Hi, Bill, We've had the problem once or twice, too. What we did was the following:
* shut down Fedora * delete the object from any tables it appears in the database * delete the object's datastreams from any tables in the database * remove the datastreams, if any, from the filesystem * remove the object from the filesystem * run fedora-rebuild.sh to rebuild both the database and the resource index * start Fedora back up. This should get you back to a clean state. If you're extra paranoid, make backups of your datastreams and objects filesystems, and of your database after shutting down but before making changes, in case you need to roll back. Anyone else, feel free to step in if you have more experience with this situation, and if I suggested anything dangerous. -- Scott Bill Parod wrote: > I neglected to mention this is in Fedora version 3.1. > > - Bill > > On Oct 14, 2010, at 12:26 PM, Bill Parod wrote: > >> We have an object that is in a corrupted state. The object is found in the >> objectPaths table but not in doFields. Also its foxml won't parse, >> apparently because it contains a namespace reference which is unresolved, >> bound to a urn. I'll include some detail below. I'm inclined to 'fix' this >> problem by deleting the specific record in the objectPaths table and >> deleting its foxml file in the fedora data subdirectory. Is this a bad idea? >> Could there be side effects to this that I'm not considering? >> >> Thanks very much in advance! >> - Bill >> >> >> Here's a rundown of the object's mysql database profile. >> This object, having pid inu:inm-ead-0001 is: >> >> not in datastreamPaths >> not in dcDates >> not in doFields >> not in doRegistry >> but is in objectPaths: >> mysql> select * from objectPaths where token like 'inu:inm-ead%'; >> +-----------+------------------+------------------------------------------------------------------------+ >> | tokenDbID | token | path >> | >> +-----------+------------------+------------------------------------------------------------------------+ >> | 437940 | inu:inm-ead-0001 | >> /farchive1/fedorastorage/data/objects/2010/1014/10/37/inu_inm-ead-0001 | >> +-----------+------------------+------------------------------------------------------------------------+ >> >> >> Searches don't find it: >> >> fedora/search?query=pid~inu:inm-ead-0001&pid=true&maxResults=10&xml=true >> <result> <resultList></resultList></result> >> >> But references to the default dissemination return auth failure rather than >> not found. I'm guessing this is because its attempting to read the object's >> foxml, but it doesn't parse and so can't obtain its policy, so denies access. >> >> fedora/get/inu:inm-ead-0001: >> >> 403 Forbidden >> >> Authorization failed >> >> Doing a viewItemIndex shows the root of the problem: >> >> fedora/get/inu:inm-ead-0001/fedora-system:3/viewItemIndex >> >> 500 Internal Server Error >> >> FOXML IO stream was bad : The prefix "ead" for element "ead:unitid" is not >> bound. >> fedora.server.errors.ObjectIntegrityException: FOXML IO stream was bad : The >> prefix "ead" for element "ead:unitid" is not bound. >> at >> fedora.server.storage.translation.FOXMLDODeserializer.deserialize(FOXMLDODeserializer.java:250) >> at >> fedora.server.storage.translation.DOTranslatorImpl.deserialize(DOTranslatorImpl.java:76) >> at >> fedora.server.storage.translation.DOTranslatorModule.deserialize(DOTranslatorModule.java:127) >> at fedora.server.storage.SimpleDOReader.(SimpleDOReader.java:92) >> at >> fedora.server.storage.DefaultDOManager.getReader(DefaultDOManager.java:659) >> at >> fedora.server.access.DefaultAccess.getDissemination(DefaultAccess.java:223) >> at >> fedora.server.access.FedoraAccessServlet.getDissemination(FedoraAccessServlet.java:730) >> at >> fedora.server.access.FedoraAccessServlet.doGet(FedoraAccessServlet.java:440) >> at javax.servlet.http.HttpServlet.service(HttpServlet.java:690) >> at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> fedora.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> fedora.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> fedora.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) >> at >> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) >> at >> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) >> at >> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) >> at >> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) >> at >> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) >> at >> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) >> at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200) >> at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283) >> at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773) >> at >> org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703) >> at >> org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:895) >> at >> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) >> at java.lang.Thread.run(Thread.java:595) >> >> >> Here's an example of what I believe is the offending foxml >> <ead:unitid xmlns:ead="urn:isbn:1-931666-22-9">autogend1e275</ead:unitid> >> >> Thanks, >> >> Bill Parod >> Library Technology Division - Enterprise Systems >> Northwestern University Library >> bill-pa...@northwestern.edu >> 847 491 5368 >> >> >> >> >> ------------------------------------------------------------------------------ >> Beautiful is writing same markup. Internet Explorer 9 supports >> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. >> Spend less time writing and rewriting code and more time creating great >> experiences on the web. Be a part of the beta today. >> http://p.sf.net/sfu/beautyoftheweb_______________________________________________ >> Fedora-commons-users mailing list >> Fedora-commons-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/fedora-commons-users > > Bill Parod > Library Technology Division - Enterprise Systems > Northwestern University Library > bill-pa...@northwestern.edu > 847 491 5368 > > > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > > > ------------------------------------------------------------------------ > > _______________________________________________ > Fedora-commons-users mailing list > Fedora-commons-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/fedora-commons-users -- Scott Prater Library, Instructional, and Research Applications (LIRA) Division of Information Technology (DoIT) University of Wisconsin - Madison pra...@wisc.edu ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Fedora-commons-users mailing list Fedora-commons-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fedora-commons-users
