forked from HBPMedical/algorithm-repository
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docker-compose.yml
92 lines (85 loc) · 3.42 KB
/
docker-compose.yml
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---
version: '2'
services:
db:
image: postgres:9.6.5-alpine
hostname: db
environment:
POSTGRES_PASSWORD: test
wait_dbs:
image: "waisbrot/wait"
restart: "no"
environment:
TARGETS: "db:5432"
TIMEOUT: 60
create_dbs:
image: "hbpmip/create-databases:1.0.0"
restart: "no"
environment:
DB_HOST: db
DB_PORT: 5432
DB_ADMIN_USER: postgres
DB_ADMIN_PASSWORD: test
DB1: features
USER1: features
PASSWORD1: featurespwd
DB2: woken
USER2: woken
PASSWORD2: wokenpwd
depends_on:
- db
sample_data_db_setup:
image: "hbpmip/sample-data-db-setup:0.6.0"
container_name: "data-db-setup"
restart: "no"
environment:
FLYWAY_DBMS: postgresql
FLYWAY_HOST: db
FLYWAY_PORT: 5432
FLYWAY_DATABASE_NAME: features
FLYWAY_USER: postgres
FLYWAY_PASSWORD: test
depends_on:
- db
woken_db_setup:
image: "hbpmip/woken-db-setup:latest"
container_name: "woken-db-setup"
restart: "no"
environment:
FLYWAY_DBMS: postgresql
FLYWAY_HOST: db
FLYWAY_PORT: 5432
FLYWAY_DATABASE_NAME: woken
FLYWAY_USER: postgres
FLYWAY_PASSWORD: test
depends_on:
- db
hedwig:
image: "hbpmip/python-jsi-hedwig:latest"
container_name: "python-jsi-hedwig"
restart: "no"
environment:
FUNCTION: python-jsi-hedwig
NODE: job_test
JOB_ID: 2
IN_DBAPI_DRIVER: postgresql
IN_USER: features
IN_PASSWORD: featurespwd
IN_HOST: db
IN_PORT: 5432
IN_DATABASE: features
OUT_DBAPI_DRIVER: postgresql
OUT_USER: woken
OUT_PASSWORD: wokenpwd
OUT_HOST: db
OUT_PORT: 5432
OUT_DATABASE: woken
PARAM_variables: "alzheimerbroadcategory"
PARAM_covariables: "lefthippocampus,subjectageyears"
PARAM_grouping: ""
PARAM_query: "SELECT lefthippocampus, subjectageyears, alzheimerbroadcategory FROM cde_features_a WHERE lefthippocampus is not null and subjectageyears is not null and alzheimerbroadcategory is not null LIMIT 100"
PARAM_meta: "{\"lefthippocampus\":{\"code\":\"lefthippocampus\",\"type\":\"real\",\"mean\":3.0,\"std\":0.35,\"minValue\":0.1,\"maxValue\":5.0},\"minimentalstate\":{\"code\":\"minimentalstate\",\"type\":\"real\",\"mean\":24.0,\"std\":5.0},\"opticchiasm\":{\"code\":\"opticchiasm\",\"type\":\"real\",\"mean\":0.08,\"std\":0.009},\"subjectage\":{\"code\":\"subjectage\",\"type\":\"real\",\"mean\":71.0,\"std\":8.0}, \"rs17125944_c\": {\"code\": \"rs17125944_c\",\"enumerations\": [{\"code\": 0,\"label\": 0},{\"code\": 1,\"label\": 1},{\"code\": 2,\"label\": 2}],\"sql_type\": \"int\",\"type\": \"polynominal\"}, \"adnicategory\": {\"code\": \"adnicategory\", \"enumerations\": [{\"code\": \"AD\", \"label\": \"Alzheimer's Disease\"}, {\"code\": \"MCI\", \"label\": \"Mild Cognitive Impairment\"}, {\"code\": \"CN\", \"label\": \"Cognitively Normal\"}], \"type\": \"polynominal\"}, \"alzheimerbroadcategory\": {\"code\": \"alzheimerbroadcategory\", \"enumerations\": [{\"code\": \"AD\", \"label\": \"Alzheimer's disease\"}, {\"code\": \"CN\", \"label\": \"Cognitively Normal\"}, {\"code\": \"Other\", \"label\": \"Other\"}], \"type\": \"polynominal\"}, \"subjectageyears\": {\"code\": \"subjectageyears\", \"label\": \"Age Years\", \"maxValue\": 130, \"minValue\": 0, \"type\": \"integer\"}}"
PARAM_MODEL_beam: 5
PARAM_MODEL_support: 0.1
links:
- "db:db"