diff --git a/dhki/vars b/dhki/vars index b728925..f7f7ecd 100644 --- a/dhki/vars +++ b/dhki/vars @@ -17,4 +17,12 @@ do done idManagementSetup -obds2fhirRestSetup \ No newline at end of file +obds2fhirRestSetup + +for module in modules/*.sh +do + log DEBUG "sourcing $module" + source $module +done + +routineConnectorSetup \ No newline at end of file diff --git a/modules/transfair-compose.yml b/modules/transfair-compose.yml new file mode 100644 index 0000000..863ae4a --- /dev/null +++ b/modules/transfair-compose.yml @@ -0,0 +1,19 @@ + +services: + transfair: + image: samply/routine-connector:latest # TODO: Harbor image and new name ofc + container_name: bridgehead-transfair + environment: + INSTITUTE_TTP_URL: "${INSTITUTE_TTP_URL}" + INSTITUTE_TTP_API_KEY: "${INSTITUTE_TTP_API_KEY}" + PROJECT_ID_SYSTEM: "${PROJECT_ID_SYSTEM}" + FHIR_REQUEST_URL: "${FHIR_REQUEST_URL}" + FHIR_INPUT_URL: "${FHIR_INPUT_URL}" + FHIR_OUTPUT_URL: "${FHIR_OUTPUT_URL}" + FHIR_REQUEST_CREDENTIALS: "${FHIR_REQUEST_CREDENTIALS}" + FHIR_INPUT_CREDENTIALS: "${FHIR_INPUT_CREDENTIALS}" + FHIR_OUTPUT_CREDENTIALS: "${FHIR_OUTPUT_CREDENTIALS}" + EXCHANGE_ID_SYSTEM: "SESSION_ID" + DATABASE_URL: "sqlite://transfair/data_requests.sql?mode=rwc" + volumes: + - /var/cache/bridgehead/${PROJECT}/transfair:/transfair diff --git a/modules/transfair-output-blaze-compose.yml b/modules/transfair-output-blaze-compose.yml new file mode 100644 index 0000000..9f8583b --- /dev/null +++ b/modules/transfair-output-blaze-compose.yml @@ -0,0 +1,17 @@ + +services: + transfair-blaze: + image: docker.verbis.dkfz.de/cache/samply/blaze:0.28 + container_name: bridgehead-transfair-blaze + environment: + BASE_URL: "http://bridgehead-ccp-blaze:8080" + JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m" + DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000} + DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP} + CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32} + ENFORCE_REFERENTIAL_INTEGRITY: "false" + volumes: + - "transfair-blaze-data:/app/data" + +volumes: + transfair-balze-data: \ No newline at end of file diff --git a/modules/transfair-setup.sh b/modules/transfair-setup.sh new file mode 100755 index 0000000..6dff9c2 --- /dev/null +++ b/modules/transfair-setup.sh @@ -0,0 +1,13 @@ +#!/bin/bash -e + +function transfairSetup() { + assertVarsNotEmpty INSTITUTE_TTP_URL INSTITUTE_TTP_API_KEY PROJECT_ID_SYSTEM FHIR_REQUEST_URL FHIR_INPUT_URL + OVERRIDE+=" -f ./modules/transfair-compose.yml" + if [ -n "$FHIR_OUTPUT_URL" ]; then + log INFO "TransFAIR output fhir store set to external $FHIR_OUTPUT_URL" + else + log INFO "TransFAIR output fhir store not set writing to internal blaze" + FHIR_OUTPUT_URL="http://transfair-blaze:8080" + OVERRIDE+=" -f ./modules/transfair-compose.yml" + fi +}