Load UMLS data into TermGraph and allow triggering in cloud container

[ibmatc]

These changes enable loading UMLS data (Concepts, Relationships, and now map edges between Snomed and ICD) into FHIR TermGraph. This also includes example yml for setting up Cassandra and ElasticSearch for JanusGraph to use.

Signed-off-by: Adam T. Clark atclark@us.ibm.com

[prb112]

 on: pull_request
Integration on: pull_request
3
Build and Tests on: pull_request
Integration - Audit on: pull_request
3
e2e-audit (openjdk11, kafka)
Integration - Windows on: pull_request
2
Integration - Persistence on: pull_request
3
e2e-audit (openjdk11, kafka)
failed 8 minutes ago in 2m 30s
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2m 1s
[INFO] fhir-audit ......................................... SUCCESS [  0.899 s]
[INFO] fhir-registry ...................................... SUCCESS [  5.265 s]
[INFO] fhir-term .......................................... SUCCESS [  0.721 s]
[INFO] fhir-term-graph .................................... FAILURE [  6.405 s]
[INFO] fhir-provider ...................................... SKIPPED
[INFO] fhir-term-remote ................................... SKIPPED
[INFO] fhir-profile ....................................... SKIPPED
[INFO] fhir-path .......................................... SKIPPED
[INFO] fhir-validation .................................... SKIPPED
[INFO] fhir-ig-us-core .................................... SKIPPED
[INFO] fhir-ig-carin-bb ................................... SKIPPED
[INFO] fhir-ig-mcode ...................................... SKIPPED
[INFO] fhir-ig-davinci-pdex-plan-net ...................... SKIPPED
[INFO] fhir-ig-davinci-pdex-formulary ..................... SKIPPED
[INFO] fhir-ig-davinci-pdex ............................... SKIPPED
[INFO] fhir-ig-davinci-hrex ............................... SKIPPED
[INFO] fhir-ig-spl ........................................ SKIPPED
[INFO] fhir-search ........................................ SKIPPED
[INFO] fhir-persistence ................................... SKIPPED
[INFO] fhir-persistence-schema ............................ SKIPPED
[INFO] fhir-persistence-jdbc .............................. SKIPPED
[INFO] fhir-notification .................................. SKIPPED
[INFO] fhir-notification-websocket ........................ SKIPPED
[INFO] fhir-notification-kafka ............................ SKIPPED
[INFO] fhir-notification-nats ............................. SKIPPED
[INFO] fhir-server ........................................ SKIPPED
[INFO] fhir-operation-test ................................ SKIPPED
[INFO] fhir-operation-validate ............................ SKIPPED
[INFO] fhir-operation-document ............................ SKIPPED
[INFO] fhir-operation-healthcheck ......................... SKIPPED
[INFO] fhir-operation-apply ............................... SKIPPED
[INFO] fhir-operation-convert ............................. SKIPPED
[INFO] fhir-operation-term ................................ SKIPPED
[INFO] fhir-operation-term-cache .......................... SKIPPED
[INFO] fhir-operation-reindex ............................. SKIPPED
[INFO] fhir-operation-bulkdata ............................ SKIPPED
[INFO] fhir-operation-everything .......................... SKIPPED
[INFO] fhir-operation-erase ............................... SKIPPED
[INFO] fhir-bulkdata-webapp ............................... SKIPPED
[INFO] fhir-client ........................................ SKIPPED
[INFO] fhir-server-webapp ................................. SKIPPED
[INFO] fhir-server-test ................................... SKIPPED
[INFO] fhir-smart ......................................... SKIPPED
[INFO] fhir-bucket ........................................ SKIPPED
[INFO] fhir-swagger-generator ............................. SKIPPED
[INFO] fhir-openapi ....................................... SKIPPED
[INFO] fhir-install ....................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  55.365 s
[INFO] Finished at: 2021-09-22T19:06:21Z
[INFO] ------------------------------------------------------------------------
Error:  Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project fhir-term-graph: Compilation failure: Compilation failure: 
Error:  /home/runner/work/FHIR/FHIR/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/UMLSTermGraphLoader.java:[84,9] no suitable constructor found for AbstractTermGraphLoader(java.util.Map<java.lang.String,java.lang.String>,org.apache.commons.configuration.Configuration)
Error:      constructor com.ibm.fhir.term.graph.loader.impl.AbstractTermGraphLoader.AbstractTermGraphLoader(java.util.Map<java.lang.String,java.lang.String>,org.apache.commons.configuration2.Configuration) is not applicable
Error:        (argument mismatch; org.apache.commons.configuration.Configuration cannot be converted to org.apache.commons.configuration2.Configuration)
Error:      constructor com.ibm.fhir.term.graph.loader.impl.AbstractTermGraphLoader.AbstractTermGraphLoader(java.util.Map<java.lang.String,java.lang.String>,com.ibm.fhir.term.graph.FHIRTermGraph) is not applicable
Error:        (argument mismatch; org.apache.commons.configuration.Configuration cannot be converted to com.ibm.fhir.term.graph.FHIRTermGraph)
Error:  /home/runner/work/FHIR/FHIR/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/SnoMedICD10MapTermGraphLoader.java:[154,9] no suitable constructor found for AbstractTermGraphLoader(java.util.Map<java.lang.String,java.lang.String>,org.apache.commons.configuration.Configuration)
Error:      constructor com.ibm.fhir.term.graph.loader.impl.AbstractTermGraphLoader.AbstractTermGraphLoader(java.util.Map<java.lang.String,java.lang.String>,org.apache.commons.configuration2.Configuration) is not applicable
Error:        (argument mismatch; org.apache.commons.configuration.Configuration cannot be converted to org.apache.commons.configuration2.Configuration)
Error:      constructor com.ibm.fhir.term.graph.loader.impl.AbstractTermGraphLoader.AbstractTermGraphLoader(java.util.Map<java.lang.String,java.lang.String>,com.ibm.fhir.term.graph.FHIRTermGraph) is not applicable
Error:        (argument mismatch; org.apache.commons.configuration.Configuration cannot be converted to com.ibm.fhir.term.graph.FHIRTermGraph)

Compilation failures

[JohnTimm]

Good stuff!

[prb112]

LGTM

[lmsurpre]

We were already using this in fhir-bulkdata-webapp, but this is a new dependency for the fhir-server-webapp. I think it pulls in much of the aws sdk.
Since its not actually needed by the server during runtime, I think we should work to split out this new loading tool work so that it doesn't end up in the webapp.

[prb112]

agreed #2799

[lmsurpre]

ah, I read that as more of creating a utility class to encapsulate the code that accesses COS. i didn't think it went quite as far as what i'm suggesting here which is to split fhir-term-graph into two totally separate modules:

1. the loading stuff the creates/populates the graph db
2. the provider stuff that uses the graph and ships with the server

[lmsurpre]

Thanks @ibmatc !