Merge pull request #6 from lca1/dev

MedCo v0.2.1
ldsec · Aug 15, 2019 · a700026 · a700026
2 parents 6254a73 + 398f2c6
commit a700026
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Showing 45 changed files with 2,542 additions and 139 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 .DS_Store
 configuration-profiles/dev/
+resources/data/
diff --git a/compose-profiles/dev-local-3nodes/.env b/compose-profiles/dev-local-3nodes/.env
@@ -0,0 +1,9 @@
+I2B2_VERSION=dev
+MEDCO_UNLYNX_VERSION=dev
+NGINX_VERSION=dev
+PHP_FPM_VERSION=dev
+PGADMIN_VERSION=dev
+KEYCLOAK_VERSION=dev
+PICSURE_VERSION=dev
+MEDCO_CONNECTOR_VERSION=dev
+MEDCO_LOADER_VERSION=dev
diff --git a/compose-profiles/dev-local-3nodes/docker-compose.tools.yml b/compose-profiles/dev-local-3nodes/docker-compose.tools.yml
@@ -0,0 +1,35 @@
+version: '2.4'
+services:
+  medco-cli-client:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-cli-client
+    environment:
+      - LOG_LEVEL=5
+
+  medco-loader-srv0:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-loader
+    environment:
+      - LOG_LEVEL=5
+      - DB_NAME=i2b2medcosrv0
+      - UNLYNX_GROUP_FILE_IDX=0
+
+  medco-loader-srv1:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-loader
+    environment:
+      - LOG_LEVEL=5
+      - DB_NAME=i2b2medcosrv1
+      - UNLYNX_GROUP_FILE_IDX=1
+
+  medco-loader-srv2:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-loader
+    environment:
+      - LOG_LEVEL=5
+      - DB_NAME=i2b2medcosrv2
+      - UNLYNX_GROUP_FILE_IDX=2
diff --git a/compose-profiles/dev-local-3nodes/docker-compose.yml b/compose-profiles/dev-local-3nodes/docker-compose.yml
@@ -4,7 +4,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: i2b2
-    image: medco/i2b2:dev
     environment:
       - I2B2_DB_NAME=i2b2medcosrv0
       - I2B2_DOMAIN_NAME=i2b2medcosrv0
@@ -22,7 +21,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: medco-unlynx
-    image: medco/medco-unlynx:dev
     ports:
       - "2000:2000"
       - "2001:2001"
@@ -38,7 +36,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: medco-connector
-    image: medco/medco-connector:dev
     ports:
       - "1990:1999"
     environment:
@@ -57,7 +54,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: i2b2
-    image: medco/i2b2:dev
     environment:
       - I2B2_DB_NAME=i2b2medcosrv1
       - I2B2_DOMAIN_NAME=i2b2medcosrv1
@@ -75,7 +71,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: medco-unlynx
-    image: medco/medco-unlynx:dev
     ports:
       - "2002:2002"
       - "2003:2003"
@@ -91,7 +86,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: medco-connector
-    image: medco/medco-connector:dev
     ports:
       - "1991:1999"
     environment:
@@ -110,7 +104,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: i2b2
-    image: medco/i2b2:dev
     environment:
       - I2B2_DB_NAME=i2b2medcosrv2
       - I2B2_DOMAIN_NAME=i2b2medcosrv2
@@ -128,7 +121,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: medco-unlynx
-    image: medco/medco-unlynx:dev
     ports:
       - "2004:2004"
       - "2005:2005"
@@ -144,7 +136,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: medco-connector
-    image: medco/medco-connector:dev
     ports:
       - "1992:1999"
     environment:
@@ -163,11 +154,8 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: nginx
-    image: medco/nginx:dev
     ports:
     - "80:80"
-    environment:
-      - HTTP_SCHEME=http
     networks:
       intra-node-srv0:
       inter-nodes:
@@ -177,7 +165,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: php-fpm
-    image: medco/php-fpm:dev
     environment:
       - I2B2_DB_NAME=i2b2medcosrv0
       - I2B2_DOMAIN_NAME=i2b2medcosrv0
@@ -201,7 +188,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: pg-admin
-    image: medco/pgadmin4:dev
     ports:
       - "81:80"
     networks:
@@ -212,7 +198,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: keycloak
-    image: medco/keycloak:dev
     ports:
       - "8081:8080"
     depends_on:
@@ -225,7 +210,6 @@ services:
     extends:
       file: ../docker-compose-definitions.yml
       service: picsure
-    image: medco/picsure:dev
     ports:
       - "8082:8080"
       - "9992:9990"

diff --git a/compose-profiles/docker-compose-definitions.yml b/compose-profiles/docker-compose-definitions.yml
@@ -1,7 +1,7 @@
 version: '2.4'
 services:
   i2b2:
-    image: medco/i2b2:MedCo-v0.2.0
+    image: medco/i2b2:${I2B2_VERSION:-MedCo-v0.2.1}
     build:
       context: ../docker-images/i2b2
     environment:
@@ -17,7 +17,7 @@ services:
       - AXIS2_LOGLEVEL=INFO
 
   medco-unlynx:
-    image: medco/medco-unlynx:v0.2.0
+    image: medco/medco-unlynx:${MEDCO_UNLYNX_VERSION:-v0.2.1}
     ports:
     - "2000"
     - "2001"
@@ -28,7 +28,7 @@ services:
     - ../configuration-profiles/dev-local-3nodes:/medco-configuration
 
   nginx:
-    image: medco/nginx:MedCo-v0.2.0
+    image: medco/nginx:${NGINX_VERSION:-MedCo-v0.2.1}
     build:
       context: ../docker-images/web
       dockerfile: nginx.Dockerfile
@@ -37,13 +37,14 @@ services:
       - "443"
     environment:
       - HTTP_SCHEME=http
+      - ALL_TIMEOUTS_SECONDS=600
     volumes:
       - ../docker-images/web/www-data:/www-data
       - ../docker-images/web/nginx-conf.d:/etc/nginx/conf.d
       - ../configuration-profiles/dev-local-3nodes/group.toml:/medco-configuration/group.toml
 
   php-fpm:
-    image: medco/php-fpm:MedCo-v0.2.0
+    image: medco/php-fpm:${PHP_FPM_VERSION:-MedCo-v0.2.1}
     build:
       context: ../docker-images/web
       dockerfile: php-fpm.Dockerfile
@@ -69,15 +70,15 @@ services:
     - ../docker-images/postgresql/initdb-data:/docker-entrypoint-initdb.d
 
   pg-admin:
-    image: medco/pgadmin4:MedCo-v0.2.0
+    image: medco/pgadmin4:${PGADMIN_VERSION:-MedCo-v0.2.1}
     build:
       context: ../docker-images/pgadmin
     environment:
       - PGADMIN_DEFAULT_EMAIL=admin
       - PGADMIN_DEFAULT_PASSWORD=admin
 
   keycloak:
-    image: medco/keycloak:MedCo-v0.2.0
+    image: medco/keycloak:${KEYCLOAK_VERSION:-MedCo-v0.2.1}
     build:
       context: ../docker-images/keycloak
     environment:
@@ -91,7 +92,7 @@ services:
       - DB_PASSWORD=keycloak
 
   glowing-bear-medco:
-    image: medco/glowing-bear-medco:v0.2.0
+    image: medco/glowing-bear-medco:${GLOWING_BEAR_MEDCO_VERSION:-v0.2.1}
     ports:
       - "80"
     environment:
@@ -107,7 +108,7 @@ services:
       - MEDCO_NODES_NAME=a,b,c
 
   picsure:
-    image: medco/picsure:MedCo-v0.2.0
+    image: medco/picsure:${PICSURE_VERSION:-MedCo-v0.2.1}
     build:
       context: ../docker-images/picsure
     environment:
@@ -124,23 +125,61 @@ services:
       - MEDCO_NETWORK_NAME=testnetwork
       - MEDCO_NODES_NAME=a,b,c
       - MEDCO_NODES_CONNECTOR_URL=http://medco-connector-srv0:1999/medco-connector/picsure2,http://medco-connector-srv1:1999/medco-connector/picsure2,http://medco-connector-srv2:1999/medco-connector/picsure2
+      - HTTP_CLIENT_TIMEOUT_SECONDS=600
 
   medco-connector:
-    image: medco/medco-connector:v0.2.0
+    image: medco/medco-connector:${MEDCO_CONNECTOR_VERSION:-v0.2.1}
     ports:
       - "1999"
     environment:
+      - SERVER_HTTP_WRITE_TIMEOUT_SECONDS=600
       - I2B2_HIVE_URL=http://i2b2:8080/i2b2/services
       - I2B2_LOGIN_DOMAIN=i2b2medco
       - I2B2_LOGIN_PROJECT=MedCo
       - I2B2_LOGIN_USER=medcouser
       - I2B2_LOGIN_PASSWORD=demouser
+      - I2B2_WAIT_TIME_SECONDS=450
       - LOG_LEVEL=3
       - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
       - UNLYNX_GROUP_FILE_IDX=0
+      - UNLYNX_TIMEOUT_SECONDS=150
       - JWKS_URL=http://keycloak:8080/auth/realms/master/protocol/openid-connect/certs
       - OIDC_JWT_ISSUER=http://localhost/auth/realms/master
       - OIDC_CLIENT_ID=medco
       - OIDC_JWT_USER_ID_CLAIM=preferred_username
+      - MEDCO_OBFUSCATION_MIN=5
     volumes:
       - ../configuration-profiles/dev-local-3nodes:/medco-configuration
+
+  medco-cli-client:
+    image: medco/medco-cli-client:${MEDCO_CONNECTOR_VERSION:-v0.2.1}
+    environment:
+      - LOG_LEVEL=3
+      - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
+      - UNLYNX_GROUP_FILE_IDX=0
+      - OIDC_CLIENT_ID=medco
+      - CLIENT_QUERY_TIMEOUT_SECONDS=660
+      - PICSURE2_API_HOST=localhost
+      - PICSURE2_API_BASE_PATH=/pic-sure-api-2/PICSURE
+      - PICSURE2_API_SCHEME=http
+      - PICSURE2_RESOURCES=MEDCO_testnetwork_0_a,MEDCO_testnetwork_1_b,MEDCO_testnetwork_2_c
+      - OIDC_REQ_TOKEN_URL=http://localhost/auth/realms/master/protocol/openid-connect/token
+    volumes:
+      - ../configuration-profiles/dev-local-3nodes:/medco-configuration
+    network_mode: host
+
+  medco-loader:
+    image: medco/medco-loader:${MEDCO_LOADER_VERSION:-v0.2.1}
+    environment:
+      - LOG_LEVEL=3
+      - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
+      - UNLYNX_GROUP_FILE_IDX=0
+      - DB_HOST=localhost
+      - DB_PORT=5432
+      - DB_NAME=i2b2medco
+      - DB_USER=i2b2
+      - DB_PASSWORD=i2b2
+    volumes:
+      - ../resources/data:/data
+      - ../configuration-profiles/dev-local-3nodes:/medco-configuration
+    network_mode: host
diff --git a/compose-profiles/test-local-3nodes/.env b/compose-profiles/test-local-3nodes/.env
@@ -1,5 +1,5 @@
-MEDCO_NODE_URL=http://localhost
-HTTP_SCHEME=http
+MEDCO_NODE_HOST=localhost
+MEDCO_NODE_HTTP_SCHEME=http
 POSTGRES_PASSWORD=postgres1
 PGADMIN_PASSWORD=admin
 KEYCLOAK_PASSWORD=keycloak

diff --git a/compose-profiles/test-local-3nodes/docker-compose.tools.yml b/compose-profiles/test-local-3nodes/docker-compose.tools.yml
@@ -0,0 +1,45 @@
+version: '2.4'
+services:
+  medco-cli-client:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-cli-client
+    environment:
+      - PICSURE2_API_HOST=${MEDCO_NODE_HOST:?}
+      - PICSURE2_API_SCHEME=${MEDCO_NODE_HTTP_SCHEME:?}
+      - OIDC_REQ_TOKEN_URL=${MEDCO_NODE_HTTP_SCHEME:?}://${MEDCO_NODE_HOST:?}/auth/realms/master/protocol/openid-connect/token
+    volumes:
+      - ../../configuration-profiles/test-local-3nodes:/medco-configuration
+
+  medco-loader-srv0:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-loader
+    environment:
+      - DB_NAME=i2b2medcosrv0
+      - UNLYNX_GROUP_FILE_IDX=0
+      - DB_HOST=${MEDCO_NODE_HOST:?}
+    volumes:
+      - ../../configuration-profiles/test-local-3nodes:/medco-configuration
+
+  medco-loader-srv1:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-loader
+    environment:
+      - DB_NAME=i2b2medcosrv1
+      - UNLYNX_GROUP_FILE_IDX=1
+      - DB_HOST=${MEDCO_NODE_HOST:?}
+    volumes:
+      - ../../configuration-profiles/test-local-3nodes:/medco-configuration
+
+  medco-loader-srv2:
+    extends:
+      file: ../docker-compose-definitions.yml
+      service: medco-loader
+    environment:
+      - DB_NAME=i2b2medcosrv2
+      - UNLYNX_GROUP_FILE_IDX=2
+      - DB_HOST=${MEDCO_NODE_HOST:?}
+    volumes:
+      - ../../configuration-profiles/test-local-3nodes:/medco-configuration