From a3ba98a2fdb1d950ab4fbcb2d1a9302692086816 Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Wed, 7 Dec 2022 15:46:19 +0100 Subject: [PATCH 1/4] Added Configuration for Local ID-Management --- ccp/modules/id-management-setup.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh index 0f361dc..b02ef66 100644 --- a/ccp/modules/id-management-setup.sh +++ b/ccp/modules/id-management-setup.sh @@ -1,7 +1,8 @@ #!/bin/bash function idManagementSetup() { - if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then +# if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then + 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" From e2d90447f7e3ad6ee981c16de6d02b048cfdebf2 Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Thu, 15 Dec 2022 16:39:03 +0100 Subject: [PATCH 2/4] refactor: Changed Trigger of the IDM Module --- ccp/modules/id-management-setup.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh index b02ef66..c8ea707 100644 --- a/ccp/modules/id-management-setup.sh +++ b/ccp/modules/id-management-setup.sh @@ -1,7 +1,6 @@ #!/bin/bash function idManagementSetup() { -# if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then if [ -n "$ENABLE_ID_MANAGEMENT" ]; then log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)." OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml" From bce28342f90482205a5eba1d284fb5dffb6e6cce Mon Sep 17 00:00:00 2001 From: "p.delpy@dkfz-heidelberg.de" Date: Wed, 18 Jan 2023 13:42:36 +0100 Subject: [PATCH 3/4] update docker and host paths --- ccp/mtba-compose.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ccp/mtba-compose.yml b/ccp/mtba-compose.yml index 857ff34..ad25dd0 100644 --- a/ccp/mtba-compose.yml +++ b/ccp/mtba-compose.yml @@ -17,16 +17,16 @@ services: PATIENT_CSV_BIRTHDAY_HEADER: ${PATIENT_CSV_BIRTHDAY_HEADER:-"BIRTHDAY"} CBIOPORTAL_URL: http://bridgehead-ccp-cbioportal:8080 MUTATIONS_CSV_SCRIPT_INTERPRETER: "python3" + NEW_FILES_DIRECTORY: "/app/input" + PERSIST_DIRECTORY: "/app/persist" labels: - "traefik.enable=true" - "traefik.http.routers.mtba.rule=PathPrefix(`/`)" - "traefik.http.services.mtba.loadbalancer.server.port=80" - "traefik.http.routers.mtba.tls=true" volumes: - # This directory persists the FHIR Resources that are needed to import data into blaze. - - mtba-data:/app/mtba-files/persist - # Place new import files in this directory - - /tmp/bridgehead/mtba/:/app/mtba-files/input + - /tmp/bridgehead/mtba/input:/app/input + - /tmp/bridgehead/mtba/persist:/app/persist # TODO: Include CBioPortal in Deployment ... # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted! From e9455a5558dd33de59bb46e3c048368f4c30df34 Mon Sep 17 00:00:00 2001 From: "p.delpy@dkfz-heidelberg.de" Date: Fri, 27 Jan 2023 11:13:49 +0100 Subject: [PATCH 4/4] update mtba config --- ccp/modules/id-management-setup.sh | 2 +- ccp/mtba-compose.yml | 20 ++++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/ccp/modules/id-management-setup.sh b/ccp/modules/id-management-setup.sh index c8ea707..0f361dc 100644 --- a/ccp/modules/id-management-setup.sh +++ b/ccp/modules/id-management-setup.sh @@ -1,7 +1,7 @@ #!/bin/bash function idManagementSetup() { - if [ -n "$ENABLE_ID_MANAGEMENT" ]; then + if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)." OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml" diff --git a/ccp/mtba-compose.yml b/ccp/mtba-compose.yml index ad25dd0..bb90059 100644 --- a/ccp/mtba-compose.yml +++ b/ccp/mtba-compose.yml @@ -5,20 +5,20 @@ services: image: samply/mtba:develop container_name: bridgehead-mtba environment: - BLAZE_STORE_URL: http://bridgehead-ccp-blaze:8080/fhir + 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://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" - NEW_FILES_DIRECTORY: "/app/input" - PERSIST_DIRECTORY: "/app/persist" + 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(`/`)"