preparing for quickstart release 18.1(not beta)

i2b2-tranSMART · Dec 16, 2018 · 0d90a4b · 0d90a4b
1 parent b3a9d83
commit 0d90a4b
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Showing 3 changed files with 44 additions and 48 deletions.
diff --git a/.env b/.env
@@ -1,16 +1,5 @@
 ### for all environments ####
 
-# versions
-nginx_version=i2b2tm.release-18.1
-i2b2transmart_version=18.1-beta-17
-db_version=oracle.12.2.0.1-ee-i2b2.1.7.09-tm.release-18.1-v.1.4.1-nhanes
-rserve_version=3.2.1-tm.release-18.1
-solr_version=4.5.0-tm.release-18.1
-i2b2_wildfly_version=1.7.09c-18.1-beta-hotfix
-irct_version=1.4.2c
-irctdb_version=mysql.5.7.22-irct.1.4.2-i2b2-wildfly
-fractalis_version=1.3.1
-
 ## labeling
 STACK_ENV=i2b2tm.release-18.1-beta
 STACK_NAME=quickstart

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,32 +1,17 @@
 version: '3.3'
 services:
 
-  # nginx
-  nginx:
-    image: dbmi/nginx:${nginx_version}
-    labels:
-      - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
-      - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
-    restart: always
-    networks:
-      - public
-    # application stack exposed ports
-    ports:
-      - ${HTTP_PORT:-80}:80
-      - ${HTTPS_PORT:-443}:443
-
   ## i2b2transmart stack ##
   # transmart
   transmart:
-    image: dbmi/i2b2transmart:${i2b2transmart_version}
+    image: dbmi/i2b2transmart:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
     env_file:
       - ${ENV_FILE}
     restart: always
     depends_on:
-      - nginx
       - solr
       - rserve
       - db
@@ -39,7 +24,7 @@ services:
 
   # i2b2transmart database
   db:
-    image: dbmi/i2b2transmart-db:${db_version}
+    image: dbmi/i2b2transmart-db:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -54,7 +39,7 @@ services:
 
   # Rserve
   rserve:
-    image: dbmi/rserve:${rserve_version}
+    image: dbmi/rserve:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -67,7 +52,7 @@ services:
       - public
 
   solr:
-    image: dbmi/solr:${solr_version}
+    image: dbmi/solr:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -81,12 +66,7 @@ services:
 
   ## Fractalis Stack ##
   fractalis:
-    build:
-      context: .
-      dockerfile: Dockerfile-fractalis
-      args:
-        fractalis_version: "${fractalis_version}"
-    image: sherzinger/fractalis:${fractalis_version}-${STACK_NAME}
+    image: dbmi/fractalis:1.3.1-quickstart-hotfix
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -103,16 +83,10 @@ services:
       - irct
       - redis
       - rabbitmq
-      - nginx
       - worker
 
   worker:
-    build:
-      context: .
-      dockerfile: Dockerfile-fractalis
-      args:
-        fractalis_version: "${fractalis_version}"
-    image: sherzinger/fractalis:${fractalis_version}-${STACK_NAME}
+    image: dbmi/fractalis:1.3.1-quickstart-hotfix
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -154,13 +128,12 @@ services:
   ## PIC-SURE API Stack ##
   # IRCT
   irct:
-    image: dbmi/irct:${irct_version}
+    image: dbmi/irct:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
     depends_on:
       - irctdb
-      - nginx
       - i2b2-wildfly
     env_file:
       - ${ENV_FILE}
@@ -172,7 +145,7 @@ services:
 
   # PIC-SURE i2b2-wildfly resource
   i2b2-wildfly:
-    image: dbmi/i2b2-wildfly:${i2b2_wildfly_version}
+    image: dbmi/i2b2-wildfly:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -188,7 +161,7 @@ services:
 
   # IRCT DB
   irctdb:
-    image: dbmi/irct-db:${irctdb_version}
+    image: dbmi/irct-db:18.1-Quickstart
     labels:
       - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
       - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
@@ -206,6 +179,31 @@ services:
     volumes:
       - irct-data:/mysql/data
 
+  nhaneshpds:
+    image: dbmi/pic-sure-hpds-nhanes:18.1-Quickstart
+    labels:
+      - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
+      - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
+    env_file:
+      - ${ENV_FILE}
+    restart: always
+    networks:
+      - public
+    expose:
+      - 8080
+
+  hpdsui:
+    image: dbmi/pic-sure-hpds-ui:18.1-Quickstart
+    restart: always
+    env_file:
+      - ${ENV_FILE}
+    expose:
+      - 80
+    ports:
+      - 80:80
+    networks:
+      - public
+
 volumes:
   # PIC-SURE database
   irct-data:

diff --git a/quickstart.env b/quickstart.env
@@ -27,7 +27,7 @@ HIDE_WORKSPACE=true
 # fractalis
 FRACTALIS_ACTIVE=true
 FRACTALIS_NODE=/fractalis
-FRACTALIS_DATA_SOURCE=https://nginx/rest/v1
+FRACTALIS_DATA_SOURCE=http://hpdsui/rest/v1
 FRACTALIS_RESOURCE_NAME=i2b2-wildfly-default/Demo
 
 # i2b2-wildfly
@@ -57,3 +57,12 @@ [email protected]
 CONTACT_US=[email protected]
 BUG_REPORT_URL=https://jira.transmartfoundation.org/projects/I2B2TM
 USER_GUIDE_URL=http://s3.amazon.com/dbmi-public-docs/i2b2_transmart_userguide.pdf
+
+# HPDS settings
+HEAPSIZE=1024
+CACHESIZE=500
+SMALL_TASK_THREADS=1
+LARGE_TASK_THREADS=1
+SMALL_JOB_LIMIT=100
+ID_BATCH_SIZE=50000
+SURVIVOR_RATIO=255