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July 3, 2018 20:52
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| WARNING: exception encountered when trying to cache the index files: | |
| Traceback (most recent call last): | |
| File "/kb/module/lib/kb_Bowtie2/util/Bowtie2IndexBuilder.py", line 178, in _put_cached_index | |
| save_result = ws.save_objects(save_params) | |
| File "/kb/module/lib/Workspace/WorkspaceClient.py", line 901, in save_objects | |
| [params], self._service_ver, context) | |
| File "/kb/module/lib/Workspace/baseclient.py", line 268, in call_method | |
| return self._call(url, service_method, args, context) | |
| File "/kb/module/lib/Workspace/baseclient.py", line 183, in _call | |
| raise ServerError(**err['error']) | |
| ServerError: JSONRPCError: -32500. Object #1, bowtie2_index_153030841313 failed type checking: | |
| Unable to locate type: KBaseRNASeq.Bowtie2IndexV2 | |
| us.kbase.typedobj.exceptions.TypedObjectValidationException: Object #1, bowtie2_index_153030841313 failed type checking: | |
| Unable to locate type: KBaseRNASeq.Bowtie2IndexV2 | |
| at us.kbase.workspace.database.Workspace.validate(Workspace.java:869) | |
| at us.kbase.workspace.database.Workspace.validateObjectsAndExtractReferences(Workspace.java:770) | |
| at us.kbase.workspace.database.Workspace.saveObjects(Workspace.java:652) | |
| at us.kbase.workspace.kbase.WorkspaceServerMethods.saveObjects(WorkspaceServerMethods.java:395) | |
| at us.kbase.workspace.WorkspaceServer.saveObjects(WorkspaceServer.java:596) | |
| at sun.reflect.GeneratedMethodAccessor133.invoke(Unknown Source) | |
| at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) | |
| Unable to locate type: KBaseRNASeq.Bowtie2IndexV2 | |
| us.kbase.typedobj.exceptions.TypedObjectValidationException: Object #1, bowtie2_index_153030841313 failed type checking: | |
| Unable to locate type: KBaseRNASeq.Bowtie2IndexV2 | |
| at us.kbase.workspace.database.Workspace.validate(Workspace.java:869) | |
| at us.kbase.workspace.database.Workspace.validateObjectsAndExtractReferences(Workspace.java:770) | |
| at us.kbase.workspace.database.Workspace.saveObjects(Workspace.java:652) | |
| at us.kbase.workspace.kbase.WorkspaceServerMethods.saveObjects(WorkspaceServerMethods.java:395) | |
| at us.kbase.workspace.WorkspaceServer.saveObjects(WorkspaceServer.java:596) | |
| at sun.reflect.GeneratedMethodAccessor133.invoke(Unknown Source) | |
| at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) | |
| at java.lang.reflect.Method.invoke(Method.java:498) | |
| at us.kbase.common.service.JsonServerServlet.processRpcCall(JsonServerServlet.java:610) | |
| at us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:463) | |
| at javax.servlet.http.HttpServlet.service(HttpServlet.java:661) | |
| at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) | |
| at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) | |
| at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) | |
| at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) | |
| at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) | |
| at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) | |
| at java.lang.reflect.Method.invoke(Method.java:498) | |
| at us.kbase.common.service.JsonServerServlet.processRpcCall(JsonServerServlet.java:610) | |
| at us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:463) | |
| at javax.servlet.http.HttpServlet.service(HttpServlet.java:661) | |
| at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) | |
| at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) | |
| at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) | |
| at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) | |
| at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) | |
| at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) | |
| at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199) | |
| at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) | |
| at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478) | |
| at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140) | |
| at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80) | |
| at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:624) | |
| at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) | |
| at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) | |
| at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799) | |
| at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) | |
| at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:861) | |
| at org.apache.tomcat.util.net.Nio2Endpoint$SocketProcessor.doRun(Nio2Endpoint.java:1697) | |
| at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) | |
| at org.apache.tomcat.util.net.AbstractEndpoint.processSocket(AbstractEndpoint.java:934) | |
| at org.apache.tomcat.util.net.Nio2Endpoint$Nio2SocketWrapper$4.completed(Nio2Endpoint.java:626) | |
| at org.apache.tomcat.util.net.Nio2Endpoint$Nio2SocketWrapper$4.completed(Nio2Endpoint.java:604) | |
| at sun.nio.ch.Invoker.invokeUnchecked(Invoker.java:126) | |
| at sun.nio.ch.UnixAsynchronousSocketChannelImpl.finishRead(UnixAsynchronousSocketChannelImpl.java:430) | |
| at sun.nio.ch.UnixAsynchronousSocketChannelImpl.finish(UnixAsynchronousSocketChannelImpl.java:191) | |
| at sun.nio.ch.UnixAsynchronousSocketChannelImpl.onEvent(UnixAsynchronousSocketChannelImpl.java:213) | |
| at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:861) | |
| at org.apache.tomcat.util.net.Nio2Endpoint$SocketProcessor.doRun(Nio2Endpoint.java:1697) | |
| at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) | |
| at org.apache.tomcat.util.net.AbstractEndpoint.processSocket(AbstractEndpoint.java:934) | |
| at org.apache.tomcat.util.net.Nio2Endpoint$Nio2SocketWrapper$4.completed(Nio2Endpoint.java:626) | |
| at org.apache.tomcat.util.net.Nio2Endpoint$Nio2SocketWrapper$4.completed(Nio2Endpoint.java:604) | |
| at sun.nio.ch.Invoker.invokeUnchecked(Invoker.java:126) | |
| at sun.nio.ch.UnixAsynchronousSocketChannelImpl.finishRead(UnixAsynchronousSocketChannelImpl.java:430) | |
| at sun.nio.ch.UnixAsynchronousSocketChannelImpl.finish(UnixAsynchronousSocketChannelImpl.java:191) | |
| at sun.nio.ch.UnixAsynchronousSocketChannelImpl.onEvent(UnixAsynchronousSocketChannelImpl.java:213) | |
| at sun.nio.ch.EPollPort$EventHandlerTask.run(EPollPort.java:293) | |
| at sun.nio.ch.AsynchronousChannelGroupImpl$1.run(AsynchronousChannelGroupImpl.java:112) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) | |
| at java.lang.Thread.run(Thread.java:748) | |
| Caused by: us.kbase.typedobj.exceptions.NoSuchTypeException: Unable to locate type: KBaseRNASeq.Bowtie2IndexV2 | |
| at us.kbase.typedobj.db.TypeDefinitionDB.throwNoSuchTypeException(TypeDefinitionDB.java:727) | |
| at us.kbase.typedobj.db.TypeDefinitionDB.resolveTypeDefIdNL(TypeDefinitionDB.java:429) | |
| at us.kbase.typedobj.db.TypeDefinitionDB.resolveTypeDefId(TypeDefinitionDB.java:409) | |
| at us.kbase.typedobj.core.LocalTypeProvider.resolveTypeDef(LocalTypeProvider.java:32) | |
| at sun.nio.ch.EPollPort$EventHandlerTask.run(EPollPort.java:293) | |
| at sun.nio.ch.AsynchronousChannelGroupImpl$1.run(AsynchronousChannelGroupImpl.java:112) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) | |
| at java.lang.Thread.run(Thread.java:748) | |
| Caused by: us.kbase.typedobj.exceptions.NoSuchTypeException: Unable to locate type: KBaseRNASeq.Bowtie2IndexV2 | |
| at us.kbase.typedobj.db.TypeDefinitionDB.throwNoSuchTypeException(TypeDefinitionDB.java:727) | |
| at us.kbase.typedobj.db.TypeDefinitionDB.resolveTypeDefIdNL(TypeDefinitionDB.java:429) | |
| at us.kbase.typedobj.db.TypeDefinitionDB.resolveTypeDefId(TypeDefinitionDB.java:409) | |
| at us.kbase.typedobj.core.LocalTypeProvider.resolveTypeDef(LocalTypeProvider.java:32) | |
| at us.kbase.typedobj.core.TypedObjectValidator.validate(TypedObjectValidator.java:175) | |
| at us.kbase.workspace.database.Workspace.validate(Workspace.java:864) | |
| ... 41 more | |
| END WARNING: exception encountered when trying to cache the index files |
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