Hi Scott, Good find. Yes, please submit it to the Akubra tracker. It appears that java.nio.file.Path is a Java 1.7+ class, so it doesn't look like we can use it, but I'm sure we can muster up a suitable 1.6-compatible workaround.
- Chris On Tue, Oct 5, 2010 at 5:03 PM, Scott Prater <[email protected]> wrote: > I think I may have found the source of the problem. > > In org.akubraproject.fs.FSBlob, this is what happens when an object gets > moved: > > if (!file.renameTo(other)) { > if (!file.exists()) > throw new MissingBlobException(getId()); > > throw new IOException("Rename failed for an unknown reason."); > } > > file.renameTo() is a java.io.File method that may or may not move files > across symlinks and filesystems, depending on your platform (I'm running > Solaris 10, so go figure): > > http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 > > Googling turns up a rich history of problems with the java.io.File renameTo() > method when other filesystems and symlinks are involved. Best practice these > days seems to be to use java.nio.file instead: > > http://download.oracle.com/javase/tutorial/essential/io/legacy.html > > Chris: shall I open to a bug report in the Akubra JIRA issue tracker? > > -- Scott > > On 10/05/10, "Scott Prater" <[email protected]> wrote: > >> Another item of information: Ingesting FOXML files works without a problem, >> induicating that this may be a problem with the copy/replace functionality? >> >> Also, I simplified the process somewhat: really, the new data is spread >> across three different filesystems, with the symlinks occuring at the >> top-level hash character directories: >> >> /fedora/data/objects/0 -> /fedora/db01/objects/0 >> /fedora/data/objects/1 -> /fedora/db02/objects/1 >> etc. >> >> I mention this, as it occurs to me that perhaps Akubra, as part of its safe >> move/rename function, is attempting to create temporary hard links across >> filesystems? Just a guess... >> >> -- Scott >> >> On 10/05/10, "Scott Prater" <[email protected]> wrote: >> >> > We encountered a worrisome problem today after filling up a filesystem and >> > being forced to move our data to another filesystem. After the move and >> > rebuild, we can no longer add datastreams to objects. >> > >> > I'm running Fedora 3.4, with the default Akubra low-level storage module. >> > >> > Here's what happened: >> > >> > 1. filesystem /fedora/data filled up, Fedora (and Tomcat) hung. >> > 2. I shut down Fedora, Tomcat, Postgres. >> > 3. I moved the directory /fedora/data/objects to another filesystem, >> > /fedora/db01/objects. >> > 4. I moved the directory /fedora/data/datastreams to another filesystem, >> > /fedora/db01/datastreams. >> > 5. I made symlinks from the original locations to the new locations: >> > /fedora/data/objects -> /fedora/db01/objects >> > /fedora/data/datastreams -> /fedora/db01/datastreams >> > 6. I started up Postgres, and ran fedora-rebuild.sh twice, once to >> > rebuild the database and once to rebuild the resource index. The rebuild >> > completed successfully. >> > 7. I then started up Tomcat + Fedora, and I was able to view all the >> > objects. >> > 8. I then did a test ingest of an object, and a stub object was >> > successfully created, with a DC datastream. I verified that I could find >> > the object and the datastream on the filesystem (both through the direct >> > path and through the symlinked path). I verified that permsissions were >> > correct at every directory level, and at the file level. >> > >> > I then try to add a datastream to the test object, and I receive this >> > error (truncated): >> > >> > ERROR 2010-10-05 14:51:16.424 [http-9090-1] (WebApplicationImpl) Internal >> > server error >> > javax.ws.rs.WebApplicationException: >> > org.fcrepo.server.errors.GeneralException: Unable to add or modify object >> > (commit canceled) >> > [...] >> > Caused by: java.io.IOException: Rename failed for an unknown reason. >> > at org.akubraproject.fs.FSBlob.moveTo(FSBlob.java:151) >> > [akubra-fs-0.3.jar:na] >> > >> > I've tested this with the REST API, through the web admin interface, and >> > through the java GUI admin tool, and the results are the same in all three >> > cases. This error occurs regardless of whether I'm adding a datastream to >> > a newly-created object or attempting to add a datastream to an older >> > object. >> > >> > This may properly be an Akubra matter, but I thought I would bring it up >> > here, first. Any suggestions or help would be greatly appreciated. >> > >> > thanks, >> > >> > -- Scott >> > >> > Following is the full stack trace: >> > >> > ERROR 2010-10-05 14:51:16.424 [http-9090-1] (WebApplicationImpl) Internal >> > server error >> > javax.ws.rs.WebApplicationException: >> > org.fcrepo.server.errors.GeneralException: Unable to add or modify object >> > (commit canceled) >> > at >> > org.fcrepo.server.rest.BaseRestResource.handleException(BaseRestResource.java:168) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.rest.DatastreamResource.addOrUpdateDatastream(DatastreamResource.java:583) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.rest.DatastreamResource.addDatastream(DatastreamResource.java:358) >> > [fcrepo-server-3.4.jar:na] >> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> > [na:1.6.0_21] >> > at >> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> > [na:1.6.0_21] >> > at >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> > [na:1.6.0_21] >> > at java.lang.reflect.Method.invoke(Method.java:597) [na:1.6.0_21] >> > at >> > com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:175) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:67) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:163) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:111) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:71) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:111) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:63) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:689) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:647) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:638) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:309) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:425) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at >> > com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:590) >> > [jersey-bundle-1.0.3.1.jar:1.0.3.1] >> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) >> > [servlet-api.jar:na] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) >> > [catalina.jar:6.0.29] >> > at >> > org.fcrepo.server.security.servletfilters.FilterRestApiFlash.doFilter(FilterRestApiFlash.java:66) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) >> > [catalina.jar:6.0.29] >> > at >> > org.fcrepo.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) >> > [catalina.jar:6.0.29] >> > at >> > org.fcrepo.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) >> > [catalina.jar:6.0.29] >> > at >> > org.fcrepo.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) >> > [catalina.jar:6.0.29] >> > at >> > org.fcrepo.server.security.servletfilters.FilterSetup.doFilter(FilterSetup.java:235) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:563) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:269) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:555) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) >> > [catalina.jar:6.0.29] >> > at >> > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857) >> > [tomcat-coyote.jar:6.0.29] >> > at >> > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) >> > [tomcat-coyote.jar:6.0.29] >> > at >> > org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) >> > [tomcat-coyote.jar:6.0.29] >> > at java.lang.Thread.run(Thread.java:619) [na:1.6.0_21] >> > Caused by: org.fcrepo.server.errors.GeneralException: Unable to add or >> > modify object (commit canceled) >> > at >> > org.fcrepo.server.storage.DefaultDOManager.doCommit(DefaultDOManager.java:1438) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.storage.SimpleDOWriter.commit(SimpleDOWriter.java:508) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.management.DefaultManagement.addDatastream(DefaultManagement.java:572) >> > [fcrepo-server-3.4.jar:na] >> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> > [na:1.6.0_21] >> > at >> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> > [na:1.6.0_21] >> > at >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> > [na:1.6.0_21] >> > at java.lang.reflect.Method.invoke(Method.java:597) [na:1.6.0_21] >> > at >> > org.fcrepo.server.messaging.NotificationInvocationHandler.invoke(NotificationInvocationHandler.java:68) >> > [fcrepo-server-3.4.jar:na] >> > at $Proxy0.addDatastream(Unknown Source) [na:na] >> > at >> > org.fcrepo.server.management.ManagementModule.addDatastream(ManagementModule.java:227) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.rest.DatastreamResource.addOrUpdateDatastream(DatastreamResource.java:467) >> > [fcrepo-server-3.4.jar:na] >> > ... 50 common frames omitted >> > Caused by: org.fcrepo.common.FaultException: java.io.IOException: Rename >> > failed for an unknown reason. >> > at >> > org.fcrepo.server.storage.lowlevel.akubra.AkubraLowlevelStorage.rename(AkubraLowlevelStorage.java:363) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.storage.lowlevel.akubra.AkubraLowlevelStorage.safeOverwrite(AkubraLowlevelStorage.java:306) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.storage.lowlevel.akubra.AkubraLowlevelStorage.replace(AkubraLowlevelStorage.java:244) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.storage.lowlevel.akubra.AkubraLowlevelStorage.replaceObject(AkubraLowlevelStorage.java:150) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.storage.lowlevel.akubra.AkubraLowlevelStorageModule.replaceObject(AkubraLowlevelStorageModule.java:79) >> > [fcrepo-server-3.4.jar:na] >> > at >> > org.fcrepo.server.storage.DefaultDOManager.doCommit(DefaultDOManager.java:1334) >> > [fcrepo-server-3.4.jar:na] >> > ... 60 common frames omitted >> > Caused by: java.io.IOException: Rename failed for an unknown reason. >> > at org.akubraproject.fs.FSBlob.moveTo(FSBlob.java:151) >> > [akubra-fs-0.3.jar:na] >> > at >> > org.akubraproject.map.IdMappingBlob.moveTo(IdMappingBlob.java:69) >> > [akubra-map-0.3.jar:na] >> > at >> > org.fcrepo.server.storage.lowlevel.akubra.AkubraLowlevelStorage.rename(AkubraLowlevelStorage.java:361) >> > [fcrepo-server-3.4.jar:na] >> > ... 65 common frames omitted >> > -- >> > Scott Prater >> > Library, Instructional, and Research Applications (LIRA) >> > Division of Information Technology (DoIT) >> > University of Wisconsin - Madison >> > [email protected] > > ------------------------------------------------------------------------------ > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/fedora-commons-users > ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/fedora-commons-users
