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  1. Sep 30, 2011 1:41:50 PM org.apache.catalina.core.AprLifecycleListener init
  2. INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /opt/jdk1.6.0_22/jre/lib/amd64/server:/opt/jdk1.6.0_22/jre/lib/amd64:/opt/jdk1.6.0_22/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
  3. Sep 30, 2011 1:41:50 PM org.apache.coyote.http11.Http11Protocol init
  4. INFO: Initializing Coyote HTTP/1.1 on http-8080
  5. Sep 30, 2011 1:41:50 PM org.apache.coyote.http11.Http11Protocol init
  6. INFO: Initializing Coyote HTTP/1.1 on http-443
  7. Sep 30, 2011 1:41:50 PM org.apache.coyote.http11.Http11Protocol init
  8. INFO: Initializing Coyote HTTP/1.1 on http-8443
  9. Sep 30, 2011 1:41:50 PM org.apache.catalina.startup.Catalina load
  10. INFO: Initialization processed in 977 ms
  11. Sep 30, 2011 1:41:51 PM org.apache.catalina.core.StandardService start
  12. INFO: Starting service Catalina
  13. Sep 30, 2011 1:41:51 PM org.apache.catalina.core.StandardEngine start
  14. INFO: Starting Servlet Engine: Apache Tomcat/6.0.29
  15. Sep 30, 2011 1:41:51 PM org.apache.catalina.startup.HostConfig deployDescriptor
  16. INFO: Deploying configuration descriptor grouper.xml
  17. Sep 30, 2011 1:41:51 PM org.apache.catalina.startup.HostConfig deployDescriptor
  18. WARNING: A docBase /opt/tomcat/webapps/grouper inside the host appBase has been specified, and will be ignored
  19. Sep 30, 2011 1:41:55 PM org.apache.catalina.core.ApplicationContext log
  20. INFO: Grouper starting up: version: 2.0.0, build date: 2011/09/06 07:57:48, env: <no label configured>
  21. grouper.properties read from: /opt/tomcat/webapps/grouper/WEB-INF/classes/grouper.properties
  22. Grouper current directory is: /opt/tomcat/webapps/grouper/WEB-INF/classes
  23. log4j.properties read from: /opt/tomcat/webapps/grouper/WEB-INF/classes/log4j.properties
  24. Grouper warning, it is detected that you are logging edu.internet2.middleware.grouper as ERROR and not WARN level. It is recommended to log at at least WARN level in log4j.properties
  25. Grouper is logging to file: /var/log/log4jgrouper_ui.log, console, at min level ERROR for package: edu.internet2.middleware.grouper, based on log4j.properties
  26. grouper.hibernate.properties: /opt/tomcat/webapps/grouper/WEB-INF/classes/grouper.hibernate.properties
  27. grouper.hibernate.properties: sa@jdbc:hsqldb:hsql://localhost/grouper
  28. sources.xml read from: /opt/tomcat/webapps/grouper/WEB-INF/classes/sources.xml
  29. sources.xml groupersource id: g:gsa
  30. sources.xml jdbc source id: example: GrouperJdbcConnectionProvider
  31. 2011-09-30 13:41:54,224: [main] WARN EhCacheProvider.buildCache(86) - Could not find configuration [edu.internet2.middleware.grouper.externalSubjects.ExternalSubject]; using defaults.
  32. 2011-09-30 13:41:54,341: [main] WARN EhCacheProvider.buildCache(86) - Could not find configuration [edu.internet2.middleware.grouper.externalSubjects.ExternalSubjectAttribute]; using defaults.
  33. 2011-09-30 13:41:54,498: [main] WARN EhCacheProvider.buildCache(86) - Could not find configuration [edu.internet2.middleware.grouper.attr.value.AttributeAssignValue]; using defaults.
  34. Grouper ddl object type 'Grouper' has dbVersion: 23 and java version: 25
  35. 2011-09-30 13:41:54,669: [main] ERROR GrouperDdlUtils.bootstrapHelper(406) - Grouper ddl object type 'Grouper' has dbVersion: 23 and java version: 25
  36. 2011-09-30 13:41:55,735: [main] ERROR GrouperDdlUtils.bootstrapHelper(666) - Grouper database schema DDL requires updates
  37. (should run script manually and carefully, in sections, verify data before drop statements, backup/export important data before starting, follow change log on confluence, dont run exact same script in multiple envs - generate a new one for each env),
  38. script file is:
  39. /opt/tomcat/webapps/grouper/WEB-INF/classes/ddlScripts/grouperDdl_20110930_13_41_55_727.sql
  40. Grouper database schema DDL requires updates
  41. (should run script manually and carefully, in sections, verify data before drop statements, backup/export important data before starting, follow change log on confluence, dont run exact same script in multiple envs - generate a new one for each env),
  42. script file is:
  43. /opt/tomcat/webapps/grouper/WEB-INF/classes/ddlScripts/grouperDdl_20110930_13_41_55_727.sql
  44. Couldnt startup grouper: unable to retrieve GrouperSystem: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,
  45. Problem in HibernateSession: null,
  46. Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where m.subjectIdDb = :sid and m.subjectSourceIdDb = :source and m.subjectTypeId = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',
  47. edu.internet2.middleware.grouper.exception.GrouperException: unable to retrieve GrouperSystem: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,
  48. Problem in HibernateSession: null,
  49. Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where m.subjectIdDb = :sid and m.subjectSourceIdDb = :source and m.subjectTypeId = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',
  50. at edu.internet2.middleware.grouper.SubjectFinder.findRootSubject(SubjectFinder.java:550)
  51. at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:221)
  52. at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:239)
  53. at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(GrouperCheckConfig.java:450)
  54. at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:417)
  55. at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:109)
  56. at edu.internet2.middleware.grouper.ui.GrouperUiFilter.init(GrouperUiFilter.java:613)
  57. at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:287)
  58. at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:422)
  59. at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:115)
  60. at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4001)
  61. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4651)
  62. at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
  63. at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
  64. at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
  65. at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
  66. at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
  67. at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
  68. at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
  69. at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
  70. at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
  71. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
  72. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  73. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  74. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
  75. at org.apache.catalina.core.StandardService.start(StandardService.java:519)
  76. at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
  77. at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
  78. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  79. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
  80. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
  81. at java.lang.reflect.Method.invoke(Method.java:597)
  82. at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
  83. at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
  84. 2011-09-30 13:41:55,935: [main] ERROR GrouperStartup.startup(142) - Couldnt startup grouper: unable to retrieve GrouperSystem: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,
  85. Problem in HibernateSession: null,
  86. Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where m.subjectIdDb = :sid and m.subjectSourceIdDb = :source and m.subjectTypeId = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',
  87. edu.internet2.middleware.grouper.exception.GrouperException: unable to retrieve GrouperSystem: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,
  88. Problem in HibernateSession: null,
  89. Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where m.subjectIdDb = :sid and m.subjectSourceIdDb = :source and m.subjectTypeId = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',
  90. at edu.internet2.middleware.grouper.SubjectFinder.findRootSubject(SubjectFinder.java:550)
  91. at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:221)
  92. at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:239)
  93. at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(GrouperCheckConfig.java:450)
  94. at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:417)
  95. at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:109)
  96. at edu.internet2.middleware.grouper.ui.GrouperUiFilter.init(GrouperUiFilter.java:613)
  97. at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:287)
  98. at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:422)
  99. at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:115)
  100. at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4001)
  101. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4651)
  102. at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
  103. at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
  104. at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
  105. at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
  106. at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
  107. at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
  108. at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
  109. at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
  110. at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
  111. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
  112. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  113. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  114. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
  115. at org.apache.catalina.core.StandardService.start(StandardService.java:519)
  116. at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
  117. at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
  118. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  119. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
  120. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
  121. at java.lang.reflect.Method.invoke(Method.java:597)
  122. at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
  123. at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
  124.  
  125. Sep 30, 2011 1:41:55 PM org.apache.catalina.core.StandardContext filterStart
  126. SEVERE: Exception starting filter GrouperUi
  127. edu.internet2.middleware.grouper.exception.GrouperException: unable to retrieve GrouperSystem: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,
  128. Problem in HibernateSession: null,
  129. Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where m.subjectIdDb = :sid and m.subjectSourceIdDb = :source and m.subjectTypeId = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',
  130. at edu.internet2.middleware.grouper.SubjectFinder.findRootSubject(SubjectFinder.java:550)
  131. at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:221)
  132. at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:239)
  133. at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(GrouperCheckConfig.java:450)
  134. at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:417)
  135. at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:109)
  136. at edu.internet2.middleware.grouper.ui.GrouperUiFilter.init(GrouperUiFilter.java:613)
  137. at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:287)
  138. at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:422)
  139. at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:115)
  140. at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4001)
  141. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4651)
  142. at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
  143. at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
  144. at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
  145. at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
  146. at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
  147. at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
  148. at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
  149. at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
  150. at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
  151. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
  152. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  153. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  154. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
  155. at org.apache.catalina.core.StandardService.start(StandardService.java:519)
  156. at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
  157. at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
  158. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  159. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
  160. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
  161. at java.lang.reflect.Method.invoke(Method.java:597)
  162. at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
  163. at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
  164. Sep 30, 2011 1:41:55 PM org.apache.catalina.core.StandardContext start
  165. SEVERE: Error filterStart
  166. Sep 30, 2011 1:41:55 PM org.apache.catalina.core.StandardContext start
  167. SEVERE: Context [/grouper] startup failed due to previous errors
  168. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
  169. SEVERE: The web application [/grouper] registered the JBDC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
  170. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
  171. SEVERE: The web application [/grouper] registered the JBDC driver [com.microsoft.sqlserver.jdbc.SQLServerDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
  172. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
  173. SEVERE: The web application [/grouper] registered the JBDC driver [org.hsqldb.jdbcDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
  174. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
  175. SEVERE: The web application [/grouper] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
  176. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
  177. SEVERE: The web application [/grouper] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0] but has failed to stop it. This is very likely to create a memory leak.
  178. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
  179. SEVERE: The web application [/grouper] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1] but has failed to stop it. This is very likely to create a memory leak.
  180. Sep 30, 2011 1:41:55 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
  181. SEVERE: The web application [/grouper] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2] but has failed to stop it. This is very likely to create a memory leak.
  182. log4j:ERROR LogMananger.repositorySelector was null likely due to error in class reloading, using NOPLoggerRepository.
  183. Sep 30, 2011 1:41:56 PM org.apache.catalina.startup.HostConfig deployDescriptor
  184. INFO: Deploying configuration descriptor host-manager.xml
  185. Sep 30, 2011 1:41:56 PM org.apache.catalina.startup.HostConfig deployDescriptor
  186. INFO: Deploying configuration descriptor idp.xml
  187. Sep 30, 2011 1:42:00 PM org.apache.catalina.startup.HostConfig deployDescriptor
  188. INFO: Deploying configuration descriptor manager.xml
  189. Sep 30, 2011 1:42:00 PM org.apache.catalina.startup.HostConfig deployDirectory
  190. INFO: Deploying web application directory ddlScripts
  191. Sep 30, 2011 1:42:00 PM org.apache.catalina.startup.HostConfig deployDirectory
  192. INFO: Deploying web application directory ROOT
  193. Sep 30, 2011 1:42:00 PM org.apache.catalina.startup.HostConfig deployDirectory
  194. INFO: Deploying web application directory docs
  195. Sep 30, 2011 1:42:00 PM org.apache.catalina.startup.HostConfig deployDirectory
  196. INFO: Deploying web application directory examples
  197. Sep 30, 2011 1:42:00 PM org.apache.coyote.http11.Http11Protocol start
  198. INFO: Starting Coyote HTTP/1.1 on http-8080
  199. Sep 30, 2011 1:42:00 PM org.apache.jk.common.ChannelSocket init
  200. INFO: JK: ajp13 listening on /0.0.0.0:8009
  201. Sep 30, 2011 1:42:00 PM org.apache.jk.server.JkMain start
  202. INFO: Jk running ID=0 time=0/14 config=null
  203. Sep 30, 2011 1:42:00 PM org.apache.coyote.http11.Http11Protocol start
  204. INFO: Starting Coyote HTTP/1.1 on http-443
  205. Sep 30, 2011 1:42:00 PM org.apache.coyote.http11.Http11Protocol start
  206. INFO: Starting Coyote HTTP/1.1 on http-8443
  207. Sep 30, 2011 1:42:00 PM org.apache.catalina.startup.Catalina start
  208. INFO: Server startup in 9273 ms
  209.  
  210.  
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