Initial config for OpenFn HAPI FHIR & OpenHIM

openfn/README.md

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+# OpenFn Microservice
+
+A demo package using OpenFn Microservice, OpenHIM and HAPI FHIR using Instant OpenHIE.
+
+The `microservice` project.yaml file is located here: [`openfn/docker/config/project.yaml`](./docker/config/project.yaml).
+
+## Getting Started
+
+### Docker
+
+To start up the service
+
+```sh
+yarn
+yarn docker:build
+yarn docker:instant init -t docker openfn
+```
+
+To tear down the deployment use the opposing command:
+
+```bash
+yarn docker:instant down -t docker openfn
+```
+
+To start up the service after a tear down, use the following command:
+
+```bash
+yarn docker:instant up -t docker openfn
+```
+
+To completely remove all package components use the following option:
+
+```bash
+yarn docker:instant destroy -t docker openfn
+```
+
+### Kubernetes
+
+To start up the service
+
+```sh
+yarn
+yarn docker:build
+yarn docker:instant init -t k8s openfn
+```
+
+To tear down the deployment use the opposing command:
+
+```bash
+yarn docker:instant down -t k8s openfn
+```
+
+To start up the service after a tear down, use the following command:
+
+```bash
+yarn docker:instant up -t k8s openfn
+```
+
+To completely remove all package components use the following option:
+
+```bash
+yarn docker:instant destroy -t k8s openfn
+```
+
+## How data gets to HAPI FHIR
+
+Using the example payload [commcare_sample.json](./fixtures/commcare_sample.json)
+we send that to the configured OpenFn Microservice.
+
+Microservice is configurated to run a job based on the shape of the incoming 
+payload _see [project.yaml](./docker/config/project.yaml)_.
+
+The job `commcare-to-him` will match against this message and will be invoked
+performing the following actions:
+
+- creates a payload in the FHIR standard containing
+  - a Encounter resource that contains (`contained` resource field) a Patient resource
+- sends the payload to OpenHIM
+- which in turn sends the payload to HAPI FHIR
+
+
+### In Docker
+
+* URL - `http://localhost:4001`
+
+### In Kubernetes
+
+Use the host ip or DNS, and the port `4001`. If the deployment has been done to a [minikube](https://kubernetes.io/docs/setup/learning-environment/minikube/) cluster, get the external ip and port for the `openfn-service` service by running the following command
+
+```sh
+kubectl get services
+```
+
+## Notes
+
+- The HAPI FHIR service runs on port `3447`
+- The OpenHIM channel that we go through is on port `5001`.  
+  The API is identical, with the exception of a required `Authorization` header.
+

openfn/docker/compose.sh

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+#!/bin/bash
+
+composeFilePath=$(dirname $(readlink -f $0))
+
+# Create a volume and copy the project configuration in before starting the stack.
+docker volume create microservice_him_hapi
+docker container create --name dummy -v microservice_him_hapi:/mnt tianon/true 
+docker cp $composeFilePath/config/project.yaml dummy:/mnt/
+docker rm dummy
+
+if [ "$1" == "init" ]; then
+    docker-compose -p openfn \
+    -f "$composeFilePath"/docker-compose.yml \
+    -f "$composeFilePath"/docker-compose.dev.yml \
+    -f "$composeFilePath"/docker-compose.config.yml \
+    up -d
+elif [ "$1" == "up" ]; then
+    docker-compose -p openfn \
+    -f "$composeFilePath"/docker-compose.yml \
+    -f "$composeFilePath"/docker-compose.dev.yml \
+    -f "$composeFilePath"/docker-compose.config.yml \
+    up -d
+elif [ "$1" == "down" ]; then
+    docker-compose -p openfn \
+    -f "$composeFilePath"/docker-compose.yml \
+    -f "$composeFilePath"/docker-compose.dev.yml \
+    -f "$composeFilePath"/docker-compose.config.yml \
+    stop
+elif [ "$1" == "destroy" ]; then
+    docker-compose -p openfn \
+    -f "$composeFilePath"/docker-compose.yml \
+    -f "$composeFilePath"/docker-compose.dev.yml \
+    -f "$composeFilePath"/docker-compose.config.yml \
+    down
+else
+    echo "Valid options are: init, up, down, or destroy"
+fi

openfn/docker/config/project.yaml

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+jobs:
+  create-patient:
+    expression: >
+      post('Patient', {
+        body: dataValue('$'),
+        headers: {
+          'Content-Type': 'application/json',
+          Authorization: 'Custom test',
+          'If-None-Exist': state =>
+            `identifier=${dataValue('identifier[0].value')(state)}`,
+        },
+      });
+    adaptor: '@openfn/language-http'
+    trigger: patient-message
+    credential: openhim
+
+  create-organization:
+    expression: >
+      post('Organization', {
+        body: dataValue('$'),
+        headers: {
+          'Content-Type': 'application/json',
+          Authorization: 'Custom test',
+          'If-None-Exist': state =>
+            `identifier=${dataValue('identifier[0].value')(state)}`,
+        },
+      });
+    adaptor: '@openfn/language-http'
+    trigger: organization-message
+    credential: openhim
+
+  commcare-to-openhim:
+    expression: >
+      post("Patient", {
+        body: fields(
+          field("resourceType", "Patient"),
+          field("id", dataValue("$form.patient_data.patient_id")),
+          field("identifier", [
+            {
+              use: "usual",
+              type: {
+                coding: [
+                  {
+                    system: "http://terminology.hl7.org/CodeSystem/v2-0203",
+                    code: "MR",
+                  },
+                ],
+              },
+              system: "urn:oid:0.1.2.3.4.5.6.7",
+              value: dataValue("$form.patient_data.patient_id"),
+            },
+          ]),
+          field("name", [
+            {
+              use: "official",
+              family: dataValue("$form.patient_data.age.last_name"),
+              given: [dataValue("$form.patient_data.age.first_name")],
+            },
+          ]),
+          field("gender", dataValue("$form.patient_data.age.gender")),
+          field("birthDate", dataValue("$form.patient_data.age.birthDate"))
+        ),
+        headers: {
+          "Content-Type": "application/json",
+          Authorization: "Custom test",
+          "If-None-Exist": (state) =>
+            `identifier=${dataValue("$form.patient_data.patient_id")(state)}`,
+        },
+      });
+
+      post("Encounter", {
+        body: fields(
+          field("resourceType", "Encounter"),
+          field("status", "finished"),
+          field(
+            "subject",
+            field("reference", (state) => `Patient/${dataValue("id")(state)}`)
+          )
+        ),
+        headers: {
+          "Content-Type": "application/json",
+          Authorization: "Custom test",
+        },
+      });
+    adaptor: '@openfn/language-http'
+    trigger: commcare-message
+    credential: openhim
+
+  kobo-to-openhim:
+    expression: >
+      post("Patient", {
+        body: fields(
+          field("resourceType", "Patient"),
+          field("id", dataValue("$body.Godata_ID")),
+          field("identifier", [
+            {
+              use: "usual",
+              type: {
+                coding: [
+                  {
+                    system: "http://terminology.hl7.org/CodeSystem/v2-0203",
+                    code: "MR",
+                  },
+                ],
+              },
+              system: "urn:oid:0.1.2.3.4.5.6.7",
+              value: dataValue("$body.Godata_ID"),
+            },
+          ]),
+          field("name", [
+            {
+              use: "official",
+              text: dataValue("$body.Patient_name"),
+            },
+          ]),
+          field("gender", dataValue("$body.Sex")),
+          field("birthDate", (state) => {
+            const year =
+              Intl.DateTimeFormat("en", { year: "numeric" }).format() -
+              Number(dataValue("$body.Age_in_year")(state));
+            return `${year}-01-01`;
+          })
+        ),
+        headers: {
+          "Content-Type": "application/json",
+          Authorization: "Custom test",
+          "If-None-Exist": (state) =>
+            `identifier=${dataValue("$body.Godata_ID")(state)}`,
+        },
+      });
+
+      post("Encounter", {
+        body: fields(
+          field("resourceType", "Encounter"),
+          field("status", "finished"),
+          field(
+            "subject",
+            field(
+              "reference",
+              (state) => `Patient/${dataValue("id")(state)}`
+            )
+          )
+        ),
+        headers: {
+          "Content-Type": "application/json",
+          Authorization: "Custom test",
+        },
+      });
+
+    adaptor: '@openfn/language-http'
+    trigger: kobo-message
+    credential: openhim
+
+
+triggers:
+  patient-message:
+    criteria: '{"resourceType":"Patient"}'
+  organization-message:
+    criteria: '{"resourceType":"Organization"}'
+  kobo-message:
+    criteria: '{"form":"covid19-registration"}'
+  commcare-message:
+    criteria: '{"app_id":"aa"}'
+
+credentials:
+  openhim:
+    baseUrl: "http://openhim-core:5001/fhir/"

openfn/docker/docker-compose.config.yml

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+version: "3.3"
+
+services:
+  openfn:
+    environment:
+      PROJECT_DIR: /opt/app/project
+      # MIX_ENV: prod
+    volumes:
+      - microservice_him_hapi:/opt/app/project
+
+volumes:
+  microservice_him_hapi:
+    external: true
+
+networks:
+  default:
+    external:
+      name: instant_default

openfn/docker/docker-compose.dev.yml

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+version: '3.3'
+
+services:
+  openfn:
+    ports:
+      - '4001:4001'

openfn/docker/docker-compose.yml

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+version: '3.3'
+
+services:
+  openfn:
+    image: openfn/microservice:v0.3.3
+    container_name: openfn_him_hapi
+    environment:
+      HOST_URL: localhost
+      PORT: 4001
+      ENDPOINT_STYLE: async

openfn/fixtures/commcare_sample.json

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+{
+  "app_id": "aa",
+  "archived": false,
+  "attachments": {
+    "form.xml": {
+      "content_type": "text/xml",
+      "length": 11528,
+      "url": "https://www.commcarehq.org/a/x.xml"
+    }
+  },
+  "form": {
+    "#type": "data",
+    "@name": "Register New Patient",
+    "@uiVersion": "1",
+    "@version": "1",
+    "patient_data": {
+      "age": {
+        "age_at_registration_days": "181",
+        "gender": "female",
+        "birthDate": "2020-10-11",
+        "first_name": "test",
+        "last_name": "case"
+      },
+      "locations": {
+        "city": "k",
+        "clinic_code": "test_clinic",
+        "country": "Kenya"
+      },
+      "patient_id": "test_clinic-0009-01"
+    },
+    "case": {
+      "@case_id": "xxx",
+      "@date_modified": "2021-01-21T07:08:19.431000Z",
+      "@user_id": "aaa",
+      "@xmlns": "http://commcarehq.org/case/transaction/v2",
+      "create": {
+        "case_name": "test case",
+        "case_type": "patient",
+        "owner_id": "aaa"
+      }
+    }   
+}
+}