mirror of
https://github.com/samply/bridgehead.git
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Changes made for EHDS2
The EHDS2 project has initiated a use case for antibiotic resistance under the control of the ECDC. This branch caters for the ECDC requirements. Specifically, it contains the ETL to transform the ECDC CSV format to FHIR, plus additional configuration options that have been packaged into the bbmri project.
This commit is contained in:
Croft
59
bbmri/modules/ehds2-compose.yml
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59
bbmri/modules/ehds2-compose.yml
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version: "3.7"
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services:
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focus-ehds2:
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image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
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container_name: bridgehead-focus-ehds2
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environment:
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API_KEY: ${EHDS2_FOCUS_BEAM_SECRET_SHORT}
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BEAM_APP_ID_LONG: focus.${EHDS2_PROXY_ID}
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PROXY_ID: ${EHDS2_PROXY_ID}
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BLAZE_URL: "http://blaze:8080/fhir/"
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BEAM_PROXY_URL: http://beam-proxy-ehds2:8081
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RETRY_COUNT: ${FOCUS_RETRY_COUNT}
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depends_on:
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- "beam-proxy-ehds2"
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- "blaze"
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beam-proxy-ehds2:
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image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
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container_name: bridgehead-beam-proxy-ehds2
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environment:
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BROKER_URL: ${EHDS2_BROKER_URL}
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PROXY_ID: ${EHDS2_PROXY_ID}
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APP_focus_KEY: ${EHDS2_FOCUS_BEAM_SECRET_SHORT}
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PRIVKEY_FILE: /run/secrets/proxy.pem
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ALL_PROXY: http://forward_proxy:3128
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TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
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ROOTCERT_FILE: /conf/root.crt.pem
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secrets:
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- proxy.pem
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depends_on:
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- "forward_proxy"
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volumes:
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- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
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- /srv/docker/bridgehead/bbmri/modules/${EHDS2_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
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# Convert ECDC CSV file into FHIR and push to Blaze
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transfair:
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container_name: transfair
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image: samply/transfair
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environment:
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FHIR_INPUT_URL: "http://source_blaze:8080/fhir"
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FHIR_OUTPUT_URL: "http://bridgehead-bbmri-blaze:8080/fhir"
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PROFILE: "amr2fhir"
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#WRITE_BUNDLES_TO_FILE: "true"
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AMR_FILE_PATH: "/app/data"
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restart: on-failure
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command: sh -c "sleep 60 && rm -rf /app/test/* && java -jar transFAIR.jar && tail -f /dev/null"
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#command: sh -c "rm -rf /app/test/* && java -jar transFAIR.jar"
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volumes:
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- /home/gerhard/Projects/EHDS2/PrototypeSpring2024/test/:/app/test/
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- /home/gerhard/Projects/EHDS2/PrototypeSpring2024/Data/:/app/data/
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# Report on the data pushed to Blaze by TransFAIR
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blazectl:
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container_name: blazectl
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image: samply/blazectl
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command: sh -c "sleep 300 && echo Source store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"
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28
bbmri/modules/ehds2-setup.sh
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28
bbmri/modules/ehds2-setup.sh
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#!/bin/bash
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if [ "${ENABLE_EHDS2}" == "true" ]; then
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log INFO "EHDS2 setup detected -- will start services for German Biobank Node."
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OVERRIDE+=" -f ./$PROJECT/modules/ehds2-compose.yml"
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# The environment needs to be defined in /etc/bridgehead
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case "$ENVIRONMENT" in
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"production")
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export EHDS2_BROKER_ID=broker.bbmri.samply.de
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export EHDS2_ROOT_CERT=ehds2
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;;
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"test")
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export EHDS2_BROKER_ID=broker.test.bbmri.samply.de
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export EHDS2_ROOT_CERT=ehds2.test
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;;
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*)
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report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
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export EHDS2_BROKER_ID=broker.bbmri.samply.de
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export EHDS2_ROOT_CERT=ehds2
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;;
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esac
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EHDS2_BROKER_URL=https://${EHDS2_BROKER_ID}
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EHDS2_PROXY_ID=${SITE_ID}.${EHDS2_BROKER_ID}
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EHDS2_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
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EHDS2_SUPPORT_EMAIL=feedback@germanbiobanknode.de
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fi
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20
bbmri/modules/ehds2.root.crt.pem
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20
bbmri/modules/ehds2.root.crt.pem
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-----BEGIN CERTIFICATE-----
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MIIDNTCCAh2gAwIBAgIUMy/n0zFRihhVR3aAD54LumzeYdwwDQYJKoZIhvcNAQEL
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BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjIxMDI1MDczNTA4WhcNMzIx
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MDIyMDczNTM3WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
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wcMUK+igv3/K
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-----END CERTIFICATE-----
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20
bbmri/modules/ehds2.test.root.crt.pem
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20
bbmri/modules/ehds2.test.root.crt.pem
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-----BEGIN CERTIFICATE-----
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MIIDNTCCAh2gAwIBAgIUJ0g7k2vrdAwNTU38S1/mU8NO26MwDQYJKoZIhvcNAQEL
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BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwNzEwMTIyMzQxWhcNMzMw
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NzA3MTIyNDExWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
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AQEBBQADggEPADCCAQoCggEBALMvc/fApbsAl+/NXDszNgffNR5llAb9CfxzdnRn
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ryoBqZdPevBYZZfKBARRKjFbXRDdPWbE7erDeo1LiCM6PObXCuT9wmGWJtvfkmqW
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UNe/254bc0vqHEPT6VI/86c7qAmk1xR0RUfrnKAEqZtUeuoj2fe1L/6yOB16fxt5
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3V3oim7EO6eZCTjDo9fU5DaFiqSMe7WVdr03Na0cWet60XKRH/xaiC6gMWdHWcbh
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vZdXnV1qjlM2
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-----END CERTIFICATE-----
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