wip: routine connector

dhki/vars

@@ -17,4 +17,12 @@ do
 done
 
 idManagementSetup
-obds2fhirRestSetup
+obds2fhirRestSetup
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+routineConnectorSetup

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

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:

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
+}