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IHTSDO / health-data-analytics

Snolytical - Health Data Analytics Demonstrator
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NullPointerException: ClinicalEncounter.hashCode #5

Closed johngrimes closed 5 years ago

johngrimes commented 5 years ago

I've built the JAR using mvn clean package, then extracted the July 2018 international release into target/release.

Upon running java -Xmx3g -jar health-data-analytics*.jar --generate-population=10000, I get the following error:

java.lang.IllegalStateException: Failed to execute ApplicationRunner
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:770) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:757) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.afterRefresh(SpringApplication.java:747) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1162) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1151) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.snomed.heathanalytics.Application.main(Application.java:60) ~[classes!/:1.1.0]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48) ~[health-data-analytics-1.1.0.jar:1.1.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:87) ~[health-data-analytics-1.1.0.jar:1.1.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:50) ~[health-data-analytics-1.1.0.jar:1.1.0]
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51) ~[health-data-analytics-1.1.0.jar:1.1.0]
Caused by: java.lang.NullPointerException: null
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:na]
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:678) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:737) ~[na:na]
    at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateParallel(ForEachOps.java:159) ~[na:na]
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfInt.evaluateParallel(ForEachOps.java:188) ~[na:na]
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233) ~[na:na]
    at java.base/java.util.stream.IntPipeline.forEach(IntPipeline.java:439) ~[na:na]
    at java.base/java.util.stream.IntPipeline$Head.forEach(IntPipeline.java:596) ~[na:na]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.stream(ExampleDataGenerator.java:38) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.Application.generatePopulation(Application.java:114) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.Application.run(Application.java:72) ~[classes!/:1.1.0]
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:767) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    ... 14 common frames omitted
Caused by: java.lang.NullPointerException: null
    at org.snomed.heathanalytics.domain.ClinicalEncounter.hashCode(ClinicalEncounter.java:104) ~[classes!/:1.1.0]
    at java.base/java.util.HashMap.hash(HashMap.java:339) ~[na:na]
    at java.base/java.util.HashMap.put(HashMap.java:607) ~[na:na]
    at java.base/java.util.HashSet.add(HashSet.java:220) ~[na:na]
    at org.snomed.heathanalytics.domain.Patient.addEncounter(Patient.java:54) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.scenarioPulmEmbGIBleed(ExampleDataGenerator.java:304) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.generateExamplePatientAndActs(ExampleDataGenerator.java:86) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.lambda$stream$0(ExampleDataGenerator.java:44) ~[classes!/:1.1.0]
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfInt.accept(ForEachOps.java:204) ~[na:na]
    at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104) ~[na:na]
    at java.base/java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:699) ~[na:na]
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) ~[na:na]
    at java.base/java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:290) ~[na:na]
    at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:746) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:177) ~[na:na]
kaicode commented 5 years ago

Hi @johngrimes, thanks for getting in touch.

The release directory should be in the root of the project directory or wherever you run the java -jar ... command from.

When it's working you should see the counts of SNOMED CT concepts loaded and written to the index:

2018-12-18 09:45:00.924  INFO 9442 --- [pool-1-thread-1] o.i.o.s.ReleaseImporter$ImportRun        : Reading relationships 
2018-12-18 09:45:00.924  INFO 9442 --- [pool-1-thread-2] o.i.o.s.ReleaseImporter$ImportRun        : Reading descriptions 
2018-12-18 09:45:00.924  INFO 9442 --- [pool-1-thread-3] o.i.o.s.ReleaseImporter$ImportRun        : Reading descriptions 
2018-12-18 09:45:01.016  INFO 9442 --- [pool-1-thread-3] o.i.o.s.ReleaseImporter$ImportRun        : 5021 descriptions read from sct2_TextDefinition_Snapshot-en_INT_20180731.txt
2018-12-18 09:45:05.641  INFO 9442 --- [pool-1-thread-2] o.i.o.s.ReleaseImporter$ImportRun        : 1407643 descriptions read from sct2_Description_Snapshot-en_INT_20180731.txt
2018-12-18 09:45:08.263  INFO 9442 --- [pool-1-thread-1] o.i.o.s.ReleaseImporter$ImportRun        : 2755736 relationships read from sct2_Relationship_Snapshot_INT_20180731.txt
2018-12-18 09:45:08.263  INFO 9442 --- [           main] o.i.o.s.ReleaseImporter$ImportRun        : Release files read. JVM total memory is approx 1,547 MB.
2018-12-18 09:45:08.264  INFO 9442 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : All in memory. Using approx 1,547 MB of memory.
2018-12-18 09:45:08.264  INFO 9442 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : Writing to index...
2018-12-18 09:45:15.159  INFO 9442 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 100000 concepts added to index...
2018-12-18 09:45:19.925  INFO 9442 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 200000 concepts added to index...
2018-12-18 09:45:25.125  INFO 9442 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 300000 concepts added to index...
2018-12-18 09:45:26.824  INFO 9442 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 340659 concepts added to index in total.

Different versions of SNOMED CT will give different counts of content but you should be getting 400,000 or more. The loaded count includes active and inactive concepts. The count of concepts written to the index is lower because only the active concepts are kept.

I hope you find this project useful. Please drop me a note if you manage to load any of your own clinical data, I'm always interested to hear how this project has been used in the wild 😸

Kind regards, Kai

johngrimes commented 5 years ago

Hi @kaicode,

I don't think the location of the release directory is the issue, the import appears to complete successfully, adding 340,659 concepts to the index according to the log.

The aforementioned error occurs after the import, here is the full log for context. Thanks in advance for any help.

  ____  _   _  ___  __  __ _____ ____    ____        _             _                _       _   _
 / ___|| \ | |/ _ \|  \/  | ____|  _ \  |  _ \  __ _| |_ __ _     / \   _ __   __ _| |_   _| |_(_) ___ ___
 \___ \|  \| | | | | |\/| |  _| | | | | | | | |/ _` | __/ _` |   / _ \ | '_ \ / _` | | | | | __| |/ __/ __|
  ___) | |\  | |_| | |  | | |___| |_| | | |_| | (_| | || (_| |  / ___ \| | | | (_| | | |_| | |_| | (__\__ \
 |____/|_| \_|\___/|_|  |_|_____|____/  |____/ \__,_|\__\__,_| /_/   \_\_| |_|\__,_|_|\__, |\__|_|\___|___/
                                                                                      |___/
 :: SNOMED CT Health Data Analytics Demonstrator :: (v1.1.0)

2019-01-14 15:04:58.520  INFO 94989 --- [           main] org.snomed.heathanalytics.Application    : Starting Application v1.1.0 on rockbourne-RBH with PID 94989 (/Users/gri306/Code/health-data-analytics/target/health-data-analytics-1.1.0.jar started by gri306 in /Users/gri306/Code/health-data-analytics/target)
2019-01-14 15:04:58.526  INFO 94989 --- [           main] org.snomed.heathanalytics.Application    : No active profile set, falling back to default profiles: default
2019-01-14 15:04:58.599  INFO 94989 --- [           main] ationConfigEmbeddedWebApplicationContext : Refreshing org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext@43195e57: startup date [Mon Jan 14 15:04:58 AEST 2019]; root of context hierarchy
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.springframework.cglib.core.ReflectUtils$1 (jar:file:/Users/gri306/Code/health-data-analytics/target/health-data-analytics-1.1.0.jar!/BOOT-INF/lib/spring-core-4.3.6.RELEASE.jar!/) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of org.springframework.cglib.core.ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2019-01-14 15:05:00.091  INFO 94989 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.boot.autoconfigure.validation.ValidationAutoConfiguration' of type [class org.springframework.boot.autoconfigure.validation.ValidationAutoConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2019-01-14 15:05:00.216  INFO 94989 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'validator' of type [class org.springframework.validation.beanvalidation.LocalValidatorFactoryBean] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2019-01-14 15:05:00.542  INFO 94989 --- [           main] s.b.c.e.t.TomcatEmbeddedServletContainer : Tomcat initialized with port(s): 8080 (http)
2019-01-14 15:05:00.556  INFO 94989 --- [           main] o.apache.catalina.core.StandardService   : Starting service Tomcat
2019-01-14 15:05:00.558  INFO 94989 --- [           main] org.apache.catalina.core.StandardEngine  : Starting Servlet Engine: Apache Tomcat/8.5.11
2019-01-14 15:05:00.643  INFO 94989 --- [ost-startStop-1] o.a.c.c.C.[.[.[/health-analytics-api]    : Initializing Spring embedded WebApplicationContext
2019-01-14 15:05:00.644  INFO 94989 --- [ost-startStop-1] o.s.web.context.ContextLoader            : Root WebApplicationContext: initialization completed in 2051 ms
2019-01-14 15:05:00.774  INFO 94989 --- [ost-startStop-1] o.s.b.w.servlet.ServletRegistrationBean  : Mapping servlet: 'dispatcherServlet' to [/]
2019-01-14 15:05:00.779  INFO 94989 --- [ost-startStop-1] o.s.b.w.servlet.FilterRegistrationBean   : Mapping filter: 'characterEncodingFilter' to: [/*]
2019-01-14 15:05:00.779  INFO 94989 --- [ost-startStop-1] o.s.b.w.servlet.FilterRegistrationBean   : Mapping filter: 'hiddenHttpMethodFilter' to: [/*]
2019-01-14 15:05:00.779  INFO 94989 --- [ost-startStop-1] o.s.b.w.servlet.FilterRegistrationBean   : Mapping filter: 'httpPutFormContentFilter' to: [/*]
2019-01-14 15:05:00.780  INFO 94989 --- [ost-startStop-1] o.s.b.w.servlet.FilterRegistrationBean   : Mapping filter: 'requestContextFilter' to: [/*]
2019-01-14 15:05:01.050  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] version[2.4.4], pid[94989], build[fcbb46d/2017-01-03T11:33:16Z]
2019-01-14 15:05:01.050  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] initializing ...
2019-01-14 15:05:01.057  INFO 94989 --- [           main] org.elasticsearch.plugins                : [Midgard Serpent] modules [], plugins [], sites []
2019-01-14 15:05:01.095  INFO 94989 --- [           main] org.elasticsearch.env                    : [Midgard Serpent] using [1] data paths, mounts [[/ (/dev/disk1s1)]], net usable_space [711.3gb], net total_space [931.5gb], spins? [unknown], types [apfs]
2019-01-14 15:05:01.095  INFO 94989 --- [           main] org.elasticsearch.env                    : [Midgard Serpent] heap size [3gb], compressed ordinary object pointers [true]
2019-01-14 15:05:01.098  WARN 94989 --- [           main] org.elasticsearch.env                    : [Midgard Serpent] max file descriptors [10240] for elasticsearch process likely too low, consider increasing to at least [65536]
2019-01-14 15:05:03.056  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] initialized
2019-01-14 15:05:03.056  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] starting ...
2019-01-14 15:05:03.059  INFO 94989 --- [           main] org.elasticsearch.transport              : [Midgard Serpent] publish_address {local[1]}, bound_addresses {local[1]}
2019-01-14 15:05:03.061  INFO 94989 --- [           main] org.elasticsearch.discovery              : [Midgard Serpent] elasticsearch/DSWndQjcTsmwCgTR9NvWaA
2019-01-14 15:05:03.068  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.service        : [Midgard Serpent] new_master {Midgard Serpent}{DSWndQjcTsmwCgTR9NvWaA}{local}{local[1]}{local=true}, reason: local-disco-initial_connect(master)
2019-01-14 15:05:03.075  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] started
2019-01-14 15:05:03.141  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.gateway                : [Midgard Serpent] recovered [0] indices into cluster_state
2019-01-14 15:05:03.358  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [patient] creating index, cause [api], templates [], shards [5]/[1], mappings []
2019-01-14 15:05:03.733  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [patient] create_mapping [patient]
2019-01-14 15:05:03.866  INFO 94989 --- [pdateTask][T#1]] o.e.cluster.routing.allocation           : [Midgard Serpent] Cluster health status changed from [RED] to [YELLOW] (reason: [shards started [[patient][4], [patient][4]] ...]).
2019-01-14 15:05:03.887  INFO 94989 --- [           main] ication$$EnhancerBySpringCGLIB$$5982df74 : SRS Index does not yet exist. Importing release to build disk based index.
2019-01-14 15:05:03.900  INFO 94989 --- [           main] o.i.o.s.ReleaseImporter$ImportRun        : Loading release files ReleaseFiles{conceptPath=release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Terminology/sct2_Concept_Snapshot_INT_20180731.txt, descriptionPath=release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Terminology/sct2_Description_Snapshot-en_INT_20180731.txt, textDefinitionPath=release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Terminology/sct2_TextDefinition_Snapshot-en_INT_20180731.txt, relationshipPath=release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20180731.txt, statedRelationshipPath=release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Terminology/sct2_StatedRelationship_Snapshot_INT_20180731.txt, refsetPaths=[release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Content/der2_cRefset_AttributeValueSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Content/der2_cRefset_AssociationSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Content/der2_Refset_SimpleSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Language/der2_cRefset_LanguageSnapshot-en_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Map/der2_iisssccRefset_ExtendedMapSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Map/der2_sRefset_SimpleMapSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_sssssssRefset_MRCMDomainSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_cRefset_MRCMModuleScopeSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_cciRefset_RefsetDescriptorSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_ssRefset_ModuleDependencySnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_ciRefset_DescriptionTypeSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_cissccRefset_MRCMAttributeDomainSnapshot_INT_20180731.txt, release/SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Snapshot/Refset/Metadata/der2_ssccRefset_MRCMAttributeRangeSnapshot_INT_20180731.txt]}
2019-01-14 15:05:03.902  INFO 94989 --- [           main] o.i.o.s.ReleaseImporter$ImportRun        : Reading concepts
2019-01-14 15:05:04.931  INFO 94989 --- [           main] o.i.o.s.ReleaseImporter$ImportRun        : 454709 concepts read from sct2_Concept_Snapshot_INT_20180731.txt
2019-01-14 15:05:04.933  INFO 94989 --- [pool-1-thread-1] o.i.o.s.ReleaseImporter$ImportRun        : Reading relationships
2019-01-14 15:05:04.934  INFO 94989 --- [pool-1-thread-2] o.i.o.s.ReleaseImporter$ImportRun        : Reading descriptions
2019-01-14 15:05:04.934  INFO 94989 --- [pool-1-thread-3] o.i.o.s.ReleaseImporter$ImportRun        : Reading descriptions
2019-01-14 15:05:04.970  INFO 94989 --- [pool-1-thread-3] o.i.o.s.ReleaseImporter$ImportRun        : 5021 descriptions read from sct2_TextDefinition_Snapshot-en_INT_20180731.txt
2019-01-14 15:05:08.875  INFO 94989 --- [pool-1-thread-2] o.i.o.s.ReleaseImporter$ImportRun        : 1407643 descriptions read from sct2_Description_Snapshot-en_INT_20180731.txt
2019-01-14 15:05:13.609  INFO 94989 --- [pool-1-thread-1] o.i.o.s.ReleaseImporter$ImportRun        : 2755736 relationships read from sct2_Relationship_Snapshot_INT_20180731.txt
2019-01-14 15:05:13.609  INFO 94989 --- [           main] o.i.o.s.ReleaseImporter$ImportRun        : Release files read. JVM total memory is approx 2,581 MB.
2019-01-14 15:05:13.609  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : All in memory. Using approx 2,581 MB of memory.
2019-01-14 15:05:13.609  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : Writing to index...
2019-01-14 15:05:20.579  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 100000 concepts added to index...
2019-01-14 15:05:26.151  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 200000 concepts added to index...
2019-01-14 15:05:31.955  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 300000 concepts added to index...
2019-01-14 15:05:33.795  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : 340659 concepts added to index in total.
2019-01-14 15:05:33.796  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : Closing index writer.
2019-01-14 15:05:34.407  INFO 94989 --- [           main] o.i.o.sqs.service.ReleaseImportManager   : Finished creating index. Using approx 170 MB of memory.
2019-01-14 15:05:34.495  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [subset] creating index, cause [api], templates [], shards [5]/[1], mappings []
2019-01-14 15:05:34.630  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [subset] create_mapping [subset]
2019-01-14 15:05:34.818  INFO 94989 --- [pdateTask][T#1]] o.e.cluster.routing.allocation           : [Midgard Serpent] Cluster health status changed from [RED] to [YELLOW] (reason: [shards started [[subset][4]] ...]).
2019-01-14 15:05:34.838  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [cohort] creating index, cause [api], templates [], shards [5]/[1], mappings []
2019-01-14 15:05:34.993  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [cohort] create_mapping [cohortcriteria]
2019-01-14 15:05:35.160  INFO 94989 --- [pdateTask][T#1]] o.e.cluster.routing.allocation           : [Midgard Serpent] Cluster health status changed from [RED] to [YELLOW] (reason: [shards started [[cohort][4]] ...]).
2019-01-14 15:05:35.450  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/stats],methods=[GET],produces=[application/json]}" onto public org.snomed.heathanalytics.pojo.Stats org.snomed.heathanalytics.rest.StatsController.getStats()
2019-01-14 15:05:35.451  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/],methods=[GET]}" onto public void org.snomed.heathanalytics.rest.RootController.getRoot(javax.servlet.http.HttpServletResponse) throws java.io.IOException
2019-01-14 15:05:35.452  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/subsets/{subsetId}],methods=[GET],produces=[application/json]}" onto public org.snomed.heathanalytics.domain.Subset org.snomed.heathanalytics.rest.SubsetController.getSubset(java.lang.String) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.452  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/subsets],methods=[GET],produces=[application/json]}" onto public org.springframework.data.domain.Page<org.snomed.heathanalytics.domain.Subset> org.snomed.heathanalytics.rest.SubsetController.listSubsets(int,int) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.452  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/subsets],methods=[POST],produces=[application/json]}" onto public org.snomed.heathanalytics.domain.Subset org.snomed.heathanalytics.rest.SubsetController.saveSubset(org.snomed.heathanalytics.domain.Subset) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.453  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/subsets/{subsetId}],methods=[PUT],produces=[application/json]}" onto public org.snomed.heathanalytics.domain.Subset org.snomed.heathanalytics.rest.SubsetController.updateSubset(java.lang.String,org.snomed.heathanalytics.domain.Subset) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.453  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/subsets/{subsetId}],methods=[DELETE],produces=[application/json]}" onto public org.snomed.heathanalytics.pojo.EmptyPojo org.snomed.heathanalytics.rest.SubsetController.deleteSubset(java.lang.String) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.454  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts],methods=[POST],produces=[application/json]}" onto public org.springframework.http.ResponseEntity<java.lang.Void> org.snomed.heathanalytics.rest.CohortController.saveCohort(org.snomed.heathanalytics.domain.CohortCriteria)
2019-01-14 15:05:35.454  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts],methods=[GET],produces=[application/json]}" onto public java.util.List<org.snomed.heathanalytics.domain.CohortCriteria> org.snomed.heathanalytics.rest.CohortController.listCohorts()
2019-01-14 15:05:35.454  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts/{cohortId}],methods=[GET],produces=[application/json]}" onto public org.snomed.heathanalytics.domain.CohortCriteria org.snomed.heathanalytics.rest.CohortController.getCohort(java.lang.String)
2019-01-14 15:05:35.455  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts/{cohortId}],methods=[PUT],produces=[application/json]}" onto public org.snomed.heathanalytics.domain.CohortCriteria org.snomed.heathanalytics.rest.CohortController.updateCohort(java.lang.String,org.snomed.heathanalytics.domain.CohortCriteria) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.455  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts/{cohortId}],methods=[DELETE],produces=[application/json]}" onto public org.snomed.heathanalytics.pojo.EmptyPojo org.snomed.heathanalytics.rest.CohortController.deleteCohort(java.lang.String)
2019-01-14 15:05:35.455  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts/select],methods=[POST],produces=[application/json]}" onto public org.springframework.data.domain.Page<org.snomed.heathanalytics.domain.Patient> org.snomed.heathanalytics.rest.CohortController.runCohortSelection(org.snomed.heathanalytics.domain.CohortCriteria,int,int) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.455  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts/statistical-test],methods=[POST],produces=[application/json]}" onto public org.snomed.heathanalytics.service.StatisticalTestResult org.snomed.heathanalytics.rest.CohortController.runStatisticalTest(org.snomed.heathanalytics.domain.CohortCriteria) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.455  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/cohorts/statistical-test-dev],methods=[POST],produces=[application/json]}" onto public org.snomed.heathanalytics.service.StatisticalTestResult org.snomed.heathanalytics.rest.CohortController.runStatisticalTestDevResults(org.snomed.heathanalytics.domain.CohortCriteria) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.458  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/concepts],methods=[GET],produces=[application/json]}" onto public org.ihtsdo.otf.sqs.service.dto.ConceptResults org.snomed.heathanalytics.rest.ConceptController.findConcepts(java.lang.String,java.lang.String,int) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.458  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/concepts/{conceptId}],methods=[GET],produces=[application/json]}" onto public org.ihtsdo.otf.sqs.service.dto.ConceptResult org.snomed.heathanalytics.rest.ConceptController.findConcepts(java.lang.String) throws org.snomed.heathanalytics.service.ServiceException
2019-01-14 15:05:35.458  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/v2/api-docs],methods=[GET],produces=[application/json || application/hal+json]}" onto public org.springframework.http.ResponseEntity<springfox.documentation.spring.web.json.Json> springfox.documentation.swagger2.web.Swagger2Controller.getDocumentation(java.lang.String,javax.servlet.http.HttpServletRequest)
2019-01-14 15:05:35.462  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/swagger-resources/configuration/security]}" onto org.springframework.http.ResponseEntity<springfox.documentation.swagger.web.SecurityConfiguration> springfox.documentation.swagger.web.ApiResourceController.securityConfiguration()
2019-01-14 15:05:35.462  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/swagger-resources/configuration/ui]}" onto org.springframework.http.ResponseEntity<springfox.documentation.swagger.web.UiConfiguration> springfox.documentation.swagger.web.ApiResourceController.uiConfiguration()
2019-01-14 15:05:35.463  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/swagger-resources]}" onto org.springframework.http.ResponseEntity<java.util.List<springfox.documentation.swagger.web.SwaggerResource>> springfox.documentation.swagger.web.ApiResourceController.swaggerResources()
2019-01-14 15:05:35.465  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/error]}" onto public org.springframework.http.ResponseEntity<java.util.Map<java.lang.String, java.lang.Object>> org.springframework.boot.autoconfigure.web.BasicErrorController.error(javax.servlet.http.HttpServletRequest)
2019-01-14 15:05:35.465  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerMapping : Mapped "{[/error],produces=[text/html]}" onto public org.springframework.web.servlet.ModelAndView org.springframework.boot.autoconfigure.web.BasicErrorController.errorHtml(javax.servlet.http.HttpServletRequest,javax.servlet.http.HttpServletResponse)
2019-01-14 15:05:35.628  INFO 94989 --- [           main] s.w.s.m.m.a.RequestMappingHandlerAdapter : Looking for @ControllerAdvice: org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext@43195e57: startup date [Mon Jan 14 15:04:58 AEST 2019]; root of context hierarchy
2019-01-14 15:05:35.696  INFO 94989 --- [           main] o.s.w.s.handler.SimpleUrlHandlerMapping  : Mapped URL path [/webjars/**] onto handler of type [class org.springframework.web.servlet.resource.ResourceHttpRequestHandler]
2019-01-14 15:05:35.696  INFO 94989 --- [           main] o.s.w.s.handler.SimpleUrlHandlerMapping  : Mapped URL path [/**] onto handler of type [class org.springframework.web.servlet.resource.ResourceHttpRequestHandler]
2019-01-14 15:05:35.715  INFO 94989 --- [           main] .m.m.a.ExceptionHandlerExceptionResolver : Detected @ExceptionHandler methods in controllerAdvice
2019-01-14 15:05:35.736  INFO 94989 --- [           main] o.s.w.s.handler.SimpleUrlHandlerMapping  : Mapped URL path [/**/favicon.ico] onto handler of type [class org.springframework.web.servlet.resource.ResourceHttpRequestHandler]
2019-01-14 15:05:35.760  INFO 94989 --- [           main] oConfiguration$WelcomePageHandlerMapping : Adding welcome page: class path resource [static/index.html]
2019-01-14 15:05:35.886  INFO 94989 --- [           main] o.s.j.e.a.AnnotationMBeanExporter        : Registering beans for JMX exposure on startup
2019-01-14 15:05:35.896  INFO 94989 --- [           main] o.s.c.support.DefaultLifecycleProcessor  : Starting beans in phase 2147483647
2019-01-14 15:05:35.896  INFO 94989 --- [           main] d.s.w.p.DocumentationPluginsBootstrapper : Context refreshed
2019-01-14 15:05:35.921  INFO 94989 --- [           main] d.s.w.p.DocumentationPluginsBootstrapper : Found 1 custom documentation plugin(s)
2019-01-14 15:05:35.929  INFO 94989 --- [           main] s.d.s.w.s.ApiListingReferenceScanner     : Scanning for api listing references
2019-01-14 15:05:36.120  INFO 94989 --- [           main] .d.s.w.r.o.CachingOperationNameGenerator : Generating unique operation named: findConceptsUsingGET_1
2019-01-14 15:05:36.216  INFO 94989 --- [           main] s.b.c.e.t.TomcatEmbeddedServletContainer : Tomcat started on port(s): 8080 (http)
2019-01-14 15:05:36.241  INFO 94989 --- [           main] ication$$EnhancerBySpringCGLIB$$5982df74 : ******** Generating data for 10,000 patients ...
2019-01-14 15:05:36.304  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [patient] creating index, cause [auto(index api)], templates [], shards [5]/[1], mappings []
2019-01-14 15:05:36.392  INFO 94989 --- [nPool-worker-17] o.i.otf.sqs.service.SnomedQueryService   : ec:'<69896004', unprocessed-lucene:'ancestor:69896004'
2019-01-14 15:05:36.487  INFO 94989 --- [nPool-worker-17] o.i.otf.sqs.service.SnomedQueryService   : ec:'<69896004', lucene:'ancestor:69896004', totalHits:56
2019-01-14 15:05:36.493  INFO 94989 --- [nPool-worker-21] o.i.otf.sqs.service.SnomedQueryService   : ec:'<420868002', unprocessed-lucene:'ancestor:420868002'
2019-01-14 15:05:36.530  INFO 94989 --- [nPool-worker-21] o.i.otf.sqs.service.SnomedQueryService   : ec:'<420868002', lucene:'ancestor:420868002', totalHits:64
2019-01-14 15:05:36.532  INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService   : ec:'<13645005', unprocessed-lucene:'ancestor:13645005'
2019-01-14 15:05:36.558  INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService   : ec:'<13645005', lucene:'ancestor:13645005', totalHits:37
2019-01-14 15:05:36.558  INFO 94989 --- [pdateTask][T#1]] o.e.cluster.routing.allocation           : [Midgard Serpent] Cluster health status changed from [RED] to [YELLOW] (reason: [shards started [[patient][4]] ...]).
2019-01-14 15:05:36.599  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [patient] create_mapping [patient]
2019-01-14 15:05:36.605  INFO 94989 --- [pdateTask][T#1]] org.elasticsearch.cluster.metadata       : [Midgard Serpent] [patient] update_mapping [patient]
2019-01-14 15:05:36.797  INFO 94989 --- [onPool-worker-7] o.i.otf.sqs.service.SnomedQueryService   : ec:'<416897008', unprocessed-lucene:'ancestor:416897008'
2019-01-14 15:05:36.807  INFO 94989 --- [onPool-worker-7] o.i.otf.sqs.service.SnomedQueryService   : ec:'<416897008', lucene:'ancestor:416897008', totalHits:7
2019-01-14 15:05:36.917  INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService   : ec:'<59282003', unprocessed-lucene:'ancestor:59282003'
2019-01-14 15:05:36.967  INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService   : ec:'<59282003', lucene:'ancestor:59282003', totalHits:59
2019-01-14 15:05:36.969  INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService   : ec:'<350468007', unprocessed-lucene:'ancestor:350468007'
2019-01-14 15:05:36.971  INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService   : ec:'<350468007', lucene:'ancestor:350468007', totalHits:0
2019-01-14 15:05:37.024  INFO 94989 --- [onPool-worker-3] o.i.otf.sqs.service.SnomedQueryService   : ec:'<40845000', unprocessed-lucene:'ancestor:40845000'
2019-01-14 15:05:37.142  INFO 94989 --- [onPool-worker-3] o.i.otf.sqs.service.SnomedQueryService   : ec:'<40845000', lucene:'ancestor:40845000', totalHits:339
2019-01-14 15:05:38.121  INFO 94989 --- [onPool-worker-5] o.i.otf.sqs.service.SnomedQueryService   : ec:'<22298006', unprocessed-lucene:'ancestor:22298006'
2019-01-14 15:05:38.154  INFO 94989 --- [onPool-worker-5] o.i.otf.sqs.service.SnomedQueryService   : ec:'<22298006', lucene:'ancestor:22298006', totalHits:84
2019-01-14 15:05:38.699  INFO 94989 --- [nPool-worker-23] o.i.otf.sqs.service.SnomedQueryService   : ec:'<53084003', unprocessed-lucene:'ancestor:53084003'
2019-01-14 15:05:38.720  INFO 94989 --- [nPool-worker-23] o.i.otf.sqs.service.SnomedQueryService   : ec:'<53084003', lucene:'ancestor:53084003', totalHits:79
2019-01-14 15:05:40.649  INFO 94989 --- [onPool-worker-5] o.i.otf.sqs.service.SnomedQueryService   : ec:'<302226006', unprocessed-lucene:'ancestor:302226006'
2019-01-14 15:05:40.808  INFO 94989 --- [onPool-worker-5] o.i.otf.sqs.service.SnomedQueryService   : ec:'<302226006', lucene:'ancestor:302226006', totalHits:1012
2019-01-14 15:05:52.011  INFO 94989 --- [           main] utoConfigurationReportLoggingInitializer :

Error starting ApplicationContext. To display the auto-configuration report re-run your application with 'debug' enabled.
2019-01-14 15:05:52.028 ERROR 94989 --- [           main] o.s.boot.SpringApplication               : Application startup failed

java.lang.IllegalStateException: Failed to execute ApplicationRunner
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:770) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:757) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.afterRefresh(SpringApplication.java:747) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1162) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1151) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    at org.snomed.heathanalytics.Application.main(Application.java:60) ~[classes!/:1.1.0]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48) ~[health-data-analytics-1.1.0.jar:1.1.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:87) ~[health-data-analytics-1.1.0.jar:1.1.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:50) ~[health-data-analytics-1.1.0.jar:1.1.0]
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51) ~[health-data-analytics-1.1.0.jar:1.1.0]
Caused by: java.lang.NullPointerException: null
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:na]
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:678) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:737) ~[na:na]
    at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateParallel(ForEachOps.java:159) ~[na:na]
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfInt.evaluateParallel(ForEachOps.java:188) ~[na:na]
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233) ~[na:na]
    at java.base/java.util.stream.IntPipeline.forEach(IntPipeline.java:439) ~[na:na]
    at java.base/java.util.stream.IntPipeline$Head.forEach(IntPipeline.java:596) ~[na:na]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.stream(ExampleDataGenerator.java:38) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.Application.generatePopulation(Application.java:114) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.Application.run(Application.java:72) ~[classes!/:1.1.0]
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:767) ~[spring-boot-1.5.1.RELEASE.jar!/:1.5.1.RELEASE]
    ... 14 common frames omitted
Caused by: java.lang.NullPointerException: null
    at org.snomed.heathanalytics.domain.ClinicalEncounter.hashCode(ClinicalEncounter.java:104) ~[classes!/:1.1.0]
    at java.base/java.util.HashMap.hash(HashMap.java:339) ~[na:na]
    at java.base/java.util.HashMap.put(HashMap.java:607) ~[na:na]
    at java.base/java.util.HashSet.add(HashSet.java:220) ~[na:na]
    at org.snomed.heathanalytics.domain.Patient.addEncounter(Patient.java:54) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.scenarioPulmEmbGIBleed(ExampleDataGenerator.java:304) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.generateExamplePatientAndActs(ExampleDataGenerator.java:86) ~[classes!/:1.1.0]
    at org.snomed.heathanalytics.ingestion.exampledata.ExampleDataGenerator.lambda$stream$0(ExampleDataGenerator.java:44) ~[classes!/:1.1.0]
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfInt.accept(ForEachOps.java:204) ~[na:na]
    at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104) ~[na:na]
    at java.base/java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:699) ~[na:na]
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) ~[na:na]
    at java.base/java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:290) ~[na:na]
    at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:746) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) ~[na:na]
    at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:177) ~[na:na]

2019-01-14 15:05:52.031  INFO 94989 --- [           main] ationConfigEmbeddedWebApplicationContext : Closing org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext@43195e57: startup date [Mon Jan 14 15:04:58 AEST 2019]; root of context hierarchy
2019-01-14 15:05:52.032  INFO 94989 --- [           main] o.s.c.support.DefaultLifecycleProcessor  : Stopping beans in phase 2147483647
2019-01-14 15:05:52.033  INFO 94989 --- [           main] o.s.j.e.a.AnnotationMBeanExporter        : Unregistering JMX-exposed beans on shutdown
2019-01-14 15:05:52.035  INFO 94989 --- [           main] s.b.a.d.e.ElasticsearchAutoConfiguration : Closing Elasticsearch client
2019-01-14 15:05:52.035  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] stopping ...
10,000/10,000
2019-01-14 15:05:52.056  WARN 94989 --- [t][index][T#10]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7591]
2019-01-14 15:05:52.057  WARN 94989 --- [][refresh][T#3]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7542]
2019-01-14 15:05:52.057  WARN 94989 --- [][refresh][T#4]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7559]
2019-01-14 15:05:52.057  WARN 94989 --- [][refresh][T#1]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7560]
2019-01-14 15:05:52.057  WARN 94989 --- [][refresh][T#5]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7550]
2019-01-14 15:05:52.057  WARN 94989 --- [][refresh][T#2]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7570]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#6]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7547]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#4]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7572]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#5]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7574]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#3]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7571]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#1]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7573]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#2]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7575]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#6]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7576]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#4]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7577]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#5]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7578]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#3]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7579]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#1]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7580]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#2]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7581]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#6]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7582]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#4]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7583]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#5]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7584]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#3]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7585]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#1]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7586]
2019-01-14 15:05:52.058  WARN 94989 --- [][refresh][T#2]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7587]
2019-01-14 15:05:52.059  WARN 94989 --- [][refresh][T#6]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7588]
2019-01-14 15:05:52.059  WARN 94989 --- [][refresh][T#4]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7589]
2019-01-14 15:05:52.059  WARN 94989 --- [][refresh][T#5]] org.elasticsearch.transport              : [Midgard Serpent] Transport response handler not found of id [7590]
2019-01-14 15:05:52.309  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] stopped
2019-01-14 15:05:52.310  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] closing ...
2019-01-14 15:05:52.313  INFO 94989 --- [           main] org.elasticsearch.node                   : [Midgard Serpent] closed
kaicode commented 5 years ago

Hi @johngrimes

Thanks for your output.

This line is causing the problem: 2019-01-14 15:05:36.971 INFO 94989 --- [nPool-worker-13] o.i.otf.sqs.service.SnomedQueryService : ec:'<350468007', lucene:'ancestor:350468007', totalHits:0 Since the 20180731 international release this concept no longer has any children so this concept query is not returning any results. This is causing the generation of the clinical encounter to fall over.

I'll update the query to work on the latest dataset later today.