Bring in and use Blazegraph-enabled Minerva

[kltm]

This ticket will be closed when the Blazegraph-enabled Minerva JAR is the default. To this end, several items must be met:

• [x] minerva-requests and bbop-manager-minerva support the blazegraph flush-to-disk commands
• [x] any new needed startup.yaml variables are threaded through
• [x] the gulpfile commands for running minerva
• [x] remove all things epione
• [x] the minerva-cli.jar in noctua is built from the merged minerva off of minerva master

[kltm]

Related to and following geneontology/minerva#39.

[kltm]

@balhoff I'm unsure where I'm running into this issue, but I am so far unable to complete the "export-all" command against minerva. It looks like minerva, but there are other places in might be (a lot of new stuff running around). Against the current noctua-models, run with:

    'java',
    '-Xmx' + minerva_max_mem + 'G',
    '-cp', './java/lib/minerva-cli.jar',
    'org.geneontology.minerva.server.StartUpTool',
    '--use-golr-url-logging', // possibly unnecessary in non-lookup cases
    '--use-request-logging',
    '--slme-elk',
    '-g', ontology_list,
    '--set-important-relation-parent', 'http://purl.obolibrary.org/obo/LEGOREL_0000000',
    '--port', minerva_port,
    '-f', noctua_store,
    '-export-folder', noctua_models

The command:

http "http://localhost:6800/m3BatchPrivileged?intention=query&requests=%5B%7B%22entity%22%3A%22meta%22%2C%22operation%22%3A%22export-all%22%2C%22arguments%22%3A%7B%7D%7D%5D&uid=GOC%3Akltm"

{ "token": 123,
  "intention": "query",
  "requests": [ { "entity": "meta", "operation": "export-all", "arguments": {} } ] }

returns:

{
    "commentary": "java.lang.NullPointerException\n\tat java.io.File.<init>(File.java:277)\n\tat org.geneontology.minerva.BlazegraphMolecularModelManager.dumpAllStoredModels(BlazegraphMolecularModelManager.java:595)\n\tat org.geneontology.minerva.server.handler.OperationsImpl.exportAllModels(OperationsImpl.java:629)\n\tat org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3Batch(JsonOrJsonpBatchHandler.java:184)\n\tat org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3Batch(JsonOrJsonpBatchHandler.java:132)\n\tat org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3BatchGetPrivileged(JsonOrJsonpBatchHandler.java:79)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\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$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)\n\tat org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:151)\n\tat org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:171)\n\tat org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:195)\n\tat org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:104)\n\tat org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:402)\n\tat org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:349)\n\tat org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:106)\n\tat org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:259)\n\tat org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)\n\tat org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)\n\tat org.glassfish.jersey.internal.Errors.process(Errors.java:315)\n\tat org.glassfish.jersey.internal.Errors.process(Errors.java:297)\n\tat org.glassfish.jersey.internal.Errors.process(Errors.java:267)\n\tat org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:318)\n\tat org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:236)\n\tat org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1010)\n\tat org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373)\n\tat org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:382)\n\tat org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:345)\n\tat org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:220)\n\tat org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:547)\n\tat org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:480)\n\tat org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:225)\n\tat org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:941)\n\tat org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:409)\n\tat org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:186)\n\tat org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:875)\n\tat org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)\n\tat org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:110)\n\tat org.eclipse.jetty.server.Server.handle(Server.java:349)\n\tat org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:441)\n\tat org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:919)\n\tat org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:582)\n\tat org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:218)\n\tat org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:51)\n\tat org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:586)\n\tat org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:44)\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:598)\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:533)\n\tat java.lang.Thread.run(Thread.java:745)\n", 
    "intention": "query", 
    "is-reasoned": false, 
    "message": "Could not successfully handle batch request. Exception: java.lang.NullPointerException.", 
    "message-type": "error", 
    "packet-id": "2db391da79de3", 
    "provided-by": [], 
    "uid": "GOC:kltm"
}

[balhoff]

Oh I see! You used -export-folder instead of --export-folder. See if that fixes it.

[balhoff]

The error handling/reporting could be better here.

[cmungall]

It inherits owltools command line handling - only so much to be done...

[kltm]

Ahhhh! I never would have caught that. Thanks!

[kltm]

Looks like this is done--thanks @balhoff ! Nothing left but the merge of all these noctua branches.