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