mirror of
https://github.com/samply/bridgehead.git
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QR basic auth; teiler, exporter, reporter -> min
This commit is contained in:
Enola Knezevic
@ -1,6 +0,0 @@
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# Full Excel Export
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curl --location --request POST 'https://${HOST}/ccp-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}/ccp-reporter/generate?template-id=ccp'
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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-${PLATFORM}-exporter
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environment:
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JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
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LOG_LEVEL: "INFO"
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EXPORTER_API_KEY: "${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: "/${PLATFORM}-exporter"
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SITE: "${SITE_ID}"
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HTTP_SERVLET_REQUEST_SCHEME: "https"
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OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.exporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-exporter`)"
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- "traefik.http.services.exporter_${PLATFORM}.loadbalancer.server.port=8092"
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- "traefik.http.routers.exporter_${PLATFORM}.tls=true"
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- "traefik.http.middlewares.exporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-exporter"
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- "traefik.http.routers.exporter_${PLATFORM}.middlewares=exporter_${PLATFORM}_strip"
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volumes:
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- "/var/cache/bridgehead/${PLATFORM}/exporter-files:/app/exporter-files/output"
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exporter-db:
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image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
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container_name: bridgehead-${PLATFORM}-exporter-db
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environment:
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POSTGRES_USER: "exporter"
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POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
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POSTGRES_DB: "exporter"
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volumes:
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# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
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- "/var/cache/bridgehead/${PLATFORM}/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-${PLATFORM}-reporter
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environment:
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JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
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LOG_LEVEL: "INFO"
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CROSS_ORIGINS: "https://${HOST}"
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HTTP_RELATIVE_PATH: "/${PLATFORM}-reporter"
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SITE: "${SITE_ID}"
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EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
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EXPORTER_URL: "http://exporter:8092"
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LOG_FHIR_VALIDATION: "false"
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HTTP_SERVLET_REQUEST_SCHEME: "https"
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# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
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# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
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# a process that can take several hours, because it depends on the exporter.
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# There is a risk that the bridgehead restarts, losing the already created export.
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volumes:
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- "/var/cache/bridgehead/${PLATFORM}/reporter-files:/app/reports"
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.reporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-reporter`)"
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- "traefik.http.services.reporter_${PLATFORM}.loadbalancer.server.port=8095"
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- "traefik.http.routers.reporter_${PLATFORM}.tls=true"
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- "traefik.http.middlewares.reporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-reporter"
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- "traefik.http.routers.reporter_${PLATFORM}.middlewares=reporter_${PLATFORM}_strip"
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@ -1,8 +0,0 @@
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#!/bin/bash -e
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if [ "$ENABLE_EXPORTER" == true ]; then
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log INFO "Exporter setup detected -- will start Exporter service."
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OVERRIDE+=" -f ./ccp/modules/exporter-compose.yml"
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EXPORTER_DB_PASSWORD="$(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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@ -1,15 +0,0 @@
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# Exporter and Reporter
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## Exporter
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The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
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It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
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## Exporter-DB
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It is a database to save queries for its execution in the exporter.
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The exporter manages also the different executions of the same query in through the database.
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## Reporter
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This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
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It is compatible with different template engines as Groovy, Thymeleaf,...
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It is perfect to generate a document as our traditional CCP quality report.
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@ -1,82 +0,0 @@
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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_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler`)"
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- "traefik.http.services.teiler_orchestrator_${PLATFORM}.loadbalancer.server.port=9000"
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- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.tls=true"
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- "traefik.http.middlewares.teiler_orchestrator_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler"
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- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.middlewares=teiler_orchestrator_${PLATFORM}_strip"
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environment:
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TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
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TEILER_DASHBOARD_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard"
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DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
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HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
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teiler-dashboard:
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#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
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image: docker.verbis.dkfz.de/ccp/samply/teiler-dashboard:bbmri
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container_name: bridgehead-teiler-dashboard
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.teiler_dashboard_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler-dashboard`)"
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- "traefik.http.services.teiler_dashboard_${PLATFORM}.loadbalancer.server.port=80"
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- "traefik.http.routers.teiler_dashboard_${PLATFORM}.tls=true"
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- "traefik.http.middlewares.teiler_dashboard_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler-dashboard"
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- "traefik.http.routers.teiler_dashboard_${PLATFORM}.middlewares=teiler_dashboard_${PLATFORM}_strip"
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environment:
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DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
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TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-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}/${PLATFORM}-teiler"
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TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler-dashboard"
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TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
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TEILER_USER: "${OIDC_USER_GROUP}"
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TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
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REPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}-qb"
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EXPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}"
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teiler-backend:
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image: docker.verbis.dkfz.de/ccp/${PROJECT}-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_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler-backend`)"
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- "traefik.http.services.teiler_backend_${PLATFORM}.loadbalancer.server.port=8085"
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- "traefik.http.routers.teiler_backend_${PLATFORM}.tls=true"
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- "traefik.http.middlewares.teiler_backend_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler-backend"
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- "traefik.http.routers.teiler_backend_${PLATFORM}.middlewares=teiler_backend_${PLATFORM}_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/project-conf"
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TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
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TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PLATFORM}-teiler"
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TEILER_DASHBOARD_DE_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard/de"
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TEILER_DASHBOARD_EN_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard/en"
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CENTRAX_URL: "${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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secrets:
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- project-conf
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secrets:
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project-conf:
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file: "/etc/bridgehead/${PROJECT}.conf"
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@ -1,9 +0,0 @@
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#!/bin/bash -e
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if [ "$ENABLE_TEILER" == true ];then
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log INFO "Teiler setup detected -- will start Teiler services."
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OVERRIDE+=" -f ./ccp/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 "/ccp-teiler/*"
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fi
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@ -1,19 +0,0 @@
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# Teiler
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This module orchestrates the different microfrontends of the bridgehead as a single page application.
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## Teiler Orchestrator
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Single SPA component that consists on the root HTML site of the single page application and a javascript code that
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gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
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resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly.
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The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
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This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
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There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
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## Teiler Dashboard
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It consists on the main dashboard and a set of embedded services.
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### Login
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user and password in ccp.local.conf
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## Teiler Backend
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In this component, the microfrontends are configured.
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