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redo transfair setup

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janskiba
2025-01-23 12:42:59 +00:00
parent 2058a7a5c9
commit 139fcecabe
4 changed files with 52 additions and 26 deletions
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2
dhki/vars
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@@ -25,4 +25,4 @@ do
source $module source $module
done done
routineConnectorSetup transfairSetup

36
modules/transfair-compose.yml
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@@ -9,11 +9,43 @@ services:
PROJECT_ID_SYSTEM: "${PROJECT_ID_SYSTEM}" PROJECT_ID_SYSTEM: "${PROJECT_ID_SYSTEM}"
FHIR_REQUEST_URL: "${FHIR_REQUEST_URL}" FHIR_REQUEST_URL: "${FHIR_REQUEST_URL}"
FHIR_INPUT_URL: "${FHIR_INPUT_URL}" FHIR_INPUT_URL: "${FHIR_INPUT_URL}"
FHIR_OUTPUT_URL: "${FHIR_OUTPUT_URL}" FHIR_OUTPUT_URL: "${FHIR_OUTPUT_URL:-http://blaze:8080}"
FHIR_REQUEST_CREDENTIALS: "${FHIR_REQUEST_CREDENTIALS}" FHIR_REQUEST_CREDENTIALS: "${FHIR_REQUEST_CREDENTIALS}"
FHIR_INPUT_CREDENTIALS: "${FHIR_INPUT_CREDENTIALS}" FHIR_INPUT_CREDENTIALS: "${FHIR_INPUT_CREDENTIALS}"
FHIR_OUTPUT_CREDENTIALS: "${FHIR_OUTPUT_CREDENTIALS}" FHIR_OUTPUT_CREDENTIALS: "${FHIR_OUTPUT_CREDENTIALS}"
EXCHANGE_ID_SYSTEM: "SESSION_ID" EXCHANGE_ID_SYSTEM: "${EXCHANGE_ID_SYSTEM:-SESSION_ID}"
DATABASE_URL: "sqlite://transfair/data_requests.sql?mode=rwc" DATABASE_URL: "sqlite://transfair/data_requests.sql?mode=rwc"
volumes: volumes:
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
transfair-input-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-transfair-input-blaze
environment:
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${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: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-input-blaze-data:/app/data"
profiles: ["transfair-input-blaze"]
transfair-request-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-transfair-requests-blaze
environment:
BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${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-request-blaze-data:/app/data"
profiles: ["transfair-request-blaze"]
volumes:
transfair-input-blaze-data:
transfair-request-blaze-data:

17
modules/transfair-output-blaze-compose.yml
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@@ -1,17 +0,0 @@
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:

23
modules/transfair-setup.sh
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@@ -1,13 +1,24 @@
#!/bin/bash -e #!/bin/bash -e
function transfairSetup() { function transfairSetup() {
assertVarsNotEmpty INSTITUTE_TTP_URL INSTITUTE_TTP_API_KEY PROJECT_ID_SYSTEM FHIR_REQUEST_URL FHIR_INPUT_URL if [[ -n "$INSTITUTE_TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
echo "Starting transfair."
else
return
fi
OVERRIDE+=" -f ./modules/transfair-compose.yml" OVERRIDE+=" -f ./modules/transfair-compose.yml"
if [ -n "$FHIR_OUTPUT_URL" ]; then if [ -n "$FHIR_INPUT_URL" ]; then
log INFO "TransFAIR output fhir store set to external $FHIR_OUTPUT_URL" log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
else else
log INFO "TransFAIR output fhir store not set writing to internal blaze" log INFO "TransFAIR input fhir store not set writing to internal blaze"
FHIR_OUTPUT_URL="http://transfair-blaze:8080" FHIR_INPUT_URL="http://bridgehead-transfair-input-blaze:8080"
OVERRIDE+=" -f ./modules/transfair-compose.yml" OVERRIDE+=" --profile transfair-input-blaze"
fi
if [ -n "$FHIR_REQUEST_URL" ]; then
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
else
log INFO "TransFAIR request fhir store not set writing to internal blaze"
FHIR_REQUEST_URL="http://bridgehead-transfair-requests-blaze:8080"
OVERRIDE+=" --profile transfair-request-blaze"
fi fi
} }