From 99c0e7f28354bcb6ae49f30556df78d1a9e1da07 Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Wed, 7 Dec 2022 15:46:19 +0100 Subject: [PATCH 1/7] Added Configuration for Local ID-Management --- ccp/modules/id-management-compose.yml | 75 +++++++++++++++++++++++++++ ccp/modules/id-management-setup.sh | 17 ++++++ ccp/vars | 3 ++ lib/functions.sh | 2 +- 4 files changed, 96 insertions(+), 1 deletion(-) create mode 100644 ccp/modules/id-management-compose.yml create mode 100644 ccp/modules/id-management-setup.sh diff --git a/ccp/modules/id-management-compose.yml b/ccp/modules/id-management-compose.yml new file mode 100644 index 0000000..0968048 --- /dev/null +++ b/ccp/modules/id-management-compose.yml @@ -0,0 +1,75 @@ +version: "3.7" +services: + id-manager: + image: docker.verbis.dkfz.de/bridgehead/magicpl + environment: + TOMCAT_REVERSEPROXY_FQDN: ${HOST} + MAGICPL_SITE: ${SITE_ID} + MAGICPL_ALLOWED_ORIGINS: https://${HOST} + MAGICPL_LOCAL_PATIENTLIST_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} + MAGICPL_CENTRAXX_APIKEY: ${IDMANAGER_CENTRAXX_APIKEY} + MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_CONNECTOR_APIKEY} + MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY} + MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY} + MAGICPL_OIDC_CLIENT_ID: ${IDMANAGER_AUTH_CLIENT_ID} + MAGICPL_OIDC_CLIENT_SECRET: ${IDMANAGER_AUTH_CLIENT_SECRET} + depends_on: + - patientlist + labels: + - "traefik.enable=true" + - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)" + - "traefik.http.services.id-manager.loadbalancer.server.port=8080" + - "traefik.http.routers.id-manager.tls=true" + + patientlist: + image: docker.verbis.dkfz.de/bridgehead/mainzelliste + environment: + - TOMCAT_REVERSEPROXY_FQDN=${HOST} + - ML_SITE=${SITE_ID} + - ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD} + - ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} + # Add Variables from /etc/patientlist-id-generators.env + - ML_BK_IDGENERATOR_RANDOM_1 + - ML_BK_IDGENERATOR_RANDOM_2 + - ML_BK_IDGENERATOR_RANDOM_3 + - ML_MDS_IDGENERATOR_RANDOM_1 + - ML_MDS_IDGENERATOR_RANDOM_2 + - ML_MDS_IDGENERATOR_RANDOM_3 + - ML_DKTK000001985_IDGENERATOR_RANDOM_1 + - ML_DKTK000001985_IDGENERATOR_RANDOM_2 + - ML_DKTK000001985_IDGENERATOR_RANDOM_3 + - ML_DKTK000001986_IDGENERATOR_RANDOM_1 + - ML_DKTK000001986_IDGENERATOR_RANDOM_2 + - ML_DKTK000001986_IDGENERATOR_RANDOM_3 + - ML_DKTK000001950_IDGENERATOR_RANDOM_1 + - ML_DKTK000001950_IDGENERATOR_RANDOM_2 + - ML_DKTK000001950_IDGENERATOR_RANDOM_3 + - ML_DKTK000001951_IDGENERATOR_RANDOM_1 + - ML_DKTK000001951_IDGENERATOR_RANDOM_2 + - ML_DKTK000001951_IDGENERATOR_RANDOM_3 + - ML_DKTK999999999_IDGENERATOR_RANDOM_1 + - ML_DKTK999999999_IDGENERATOR_RANDOM_2 + - ML_DKTK999999999_IDGENERATOR_RANDOM_3 + - ML_DKTK000002089_IDGENERATOR_RANDOM_1 + - ML_DKTK000002089_IDGENERATOR_RANDOM_2 + - ML_DKTK000002089_IDGENERATOR_RANDOM_3 + labels: + - "traefik.enable=true" + - "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)" + - "traefik.http.services.patientlist.loadbalancer.server.port=8080" + - "traefik.http.routers.patientlist.tls=true" + depends_on: + - patientlist-db + + patientlist-db: + image: postgres:14-alpine + environment: + POSTGRES_USER: "mainzelliste" + POSTGRES_DB: "mainzelliste" + POSTGRES_PASSWORD: ${PATIENTLIST_POSTGRES_PASSWORD} + volumes: + - "patientlist-db-data:/var/lib/postgresql/data" + +volumes: + patientlist-db-data: + diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh new file mode 100644 index 0000000..ca939fb --- /dev/null +++ b/ccp/modules/id-management-setup.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +function idManagementSetup() { + if [ -n "$ENABLE_ID_MANAGEMENT" ]; then + log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)." + OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml" + + # Auto Generate local Passwords + PATIENTLIST_POSTGRES_PASSWORD="$(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/${SITE_ID}.priv.pem | base64 | head -c 30)" + IDMANAGER_LOCAL_PATIENTLIST_APIKEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)" + + # Source the ID Generators Configuration + source /etc/bridgehead/patientlist-id-generators.env + log INFO "ID-Management Generator 1: ${ML_BK_IDGENERATOR_RANDOM_1}" + fi + +} diff --git a/ccp/vars b/ccp/vars index 63def80..89deae0 100644 --- a/ccp/vars +++ b/ccp/vars @@ -8,6 +8,9 @@ REPORTHUB_BEAM_SECRET_LONG="ApiKey report-hub.${PROXY_ID} ${REPORTHUB_BEAM_SECRE SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem +# This will load id-management setup. Effective only if id-management configuration is defined. +source $PROJECT/modules/id-management-setup.sh +idManagementSetup # This will load nngm setup. Effective only if nngm configuration is defined. source $PROJECT/nngm-setup.sh nngmSetup diff --git a/lib/functions.sh b/lib/functions.sh index 4f40fd0..355ebaa 100644 --- a/lib/functions.sh +++ b/lib/functions.sh @@ -131,7 +131,7 @@ fail_and_report() { setHostname() { if [ -z "$HOST" ]; then - export HOST=$(hostname -f) + export HOST=$(hostname -f | tr "[:upper:]" "[:lower:]") log DEBUG "Using auto-detected hostname $HOST." fi } From 5e063003ace490b3835e30fcebbafd6465ed4586 Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Tue, 13 Dec 2022 16:51:32 +0100 Subject: [PATCH 2/7] feature: Added automated Backups for PostgreSQL --- README.md | 9 +++++++ ccp/modules/id-management-compose.yml | 11 ++++---- lib/functions.sh | 11 ++++++++ lib/install-bridgehead.sh | 10 ++++--- lib/update-bridgehead.sh | 39 +++++++++++++++++++++++++++ 5 files changed, 72 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index b57c10e..24ebdf2 100644 --- a/README.md +++ b/README.md @@ -128,6 +128,8 @@ All of the Bridgehead's outgoing connections are secured by transport encryption - `/etc/bridgehead/traefik-tls` contains your Bridgehead's reverse proxies TLS certificates for [HTTPS access](#https-access). - `/etc/bridgehead/pki` contains your Bridgehead's private key (e.g., but not limited to Samply.Beam), generated as part of the [Samply.Beam enrollment](#register-with-samplybeam). - `/etc/bridgehead/trusted-ca-certs` contains third-party certificates to be trusted by the Bridgehead. For example, you want to place the certificates of your [TLS-terminating proxy](#network) here. +- `/var/data/bridgehead` contains persistent data of the bridgehead + - `/var/data/bridgehead/backups` contains automatically created backups of the databases. Your Bridgehead's actual data is not stored in the above directories, but in named docker volumes, see `docker volume ls` and `docker volume inspect `. @@ -139,6 +141,13 @@ Your Bridgehead will automatically and regularly check for updates. Whenever som If you would like to understand what happens exactly and when, please check the systemd units deployed during the [installation](#base-installation) via `systemctl cat bridgehead-update@.service` and `systemctl cat bridgehead-update@ \ + "$1/$2/$(date +%Y-KW%V).sql" +} + + # from: https://gist.github.com/sj26/88e1c6584397bb7c13bd11108a579746 # ex. use: retry 5 /bin/false function retry { diff --git a/lib/install-bridgehead.sh b/lib/install-bridgehead.sh index 5e3add3..7cbd8ef 100755 --- a/lib/install-bridgehead.sh +++ b/lib/install-bridgehead.sh @@ -22,8 +22,8 @@ Cmnd_Alias BRIDGEHEAD${PROJECT^^} = \\ /bin/systemctl stop bridgehead@${PROJECT}.service, \\ /bin/systemctl restart bridgehead@${PROJECT}.service, \\ /bin/systemctl restart bridgehead@*.service, \\ - /bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead, \\ - /usr/bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead + /bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead /var/data/bridgehead, \\ + /usr/bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead /var/data/bridgehead bridgehead ALL= NOPASSWD: BRIDGEHEAD${PROJECT^^} EOF @@ -37,6 +37,10 @@ if [ -z "$LDM_PASSWORD" ]; then echo -e "## Local Data Management Basic Authentication\n# User: $PROJECT\nLDM_PASSWORD=$generated_passwd" >> /etc/bridgehead/${PROJECT}.local.conf; fi +log "INFO" "Creating directory /var/data/bridgehead for storage of persistent data." +mkdir -p /var/data/bridgehead +chown -R bridgehead /var/data/bridgehead + log "INFO" "Registering system units for bridgehead and bridgehead-update" cp -v \ lib/systemd/bridgehead\@.service \ @@ -63,4 +67,4 @@ else STR="Success. Next, enroll into the $PROJECT broker by creating a cryptographic certificate. To do so, run\n\n /srv/docker/bridgehead/bridgehead enroll $PROJECT\n\nThen, you may start the bridgehead by running$STR" fi -log "INFO" "$STR" \ No newline at end of file +log "INFO" "$STR" diff --git a/lib/update-bridgehead.sh b/lib/update-bridgehead.sh index 897c8a2..cc1d55f 100755 --- a/lib/update-bridgehead.sh +++ b/lib/update-bridgehead.sh @@ -1,6 +1,45 @@ #!/bin/bash source lib/functions.sh +AUTO_BACKUP=${AUTO_BACKUP:-true} + +if [ "$AUTO_BACKUP" == "true" ]; then + BACKUP_DIRECTORY="/var/data/bridgehead/backups" + if [ ! -d /var/data ]; then + log DEBUG "Created /var/data" + mkdir /var/data + fi + if [ ! -d /var/data/bridgehead ]; then + log DEBUG "Created /var/data/bridgehead" + mkdir /var/data/bridgehead + fi + if [ ! -d $BACKUP_DIRECTORY ]; then + message="Performing automatic maintenance: Creating Backup directory $BACKUP_DIRECTORY." + hc_send log "$message" + log INFO "$message" + mkdir -p $BACKUP_DIRECTORY + fi + BACKUP_SERVICES="$(docker ps --filter ancestor=postgres:14-alpine --format "{{.Names}}" | tr "\n" "\ ")" + log INFO "Performing automatic maintenance: Creating Backups for $BACKUP_SERVICES"; + for service in $BACKUP_SERVICES; do + if [ ! -d $BACKUP_DIRECTORY/$service ]; then + message="Performing automatic maintenance: Creating Backup directory for $service in $BACKUP_DIRECTORY." + hc_send log "$message" + log INFO "$message" + mkdir -p $BACKUP_DIRECTORY/$service + fi + if createEncryptedPostgresBackup "$BACKUP_DIRECTORY" "$service"; then + message="Performing automatic maintenance: Stored encrypted Backup for $service in $BACKUP_DIRECTORY." + hc_send log "$message" + log INFO "$message" + else + fail_and_report 5 "Failed to create encrypted update for $service" + fi + done +else + log WARN "Automated backups are disabled (variable AUTO_BACKUPS != \"true\")" +fi + AUTO_HOUSEKEEPING=${AUTO_HOUSEKEEPING:-true} if [ "$AUTO_HOUSEKEEPING" == "true" ]; then From 125bb5e26232be6f5279d1fb771a99710d8fe012 Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Thu, 15 Dec 2022 16:39:03 +0100 Subject: [PATCH 3/7] refactor: Changed Trigger of the IDM Module --- ccp/modules/id-management-setup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh index ca939fb..790f846 100644 --- a/ccp/modules/id-management-setup.sh +++ b/ccp/modules/id-management-setup.sh @@ -1,7 +1,7 @@ #!/bin/bash function idManagementSetup() { - if [ -n "$ENABLE_ID_MANAGEMENT" ]; then + if [ -n "$IDMANAGER_CENTRAXX_APIKEY" ]; then log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)." OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml" From bc72093be9c42db534d12a4d418106cf7e21409d Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Thu, 15 Dec 2022 16:39:23 +0100 Subject: [PATCH 4/7] docs: Added Documentation for the IDM Module --- ccp/modules/id-management.md | 58 ++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 ccp/modules/id-management.md diff --git a/ccp/modules/id-management.md b/ccp/modules/id-management.md new file mode 100644 index 0000000..8de2f5a --- /dev/null +++ b/ccp/modules/id-management.md @@ -0,0 +1,58 @@ +# Module: Id-Management +This module provides integration with the CCP-Pseudonymiziation Service. To learn more on the backgrounds of this service, you can refer to the [CCP-DSK](https://dktk.dkfz.de/application/files/5016/2030/2474/20_11_23_Datenschutzkonzept_CCP-IT_inkl_Anlagen.pdf). + +## Getting Started +You must add following configuration variables to your sites-configuration repository: + +``` +IDMANAGER_CENTRAXX_APIKEY="" +IDMANAGER_CONNECTOR_APIKEY="" +IDMANAGER_CENTRAL_PATIENTLIST_APIKEY="" +IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY="" +IDMANAGER_AUTH_CLIENT_ID="" +IDMANAGER_AUTH_CLIENT_SECRET="" +``` + +Additionally, the ccp-it needs to add a new file "patientlist-id-generators.env" to your site configuration. This file will hold the seeds for the different id-generators used in all projects. + +After adding the configuration, you simply need to update your bridgehead and 3 new services will run on your server: + +- `bridgehead-id-manager`, accessible by "https:///id-manager". This component adds a common interface for creating pseudonymes in the bridgehead. +- `bridgehead-patientlist`, accessible by "https:// NOTE: Please create the postgres dump with the options "--no-owner" and "--no-privileges". Additionally ensure the dump is created in the plain format (SQL). + +After this, you can restart your bridgehead and the dump will be imported: +``` +systemctl start bridgehead@ccp +``` + +### How to connect your local data-management +Typically, the sites connect their local data-management for the pseudonym creation with the id-management in the bridgehead. In the following two sections, you can read where you can change the configuration: +#### Sites using CentraXX +On your CentraXX Server, you need to change following settings in the "centraxx-dev.properties" file. +``` +dktk.idmanagement.url=https:///id-manager/translator/getId +dktk.idmanagement.apiKey= +``` +They typically already exist, but need to be changed to the new values! +#### Sites using ADT2FHIR +@Pierre + + +### How to connect the legacy windows bridgehead +You need to change the configuration file "..." of your Windows Bridgehead. TODO... From 276be28db1792c4f276191e24bbb3b7cbd8f852c Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Fri, 16 Dec 2022 12:02:49 +0100 Subject: [PATCH 5/7] fix: Included Legacy ID-Mapping (Please Complete) --- ccp/modules/id-management-compose.yml | 6 +++--- ccp/modules/id-management-setup.sh | 24 ++++++++++++++++++++++-- ccp/modules/id-management.md | 6 +++--- 3 files changed, 28 insertions(+), 8 deletions(-) diff --git a/ccp/modules/id-management-compose.yml b/ccp/modules/id-management-compose.yml index d1639af..4baaba7 100644 --- a/ccp/modules/id-management-compose.yml +++ b/ccp/modules/id-management-compose.yml @@ -5,11 +5,11 @@ services: container_name: bridgehead-id-manager environment: TOMCAT_REVERSEPROXY_FQDN: ${HOST} - MAGICPL_SITE: ${SITE_ID} + MAGICPL_SITE: ${IDMANAGEMENT_FRIENDLY_ID} MAGICPL_ALLOWED_ORIGINS: https://${HOST} MAGICPL_LOCAL_PATIENTLIST_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} - MAGICPL_CENTRAXX_APIKEY: ${IDMANAGER_CENTRAXX_APIKEY} - MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_CONNECTOR_APIKEY} + MAGICPL_CENTRAXX_APIKEY: ${IDMANAGER_UPLOAD_APIKEY} + MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY} MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY} MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY} MAGICPL_OIDC_CLIENT_ID: ${IDMANAGER_AUTH_CLIENT_ID} diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh index 790f846..d2449c7 100644 --- a/ccp/modules/id-management-setup.sh +++ b/ccp/modules/id-management-setup.sh @@ -1,7 +1,7 @@ #!/bin/bash function idManagementSetup() { - if [ -n "$IDMANAGER_CENTRAXX_APIKEY" ]; then + if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)." OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml" @@ -11,7 +11,27 @@ function idManagementSetup() { # Source the ID Generators Configuration source /etc/bridgehead/patientlist-id-generators.env - log INFO "ID-Management Generator 1: ${ML_BK_IDGENERATOR_RANDOM_1}" + + # Ensure old ids are working !!! + legacyIdMapping fi } + +# TODO: Map all old site ids to the new ones +function legacyIdMapping() { + case ${SITE_ID} in + "berlin") + export IDMANAGEMENT_FRIENDLY_ID=Berlin + ;; + "dresden") + export IDMANAGEMENT_FRIENDLY_ID=Dresden + ;; + "frankfurt") + export IDMANAGEMENT_FRIENDLY_ID=Frankfurt + ;; + *) + export IDMANAGEMENT_FRIENDLY_ID=$SITE_ID + ;; + esac +} diff --git a/ccp/modules/id-management.md b/ccp/modules/id-management.md index 8de2f5a..89ff65c 100644 --- a/ccp/modules/id-management.md +++ b/ccp/modules/id-management.md @@ -5,8 +5,8 @@ This module provides integration with the CCP-Pseudonymiziation Service. To lear You must add following configuration variables to your sites-configuration repository: ``` -IDMANAGER_CENTRAXX_APIKEY="" -IDMANAGER_CONNECTOR_APIKEY="" +IDMANAGER_UPLOAD_APIKEY="" +IDMANAGER_READ_APIKEY="" IDMANAGER_CENTRAL_PATIENTLIST_APIKEY="" IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY="" IDMANAGER_AUTH_CLIENT_ID="" @@ -47,7 +47,7 @@ Typically, the sites connect their local data-management for the pseudonym creat On your CentraXX Server, you need to change following settings in the "centraxx-dev.properties" file. ``` dktk.idmanagement.url=https:///id-manager/translator/getId -dktk.idmanagement.apiKey= +dktk.idmanagement.apiKey= ``` They typically already exist, but need to be changed to the new values! #### Sites using ADT2FHIR From 828312e04510315dd9ee87c3d5b9f53a4099852d Mon Sep 17 00:00:00 2001 From: "p.delpy@dkfz-heidelberg.de" Date: Fri, 2 Dec 2022 15:38:33 +0100 Subject: [PATCH 6/7] 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 From e1e7ffece8899a57ce6c22b1e5f55ebdf083225c Mon Sep 17 00:00:00 2001 From: "p.delpy@dkfz-heidelberg.de" Date: Fri, 16 Dec 2022 15:01:04 +0100 Subject: [PATCH 7/7] set magicpl instead of patientlist --- ccp/mtba-compose.yml | 4 ++-- ccp/nngm-setup.sh | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ccp/mtba-compose.yml b/ccp/mtba-compose.yml index 53fd327..d492ae0 100644 --- a/ccp/mtba-compose.yml +++ b/ccp/mtba-compose.yml @@ -7,8 +7,8 @@ services: 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} + # 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://bridgehead-id-manager:8080 PATIENT_CSV_FIRST_NAME_HEADER: ${PATIENT_CSV_FIRST_NAME_HEADER:-"FIRST_NAME"} diff --git a/ccp/nngm-setup.sh b/ccp/nngm-setup.sh index b55d48e..ba2e77f 100644 --- a/ccp/nngm-setup.sh +++ b/ccp/nngm-setup.sh @@ -12,7 +12,7 @@ function mtbaSetup() { # TODO: Check if ID-Management Module is activated! if [ -n "$ENABLE_MTBA" ];then log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal." - if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then + if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!" exit 1; fi