Merge pull request #249 from jembi/hotfix-hapi-fhir-tag-fixing

Hotfix: hapi fhir tag fixing

.env.cluster

@@ -19,6 +19,8 @@ OPENHIM_MONGO_ATNAURL=mongodb://mongo-1:27017,mongo-2:27017,mongo-3:27017/openhi
 
 # FHIR Datastore - HAPI FHIR
 HAPI_FHIR_INSTANCES=3
+# (pool size * instances) should be less than 100
+HF_MAX_POOL_SIZE=30
 REPMGR_PARTNER_NODES=postgres-1,postgres-2,postgres-3
 POSTGRES_REPLICA_SET=postgres-1:5432,postgres-2:5432,postgres-3:5432
 HAPI_DB_SET=pgpool-1:5432,pgpool-2:5432,pgpool-3:5432

.env.remote

@@ -15,6 +15,8 @@ ES_HOSTS="\"analytics-datastore-elastic-search-01:9200","analytics-datastore-ela
 CLICKHOUSE_HOST=analytics-datastore-clickhouse-01
 
 # FHIR Datastore - HAPI FHIR
+HAPI_FHIR_INSTANCES=3
+HF_MAX_POOL_SIZE=30
 REPMGR_PARTNER_NODES=postgres-1,postgres-2,postgres-3
 POSTGRES_REPLICA_SET=postgres-1:5432,postgres-2:5432,postgres-3:5432
 HAPI_DB_SET=postgres-1:5432,postgres-2:5432,postgres-3:5432

config.yaml

@@ -1,5 +1,5 @@
 projectName: platform
-image: jembi/platform:2.4.1
+image: jembi/platform:2.4.2
 logPath: /tmp/logs
 
 packages:

fhir-datastore-hapi-fhir/config/custom_pgpool.conf

@@ -1,14 +1,9 @@
-failover_on_backend_error='on'
-detach_false_primary='on'
 auto_failback='on'
 health_check_period=25
 health_check_max_retries=3
 health_check_user='postgres'
-reserved_connections=1
-max_pool=6
+max_pool=5
 client_idle_limit=300
-connection_life_time=300
-child_max_connections=25
 
 use_watchdog='on'
 hostname0='pgpool-1'

fhir-datastore-hapi-fhir/config/custom_postgresql.conf

@@ -0,0 +1,2 @@
+max_connections = 250
+shared_buffers = 768MB

fhir-datastore-hapi-fhir/docker-compose-pgpool.cluster.yml

@@ -0,0 +1,126 @@
+version: '3.9'
+
+services:
+ pgpool-1:
+ image: bitnami/pgpool:4.4.3
+ deploy:
+ placement:
+ constraints:
+ - "node.labels.name==node-1"
+ replicas: 1
+ resources:
+ limits:
+ cpus: ${HF_PGPOOL_CPU_LIMIT}
+ memory: ${HF_PGPOOL_MEMORY_LIMIT}
+ reservations:
+ cpus: ${HF_PGPOOL_CPU_RESERVE}
+ memory: ${HF_PGPOOL_MEMORY_RESERVE}
+ configs:
+ - target: /config/custom_pgpool.conf
+ source: pgpool.conf
+ - target: /opt/bitnami/pgpool/conf/pgpool_node_id
+ source: pgpool_node_id0.conf
+ environment:
+ PGPOOL_BACKEND_NODES: ${HF_PGPOOL_NODES}
+ PGPOOL_BACKEND_APPLICATION_NAMES: ${REPMGR_PARTNER_NODES}
+ PGPOOL_SR_CHECK_USER: postgres
+ PGPOOL_SR_CHECK_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ PGPOOL_POSTGRES_USERNAME: postgres
+ PGPOOL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ PGPOOL_ADMIN_USERNAME: ${HF_PGPOOL_USERNAME}
+ PGPOOL_ADMIN_PASSWORD: ${HF_PGPOOL_PASSWORD}
+ PGPOOL_POSTGRES_CUSTOM_USERS: ${HF_POSTGRESQL_USERNAME}
+ PGPOOL_POSTGRES_CUSTOM_PASSWORDS: ${HF_POSTGRESQL_PASSWORD}
+ PGPOOL_ENABLE_LOAD_BALANCING: "no"
+ PGPOOL_AUTO_FAILBACK: "yes"
+ PGPOOL_USER_CONF_FILE: "/config/custom_pgpool.conf"
+
+ pgpool-2:
+ image: bitnami/pgpool:4.4.3
+ deploy:
+ placement:
+ constraints:
+ - "node.labels.name==node-2"
+ replicas: 1
+ resources:
+ limits:
+ cpus: ${HF_PGPOOL_CPU_LIMIT}
+ memory: ${HF_PGPOOL_MEMORY_LIMIT}
+ reservations:
+ cpus: ${HF_PGPOOL_CPU_RESERVE}
+ memory: ${HF_PGPOOL_MEMORY_RESERVE}
+ configs:
+ - target: /config/custom_pgpool.conf
+ source: pgpool.conf
+ - target: /opt/bitnami/pgpool/conf/pgpool_node_id
+ source: pgpool_node_id1.conf
+ environment:
+ PGPOOL_BACKEND_NODES: ${HF_PGPOOL_NODES}
+ PGPOOL_BACKEND_APPLICATION_NAMES: ${REPMGR_PARTNER_NODES}
+ PGPOOL_SR_CHECK_USER: postgres
+ PGPOOL_SR_CHECK_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ PGPOOL_POSTGRES_USERNAME: postgres
+ PGPOOL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ PGPOOL_ADMIN_USERNAME: ${HF_PGPOOL_USERNAME}
+ PGPOOL_ADMIN_PASSWORD: ${HF_PGPOOL_PASSWORD}
+ PGPOOL_POSTGRES_CUSTOM_USERS: ${HF_POSTGRESQL_USERNAME}
+ PGPOOL_POSTGRES_CUSTOM_PASSWORDS: ${HF_POSTGRESQL_PASSWORD}
+ PGPOOL_ENABLE_LOAD_BALANCING: "no"
+ PGPOOL_AUTO_FAILBACK: "yes"
+ PGPOOL_USER_CONF_FILE: "/config/custom_pgpool.conf"
+
+ pgpool-3:
+ image: bitnami/pgpool:4.4.3
+ deploy:
+ placement:
+ constraints:
+ - "node.labels.name==node-3"
+ replicas: 1
+ resources:
+ limits:
+ cpus: ${HF_PGPOOL_CPU_LIMIT}
+ memory: ${HF_PGPOOL_MEMORY_LIMIT}
+ reservations:
+ cpus: ${HF_PGPOOL_CPU_RESERVE}
+ memory: ${HF_PGPOOL_MEMORY_RESERVE}
+ configs:
+ - target: /config/custom_pgpool.conf
+ source: pgpool.conf
+ - target: /opt/bitnami/pgpool/conf/pgpool_node_id
+ source: pgpool_node_id2.conf
+ environment:
+ PGPOOL_BACKEND_NODES: ${HF_PGPOOL_NODES}
+ PGPOOL_BACKEND_APPLICATION_NAMES: ${REPMGR_PARTNER_NODES}
+ PGPOOL_SR_CHECK_USER: postgres
+ PGPOOL_SR_CHECK_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ PGPOOL_POSTGRES_USERNAME: postgres
+ PGPOOL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ PGPOOL_ADMIN_USERNAME: ${HF_PGPOOL_USERNAME}
+ PGPOOL_ADMIN_PASSWORD: ${HF_PGPOOL_PASSWORD}
+ PGPOOL_POSTGRES_CUSTOM_USERS: ${HF_POSTGRESQL_USERNAME}
+ PGPOOL_POSTGRES_CUSTOM_PASSWORDS: ${HF_POSTGRESQL_PASSWORD}
+ PGPOOL_ENABLE_LOAD_BALANCING: "no"
+ PGPOOL_AUTO_FAILBACK: "yes"
+ PGPOOL_USER_CONF_FILE: "/config/custom_pgpool.conf"
+
+configs:
+ pgpool.conf:
+ name: pgpool_conf-${pgpool_conf_DIGEST:?err}
+ file: ./config/custom_pgpool.conf
+ labels:
+ name: hapi-fhir
+ pgpool_node_id0.conf:
+ name: pgpool_node_id0-${pgpool_node_id0_DIGEST:?err}
+ file: ./config/pgpool_node_id0
+ labels:
+ name: hapi-fhir
+ pgpool_node_id1.conf:
+ name: pgpool_node_id1-${pgpool_node_id1_DIGEST:?err}
+ file: ./config/pgpool_node_id1
+ labels:
+ name: hapi-fhir
+ pgpool_node_id2.conf:
+ name: pgpool_node_id2-${pgpool_node_id2_DIGEST:?err}
+ file: ./config/pgpool_node_id2
+ labels:
+ name: hapi-fhir

fhir-datastore-hapi-fhir/docker-compose-postgres.cluster.yml

@@ -22,8 +22,13 @@ services:
  REPMGR_PRIMARY_HOST: ${REPMGR_PRIMARY_HOST}
  REPMGR_PARTNER_NODES: ${REPMGR_PARTNER_NODES}
  POSTGRESQL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ REPMGR_FAILOVER: ${HF_POSTGRES_FAILOVER}
+ REPMGR_DEGRADED_MONITORING_TIMEOUT: ${HF_POSTGRES_DEGRADED_MONITORING_TIMEOUT}
  volumes:
  - 'hapi-postgres-2-data:/bitnami/postgresql'
+ configs:
+ - target: /bitnami/postgresql/conf/conf.d/custom_postgresql.conf
+ source: postgresql.conf
  deploy:
  placement:
  constraints:
@@ -53,8 +58,13 @@ services:
  REPMGR_PRIMARY_HOST: ${REPMGR_PRIMARY_HOST}
  REPMGR_PARTNER_NODES: ${REPMGR_PARTNER_NODES}
  POSTGRESQL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ REPMGR_FAILOVER: ${HF_POSTGRES_FAILOVER}
+ REPMGR_DEGRADED_MONITORING_TIMEOUT: ${HF_POSTGRES_DEGRADED_MONITORING_TIMEOUT}
  volumes:
  - 'hapi-postgres-3-data:/bitnami/postgresql'
+ configs:
+ - target: /bitnami/postgresql/conf/conf.d/custom_postgresql.conf
+ source: postgresql.conf
  deploy:
  placement:
  constraints:
@@ -71,130 +81,6 @@ services:
  default:
  pg_backup_net:
 
- pgpool-1:
- image: bitnami/pgpool:4.4.3
- deploy:
- placement:
- max_replicas_per_node: 1
- resources:
- limits:
- cpus: ${HF_PGPOOL_CPU_LIMIT}
- memory: ${HF_PGPOOL_MEMORY_LIMIT}
- reservations:
- cpus: ${HF_PGPOOL_CPU_RESERVE}
- memory: ${HF_PGPOOL_MEMORY_RESERVE}
- configs:
- - target: /config/custom_pgpool.conf
- source: pgpool.conf
- - target: /opt/bitnami/pgpool/conf/pgpool_node_id
- source: pgpool_node_id0.conf
- environment:
- PGPOOL_BACKEND_NODES: ${HF_PGPOOL_NODES}
- PGPOOL_BACKEND_APPLICATION_NAMES: ${REPMGR_PARTNER_NODES}
- PGPOOL_SR_CHECK_USER: postgres
- PGPOOL_SR_CHECK_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
- PGPOOL_POSTGRES_USERNAME: postgres
- PGPOOL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
- PGPOOL_ADMIN_USERNAME: ${HF_PGPOOL_USERNAME}
- PGPOOL_ADMIN_PASSWORD: ${HF_PGPOOL_PASSWORD}
- PGPOOL_POSTGRES_CUSTOM_USERS: ${HF_POSTGRESQL_USERNAME}
- PGPOOL_POSTGRES_CUSTOM_PASSWORDS: ${HF_POSTGRESQL_PASSWORD}
- PGPOOL_ENABLE_LOAD_BALANCING: "no"
- PGPOOL_AUTO_FAILBACK: "yes"
- PGPOOL_USER_CONF_FILE: "/config/custom_pgpool.conf"
- networks:
- default:
-
- pgpool-2:
- image: bitnami/pgpool:4.4.3
- deploy:
- placement:
- max_replicas_per_node: 1
- resources:
- limits:
- cpus: ${HF_PGPOOL_CPU_LIMIT}
- memory: ${HF_PGPOOL_MEMORY_LIMIT}
- reservations:
- cpus: ${HF_PGPOOL_CPU_RESERVE}
- memory: ${HF_PGPOOL_MEMORY_RESERVE}
- configs:
- - target: /config/custom_pgpool.conf
- source: pgpool.conf
- - target: /opt/bitnami/pgpool/conf/pgpool_node_id
- source: pgpool_node_id1.conf
- environment:
- PGPOOL_BACKEND_NODES: ${HF_PGPOOL_NODES}
- PGPOOL_BACKEND_APPLICATION_NAMES: ${REPMGR_PARTNER_NODES}
- PGPOOL_SR_CHECK_USER: postgres
- PGPOOL_SR_CHECK_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
- PGPOOL_POSTGRES_USERNAME: postgres
- PGPOOL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
- PGPOOL_ADMIN_USERNAME: ${HF_PGPOOL_USERNAME}
- PGPOOL_ADMIN_PASSWORD: ${HF_PGPOOL_PASSWORD}
- PGPOOL_POSTGRES_CUSTOM_USERS: ${HF_POSTGRESQL_USERNAME}
- PGPOOL_POSTGRES_CUSTOM_PASSWORDS: ${HF_POSTGRESQL_PASSWORD}
- PGPOOL_ENABLE_LOAD_BALANCING: "no"
- PGPOOL_AUTO_FAILBACK: "yes"
- PGPOOL_USER_CONF_FILE: "/config/custom_pgpool.conf"
- networks:
- default:
-
- pgpool-3:
- image: bitnami/pgpool:4.4.3
- deploy:
- placement:
- max_replicas_per_node: 1
- resources:
- limits:
- cpus: ${HF_PGPOOL_CPU_LIMIT}
- memory: ${HF_PGPOOL_MEMORY_LIMIT}
- reservations:
- cpus: ${HF_PGPOOL_CPU_RESERVE}
- memory: ${HF_PGPOOL_MEMORY_RESERVE}
- configs:
- - target: /config/custom_pgpool.conf
- source: pgpool.conf
- - target: /opt/bitnami/pgpool/conf/pgpool_node_id
- source: pgpool_node_id2.conf
- environment:
- PGPOOL_BACKEND_NODES: ${HF_PGPOOL_NODES}
- PGPOOL_BACKEND_APPLICATION_NAMES: ${REPMGR_PARTNER_NODES}
- PGPOOL_SR_CHECK_USER: postgres
- PGPOOL_SR_CHECK_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
- PGPOOL_POSTGRES_USERNAME: postgres
- PGPOOL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
- PGPOOL_ADMIN_USERNAME: ${HF_PGPOOL_USERNAME}
- PGPOOL_ADMIN_PASSWORD: ${HF_PGPOOL_PASSWORD}
- PGPOOL_POSTGRES_CUSTOM_USERS: ${HF_POSTGRESQL_USERNAME}
- PGPOOL_POSTGRES_CUSTOM_PASSWORDS: ${HF_POSTGRESQL_PASSWORD}
- PGPOOL_ENABLE_LOAD_BALANCING: "no"
- PGPOOL_AUTO_FAILBACK: "yes"
- PGPOOL_USER_CONF_FILE: "/config/custom_pgpool.conf"
- networks:
- default:
-
-configs:
- pgpool.conf:
- name: pgpool_conf-${pgpool_conf_DIGEST:?err}
- file: ./config/custom_pgpool.conf
- labels:
- name: hapi-fhir
- pgpool_node_id0.conf:
- name: pgpool_node_id0-${pgpool_node_id0_DIGEST:?err}
- file: ./config/pgpool_node_id0
- labels:
- name: hapi-fhir
- pgpool_node_id1.conf:
- name: pgpool_node_id1-${pgpool_node_id1_DIGEST:?err}
- file: ./config/pgpool_node_id1
- labels:
- name: hapi-fhir
- pgpool_node_id2.conf:
- name: pgpool_node_id2-${pgpool_node_id2_DIGEST:?err}
- file: ./config/pgpool_node_id2
- labels:
- name: hapi-fhir
-
 volumes:
  hapi-postgres-2-data:
  hapi-postgres-3-data:

fhir-datastore-hapi-fhir/docker-compose-postgres.yml

@@ -14,8 +14,13 @@ services:
  REPMGR_PRIMARY_HOST: ${REPMGR_PRIMARY_HOST}
  REPMGR_PARTNER_NODES: ${REPMGR_PARTNER_NODES}
  POSTGRESQL_POSTGRES_PASSWORD: ${HAPI_POSTGRES_PASSWORD}
+ REPMGR_FAILOVER: ${HF_POSTGRES_FAILOVER}
+ REPMGR_DEGRADED_MONITORING_TIMEOUT: ${HF_POSTGRES_DEGRADED_MONITORING_TIMEOUT}
  volumes:
  - "hapi-postgres-1-data:/bitnami/postgresql"
+ configs:
+ - target: /bitnami/postgresql/conf/conf.d/custom_postgresql.conf
+ source: postgresql.conf
  deploy:
  replicas: 1
  resources:
@@ -33,6 +38,13 @@ services:
 volumes:
  hapi-postgres-1-data:
 
+configs:
+ postgresql.conf:
+ name: postgresql_conf-${postgresql_conf_DIGEST:?err}
+ file: ./config/custom_postgresql.conf
+ labels:
+ name: hapi-fhir
+
 networks:
  default:
  hapi-fhir-postgres:

fhir-datastore-hapi-fhir/docker-compose.yml

@@ -2,7 +2,7 @@ version: '3.9'
 
 services:
  hapi-fhir:
- image: jembi/hapi:v6.0.1-wget
+ image: jembi/hapi:${HF_IMAGE_TAG}
  networks:
  mpi:
  public:
@@ -13,7 +13,7 @@ services:
  - spring.datasource.password=${HF_POSTGRESQL_PASSWORD}
  - spring.datasource.driverClassName=org.postgresql.Driver
  - spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.PostgreSQL95Dialect
- - spring.datasource.hikari.maximumPoolSize=250
+ - spring.datasource.hikari.maximumPoolSize=${HF_MAX_POOL_SIZE}
  - spring.datasource.hikari.minimumIdle=20
  - spring.datasource.hikari.connectionTimeout=60000
  - spring.datasource.hikari.idleTimeout=600000
@@ -36,8 +36,8 @@ services:
  healthcheck:
  test: /bin/wget --no-verbose --tries=1 --spider http://localhost:8080/fhir/Organization?identifier=urn:healthcheck
  interval: 30s
- timeout: 30s
- retries: 2
+ timeout: 5s
+ retries: 5
  start_period: 2m
 
 networks:

fhir-datastore-hapi-fhir/package-metadata.json

@@ -32,6 +32,11 @@
  "HF_PGPOOL_MEMORY_LIMIT": "500M",
  "HF_PGPOOL_CPU_RESERVE": "0.05",
  "HF_PGPOOL_MEMORY_RESERVE": "50M",
- "HF_JAVA_OPTS": "-Xmx2g"
+ "HF_JAVA_OPTS": "-Xmx2g",
+ "HF_IMAGE_TAG": "v6.0.1-wget",
+ "HF_MAX_POOL_SIZE": "80",
+ "HF_PGPOOL_ENABLED": "true",
+ "HF_POSTGRES_FAILOVER": "automatic",
+ "HF_POSTGRES_DEGRADED_MONITORING_TIMEOUT": "5"
  }
 }