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Snolytical - Health Data Analytics Demonstrator

License: Other

Shell 0.29% Java 77.10% JavaScript 0.09% HTML 0.19% Vue 21.00% TypeScript 1.33%

snomed data-analysis snomed-ct snomed-api opensource healthcare

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dmmn1992 divyanshchaudhary85 pimvolkert hmelberg danka74 nipunbalan wapophis koushal1996 zaus71 christk rarecarewa

health-data-analytics's Issues

How can I load the data into an external Elastic Search instance?

Looking to try this out but would like to be able to use an external Elastic Search Instance. Wondering if there is a how-to / example config/ any notes on if a specific version of es must be used etc.

Thanks

Add import for FHIR Bulk Data

Allow FHIR resources to be imported into the store for analysis.
Use the FHIR Bulk Data standard.

Failure to find org.ihtsdo.otf:snomed-boot:jar:1.1.0

The artifact org.ihtsdo.otf:snomed-boot does not seem to be currently present in the repository: https://nexus3.ihtsdotools.org/repository/maven-releases/

Also, I can't build it from https://github.com/IHTSDO/snomed-boot, as 1.1.0 is not the subject of a tagged commit.

Cohort always empty when gender selected

If a gender is given in the selection criteria the resulting cohort always empty.

Please explain the "then within" part of the cohort criteria.

Sharing a question from someone in the community:

I was just reviewing the slides from the data analytics demonstrator & was wondering about the background to the cohorts model and where the “then within” parts come in?

NullPointerException: ClinicalEncounter.hashCode

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]

Is MinAge for time of encounter or at present?

For cohort selection - when I set MinAge, will it filter based on age at the encounter which matches the ECL, or current age (which will not be relevant for historic data)?
Thanks

Error on some ElasticSearch field annotations

I get org.elasticsearch.index.mapper.MapperParsingException: No type specified for field [dob] for field dob on Patient.java.
This exception also occurs for field gender (also on Patient.java) and on fields name and description of file CohortCriteria.java.

Specifically the annotation seems to lack the type added to it, at least for me.

Application does not start after generating population

After using the --generate-population argument to generate the population I am finding that the application will not start again.

Startup fails with an Elasticsearch error:
java.lang.IllegalArgumentException: mapper [dobYear] of different type, current_type [long], merged_type [integer].

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