Add nngm and exliquid modules

ccp/modules/exliquid-compose.yml

@@ -0,0 +1,34 @@
+version: "3.7"
+
+services:
+  exliquid-task-store:
+    image: "samply/blaze:0.19"
+    container_name: bridgehead-exliquid-task-store
+    environment:
+      BASE_URL: "http://bridgehead-exliquid-task-store:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+    volumes:
+    - "exliquid-task-store-data:/app/data"
+    labels:
+      - "traefik.enable=false"
+
+  exliquid-report-hub:
+    image: "samply/report-hub:latest"
+    container_name: bridgehead-exliquid-report-hub
+    environment:
+      SPRING_WEBFLUX_BASE_PATH: "/exliquid"
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      APP_BEAM_APPID: "report-hub.${PROXY_ID}"
+      APP_BEAM_SECRET: ${REPORTHUB_BEAM_SECRET_SHORT}
+      APP_BEAM_PROXY_BASEURL: http://beam-proxy:8081
+      APP_TASKSTORE_BASEURL: "http://bridgehead-exliquid-task-store:8080/fhir"
+      APP_DATASTORE_BASEURL:  http://bridgehead-ccp-blaze:8080/fhir
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.report-ccp.rule=PathPrefix(`/exliquid`)"
+      - "traefik.http.services.report-ccp.loadbalancer.server.port=8080"
+      - "traefik.http.routers.report-ccp.tls=true"
+
+volumes:
+  exliquid-task-store-data:

ccp/modules/exliquid-setup.sh

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+#!/bin/bash
+
+function exliquidSetup() {
+	case ${SITE_ID} in
+		berlin|dresden|essen|frankfurt|freiburg|luebeck|mainz|muenchen-lmu|muenchen-tu|mannheim|tuebingen)
+			EXLIQUID=1
+			;;
+		dktk-test)
+			EXLIQUID=1
+			;;
+		*)
+			EXLIQUID=0
+			;;
+	esac
+	if [[ $EXLIQUID -eq 1 ]]; then
+		log INFO "EXLIQUID setup detected -- will start Report-Hub."
+		OVERRIDE+=" -f ./$PROJECT/exliquid-compose.yml"
+	fi
+}

ccp/modules/mtba-compose.yml

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+version: "3.7"
+
+services:
+  mtba:
+    image: samply/mtba:develop
+    container_name: bridgehead-mtba
+    environment:
+      BLAZE_STORE_URL: http://blaze:8080
+      # NOTE: Aktuell Berechtigungen wie MagicPL!!!
+      # TODO: Add separate ApiKey to MagicPL only for MTBA!
+      ID_MANAGER_API_KEY: ${IDMANAGER_UPLOAD_APIKEY}
+      ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
+      ID_MANAGER_URL: http://id-manager:8080/id-manager
+      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER}
+      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
+      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
+      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
+      CBIOPORTAL_URL:  http://cbioportal:8080
+      FILE_CHARSET: ${MTBA_FILE_CHARSET}
+      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
+      CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
+      - "traefik.http.services.mtba.loadbalancer.server.port=80"
+      - "traefik.http.routers.mtba.tls=true"
+    volumes:
+      - /tmp/bridgehead/mtba/input:/app/input
+      - /tmp/bridgehead/mtba/persist:/app/persist
+
+  # TODO: Include CBioPortal in Deployment ...
+  # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!
+  # TODO: Find a trigger to let mtba signal a restart for CBioPortal
+
+volumes:
+  mtba-data:

ccp/modules/mtba-setup.sh

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+#!/bin/bash
+
+function mtbaSetup() {
+	# TODO: Check if ID-Management Module is activated!
+	if [ -n "$ENABLE_MTBA" ];then
+		log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
+		if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+			log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
+			exit 1;
+		fi
+		OVERRIDE+=" -f ./$PROJECT/mtba-compose.yml"
+	fi
+}

ccp/modules/nngm-compose.yml

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+version: "3.7"
+
+services:
+  connector:
+    container_name: bridgehead-connector
+    image: docker.verbis.dkfz.de/ccp/connector:bk2
+    environment:
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASSWORD}
+      NNGM_MAGICPL_APIKEY: ${NNGM_MAGICPL_APIKEY}
+      NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
+      NNGM_CTS_APIKEY: ${NNGM_CTS_APIKEY}
+      NNGM_CRYPTKEY: ${NNGM_CRYPTKEY}
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.connector.rule=PathPrefix(`/ccp-connector`)"
+      - "traefik.http.services.connector.loadbalancer.server.port=8080"
+      - "traefik.http.routers.connector.tls=true"
+
+  connector_db:
+    image: postgres:9.5-alpine
+    container_name: bridgehead-ccp-connector-db
+    volumes:
+      - "connector_db_data:/var/lib/postgresql/data"
+    environment:
+      POSTGRES_DB: "samplyconnector"
+      POSTGRES_USER: "samplyconnector"
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASSWORD}
+    restart: always
+
+volumes:
+  connector_db_data:

ccp/modules/nngm-setup.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+function nngmSetup() {
+	if [ -n "$NNGM_CTS_APIKEY" ]; then
+		log INFO "nNGM setup detected -- will start nNGM Connector."
+		OVERRIDE+=" -f ./$PROJECT/nngm-compose.yml"
+	fi
+	CONNECTOR_POSTGRES_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+}

ccp/modules/teiler-setup.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 function teilerSetup() {
 	if [ -n "$ENABLE_TEILER" ];then
 		log INFO "Teiler setup detected -- will start Teiler service."

ccp/modules/teiler-ui-setup.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 function teilerUiSetup() {
 	if [ -n "$ENABLE_TEILER" ];then
 		log INFO "Teiler-UI setup detected -- will start Teiler-UI services."