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