Merge pull request #20 from ldsec/dev

medco-deployment v0.3.1

compose-profiles/dev-local-3nodes/docker-compose.yml

@@ -221,3 +221,6 @@ networks:
     driver: bridge
   intra-node-srv2:
     driver: bridge
+
+volumes:
+  medcodb:

compose-profiles/docker-compose-definitions.yml

@@ -1,23 +1,23 @@
 version: '2.4'
 services:
   i2b2:
-    image: medco/i2b2:${I2B2_VERSION:-MedCo-v0.3.0}
+    image: medco/i2b2:${I2B2_VERSION:-v0.3.0-MedCo}
     build:
       context: ../docker-images/i2b2
     environment:
       - I2B2_DB_HOST=postgresql
       - I2B2_DB_PORT=5432
       - I2B2_DB_USER=i2b2
       - I2B2_DB_PW=i2b2
-      - I2B2_DB_NAME=i2b2medcosrv
+      - I2B2_DB_NAME=i2b2medco
       - WILDFLY_ADMIN_PASSWORD=admin
       - I2B2_DOMAIN_NAME=i2b2medco
       - I2B2_SERVICE_PASSWORD=pFjy3EjDVwLfT2rB9xkK
       - DEFAULT_USER_PASSWORD=demouser
       - AXIS2_LOGLEVEL=INFO
 
   medco-unlynx:
-    image: medco/medco-unlynx:${MEDCO_UNLYNX_VERSION:-v0.3.0}
+    image: medco/medco-unlynx:${MEDCO_UNLYNX_VERSION:-v0.3.1}
     ports:
     - "2000"
     - "2001"
@@ -28,7 +28,7 @@ services:
     - ../configuration-profiles/dev-local-3nodes:/medco-configuration
 
   nginx:
-    image: medco/nginx:${NGINX_VERSION:-MedCo-v0.3.0}
+    image: medco/nginx:${NGINX_VERSION:-v0.3.1-MedCo}
     build:
       context: ../docker-images/nginx
     ports:
@@ -40,7 +40,6 @@ services:
     volumes:
       - ../docker-images/nginx/www-data:/www-data
       - ../docker-images/nginx/conf.d:/etc/nginx/conf.d
-      - ../configuration-profiles/dev-local-3nodes/group.toml:/medco-configuration/group.toml
 
   postgresql:
     image: postgres:9.6
@@ -49,18 +48,19 @@ services:
     ports:
     - "5432"
     volumes:
+    - medcodb:/var/lib/postgresql/data
     - ../docker-images/postgresql/initdb-data:/docker-entrypoint-initdb.d
 
   pg-admin:
-    image: medco/pgadmin4:${PGADMIN_VERSION:-MedCo-v0.3.0}
+    image: medco/pgadmin4:${PGADMIN_VERSION:-v0.3.1-MedCo}
     build:
       context: ../docker-images/pgadmin
     environment:
       - PGADMIN_DEFAULT_EMAIL=admin
       - PGADMIN_DEFAULT_PASSWORD=admin
 
   keycloak:
-    image: medco/keycloak:${KEYCLOAK_VERSION:-MedCo-v0.3.0}
+    image: medco/keycloak:${KEYCLOAK_VERSION:-v0.3.1-MedCo}
     build:
       context: ../docker-images/keycloak
     environment:
@@ -74,7 +74,7 @@ services:
       - DB_PASSWORD=keycloak
 
   glowing-bear-medco:
-    image: medco/glowing-bear-medco:${GLOWING_BEAR_MEDCO_VERSION:-v0.3.0}
+    image: medco/glowing-bear-medco:${GLOWING_BEAR_MEDCO_VERSION:-v0.3.1}
     ports:
       - "80"
     environment:
@@ -85,7 +85,7 @@ services:
       - GB_FOOTER_TEXT=
 
   medco-connector:
-    image: medco/medco-connector:${MEDCO_CONNECTOR_VERSION:-v0.3.0}
+    image: medco/medco-connector:${MEDCO_CONNECTOR_VERSION:-v0.3.1}
     ports:
       - "1999"
     environment:
@@ -116,7 +116,7 @@ services:
       - ../configuration-profiles/dev-local-3nodes:/medco-configuration
 
   medco-cli-client:
-    image: medco/medco-cli-client:${MEDCO_CONNECTOR_VERSION:-v0.3.0}
+    image: medco/medco-cli-client:${MEDCO_CONNECTOR_VERSION:-v0.3.1}
     environment:
       - LOG_LEVEL=3
       - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
@@ -132,7 +132,7 @@ services:
     network_mode: host
 
   medco-loader:
-    image: medco/medco-loader:${MEDCO_LOADER_VERSION:-v0.3.0}
+    image: medco/medco-loader:${MEDCO_LOADER_VERSION:-v0.3.1}
     environment:
       - LOG_LEVEL=3
       - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml

compose-profiles/test-local-3nodes/docker-compose.yml

@@ -197,7 +197,6 @@ services:
       intra-node-srv0:
       inter-nodes:
     volumes:
-    - ../../configuration-profiles/test-local-3nodes/group.toml:/medco-configuration/group.toml
     - ../../configuration-profiles/test-local-3nodes/certificate.crt:/medco-configuration/certificate.crt
     - ../../configuration-profiles/test-local-3nodes/certificate.key:/medco-configuration/certificate.key
 
@@ -249,3 +248,6 @@ networks:
     driver: bridge
   intra-node-srv2:
     driver: bridge
+
+volumes:
+  medcodb:

resources/profile-generation-scripts/test-network/docker-compose.yml

@@ -85,3 +85,6 @@ services:
       - KEYCLOAK_PASSWORD=${KEYCLOAK_PASSWORD:?}
     depends_on:
       - postgresql
+
+volumes:
+  medcodb:

resources/profile-generation-scripts/test-network/step1.sh

@@ -20,7 +20,7 @@ PRIV_KEY="${5-}"
 # convenience variables
 PROFILE_NAME="test-network-${NETWORK_NAME}-node${NODE_IDX}"
 SCRIPT_FOLDER="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-MEDCO_UNLYNX_VER="v0.3.0"
+MEDCO_UNLYNX_VER="v0.3.1"
 CONF_FOLDER="${SCRIPT_FOLDER}/../../../configuration-profiles/${PROFILE_NAME}"
 COMPOSE_FOLDER="${SCRIPT_FOLDER}/../../../compose-profiles/${PROFILE_NAME}"
 if [[ -d ${CONF_FOLDER} ]] || [[ -d ${COMPOSE_FOLDER} ]]; then
@@ -30,8 +30,10 @@ fi
 
 read -rp "### About to generate configuration of node ${NODE_IDX} (${NODE_DNS_NAME}) for profile ${PROFILE_NAME}, <Enter> to continue, <Ctrl+C> to abort."
 
-echo "### Dependencies check, script will abort if dependency if not found"
-which docker openssl
+echo "### Dependency on Docker check, script will abort if not found"
+which docker
+echo "### Dependency on OpenSSL check, script will abort if not found"
+which openssl
 
 # ===================== pre-requisites ======================
 mkdir "${CONF_FOLDER}" "${COMPOSE_FOLDER}"

resources/profile-generation-scripts/test-network/step2.sh

@@ -14,7 +14,7 @@ SECRETS="${3-}"
 # convenience variables
 PROFILE_NAME="test-network-${NETWORK_NAME}-node${NODE_IDX}"
 SCRIPT_FOLDER="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-MEDCO_UNLYNX_VER="v0.3.0"
+MEDCO_UNLYNX_VER="v0.3.1"
 CONF_FOLDER="${SCRIPT_FOLDER}/../../../configuration-profiles/${PROFILE_NAME}"
 COMPOSE_FOLDER="${SCRIPT_FOLDER}/../../../compose-profiles/${PROFILE_NAME}"
 if [[ ! -d ${CONF_FOLDER} ]] || [[ ! -d ${COMPOSE_FOLDER} ]] || [[ -f ${CONF_FOLDER}/group.toml ]]; then