apache.axis.transport.http.AdminServlet</servlet-class>\r
 178                 <load-on-startup>100</load-on-startup>\r
 179         </servlet>\r
 180 \r
 181         <!-- JABAWS servlet mappings -->\r
 182         <servlet-mapping>\r
 183                 <servlet-name>listings</servlet-name>\r
 184                 <url-pattern>/</url-pattern>\r
 185         </servlet-mapping>\r
 186 \r
 187         <servlet-mapping>\r
 188                 <servlet-name>DownloadRedirector</servlet-name>\r
 189                 <url-pattern>/download</url-pattern>\r
 190         </servlet-mapping>\r
 191 \r
 192         <servlet-mapping>\r
 193                 <servlet-name>DisplayStat</servlet-name>\r
 194                 <url-pattern>/DisplayStat</url-pattern>\r
 195         </servlet-mapping>\r
 196 \r
 197         <servlet-mapping>\r
 198                 <servlet-name>ServiceStatus</servlet-name>\r
 199                 <url-pattern>/ServiceStatus</url-pattern>\r
 200         </servlet-mapping>\r
 201 \r
 202         <servlet-mapping>\r
 203                 <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
 204                 <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
 205         </servlet-mapping>\r
 206 \r
 207         <servlet-mapping>\r
 208                 <servlet-name>AnnualStat</servlet-name>\r
 209                 <url-pattern>/AnnualStat</url-pattern>\r
 210         </servlet-mapping>\r
 211 \r
 212         <servlet-mapping>\r
 213                 <servlet-name>PublicAnnualStat</servlet-name>\r
 214                 <url-pattern>/PublicAnnualStat</url-pattern>\r
 215         </servlet-mapping>\r
 216 \r
 217         <servlet-mapping>\r
 218                 <servlet-name>Joblist</servlet-name>\r
 219                 <url-pattern>/Joblist</url-pattern>\r
 220         </servlet-mapping>\r
 221 \r
 222         <servlet-mapping>\r
 223                 <servlet-name>RegistryWS</servlet-name>\r
 224                 <url-pattern>/RegistryWS</url-pattern>\r
 225         </servlet-mapping>\r
 226 \r
 227         <servlet-mapping>\r
 228                 <servlet-name>ClustalWS</servlet-name>\r
 229                 <url-pattern>/ClustalWS</url-pattern>\r
 230         </servlet-mapping>\r
 231 \r
 232         <servlet-mapping>\r
 233                 <servlet-name>ClustalOWS</servlet-name>\r
 234                 <url-pattern>/ClustalOWS</url-pattern>\r
 235         </servlet-mapping>\r
 236 \r
 237         <servlet-mapping>\r
 238                 <servlet-name>MuscleWS</servlet-name>\r
 239                 <url-pattern>/MuscleWS</url-pattern>\r
 240         </servlet-mapping>\r
 241 \r
 242         <servlet-mapping>\r
 243                 <servlet-name>MafftWS</servlet-name>\r
 244                 <url-pattern>/MafftWS</url-pattern>\r
 245         </servlet-mapping>\r
 246 \r
 247         <servlet-mapping>\r
 248                 <servlet-name>TcoffeeWS</servlet-name>\r
 249                 <url-pattern>/TcoffeeWS</url-pattern>\r
 250         </servlet-mapping>\r
 251 \r
 252         <servlet-mapping>\r
 253                 <servlet-name>ProbconsWS</servlet-name>\r
 254                 <url-pattern>/ProbconsWS</url-pattern>\r
 255         </servlet-mapping>\r
 256 \r
 257         <servlet-mapping>\r
 258                 <servlet-name>AAConWS</servlet-name>\r
 259                 <url-pattern>/AAConWS</url-pattern>\r
 260         </servlet-mapping>\r
 261 \r
 262         <servlet-mapping>\r
 263                 <servlet-name>JronnWS</servlet-name>\r
 264                 <url-pattern>/JronnWS</url-pattern>\r
 265         </servlet-mapping>\r
 266 \r
 267         <servlet-mapping>\r
 268                 <servlet-name>DisemblWS</servlet-name>\r
 269                 <url-pattern>/DisemblWS</url-pattern>\r
 270         </servlet-mapping>\r
 271 \r
 272         <servlet-mapping>\r
 273                 <servlet-name>GlobPlotWS</servlet-name>\r
 274                 <url-pattern>/GlobPlotWS</url-pattern>\r
 275         </servlet-mapping>\r
 276 \r
 277         <servlet-mapping>\r
 278                 <servlet-name>IUPredWS</servlet-name>\r
 279                 <url-pattern>/IUPredWS</url-pattern>\r
 280         </servlet-mapping>\r
 281         \r
 282         <servlet-mapping>\r
 283                 <servlet-name>RNAalifoldWS</servlet-name>\r
 284                 <url-pattern>/RNAalifoldWS</url-pattern>\r
 285         </servlet-mapping>\r
 286         <servlet-mapping>\r
 287                 <servlet-name>AxisServlet</servlet-name>\r
 288                 <url-pattern>/servlet/AxisServlet</url-pattern>\r
 289         </servlet-mapping>\r
 290         <servlet-mapping>\r
 291                 <servlet-name>AxisServlet</servlet-name>\r
 292                 <url-pattern>*.jws</url-pattern>\r
 293         </servlet-mapping>\r
 294         <servlet-mapping>\r
 295                 <servlet-name>AxisServlet</servlet-name>\r
 296                 <url-pattern>/services/*</url-pattern>\r
 297         </servlet-mapping>\r
 298         <servlet-mapping>\r
 299                 <servlet-name>AdminServlet</servlet-name>\r
 300                 <url-pattern>/servlet/AdminServlet</url-pattern>\r
 301         </servlet-mapping>\r
 302 \r
 303 \r
 304 \r
 305         <!-- JABAWS security constraints -->\r
 306         <security-constraint>\r
 307                 <web-resource-collection>\r
 308                 <web-resource-name>Administrator pages</web-resource-name>\r
 309                         <!-- Prohibit access to any resources -->\r
 310                         <url-pattern>/DisplayStat</url-pattern>\r
 311                         <url-pattern>/Joblist</url-pattern>\r
 312                         <url-pattern>/AnnualStat</url-pattern>\r
 313                         <url-pattern>/conf/*</url-pattern>\r
 314                         <url-pattern>/binaries/*</url-pattern>\r
 315                         <url-pattern>/jobsout/*</url-pattern>\r
 316                         <url-pattern>/testsrc/*</url-pattern>\r
 317                         <url-pattern>/lib/*</url-pattern>\r
 318                         <url-pattern>/test-output/*</url-pattern>\r
 319                         <!-- Uncomment this to secure services status checker \r
 320                         <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
 321                         <url-pattern>/ServiceStatus</url-pattern>\r
 322                         -->\r
 323                         <!-- No http-method means all methods are constrained -->\r
 324                 </web-resource-collection>\r
 325                 <auth-constraint>\r
 326                         <role-name>admin</role-name>\r
 327                 </auth-constraint>\r
 328         </security-constraint>\r
 329 \r
 330 \r
 331         <!-- unsupported HTTP methods -->\r
 332         <security-constraint>\r
 333                 <web-resource-collection>\r
 334                         <web-resource-name>unsupported HTTP methods</web-resource-name>\r
 335                         <url-pattern>/*</url-pattern>\r
 336                         <http-method>PUT</http-method>\r
 337                         <http-method>DELETE</http-method>\r
 338                         <http-method>TRACE</http-method>\r
 339                         <http-method>OPTIONS</http-method>\r
 340                 </web-resource-collection>\r
 341                 <auth-constraint/>\r
 342         </security-constraint>\r
 343 \r
 344 \r
 345         <!-- Define the Login Configuration for this Application -->\r
 346         <login-config>\r
 347                 <auth-method>BASIC</auth-method>\r
 348                 <realm-name>JABAWS administrators</realm-name>\r
 349         </login-config>\r
 350 \r
 351 \r
 352         <!-- Security roles referenced by this web application -->\r
 353         <security-role>\r
 354                 <description>The role that is required to log in and view JABAWS internals</description>\r
 355                 <role-name>admin</role-name>\r
 356         </security-role>\r
 357 \r
 358 </web-app>\r