Added extra stuff for EHDS2

This includes docker-compose files that include transfair plus
configuration variables specific to EHDS2.

bbmri/modules/ehds2-compose.yml

@@ -0,0 +1,60 @@
+version: "3.7"
+
+services:
+  focus-ehds2:
+    #image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: samply/focus
+    container_name: bridgehead-focus-ehds2
+    environment:
+      API_KEY: ${EHDS2_FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${EHDS2_PROXY_ID}
+      PROXY_ID: ${EHDS2_PROXY_ID}
+      BLAZE_URL: "http://blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy-ehds2:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+    depends_on:
+      - "beam-proxy-ehds2"
+      - "blaze"
+
+  beam-proxy-ehds2:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-beam-proxy-ehds2
+    environment:
+      BROKER_URL: ${EHDS2_BROKER_URL}
+      PROXY_ID: ${EHDS2_PROXY_ID}
+      APP_focus_KEY: ${EHDS2_FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/bbmri/modules/${EHDS2_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+
+  # Convert ECDC CSV file into FHIR and push to Blaze
+  transfair:
+    container_name: transfair
+    image: samply/transfair
+    environment:
+      FHIR_INPUT_URL: "http://source_blaze:8080/fhir"
+      FHIR_OUTPUT_URL: "http://bridgehead-bbmri-blaze:8080/fhir"
+      PROFILE: "amr2fhir"
+      #WRITE_BUNDLES_TO_FILE: "true"
+      AMR_FILE_PATH: "/app/data"
+    restart: on-failure
+    command: sh -c "sleep 60 && rm -rf /app/test/* && java -jar transFAIR.jar && tail -f /dev/null"
+    #command: sh -c "rm -rf /app/test/* && java -jar transFAIR.jar"
+    volumes:
+      - /home/gerhard/Projects/EHDS2/PrototypeSpring2024/test/:/app/test/
+      - /home/gerhard/Projects/EHDS2/PrototypeSpring2024/Data/:/app/data/
+
+  # Report on the data pushed to Blaze by TransFAIR
+  blazectl:
+    container_name: blazectl
+    image: samply/blazectl
+    command: sh -c "sleep 300 && echo Source store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"
+

bbmri/modules/ehds2-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+if [ "${ENABLE_EHDS2}" == "true" ]; then
+	log INFO "EHDS2 setup detected -- will start services for German Biobank Node."
+	OVERRIDE+=" -f ./$PROJECT/modules/ehds2-compose.yml"
+
+	# The environment needs to be defined in /etc/bridgehead
+	case "$ENVIRONMENT" in
+		"production")
+			export EHDS2_BROKER_ID=broker.bbmri.samply.de
+			export EHDS2_ROOT_CERT=ehds2
+			;;
+		"test")
+			export EHDS2_BROKER_ID=broker.test.bbmri.samply.de
+			export EHDS2_ROOT_CERT=ehds2.test
+			;;
+		*)
+			report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			export EHDS2_BROKER_ID=broker.bbmri.samply.de
+			export EHDS2_ROOT_CERT=ehds2
+			;;
+	esac
+	
+	EHDS2_BROKER_URL=https://${EHDS2_BROKER_ID}
+	EHDS2_PROXY_ID=${SITE_ID}.${EHDS2_BROKER_ID}
+	EHDS2_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+	EHDS2_SUPPORT_EMAIL=feedback@germanbiobanknode.de
+fi

bbmri/modules/ehds2.root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----
+MIIDNTCCAh2gAwIBAgIUMy/n0zFRihhVR3aAD54LumzeYdwwDQYJKoZIhvcNAQEL
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+-----END CERTIFICATE-----

bbmri/modules/ehds2.test.root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----
+MIIDNTCCAh2gAwIBAgIUJ0g7k2vrdAwNTU38S1/mU8NO26MwDQYJKoZIhvcNAQEL
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+-----END CERTIFICATE-----