The IBM FHIR Server Terminology module fhir-term provides a FHIR terminology service provider interface (SPI) and a default implementation that implements terminology services using CodeSystem, ValueSet, and ConceptMap resources that have been made available through the FHIR registry module fhir-registry.
This document outlines a small test environment to setup Cassandra and ElasticSearch to run the Terminology and run a simple test.
Recipe
- Clone the IBM FHIR Server repository and switch to the cloned repository.
git clone https://github.com/IBM/FHIR.git && cd $(basename $_ .git)
- Setup the examples
mvn clean install -f fhir-examples -DskipTests
- Edit line 68 –
term/fhir-term-graph/pom.xml, changeprovidedtocompile
<dependency>
<groupId>org.janusgraph</groupId>
<artifactId>janusgraph-cql</artifactId>
<scope>compile</scope>
- Edit line 174 –
term/fhir-term-graph/pom.xml, changeprovidedtocompile
<dependency>
<groupId>org.janusgraph</groupId>
<artifactId>janusgraph-es</artifactId>
<scope>compile</scope>
</dependency>
- Setup the fhir projects
mvn clean install -f fhir-parent -DskipTests
- Build the IBM FHIR Server
export WORKSPACE=$(pwd)
export BUILD_ID=4.11.0-SNAPSHOT
docker logout
nerdctl build fhir-install -t ibmcom/ibm-fhir-server:graph
You’ll see:
Successfully built 196dd54732a4
Successfully tagged ibmcom/ibm-fhir-server:latest
- Build the Graph Terminology Loader
pushd
cd ${WORKSPACE}/fhir-install/src/main/docker/ibm-fhir-term-graph-loader/
mkdir -p target/
cp ${WORKSPACE}/term/fhir-term-graph-loader/target/fhir-term-graph-loader-*-cli.jar target/
cp ${WORKSPACE}/LICENSE target/
nerdctl build --build-arg FHIR_VERSION=${BUILD_ID} -t ibmcom/ibm-fhir-term-loader:latest .
popd
- Download the
janusgraph-cassandra-elasticsearch.properties
curl -o janusgraph-cassandra-elasticsearch.properties -L \
https://raw.githubusercontent.com/IBM/FHIR/main/term/fhir-term-graph-loader/src/test/resources/conf/janusgraph-cassandra-elasticsearch.properties
- Download the fhir-server-config.json
curl -o fhir-server-config.json -L \
https://gist.githubusercontent.com/prb112/c08613e6e21e77b92cfc0ea19c56f081/raw/a9e17bb2924b59de14bd04aa9fbbcc8ff38afb10/fhir-server-config-term.json
- Download the docker-compose.yml
curl -o docker-compose.yml -L \
https://gist.githubusercontent.com/prb112/1461e66d28767ba169843bded4b0aad8/raw/a4ed5b59fd8eb430745c173536dc5ab304186c7a/docker-compose.yml
- Startup the cassandra container
nerdctl compose up cassandra
- Check the logs until you see:
fhir-cassandra |INFO [main] 2022-02-19 00:36:18,884 CassandraDaemon.java:780 - Startup complete
- Startup the elasticsearch container
nerdctl compose up elasticsearch -d
- Check the logs for "Yellow to Green"
Cluster health status changed from [YELLOW] to [GREEN]
- Start the IBM FHIR Server
nerdctl compose up fhir-server -d
- Check the logs for smarter planet
fhir-server_1 |[2/19/22, 0:40:09:547 UTC] 00000026 FeatureManage A CWWKF0011I: The defaultServer server is ready to run a smarter planet. The defaultServer server started in 27.170 seconds.
You should also see the schema created:
fhir-server |[2/19/22, 1:20:11:487 UTC] 00000027 FHIRTermGraph I Creating schema...
fhir-server |[2/19/22, 1:20:13:840 UTC] 00000027 FHIRTermGraph I
fhir-server |------------------------------------------------------------------------------------------------
fhir-server |Vertex Label Name | Partitioned | Static |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |CodeSystem | false | false |
fhir-server |Concept | false | false |
fhir-server |Designation | false | false |
fhir-server |Property_ | false | false |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |Edge Label Name | Directed | Unidirected | Multiplicity |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |isa | true | false | MULTI |
fhir-server |concept | true | false | MULTI |
fhir-server |designation | true | false | MULTI |
fhir-server |property_ | true | false | MULTI |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |Property Key Name | Cardinality | Data Type |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |valueCode | SINGLE | class java.lang.String |
fhir-server |display | SINGLE | class java.lang.String |
fhir-server |version | SINGLE | class java.lang.String |
fhir-server |code | SINGLE | class java.lang.String |
fhir-server |codeLowerCase | SINGLE | class java.lang.String |
fhir-server |url | SINGLE | class java.lang.String |
fhir-server |value | SINGLE | class java.lang.String |
fhir-server |valueBoolean | SINGLE | class java.lang.Boolean |
fhir-server |valueDateTimeLong | SINGLE | class java.lang.Long |
fhir-server |valueDecimal | SINGLE | class java.lang.Double |
fhir-server |valueInteger | SINGLE | class java.lang.Integer |
fhir-server |valueString | SINGLE | class java.lang.String |
fhir-server |count | SINGLE | class java.lang.Integer |
fhir-server |group | SINGLE | class java.lang.String |
fhir-server |language | SINGLE | class java.lang.String |
fhir-server |system | SINGLE | class java.lang.String |
fhir-server |use | SINGLE | class java.lang.String |
fhir-server |valueDateTime | SINGLE | class java.lang.String |
fhir-server |valueDecimalString | SINGLE | class java.lang.String |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |Graph Index (Vertex) | Type | Unique | Backing | Key: Status |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |byUrl | Composite | false | internalindex | url: ENABLED |
fhir-server |byCode | Composite | false | internalindex | code: ENABLED |
fhir-server |byCodeLowerCase | Composite | false | internalindex | codeLowerCase: ENABLED |
fhir-server |byDisplay | Composite | false | internalindex | display: ENABLED |
fhir-server |byUrlAndVersion | Composite | false | internalindex | url: ENABLED |
fhir-server | | | | | version: ENABLED |
fhir-server |byValue | Composite | false | internalindex | value: ENABLED |
fhir-server |byValueBoolean | Composite | false | internalindex | valueBoolean: ENABLED |
fhir-server |byValueCode | Composite | false | internalindex | valueCode: ENABLED |
fhir-server |byValueDateTimeLong | Composite | false | internalindex | valueDateTimeLong: ENABLED |
fhir-server |byValueDecimal | Composite | false | internalindex | valueDecimal: ENABLED |
fhir-server |byValueInteger | Composite | false | internalindex | valueInteger: ENABLED |
fhir-server |byValueString | Composite | false | internalindex | valueString: ENABLED |
fhir-server |vertices | Mixed | false | search | display: ENABLED |
fhir-server | | | | | value: ENABLED |
fhir-server | | | | | valueCode: ENABLED |
fhir-server | | | | | valueString: ENABLED |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |Graph Index (Edge) | Type | Unique | Backing | Key: Status |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |Relation Index (VCI) | Type | Direction | Sort Key | Order | Status |
fhir-server |---------------------------------------------------------------------------------------------------
fhir-server |
fhir-server |[2/19/22, 1:20:15:061 UTC] 00000071 Clock I com.datastax.oss.driver.internal.core.time.Clock getInstance Using native clock for microsecond precision
fhir-server |[2/19/22, 1:20:15:132 UTC] 00000027 ExecutorServi I org.janusgraph.diskstorage.configuration.ExecutorServiceBuilder buildFixedExecutorService Initiated fixed thread pool of size 10
fhir-server |[2/19/22, 1:20:15:197 UTC] 00000027 UniqueInstanc I org.janusgraph.graphdb.idmanagement.UniqueInstanceIdRetriever getOrGenerateUniqueInstanceId Generated unique-instance-id=0a04031316-fhir2
fhir-server |[2/19/22, 1:20:15:256 UTC] 00000084 Clock I com.datastax.oss.driver.internal.core.time.Clock getInstance Using native clock for microsecond precision
fhir-server |[2/19/22, 1:20:15:331 UTC] 00000027 ExecutorServi I org.janusgraph.diskstorage.configuration.ExecutorServiceBuilder buildFixedExecutorService Initiated fixed thread pool of size 10
fhir-server |[2/19/22, 1:20:15:332 UTC] 00000027 Backend I org.janusgraph.diskstorage.Backend getIndexes Configuring index [search]
fhir-server |[2/19/22, 1:20:15:373 UTC] 00000027 ExecutorServi I org.janusgraph.diskstorage.configuration.ExecutorServiceBuilder buildFixedExecutorService Initiated fixed thread pool of size 4
fhir-server |[2/19/22, 1:20:15:541 UTC] 00000027 KCVSLog I org.janusgraph.diskstorage.log.kcvs.KCVSLog$MessagePuller initializeTimepoint Loaded unidentified ReadMarker start time 2022-02-19T01:20:15.541046Z into org.janusgraph.diskstorage.log.kcvs.KCVSLog$MessagePuller@2c491de4
- Check the Capabilities endpoint, it should respond with a wealth of input
curl --request GET \
--url https://localhost:9443/fhir-server/api/v4/metadata \
--header 'Content-Type: application/fhir+json' \
--header 'X-FHIR-TENANT-ID: default' \
-k -o /dev/null -I
-
Copy over the Jar file
term/fhir-term-graph-loader/target/fhir-term-graph-loader-4.11.0-SNAPSHOT-cli.jar -
Loading the Data for your specific use-case.
- CodeSystem
java -jar fhir-term-graph-loader-4.11.0-SNAPSHOT-cli.jar -config ./janusgraph-cassandra-elasticsearch.properties -file CodeSystem.json
Also -url
- Snomed
java -jar fhir-term-graph-loader-4.11.0-SNAPSHOT-cli.jar -config ./janusgraph-cassandra-elasticsearch.properties \
-base snomed/ \
-concept concept.cpt \
-relation relation.rt \
-desc desc.file \
-lang lang.file
- UMLS
java -jar fhir-term-graph-loader-4.11.0-SNAPSHOT-cli.jar -config ./janusgraph-cassandra-elasticsearch.properties
I don’t actually execute these commands in this blog as it is licensed content.
- Execute the queries for the terminology system.
There are some ancillary tasks you should do when done:
A. Shutdown the Containers when you are done.
nerdctl compose down
B. List current moby images.
nerdctl images
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