geneontology / minerva

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id lookup failure on model save. #305

Closed tmushayahama closed 4 years ago

tmushayahama commented 4 years ago

Trying to save model is giving an error "Could not find a property for id: ID"

tagging @goodb @kltm

Extra Detail:

The whole error is { "packet-id":"30deb67d9cab1f167", "uid":"http://orcid.org/0000-0002-2874-6934", "provided-by":[ "http://geneontology.org" ], "is-reasoned":false, "intention":"action", "message-type":"error", "message":"Could not successfully handle batch request. Exception: org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException. Could not find a property for id: RO:0002333", "commentary":"org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException: Could not find a property for id: RO:0002333\n\tat org.geneontology.minerva.server.handler.OperationsImpl.getProperty(OperationsImpl.java:307)\n\tat org.geneontology.minerva.server.handler.OperationsImpl.handleRequestForEdge(OperationsImpl.java:334)\n\tat org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3Batch(JsonOrJsonpBatchHandler.java:160)\n\tat org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3Batch(JsonOrJsonpBatchHandler.java:129)\n\tat org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3BatchPostPrivileged(JsonOrJsonpBatchHandler.java:88)\n\tat sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.lang.reflect.Method.invoke(Method.java:498)\n\tat org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)\n\tat org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:124)\n\tat org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:167)\n\tat org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:219)\n\tat org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:79)\n\tat org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:469)\n\tat org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:391)\n\tat org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:80)\n\tat org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:253)\n\tat org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)\n\tat org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)\n\tat org.glassfish.jersey.internal.Errors.process(Errors.java:292)\n\tat org.glassfish.jersey.internal.Errors.process(Errors.java:274)\n\tat org.glassfish.jersey.internal.Errors.process(Errors.java:244)\n\tat org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)\n\tat org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:232)\n\tat org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:680)\n\tat org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:392)\n\tat org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)\n\tat org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:365)\n\tat org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:318)\n\tat org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)\n\tat org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:769)\n\tat org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)\n\tat org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221)\n\tat org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)\n\tat org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)\n\tat org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)\n\tat org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1059)\n\tat org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)\n\tat org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)\n\tat org.eclipse.jetty.server.Server.handle(Server.java:497)\n\tat org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:311)\n\tat org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:248)\n\tat org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:610)\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:539)\n\tat java.lang.Thread.run(Thread.java:748)\n" }

tmushayahama commented 4 years ago

@vanaukenk I went ahead and put as high priority because models cannot be created in noctua-form.

goodb commented 4 years ago

believe this was resolved in conversion to blazegraph ontology manager.