diff --git a/README.md b/README.md index bc3e1db..b8ccb73 100644 --- a/README.md +++ b/README.md @@ -399,6 +399,7 @@ The Exporter is a dedicated service for extracting and exporting Bridgehead data ```bash ENABLE_EXPORTER=true +``` #### Data Quality Report To assess the quality and plausibility of your imported data, the Reporter component is pre-configured to generate Excel reports with data quality metrics and statistical analyses. Reporter is part of the Exporter and can be enabled by setting the same environment variable in your `.conf` file: diff --git a/bbmri/modules/exporter.md b/bbmri/modules/exporter.md deleted file mode 100644 index 24e81b0..0000000 --- a/bbmri/modules/exporter.md +++ /dev/null @@ -1,15 +0,0 @@ -# Exporter and Reporter - - -## Exporter -The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables. -It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal. - -## Exporter-DB -It is a database to save queries for its execution in the exporter. -The exporter manages also the different executions of the same query in through the database. - -## Reporter -This component is a plugin of the exporter that allows to create more complex Excel reports described in templates. -It is compatible with different template engines as Groovy, Thymeleaf,... -It is perfect to generate a document as our traditional CCP quality report. diff --git a/bbmri/modules/teiler-compose.yml b/bbmri/modules/teiler-compose.yml index 417bc00..33274a2 100644 --- a/bbmri/modules/teiler-compose.yml +++ b/bbmri/modules/teiler-compose.yml @@ -13,8 +13,8 @@ services: - "traefik.http.middlewares.teiler_orchestrator_bbmri_strip.stripprefix.prefixes=/bbmri-teiler" - "traefik.http.routers.teiler_orchestrator_bbmri.middlewares=teiler_orchestrator_bbmri_strip" environment: - TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard" + TEILER_BACKEND_URL: "/bbmri-teiler-backend" + TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}" HTTP_RELATIVE_PATH: "/bbmri-teiler" @@ -30,20 +30,15 @@ services: - "traefik.http.routers.teiler_dashboard_bbmri.middlewares=teiler_dashboard_bbmri_strip" environment: DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" - TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard" - OIDC_URL: "${OIDC_URL}" - OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" - OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}" + TEILER_BACKEND_URL: "/bbmri-teiler-backend" + TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard" TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}" TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}" TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" TEILER_PROJECT: "${PROJECT}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler" + TEILER_ORCHESTRATOR_URL: "/bbmri-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler" - TEILER_USER: "${OIDC_USER_GROUP}" - TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb" EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri" @@ -61,10 +56,9 @@ services: environment: LOG_LEVEL: "INFO" APPLICATION_PORT: "8085" - APPLICATION_ADDRESS: "${HOST}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler" - TEILER_DASHBOARD_DE_URL: "https://${HOST}/bbmri-teiler-dashboard/de" - TEILER_DASHBOARD_EN_URL: "https://${HOST}/bbmri-teiler-dashboard/en" + TEILER_ORCHESTRATOR_URL: "/bbmri-teiler" + TEILER_DASHBOARD_DE_URL: "/bbmri-teiler-dashboard/de" + TEILER_DASHBOARD_EN_URL: "/bbmri-teiler-dashboard/en" HTTP_PROXY: "http://forward_proxy:3128" diff --git a/bbmri/modules/teiler.md b/bbmri/modules/teiler.md deleted file mode 100644 index 51e94e4..0000000 --- a/bbmri/modules/teiler.md +++ /dev/null @@ -1,19 +0,0 @@ -# Teiler -This module orchestrates the different microfrontends of the bridgehead as a single page application. - -## Teiler Orchestrator -Single SPA component that consists on the root HTML site of the single page application and a javascript code that -gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the -resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. - -The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...) -This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem). -There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler. - -## Teiler Dashboard -It consists on the main dashboard and a set of embedded services. -### Login -user and password in ccp.local.conf - -## Teiler Backend -In this component, the microfrontends are configured. diff --git a/bridgehead b/bridgehead index 395504a..1951a7f 100755 --- a/bridgehead +++ b/bridgehead @@ -162,7 +162,7 @@ case "$ACTION" in adduser) loadVars log "INFO" "Adding encrypted credentials in /etc/bridgehead/$PROJECT.local.conf" - read -p "Please choose the component (LDM_AUTH|NNGM_AUTH) you want to add a user to : " COMPONENT + read -p "Please choose the component (LDM_AUTH|NNGM_AUTH|EXPORTER_USER) you want to add a user to : " COMPONENT read -p "Please enter a username: " USER read -s -p "Please enter a password (will not be echoed): "$'\n' PASSWORD add_basic_auth_user $USER $PASSWORD $COMPONENT $PROJECT diff --git a/cce/modules/exporter-compose.yml b/cce/modules/exporter-compose.yml new file mode 100644 index 0000000..af31465 --- /dev/null +++ b/cce/modules/exporter-compose.yml @@ -0,0 +1,87 @@ +version: "3.7" + +services: + + exporter: + image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest + container_name: bridgehead-cce-exporter + environment: + JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" + LOG_LEVEL: "INFO" + EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh + CROSS_ORIGINS: "https://${HOST}" + EXPORTER_DB_USER: "exporter" + EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh + EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter" + HTTP_RELATIVE_PATH: "/cce-exporter" + SITE: "${SITE_ID}" + HTTP_SERVLET_REQUEST_SCHEME: "https" + OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}" + labels: + - "traefik.enable=true" + - "traefik.http.routers.exporter_cce.rule=PathPrefix(`/cce-exporter`)" + - "traefik.http.services.exporter_cce.loadbalancer.server.port=8092" + - "traefik.http.routers.exporter_cce.tls=true" + - "traefik.http.middlewares.exporter_cce_strip.stripprefix.prefixes=/cce-exporter" + - "traefik.http.routers.exporter_cce.middlewares=exporter_cce_strip" + # Main router + - "traefik.http.routers.exporter_cce.priority=20" + + # API router + - "traefik.http.routers.exporter_cce_api.middlewares=exporter_cce_strip,exporter_auth" + - "traefik.http.routers.exporter_cce_api.rule=PathRegexp(`/cce-exporter/.+`)" + - "traefik.http.routers.exporter_cce_api.tls=true" + - "traefik.http.routers.exporter_cce_api.priority=25" + + # Shared middlewares + - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}" + + volumes: + - "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output" + + exporter-db: + image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG} + container_name: bridgehead-cce-exporter-db + environment: + POSTGRES_USER: "exporter" + POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh + POSTGRES_DB: "exporter" + volumes: + # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer. + - "/var/cache/bridgehead/cce/exporter-db:/var/lib/postgresql/data" + + reporter: + image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest + container_name: bridgehead-cce-reporter + environment: + JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" + LOG_LEVEL: "INFO" + CROSS_ORIGINS: "https://${HOST}" + HTTP_RELATIVE_PATH: "/cce-reporter" + SITE: "${SITE_ID}" + EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh + EXPORTER_URL: "http://exporter:8092" + LOG_FHIR_VALIDATION: "false" + HTTP_SERVLET_REQUEST_SCHEME: "https" + + # In this initial development state of the bridgehead, we are trying to have so many volumes as possible. + # However, in the first executions in the cce sites, this volume seems to be very important. A report is + # a process that can take several hours, because it depends on the exporter. + # There is a risk that the bridgehead restarts, losing the already created export. + + volumes: + - "/var/cache/bridgehead/cce/reporter-files:/app/reports" + labels: + - "traefik.enable=true" + - "traefik.http.routers.reporter_cce.rule=PathPrefix(`/cce-reporter`)" + - "traefik.http.services.reporter_cce.loadbalancer.server.port=8095" + - "traefik.http.routers.reporter_cce.tls=true" + - "traefik.http.middlewares.reporter_cce_strip.stripprefix.prefixes=/cce-reporter" + - "traefik.http.routers.reporter_cce.middlewares=reporter_cce_strip" + - "traefik.http.routers.reporter_cce.priority=20" + + - "traefik.http.routers.reporter_cce_api.middlewares=reporter_cce_strip,exporter_auth" + - "traefik.http.routers.reporter_cce_api.rule=PathRegexp(`/cce-reporter/.+`)" + - "traefik.http.routers.reporter_cce_api.tls=true" + - "traefik.http.routers.reporter_cce_api.priority=25" + diff --git a/cce/modules/exporter-setup.sh b/cce/modules/exporter-setup.sh new file mode 100644 index 0000000..9b947a6 --- /dev/null +++ b/cce/modules/exporter-setup.sh @@ -0,0 +1,8 @@ +#!/bin/bash -e + +if [ "$ENABLE_EXPORTER" == true ]; then + log INFO "Exporter setup detected -- will start Exporter service." + OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml" + 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)" + 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)" +fi diff --git a/cce/modules/lens-compose.yml b/cce/modules/lens-compose.yml index 12b95ce..d9ec6e2 100644 --- a/cce/modules/lens-compose.yml +++ b/cce/modules/lens-compose.yml @@ -17,7 +17,6 @@ services: BEAM_PROXY_ID: ${SITE_ID} BEAM_BROKER_ID: ${BROKER_ID} BEAM_APP_ID: "focus" - PROJECT_METADATA: "cce_supervisors" depends_on: - "beam-proxy" labels: @@ -30,4 +29,4 @@ services: - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)" - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend" - "traefik.http.routers.spot.tls=true" - - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot" + - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth" diff --git a/cce/modules/teiler-compose.yml b/cce/modules/teiler-compose.yml new file mode 100644 index 0000000..a2845bf --- /dev/null +++ b/cce/modules/teiler-compose.yml @@ -0,0 +1,64 @@ +version: "3.7" + +services: + + teiler-orchestrator: + image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest + container_name: bridgehead-teiler-orchestrator + labels: + - "traefik.enable=true" + - "traefik.http.routers.teiler_orchestrator_cce.rule=PathPrefix(`/cce-teiler`)" + - "traefik.http.services.teiler_orchestrator_cce.loadbalancer.server.port=9000" + - "traefik.http.routers.teiler_orchestrator_cce.tls=true" + - "traefik.http.middlewares.teiler_orchestrator_cce_strip.stripprefix.prefixes=/cce-teiler" + - "traefik.http.routers.teiler_orchestrator_cce.middlewares=teiler_orchestrator_cce_strip" + environment: + TEILER_BACKEND_URL: "/cce-teiler-backend" + TEILER_DASHBOARD_URL: "/cce-teiler-dashboard" + DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}" + HTTP_RELATIVE_PATH: "/cce-teiler" + + teiler-dashboard: + image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop + container_name: bridgehead-teiler-dashboard + labels: + - "traefik.enable=true" + - "traefik.http.routers.teiler_dashboard_cce.rule=PathPrefix(`/cce-teiler-dashboard`)" + - "traefik.http.services.teiler_dashboard_cce.loadbalancer.server.port=80" + - "traefik.http.routers.teiler_dashboard_cce.tls=true" + - "traefik.http.middlewares.teiler_dashboard_cce_strip.stripprefix.prefixes=/cce-teiler-dashboard" + - "traefik.http.routers.teiler_dashboard_cce.middlewares=teiler_dashboard_cce_strip" + environment: + DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" + TEILER_BACKEND_URL: "/cce-teiler-backend" + TEILER_DASHBOARD_URL: "/cce-teiler-dashboard" + TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}" + TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}" + TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" + TEILER_PROJECT: "${PROJECT}" + EXPORTER_API_KEY: "${EXPORTER_API_KEY}" + TEILER_ORCHESTRATOR_URL: "/cce-teiler" + TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler" + REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb" + EXPORTER_DEFAULT_TEMPLATE_ID: "cce" + + + teiler-backend: + image: docker.verbis.dkfz.de/ccp/cce-teiler-backend:latest + container_name: bridgehead-teiler-backend + labels: + - "traefik.enable=true" + - "traefik.http.routers.teiler_backend_cce.rule=PathPrefix(`/cce-teiler-backend`)" + - "traefik.http.services.teiler_backend_cce.loadbalancer.server.port=8085" + - "traefik.http.routers.teiler_backend_cce.tls=true" + - "traefik.http.middlewares.teiler_backend_cce_strip.stripprefix.prefixes=/cce-teiler-backend" + - "traefik.http.routers.teiler_backend_cce.middlewares=teiler_backend_cce_strip" + environment: + LOG_LEVEL: "INFO" + APPLICATION_PORT: "8085" + DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" + TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler" + TEILER_ORCHESTRATOR_URL: "/cce-teiler" + TEILER_DASHBOARD_DE_URL: "/cce-teiler-dashboard/de" + TEILER_DASHBOARD_EN_URL: "/cce-teiler-dashboard/en" + HTTP_PROXY: "http://forward_proxy:3128" diff --git a/cce/modules/teiler-setup.sh b/cce/modules/teiler-setup.sh new file mode 100644 index 0000000..dc8dfc4 --- /dev/null +++ b/cce/modules/teiler-setup.sh @@ -0,0 +1,8 @@ +#!/bin/bash -e + +if [ "$ENABLE_TEILER" == true ];then + log INFO "Teiler setup detected -- will start Teiler services." + OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml" + TEILER_DEFAULT_LANGUAGE=EN + TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,} +fi diff --git a/ccp/modules/datashield-compose.yml b/ccp/modules/datashield-compose.yml index a20e9e6..2e8c945 100644 --- a/ccp/modules/datashield-compose.yml +++ b/ccp/modules/datashield-compose.yml @@ -1,25 +1,6 @@ version: "3.7" services: - rstudio: - container_name: bridgehead-rstudio - image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest - environment: - #DEFAULT_USER: "rstudio" # This line is kept for informational purposes - PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled - DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use - HTTP_RELATIVE_PATH: "/rstudio" - ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html - labels: - - "traefik.enable=true" - - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)" - - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787" - - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio" - - "traefik.http.routers.rstudio_ccp.tls=true" - - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip" - networks: - - rstudio - opal: container_name: bridgehead-opal image: docker.verbis.dkfz.de/ccp/dktk-opal:latest @@ -44,7 +25,7 @@ services: APP_CONTEXT_PATH: "/opal" OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem" OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem" - OIDC_URL: "${OIDC_URL}" + OIDC_URL: "${OIDC_PRIVATE_URL}" OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}" OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}" @@ -92,79 +73,14 @@ services: - beam-proxy volumes: - /tmp/bridgehead/opal-map/:/map/:ro - networks: - - default - - rstudio - - traefik: - labels: - - "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2-proxy:4180/" - - "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true" - - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization" - networks: - - default - - rstudio - forward_proxy: - networks: - - default - - rstudio beam-proxy: environment: APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET} APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET} - # TODO: Allow users of group /DataSHIELD and OIDC_USER_GROUP at the same time: - # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/configuration/oauth_provider): - # --allowed-groups=/DataSHIELD,OIDC_USER_GROUP - oauth2-proxy: - image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest - container_name: bridgehead-oauth2proxy - command: >- - --allowed-group=DataSHIELD - --oidc-groups-claim=${OIDC_GROUP_CLAIM} - --auth-logging=true - --whitelist-domain=${HOST} - --http-address="0.0.0.0:4180" - --reverse-proxy=true - --upstream="static://202" - --email-domain="*" - --cookie-name="_BRIDGEHEAD_oauth2" - --cookie-secret="${OAUTH2_PROXY_SECRET}" - --cookie-expire="12h" - --cookie-secure="true" - --cookie-httponly="true" - #OIDC settings - --provider="keycloak-oidc" - --provider-display-name="VerbIS Login" - --client-id="${OIDC_PRIVATE_CLIENT_ID}" - --client-secret="${OIDC_CLIENT_SECRET}" - --redirect-url="https://${HOST}${OAUTH2_CALLBACK}" - --oidc-issuer-url="${OIDC_URL}" - --scope="openid email profile" - --code-challenge-method="S256" - --skip-provider-button=true - #X-Forwarded-Header settings - true/false depending on your needs - --pass-basic-auth=true - --pass-user-headers=false - --pass-access-token=false - labels: - - "traefik.enable=true" - - "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)" - - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180" - - "traefik.http.routers.oauth2_proxy.tls=true" - environment: - http_proxy: "http://forward_proxy:3128" - https_proxy: "http://forward_proxy:3128" - depends_on: - forward_proxy: - condition: service_healthy - secrets: opal-cert.pem: file: /tmp/bridgehead/opal-cert.pem opal-key.pem: file: /tmp/bridgehead/opal-key.pem - -networks: - rstudio: diff --git a/ccp/modules/datashield-setup.sh b/ccp/modules/datashield-setup.sh index 9692fb9..e5f7f61 100644 --- a/ccp/modules/datashield-setup.sh +++ b/ccp/modules/datashield-setup.sh @@ -5,17 +5,12 @@ if [ "$ENABLE_DATASHIELD" == true ]; then if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'." fi - OAUTH2_CALLBACK=/oauth2/callback - OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)" - add_private_oidc_redirect_url "${OAUTH2_CALLBACK}" - log INFO "DataSHIELD setup detected -- will start DataSHIELD services." OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml" EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")" TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")" OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)" OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")" - RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")" DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)" TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)" if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then @@ -23,18 +18,13 @@ if [ "$ENABLE_DATASHIELD" == true ]; then openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE" fi mkdir -p /tmp/bridgehead/opal-map - sites="$(cat ./$PROJECT/modules/datashield-sites.json)" - echo "$sites" | docker_jq -n --args '{"sites": input | map({ - "name": ., - "id": ., - "virtualhost": "\(.):443", - "beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'" - })}' $sites >/tmp/bridgehead/opal-map/central.json - echo "$sites" | docker_jq -n --args '[{ - "external": "'"$SITE_ID"':443", + echo '{"sites": []}' >/tmp/bridgehead/opal-map/central.json + # Only allow connections from the central beam proxy that is used by all coder workspaces + echo '[{ + "external": "'$SITE_ID':443", "internal": "opal:8443", - "allowed": input | map("\(.).'"$BROKER_ID"'") - }]' >/tmp/bridgehead/opal-map/local.json + "allowed": ["central-ds-orchestrator.'$BROKER_ID'"] + }]' > /tmp/bridgehead/opal-map/local.json if [ "$USER" == "root" ]; then chown -R bridgehead:docker /tmp/bridgehead chmod g+wr /tmp/bridgehead/opal-map/* diff --git a/ccp/modules/datashield-sites.json b/ccp/modules/datashield-sites.json deleted file mode 100644 index 600534d..0000000 --- a/ccp/modules/datashield-sites.json +++ /dev/null @@ -1,15 +0,0 @@ -[ - "berlin", - "muenchen-lmu", - "dresden", - "freiburg", - "muenchen-tum", - "tuebingen", - "mainz", - "frankfurt", - "essen", - "dktk-datashield-test", - "dktk-test", - "mannheim", - "central-ds-orchestrator" -] diff --git a/ccp/modules/dnpm-node-compose.yml b/ccp/modules/dnpm-node-compose.yml index c1f7dde..62e04b7 100644 --- a/ccp/modules/dnpm-node-compose.yml +++ b/ccp/modules/dnpm-node-compose.yml @@ -43,7 +43,7 @@ services: - "traefik.http.routers.dnpm-auth.tls=true" dnpm-portal: - image: ghcr.io/dnpm-dip/portal:latest + image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-latest} container_name: bridgehead-dnpm-portal environment: - NUXT_API_URL=http://dnpm-backend:9000/ @@ -58,7 +58,7 @@ services: dnpm-backend: container_name: bridgehead-dnpm-backend - image: ghcr.io/dnpm-dip/backend:latest + image: ghcr.io/dnpm-dip/backend:{DNPM_IMAGE_TAG:-latest} environment: - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1} diff --git a/ccp/modules/id-management-compose.yml b/ccp/modules/id-management-compose.yml index 4e3e90a..86c6a96 100644 --- a/ccp/modules/id-management-compose.yml +++ b/ccp/modules/id-management-compose.yml @@ -14,6 +14,7 @@ services: MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY} MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY} MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY} + MAGICPL_OIDC_PROVIDER: ${OIDC_PRIVATE_URL} depends_on: - patientlist - traefik-forward-auth @@ -71,12 +72,14 @@ services: - https_proxy=http://forward_proxy:3128 - OAUTH2_PROXY_PROVIDER=oidc - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true - - OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master - - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID} - - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET} + - OAUTH2_PROXY_OIDC_ISSUER_URL=${OIDC_PRIVATE_URL} + - OAUTH2_PROXY_CLIENT_ID=${OIDC_PRIVATE_CLIENT_ID} + - OAUTH2_PROXY_CLIENT_SECRET=${OIDC_CLIENT_SECRET} - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET} - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST} + - OAUTH2_PROXY_COOKIE_REFRESH=4m + - OAUTH2_PROXY_COOKIE_EXPIRE=24h - OAUTH2_PROXY_HTTP_ADDRESS=:4180 - OAUTH2_PROXY_REVERSE_PROXY=true - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST} @@ -87,8 +90,8 @@ services: - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true - OAUTH2_PROXY_SET_XAUTHREQUEST=true # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that - - OAUTH2_PROXY_COOKIE_REFRESH=60s - - OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN + - OAUTH2_PROXY_ALLOWED_GROUPS=${OIDC_PSP_GROUP} + - OAUTH2_PROXY_OIDC_GROUPS_CLAIM=${OIDC_GROUP_CLAIM} - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm labels: - "traefik.enable=true" diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh index 333b512..a764459 100644 --- a/ccp/modules/id-management-setup.sh +++ b/ccp/modules/id-management-setup.sh @@ -14,6 +14,8 @@ function idManagementSetup() { # Ensure old ids are working !!! export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID") + + add_private_oidc_redirect_url "/oauth2-idm/callback" fi } diff --git a/ccp/modules/mtba-compose.yml b/ccp/modules/mtba-compose.yml index 8f89449..1c01340 100644 --- a/ccp/modules/mtba-compose.yml +++ b/ccp/modules/mtba-compose.yml @@ -22,8 +22,14 @@ services: HTTP_RELATIVE_PATH: "/mtba" OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}" OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}" - OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" - OIDC_URL: "${OIDC_URL}" + # TODO: Add following variables after moving to Authentik: + #OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" + #OIDC_URL: "${OIDC_URL}" + # TODO: Remove following variables after moving to Authentik: + # Please add KECLOAK_CLIENT_SECRET in ccp.conf + OIDC_CLIENT_SECRET: "${KEYCLOAK_CLIENT_SECRET}" + OIDC_URL: "https://login.verbis.dkfz.de/realms/test-realm-01" + OIDC_ADMIN_URL: "https://login.verbis.dkfz.de/admin/realms/test-realm-01" labels: - "traefik.enable=true" diff --git a/ccp/modules/teiler-compose.yml b/ccp/modules/teiler-compose.yml index 1a5ca9e..15dbd08 100644 --- a/ccp/modules/teiler-compose.yml +++ b/ccp/modules/teiler-compose.yml @@ -13,8 +13,8 @@ services: - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler" - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip" environment: - TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard" + TEILER_BACKEND_URL: "/ccp-teiler-backend" + TEILER_DASHBOARD_URL: "/ccp-teiler-dashboard" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}" HTTP_RELATIVE_PATH: "/ccp-teiler" @@ -30,8 +30,8 @@ services: - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip" environment: DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" - TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard" + TEILER_BACKEND_URL: "/ccp-teiler-backend" + TEILER_DASHBOARD_URL: "/ccp-teiler-dashboard" OIDC_URL: "${OIDC_URL}" OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}" @@ -40,7 +40,7 @@ services: TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" TEILER_PROJECT: "${PROJECT}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" + TEILER_ORCHESTRATOR_URL: "/ccp-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" TEILER_USER: "${OIDC_USER_GROUP}" TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" @@ -61,12 +61,11 @@ services: environment: LOG_LEVEL: "INFO" APPLICATION_PORT: "8085" - APPLICATION_ADDRESS: "${HOST}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" - TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de" - TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en" + TEILER_ORCHESTRATOR_URL: "/ccp-teiler" + TEILER_DASHBOARD_DE_URL: "/ccp-teiler-dashboard/de" + TEILER_DASHBOARD_EN_URL: "/ccp-teiler-dashboard/en" HTTP_PROXY: "http://forward_proxy:3128" ENABLE_MTBA: "${ENABLE_MTBA}" ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}" diff --git a/ccp/vars b/ccp/vars index f415bd3..2377b83 100644 --- a/ccp/vars +++ b/ccp/vars @@ -10,9 +10,11 @@ BROKER_URL_FOR_PREREQ=$BROKER_URL OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})" OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter" +OIDC_PSP_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_PSP" OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public -OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01" +OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/" +OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/" OIDC_GROUP_CLAIM="groups" for module in $PROJECT/modules/*.sh diff --git a/itcc/modules/lens-compose.yml b/itcc/modules/lens-compose.yml index 2bbddbe..d9ec6e2 100644 --- a/itcc/modules/lens-compose.yml +++ b/itcc/modules/lens-compose.yml @@ -17,7 +17,6 @@ services: BEAM_PROXY_ID: ${SITE_ID} BEAM_BROKER_ID: ${BROKER_ID} BEAM_APP_ID: "focus" - PROJECT_METADATA: "dktk_supervisors" depends_on: - "beam-proxy" labels: @@ -30,4 +29,4 @@ services: - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)" - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend" - "traefik.http.routers.spot.tls=true" - - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot" + - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth" diff --git a/kr/modules/exporter-compose.yml b/kr/modules/exporter-compose.yml index d5eb227..c5e6984 100644 --- a/kr/modules/exporter-compose.yml +++ b/kr/modules/exporter-compose.yml @@ -1,9 +1,10 @@ version: "3.7" services: + exporter: image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest - container_name: bridgehead-ccp-exporter + container_name: bridgehead-kr-exporter environment: JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" LOG_LEVEL: "INFO" @@ -12,39 +13,51 @@ services: EXPORTER_DB_USER: "exporter" EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter" - HTTP_RELATIVE_PATH: "/ccp-exporter" + HTTP_RELATIVE_PATH: "/kr-exporter" SITE: "${SITE_ID}" HTTP_SERVLET_REQUEST_SCHEME: "https" OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}" labels: - "traefik.enable=true" - - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)" - - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092" - - "traefik.http.routers.exporter_ccp.tls=true" - - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter" - - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip" + - "traefik.http.routers.exporter_kr.rule=PathPrefix(`/kr-exporter`)" + - "traefik.http.services.exporter_kr.loadbalancer.server.port=8092" + - "traefik.http.routers.exporter_kr.tls=true" + - "traefik.http.middlewares.exporter_kr_strip.stripprefix.prefixes=/kr-exporter" + - "traefik.http.routers.exporter_kr.middlewares=exporter_kr_strip" + # Main router + - "traefik.http.routers.exporter_kr.priority=20" + + # API router + - "traefik.http.routers.exporter_kr_api.middlewares=exporter_kr_strip,exporter_auth" + - "traefik.http.routers.exporter_kr_api.rule=PathRegexp(`/kr-exporter/.+`)" + - "traefik.http.routers.exporter_kr_api.tls=true" + - "traefik.http.routers.exporter_kr_api.priority=25" + + # Shared middlewares + - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}" + volumes: - - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output" + - "/var/cache/bridgehead/kr/exporter-files:/app/exporter-files/output" exporter-db: image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG} - container_name: bridgehead-ccp-exporter-db + container_name: bridgehead-kr-exporter-db environment: POSTGRES_USER: "exporter" POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh POSTGRES_DB: "exporter" volumes: # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer. - - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data" + - "/var/cache/bridgehead/kr/exporter-db:/var/lib/postgresql/data" reporter: image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest - container_name: bridgehead-ccp-reporter + container_name: bridgehead-kr-reporter environment: JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" LOG_LEVEL: "INFO" CROSS_ORIGINS: "https://${HOST}" - HTTP_RELATIVE_PATH: "/ccp-reporter" + HTTP_RELATIVE_PATH: "/kr-reporter" SITE: "${SITE_ID}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh EXPORTER_URL: "http://exporter:8092" @@ -52,16 +65,23 @@ services: HTTP_SERVLET_REQUEST_SCHEME: "https" # In this initial development state of the bridgehead, we are trying to have so many volumes as possible. - # However, in the first executions in the CCP sites, this volume seems to be very important. A report is + # However, in the first executions in the kr sites, this volume seems to be very important. A report is # a process that can take several hours, because it depends on the exporter. # There is a risk that the bridgehead restarts, losing the already created export. volumes: - - "/var/cache/bridgehead/ccp/reporter-files:/app/reports" + - "/var/cache/bridgehead/kr/reporter-files:/app/reports" labels: - "traefik.enable=true" - - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)" - - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095" - - "traefik.http.routers.reporter_ccp.tls=true" - - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter" - - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip" + - "traefik.http.routers.reporter_kr.rule=PathPrefix(`/kr-reporter`)" + - "traefik.http.services.reporter_kr.loadbalancer.server.port=8095" + - "traefik.http.routers.reporter_kr.tls=true" + - "traefik.http.middlewares.reporter_kr_strip.stripprefix.prefixes=/kr-reporter" + - "traefik.http.routers.reporter_kr.middlewares=reporter_kr_strip" + - "traefik.http.routers.reporter_kr.priority=20" + + - "traefik.http.routers.reporter_kr_api.middlewares=reporter_kr_strip,exporter_auth" + - "traefik.http.routers.reporter_kr_api.rule=PathRegexp(`/kr-reporter/.+`)" + - "traefik.http.routers.reporter_kr_api.tls=true" + - "traefik.http.routers.reporter_kr_api.priority=25" + diff --git a/kr/modules/exporter.md b/kr/modules/exporter.md deleted file mode 100644 index 24e81b0..0000000 --- a/kr/modules/exporter.md +++ /dev/null @@ -1,15 +0,0 @@ -# Exporter and Reporter - - -## Exporter -The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables. -It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal. - -## Exporter-DB -It is a database to save queries for its execution in the exporter. -The exporter manages also the different executions of the same query in through the database. - -## Reporter -This component is a plugin of the exporter that allows to create more complex Excel reports described in templates. -It is compatible with different template engines as Groovy, Thymeleaf,... -It is perfect to generate a document as our traditional CCP quality report. diff --git a/kr/modules/teiler-compose.yml b/kr/modules/teiler-compose.yml index 25a3423..db42513 100644 --- a/kr/modules/teiler-compose.yml +++ b/kr/modules/teiler-compose.yml @@ -7,73 +7,58 @@ services: container_name: bridgehead-teiler-orchestrator labels: - "traefik.enable=true" - - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)" - - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000" - - "traefik.http.routers.teiler_orchestrator_ccp.tls=true" - - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler" - - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip" + - "traefik.http.routers.teiler_orchestrator_kr.rule=PathPrefix(`/kr-teiler`)" + - "traefik.http.services.teiler_orchestrator_kr.loadbalancer.server.port=9000" + - "traefik.http.routers.teiler_orchestrator_kr.tls=true" + - "traefik.http.middlewares.teiler_orchestrator_kr_strip.stripprefix.prefixes=/kr-teiler" + - "traefik.http.routers.teiler_orchestrator_kr.middlewares=teiler_orchestrator_kr_strip" environment: - TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard" + TEILER_BACKEND_URL: "/kr-teiler-backend" + TEILER_DASHBOARD_URL: "/kr-teiler-dashboard" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}" - HTTP_RELATIVE_PATH: "/ccp-teiler" + HTTP_RELATIVE_PATH: "/kr-teiler" teiler-dashboard: image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop container_name: bridgehead-teiler-dashboard labels: - "traefik.enable=true" - - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)" - - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80" - - "traefik.http.routers.teiler_dashboard_ccp.tls=true" - - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard" - - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip" + - "traefik.http.routers.teiler_dashboard_kr.rule=PathPrefix(`/kr-teiler-dashboard`)" + - "traefik.http.services.teiler_dashboard_kr.loadbalancer.server.port=80" + - "traefik.http.routers.teiler_dashboard_kr.tls=true" + - "traefik.http.middlewares.teiler_dashboard_kr_strip.stripprefix.prefixes=/kr-teiler-dashboard" + - "traefik.http.routers.teiler_dashboard_kr.middlewares=teiler_dashboard_kr_strip" environment: DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" - TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard" - OIDC_URL: "${OIDC_URL}" - OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" - OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}" + TEILER_BACKEND_URL: "/kr-teiler-backend" + TEILER_DASHBOARD_URL: "/kr-teiler-dashboard" TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}" TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}" TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" TEILER_PROJECT: "${PROJECT}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" - TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" - TEILER_USER: "${OIDC_USER_GROUP}" - TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" + TEILER_ORCHESTRATOR_URL: "/kr-teiler" + TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-teiler" REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb" EXPORTER_DEFAULT_TEMPLATE_ID: "ccp" teiler-backend: - image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest + image: docker.verbis.dkfz.de/ccp/kr-teiler-backend:latest container_name: bridgehead-teiler-backend labels: - "traefik.enable=true" - - "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)" - - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085" - - "traefik.http.routers.teiler_backend_ccp.tls=true" - - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend" - - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip" + - "traefik.http.routers.teiler_backend_kr.rule=PathPrefix(`/kr-teiler-backend`)" + - "traefik.http.services.teiler_backend_kr.loadbalancer.server.port=8085" + - "traefik.http.routers.teiler_backend_kr.tls=true" + - "traefik.http.middlewares.teiler_backend_kr_strip.stripprefix.prefixes=/kr-teiler-backend" + - "traefik.http.routers.teiler_backend_kr.middlewares=teiler_backend_kr_strip" environment: LOG_LEVEL: "INFO" APPLICATION_PORT: "8085" - APPLICATION_ADDRESS: "${HOST}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" - CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf" - TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" - TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de" - TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en" + TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-teiler" + TEILER_ORCHESTRATOR_URL: "/kr-teiler" + TEILER_DASHBOARD_DE_URL: "/kr-teiler-dashboard/de" + TEILER_DASHBOARD_EN_URL: "/kr-teiler-dashboard/en" HTTP_PROXY: "http://forward_proxy:3128" - ENABLE_MTBA: "${ENABLE_MTBA}" - ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}" - secrets: - - ccp.conf - -secrets: - ccp.conf: - file: /etc/bridgehead/ccp.conf diff --git a/kr/modules/teiler-setup.sh b/kr/modules/teiler-setup.sh index eed3f81..dc8dfc4 100644 --- a/kr/modules/teiler-setup.sh +++ b/kr/modules/teiler-setup.sh @@ -3,7 +3,6 @@ if [ "$ENABLE_TEILER" == true ];then log INFO "Teiler setup detected -- will start Teiler services." OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml" - TEILER_DEFAULT_LANGUAGE=DE + TEILER_DEFAULT_LANGUAGE=EN TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,} - add_public_oidc_redirect_url "/ccp-teiler/*" fi diff --git a/kr/modules/teiler.md b/kr/modules/teiler.md deleted file mode 100644 index 51e94e4..0000000 --- a/kr/modules/teiler.md +++ /dev/null @@ -1,19 +0,0 @@ -# Teiler -This module orchestrates the different microfrontends of the bridgehead as a single page application. - -## Teiler Orchestrator -Single SPA component that consists on the root HTML site of the single page application and a javascript code that -gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the -resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. - -The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...) -This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem). -There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler. - -## Teiler Dashboard -It consists on the main dashboard and a set of embedded services. -### Login -user and password in ccp.local.conf - -## Teiler Backend -In this component, the microfrontends are configured. diff --git a/lib/functions.sh b/lib/functions.sh index 680032c..12308c0 100644 --- a/lib/functions.sh +++ b/lib/functions.sh @@ -301,19 +301,33 @@ function sync_secrets() { if [[ $secret_sync_args == "" ]]; then return fi + + if [ "$PROJECT" == "bbmri" ]; then + # If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker + proxy_id=$ERIC_PROXY_ID + broker_url=$ERIC_BROKER_URL + broker_id=$ERIC_BROKER_ID + root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem" + else + proxy_id=$PROXY_ID + broker_url=$BROKER_URL + broker_id=$BROKER_ID + root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem" + fi + mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again." touch /var/cache/bridgehead/secrets/oidc docker run --rm \ -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \ -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \ - -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \ + -v $root_crt_file:/run/secrets/root.crt.pem:ro \ -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \ -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \ -e NO_PROXY=localhost,127.0.0.1 \ -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \ - -e PROXY_ID=$PROXY_ID \ - -e BROKER_URL=$BROKER_URL \ - -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \ + -e PROXY_ID=$proxy_id \ + -e BROKER_URL=$broker_url \ + -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \ -e SECRET_DEFINITIONS=$secret_sync_args \ docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest @@ -436,7 +450,3 @@ generate_simple_password(){ local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret." echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g' } - -docker_jq() { - docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@" -} diff --git a/minimal/modules/dnpm-node-compose.yml b/minimal/modules/dnpm-node-compose.yml index 8c2b146..6c220e7 100644 --- a/minimal/modules/dnpm-node-compose.yml +++ b/minimal/modules/dnpm-node-compose.yml @@ -43,7 +43,7 @@ services: - "traefik.http.routers.dnpm-auth.tls=true" dnpm-portal: - image: ghcr.io/dnpm-dip/portal:latest + image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-latest} container_name: bridgehead-dnpm-portal environment: - NUXT_API_URL=http://dnpm-backend:9000/ @@ -58,7 +58,7 @@ services: dnpm-backend: container_name: bridgehead-dnpm-backend - image: ghcr.io/dnpm-dip/backend:latest + image: ghcr.io/dnpm-dip/backend:{DNPM_IMAGE_TAG:-latest} environment: - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}