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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
37 stars 13 forks source link

Error message when creating a function annoton #219

Closed vanaukenk closed 8 years ago

vanaukenk commented 8 years ago

Hi, I'm getting the following error message when trying to create an annoton this morning:

Error (error): Could not successfully handle batch request. Exception: org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException. Could not retrieve a class for id: WB:WBGene00001674; your operation was likely not performed. org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException: Could not retrieve a class for id: WB:WBGene00001674

This happens for multiple WB genes when I try to add a free form function.

Thanks, --Kimberly

kltm commented 8 years ago

Duplicated, use "gpe-12".

kltm commented 8 years ago

@hdietze any ideas here?

I've restarted everything, but the error persists (I initially thought that minerva might be using the wrong URL to resolve IDs, but that does not seem to be it). The GOlr service can be examined at: 

http://noctua-amigo.berkeleybop.org/amigo/gene_product/WB:WBGene00001674
http://noctua-golr.berkeleybop.org/select?defType=edismax&qt=standard&indent=on&wt=json&rows=10&start=0&fl=*,score&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&hl=true&hl.simple.pre=%3Cem%20class=%22hilite%22%3E&fq=document_category:%22annotation%22&fq=bioentity:%22WB:WBGene00001674%22&facet.field=source&facet.field=assigned_by&facet.field=aspect&facet.field=evidence_type_closure&facet.field=panther_family_label&facet.field=qualifier&facet.field=taxon_label&facet.field=annotation_class_label&facet.field=regulates_closure_label&facet.field=annotation_extension_class_closure_label&q=*:*&packet=1&callback_type=search

Minerva's command is:

java -Xmx4G -cp ./java/lib/minerva-cli.jar org.geneontology.minerva.server.StartUpTool --use-request-logging --slme-elk -g http://purl.obolibrary.org/obo/go/extensions/go-lego.owl --set-important-relation-parent http://purl.obolibrary.org/obo/LEGOREL_0000000 --golr-labels http://noctua-golr.berkeleybop.org/ -c /home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/catalog-v001.xml -f /home/swdev/local/src/git/noctua-models/models/ --port 6800

Minerva's startup looks like:

[13:14:54] Starting 'run-minerva'...
java -Xmx4G -cp ./java/lib/minerva-cli.jar org.geneontology.minerva.server.StartUpTool --use-request-logging --slme-elk -g http://purl.obolibrary.org/obo/go/extensions/go-lego.owl --set-important-relation-parent http://purl.obolibrary.org/obo/LEGOREL_0000000 --golr-labels http://noctua-golr.berkeleybop.org/ -c ~/local/src/svn/geneontology.org/trunk/ontology/extensions/catalog-v001.xml -f ~/local/src/git/noctua-models/models/ --port 6800
Pinged: https://s3-us-west-1.amazonaws.com/go-noctua-usage-master/ping.json
2015-11-17 13:14:54,703 INFO  (GolrExternalLookupService:47) Creating Golr lookup service for minerva: http://noctua-golr.berkeleybop.org/
2015-11-17 13:14:54,705 INFO  (StartUpTool:210) Setting up Golr cache with size: 100000 duration: 24 HOURS
2015-11-17 13:14:54,742 INFO  (StartUpTool:269) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-lego.owl
2015-11-17 13:14:54,855 INFO  (StartUpTool:273) Adding catalog xml: /home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/catalog-v001.xml
2015-11-17 13:14:54,909 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-lego.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/go-lego.owl
2015-11-17 13:14:55,080 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/legorel.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/legorel.owl
2015-11-17 13:14:55,216 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/legorel.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/legorel.owl
2015-11-17 13:14:55,216 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/go-plus.owl
2015-11-17 13:14:55,227 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/chebi_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/chebi_import.owl
2015-11-17 13:14:56,797 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/chebi_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/chebi_import.owl
2015-11-17 13:14:56,810 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/cl_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/cl_import.owl
2015-11-17 13:14:56,953 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/cl_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/cl_import.owl
2015-11-17 13:14:56,958 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/ncbitaxon_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/ncbitaxon_import.owl
2015-11-17 13:14:57,038 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/ncbitaxon_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/ncbitaxon_import.owl
2015-11-17 13:14:57,044 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/oba_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/oba_import.owl
2015-11-17 13:14:57,069 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/oba_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/oba_import.owl
2015-11-17 13:14:57,074 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/pato_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/pato_import.owl
2015-11-17 13:14:57,079 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/pato_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/pato_import.owl
2015-11-17 13:14:57,081 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/po_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/po_import.owl
2015-11-17 13:14:57,156 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/po_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/po_import.owl
2015-11-17 13:14:57,159 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/pr_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/pr_import.owl
2015-11-17 13:14:57,207 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/pr_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/pr_import.owl
2015-11-17 13:14:57,210 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/ro_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/ro_import.owl
2015-11-17 13:14:57,257 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/ro_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/ro_import.owl
2015-11-17 13:14:57,260 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/ro_pending.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/ro_pending.owl
2015-11-17 13:14:57,277 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/ro_pending.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/ro_pending.owl
2015-11-17 13:14:57,281 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/so_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/so_import.owl
2015-11-17 13:14:57,293 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/so_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/so_import.owl
2015-11-17 13:14:57,295 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/uberon_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/uberon_import.owl
2015-11-17 13:14:58,359 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/uberon_import.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/uberon_import.owl
2015-11-17 13:14:58,364 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/x-disjoint.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/x-disjoint.owl
2015-11-17 13:14:58,384 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/x-disjoint.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/x-disjoint.owl
2015-11-17 13:15:22,360 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/go-plus.owl
2015-11-17 13:15:22,360 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-bfo-bridge.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/go-bfo-bridge.owl
2015-11-17 13:15:22,366 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-bfo-bridge.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/go-bfo-bridge.owl
2015-11-17 13:15:22,366 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
2015-11-17 13:15:25,185 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
2015-11-17 13:15:25,186 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
2015-11-17 13:15:27,493 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
2015-11-17 13:15:27,493 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/eco.owl from: http://purl.obolibrary.org/obo/eco.owl
2015-11-17 13:15:28,279 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/eco.owl from: http://purl.obolibrary.org/obo/eco.owl
2015-11-17 13:15:28,280 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/wbbt.owl from: http://purl.obolibrary.org/obo/wbbt.owl
2015-11-17 13:15:29,657 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/wbbt.owl from: http://purl.obolibrary.org/obo/wbbt.owl
2015-11-17 13:15:29,659 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go/extensions/go-lego.owl from: file:/home/swdev/local/src/svn/geneontology.org/trunk/ontology/extensions/go-lego.owl
2015-11-17 13:15:29,661 INFO  (StartUpTool:295) Start initializing Minerva
2015-11-17 13:15:29,666 INFO  (StartUpTool:303) Model path: /home/swdev/local/src/git/noctua-models/models/
2015-11-17 13:15:29,666 INFO  (StartUpTool:313) Setup Jetty config.
2015-11-17 13:15:29,714 INFO  (StartUpTool:324) BatchHandler config useReasoner: true
2015-11-17 13:15:29,714 INFO  (StartUpTool:325) BatchHandler config useModuleReasoner: true
2015-11-17 13:15:29,717 INFO  (StartUpTool:326) BatchHandler config importantRelations: [<http://purl.obolibrary.org/obo/BFO_0000066>, <http://purl.obolibrary.org/obo/RO_0002233>, <http://purl.obolibrary.org/obo/RO_0002408>, <http://purl.obolibrary.org/obo/RO_0002224>, <http://purl.obolibrary.org/obo/RO_0002230>, <http://purl.obolibrary.org/obo/RO_0002406>, <http://purl.obolibrary.org/obo/RO_0002413>, <http://purl.obolibrary.org/obo/RO_0002333>, <http://purl.obolibrary.org/obo/BFO_0000050>, <http://purl.obolibrary.org/obo/RO_0002234>]
2015-11-17 13:15:29,717 INFO  (StartUpTool:327) BatchHandler config lookupService: Caching(Golr: http://noctua-golr.berkeleybop.org/)
2015-11-17 13:15:29,717 INFO  (StartUpTool:328) BatchHandler config checkLiteralIds: true
2015-11-17 13:15:29,717 INFO  (StartUpTool:329) BatchHandler config useRequestLoggingtrue
2015-11-17 13:15:29,717 INFO  (StartUpTool:330) SeedHandler config golrUrl: http://noctua-golr.berkeleybop.org/
2015-11-17 13:15:29,774 INFO  (StartUpTool:354) Start server on port: 6800 context: /
2015-11-17 13:15:29,774 INFO  (Server:252) jetty-7.x.y-SNAPSHOT
2015-11-17 13:15:29,804 INFO  (ContextHandler:647) started o.e.j.s.ServletContextHandler{/,null}
Nov 17, 2015 1:15:29 PM org.glassfish.hk2.internal.ServiceLocatorFactoryImpl getGenerator
WARNING: Cannot find a default implementation of the HK2 ServiceLocatorGenerator
Nov 17, 2015 1:15:29 PM org.glassfish.jersey.server.ApplicationHandler initialize
INFO: Initiating Jersey application, version Jersey: 2.5 2013-12-18 14:27:29...
2015-11-17 13:15:30,271 INFO  (LoggingApplicationEventListener:19) Application null initialization finished.
2015-11-17 13:15:30,282 INFO  (AbstractConnector:320) Started SelectChannelConnector@0.0.0.0:6800 STARTING

The full error is:

Error (error): Could not successfully handle batch request. Exception: org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException. Could not retrieve a class for id: WB:WBGene00001674; your operation was likely not performed.
org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException: Could not retrieve a class for id: WB:WBGene00001674
    at org.geneontology.minerva.server.handler.M3ExpressionParser.parse(M3ExpressionParser.java:73)
    at org.geneontology.minerva.server.handler.M3ExpressionParser.parse(M3ExpressionParser.java:42)
    at org.geneontology.minerva.server.handler.OperationsImpl.parseM3Expression(OperationsImpl.java:318)
    at org.geneontology.minerva.server.handler.OperationsImpl.handleRequestForIndividual(OperationsImpl.java:163)
    at org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3Batch(JsonOrJsonpBatchHandler.java:159)
    at org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3Batch(JsonOrJsonpBatchHandler.java:135)
    at org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler.m3BatchGetPrivileged(JsonOrJsonpBatchHandler.java:87)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:151)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:171)
    at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:195)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:104)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:402)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:349)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:106)
    at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:259)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:318)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:236)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1010)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:382)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:345)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:220)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:547)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:480)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:225)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:941)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:409)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:186)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:875)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:110)
    at org.eclipse.jetty.server.Server.handle(Server.java:349)
    at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:441)
    at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:919)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:582)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:218)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:51)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:586)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:44)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:598)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:533)
    at java.lang.Thread.run(Thread.java:745)
kltm commented 8 years ago

@vanaukenk With some legwork from @hdietze, the application has been redeployed and should now work as expected.

cmungall commented 8 years ago

How was this resolved?

On 17 Nov 2015, at 15:05, kltm wrote:

@vanaukenk With some legwork from @hdietze, the application has been redeployed and should now work as expected.

Reply to this email directly or view it on GitHub: https://github.com/geneontology/noctua/issues/219#issuecomment-157538525

vanaukenk commented 8 years ago

Hi @ktlm,

All seems to be working fine this morning. Thanks for the fix.

--K.

kltm commented 8 years ago

@cmungall from the tracker tags: https://github.com/geneontology/noctua/issues/219#ref-commit-1413d8c https://github.com/geneontology/minerva/commit/1413d8c06a4d47a8c6abda1191877552576ff4ca