Added MTBA Module

This commit is contained in:
p.delpy@dkfz-heidelberg.de 2022-12-02 15:38:33 +01:00
parent 276be28db1
commit 828312e045
3 changed files with 46 additions and 0 deletions

33
ccp/mtba-compose.yml Normal file
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@ -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

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@ -7,3 +7,15 @@ function nngmSetup() {
fi 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)" 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
}

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@ -16,3 +16,4 @@ source $PROJECT/nngm-setup.sh
nngmSetup nngmSetup
source $PROJECT/exliquid-setup.sh source $PROJECT/exliquid-setup.sh
exliquidSetup exliquidSetup
mtbaSetup