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docker-compose.yml
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name: ${PROJECT_NAME:-d2e}
networks:
alp:
data:
volumes:
caddy:
cachedb-data-1:
cdw-config-cachedb-data-1:
minio-data-1:
pg-minerva-data-1:
r-libs:
trex:
fhir-schema-file-1:
demodb-data:
x-envs:
db-svc: &x-dbsvc
DB_SVC__IDP_SUBJECT_PROP: sub
DB_SVC__LOG_LEVEL: info
DB_SVC__PATH: /alpdb
DISABLE_SSL: "TRUE"
HANA__READ_ROLE: TENANT_READ_ROLE
LB__LOG_LEVEL: ${LB__LOG_LEVEL:-FINE}
PG__READ_ROLE: postgres_tenant_read_role
env_converter: &x-converter
DB_CREDENTIALS_MGR__API_URL: http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/db-credentials/db/
DB_CREDENTIALS__PRIVATE_KEY: ${DB_CREDENTIALS__INTERNAL__DECRYPT_PRIVATE_KEY}
IDP__ALP_SVC__CLIENT_ID: ${LOGTO__ALP_SVC__CLIENT_ID}
IDP__ALP_SVC__CLIENT_SECRET: ${LOGTO__ALP_SVC__CLIENT_SECRET}
IDP__SCOPE: https://alp-default
IDP_SUBJECT_PROP: sub
minio: &x-minio
MINIO__ACCESS_KEY: ${MINIO__ACCESS_KEY:-root}
MINIO__ENDPOINT: ${MINIO__ENDPOINT:-${PROJECT_NAME:-d2e}-minerva-s3}
MINIO__PORT: ${MINIO__PORT:-9000}
MINIO__REGION: ${MINIO__REGION:-ap-southeast-1}
MINIO__SECRET_KEY: ${MINIO__SECRET_KEY}
MINIO__SSL: ${MINIO__SSL:-false}
pg: &x-pg
PG__DB_NAME: alp
## Flag to display executed Knex queries in log
PG__DEBUG: ${PG_DEBUG:-1}
PG__HOST: ${PG_HOST:-${PROJECT_NAME:-d2e}-minerva-postgres-1}
PG__MAX_POOL: 10
PG__MIN_POOL: 0
PG__PORT: ${PG_PORT:-5432}
PG__IDLE_TIMEOUT_IN_MS: 1000
PG__DIALECT: postgresql
fhir: &x-fhir
FHIR__CLIENT_ID: db6b2304-f236-45ec-b10c-a852681e7129
FHIR__CLIENT_SECRET: ${FHIR__CLIENT_SECRET}
perseus: &x-perseus
PERSEUS__FILES_MANAGER_HOST: trex
redis: &x-redis
REDIS_HOST: ${REDIS_HOST:-${PROJECT_NAME:-d2e}-minerva-redis-1}
REDIS_PORT: ${REDIS_PORT:-6379}
service: &x-routes
SERVICE_ROUTES: |-
{
"analytics": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"bookmark": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/analytics-svc/api/services/bookmark",
"cdw": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"paConfig": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/pa-config-svc",
"d2e-webapi": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/webapi",
"queryGen": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"jobplugins": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"portalServer": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/system-portal",
"dataflowMgmt": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"dbCredentialsMgr": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/db-credentials",
"usermgmt": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/usermgmt/api",
"terminology": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/terminology",
"prefect": "http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api",
"idIssuerUrl": "http://${PROJECT_NAME:-d2e}-logto-1:3001/oidc",
"minio": "",
"fhir": "http://${PROJECT_NAME:-d2e}-minerva-fhir-server-1:8103/fhir/R4",
"fhirTokenUrl": "http://${PROJECT_NAME:-d2e}-minerva-fhir-server-1:8103/oauth2/token",
"dicomServer": "http://${PROJECT_NAME:-d2e}-dicom-server:8042",
"fhirSvc": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/gateway/api/fhir",
"trex": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001"
}
# "https://${PROJECT_NAME:-d2e}-minerva-portal-server-1.${TLS__INTERNAL__DOMAIN:-alp.local}:41105",
tls: &x-tls
TLS__INTERNAL__CA_CRT: ${TLS__INTERNAL__CA_CRT}
TLS__INTERNAL__CRT: ${TLS__INTERNAL__CRT}
TLS__INTERNAL__DOMAIN: ${TLS__INTERNAL__DOMAIN:-alp.local}
TLS__INTERNAL__KEY: ${TLS__INTERNAL__KEY}
cachedb: &cachedb
CACHEDB__HOST: ${PROJECT_NAME:-d2e}-cachedb
CACHEDB__PORT: 41191
CACHEDB__POOL_SIZE: ${CACHEDB__POOL_SIZE:-10}
python-internal-ssl: &python-internal-ssl
PYTHON_VERIFY_SSL: false # Only use this for apis calling internal docker urls
services:
trex:
container_name: &c84 ${PROJECT_NAME:-d2e}-trex
init: true
command: npm run start
depends_on:
alp-minerva-pg-mgmt-init:
condition: service_completed_successfully
alp-logto-post-init:
condition: service_completed_successfully
alp-minio-post-init:
condition: service_completed_successfully
hostname: ${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/d2e-trex-base:${DOCKER_TREX_TAG_NAME:-develop}
pull_policy: ${TREX_PULL_POLICY:-missing}
platform: linux/amd64
logging:
options:
tag: *c84
networks:
alp:
priority: 20
data:
priority: 10
volumes:
- trex:/usr/src/data
healthcheck:
interval: 60s
retries: 30
start_period: 60s
test:
- CMD
- npm
- run
- health
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
environment:
<<:
- *x-converter
- *x-tls
- *x-fhir
- *x-minio
- *x-pg
REP_PG: postgres://postgres:mypass@broadsea-atlasdb:5432/postgres
SERVICE_ENV: |-
{
"_shared": {
"DB_SVC__IDP_SUBJECT_PROP": "sub",
"DB_SVC__LOG_LEVEL": "info",
"DB_SVC__PATH": "/alpdb",
"DISABLE_SSL": "TRUE",
"HANA__READ_ROLE": "TENANT_READ_ROLE",
"LB__LOG_LEVEL": "${LB__LOG_LEVEL:-FINE}",
"PG__READ_ROLE": "postgres_tenant_read_role",
"DB_CREDENTIALS_MGR__API_URL": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/db-credentials/db/",
"IDP__ALP_SVC__CLIENT_ID": "${LOGTO__ALP_SVC__CLIENT_ID}",
"IDP__ALP_SVC__CLIENT_SECRET": "${LOGTO__ALP_SVC__CLIENT_SECRET}",
"IDP__SCOPE": "https://alp-default",
"IDP_SUBJECT_PROP": "sub",
"MINIO__ACCESS_KEY": "${MINIO__ACCESS_KEY:-root}",
"MINIO__ENDPOINT": "${MINIO__ENDPOINT:-${PROJECT_NAME:-d2e}-minerva-s3}",
"MINIO__PORT": ${MINIO__PORT:-9000},
"MINIO__REGION": "${MINIO__REGION:-ap-southeast-1}",
"MINIO__SECRET_KEY": "${MINIO__SECRET_KEY}",
"MINIO__SSL": "${MINIO__SSL:-false}",
"CACHEDB__PORT": 41191,
"CACHEDB__HOST": "${PROJECT_NAME:-d2e}-cachedb",
"CACHEDB__POOL_SIZE": "${CACHEDB__POOL_SIZE:-10}",
"NODE_ENV": "${NODE_ENV:-development}",
"PG__DB_NAME": "alp",
"PG__DEBUG": "${PG_DEBUG:-1}",
"PG__HOST": "${PG_HOST:-${PROJECT_NAME:-d2e}-minerva-postgres-1}",
"PG__MAX_POOL": 10,
"PG__MIN_POOL": 0,
"PG__PORT": ${PG_PORT:-5432},
"PG__IDLE_TIMEOUT_IN_MS": 1000,
"PG__DIALECT": "postgresql",
"LOCAL_DEBUG": "false",
"isHttpTestRun": "${isHttpTestRun}",
"SERVICE_ROUTES": {
"analytics": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"bookmark": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/analytics-svc/api/services/bookmark",
"cdw": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"paConfig": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/pa-config-svc",
"trex": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"queryGen": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"dataflowMgmt": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/dataflow-mgmt",
"jobplugins": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"portalServer": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/system-portal",
"dataset": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/gateway/api/dataset",
"dbCredentialsMgr": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/db-credentials",
"usermgmt": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/usermgmt/api",
"terminology": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/terminology",
"prefect": "http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api",
"idIssuerUrl": "http://${PROJECT_NAME:-d2e}-logto-1:3001/oidc",
"minio": "",
"fhir": "http://${PROJECT_NAME:-d2e}-minerva-fhir-server-1:8103/fhir/R4",
"fhirTokenUrl": "http://${PROJECT_NAME:-d2e}-minerva-fhir-server-1:8103/oauth2/token",
"fhirSvc": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/gateway/api/fhir",
"alpdb": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/gateway/api/db",
"dicomServer": "http://${PROJECT_NAME:-d2e}-dicom-server:8042",
"logto": "http://${PROJECT_NAME:-d2e}-logto-1:3001"
}
},
"analytics-svc": {
"ALP_GATEWAY_OAUTH__URL": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/oauth/token",
"ALP__SYSTEM_ID": "${ALP__SYSTEM_ID:-alp-research}",
"ANALYTICS_SVC__DEFAULT_ASSIGNMENT_NAME": "PUBLIC-CHART_DEFAULT-ASSIGNMENT",
"ANALYTICS_SVC__PORT": 41102,
"ANALYTICS_SVC__STUDIES_METADATA__TTL_IN_SECONDS": 600,
"SQL_RETURN_ON": "${SQL_RETURN_ON:-false}",
"DUCKDB__DATA_FOLDER": "/home/docker/src/alp-data-node/app/duckdb_data",
"LOCAL_DEBUG": "false",
"USE_DUCKDB": "${USE_DUCKDB:-true}",
"USE_CACHEDB": "${USE_CACHEDB:-true}",
"USE_HANA_JWT_AUTHC": "${USE_HANA_JWT_AUTHC:-false}",
"USE_EXTENSION_FOR_COHORT_CREATION": "false",
"isTestEnv": "${isTestEnv}",
"local": "${local}",
"TESTSCHEMA": "${TESTSCHEMA}",
"ANALYTICS_PATIENT_LIST_BATCH_SIZE": "${ANALYTICS_PATIENT_LIST_BATCH_SIZE:-1000}"
},
"mri-pg-config": {
"PG_ADMIN_PASSWORD": "${PG_ADMIN_PASSWORD}",
"PG_ADMIN_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG_PASSWORD": "${PG_WRITE_PASSWORD}",
"PG_SCHEMA": "cdw_config",
"PG_USER": "${PG_WRITE_USER:-alp_pg_write_user}"
},
"alp-db-credentials": {
"PG__DB_CREDENTIALS_MGR__MANAGE_PASSWORD": "${PG_ADMIN_PASSWORD}",
"PG__DB_CREDENTIALS_MGR__MANAGE_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG__DB_CREDENTIALS_MGR__PASSWORD": "${PG_WRITE_PASSWORD}",
"PG__DB_CREDENTIALS_MGR__SCHEMA": "db_credentials_mgr",
"PG__DB_CREDENTIALS_MGR__USER": "${PG_WRITE_USER:-alp_pg_write_user}",
"DB_CREDENTIALS_MGR__VOCAB_SCHEMAS": ${DB_CREDENTIALS_MGR__VOCAB_SCHEMAS:-{ "postgres": ["cdmvocab"], "hana": ["CDMVOCAB"] }},
"DATABASE_CREDENTIALS": ${DATABASE_CREDENTIALS:-{}}
},
"alp-fhir-svc": {
"FHIR__LOG_LEVEL": "debug",
"PORT": 41112,
"FHIR__CLIENT_ID": "db6b2304-f236-45ec-b10c-a852681e7129",
"FHIR__CLIENT_SECRET": "${FHIR__CLIENT_SECRET}",
"FHIR_SCHEMA_PATH": "/home/docker/fhir",
"FHIR_SCHEMA_FILE_NAME": "fhir.schema.json",
"ALP_GATEWAY_OAUTH__URL": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/oauth/token",
"IDP__ALP_DATA_CLIENT_ID": "${LOGTO__ALP_DATA__CLIENT_ID}",
"IDP__ALP_DATA__CLIENT_SECRET": "${LOGTO__ALP_DATA__CLIENT_SECRET}"
},
"alp-fhir-init": {
"PG_SUPER_PASSWORD": "${PG_SUPER_PASSWORD}",
"PG_SUPER_USER": "${PG_SUPER_USER:-postgres}",
"FHIR__LOG_LEVEL": "debug",
"PORT": 41112,
"FHIR__CLIENT_ID": "db6b2304-f236-45ec-b10c-a852681e7129",
"FHIR__CLIENT_SECRET": "${FHIR__CLIENT_SECRET}",
"DUCKDB_PATH": "/home/docker/alp-data-node/app/src/duckdb",
"PLUGIN_PATH": "/usr/src/plugins/d2ef/alp-fhir-init",
"IDP__ALP_DATA_CLIENT_ID": "${LOGTO__ALP_DATA__CLIENT_ID}",
"IDP__ALP_DATA__CLIENT_SECRET": "${LOGTO__ALP_DATA__CLIENT_SECRET}",
"ALP_GATEWAY_OAUTH__URL": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/oauth/token"
},
"query-gen-svc": {
"SQL_RETURN_ON": "${SQL_RETURN_ON:-false}",
"isTestEnv": "${isTestEnv}",
"TESTSCHEMA": "${TESTSCHEMA}",
"NOT_EQ_CHECK_FILTERCARDS": "${NOT_EQ_CHECK_FILTERCARDS:-true}"
},
"alp-usermgmt": {
"ALP__SYSTEM_NAME": "${ALP__SYSTEM_NAME:-Research System}",
"APP__TENANT_ID": "${APP__TENANT_ID:-e0348e4d-2e17-43f2-a3c6-efd752d17c23}",
"IDP__ALP_ADMIN__CLIENT_ID": "${LOGTO_API_M2M_CLIENT_ID}",
"IDP__ALP_ADMIN__CLIENT_SECRET": "${LOGTO_API_M2M_CLIENT_SECRET}",
"IDP__ALP_ADMIN__RESOURCE": "https://default.logto.app/api",
"IDP__BASE_URL": "http://${PROJECT_NAME:-d2e}-logto-1:3001",
"IDP__FETCH_USER_INFO_TYPE": "logto",
"IDP__INITIAL_USER__NAME": "${IDP__INITIAL_USER__NAME:-admin}",
"IDP__INITIAL_USER__UUID": "a6660e40-261e-4782-873e-f76b4328aecf",
"IDP__RELYING_PARTY": "${IDP__RELYING_PARTY}",
"NIFI_MGMT__BASE_URL": "http://${PROJECT_NAME:-d2e}-minerva-nifi-mgmt-svc-1:4444/alp-nifi-api/",
"PG__USER_MGMT__ADMIN_PASSWORD": "${PG_ADMIN_PASSWORD}",
"PG__USER_MGMT__ADMIN_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG__USER_MGMT__DB_NAME": "${PG_DB_NAME:-alp}",
"PG__USER_MGMT__PASSWORD": "${PG_WRITE_PASSWORD}",
"PG__USER_MGMT__SCHEMA": "usermgmt",
"PG__USER_MGMT__USER": "${PG_WRITE_USER:-alp_pg_write_user}",
"USER_MGMT__IDP_SUBJECT_PROP": "sub",
"USER_MGMT__LOG_LEVEL": "info",
"USER_MGMT__PATH": "/usermgmt/",
"USER_MGMT__PORT": 41104
},
"bookmark-svc": {
"PG_USER": "${PG_WRITE_USER:-alp_pg_write_user}",
"PG_PASSWORD": "${PG_WRITE_PASSWORD}"
},
"mri-pa-config": {
"PG_ADMIN_PASSWORD": "${PG_ADMIN_PASSWORD}",
"PG_ADMIN_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG_PASSWORD": "${PG_WRITE_PASSWORD}",
"PG_SCHEMA": "cdw_config",
"PG_USER": "${PG_WRITE_USER:-alp_pg_write_user}"
},
"cdw-svc": {
"PG_PASSWORD": "${PG_WRITE_PASSWORD}",
"PG_SCHEMA": "cdw_config",
"PG_USER": "${PG_WRITE_USER:-alp_pg_write_user}",
"PORT": 41114,
"USE_CACHEDB": "${USE_CACHEDB:-true}",
"USE_DUCKDB": "${USE_DUCKDB:-true}",
"isTestEnv": "${isTestEnv}",
"DUCKDB_PATH": "/home/docker/src/services/app/src/duckdb",
"BUILT_IN_DUCKDB_PATH": "/home/docker/src/services/app/src/duckdb"
},
"jobplugins": {
"PREFECT_API_URL": "http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api",
"PG_USER": "${PG_WRITE_USER:-alp_pg_write_user}",
"PG_PASSWORD": "${PG_WRITE_PASSWORD}",
"PG_ADMIN_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG_ADMIN_PASSWORD": "${PG_ADMIN_PASSWORD}",
"IDP__ALP_DATA_CLIENT_ID": "${LOGTO__ALP_DATA__CLIENT_ID}",
"IDP__ALP_DATA__CLIENT_SECRET": "${LOGTO__ALP_DATA__CLIENT_SECRET}"
},
"dataset": {
"GATEWAY_WO_PROTOCOL_FQDN": "${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}"
},
"alpdb": {},
"concept-mapping": {},
"portal": {
"PG_MANAGE_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG_MANAGE_PASSWORD": "${PG_ADMIN_PASSWORD}",
"PG_USER": "${PG_WRITE_USER:-alp_pg_write_user}",
"PG_PASSWORD": "${PG_WRITE_PASSWORD}",
"PG_SCHEMA": "portal",
"PG_HOST": "${PG_HOST:-${PROJECT_NAME:-d2e}-minerva-postgres-1}",
"PG_PORT": "${PG_PORT:-5432}",
"PG_DATABASE": "${PG_DB_NAME:-alp}",
"APP__TENANT_ID": "${APP__TENANT_ID:-e0348e4d-2e17-43f2-a3c6-efd752d17c23}",
"APP__TENANT_NAME": "${APP__TENANT_NAME:-Tenant}",
"ALP__SYSTEM_NAME": "${ALP__SYSTEM_NAME:-Research System}"
},
"files-manager": {
"PG_ADMIN_PASSWORD": "${PG_ADMIN_PASSWORD}",
"PG_ADMIN_USER": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"PG_SCHEMA": "files_manager"
},
"terminology-svc": {},
"code-suggestion": {
"COGNITO_CLIENT_ID": "${COGNITO_CLIENT_ID:-null}",
"COGNITO_CLIENT_SECRET": "${COGNITO_CLIENT_SECRET:-null}",
"COGNITO_TOKEN_ENDPOINT": "${COGNITO_TOKEN_ENDPOINT:-null}",
"LAMBDA_API_ENDPOINT": "${LAMBDA_API_ENDPOINT:-null}"
},
"demo": {
"DEMO__DB_CODE": "demo_database",
"DEMO__DB_CDM_SCHEMA": "demo_cdm",
"DEMO__DB_DEFAULT": "{ \"name\": \"postgres\", \"dialect\": \"postgres\", \"host\": \"broadsea-atlasdb\", \"port\": 5432, \"extra\": { \"Internal\": { \"statementTimeout\": 60000, \"queryTimeout\": 60000, \"idleTimeoutMillis\": 300000, \"idleInTransactionSessionTimeout\": 300000, \"max\": 50 } }, \"credentials\": [] }",
"DEMO__DB_USER": "${DEMO__DB_USER:-postgres}",
"DEMO__DB_PASSWORD": "${DEMO__DB_PASSWORD:-mypass}",
"DEMO__DATASET": "{ \"tokenStudyCode\": \"demo\", \"type\": \"demo\", \"tenantId\": \"${APP__TENANT_ID:-e0348e4d-2e17-43f2-a3c6-efd752d17c23}\", \"schemaOption\": \"existing_cdm\", \"dialect\": \"postgres\", \"dataModel\": \"omop5-4\", \"plugin\": \"omop_cdm_plugin\", \"paConfigId\": \"4fce3cb7-32bf-4b46-8cba-32e4f77a14dd\", \"visibilityStatus\": \"DEFAULT\", \"detail\": { \"name\": \"Demo dataset\", \"summary\": \"Demo dataset\", \"description\": \"Demo dataset\", \"showRequestAccess\": false }, \"dashboards\": [], \"attributes\": [], \"tags\": [] }"
},
"d2e-webapi": {}
}
SERVICE_ROUTES: |-
{
"analytics": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"bookmark": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/analytics-svc/api/services/bookmark",
"cdw": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"paConfig": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/pa-config-svc",
"trex": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"queryGen": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001",
"dataflowMgmt": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/dataflow-mgmt",
"dbCredentialsMgr": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/db-credentials",
"portalServer": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/system-portal",
"usermgmt": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/usermgmt/api",
"terminology": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/terminology",
"prefect": "http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api",
"idIssuerUrl": "http://${PROJECT_NAME:-d2e}-logto-1:3001/oidc",
"minio": "",
"fhir": "http://${PROJECT_NAME:-d2e}-minerva-fhir-server-1:8103/fhir/R4",
"fhirTokenUrl": "http://${PROJECT_NAME:-d2e}-minerva-fhir-server-1:8103/oauth2/token",
"alpdb": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/gateway/api/db",
"dicomServer": "http://${PROJECT_NAME:-d2e}-dicom-server:8042",
"logto": "http://${PROJECT_NAME:-d2e}-logto-1:3001",
"fhirSvc": "http://${PROJECT_NAME:-d2e}-trex.${TLS__INTERNAL__DOMAIN:-alp.local}:33001/gateway/api/fhir"
}
PG_SUPER_PASSWORD: ${PG_SUPER_PASSWORD}
PG_SUPER_USER: ${PG_SUPER_USER:-postgres}
PG_MANAGE_PASSWORD: ${PG_ADMIN_PASSWORD}
PG_MANAGE_USER: ${PG_ADMIN_USER:-alp_pg_admin_user}
PG_PASSWORD: ${PG_WRITE_PASSWORD}
PG_USER: ${PG_WRITE_USER:-alp_pg_write_user}
PREFECT_API_URL: http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api
DB_CREDENTIALS__PUBLIC_KEYS: |-
{
"DataPlatform": "",
"Internal": "${DB_CREDENTIALS__INTERNAL__PUBLIC_KEY}"
}
DB_CREDENTIALS__PRIVATE_KEY: ${DB_CREDENTIALS__INTERNAL__DECRYPT_PRIVATE_KEY}
GATEWAY__IDP_AUTH_TYPE: logto
GATEWAY__IDP_SUBJECT_PROP: sub
GATEWAY__WO_PROTOCOL_FQDN: ${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}
CADDY__ALP__PUBLIC_FQDN: ${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}
IDP__ALP_DATA_CLIENT_ID: ${LOGTO__ALP_DATA__CLIENT_ID}
IDP__ALP_SVC_CLIENT_ID: ${LOGTO__ALP_SVC__CLIENT_ID}
IDP__RELYING_PARTY: ${IDP__RELYING_PARTY}
LOGTO__AUDIENCES: https://alp-default
LOGTO__CLIENT_ID: ${LOGTO__ALP_APP__CLIENT_ID}
LOGTO__CLIENT_SECRET: ${LOGTO__ALP_APP__CLIENT_SECRET}
LOGTO__ISSUER: http://${PROJECT_NAME:-d2e}-logto-1:3001/oidc
LOGTO__RESOURCE_API: https://alp-default
LOGTO__SCOPE: openid offline_access profile email
LOGTO__SVC_CLIENT_ID: ${LOGTO__ALP_SVC__CLIENT_ID}
LOGTO__SVC_CLIENT_SECRET: ${LOGTO__ALP_SVC__CLIENT_SECRET}
LOGTO__TOKEN_URL: http://${PROJECT_NAME:-d2e}-logto-1:3001/oidc/token
NODE_ENV: development
PREFECT_DOCKER_VOLUMES: '["${PROJECT_NAME:-d2e}_cachedb-data-1:/app/duckdb_data", "${PROJECT_NAME:-d2e}_cdw-config-cachedb-data-1:/app/cdw-config/duckdb_data", "${PROJECT_NAME:-d2e}_r-libs:/home/docker/plugins/R/site-library", "${PROJECT_NAME:-d2e}_fhir-schema-file-1:/home/docker/fhir"]'
GH_TOKEN: ${GH_TOKEN}
PLUGINS_SEED: '["d2e-functions", "d2e-ui", "d2e-flows"]'
PLUGINS_API_VERSION: ${PLUGINS_API_VERSION:-latest}
PLUGINS_SEED_UPDATE: ${PLUGINS_SEED_UPDATE:-false}
alp-minerva-pg-mgmt-init:
container_name: &c15 ${PROJECT_NAME:-d2e}-minerva-pg-mgmt-init-1
depends_on:
alp-minerva-postgres:
condition: service_healthy
hostname: ${PROJECT_NAME:-d2e}-minerva-pg-mgmt-init-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/d2e-pg-mgmt-init:${DOCKER_TAG_NAME:-develop}
logging:
options:
tag: *c15
networks:
alp:
priority: 20
environment:
<<:
- *x-tls
NODE_ENV: development
ALP_DB_LOGLEVEL: ${ALP_DB_LOGLEVEL:-info}
POSTGRES_CONNECTION_CONFIG: |-
{
"connectionTimeoutMillis": 60000,
"database": "${PG_DB_NAME:-alp}",
"host": "${PG_HOST:-${PROJECT_NAME:-d2e}-minerva-postgres-1}",
"idle_in_transaction_session_timeout": 60000,
"password": "${PG_SUPER_PASSWORD}",
"port": "${PG_PORT:-5432}",
"query_timeout": 60000,
"statement_timeout": 60000,
"user": "${PG_SUPER_USER:-postgres}"
}
POSTGRES_MANAGE_CONFIG: |-
{
"databases": {
"+${PG_DB_NAME:-alp}": {
"schemas": {
"+cdw_config": {},
"+dataflow": {},
"+db_credentials_mgr": {},
"+portal": {},
"+public": {},
"+qe_config": {},
"+terminology": {},
"+usermgmt": {},
"+files_manager": {},
"+perseus": {},
"+white_rabbit": {},
"+trex": {}
}
}
}
}
POSTGRES_MANAGE_USERS: |-
{
"${PG_DB_NAME:-alp}": {
"manager": "${PG_ADMIN_USER:-alp_pg_admin_user}",
"managerPassword": "${PG_ADMIN_PASSWORD}",
"reader": "${PG_WRITE_USER:-alp_pg_write_user}",
"readerPassword": "${PG_WRITE_PASSWORD}",
"writer": "${PG_WRITE_USER:-alp_pg_write_user}",
"writerPassword": "${PG_WRITE_PASSWORD}"
}
}
POSTGRES_SUPERUSER: ${PG_SUPER_USER:-postgres}
POSTGRES_SUPERUSER_PASSWORD: ${PG_SUPER_PASSWORD}
PORT: 41110
sqlOnly: false
alp-caddy:
command: caddy run --environ --config /srv/caddy-config/Caddyfile --adapter caddyfile
container_name: &c1 ${PROJECT_NAME:-d2e}-caddy
hostname: ${PROJECT_NAME:-d2e}-caddy.${TLS__INTERNAL__DOMAIN:-alp.local}
image: caddy:2.8-alpine
logging:
options:
tag: *c1
networks:
alp:
priority: 20
platform: linux/amd64
ports:
- ${CADDY_PORT:-${PORT:-443}}:443
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
volumes:
- caddy:/data
- ${CADDY__CONFIG:-./deploy/caddy-config}:/srv/caddy-config
environment:
CADDY__ALP__PUBLIC_FQDN: ${CADDY__ALP__PUBLIC_FQDN:-localhost}:443
TLS__CADDY_DIRECTIVE: ${TLS__CADDY_DIRECTIVE:-tls internal}
INSTANCE_SPECIFIC_CONFIG: ${INSTANCE_SPECIFIC_CONFIG:-}
CADDY__ALP__ALIAS_PUBLIC_FQDN: ${CADDY__ALP__ALIAS_PUBLIC_FQDN:-}
PROJECT_NAME: ${PROJECT_NAME:-d2e}
alp-dataflow-gen:
command:
- sh
- -c
- "apt-get update && apt-get install -y curl && prefect server start"
container_name: &c2 ${PROJECT_NAME:-d2e}-dataflow-gen-1
depends_on:
trex:
condition: service_healthy
alp-logto-post-init:
condition: service_completed_successfully
healthcheck:
interval: 30s
retries: 30
start_period: 30s
test:
- CMD
- curl
- -f
- http://localhost:41120/api/health
timeout: 30s
hostname: ${PROJECT_NAME:-d2e}-dataflow-gen-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: prefecthq/prefect:3.0.3-python3.11
logging:
options:
tag: *c2
networks:
alp:
priority: 20
data:
priority: 10
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
environment:
<<:
- *x-converter
- *x-pg
- *x-tls
LOCAL_DEBUG: "false"
PREFECT_API_DATABASE_CONNECTION_URL: postgresql+asyncpg://${PG_SUPER_USER:-postgres}:${PG_SUPER_PASSWORD}@${PG_HOST:-${PROJECT_NAME:-d2e}-minerva-postgres-1}:${PG_PORT:-5432}/${PG_DB_NAME:-alp}
PREFECT_API_DEFAULT_LIMIT: 5000
PREFECT_API_URL: http://0.0.0.0:41120/api
PREFECT_LOGGING_LEVEL: DEBUG
PREFECT_LOGGING_SERVER_LEVEL: WARNING
PREFECT_SERVER_ANALYTICS_ENABLED: "false"
PREFECT_SERVER_API_HOST: 0.0.0.0
PREFECT_UI_STATIC_DIRECTORY: /app/ui-files
PREFECT_SERVER_API_PORT: 41120
PREFECT_API_ENABLE_HTTP2: False
alp-dataflow-gen-worker:
command:
- sh
- -c
- "apt-get update && apt-get install -y curl && pip install prefect[docker]==3.0.3 && python3 ../../create_workpool_json.py && prefect work-pool create 'docker-pool' --type docker --base-job-template ./custom-docker-workpool.json --overwrite; prefect worker start --pool 'docker-pool' --type docker --name prefect-docker-worker"
container_name: &c83 ${PROJECT_NAME:-d2e}-dataflow-gen-worker
depends_on:
alp-minio-post-init:
condition: service_completed_successfully
trex:
condition: service_healthy
alp-logto-post-init:
condition: service_completed_successfully
alp-dataflow-gen-init:
condition: service_completed_successfully
alp-dataflow-gen:
condition: service_healthy
healthcheck:
interval: 30s
retries: 30
start_period: 30s
test:
- CMD
- curl
- -f
- http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api/health
timeout: 30s
hostname: ${PROJECT_NAME:-d2e}-dataflow-gen-worker.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/d2e-dataflow-gen:${DOCKER_TAG_NAME:-develop}
logging:
options:
tag: *c83
networks:
data:
priority: 20
volumes:
- /var/run/docker.sock:/var/run/docker.sock
environment:
PREFECT_API_URL: http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api
PREFECT_API_ENABLE_HTTP2: False
D2E_MEMORY_LIMIT: ${D2E_MEMORY_LIMIT:-16G}
D2E_SWAP_LIMIT: ${D2E_SWAP_LIMIT:-64G}
DOCKER_REGISTRY_USERNAME: ${GH_USERNAME:-tech-user-pull}
DOCKER_REGISTRY_PASSWORD: ${GH_TOKEN}
DOCKER_REGISTRY_URL: ${DOCKER_REGISTRY_URL:-ghcr.io}
alp-dataflow-gen-init:
command:
- sh
- -c
- "yarn generate:envs -s alp-minerva-db-mgmt-svc && . ../generated-env.sh && python ../init.py"
container_name: &c4 ${PROJECT_NAME:-d2e}-dataflow-gen-init-1
depends_on:
alp-dataflow-gen:
condition: service_healthy
trex:
condition: service_healthy
alp-minio-post-init:
condition: service_completed_successfully
hostname: ${PROJECT_NAME:-d2e}-dataflow-gen-init-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/d2e-dataflow-gen:${DOCKER_TAG_NAME:-develop}
logging:
options:
tag: *c4
networks:
alp:
priority: 20
platform: linux/amd64
environment:
<<:
- *x-minio
- *x-tls
- *x-dbsvc
- *x-converter
- *x-routes
- *cachedb
- *python-internal-ssl
NODE_ENV: development
DATAFLOW_MGMT__FLOWS__RESULTS_SB_NAME: flow-results
DATAFLOW_MGMT__FLOWS__RESULTS__S3_DIR_PATH: s3://flows/results
PREFECT_API_URL: http://${PROJECT_NAME:-d2e}-dataflow-gen-1:41120/api
R_LIBS_USER: /home/docker/plugins/R/site-library
DUCKDB__DATA_FOLDER: /app/duckdb_data
CDW_CONFIG_DUCKDB__DATA_FOLDER: /app/cdw-config/duckdb_data
ALP__SYSTEM_ID: ${ALP__SYSTEM_ID:-alp-research}
OHDSI__R_COHORT_GENERATOR_MODULE_SETTINGS_URL: https://raw.githubusercontent.com/OHDSI/CohortGeneratorModule/v0.3.0/SettingsFunctions.R
OHDSI__R_COHORT_DIAGNOSTICS_MODULE_SETTINGS_URL: https://raw.githubusercontent.com/OHDSI/CohortDiagnosticsModule/v0.2.0/SettingsFunctions.R
STRATEGUS__KEYRING_PASSWORD: ${STRATEGUS__KEYRING_PASSWORD}
IDP__ALP_DATA__CLIENT_ID: ${LOGTO__ALP_DATA__CLIENT_ID}
IDP__ALP_DATA__CLIENT_SECRET: ${LOGTO__ALP_DATA__CLIENT_SECRET}
FHIR_SCHEMA_JSON_PATH: /home/docker/fhir
ACHILLES_THREAD_COUNT: ${ACHILLES_THREAD_COUNT:-5}
# Needed only for future alterations of schema when version upgrades
# alp-logto-db-post-alterations-init:
# depends_on:
# alp-minerva-postgres:
# condition: service_healthy
# image: ghcr.io/logto-io/logto:1.12
# entrypoint: ["sh", "-c", "npm run alteration deploy latest"]
# environment:
# CI: true
# DB_URL: postgres://${PG_SUPER_USER:-postgres}:${PG_SUPER_PASSWORD}@alp-minerva-postgres-1:${PG_PORT:-5432}/${PG_DB_NAME:-postgres}
# networks:
# - alp
alp-logto-post-init:
container_name: ${PROJECT_NAME:-d2e}-logto-post-init-1
depends_on:
alp-logto:
condition: service_healthy
image: ghcr.io/data2evidence/d2e-logto-post-init:${DOCKER_TAG_NAME:-develop}
networks:
alp:
priority: 20
environment:
ENV_TYPE: ${ENV_TYPE:-local}
PG__DB_NAME: logto
PG__HOST: ${PG_HOST:-${PROJECT_NAME:-d2e}-minerva-postgres-1}
PG__PASSWORD: ${PG_SUPER_PASSWORD}
PG__PORT: ${PG_PORT:-5432}
PG__USER: ${PG_SUPER_USER:-postgres}
# LOGTO__CUSTOM_JWT: '{"script": "/**\n* This function is called during the access token generation process to get custom claims for the JWT token.\n* Limit custom claims to under 50KB.\n*\n* @param {Object} payload - The input payload of the function.\n* @param {AccessTokenPayload} payload.token -The JWT token.\n* @param {Context} payload.context - Logto internal data that can be used to pass additional information\n* @param {EnvironmentVariables} [payload.environmentVariables] - The environment variables.\n*\n* @returns The custom claims.\n*/\n\n// @ts-ignore\nconst getCustomJwtClaims = async ({ token, context, environmentVariables, extra }) => {\n return { ...extra };\n}", "tokenSample": {"aud": "http://localhost:3000/api/test", "gty": "authorization_code", "jti": "f1d3d2d1-1f2d-3d4e-5d6f-7d8a9d0e1d2", "kind": "AccessToken", "scope": "read write", "grantId": "grant_123", "clientId": "my_app", "accountId": "uid_123"}, "contextSample": {"user": {"id": "123", "name": "Foo Bar", "roles": [], "avatar": "https://example.com/avatar.png", "profile": {}, "username": "foo", "customData": {}, "identities": {}, "hasPassword": false, "primaryEmail": "[email protected]", "primaryPhone": "+1234567890", "applicationId": "my-app", "organizations": [], "ssoIdentities": [], "organizationRoles": [], "mfaVerificationFactors": []}}}'
LOGTO__CLIENT_APPS: '[{"name":"alp-svc","description":"alp-svc","type":"MachineToMachine", "id": "${LOGTO__ALP_SVC__CLIENT_ID}", "secret": "${LOGTO__ALP_SVC__CLIENT_SECRET}"},{"name":"alp-data","description":"alp-data","type":"MachineToMachine", "id": "${LOGTO__ALP_DATA__CLIENT_ID}", "secret": "${LOGTO__ALP_DATA__CLIENT_SECRET}"},{"name":"alp-app","description":"alp-app","type":"Traditional", "id": "${LOGTO__ALP_APP__CLIENT_ID}", "secret": "${LOGTO__ALP_APP__CLIENT_SECRET}", "oidcClientMetadata":{"redirectUris":["https://${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}/portal/login-callback","https://localhost:4000/portal/login-callback","https://localhost:8081"],"postLogoutRedirectUris":["https://${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}/portal","https://localhost:4000/portal","https://localhost:8081"]},"customClientMetadata":{"corsAllowedOrigins":[],"refreshTokenTtlInDays":14,"alwaysIssueRefreshToken":true,"rotateRefreshToken":true}}]'
LOGTO__RESOURCE: '{"name":"alp-default","indicator":"https://alp-default","accessTokenTtl":3600}'
LOGTO__USER: '{"username":"admin","initialPassword":"Updatepassword12345"}'
LOGTO__ROLES: '[{"name":"role.systemadmin","description":"ALP System admin","type":"User"},{"name":"role.useradmin","description":"ALP User admin","type":"User"},{"name":"role.tenantviewer","description":"ALP Tenant viewer","type":"User"},{"name":"role.dashboardviewer","description":"ALP Dashboard viewer","type":"User"}]'
LOGTO__SCOPES: '[{"name":"role.systemadmin","description":"ALP System admin"},{"name":"role.useradmin","description":"ALP User admin"},{"name":"role.tenantviewer","description":"ALP Tenant viewer"},{"name":"role.dashboardviewer","description":"ALP Dashboard viewer"}]'
LOGTO__ADMIN_SERVER__FQDN_URL: "http://${PROJECT_NAME:-d2e}-logto-1:3002"
LOGTO__CLIENTID_PASSWORD__BASIC_AUTH: ${LOGTO__CLIENTID_PASSWORD__BASIC_AUTH}
LOGTO__ALP_ADMIN_APP: '{"application": {"id": "${LOGTO_API_M2M_CLIENT_ID}", "name":"alp-admin","description":"alp-admin", "secret": "${LOGTO_API_M2M_CLIENT_SECRET}"}, "role": { "name":"api-access","description":"Logto API access"}}'
CADDY__ALP__PUBLIC_FQDN: ${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}
alp-logto:
container_name: &c8 ${PROJECT_NAME:-d2e}-logto-1
depends_on:
alp-minerva-pg-mgmt-init:
condition: service_completed_successfully
healthcheck:
interval: 20s
retries: 30
start_period: 120s
test:
- CMD
- wget
- -O
- logto.status
- http://localhost:3001/api/status
hostname: ${PROJECT_NAME:-d2e}-logto-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/d2e-logto:${DOCKER_TAG_NAME:-develop}
logging:
options:
tag: *c8
networks:
alp:
priority: 20
data:
priority: 10
# Enable if need to access admin console
# ports:
# - 3002:3002
entrypoint:
- sh
- -c
- npm run cli db seed -- --swe && npx @logto/cli db alteration deploy 1.18.0 && npm start
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
environment:
<<:
- *x-tls
ADMIN_DISABLE_LOCALHOST: ${LOGTO__DISABLE_ADMIN_CONSOLE:-false}
# ADMIN_ENDPOINT: http://${CADDY__ALP__PUBLIC_FQDN:-localhost}:3002 # Enable if need to access admin console
DB_URL: postgres://postgres:${PG_SUPER_PASSWORD}@${PROJECT_NAME:-d2e}-minerva-postgres-1:${PG_PORT:-5432}/logto
ENDPOINT: https://${CADDY__ALP__PUBLIC_FQDN:-localhost}${PORT:+:${PORT:-443}}
LOGTO_API_M2M_CLIENT_ID: ${LOGTO_API_M2M_CLIENT_ID}
LOGTO_API_M2M_CLIENT_SECRET: ${LOGTO_API_M2M_CLIENT_SECRET}
LOGTO_ROLES_AZ_GROUPS_MAPPING: ${LOGTO_ROLES_AZ_GROUPS_MAPPING:-{"role.systemadmin":"37b5364a-348c-494f-b67f-a59a40e52ab7","role.useradmin":"90597adc-92af-4649-8151-68c3b7feb66c","role.tenantviewer":"50a3b140-21eb-46dd-9d81-61a77cbc81f5","role.dashboardviewer":"50a3b140-21eb-46dd-9d81-61a77cbc81f5"}}
NODE_ENV: test
PROJECT_NAME: ${PROJECT_NAME:-d2e}
PORT: 3001
TRUST_PROXY_HEADER: true
alp-minerva-postgres:
container_name: &c17 ${PROJECT_NAME:-d2e}-minerva-postgres-1
healthcheck:
interval: 20s
retries: 30
start_period: 60s
test:
- CMD-SHELL
- pg_isready
- -d
- ${POSTGRES_DB}
timeout: 30s
hostname: ${PROJECT_NAME:-d2e}-minerva-postgres-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: postgres:15-alpine
logging:
options:
tag: *c17
networks:
alp:
priority: 20
data:
priority: 10
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
shm_size: 1gb
volumes:
- pg-minerva-data-1:/var/lib/postgresql/data
- ./cache/pgbackup:/backup
environment:
<<:
- *x-tls
POSTGRES_DB: ${PG_DB_NAME:-alp}
POSTGRES_PASSWORD: ${PG_SUPER_PASSWORD}
alp-minerva-s3:
command:
- server
- /data
- --console-address
- :9090
container_name: &c19 ${PROJECT_NAME:-d2e}-minerva-s3
healthcheck:
interval: 20s
retries: 30
start_period: 60s
test:
- CMD
- curl
- -I
- http://${PROJECT_NAME:-d2e}-minerva-s3:9000/minio/health/live
timeout: 30s
hostname: ${PROJECT_NAME:-d2e}-minerva-s3.${TLS__INTERNAL__DOMAIN:-alp.local}
image: minio/minio:RELEASE.2023-10-25T06-33-25Z
logging:
options:
tag: *c19
networks:
alp:
priority: 20
data:
priority: 10
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
volumes:
- minio-data-1:/data
environment:
<<:
- *x-tls
MINIO_ROOT_PASSWORD: ${MINIO__SECRET_KEY}
MINIO_ROOT_USER: ${MINIO__ACCESS_KEY:-root}
alp-minio-post-init:
container_name: &c23 ${PROJECT_NAME:-d2e}-minio-post-init
depends_on:
alp-minerva-s3:
condition: service_healthy
hostname: ${PROJECT_NAME:-d2e}-minio-post-init.${TLS__INTERNAL__DOMAIN:-alp.local}
image: minio/mc
logging:
options:
tag: *c23
networks:
alp:
priority: 20
entrypoint: |
/bin/sh -c " /usr/bin/mc config host add myminio http://${PROJECT_NAME:-d2e}-minerva-s3:9000 ${MINIO__ACCESS_KEY:-root} ${MINIO__SECRET_KEY};
/usr/bin/mc mb -p myminio/dataflow-adhoc-flows;
/usr/bin/mc mb -p myminio/flows/results;
/usr/bin/mc mb -p myminio/dicom-images;
/usr/bin/mc policy download myminio/dataflow-adhoc-flows;
exit 0;
"
alp-cachedb:
container_name: &c30 ${PROJECT_NAME:-d2e}-cachedb
hostname: ${PROJECT_NAME:-d2e}-cachedb.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/d2e-cachedb:${DOCKER_TAG_NAME:-develop}
platform: linux/amd64
depends_on:
trex:
condition: service_healthy
alp-logto-post-init:
condition: service_completed_successfully
alp-minerva-pg-mgmt-init:
condition: service_completed_successfully
healthcheck:
interval: 20s
retries: 5
start_period: 120s
test: ["CMD", "python", "src/utils/healthcheck.py", "41191"]
timeout: 10s
logging:
options:
tag: *c30
networks:
alp:
priority: 20
data:
priority: 10
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
volumes:
- cachedb-data-1:/home/docker/duckdb_data
- cdw-config-cachedb-data-1:/home/docker/cdw_svc/duckdb_data # Volume for dynamically generated cdw-config duckdb file (refer to docs/3-configure/9-create-cdw-config-duckdb-file.md for information)
- fhir-schema-file-1:/home/docker/fhir
environment:
<<:
- *x-converter
- *x-routes
- *x-tls
- *cachedb
- *python-internal-ssl
DUCKDB__DATA_FOLDER: /home/docker/duckdb_data
CDW_SVC_DUCKDB_DATA_FOLDER: /home/docker/cdw_svc/duckdb_data
CDW_SVC_BUILT_IN_DUCKDB_DATA_FOLDER: /home/docker/cdw_svc/built_in_duckdb_data
DUCKDB_EXTENSIONS_FOLDER: /home/docker/duckdb_extensions
IDP__ALP_DATA_CLIENT_ID: ${LOGTO__ALP_DATA__CLIENT_ID}
LOCAL_DEBUG: "false"
deploy:
resources:
limits:
cpus: ${D2E_CPU_LIMIT:-2}
memory: ${D2E_MEMORY_LIMIT:-7G}
alp-perseus-backend:
image: ghcr.io/data2evidence/d2e-perseus:master
container_name: &c35 ${PROJECT_NAME:-d2e}-perseus-backend-1
environment:
<<:
- *x-pg
- *x-perseus
PERSEUS_ENV: Docker
PG_ADMIN_PASSWORD: ${PG_ADMIN_PASSWORD}
PG_ADMIN_USER: ${PG_ADMIN_USER:-alp_pg_admin_user}
depends_on:
alp-minerva-postgres:
condition: service_healthy
alp-minerva-pg-mgmt-init:
condition: service_completed_successfully
networks:
alp:
priority: 20
platform: linux/amd64
profiles: [perseus]
alp-perseus-white-rabbit:
image: ghcr.io/data2evidence/whiterabbit:master
container_name: &c36 ${PROJECT_NAME:-d2e}-perseus-white-rabbit-1
platform: linux/amd64
environment:
<<:
- *x-pg
- *x-perseus
SPRING_PROFILES_ACTIVE: docker
PG_ADMIN_PASSWORD: ${PG_ADMIN_PASSWORD}
PG_ADMIN_USER: ${PG_ADMIN_USER:-alp_pg_admin_user}
depends_on:
alp-minerva-postgres:
condition: service_healthy
alp-minerva-pg-mgmt-init:
condition: service_completed_successfully
networks:
alp:
priority: 20
entrypoint: ["sh", "-c", "./init.sh"]
profiles: [perseus]
demodb:
image: ohdsi/broadsea-atlasdb:2.0.0
container_name: ${PROJECT_NAME:-d2e}-demodb
mem_limit: "2G"
environment:
- POSTGRES_PASSWORD=mypass
networks:
alp:
priority: 20
data:
priority: 10
volumes:
- demodb-data:/var/lib/postgresql/data
- ./deploy/broadsea-atlas/cohort_patch.sql:/cohort_patch.sql
healthcheck:
test: ["CMD-SHELL", "pg_isready -U postgres"]
interval: 5s
timeout: 5s
retries: 10
profiles: [demodb]
redis:
command: redis-server --requirepass ${REDIS_PASSWORD}
container_name: &c26 ${PROJECT_NAME:-d2e}-minerva-redis-1
healthcheck:
interval: 20s
retries: 10
start_period: 60s
timeout: 30s
test: redis-cli --no-auth-warning -a ${REDIS_PASSWORD} ping | grep PONG
hostname: ${PROJECT_NAME:-d2e}-minerva-redis-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: redis:7
logging:
options:
tag: *c26
networks:
alp:
priority: 20
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
profiles: [fhir]
fhir-server:
container_name: &c6 ${PROJECT_NAME:-d2e}-minerva-fhir-server-1
depends_on:
trex:
condition: service_healthy
redis:
condition: service_healthy
healthcheck:
interval: 20s
retries: 5
start_period: 120s
test:
- CMD
- wget
- -O
- fhir.status
- http://localhost:8103/healthcheck
hostname: ${PROJECT_NAME:-d2e}-minerva-fhir-server-1.${TLS__INTERNAL__DOMAIN:-alp.local}
image: ghcr.io/data2evidence/fhir-server:${DOCKER_TAG_NAME:-develop}
logging:
options:
tag: *c6
networks:
alp:
priority: 20
restart: ${DOCKER__RESTART_POLICY:-unless-stopped}
volumes:
- fhir-schema-file-1:/home/docker/app/medplum/packages/definitions/dist/fhir/r4
environment:
<<:
- *x-pg
- *x-redis
- *x-fhir
PG_SUPER_PASSWORD: ${PG_SUPER_PASSWORD}