mirror of
https://github.com/samply/bridgehead.git
synced 2026-11-07 22:36:41 +01:00
Skiba, Jan
ca58ba4938
Adds the ITCC blaze data-model validator next to the uploader. It fetches
from the local Blaze over the compose network (BLAZE_URL), while the
resource links in its UI point at the browser-facing route
(PUBLIC_BLAZE_URL = Blaze's traefik /itcc-localdatamanagement mapping) —
the two URLs differ because everything external is relative to ${HOST}.
The UI is exposed like the uploader's: /itcc-validator with basic auth
(auth middleware) and strip-prefix.
110 lines
4.3 KiB
YAML
110 lines
4.3 KiB
YAML
services:
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omics-endpoint:
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image: samply/itcc-omics-ingest:develop
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environment:
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API_KEY: ${GENERATE_API_KEY}
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API_PORT: "6080"
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BEAM_APP_ID_LONG: omics-endpoint.${PROXY_ID}
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BEAM_SECRET: ${FOCUS_BEAM_SECRET_SHORT}
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BEAM_URL: http://beam-proxy:8081
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BLAZE_URL: http://bridgehead-itcc-blaze:8080/fhir/
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BOX_ROOT: /var/lib/itcc-maf-box
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DWH_SOCKET_ID: ${DWH_SOCKET_ID}
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DWH_TASK_ID: ${DWH_TASK_ID}
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SITE_ID: ${SITE_ID}
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ML_API_KEY: ${GENERATE_API_KEY}
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ML_URL: http://bridgehead-patientlist:8080
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UI_PORT: "3000"
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volumes:
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- "omics-maf-box:/var/lib/itcc-maf-box"
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labels:
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- "traefik.http.routers.omics.rule=Host(`${HOST}`) &&
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PathPrefix(`/api/upload`)"
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- "traefik.enable=true"
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- "traefik.http.services.omics.loadbalancer.server.port=6080"
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- "traefik.http.routers.omics.service=omics"
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- "traefik.http.routers.omics.tls=true"
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- "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api"
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- "traefik.http.routers.omics.middlewares=omics-stripprefix"
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- "traefik.http.routers.itcc-uploader.rule=Host(`${HOST}`) && PathPrefix(`/itcc-uploader`)"
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- "traefik.http.routers.itcc-uploader.service=itcc-uploader"
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- "traefik.http.routers.itcc-uploader.tls=true"
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- "traefik.http.services.itcc-uploader.loadbalancer.server.port=3000"
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- "traefik.http.middlewares.itcc-uploader-stripprefix.stripprefix.prefixes=/itcc-uploader"
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- "traefik.http.routers.itcc-uploader.middlewares=auth,itcc-uploader-stripprefix"
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# Validates the local Blaze store against the ITCC core data model and shows
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# the findings under https://${HOST}/itcc-validator. It fetches from Blaze
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# over the compose network, while the resource links in its UI must point at
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# the route the *browser* can reach: Blaze's Traefik route below maps
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# /itcc-localdatamanagement onto the same store (strip-prefix + basic auth),
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# so the two URLs differ and are configured separately.
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blaze-validator:
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image: docker.verbis.dkfz.de/cache/samply/itcc-blaze-validator:develop
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environment:
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# Bare base URL — the validator appends /fhir itself.
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BLAZE_URL: http://bridgehead-itcc-blaze:8080
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PUBLIC_BLAZE_URL: https://${HOST}/itcc-localdatamanagement
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VALIDATOR_PORT: "8091"
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depends_on:
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- "blaze"
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.itcc-validator.rule=Host(`${HOST}`) && PathPrefix(`/itcc-validator`)"
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- "traefik.http.routers.itcc-validator.service=itcc-validator"
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- "traefik.http.routers.itcc-validator.tls=true"
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- "traefik.http.services.itcc-validator.loadbalancer.server.port=8091"
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- "traefik.http.middlewares.itcc-validator-stripprefix.stripprefix.prefixes=/itcc-validator"
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- "traefik.http.routers.itcc-validator.middlewares=auth,itcc-validator-stripprefix"
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patientlist-db:
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image: postgres:${POSTGRES_TAG}
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container_name: bridgehead-patientlist-db
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restart: unless-stopped
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environment:
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POSTGRES_DB: mainzelliste
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POSTGRES_USER: ${ML_DB_USER}
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POSTGRES_PASSWORD: ${PATIENTLIST_POSTGRES_PASSWORD}
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volumes:
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- "patientlist-db-data:/var/lib/postgresql/data"
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U ${ML_DB_USER} -d mainzelliste"]
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interval: 5s
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timeout: 5s
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retries: 10
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start_period: 10s
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patientlist:
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image: medicalinformatics/mainzelliste:latest
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container_name: bridgehead-patientlist
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restart: unless-stopped
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depends_on:
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patientlist-db:
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condition: service_healthy
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environment:
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ML_API_KEY: ${GENERATE_API_KEY}
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ML_DB_HOST: patientlist-db
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ML_DB_PORT: "5432"
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ML_DB_NAME: mainzelliste
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ML_DB_USER: ${ML_DB_USER}
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ML_DB_PASS: ${PATIENTLIST_POSTGRES_PASSWORD}
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ML_DB_DRIVER: org.postgresql.Driver
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ML_DB_TYPE: postgresql
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ML_LOG_LEVEL: INFO
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ML_ALLOWEDREMOTEADDRESSES: "127.0.0.1,::1,172.16.0.0/12"
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secrets:
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- mainzelliste.docker.conf
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- source: symmetric_key
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target: /etc/resources/keys/symmetric_key.json
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volumes:
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omics-maf-box:
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patientlist-db-data:
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secrets:
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mainzelliste.docker.conf:
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file: /etc/bridgehead/mainzelliste/mainzelliste.docker.conf
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symmetric_key:
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file: /var/bridgehead/mainzelliste/keyset_siv.json
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