Whitespace formatting

When a OIDC provider is configured, you'll get redirected to authup by Keycloak which redirects you to the DNPM:DIP. 

Currently the url looks like this: https://myserver/authup//someurl
and produces an error. Manually removing the additional / fixes the issue.

README.md

@@ -23,7 +23,6 @@ This repository is the starting point for any information and tools you will nee
     - [File structure](#file-structure)
     - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
     - [Loading data](#loading-data)
-    - [Metadata feedback](#metadata-feedback)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -77,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
   * git.verbis.dkfz.de
 * To fetch docker images
   * docker.verbis.dkfz.de
-  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
+  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
     * hub.docker.com
     * registry-1.docker.io
     * production.cloudflare.docker.com
@@ -156,7 +155,6 @@ Clone the bridgehead repository:
 ```shell
 sudo mkdir -p /srv/docker/
 sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
-sudo git checkout metadata_fb # Only needed if you want to use metadata feedback
 ```
 
 Then, run the installation script:
@@ -349,26 +347,6 @@ Normally, you will need to build your own ETL to feed the Bridgehead. However, t
 
 You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
 
-### Metadata feedback
-
-The Bridgehead comes with a tool that allows you to associate metadata with samples. Multiple arbitrary text strings are allowed. A typical use case would be publications based on research using a sample. Here, one could lay down the DOI of the publication in the sample.
-
-Full details of the system can be found [here](https://github.com/samply/feedback-deployment). To avail yourself of this feature, you need to
-
-- Use the bbmri project.
-- work with the ```metadata_fb``` branch of the Bridgehead repository.
-- Build the feedback-agent Docker container (more details [here](https://github.com/samply/feedback-agent/)).
-- Build the feedback-agent-ui Docker container (more details [here](https://github.com/samply/feedback-agent-ui/)).
-
-The following extra environment variables need to be added to your ```/etc/bridgehead/bbmri.conf``` file:
-
-``` code
-ENABLE_EXPORTER=true
-ENABLE_FEEDBACK_AGENT=true
-FEEDBACK_HUB_URL=<URL for central feedback hub backend API>
-FOCUS_RETRY_COUNT=256
-```
-
 ## Things you should know
 
 ### Auto-Updates

bbmri/modules/eric-compose.yml

@@ -22,7 +22,6 @@ services:
       BROKER_URL: ${ERIC_BROKER_URL}
       PROXY_ID: ${ERIC_PROXY_ID}
       APP_focus_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
-      APP_feedback-agent_KEY: ${FEEDBACK_AGENT_BEAM_SECRET}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs

bbmri/modules/exporter-compose.yml

@@ -1,67 +0,0 @@
-version: "3.7"
-
-services:
-  exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-exporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      CROSS_ORIGINS: "https://${HOST}"
-      EXPORTER_DB_USER: "exporter"
-      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}"
-      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/ccp-exporter"
-      SITE: "${SITE_ID}"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
-    volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-exporter-db
-    environment:
-      POSTGRES_USER: "exporter"
-      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}"
-      POSTGRES_DB: "exporter"
-    volumes:
-      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
-
-  reporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-ccp-reporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/ccp-reporter"
-      SITE: "${SITE_ID}"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      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 CCP 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"
-    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"

bbmri/modules/exporter-setup.sh

@@ -1,9 +0,0 @@
-#!/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)"
-  POSTGRES_TAG=15.6-alpine
-fi

bbmri/modules/exporter.md

@@ -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.

bbmri/modules/feedback-agent-compose.yml

@@ -1,59 +0,0 @@
-version: "3.7"
-
-services:
-  feedback-agent-ui:
-    image: "samply/feedback-agent-ui"
-    environment:
-      - VUE_APP_EXPORTER_URL=https://localhost/ccp-exporter
-      - VUE_APP_FB_BACKEND_URL=http://localhost:8072
-    labels:
-     - traefik.enable=true
-     # HTTPS
-     - traefik.http.routers.feedback_agent_ui_ccp_https.rule=PathPrefix(`/ccp-feedback-agent-ui`)
-     - traefik.http.services.feedback_agent_ui_ccp_https.loadbalancer.server.port=8096
-     - traefik.http.routers.feedback_agent_ui_ccp_https.entrypoints=websecure
-     - traefik.http.routers.feedback_agent_ui_ccp_https.tls=true
-  feedback-agent:
-    image: "samply/feedback-agent"
-    environment:
-      - SPRING_DATASOURCE_URL=jdbc:postgresql://feedback-agent-db:5432/compose-postgres
-      - SPRING_DATASOURCE_USERNAME=compose-postgres
-      - SPRING_DATASOURCE_PASSWORD=${FEEDBACK_AGENT_DB_PASSWORD}
-      - SPRING_JPA_HIBERNATE_DDL_AUTO=update
-      - BEAM_PROXY_URI=http://beam-proxy-eric:8081
-      - FEEDBACK_HUB_URL=${FEEDBACK_HUB_URL}
-      - BLAZE_BASE_URL=http://blaze:8080/fhir
-      - FEEDBACK_AGENT_SECRET=${FEEDBACK_AGENT_BEAM_SECRET}
-      - FEEDBACK_AGENT_BEAM_ID=feedback-agent.${ERIC_PROXY_ID}
-      - FEEDBACK_HUB_BEAM_ID=feedback-hub.feedback-central.${ERIC_BROKER_ID}
-      - EXPORTER_API_KEY=${EXPORTER_API_KEY}
-      - CORS_ALLOWED_ORIGINS="https://${HOST}
-    networks:
-      # Only needed for local testing.
-      - feedback
-      - default
-    labels:
-     - traefik.enable=true
-     # HTTPS
-     - traefik.http.routers.feedback_agent_ccp_https.rule=PathPrefix(`/ccp-feedback-agent`)
-     - traefik.http.services.feedback_agent_ccp_https.loadbalancer.server.port=8072
-     - traefik.http.routers.feedback_agent_ccp_https.entrypoints=websecure
-     - traefik.http.middlewares.feedback_agent_ccp_https_strip.stripprefix.prefixes=/ccp-feedback-agent
-     - traefik.http.routers.feedback_agent_ccp_https.middlewares=feedback_agent_ccp_https_strip
-     - traefik.http.routers.feedback_agent_ccp_https.tls=true
-  feedback-agent-db:
-    image: 'postgres:13.1-alpine'
-    container_name: feedback-agent-db
-    environment:
-      - POSTGRES_USER=compose-postgres
-      - POSTGRES_PASSWORD=${FEEDBACK_AGENT_DB_PASSWORD}
-
-# This is needed when you run both agent and hub locally in a test
-# environment. Not necessary in production, though it probably won't
-# cause any problems.
-networks:
-  # Network to connect agent and hub.
-  feedback:
-    name: feedback
-    driver: bridge
-

bbmri/modules/feedback-agent-setup.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-if [ "$ENABLE_FEEDBACK_AGENT" == true ]; then
-  OVERRIDE+=" -f ./$PROJECT/modules/feedback-agent-compose.yml"
-  FEEDBACK_AGENT_BEAM_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-  FEEDBACK_AGENT_DB_PASSWORD="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-fi
-

bbmri/modules/feedback-agent.md

@@ -1,6 +0,0 @@
-# Metadata feedback agent
-
-This component can be used to choose the sample to be associated
-with a given piece of metadata (generally the ID of a publication
-relating to research done with the sample).
-

bridgehead

@@ -53,44 +53,17 @@ case "$PROJECT" in
 		;;
 esac
 
-# Loads config variables and runs the projects setup script
 loadVars() {
+	# Load variables from /etc/bridgehead and /srv/docker/bridgehead
 	set -a
-	# Source the project specific config file
 	source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
-	# Source the project specific local config file if present
-	# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
 	if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
 		log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
 		source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
 	fi
-	# Set execution environment on main default to prod else test
-	if [[ -z "${ENVIRONMENT+x}" ]]; then
-		if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
-			ENVIRONMENT="production"
-		else
-			ENVIRONMENT="test"
-		fi
-	fi
-	# Source the versions of the images components 
-	case "$ENVIRONMENT" in
-		"production")
-			source ./versions/prod
-			;;
-		"test")
-			source ./versions/test
-			;;
-		*)
-			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
-			source ./versions/prod
-			;;
-	esac
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
 	setHostname
 	optimizeBlazeMemoryUsage
-	# Run project specific setup if it exists
-	# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
-	# This is also where projects specify which modules to load
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -106,6 +79,26 @@ loadVars() {
 	fi
 	detectCompose
 	setupProxy
+
+	# Set some project-independent default values
+	: ${ENVIRONMENT:=production}
+	export ENVIRONMENT
+
+	case "$ENVIRONMENT" in
+		"production")
+			export FOCUS_TAG=main
+			export BEAM_TAG=main
+			;;
+		"test")
+			export FOCUS_TAG=develop
+			export BEAM_TAG=develop
+			;;
+		*)
+			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			export FOCUS_TAG=main
+			export BEAM_TAG=main
+			;;
+	esac
 }
 
 case "$ACTION" in

lib/functions.sh

@@ -116,7 +116,7 @@ assertVarsNotEmpty() {
 	MISSING_VARS=""
 
 	for VAR in $@; do
-		if [ -z "${!VAR}" ]; then
+	if [ -z "${!VAR}" ]; then
 			MISSING_VARS+="$VAR "
 		fi
 	done
@@ -318,7 +318,7 @@ function sync_secrets() {
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
 
     set -a # Export variables as environment variables
-    source /var/cache/bridgehead/secrets/oidc
+    source /var/cache/bridgehead/secrets/*
     set +a # Export variables in the regular way
 }
 

lib/gitlab-token-helper.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-[ "$1" = "get" ] || exit
-
-source /var/cache/bridgehead/secrets/gitlab_token
-
-# Any non-empty username works, only the token matters
-cat << EOF
-username=bk
-password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
-EOF

lib/gitpassword.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+if [ "$1" != "get" ]; then
+	echo "Usage: $0 get"
+	exit 1
+fi
+
+baseDir() {
+	# see https://stackoverflow.com/questions/59895
+	SOURCE=${BASH_SOURCE[0]}
+	while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+		DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+		SOURCE=$(readlink "$SOURCE")
+		[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+        done
+        DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
+        echo $DIR
+}
+
+BASE=$(baseDir)
+cd $BASE
+
+source lib/functions.sh
+
+assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
+
+PARAMS="$(cat)"
+GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
+
+fetchVarsFromVault GIT_PASSWORD
+
+if [ -z "${GIT_PASSWORD}" ]; then
+	fail_and_report 1 "gitpassword.sh failed: Git password not found."
+fi
+
+cat <<EOF
+protocol=https
+host=$GITHOST
+username=bk-${SITE_ID}
+password=${GIT_PASSWORD}
+EOF

lib/update-bridgehead.sh

@@ -19,7 +19,7 @@ fi
 
 hc_send log "Checking for bridgehead updates ..."
 
-CONFFILE=/etc/bridgehead/$PROJECT.conf
+CONFFILE=/etc/bridgehead/$1.conf
 
 if [ ! -e $CONFFILE ]; then
   fail_and_report 1 "Configuration file $CONFFILE not found."
@@ -33,43 +33,7 @@ export SITE_ID
 checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
 checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
 
-# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
+CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
-# If it is missing or expired, Secret Sync will create a new token and write it to the file.
-# The git credential helper reads the token from the file during git pull.
-mkdir -p /var/cache/bridgehead/secrets
-touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
-log "INFO" "Running Secret Sync for the GitLab token"
-docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
-docker run --rm \
-  -v /var/cache/bridgehead/secrets/gitlab_token:/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 /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=$BROKER_URL \
-  -e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-  -e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN: \
-  docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
-if [ $? -eq 0 ]; then
-  log "INFO" "Secret Sync was successful"
-  # In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
-  CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
-  git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
-  # Set the git credential helper
-  git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
-else
-  log "WARN" "Secret Sync failed"
-  # Remove the git credential helper
-  git -C /etc/bridgehead config --unset credential.helper
-fi
-
-# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
-# Let's remove it to avoid confusion. This line can be removed at some point the future when we
-# believe that it was removed on all/most production servers.
-git -C /srv/docker/bridgehead config --unset credential.helper
 
 CHANGES=""
 
@@ -81,6 +45,10 @@ for DIR in /etc/bridgehead $(pwd); do
   if [ -n "$OUT" ]; then
     report_error log "The working directory $DIR is modified. Changed files: $OUT"
   fi
+  if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
+    log "INFO" "Configuring repo to use bridgehead git credential helper."
+    git -C $DIR config credential.helper "$CREDHELPER"
+  fi
   old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
   if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
     log "INFO" "Git is using no proxy!"

versions/prod

@@ -1,2 +0,0 @@
-FOCUS_TAG=main
-BEAM_TAG=main

versions/test

@@ -1,2 +0,0 @@
-FOCUS_TAG=develop
-BEAM_TAG=develop