carnival-data / carnival-demo-biomedical

Demonstration Carnival Micronaut application.
GNU General Public License v3.0
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demo-tom: gradle run fails #20

Closed th5 closed 2 years ago

th5 commented 2 years ago

The current demo branch works. It defines a graph model and also has a working database vine.

The current demo-tom branch doesn't work. It start with what's in demo and adds in Louis's graph method and service. The service calls the graph method which calls the vine and adds nodes to the graph.

gradle build works (builds and runs the test specs) gradle run doesn't work. Running using Docker. Error output below:

20:23:51.822 [main] INFO  e.c.micronaut.ApplicationInitializer - ApplicationInitializer initialize()
20:23:51.842 [main] TRACE java.lang.Class - GraphMethods.createGraphMethodInstance methodName:LoadEncounters
20:23:51.869 [main] TRACE java.lang.Class - graph method class: example.carnival.micronaut.method.ExampleMethods$LoadEncounters
20:23:51.878 [main] TRACE java.lang.Class - Vine.createVineMethodInstance methodName:Encounters
20:23:51.894 [main] TRACE java.lang.Class - vine method class: example.carnival.micronaut.vine.ExampleDbVine$Encounters
20:23:52.007 [main] TRACE e.c.micronaut.method.ExampleMethods - rec: [REASON_DESCRIPTION:Normal pregnancy, STOP:2016-05-27 15:45:18, BASE_ENCOUNTER_COST:110.03, PAYER_COVERAGE:0.00, REASON_CODE:72892002, ORGANIZATION:60d7c1cc-fcbd-3be1-bf78-dd7840fa11bb, CODE:424619006, PAYER:b1c428d6-4f07-31e0-90f0-68ffa6ff8c76, ENCOUNTER_CLASS:ambulatory, DESCRIPTION:Prenatal visit, PROVIDER:0684c44b-7b50-3e8b-8e2e-0f24d3405baa, PATIENT:7bbb9d0b-bdbd-c4b3-7a7f-422de8cd695f, START:2016-05-27 15:30:18, ID:2211d3fe-e575-f951-fbdb-b111ee743f0c, TOTAL_CLAIM_COST:9532.11]
20:23:52.116 [main] ERROR io.micronaut.runtime.Micronaut - Error starting Micronaut server: Bean definition [example.carnival.micronaut.ApplicationInitializer] could not be loaded: Error instantiating bean of type [example.carnival.micronaut.ApplicationInitializer]: Property value can not be null
io.micronaut.context.exceptions.BeanInstantiationException: Bean definition [example.carnival.micronaut.ApplicationInitializer] could not be loaded: Error instantiating bean of type [example.carnival.micronaut.ApplicationInitializer]: Property value can not be null
        at io.micronaut.context.DefaultBeanContext.initializeContext(DefaultBeanContext.java:1565)
        at io.micronaut.context.DefaultApplicationContext.initializeContext(DefaultApplicationContext.java:219)
        at io.micronaut.context.DefaultBeanContext.readAllBeanDefinitionClasses(DefaultBeanContext.java:2857)
        at io.micronaut.context.DefaultBeanContext.start(DefaultBeanContext.java:231)
        at io.micronaut.context.DefaultApplicationContext.start(DefaultApplicationContext.java:165)
        at io.micronaut.runtime.Micronaut.start(Micronaut.java:71)
        at io.micronaut.runtime.Micronaut.run(Micronaut.java:311)
        at io.micronaut.runtime.Micronaut.run(Micronaut.java:297)
        at example.carnival.micronaut.Application.main(Application.groovy:28)
Caused by: io.micronaut.context.exceptions.BeanInstantiationException: Error instantiating bean of type [example.carnival.micronaut.ApplicationInitializer]: Property value can not be null
        at io.micronaut.context.DefaultBeanContext.doCreateBean(DefaultBeanContext.java:1972)
        at io.micronaut.context.DefaultBeanContext.createAndRegisterSingletonInternal(DefaultBeanContext.java:2724)
        at io.micronaut.context.DefaultBeanContext.loadContextScopeBean(DefaultBeanContext.java:2260)
        at io.micronaut.context.DefaultBeanContext.initializeContext(DefaultBeanContext.java:1559)
        ... 8 common frames omitted
Caused by: java.lang.IllegalArgumentException: Property value can not be null
        at org.apache.tinkerpop.gremlin.structure.Property$Exceptions.propertyValueCanNotBeNull(Property.java:143)
        at org.apache.tinkerpop.gremlin.structure.util.ElementHelper.validateProperty(ElementHelper.java:97)
        at org.apache.tinkerpop.gremlin.neo4j.structure.Neo4jVertex.property(Neo4jVertex.java:81)
        at org.apache.tinkerpop.gremlin.neo4j.structure.Neo4jVertex.property(Neo4jVertex.java:70)
        at org.apache.tinkerpop.gremlin.structure.Vertex$property.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at carnival.graph.PropertyValuesHolder$_setElementProperties_closure6.doCall(PropertyValuesHolder.groovy:132)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.callClosureForMapEntry(DefaultGroovyMethods.java:5947)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2395)
        at org.codehaus.groovy.runtime.dgm$201.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:247)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at carnival.graph.PropertyValuesHolder.setElementProperties(PropertyValuesHolder.groovy:130)
        at carnival.graph.PropertyValuesHolder$setElementProperties$0.callCurrent(Unknown Source)
        at carnival.graph.ControlledInstance.createVertex(ControlledInstance.groovy:135)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:351)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
        at carnival.graph.ControlledInstance$_vertex_closure2.doCall(ControlledInstance.groovy:83)
        at carnival.graph.ControlledInstance$_vertex_closure2.doCall(ControlledInstance.groovy)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at org.codehaus.groovy.runtime.ConvertedClosure.invokeCustom(ConvertedClosure.java:50)
        at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:110)
        at com.sun.proxy.$Proxy76.get(Unknown Source)
        at java.base/java.util.Optional.orElseGet(Optional.java:369)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoCachedMethodSiteNoUnwrap.invoke(PojoMetaMethodSite.java:203)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at carnival.graph.ControlledInstance.vertex(ControlledInstance.groovy:82)
        at carnival.graph.ControlledInstance$vertex.callCurrent(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
        at carnival.graph.ControlledInstance.ensure(ControlledInstance.groovy:66)
        at carnival.graph.ControlledInstance$ensure$2.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at example.carnival.micronaut.method.ExampleMethods$LoadEncounters$_execute_closure1.doCall(ExampleMethods.groovy:55)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:428)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2318)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2303)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2332)
        at org.codehaus.groovy.runtime.dgm$198.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:247)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at example.carnival.micronaut.method.ExampleMethods$LoadEncounters.execute(ExampleMethods.groovy:53)
        at example.carnival.micronaut.method.ExampleMethods$LoadEncounters$execute.callCurrent(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
        at carnival.core.graph.GraphMethod.call(GraphMethod.groovy:68)
        at carnival.core.graph.GraphMethod$call.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at example.carnival.micronaut.service.SyncService$_syncExample_closure1.doCall(SyncService.groovy:56)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at carnival.core.graph.GremlinTraitUtilities.withTraversal(GremlinTrait.groovy:34)
        at carnival.core.graph.GremlinTraitUtilities$withTraversal.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at carnival.core.graph.GremlinTraitUtilities$withTraversal.call(Unknown Source)
        at carnival.core.graph.GremlinTrait$Trait$Helper.withTraversal(GremlinTrait.groovy:148)
        at carnival.core.graph.GremlinTrait$Trait$Helper$withTraversal$0.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at carnival.core.graph.GremlinTrait$Trait$Helper$withTraversal$0.call(Unknown Source)
        at carnival.core.graph.CoreGraph.withTraversal(CoreGraph.groovy)
        at carnival.core.graph.GremlinTrait$withTraversal.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at example.carnival.micronaut.service.SyncService.syncExample(SyncService.groovy:54)
        at example.carnival.micronaut.service.SyncService.syncExample(SyncService.groovy)
        at example.carnival.micronaut.service.SyncService$syncExample.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
        at example.carnival.micronaut.ApplicationInitializer.initialize(ApplicationInitializer.groovy:51)
        at example.carnival.micronaut.$ApplicationInitializerDefinition.initialize(Unknown Source)
        at example.carnival.micronaut.$ApplicationInitializerDefinition.build(Unknown Source)
        at io.micronaut.context.DefaultBeanContext.doCreateBean(DefaultBeanContext.java:1943)
        ... 11 common frames omitted

> Task :run FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':run'.
> Process 'command '/opt/java/openjdk/bin/java'' finished with non-zero exit value 1