Here are my tips/setup for the IBM FHIR. I hope they help you as you setup your environment.
- Create a variable to prefix the environment resources and the resource-group name.
The following generates a date that is 14 days in the future, and is in lower case, it’s best to lower case everything in the following case:
EXPIRY_DATE=$(date -j -v +14d +%Y-%b-%d |tr '[:upper:]' '[:lower:]')
echo ${EXPIRY_DATE}
The output is like the following:
2022-mar-07
- Install the plugins
When deploying the IBM FHIR Server, you’ll need a few additional plugins than the IBM Cloud default: cloud-object-storage, kubernetes-service, container-registry, cloud-database, event-streams and the infrastructure-service.
ibmcloud plugin repo-plugins -r "IBM Cloud"
ibmcloud plugin install cloud-object-storage -f
ibmcloud plugin install container-service -f
ibmcloud plugin install container-registry -f
ibmcloud plugin install cloud-databases -f
ibmcloud plugin install event-streams -f
ibmcloud plugin install infrastructure-service -f
- Login with an API Key (much easier if you use SSO)
API_KEY=$(cat cloudpak.json | jq -r .apiKey)
ibmcloud login --apikey ${API_KEY} -r us-east
- As a first step, you can check to see if there are any exisiting resources in the account:
# List the Current Databases
ibmcloud cdb ls --json
# List the Open Shift Cluster
ibmcloud oc cluster ls --json
# List the Open Shift Cluster or the Event Streams
ibmcloud resource service-instances
- Check to see if you have an existing resource-group, if no group exists, create one.
if ! ibmcloud resource group cloudpak-testing-${EXPIRY_DATE}
then
ibmcloud resource group-create 'cloudpak-testing'-${EXPIRY_DATE}
fi
- Create a Cloud Object Storage Instance, if it does not exist.
if ! ibmcloud resource service-instance cloudpak-testing-cos-${EXPIRY_DATE}
then
ibmcloud resource service-instance-create \
cloudpak-testing-cos-${EXPIRY_DATE} \
cloud-object-storage standard global \
-g 'cloudpak-testing'-${EXPIRY_DATE}
CRN=$(ibmcloud resource service-instance \
cloudpak-testing-cos-${EXPIRY_DATE} \
--output JSON | jq -r '.[].crn')
ibmcloud cos config crn --crn "${CRN}"
ibmcloud cos create-bucket --bucket \
"fhir-cloudpak-testing-${EXPIRY_DATE}"
ibmcloud resource service-key-create \
test-user-hmac Writer --instance-id "${CRN}" \
--parameters '{"HMAC":true}'
ibmcloud resource service-key-create test-user-iam Writer \
--instance-id "${CRN}" --parameters '{"HMAC":false}'
fi
Note, this creates an IAM and HMAC login user. The IBM FHIR Server team prefers the HMAC as it enables the use of presigned urls.
- Create an Event Streams instance, if it does not exist.
if ! ibmcloud resource service-instance cloudpak-testing-es-${EXPIRY_DATE}
then
ibmcloud resource service-instance-create \
cloudpak-testing-es-${EXPIRY_DATE} messagehub standard \
us-east -g 'cloudpak-testing'-${EXPIRY_DATE}
ibmcloud resource service-key-create service_manager Manager \
--instance-name cloudpak-testing-es-${EXPIRY_DATE}
ibmcloud es init -i cloudpak-testing-es-${EXPIRY_DATE}
ibmcloud es topic-create --name FHIR_AUDIT --partitions 3
ibmcloud es topic-create --name FHIR_NOTIFICATIONS --partitions 3
fi
- Create a Db2 Instance, if it does not exist.
if ! ibmcloud resource service-instance cloudpak-testing-db2-${EXPIRY_DATE}
then
ibmcloud resource service-instance-create \
cloudpak-testing-db2-${EXPIRY_DATE} \
dashdb-for-transactions standard us-east \
-g 'cloudpak-testing'-${EXPIRY_DATE} -p '{
"datacenter": "us-south:washington d.c",
"high_availability": "no",
"key_protect_instance": "none",
"key_protect_key": "none",
"oracle_compatibility": "no",
"service-endpoints": "public-and-private"
}'
fi
Note, there are some manual steps to complete the db2 setup.
- Create a postgres instance
if ! ibmcloud resource service-instance cloudpak-testing-postgres-${EXPIRY_DATE}
then
ibmcloud resource service-instance-create \
cloudpak-testing-postgres-${EXPIRY_DATE} \
databases-for-postgresql standard us-east \
-g 'cloudpak-testing'-${EXPIRY_DATE} \
-p '{"service-endpoints": "public-and-private"}'
fi
Note, there are some manual steps to complete the postgres setup.
- Create the OpenShift Cluster. The CRN is from the prior creation of the COS instance.
if [ $(ibmcloud oc cluster ls --provider vpc-gen2 --output json \
| jq -r .[].name | grep -c cloudpak-testing) = 0 ]
then
VPC_ID=$(ibmcloud ks vpcs --provider vpc-gen2 --output json \
| jq -r .[].id)
SUBNET_ID=$(ibmcloud ks subnets --provider vpc-gen2 \
--vpc-id ${VPC_ID} --zone us-east-1 --output json \
| jq -r '.[].id')
ibmcloud oc cluster create vpc-gen2 \
--name cloudpak-${EXPIRY_DATE} --flavor bx2.4x16 \
--version 4.6_openshift \
--cos-instance ${CRN} \
--service-subnet 172.21.0.0/16 --pod-subnet 172.17.64.0/18 \
--workers 3 --zone us-east-1 --vpc-id=${VPC_ID} \
--subnet-id ${SUBNET_ID}
fi
- Once the postgres instance is up, you can create users –
fhiradminandfhirserver:
PG_PASSWORD="$(openssl rand -base64 21| base64 | sed 's|=||g' )>"
echo "Postgres: " ${PG_PASSWORD}
ibmcloud cdb deployment-user-create \
cloudpak-testing-postgres-${EXPIRY_DATE} fhiradmin
ibmcloud cdb deployment-user-create \
cloudpak-testing-postgres-${EXPIRY_DATE} fhirserver
ibmcloud resource service-key-create service_manager \
--instance-name cloudpak-testing-postgres-${EXPIRY_DATE}
ibmcloud resource service-keys \
--instance-name cloudpak-testing-postgres-${EXPIRY_DATE} \
--output json
- Using
psql, create a fhirserver user for the db:
psql "host=********.databases.appdomain.cloud port=30794 dbname=ibmclouddb user=admin sslmode=verify-full"
PGPASSWORD=******
Note, if you don’t have psql in your path, use brew install postgres to get it.
-
Login with the password from the json PGPASSWORD
-
Run the following SQL to create the
fhirserveruser.
CREATE USER fhirserver WITH LOGIN encrypted password '*****CHANGE*******';
GRANT CONNECT ON DATABASE ibmclouddb TO fhirserver;
- Check the postgres configuration, and save locally:
ibmcloud cdb deployment-connections \
cloudpak-testing-postgres-${EXPIRY_DATE} --json
- Setup the necessary
max_connectionsandmax_prepared_transactionsfor postgres
ibmcloud cdb deployment-configuration \
cloudpak-testing-postgres-${EXPIRY_DATE} \
'{"max_connections": 150}'
sleep 2m
ibmcloud cdb deployment-configuration \
cloudpak-testing-postgres-${EXPIRY_DATE} \
'{"max_prepared_transactions": 150}'
- Create the db2 service-key
ibmcloud resource service-key-create service_manager \
Manager --instance-name cloudpak-testing-db2-${EXPIRY_DATE}
- Login and create
fhirserveron the https://cloud.ibm.com
Your environment is ready to run the IBM offering for IBM FHIR Server along with the supporting resources.
