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FHIR Authorization and Transaction - Spring Boot example

Abstract

This is an example application of the camel-fhir component. We’ll be using camel-spring-boot as well for an easy setup.

Introduction

The Camel route is located in the MyCamelRouter class.

This example will read patients stored in csv files from a directory and convert them to FHIR dtsu3 patients and upload them to a configured FHIR server. Each file is uploaded in a new transaction.

The example assumes you have a running FHIR server at your disposal, which is configured for basic authentication. You may use [hapi-fhir-jpa-server-example](https://github.com/rkorytkowski/hapi-fhir/tree/basic-auth/hapi-fhir-jpaserver-example). You can start it up by running mvn jetty:run.

By default, the example uses http://localhost:8080/hapi-fhir-jpaserver-example/baseDstu3 as the FHIR server URL, DSTU3 as the FHIR version, BASIC authentication (admin as username and Admin123 as password) and target/work/fhir/input as the directory to look for csv patients.

However, you can edit the application.properties file to change the defaults and provide your own configuration.

There is an example of a test in the MyCamelApplicationTest class, which mocks out the FHIR server, thus can be run without the FHIR server.

Build

You can build this example using:

$ mvn package

Run

You can run this example using:

$ mvn spring-boot:run

When the Camel application runs, you should see a folder created under target/work/fhir/input. Copy the file hl7v2.patient located in the src/main/data folder into it. You should see the following output:

2018-07-24 11:52:51.615  INFO 30666 --- [work/fhir/input] fhir-example: Converting hl7v2.patient
2018-07-24 11:52:52.700  INFO 30666 --- [work/fhir/input] fhir-example: Inserting Patient: {"resourceType":"Patient","id":"100005056","name":[{"family":"Freeman","given":["Vincent"]}]}
2018-07-24 11:52:56.995  INFO 30666 --- [ #2 - CamelFhir] fhir-example: Patient created successfully: ca.uhn.fhir.rest.api.MethodOutcome@270f03f1

The Camel application can be stopped pressing kbd:[Ctrl+c] in the shell.

Run on Openshift

Let create a service account first with all required permissions, first:

oc new-project fhir-test
oc create sa fhir-sa
oc adm policy add-scc-to-user privileged -z fhir-sa -n fhitr-test

Deploy a fhir server through this Deployment resource:

kind: Deployment
apiVersion: apps/v1
metadata:
  name: fhir
  namespace: fhir-test
  labels:
    app: fhir
spec:
  replicas: 1
  selector:
    matchLabels:
      app: fhir
  template:
    metadata:
      creationTimestamp: null
      labels:
        app: fhir
    spec:
      containers:
        - resources: {}
          readinessProbe:
            exec:
              command:
                - bash
                - "-c"
                - |
                  curl http://localhost:8080/hapi-fhir-jpaserver-example/baseDtu3/metadata --header "Authorization: Basic YWRtaW46QWRtaW4xMjMK"
            initialDelaySeconds: 60
            timeoutSeconds: 5
            periodSeconds: 10
            successThreshold: 1
            failureThreshold: 10
          terminationMessagePath: /dev/termination-log
          name: fhir
          livenessProbe:
            exec:
              command:
                - bash
                - "-c"
                - |
                  curl http://localhost:8080/hapi-fhir-jpaserver-example/baseDtu3/metadata --header "Authorization: Basic YWRtaW46QWRtaW4xMjMK"
            initialDelaySeconds: 60
            timeoutSeconds: 5
            periodSeconds: 10
            successThreshold: 1
            failureThreshold: 10
          env:
            - name: DISABLE_AUTH
              value: 'false'
            - name: FHIR_USER
              value: admin
            - name: FHIR_PWD
              value: Admin123
            - name: hapi.fhir.fhir_version
              value: DSTU3
          securityContext:
            privileged: true
          serviceAccountName: fhir-sa
          ports:
            - name: fhir
              containerPort: 8080
              protocol: TCP
          imagePullPolicy: IfNotPresent
          terminationMessagePolicy: File
          image: 'quay.io/fuse_qe/hapi-fhir-auth:v3.0.1'
      restartPolicy: Always
      terminationGracePeriodSeconds: 30
      dnsPolicy: ClusterFirst
      securityContext:
        runAsUser: 100
      serviceAccountName: fhir-sa
      schedulerName: default-scheduler
  strategy:
    type: RollingUpdate

Replace keys in src/main/jkube/configmap.yaml with desired content in application.properties and patients.csv file.

    data:
      application.properties: |
        key1=value1
        key2=value2
        key3=value3
      patients.csv: |
        1a,Name1,SureName1
        2a,Name2,SureName2

You can run this example using:

$ mvn clean install -Popenshift -DskipTests

To get health check

To show a summary of spring boot health check

curl -XGET -s http://localhost:8080/actuator/health

Help and contributions

If you hit any problem using Camel or have some feedback, then please let us know.

We also love contributors, so get involved :-)

The Camel riders!