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

Hotfix: hapi fhir tag fixing
jembi · Sep 5, 2023 · 2d2d10d · 2d2d10d
2 parents 8f6b5ca + 51da35e
commit 2d2d10d
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Showing 11 changed files with 170 additions and 136 deletions.
diff --git a/.env.cluster b/.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

diff --git a/.env.remote b/.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

diff --git a/config.yaml b/config.yaml
@@ -1,5 +1,5 @@
 projectName: platform
-image: jembi/platform:2.4.1
+image: jembi/platform:2.4.2
 logPath: /tmp/logs
 
 packages:

diff --git a/fhir-datastore-hapi-fhir/config/custom_pgpool.conf b/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'

diff --git a/fhir-datastore-hapi-fhir/config/custom_postgresql.conf b/fhir-datastore-hapi-fhir/config/custom_postgresql.conf
@@ -0,0 +1,2 @@
+max_connections = 250
+shared_buffers = 768MB
diff --git a/fhir-datastore-hapi-fhir/docker-compose-pgpool.cluster.yml b/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
diff --git a/fhir-datastore-hapi-fhir/docker-compose-postgres.cluster.yml b/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:
diff --git a/fhir-datastore-hapi-fhir/docker-compose-postgres.yml b/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:

diff --git a/fhir-datastore-hapi-fhir/docker-compose.yml b/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:

diff --git a/fhir-datastore-hapi-fhir/package-metadata.json b/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"
   }
 }