From e0c9a5ced38a61da718b0bdf2b01208c2371f094 Mon Sep 17 00:00:00 2001
From: "p.delpy@dkfz-heidelberg.de" <p.delpy@dkfz-heidelberg.de>
Date: Fri, 2 Dec 2022 15:38:33 +0100
Subject: [PATCH] Added MTBA Module

---
 ccp/mtba-compose.yml | 33 +++++++++++++++++++++++++++++++++
 ccp/nngm-setup.sh    | 12 ++++++++++++
 ccp/vars             |  1 +
 3 files changed, 46 insertions(+)
 create mode 100644 ccp/mtba-compose.yml

diff --git a/ccp/mtba-compose.yml b/ccp/mtba-compose.yml
new file mode 100644
index 0000000..53fd327
--- /dev/null
+++ b/ccp/mtba-compose.yml
@@ -0,0 +1,33 @@
+version: "3.7"
+
+services:
+  mtba:
+    image: samply/mtba:develop
+    container_name: bridgehead-mtba
+    environment:
+      BLAZE_STORE_URL: http://bridgehead-ccp-blaze:8080/fhir
+      # NOTE: Aktuell Berechtigungen wie MagicPL!!!
+      # TODO: Add separate ApiKey to Patientlist only for MTBA!
+      ID_MANAGER_API_KEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
+      ID_MANAGER_URL: http://bridgehead-id-manager:8080
+      PATIENT_CSV_FIRST_NAME_HEADER: ${PATIENT_CSV_FIRST_NAME_HEADER:-"FIRST_NAME"}
+      PATIENT_CSV_LAST_NAME_HEADER: ${PATIENT_CSV_LAST_NAME_HEADER:-"LAST_NAME"}
+      PATIENT_CSV_GENDER_HEADER: ${PATIENT_CSV_GENDER_HEADER:-"GENDER"}
+      PATIENT_CSV_BIRTHDAY_HEADER: ${PATIENT_CSV_BIRTHDAY_HEADER:-"BIRTHDAY"}
+      CBIOPORTAL_URL:  http://bridgehead-ccp-cbioportal:8080
+      MUTATIONS_CSV_SCRIPT_INTERPRETER: "python3"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
+      - "traefik.http.services.mtba.loadbalancer.server.port=80"
+      - "traefik.http.routers.mtba.tls=true"
+    volumes:
+      # This directory persists the FHIR Resources that are needed to import data into blaze.
+      - /var/data/bridgehead/mtba:/app/mtba-files/persist
+      # Place new import files in this directory
+      - /tmp/bridgehead/mtba/:/app/mtba-files/input
+
+  # TODO: Include CBioPortal in Deployment ...
+  # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!
+  # TODO: Find a trigger to let mtba signal a restart for CBioPortal
diff --git a/ccp/nngm-setup.sh b/ccp/nngm-setup.sh
index d5b80eb..b55d48e 100644
--- a/ccp/nngm-setup.sh
+++ b/ccp/nngm-setup.sh
@@ -7,3 +7,15 @@ function nngmSetup() {
 	fi
 	CONNECTOR_POSTGRES_PASSWORD="$(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/${SITE_ID}.priv.pem | base64 | head -c 30)"
 }
+
+function mtbaSetup() {
+	# TODO: Check if ID-Management Module is activated!
+	if [ -n "$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
+}
diff --git a/ccp/vars b/ccp/vars
index 89deae0..5172d24 100644
--- a/ccp/vars
+++ b/ccp/vars
@@ -16,3 +16,4 @@ source $PROJECT/nngm-setup.sh
 nngmSetup
 source $PROJECT/exliquid-setup.sh
 exliquidSetup
+mtbaSetup
\ No newline at end of file