Updating iSantePlus setup for custom modules and mysql extraction (#85)

* Updating iSantePlus setup for custom modules and mysql extraction

* network fix

build-custom-images.sh

@@ -8,7 +8,20 @@ docker build \
     -t lnsp-mediator:local \
     -f projects/lnsp-mediator/Dockerfile \
     projects/lnsp-mediator \
-
+
+# Load Env vars from json file environmentVariables field
+filepath="./packages/emr-isanteplus/package-metadata.json"
+envs=$(jq -r '.environmentVariables | to_entries | .[] | "\(.key)=\(.value)"' $filepath)
+
+# Export each environment variable
+while IFS= read -r line; do
+  export "$line"
+done <<< "$envs"
+
+docker compose \
+    -f packages/emr-isanteplus/docker-compose.yml \
+    build
+
 # Build the Platform to contain the above custom builds
 ./build-image.sh
 

config.yaml

@@ -8,6 +8,7 @@ packages:
   - fhir-datastore-hapi-fhir
   - monitoring
   - database-postgres
+  - database-mysql
   - identity-access-manager-keycloak
   - client-registry-opencr
   - analytics-datastore-elastic-search
@@ -24,6 +25,7 @@ packages:
   - lnsp-mediator
 
 
+
 profiles:
   - name: dev
     packages:

mk.sh

@@ -25,10 +25,14 @@
 #./instant package down -n interoperability-layer-openhim --env-file .env
 #./instant package up -n interoperability-layer-openhim --env-file .env
 
+#mysql 
+#./instant package remove -n database-mysql --env-file .env
+#./instant package init -n database-mysql --env-file .env
+
 #isanteplus
 
-#./instant package remove -n emr-isanteplus --env-file .env
-#./instant package init -n emr-isanteplus --env-file .env
+./instant package remove -n emr-isanteplus --env-file .env
+./instant package init -n emr-isanteplus --env-file .env
 # ./instant package down -n emr-isanteplus --env-file .env
 # ./instant package up -n emr-isanteplus --env-file .env
 
@@ -89,8 +93,8 @@
 
 
 # LNSP Mediator
-./instant package remove -n lnsp-mediator --env-file .env
-./instant package init -n lnsp-mediator --env-file .env
+#./instant package remove -n lnsp-mediator --env-file .env
+#./instant package init -n lnsp-mediator --env-file .env -d
 # ./instant package down -n lnsp-mediator --env-file .env -d
 # ./instant package up -n lnsp-mediator --env-file .env -d
 

packages/emr-isanteplus/docker-compose-mysql.yml → packages/database-mysql/docker-compose.yml

@@ -1,20 +1,19 @@
 version: "3.9"
 
 services:
-  isanteplus-mysql:
+  mysql:
     image: ghcr.io/isanteplus/docker-isanteplus-db:vtestUpdatedDb
     command: mysqld --character-set-server=utf8 --collation-server=utf8_general_ci --sql_mode=""
-    container_name: isanteplus-mysql
     environment:
-      - MYSQL_DATABASE=${OMRS_MYSQL_DB_NAME}
-      - MYSQL_ROOT_PASSWORD=${OMRS_MYSQL_ROOT_PW}
-      - MYSQL_USER=${OMRS_CONFIG_CONNECTION_USERNAME}
-      - MYSQL_PASSWORD=${OMRS_CONFIG_CONNECTION_PASSWORD}
+      - MYSQL_DATABASE=${MYSQL_DB_NAME}
+      - MYSQL_ROOT_PASSWORD=${MYSQL_ROOT_PW}
+      - MYSQL_USER=${MYSQL_CONNECTION_USERNAME}
+      - MYSQL_PASSWORD=${MYSQL_CONNECTION_PASSWORD}
       - MYSQL_ROOT_HOST=% # Allow docker containers to connect to mysql
     volumes:
-      - "isanteplus-mysql-1-data:/var/lib/mysql"
+      - "/var/lib/mysql"
     networks:
-      - openhim
+      - mysql
     configs:
       - source: mysql.cnf
         target: /etc/mysql/conf.d/custom.cnf
@@ -24,13 +23,10 @@ configs:
     file: ./config/mysql.cnf
     name: mysql.cnf
     labels:
-      name: isanteplus
-
-volumes:
-  isanteplus-mysql-1-data:
+      name: mysql
 
 networks:
-  openhim:
+  mysql:
     external: true
-    name: openhim_public
+    name: mysql_public
 

packages/database-mysql/package-metadata.json

@@ -0,0 +1,17 @@
+{
+  "id": "database-mysql",
+  "name": "MySQL",
+  "description": "MySQL database",
+  "type": "infrastructure",
+  "version": "0.0.0",
+  "dependencies": [],
+  "environmentVariables": {
+     "MYSQL_CONNECTION_USERNAME":"mysqluser",
+     "MYSQL_CONNECTION_PASSWORD":"mysqlpw",
+     "MYSQL_DB_NAME":"openmrs",
+     "MYSQL_ROOT_PW": "debezium"
+  }
+}
+
+
+

packages/database-mysql/swarm.sh

@@ -0,0 +1,92 @@
+#!/bin/bash
+
+declare ACTION=""
+declare MODE=""
+declare COMPOSE_FILE_PATH=""
+declare UTILS_PATH=""
+declare STACK="mysql"
+
+function init_vars() {
+  ACTION=$1
+  MODE=$2
+
+  COMPOSE_FILE_PATH=$(
+    cd "$(dirname "${BASH_SOURCE[0]}")" || exit
+    pwd -P
+  )
+
+  UTILS_PATH="${COMPOSE_FILE_PATH}/../utils"
+
+  readonly ACTION
+  readonly MODE
+  readonly COMPOSE_FILE_PATH
+  readonly UTILS_PATH
+  readonly STACK
+}
+
+# shellcheck disable=SC1091
+function import_sources() {
+  source "${UTILS_PATH}/docker-utils.sh"
+  source "${UTILS_PATH}/config-utils.sh"
+  source "${UTILS_PATH}/log.sh"
+}
+
+function initialize_package() {
+
+
+  # if [ "${MODE}" == "dev" ]; then
+  #   log info "Running package in DEV mode"
+  #   postgres_dev_compose_filename="docker-compose-postgres.dev.yml"
+  #   hapi_fhir_dev_compose_filename="docker-compose.dev.yml"
+  # else
+  log info "Running package in PROD mode"
+  #fi
+
+  # if [ "${CLUSTERED_MODE}" == "true" ]; then
+  #   postgres_cluster_compose_filename="docker-compose-postgres.cluster.yml"
+  # fi
+
+  (
+    docker::deploy_service "$STACK" "${COMPOSE_FILE_PATH}" "docker-compose.yml" 
+  ) ||
+    {
+      log error "Failed to deploy package"
+      exit 1
+    }
+}
+
+function destroy_package() {
+  docker::stack_destroy "$STACK"
+
+  if [[ "${CLUSTERED_MODE}" == "true" ]]; then
+    log warn "Volumes are only deleted on the host on which the command is run. Postgres volumes on other nodes are not deleted"
+  fi
+
+  docker::prune_configs "isanteplus"
+}
+
+main() {
+  init_vars "$@"
+  import_sources
+
+  if [[ "${ACTION}" == "init" ]] || [[ "${ACTION}" == "up" ]]; then
+    if [[ "${CLUSTERED_MODE}" == "true" ]]; then
+      log info "Running package in Cluster node mode"
+    else
+      log info "Running package in Single node mode"
+    fi
+
+    initialize_package
+  elif [[ "${ACTION}" == "down" ]]; then
+    log info "Scaling down package"
+
+    docker::scale_services "$STACK" 0
+  elif [[ "${ACTION}" == "destroy" ]]; then
+    log info "Destroying package"
+    destroy_package
+  else
+    log error "Valid options are: init, up, down, or destroy"
+  fi
+}
+
+main "$@"

packages/emr-isanteplus/Dockerfile

@@ -0,0 +1,3 @@
+from ghcr.io/isanteplus/docker-isanteplus-server:v2.3.4
+
+add ./config/custom_modules /custom_modules

packages/emr-isanteplus/docker-compose.yml

@@ -2,7 +2,12 @@ version: '3.9'
 
 services:
   isanteplus:
-    image:  ghcr.io/isanteplus/docker-isanteplus-server:v2.3.4
+    #image:  ghcr.io/isanteplus/docker-isanteplus-server:v2.3.4
+    # See ./build-custom-images.sh for how to build local image to include custom modules
+    image: itechuw/docker-isanteplus-server:local
+    build:
+      context: .
+      dockerfile: Dockerfile
     environment:
       - OMRS_JAVA_MEMORY_OPTS=${OMRS_JAVA_MEMORY_OPTS}
       - OMRS_CONFIG_CONNECTION_SERVER=${OMRS_CONFIG_CONNECTION_SERVER}
@@ -19,44 +24,24 @@ services:
       - isanteplus-data:/openmrs/data
       - /etc/timezone:/etc/timezone:ro
       - /etc/localtime:/etc/localtime:ro
-    ports:
-      - 1046:1044
     networks:
       - public 
-      - openhim
-    configs:
-      - target: /custom_modules/labintegration-2.2.1-SNAPSHOT.omod
-        source: labintegration-2.2.1-SNAPSHOT.omod
-
-
-configs:
-  labintegration-2.2.1-SNAPSHOT.omod:
-    file: ./config/custom_modules/labintegration-2.2.1-SNAPSHOT.omod
-    name: labintegration-2.2.1-SNAPSHOT.omod
-    labels:
-      name: labintegration-2.2.1-SNAPSHOT
-  # isanteplusreports-1.1-SNAPSHOT.omod:
-  #   file: ./config/custom_modules/isanteplusreports-1.1-SNAPSHOT.omod
-  #   name: isanteplusreports-1.1-SNAPSHOT.omod
-  #   labels:
-  #     name: isanteplusreports
+      - reverse-proxy
+      - mysql
 
 volumes:
   isanteplus-data:
-  custom_modules:
-    driver: local
-
-  #etc/timezone:
-  #etc/localtime:
-
 
 networks:
   public:
     external: true
+    name: isanteplus_public
+  mysql:
+    external: true
+    name: mysql_public
+  reverse-proxy:
     name: reverse-proxy_public
-  openhim:
     external: true
-    name: openhim_public
 
 
 

packages/emr-isanteplus/package-metadata.json

@@ -6,21 +6,18 @@
   "version": "0.0.0",
   "dependencies": [],
   "environmentVariables": {
-     "OMRS_CONFIG_CONNECTION_SERVER": "isanteplus-mysql",
+     "OMRS_CONFIG_CONNECTION_SERVER": "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_CONNECTION_URL":"jdbc:mysql://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",
      "OMRS_DEV_DEBUG_PORT":"1044",
      "OMRS_JAVA_MEMORY_OPTS":"-Xmx8192m -Xms4096m -XX:NewSize=512m",
-     "OMRS_MYSQL_DB_NAME":"openmrs",
-     "OMRS_MYSQL_ROOT_PW": "debezium"
-
-
+     "ISANTEPLUS_VERSION": "v2.3.4"
   }
 }
 

packages/emr-isanteplus/swarm.sh

@@ -47,7 +47,7 @@ function initialize_package() {
   # fi
 
   (
-    docker::deploy_service "$STACK" "${COMPOSE_FILE_PATH}" "docker-compose-mysql.yml"
+    #docker::deploy_service "$STACK" "${COMPOSE_FILE_PATH}" "docker-compose-mysql.yml"
 
     docker::deploy_service "$STACK" "${COMPOSE_FILE_PATH}" "docker-compose.yml" 
   ) ||

packages/lnsp-mediator/docker-compose.dev.yml

@@ -2,7 +2,7 @@ services:
   lnsp-mediator:
     ports:
       - target: 3000
-        published: 3300
+        published: 3000
         mode: host
       - target: 9229
         published: 9229