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12 Commits
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Author | SHA1 | Date | |
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0967a691f4 | |||
1cb48c9192 | |||
7b3f605d6c | |||
0b7fc9c14e | |||
8d2104f074 | |||
2d6ee5b898 | |||
9c2185e68a | |||
c6bb44b107 | |||
48a297ecb2 | |||
8a7d766581 | |||
635896b8f4 | |||
b074b865cd |
6
cce/modules/export-and-qb.curl-templates
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6
cce/modules/export-and-qb.curl-templates
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@ -0,0 +1,6 @@
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# Full Excel Export
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curl --location --request POST 'https://${HOST}/cce-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
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--header 'x-api-key: ${EXPORT_API_KEY}'
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# QB
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curl --location --request POST 'https://${HOST}/cce-reporter/generate?template-id=ccp'
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72
cce/modules/exporter-compose.yml
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72
cce/modules/exporter-compose.yml
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@ -0,0 +1,72 @@
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version: "3.7"
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services:
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exporter:
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image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
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container_name: bridgehead-cce-exporter
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environment:
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JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
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LOG_LEVEL: "INFO"
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EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
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CROSS_ORIGINS: "https://${HOST}"
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EXPORTER_DB_USER: "exporter"
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EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
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EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
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HTTP_RELATIVE_PATH: "/cce-exporter"
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SITE: "${SITE_ID}"
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HTTP_SERVLET_REQUEST_SCHEME: "https"
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OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.exporter_cce.rule=PathPrefix(`/cce-exporter`)"
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- "traefik.http.services.exporter_cce.loadbalancer.server.port=8092"
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- "traefik.http.routers.exporter_cce.tls=true"
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- "traefik.http.middlewares.exporter_cce_strip.stripprefix.prefixes=/cce-exporter"
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- "traefik.http.routers.exporter_cce.middlewares=exporter_cce_strip"
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volumes:
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- "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output"
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exporter-db:
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image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
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container_name: bridgehead-cce-exporter-db
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environment:
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POSTGRES_USER: "exporter"
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POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
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POSTGRES_DB: "exporter"
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volumes:
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# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
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- "/var/cache/bridgehead/cce/exporter-db:/var/lib/postgresql/data"
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reporter:
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image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
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container_name: bridgehead-cce-reporter
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environment:
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JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
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LOG_LEVEL: "INFO"
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CROSS_ORIGINS: "https://${HOST}"
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HTTP_RELATIVE_PATH: "/cce-reporter"
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SITE: "${SITE_ID}"
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EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
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EXPORTER_URL: "http://exporter:8092"
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LOG_FHIR_VALIDATION: "false"
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HTTP_SERVLET_REQUEST_SCHEME: "https"
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# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
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# However, in the first executions in the CCE sites, this volume seems to be very important. A report is
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# a process that can take several hours, because it depends on the exporter.
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# There is a risk that the bridgehead restarts, losing the already created export.
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volumes:
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- "/var/cache/bridgehead/cce/reporter-files:/app/reports"
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.reporter_cce.rule=PathPrefix(`/cce-reporter`)"
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- "traefik.http.services.reporter_cce.loadbalancer.server.port=8095"
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- "traefik.http.routers.reporter_cce.tls=true"
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- "traefik.http.middlewares.reporter_cce_strip.stripprefix.prefixes=/cce-reporter"
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- "traefik.http.routers.reporter_cce.middlewares=reporter_cce_strip"
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focus:
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environment:
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EXPORTER_URL: "http://exporter:8092"
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EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
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8
cce/modules/exporter-setup.sh
Normal file
8
cce/modules/exporter-setup.sh
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@ -0,0 +1,8 @@
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#!/bin/bash -e
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if [ "$ENABLE_EXPORTER" == true ]; then
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log INFO "Exporter setup detected -- will start Exporter service."
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OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
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EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
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EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
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fi
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89
cce/modules/teiler-compose.yml
Normal file
89
cce/modules/teiler-compose.yml
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@ -0,0 +1,89 @@
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version: "3.7"
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services:
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teiler-orchestrator:
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image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
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container_name: bridgehead-teiler-orchestrator
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.teiler_orchestrator_cce.rule=PathPrefix(`/cce-teiler`)"
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- "traefik.http.services.teiler_orchestrator_cce.loadbalancer.server.port=9000"
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- "traefik.http.routers.teiler_orchestrator_cce.tls=true"
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- "traefik.http.middlewares.teiler_orchestrator_cce_strip.stripprefix.prefixes=/cce-teiler"
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- "traefik.http.routers.teiler_orchestrator_cce.middlewares=teiler_orchestrator_cce_strip"
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environment:
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TEILER_BACKEND_URL: "https://${HOST}/cce-teiler-backend"
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TEILER_DASHBOARD_URL: "https://${HOST}/cce-teiler-dashboard"
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DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
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HTTP_RELATIVE_PATH: "/cce-teiler"
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teiler-dashboard:
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image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
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container_name: bridgehead-teiler-dashboard
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.teiler_dashboard_cce.rule=PathPrefix(`/cce-teiler-dashboard`)"
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- "traefik.http.services.teiler_dashboard_cce.loadbalancer.server.port=80"
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- "traefik.http.routers.teiler_dashboard_cce.tls=true"
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- "traefik.http.middlewares.teiler_dashboard_cce_strip.stripprefix.prefixes=/cce-teiler-dashboard"
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- "traefik.http.routers.teiler_dashboard_cce.middlewares=teiler_dashboard_cce_strip"
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environment:
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DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
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TEILER_BACKEND_URL: "https://${HOST}/cce-teiler-backend"
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OIDC_URL: "${OIDC_URL}"
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OIDC_REALM: "${OIDC_REALM}"
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OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
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OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
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TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
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TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
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TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
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TEILER_PROJECT: "${PROJECT}"
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EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
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TEILER_ORCHESTRATOR_URL: "https://${HOST}/cce-teiler"
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TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/cce-teiler-dashboard"
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TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
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TEILER_USER: "${OIDC_USER_GROUP}"
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TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
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REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
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EXPORTER_DEFAULT_TEMPLATE_ID: "cce"
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teiler-backend:
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image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
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container_name: bridgehead-teiler-backend
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.teiler_backend_cce.rule=PathPrefix(`/cce-teiler-backend`)"
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- "traefik.http.services.teiler_backend_cce.loadbalancer.server.port=8085"
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- "traefik.http.routers.teiler_backend_cce.tls=true"
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- "traefik.http.middlewares.teiler_backend_cce_strip.stripprefix.prefixes=/cce-teiler-backend"
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- "traefik.http.routers.teiler_backend_cce.middlewares=teiler_backend_cce_strip"
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environment:
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LOG_LEVEL: "INFO"
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APPLICATION_PORT: "8085"
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APPLICATION_ADDRESS: "${HOST}"
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DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
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CONFIG_ENV_VAR_PATH: "/run/secrets/cce.conf"
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TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
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TEILER_ORCHESTRATOR_URL: "https://${HOST}/cce-teiler"
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TEILER_DASHBOARD_DE_URL: "https://${HOST}/cce-teiler-dashboard/de"
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TEILER_DASHBOARD_EN_URL: "https://${HOST}/cce-teiler-dashboard/en"
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CENTRAX_URL: "${CENTRAXX_URL}"
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HTTP_PROXY: "http://forward_proxy:3128"
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ENABLE_MTBA: "${ENABLE_MTBA}"
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ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
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TEILER_APP16_BACKENDURL: "https://${HOST}/cce-exporter"
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TEILER_APP17_BACKENDURL: "https://${HOST}/cce-exporter"
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TEILER_APP18_BACKENDURL: "https://${HOST}/cce-exporter"
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TEILER_APP35_BACKENDURL: "https://${HOST}/cce-exporter"
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TEILER_APP36_BACKENDURL: "https://${HOST}/cce-exporter"
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TEILER_APP26_BACKENDURL: "https://${HOST}/cce-reporter"
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secrets:
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- cce.conf
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secrets:
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cce.conf:
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file: /etc/bridgehead/cce.conf
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9
cce/modules/teiler-setup.sh
Normal file
9
cce/modules/teiler-setup.sh
Normal file
@ -0,0 +1,9 @@
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#!/bin/bash -e
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if [ "$ENABLE_TEILER" == true ];then
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log INFO "Teiler setup detected -- will start Teiler services."
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OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
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TEILER_DEFAULT_LANGUAGE=DE
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TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
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add_public_oidc_redirect_url "/cce-teiler/*"
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fi
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12
cce/vars
12
cce/vars
@ -7,6 +7,18 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
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PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
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BROKER_URL_FOR_PREREQ=$BROKER_URL
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POSTGRES_TAG=15.6-alpine
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OIDC_USER_GROUP="CCE_$(capitalize_first_letter ${SITE_ID})"
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OIDC_ADMIN_GROUP="CCE_$(capitalize_first_letter ${SITE_ID})_Verwalter"
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OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
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OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
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# Use "test-realm-01" for testing
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OIDC_REALM="${OIDC_REALM:-test-realm-01}"
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OIDC_URL="https://login.verbis.dkfz.de"
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OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
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OIDC_GROUP_CLAIM="groups"
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for module in $PROJECT/modules/*.sh
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do
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log DEBUG "sourcing $module"
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