i2b2transmart 1.0-GA deprecated

.env

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+### for all environments ####
+
+# versions
+nginx_version=i2b2tm.release-18.1
+i2b2transmart_version=release-18.1-beta-5
+db_version=oracle.12.2.0.1-ee-i2b2.1.7.09-tm.release-18.1-v.1.3-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=1.4.2
+irctdb_version=mysql.5.7.22-irct.1.4.2-i2b2-nhanes
+fractalis_version=0.6.0
+
+## labeling
+STACK_ENV=i2b2tm.release-18.1-beta
+STACK_NAME=quick-start
+
+COMPOSE_PROJECT_NAME=quickstart
+
+## container environment variables
+# loads these values into the container
+ENV_FILE=quick_start.env

README.md

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+# i2b2/tranSMART release-18.1 Quick-Start
+
+_Database is pre-populated with the NHANES public dataset_
+
+## Docker Host Hardware Requirements
+
+-   8GB RAM
+-   128GB Hard Drive
+-   [Docker for Mac](https://docs.docker.com/docker-for-mac) and [Docker for Windows](https://docs.docker.com/docker-for-windows/) are not supported
+
+## Docker Network Requirements
+
+-   HTTP (80) and HTTPS (443) ports (default)
+-   Edit `.env` file to assign different ports
+
+```bash
+HTTP_PORT=
+HTTPS_PORT=
+```
+
+## Compatible Docker Versions
+
+    Docker: 17.06.2+
+    docker-compose: 1.14.0+
+
+## Current Service Versions
+
+    nginx:          i2b2tm.release-18.1
+    i2b2transmart:  release-18.1-beta-5
+    database:       oracle.12.2.0.1-ee-i2b2.1.7.09-tm.release-18.1-v.1.3-nhanes
+    rserve:         3.2.1-tm.release-18.1
+    solr:           4.5.0-tm.release-18.1
+    i2b2-wildfly:   1.7.09c-18.1-beta-hotfix
+    fractalis:      0.4.2
+    irct:           1.4.2
+    irct database:  mysql.5.7.22-irct.1.4.2-i2b2-nhanes
+
+## Deploy
+
+```bash
+$ cd deployments/i2b2transmart/release-18.1/quick-start
+
+# images take several minutes to download
+$ docker-compose pull
+
+# NOTE: if you are running docker-compose version 1.21.0+
+# and the pull command fails, try:
+# $ docker-compose pull --no-parallel
+
+# deploy database *first deploy only*
+# database may hang here for a few minutes
+$ export COMPOSE_HTTP_TIMEOUT=300
+$ docker-compose up -d db
+
+# verify database is up and running *first deploy only*
+$ docker-compose logs -f db
+# db_1            |#########################
+# db_1            | DATABASE IS READY TO USE!
+# db_1            | #########################
+
+# deploy i2b2/tranSMART + fractalis
+$ docker-compose up -d
+```
+
+## Test i2b2/tranSMART release-18.1
+
+1.  Browse to your docker machine IP
+2.  i2b2/tranSMART, by default, uses self-signed certificates. If the browser complains about security, 'click OK' to allow for security exception.
+3.  Default username and passwords are used, e.g. admin/admin
+
+## Troubleshoot
+
+Biggest point of failure is deploying the database for the first time. Due to its size and resource requirements, your Docker client may timeout during first deployment of the database.
+
+Docker is transferring the data from the Docker database image to the named volume `quickstart_i2b2transmart-db`. Notice, by running `docker system df` the total volume size increase:
+
+```bash
+TYPE          TOTAL         ACTIVE        SIZE          RECLAIMABLE
+Local Volumes 11            2             25.24GB       25.24GB (100%)
+```
+
+If you run into a timeout error:
+
+```bash
+ERROR: for quickstart_db_1  HTTPSConnectionPool(host='xxxx', port=2376): Read timed out. (read timeout=60)
+```
+
+Wait for data transfer to complete and the client to re-sync with the docker machine (~100s). Resume the deployment by running `docker-compose up -d db` again.

config/fractalis/config.py

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+SECRET_KEY = 'OVERWRITE ME IN PRODUCTION!!!'
+REDIS_HOST = 'redis'
+BROKER_URL = 'amqp://guest:guest@rabbitmq:5672//'
+CELERY_RESULT_BACKEND = 'redis://redis:6379'
+ETL_VERIFY_SSL_CERT = False

docker-compose.yml

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+version: '3.3'
+services:
+
+  # nginx
+  nginx:
+    image: dbmi/nginx:${nginx_version}
+    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}
+    env_file:
+      - ${ENV_FILE}
+    restart: always
+    depends_on:
+      - nginx
+      - solr
+      - rserve
+      - db
+    volumes:
+      - rserve-jobs:/tmp:rw
+    networks:
+      - public
+    expose:
+      - 8080
+
+  # i2b2transmart database
+  db:
+    image: dbmi/i2b2transmart-db:${db_version}
+    networks:
+      - public
+    expose:
+      - 1521
+    # i2b2transmart database exposed port
+    ports:
+      - ${DOCKER_DB_PORT:-1521}:1521
+    volumes:
+      - i2b2transmart-data:/opt/oracle/oradata:rw
+
+  # Rserve
+  rserve:
+    image: dbmi/rserve:${rserve_version}
+    labels:
+      - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
+      - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
+    restart: always
+    expose:
+      - 6311
+    volumes:
+      - rserve-jobs:/tmp:rw
+    networks:
+      - public
+
+  # solr
+  solr:
+    image: dbmi/solr:${solr_version}
+    labels:
+      - "edu.hms.harvard.dbmi.stack.name=${STACK_NAME}"
+      - "edu.hms.harvard.dbmi.stack.env=${STACK_ENV}"
+    env_file:
+      - ${ENV_FILE}
+    restart: always
+    networks:
+      - public
+    expose:
+      - 8983
+
+  ## Fractalis Stack ##
+  fractalis:
+    image: sherzinger/fractalis:${fractalis_version}
+    volumes:
+        - ./config/fractalis/config.py:/config.py
+    environment:
+        - FRACTALIS_CONFIG=/config.py
+    command: gunicorn -w 3 -b :5000 --log-file - --access-logfile - fractalis:app
+    networks:
+        - public
+    expose:
+        - 5000
+    depends_on:
+        - irct
+        - redis
+        - rabbitmq
+        - nginx
+        - worker
+
+  worker:
+    image: sherzinger/fractalis:${fractalis_version}
+    volumes:
+        - ./config/fractalis/config.py:/config.py
+    environment:
+        - FRACTALIS_CONFIG=/config.py
+    command: celery worker -A fractalis:celery -l info --autoscale 16,4
+    networks:
+        - public
+    depends_on:
+        - redis
+        - rabbitmq
+
+  redis:
+    image: redis:alpine
+    command: >
+            sh -c "redis-server
+            && redis-cli CONFIG SET maxmemory 4gb
+            && redis-cli CONFIG SET maxmemory-policy allkeys-lru"
+    networks:
+        - public
+
+  rabbitmq:
+    image: rabbitmq:alpine
+    networks:
+        - public
+
+  ## PIC-SURE API Stack ##
+  # IRCT
+  irct:
+    image: dbmi/irct:${irct_version}
+    depends_on:
+        - irctdb
+        - nginx
+        - i2b2-wildfly
+    env_file:
+        - ${ENV_FILE}
+    restart: always
+
+    networks:
+      - public
+    expose:
+        - 8080
+
+  # PIC-SURE i2b2-wildfly resource
+  i2b2-wildfly:
+    image: dbmi/i2b2-wildfly:${i2b2_wildfly_version}
+    env_file:
+      - ${ENV_FILE}
+    restart: always
+    networks:
+      - public
+    expose:
+      - 9090
+
+  # IRCT DB
+  irctdb:
+    image: dbmi/irct-db:${irctdb_version}
+    env_file:
+        - ${ENV_FILE}
+    restart: always
+    command: --datadir=/mysql/data
+    networks:
+      - public
+    expose:
+        - 3306
+    # PIC-SURE database exposed port
+    ports:
+        - ${DOCKER_IRCT_DB_PORT:-3306}:3306
+    volumes:
+        - irct-data:/mysql/data
+
+
+volumes:
+  # PIC-SURE database
+  irct-data:
+  # i2b2/tranSMART database
+  i2b2transmart-data:
+  # shared volume for R jobs
+  rserve-jobs:
+
+networks:
+  public:

quick_start.env

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+# i2b2transmart database
+DB_HOST=db
+DB_USER=BIOMART_USER
+BIOMART_USER=biomart_user
+DB_PORT=1521
+DB_DB=ORCLPDB1
+
+# fractalis
+FRACTALIS_ACTIVE=true
+FRACTALIS_NODE=/fractalis
+FRACTALIS_DATA_SOURCE=https://nginx
+FRACTALIS_RESOURCE_NAME=i2b2-wildfly-nhanes/Demo
+
+# i2b2-wildfly
+I2B2HIVE=demouser
+I2B2DEMODATA=demouser
+I2B2METADATA=demouser
+I2B2PM=demouser
+I2B2WORKDATA=demouser
+
+# required for JWT tokens between i2b2/tranSMART <-> PIC-SURE
+CLIENT_SECRET=dummysecret
+CLIENT_ID=dummyid
+
+# pic-sure
+IRCTMYSQLADDRESS=irctdb
+IRCT_DB_PORT=3306
+IRCT_DB_CONNECTION_USER=root
+IRCTMYSQLPASS=password
+# use aud (audience) claim in JWT token
+IRCT_USER_FIELD=aud