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grosscol/irb_and_stack_trace

Created September 15, 2016 19:07
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Hydra PCDM::Object (FileSet) and PCDM::File (original_file) results in Fedora LDP 500 response.
Raw
irb_and_stack_trace
irb(main):004:0> file_set = FileSet.find("0c483j36g")
=> #<FileSet id: "0c483j36g", label: "Evans_Old_Field_Plant_Database.zip", relative_path: nil, import_url: nil, part_of: [], resource_type: [], creator: [], contributor: [], description: [], keyword: [], rights: [], publisher: [], date_created: [], subject: [], language: [], identifier: [], based_near: [], related_url: [], bibliographic_citation: [], source: [], head: [], tail: [], depositor: "[email protected]", title: ["Evans_Old_Field_Plant_Database.zip"], date_uploaded: "2016-03-04", date_modified: nil, access_control_id: "5b97fa6e-ed85-4293-a188-294331ac8904", embargo_id: nil, lease_id: nil>
irb(main):005:0> file_set.original_file
=> #<Hydra::PCDM::File uri="http://localhost:8301/fedora/rest/umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525" >
irb(main):006:0> file_set.original_file.metadata
=> #<ActiveFedora::WithMetadata::MetadataNode:0x3f8da1e337d0(#<ActiveFedora::WithMetadata::MetadataNode:0x007f1b43c66fa0>)>
irb(main):007:0> file_set.original_file.described_by
=> "http://localhost:8301/fedora/rest/umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata"
irb(main):008:0> file_set.original_file.save
=> true
irb(main):009:0> file_set.original_file
=> #<Hydra::PCDM::File uri="http://localhost:8301/fedora/rest/umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525" >
irb(main):010:0> file_set.original_file.save
Ldp::HttpError: STATUS: 500 java.util.NoSuchElementException
at com.google.common.collect.Iterators$1.next(Iterators.java:80)
at org.fcrepo.kernel.modeshape.rdf.impl.mappings.PropertyValueIterator.computeNext(PropertyValueIterator.java:68)
at org.fcrepo.kernel.modeshape.rdf.impl.mappings.PropertyValueIterator.computeNext(PropertyValueIterator.java:35)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at com.google.common.collect.TransformedIterator.hasNext(TransformedIterator.java:43)
at com.google.common.collect.Iterators$7.computeNext(Iterators.java:650)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at com.google.common.collect.TransformedIterator.hasNext(TransformedIterator.java:43)
at com.google.common.collect.Iterators$5.hasNext(Iterators.java:547)
at com...
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/ldp-0.5.0/lib/ldp/client/methods.rb:119:in `block in check_for_errors'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/ldp-0.5.0/lib/ldp/client/methods.rb:117:in `tap'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/ldp-0.5.0/lib/ldp/client/methods.rb:117:in `check_for_errors'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/ldp-0.5.0/lib/ldp/client/methods.rb:110:in `block in patch'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.6/lib/active_support/notifications.rb:166:in `instrument'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/ldp-0.5.0/lib/ldp/client/methods.rb:102:in `patch'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/caching_connection.rb:29:in `patch'
from /l/local/rbenv/versions/2.3.0/lib/ruby/2.3.0/delegate.rb:83:in `method_missing'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/initializing_connection.rb:47:in `patch'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/sparql_insert.rb:11:in `execute'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/with_metadata/metadata_node.rb:47:in `save'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/file.rb:167:in `block in create_or_update'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/file.rb:166:in `tap'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/file.rb:166:in `create_or_update'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/with_metadata.rb:22:in `create_or_update'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/active-fedora-10.2.0/lib/active_fedora/persistence.rb:29:in `save'
from (irb):10
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/railties-4.2.6/lib/rails/commands/console.rb:110:in `start'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/railties-4.2.6/lib/rails/commands/console.rb:9:in `start'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/railties-4.2.6/lib/rails/commands/commands_tasks.rb:68:in `console'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/railties-4.2.6/lib/rails/commands/commands_tasks.rb:39:in `run_command!'
from /hydra/umrdr-production/shared/vendor/bundle/ruby/2.3.0/gems/railties-4.2.6/lib/rails/commands.rb:17:in `<top (required)>'
from bin/rails:4:in `require'
from bin/rails:4:in `<main>'
Raw
tomcat log
INFO 15:01:30.024 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g
INFO 15:01:30.061 (FedoraLdp) GET resource 'umrdr/0c/48/3j/36/0c483j36g'
INFO 15:01:41.500 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525
INFO 15:01:41.534 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata
INFO 15:01:41.563 (FedoraLdp) GET resource 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:01:53.194 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata
INFO 15:01:53.231 (FedoraLdp) GET resource 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:02:48.010 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
WARN 15:02:48.027 (PropertyConverter) The namespace of predicate: http://pcdm.org/models#File was possibly misinterpreted as: http://pcdm.org/models#.
WARN 15:02:48.029 (PropertyConverter) The namespace of predicate: http://www.w3.org/ns/ldp#NonRDFSource was possibly misinterpreted as: http://www.w3.org/ns/ldp#.
WARN 15:02:48.030 (PropertyConverter) The namespace of predicate: http://pcdm.org/use#OriginalFile was possibly misinterpreted as: http://pcdm.org/use#.
WARN 15:02:48.030 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0versionable was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
WARN 15:02:48.031 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Resource was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.031 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0mimeType was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
WARN 15:02:48.032 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Binary was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.033 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/nt/1.0resource was possibly misinterpreted as: http://www.jcp.org/jcr/nt/1.0.
WARN 15:02:48.034 (PropertyConverter) The namespace of predicate: http://www.w3.org/ns/ldp#NonRDFSource was possibly misinterpreted as: http://www.w3.org/ns/ldp#.
WARN 15:02:48.035 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/nt/1.0resource was possibly misinterpreted as: http://www.jcp.org/jcr/nt/1.0.
WARN 15:02:48.036 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0mimeType was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
WARN 15:02:48.036 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Binary was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.036 (PropertyConverter) The namespace of predicate: http://pcdm.org/models#File was possibly misinterpreted as: http://pcdm.org/models#.
WARN 15:02:48.037 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Resource was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.037 (PropertyConverter) The namespace of predicate: http://pcdm.org/use#OriginalFile was possibly misinterpreted as: http://pcdm.org/use#.
WARN 15:02:48.038 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0versionable was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
INFO 15:02:48.096 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
WARN 15:02:48.107 (PropertyConverter) The namespace of predicate: http://pcdm.org/models#File was possibly misinterpreted as: http://pcdm.org/models#.
WARN 15:02:48.107 (PropertyConverter) The namespace of predicate: http://www.w3.org/ns/ldp#NonRDFSource was possibly misinterpreted as: http://www.w3.org/ns/ldp#.
WARN 15:02:48.107 (PropertyConverter) The namespace of predicate: http://pcdm.org/use#OriginalFile was possibly misinterpreted as: http://pcdm.org/use#.
WARN 15:02:48.108 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0versionable was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
WARN 15:02:48.119 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Resource was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.119 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0mimeType was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
WARN 15:02:48.120 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Binary was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.120 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/nt/1.0resource was possibly misinterpreted as: http://www.jcp.org/jcr/nt/1.0.
WARN 15:02:48.121 (PropertyConverter) The namespace of predicate: http://www.w3.org/ns/ldp#NonRDFSource was possibly misinterpreted as: http://www.w3.org/ns/ldp#.
WARN 15:02:48.122 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/nt/1.0resource was possibly misinterpreted as: http://www.jcp.org/jcr/nt/1.0.
WARN 15:02:48.122 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0mimeType was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
WARN 15:02:48.122 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Binary was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.123 (PropertyConverter) The namespace of predicate: http://pcdm.org/models#File was possibly misinterpreted as: http://pcdm.org/models#.
WARN 15:02:48.123 (PropertyConverter) The namespace of predicate: http://fedora.info/definitions/v4/repository#Resource was possibly misinterpreted as: http://fedora.info/definitions/v4/repository#.
WARN 15:02:48.123 (PropertyConverter) The namespace of predicate: http://pcdm.org/use#OriginalFile was possibly misinterpreted as: http://pcdm.org/use#.
WARN 15:02:48.124 (PropertyConverter) The namespace of predicate: http://www.jcp.org/jcr/mix/1.0versionable was possibly misinterpreted as: http://www.jcp.org/jcr/mix/1.0.
INFO 15:04:14.377 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:04:14.382 (WildcardExceptionMapper) Exception intercepted by WildcardExceptionMapper:
java.util.NoSuchElementException: null
at com.google.common.collect.Iterators$1.next(Iterators.java:80) ~[Iterators$1.class:na]
at org.fcrepo.kernel.modeshape.rdf.impl.mappings.PropertyValueIterator.computeNext(PropertyValueIterator.java:68) ~[PropertyValueIterator.class:4.5.0]
at org.fcrepo.kernel.modeshape.rdf.impl.mappings.PropertyValueIterator.computeNext(PropertyValueIterator.java:35) ~[PropertyValueIterator.class:4.5.0]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143) ~[AbstractIterator.class:na]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138) ~[AbstractIterator.class:na]
at com.google.common.collect.TransformedIterator.hasNext(TransformedIterator.java:43) ~[TransformedIterator.class:na]
at com.google.common.collect.Iterators$7.computeNext(Iterators.java:650) ~[Iterators$7.class:na]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143) ~[AbstractIterator.class:na]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138) ~[AbstractIterator.class:na]
at com.google.common.collect.TransformedIterator.hasNext(TransformedIterator.java:43) ~[TransformedIterator.class:na]
at com.google.common.collect.Iterators$5.hasNext(Iterators.java:547) ~[Iterators$5.class:na]
at com.google.common.collect.Iterators$5.hasNext(Iterators.java:547) ~[Iterators$5.class:na]
at com.google.common.collect.ForwardingIterator.hasNext(ForwardingIterator.java:43) ~[ForwardingIterator.class:na]
at com.google.common.collect.Iterators$5.hasNext(Iterators.java:547) ~[Iterators$5.class:na]
at com.google.common.collect.ForwardingIterator.hasNext(ForwardingIterator.java:43) ~[ForwardingIterator.class:na]
at com.google.common.collect.Iterators$7.computeNext(Iterators.java:650) ~[Iterators$7.class:na]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143) ~[AbstractIterator.class:na]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138) ~[AbstractIterator.class:na]
at com.google.common.collect.Iterators$5.hasNext(Iterators.java:547) ~[Iterators$5.class:na]
at com.google.common.collect.Iterators$5.hasNext(Iterators.java:547) ~[Iterators$5.class:na]
at org.fcrepo.kernel.api.utils.iterators.RdfStream.asModel(RdfStream.java:303) ~[RdfStream.class:4.5.0]
at org.fcrepo.kernel.modeshape.FedoraResourceImpl.updateProperties(FedoraResourceImpl.java:447) ~[FedoraResourceImpl.class:4.5.0]
at org.fcrepo.http.api.ContentExposingResource.patchResourcewithSparql(ContentExposingResource.java:630) ~[ContentExposingResource.class:4.5.0]
at org.fcrepo.http.api.FedoraLdp.updateSparql(FedoraLdp.java:438) ~[FedoraLdp.class:4.5.0]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_102]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_102]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_102]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_102]
at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81) ~[ResourceMethodInvocationHandlerFactory$1.class:na]
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:151) ~[AbstractJavaResourceMethodDispatcher$1.class:na]
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:171) ~[AbstractJavaResourceMethodDispatcher.class:na]
at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:152) ~[JavaResourceMethodDispatcherProvider$ResponseOutInvoker.class:na]
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:104) ~[AbstractJavaResourceMethodDispatcher.class:na]
at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:384) ~[ResourceMethodInvoker.class:na]
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:342) ~[ResourceMethodInvoker.class:na]
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:101) ~[ResourceMethodInvoker.class:na]
at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:271) ~[ServerRuntime$1.class:na]
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) [Errors$1.class:na]
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) [Errors$1.class:na]
at org.glassfish.jersey.internal.Errors.process(Errors.java:315) [Errors.class:na]
at org.glassfish.jersey.internal.Errors.process(Errors.java:297) [Errors.class:na]
at org.glassfish.jersey.internal.Errors.process(Errors.java:267) [Errors.class:na]
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:297) [RequestScope.class:na]
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:254) [ServerRuntime.class:na]
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1030) [ApplicationHandler.class:na]
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373) [WebComponent.class:na]
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381) [ServletContainer.class:na]
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344) [ServletContainer.class:na]
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221) [ServletContainer.class:na]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat8-websocket-8.0.14.jar:8.0.14]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) [tomcat8-catalina-8.0.14.jar:8.0.14]
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) [tomcat8-coyote-8.0.14.jar:8.0.14]
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) [tomcat8-coyote-8.0.14.jar:8.0.14]
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222) [tomcat8-coyote-8.0.14.jar:8.0.14]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1566) [tomcat8-coyote-8.0.14.jar:8.0.14]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1523) [tomcat8-coyote-8.0.14.jar:8.0.14]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_102]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_102]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat8-util-8.0.14.jar:8.0.14]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_102]
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Ran the same commands on the staging host. Fedora there has been restored from the same backup. No error. Interestingly, the patch request doesn't generate the same warnings either.

The following is what the tomcat log looks like when it goes as expected on the staging machine.

INFO 15:25:09.613 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g
INFO 15:25:09.664 (FedoraLdp) GET resource 'umrdr/0c/48/3j/36/0c483j36g'
INFO 15:25:22.341 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525
INFO 15:25:22.364 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata
INFO 15:25:22.384 (FedoraLdp) GET resource 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:25:44.736 (FedoraLdp) HEAD for: umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata
INFO 15:25:44.763 (FedoraLdp) GET resource 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:25:44.870 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:25:44.926 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:25:54.639 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'
INFO 15:25:54.688 (FedoraLdp) PATCH for 'umrdr/0c/48/3j/36/0c483j36g/files/d39bd72b-ada0-4c69-9b3d-40ec151d5525/fcr:metadata'

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