Setup and testing updates (#42)

* Readme updates and changes for #39, #40, #41 * Port setup additions * Readme updates * Healthcheck test * Readme additions * Updates to setup * Default openhim config * Docker fixes * CI setup * CI fixes * Finalizing pr
I-TECH-UW · Dec 8, 2021 · 98eb87e · 98eb87e
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diff --git a/.env b/.env
@@ -15,3 +15,6 @@ OPENHIM_PORT=9201
 
 ISANTEPLUS_DB_PORT=3307
 OPENMRS_DB_PORT=3308
+
+ADMIN_PW=openhim-pw
+POSTMAN_COLLECTION=
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -0,0 +1,89 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  release:
+    types: [published]
+  workflow_dispatch:
+jobs:
+  CI:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Pull containers
+        run: docker-compose -f docker-compose.ports.yml pull
+
+      - name: Cache containers
+        uses: satackey/[email protected]
+        continue-on-error: true
+
+      - name: generate certs
+        run: docker-compose -f docker-compose.ports.yml up -d certgen
+
+      - name: Start core containers
+        run: docker-compose -f docker-compose.ports.yml up -d nginx openhim-core openhim-console mongo-db openhim-config
+
+      - name: Sleep for 10 seconds
+        run: sleep 30
+        shell: bash
+
+      - name: Display docker logs for openhim config
+        run: docker-compose -f docker-compose.ports.yml logs openhim-config
+
+      - name: Start up support containers
+        run: docker-compose -f docker-compose.ports.yml up -d shr-fhir opencr-fhir opencr-es kafka zookeeper
+
+      - name: Sleep for 90 seconds
+        run: sleep 90
+        shell: bash
+
+      - name: Display docker logs for SHR & OpenCR
+        run: docker-compose -f docker-compose.ports.yml logs shr-fhir opencr-fhir
+
+      - name: Start up mediators
+        run: docker-compose -f docker-compose.ports.yml up -d shr opencr
+
+      - name: Sleep for 30 seconds
+        run: sleep 30
+        shell: bash
+
+      - name: Display docker logs for SHR & OpenCR
+        run: docker-compose -f docker-compose.ports.yml logs shr opencr
+
+      - name: Display container status
+        run: docker-compose -f docker-compose.ports.yml ps
+
+      - name: Run General Tests (https://www.postman.com/workspace/Haiti-SEDISH~4ada6d5c-42b6-483b-84e6-e2b5e08e1123/collection/1525496-6f854cdb-67cd-447e-950a-25cdf2d85186)
+        env:
+          POSTMAN_COLLECTION: https://www.getpostman.com/collections/46fd37386092a9f460e4
+        run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+
+      - name: Run CR Tests (https://www.postman.com/workspace/Haiti-SEDISH~4ada6d5c-42b6-483b-84e6-e2b5e08e1123/collection/1525496-943a668e-664f-44a3-86b5-a4d4bc14c0e9)
+        env:
+          POSTMAN_COLLECTION: https://www.getpostman.com/collections/4d682cbb222bb538d365
+        run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+
+      # - name: Run Laboratory Tests (https://www.postman.com/workspace/Haiti-SEDISH~4ada6d5c-42b6-483b-84e6-e2b5e08e1123/collection/1525496-f269b96a-22e3-4a1f-8333-04d2cd01c1aa)
+      #   env:
+      #     POSTMAN_COLLECTION: https://www.getpostman.com/collections/4f2328a2ce056ff876e4
+      #   run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+
+      # - name: Run Continuum of Care Tests (https://www.postman.com/workspace/Haiti-SEDISH~4ada6d5c-42b6-483b-84e6-e2b5e08e1123/collection/1525496-6514deeb-c038-49fd-b510-c55b3dc20bad)
+      #   env:
+      #     POSTMAN_COLLECTION: https://www.getpostman.com/collections/0d397620f00804b00d75
+      #   run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+
+      - name: Stop containers
+        if: always()
+        run: docker-compose -f docker-compose.ports.yml down -v
diff --git a/.gitignore b/.gitignore
@@ -47,3 +47,4 @@ server/log
 hapi.properties
 configs/shr/.env
 configs/opencr-hapi/.env
+
diff --git a/.postman/postman_env.ci.json b/.postman/postman_env.ci.json
@@ -0,0 +1,29 @@
+{
+	"id": "2432b862-e96d-4c54-8dd0-280091c4f4ad",
+	"name": "local",
+	"values": [
+		{
+			"key": "openhim-core-url",
+			"value": "https://openhim-core:8080",
+			"enabled": true
+		},
+		{
+			"key": "openhim-url",
+			"value": "https://openhim-core:5000",
+			"enabled": true
+		},
+		{
+			"key": "opencr-url",
+			"value": "http://opencr:3000",
+			"enabled": true
+		},
+		{
+			"key": "openhim-console-url",
+			"value": "http://openhim-console",
+			"enabled": true
+		}
+	],
+	"_postman_variable_scope": "environment",
+	"_postman_exported_at": "2021-12-08T04:56:15.104Z",
+	"_postman_exported_using": "Postman/9.3.1-211203-1700"
+}
diff --git a/.postman/run-tests.sh b/.postman/run-tests.sh
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+docker-compose -f docker-compose.ports.yml up certgen
+
+docker-compose -f docker-compose.ports.yml up -d nginx openhim-core openhim-console mongo-db
+
+sleep 10
+
+docker-compose -f docker-compose.ports.yml up openhim-config
+
+docker-compose -f docker-compose.ports.yml up -d shr-fhir opencr-fhir opencr-es kafka zookeeper
+
+sleep 30
+
+docker-compose -f docker-compose.ports.yml up -d shr opencr
+
+sleep 30
+
+docker-compose -f docker-compose.ports.yml logs shr opencr
+
+collections=(
+  'https://www.getpostman.com/collections/46fd37386092a9f460e4'
+  'https://www.getpostman.com/collections/4d682cbb222bb538d365'
+  'https://www.getpostman.com/collections/4f2328a2ce056ff876e4'
+  'https://www.getpostman.com/collections/0d397620f00804b00d75'
+)
+
+for collection in ${collections[@]}; do
+  echo $collection
+  export POSTMAN_COLLECTION=$collection
+  docker-compose -f docker-compose.ports.yml up newman
+done
diff --git a/README.md b/README.md
@@ -1,65 +1,141 @@
-# sedish-haiti.org Demo Site
+# SEDISH: The Haiti HIE 
+[![CI](https://github.com/I-TECH-UW/sedish-haiti.org/actions/workflows/main.yml/badge.svg)](https://github.com/I-TECH-UW/sedish-haiti.org/actions/workflows/main.yml)
+## Components
 
-Proof of Concept Environment Setup
+### 1. iSantePlus EMR
+### Links
+https://github.com/IsantePlus/openmrs-distro-isanteplus
+https://github.com/IsantePlus/docker-isanteplus-server
 
-# Components
+### 2. OpenCR
+https://github.com/intrahealth/client-registry
 
-## OpenMRS EMR
-### Host URLs
-- openmrs-server: http://localhost:8091/openmrs
-- openmrs-db: jdbc:mysql://localhost:3308/openmrs
-- fhir metadata: http://localhost:8091/openmrs/ws/fhir2/R4/metadata?_format=json
+### 3. OpenHIM
+http://openhim.org/docs/installation/docker
 
-### Links
-- https://github.com/pmanko/docker-openmrs-server
+### 4. HAPI JPA Server
+https://github.com/hapifhir/hapi-fhir-jpaserver-starter#deploy-with-docker-compose
+https://hapifhir.io/hapi-fhir/docs/server_jpa/get_started.html
+
+### 5. Shared Health Record
+https://github.com/i-tech-uw/shared-health-record
 
-### Notes
-- Server container requires restart after initial setup for some reason. 
-- Ran into issues with DB character set (https://talk.openmrs.org/t/ui-framework-error-while-attempting-to-access-registration-app/8734/6).
-  Had to specify characterset and collation in docker setup.
-- To create demo patients, you can set the `OMRS_CONFIG_ADD_DEMO_DATA` variable in the `openmrs/refapp/openmrs-server.env` file
-  or set the `createDemoPatientsOnNextStartup` global property to the number of patients you want to create and restart the 
-  container.
+## Installation
+### 1. Install Docker
 
-### OpenCR
+**Docker Engine:**
 
-### iSantePlus EMR
-- https://github.com/pmanko/isanteplus-docker/tree/shr
+https://docs.docker.com/compose/install/
 
+**Docker Compose:**
 
-### Local HAPI JPA Server
-- https://hub.docker.com/r/bhits/hapi-fhir-jpaserver/
+https://docs.docker.com/compose/install/
 
-#### Notes
-- Ran into issues with setting up Postgres due to DDL error for some table creation - the 
-  generated DLL included "blob". WOndering if we can use this script which uses `oid`. Reverting to mysql f
-  for now. (solved: dialect set twice ::sigh:: ) 
 
-### OpenHIM
-- http://openhim.org/docs/installation/docker
+### 2. Clone the Sedish Repository
 
-### SHR HAPI JPA Server
-- https://hub.docker.com/_/postgres
-- https://github.com/hapifhir/hapi-fhir-jpaserver-starter#deploy-with-docker-compose
+```sh
+git clone https://github.com/I-TECH-UW/sedish-haiti.org.git
+```
 
-## Flink & Pipeline
+### 3. Port-based Setup
 
-### Host URLs
-- flink console: https://localhost:3002
 
-- https://ci.apache.org/projects/flink/flink-docs-stable/ops/deployment/docker.html
-- https://github.com/pmanko/beam-local-sync
+**a) Pull all containers**  
 
+```sh
+sudo docker-compose -f docker-compose.ports.yml pull
+```
+**b) Start up Core Containers** 
 
+Generate self-signed certs:  
+```sh
+sudo docker-compose -f docker-compose.ports.yml up certgen
+```
 
-## Installation
-1. Install Docker
+```sh
+sudo docker-compose -f docker-compose.ports.yml up -d nginx openhim-core openhim-console mongo-db
+```
+
+**c) Load Default OpenHIM Config**
+First, make sure to choose and set a desired admin PW for OpenHIM that you'll use in all of the mediator configuration. 
+
+You can set this Password with the "ADMIN_PW" env setting. 
+
+```sh
+sudo docker-compose -f docker-compose.ports.yml up openhim-config
+```
+
+**d) Access the OpenHIM Console**  
+You should now be able to access the OpenHIM console at https://localhost, or whatever IP address the server is running on. The OpenHIM console runs on ports 80 and 443. 
+
+*Note: If you are using Chrome and get a certificate error, you can type `thisisunsafe` after clicking anywhere on the page to be able to proceed.*
+
+Make sure that the console is pointint to the correct `openhim-core` container. You should be able to access that container using `<your-ip-address>:8080/heartbeat`. You can configure this connection in `configs/openhim-console/ports.json`. 
+
+**e) Modify OpenHIM settings as desired**   
+Log in to the console, and set the admin password to `openhim` (for development), or the password of your choice if you haven't done so earlier automatically.
+
+You can also set up Clients and Roles for the following systems:
+- postman for testing
+- each isanteplus instance that will connect to the HIE
+- the Shared Health Record
+
+*Note: any changes to the OpenHIM console container might not show up until you disable/clear the browser cache. You can also disable the cache by opening Chrome dev tools with F12 and selecting the `disable cache` checkbox*
+
+**f) Start up Support Containers**  
+```sh
+sudo docker-compose -f docker-compose.ports.yml up -d shr-fhir opencr-fhir opencr-es kafka zookeeper
+```
+
+**g) Configure Mediators**  
+Open, examine, and edit the following files as needed, to update the IP address for OpenHIM and set the right passwords:
+  - `./configs/opencr/config_ports.json`
+  - `./configs/shr/config_ports.json`
+#### Start up Mediators  
+
+```sh
+sudo docker-compose -f docker-compose.ports.yml up -d shr opencr
+```
+#### Start up iSantePlus
+```sh
+sudo docker-compose -f docker-compose.ports.yml up -d isanteplus
+```
+
+## 4. Testing and Validation
+Setup a Postman environment and run tests from this workspace: https://www.postman.com/itechuw/workspace/isanteplus-pilot
+
+*Work in Progress*
+
+
+## 5. Domain-based setup
+Follow section 3.2, but use the main `docker-compose.yml` file, so without the `-f` flag. Also, set up certificate generation like so:
+#### SSL Certificate Generation & Refresh 
+Modify the configuration for the `certbot` entry in the `docker-compose.yml` file to match server settings. See the [Certbot Docs](https://certbot.eff.org/) for more information.
+
+Here are example settings for the AWS setup:
+
+```yaml
+  certbot:
+    image: certbot/dns-route53
+    container_name: certbot
+    entrypoint: "certbot certonly -n --agree-tos --email <your-email> -d <your-domain> -d '*.<your-domain>' --dns-route53 --preferred-challenges=dns"
+    environment:
+    - AWS_ACCESS_KEY_ID
+    - AWS_SECRET_ACCESS_KEY
+    volumes:
+    - certs:/etc/letsencrypt
+    - letsencrypt:/var/lib/letsencrypt
+    networks:
+    - sedish
+```
 
-2. Clone the repository
+Then, run the following command:
 
-3. Download https://www.dropbox.com/s/qp8zvaefuivqpcb/openmrs.zip?dl=1 and unzip into project directory
+```sh
+sudo docker-compose up certbot
+```
 
-4. Use docker-compose to build and start containers
+The certificates will be generated and provided to the other containers through a shared volume.
 
-5. Clone local sync pipeline code
 
diff --git a/compose.sh b/compose.sh
diff --git a/configs/isanteplus/isanteplus.env b/configs/isanteplus/isanteplus.env
@@ -0,0 +1,10 @@
+OMRS_JAVA_MEMORY_OPTS="-Xmx2048m -Xms1024m -XX:NewSize=128m"
+OMRS_CONFIG_CONNECTION_SERVER=isanteplus-mysql
+OMRS_CONFIG_CREATE_DATABASE_USER=false
+OMRS_CONFIG_CREATE_TABLES=false
+OMRS_CONFIG_ADD_DEMO_DATA=false
+OMRS_CONFIG_CONNECTION_URL=jdbc:mysql://isanteplus-mysql:3306/openmrs?autoReconnect=true
+OMRS_CONFIG_HAS_CURRENT_OPENMRS_DATABASE=true
+OMRS_JAVA_SERVER_OPTS="-Dfile.encoding=UTF-8 -server -Djava.security.egd=file:/dev/./urandom -Djava.awt.headless=true -Djava.awt.headlesslib=true"
+OMRS_CONFIG_CONNECTION_USERNAME=mysqluser
+OMRS_CONFIG_CONNECTION_PASSWORD=mysqlpw