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                 <servlet-name>DownloadRedirector</servlet-name>\r
  66                 <servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>\r
  67         </servlet>\r
  68 \r
  69         <servlet>\r
  70                 <description>WebService Status with no UI. Accepts web service name as a parameter</description>\r
  71                 <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
  72                 <servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>\r
  73         </servlet>\r
  74 \r
  75         <servlet>\r
  76                 <description>Display job list</description>\r
  77                 <servlet-name>Joblist</servlet-name>\r
  78                 <servlet-class>compbio.stat.servlet.Joblist</servlet-class>\r
  79         </servlet>\r
  80 \r
  81         <servlet>\r
  82                 <description>Display monthly summary statistics</description>\r
  83                 <servlet-name>AnnualStat</servlet-name>\r
  84                 <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
  85         </servlet>\r
  86 \r
  87         <servlet>\r
  88                 <description>Display monthly summary statistics with no links to details</description>\r
  89                 <servlet-name>PublicAnnualStat</servlet-name>\r
  90                 <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
  91         </servlet>\r
  92 \r
  93         <servlet>\r
  94                 <servlet-name>RegistryWS</servlet-name>\r
  95                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
  96                 <load-on-startup>1</load-on-startup>\r
  97         </servlet>\r
  98 \r
  99         <servlet>\r
 100                 <servlet-name>ClustalWS</servlet-name>\r
 101                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 102                 <load-on-startup>1</load-on-startup>\r
 103         </servlet>\r
 104 \r
 105         <servlet>\r
 106                 <servlet-name>ClustalOWS</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>MuscleWS</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>MafftWS</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>TcoffeeWS</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>ProbconsWS</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>MSAprobsWS</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>GLprobsWS</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>AAConWS</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>JronnWS</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>DisemblWS</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>GlobPlotWS</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>IUPredWS</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>JpredWS</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         <servlet>\r
 183                 <servlet-name>RNAalifoldWS</servlet-name>\r
 184                 <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
 185                 <load-on-startup>1</load-on-startup>\r
 186         </servlet>\r
 187 \r
 188         <!-- JABAWS servlet mappings -->\r
 189         <servlet-mapping>\r
 190                 <servlet-name>listings</servlet-name>\r
 191                 <url-pattern>/</url-pattern>\r
 192         </servlet-mapping>\r
 193 \r
 194         <servlet-mapping>\r
 195                 <servlet-name>DownloadRedirector</servlet-name>\r
 196                 <url-pattern>/download</url-pattern>\r
 197         </servlet-mapping>\r
 198 \r
 199         <servlet-mapping>\r
 200                 <servlet-name>DisplayStat</servlet-name>\r
 201                 <url-pattern>/DisplayStat</url-pattern>\r
 202         </servlet-mapping>\r
 203 \r
 204         <servlet-mapping>\r
 205                 <servlet-name>ServiceStatus</servlet-name>\r
 206                 <url-pattern>/ServiceStatus</url-pattern>\r
 207         </servlet-mapping>\r
 208 \r
 209         <servlet-mapping>\r
 210                 <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
 211                 <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
 212         </servlet-mapping>\r
 213 \r
 214         <servlet-mapping>\r
 215                 <servlet-name>AnnualStat</servlet-name>\r
 216                 <url-pattern>/AnnualStat</url-pattern>\r
 217         </servlet-mapping>\r
 218 \r
 219         <servlet-mapping>\r
 220                 <servlet-name>PublicAnnualStat</servlet-name>\r
 221                 <url-pattern>/PublicAnnualStat</url-pattern>\r
 222         </servlet-mapping>\r
 223 \r
 224         <servlet-mapping>\r
 225                 <servlet-name>Joblist</servlet-name>\r
 226                 <url-pattern>/Joblist</url-pattern>\r
 227         </servlet-mapping>\r
 228 \r
 229         <servlet-mapping>\r
 230                 <servlet-name>RegistryWS</servlet-name>\r
 231                 <url-pattern>/RegistryWS</url-pattern>\r
 232         </servlet-mapping>\r
 233 \r
 234         <servlet-mapping>\r
 235                 <servlet-name>ClustalWS</servlet-name>\r
 236                 <url-pattern>/ClustalWS</url-pattern>\r
 237         </servlet-mapping>\r
 238 \r
 239         <servlet-mapping>\r
 240                 <servlet-name>ClustalOWS</servlet-name>\r
 241                 <url-pattern>/ClustalOWS</url-pattern>\r
 242         </servlet-mapping>\r
 243 \r
 244         <servlet-mapping>\r
 245                 <servlet-name>MuscleWS</servlet-name>\r
 246                 <url-pattern>/MuscleWS</url-pattern>\r
 247         </servlet-mapping>\r
 248 \r
 249         <servlet-mapping>\r
 250                 <servlet-name>MafftWS</servlet-name>\r
 251                 <url-pattern>/MafftWS</url-pattern>\r
 252         </servlet-mapping>\r
 253 \r
 254         <servlet-mapping>\r
 255                 <servlet-name>TcoffeeWS</servlet-name>\r
 256                 <url-pattern>/TcoffeeWS</url-pattern>\r
 257         </servlet-mapping>\r
 258 \r
 259         <servlet-mapping>\r
 260                 <servlet-name>ProbconsWS</servlet-name>\r
 261                 <url-pattern>/ProbconsWS</url-pattern>\r
 262         </servlet-mapping>\r
 263 \r
 264         <servlet-mapping>\r
 265                 <servlet-name>MSAprobsWS</servlet-name>\r
 266                 <url-pattern>/MSAprobsWS</url-pattern>\r
 267         </servlet-mapping>\r
 268 \r
 269         <servlet-mapping>\r
 270                 <servlet-name>GLprobsWS</servlet-name>\r
 271                 <url-pattern>/GLprobsWS</url-pattern>\r
 272         </servlet-mapping>\r
 273 \r
 274         <servlet-mapping>\r
 275                 <servlet-name>AAConWS</servlet-name>\r
 276                 <url-pattern>/AAConWS</url-pattern>\r
 277         </servlet-mapping>\r
 278 \r
 279         <servlet-mapping>\r
 280                 <servlet-name>JronnWS</servlet-name>\r
 281                 <url-pattern>/JronnWS</url-pattern>\r
 282         </servlet-mapping>\r
 283 \r
 284         <servlet-mapping>\r
 285                 <servlet-name>DisemblWS</servlet-name>\r
 286                 <url-pattern>/DisemblWS</url-pattern>\r
 287         </servlet-mapping>\r
 288 \r
 289         <servlet-mapping>\r
 290                 <servlet-name>GlobPlotWS</servlet-name>\r
 291                 <url-pattern>/GlobPlotWS</url-pattern>\r
 292         </servlet-mapping>\r
 293 \r
 294         <servlet-mapping>\r
 295                 <servlet-name>IUPredWS</servlet-name>\r
 296                 <url-pattern>/IUPredWS</url-pattern>\r
 297         </servlet-mapping>\r
 298 \r
 299         <servlet-mapping>\r
 300                 <servlet-name>JpredWS</servlet-name>\r
 301                 <url-pattern>/JpredWS</url-pattern>\r
 302         </servlet-mapping>\r
 303 \r
 304         <servlet-mapping>\r
 305                 <servlet-name>RNAalifoldWS</servlet-name>\r
 306                 <url-pattern>/RNAalifoldWS</url-pattern>\r
 307         </servlet-mapping>\r
 308 \r
 309 \r
 310         <!-- JABAWS security constraints -->\r
 311         <security-constraint>\r
 312                 <web-resource-collection>\r
 313                 <web-resource-name>Administrator pages</web-resource-name>\r
 314                         <!-- Prohibit access to any resources -->\r
 315                         <url-pattern>/DisplayStat</url-pattern>\r
 316                         <url-pattern>/Joblist</url-pattern>\r
 317                         <url-pattern>/AnnualStat</url-pattern>\r
 318                         <url-pattern>/conf/*</url-pattern>\r
 319                         <url-pattern>/binaries/*</url-pattern>\r
 320                         <url-pattern>/jobsout/*</url-pattern>\r
 321                         <url-pattern>/testsrc/*</url-pattern>\r
 322                         <url-pattern>/lib/*</url-pattern>\r
 323                         <url-pattern>/test-output/*</url-pattern>\r
 324                         <!-- Uncomment this to secure services status checker \r
 325                         <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
 326                         <url-pattern>/ServiceStatus</url-pattern>\r
 327                         -->\r
 328                         <!-- No http-method means all methods are constrained -->\r
 329                 </web-resource-collection>\r
 330                 <auth-constraint>\r
 331                         <role-name>admin</role-name>\r
 332                 </auth-constraint>\r
 333         </security-constraint>\r
 334 \r
 335 \r
 336         <!-- unsupported HTTP methods -->\r
 337         <security-constraint>\r
 338                 <web-resource-collection>\r
 339                         <web-resource-name>unsupported HTTP methods</web-resource-name>\r
 340                         <url-pattern>/*</url-pattern>\r
 341                         <http-method>PUT</http-method>\r
 342                         <http-method>DELETE</http-method>\r
 343                         <http-method>TRACE</http-method>\r
 344                         <http-method>OPTIONS</http-method>\r
 345                 </web-resource-collection>\r
 346                 <auth-constraint/>\r
 347         </security-constraint>\r
 348 \r
 349 \r
 350         <!-- Define the Login Configuration for this Application -->\r
 351         <login-config>\r
 352                 <auth-method>BASIC</auth-method>\r
 353                 <realm-name>JABAWS administrators</realm-name>\r
 354         </login-config>\r
 355 \r
 356 \r
 357         <!-- Security roles referenced by this web application -->\r
 358         <security-role>\r
 359                 <description>The role that is required to log in and view JABAWS internals</description>\r
 360                 <role-name>admin</role-name>\r
 361         </security-role>\r
 362 \r
 363 </web-app>\r