test: use batch import branch of oBDS2FHIR-REST

bbmri/modules/eric-setup.sh

@@ -10,10 +10,6 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
 			export ERIC_BROKER_ID=broker.bbmri.samply.de
 			export ERIC_ROOT_CERT=eric
 			;;
-		"acceptance")
-			export ERIC_BROKER_ID=broker-acc.bbmri-acc.samply.de
-			export ERIC_ROOT_CERT=eric.acc
-			;;
 		"test")
 			export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
 			export ERIC_ROOT_CERT=eric.test

bbmri/modules/eric.acc.root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUE/wu6FmI+KSMOalI65b+lI3HI4cwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwOTE2MTUyMzU0WhcNMzQw
-OTE0MTUyNDI0WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAOt1I1FQt2bI4Nnjtg8JBYid29cBIkDT4MMb45Jr
-ays24y4R3WO7VJK9UjNduSq/A1jlA0W0A/szDf8Ojq6bBtg+uL92PTDjYH1QXwX0
-c7eMo2tvvyyrs/cb2/ovDBQ1lpibcxVmVAv042ASmil3SdqKKXpv3ATnF9I7V4cv
-fwB56FChaGIov5EK+9JOMjTx6oMlBEgUFR6qq/lSqM9my0HYwUFbX2W+nT9EKEIP
-9UP1eyfRZR3E/+oticnm/cS20BGCbjoYrNgLthXKyaASuhGoElKs8EZ3h9MiI+u0
-DpR0KpePhAkMLugBrgYWqkMwwD1684LfC4YVQrsLwzo5OW8CAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFPbXs3g3lMjH
-1JMe0a5aVbN7lB92MB8GA1UdIwQYMBaAFPbXs3g3lMjH1JMe0a5aVbN7lB92MBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQBM5RsXb2HN
-FpC1mYfocXAn20Zu4d603qmc/IqkiOWbp36pWo+jk1AxejyRS9hEpQalgSnvcRPQ
-1hPEhGU+wvI0WWVi/01iNjVbXmJNPQEouXQWAT17dyp9vqQkPw8LNzpSV/qdPgbT
-Z9o3sZrjUsSLsK7A7Q5ky4ePkiJBaMsHeAD+wqGwpiJ4D2Xhp8e1v36TWM0qt2EA
-gySx9isx/jeGGPBmDqYB9BCal5lrihPN56jd+5pCkyXeZqKWiiXFJKXwcwxctYZc
-ADHIiTLLPXE8LHTUJAO51it1NAZ1S24aMzax4eWDXcWO7/ybbx5pkYkMd6EqlKHd
-8riQJIhY4huX
------END CERTIFICATE-----

bridgehead

@@ -69,7 +69,7 @@ loadVars() {
 		if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
 			ENVIRONMENT="production"
 		else
-			ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility
+			ENVIRONMENT="test"
 		fi
 	fi
 	# Source the versions of the images components 
@@ -80,9 +80,6 @@ loadVars() {
 		"test")
 			source ./versions/test
 			;;
-		"acceptance")
-			source ./versions/acceptance
-			;;
 		*)
 			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
 			source ./versions/prod

ccp/modules/exporter-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:test
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
     container_name: bridgehead-ccp-exporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"

ccp/modules/obds2fhir-rest-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
   obds2fhir-rest:
     container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
+    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:fixSampleImport
     environment:
       IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
       MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

ccp/modules/teiler-compose.yml

@@ -19,8 +19,7 @@ services:
       HTTP_RELATIVE_PATH: "/ccp-teiler"
 
   teiler-dashboard:
-    #image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
-    image: samply/teiler-dashboard:develop
     container_name: bridgehead-teiler-dashboard
     labels:
       - "traefik.enable=true"
@@ -32,7 +31,6 @@ services:
     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_REALM: "${OIDC_REALM}"
       OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@@ -43,6 +41,7 @@ services:
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
       TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
       TEILER_USER: "${OIDC_USER_GROUP}"
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@@ -70,10 +69,10 @@ services:
       TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
       TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
       TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
+      CENTRAX_URL: "${CENTRAXX_URL}"
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-      IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active
     secrets:
       - ccp.conf
 

kr/modules/teiler-compose.yml

@@ -31,7 +31,6 @@ services:
     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_REALM: "${OIDC_REALM}"
       OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@@ -42,6 +41,7 @@ services:
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
       TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
       TEILER_USER: "${OIDC_USER_GROUP}"
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@@ -69,6 +69,7 @@ services:
       TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
       TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
       TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
+      CENTRAX_URL: "${CENTRAXX_URL}"
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"

lib/functions.sh

@@ -347,21 +347,18 @@ function secret_sync_gitlab_token() {
         root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
     fi
 
-    # Create a temporary directory for Secret Sync that is valid per boot
+    # Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
-    secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
-    mkdir -p $secret_sync_tempdir
-
-    # Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
     # If it is missing or expired, Secret Sync will create a new token and write it to the file.
     # The git credential helper reads the token from the file during git pull.
+    mkdir -p /var/cache/bridgehead/secrets
+    touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
     log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
     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 $root_crt_file:/run/secrets/root.crt.pem:ro \
         -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-        -v $secret_sync_tempdir:/secret-sync/ \
-        -e CACHE_PATH=/secret-sync/gitlab-token \
         -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
         -e NO_PROXY=localhost,127.0.0.1 \
         -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \

lib/gitlab-token-helper.sh

@@ -2,7 +2,7 @@
 
 [ "$1" = "get" ] || exit
 
-source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
+source /var/cache/bridgehead/secrets/gitlab_token
 
 # Any non-empty username works, only the token matters
 cat << EOF

modules/ssh-tunnel-setup.sh

@@ -2,5 +2,5 @@
 
 if [ -n "$ENABLE_SSH_TUNNEL" ]; then
 	log INFO "SSH Tunnel setup detected -- will start SSH Tunnel."
-	OVERRIDE+=" -f ./modules/ssh-tunnel-compose.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/ssh-tunnel-compose.yml"
 fi

modules/transfair-compose.yml

@@ -8,8 +8,7 @@ services:
       - TTP_URL
       - TTP_ML_API_KEY
       - TTP_GW_SOURCE
-      - TTP_GW_EPIX_DOMAIN
+      - TTP_GW_DOMAIN
-      - TTP_GW_GPAS_DOMAIN
       - TTP_TYPE
       - TTP_AUTH
       - PROJECT_ID_SYSTEM
@@ -23,9 +22,6 @@ services:
       - DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
       - RUST_LOG=${RUST_LOG:-info}
       - TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
-      - TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
-      - NO_PROXY=${TRANSFAIR_NO_PROXIES}
-      - ALL_PROXY=http://forward_proxy:3128
     volumes:
       - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
@@ -63,9 +59,9 @@ services:
 
   transfair-request-blaze:
     image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
-    container_name: bridgehead-transfair-request-blaze
+    container_name: bridgehead-transfair-requests-blaze
     environment:
-      BASE_URL: "http://bridgehead-transfair-request-blaze:8080"
+      BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx1024m"
       DB_BLOCK_CACHE_SIZE: 1024
       CQL_EXPR_CACHE_SIZE: 8

modules/transfair-setup.sh

@@ -15,7 +15,7 @@ function transfairSetup() {
 		    log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
 	    else
 		    log INFO "TransFAIR request fhir store not set writing to internal blaze"
-		    FHIR_REQUEST_URL="http://transfair-request-blaze:8080"
+		    FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
 		    OVERRIDE+=" --profile transfair-request-blaze"
 	    fi
 	    if [ -n "$TTP_GW_SOURCE" ]; then
@@ -27,9 +27,5 @@ function transfairSetup() {
         else
 		    log INFO "TransFAIR configured without ttp"
 	    fi
-        TRANSFAIR_NO_PROXIES="transfair-input-blaze,blaze,transfair-requests-blaze"
-        if [ -n "${TRANSFAIR_NO_PROXY}" ]; then
-            TRANSFAIR_NO_PROXIES+=",${TRANSFAIR_NO_PROXY}"
-        fi
     fi
 }

versions/acceptance

@@ -1,3 +0,0 @@
-FOCUS_TAG=develop
-BEAM_TAG=develop
-BLAZE_TAG=main