Process Deployment and Configuration v0.4.0

The process can be deployed by dropping the process-plugin-jar into the the DSF BPE folder /opt/bpe/process. The release notes of the process version 0.4.0 can be found here.

Data Integration Center (DIC) Configuration

Prerequisite

• The hapi-fhir-client-5.1.0.jar has to be installed as a regular DSF BPE plugin by dropping the jar file into the folder /opt/bpe/plugin.
  Make sure the file is readable by the bpe user or group, for example by executing:

  sudo chmod 440 hapi-fhir-client-5.1.0.jar
  sudo chown root:bpe hapi-fhir-client-5.1.0.jar
  

Download Process Plugin

• Add the codex-process-data-transfer-0.4.0.jar to the folder /opt/bpe/process.
  Make sure the file is readable by the bpe user or group, for example by executing:

  sudo chmod 440 codex-process-data-transfer-0.4.0.jar
  sudo chown root:bpe codex-process-data-transfer-0.4.0.jar
  

Configuration

The following list highlights environment variables that can be set in the /opt/bpe/docker-compose.yml file. See Configuration Parameters v0.4.0 for a full list of all options.

CRR public-key:

• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_CRR_PUBLIC_KEY

DIC GECCO FHIR repository:

• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_BASE_URL
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_BASICAUTH_USERNAME
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_BASICAUTH_PASSWORD_FILE

If the DIC GECCO FHIR repository is not configured, the send process generates demo data for testing purposes. This test data contains for each provided DIC pseudonym 1 FHIR Patient ressource, 1 FHIR Condition resource and 1 FHIR Observation resource.

fTTP connection to resolve Bloom Filters:

This configuration is only needed if Patient resources in the DIC GECCO FHIR repository contain a Bloom Filter and not a DIC pseudonym.

• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_SERVER_BASE_URL
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_TRUST_CERTIFICATES
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_CERTIFICATE
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_PRIVATE_KEY
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_BASICAUTH_USERNAME
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_BASICAUTH_PASSWORD_FILE
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_API_KEY
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_TARGET

If the fTTP connection is not configured and the process finds a Bloom Filter in a FHIR Patient resource, a demo DIC pseudonym with the value source2/original2 is generated and used.

Internet access via corporate proxy server:

To access the GTH DSF FHIR server, the local GECCO FHIR server or the fTTP server use the following parameters:

• BPE -> Local GECCO FHIR server
  • DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_PROXY_URL
  • DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_PROXY_USERNAME
  • DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_PROXY_PASSWORD_FILE
• BPE -> fTTP server
  • DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_PROXY_URL
  • DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_PROXY_USERNAME
  • DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_FTTP_PROXY_PASSWORD_FILE
• BPE -> GTH DSF FHIR Server
  • ORG_HIGHMED_DSF_BPE_FHIR_CLIENT_REMOTE_PROXY_URL
  • ORG_HIGHMED_DSF_BPE_FHIR_CLIENT_REMOTE_PROXY_USERNAME
  • ORG_HIGHMED_DSF_BPE_FHIR_CLIENT_REMOTE_PROXY_PASSWORD_FILE
• Local DSF FHIR Server -> GTH DSF FHIR Server (for reference validation)
  • ORG_HIGHMED_DSF_FHIR_CLIENT_PROXY_URL
  • ORG_HIGHMED_DSF_FHIR_CLIENT_PROXY_USERNAME
  • ORG_HIGHMED_DSF_FHIR_CLIENT_PROXY_PASSWORD_FILE

Local consent provider:

• No implementation yet.

Process exclude config:

• ORG_HIGHMED_DSF_BPE_PROCESS_EXCLUDED: wwwnetzwerk-universitaetsmedizinde_dataTranslate/0.4.0,wwwnetzwerk-universitaetsmedizinde_dataReceive/0.4.0
  The processes translate and receive are not needed at data integration centers (DIC).

Test Data

There exist two GECCO FHIR transaction Bundles with test data that can be used in the DIC GECCO FHIR repository for testing purposes:

• A transaction Bundle containing demo data based on a FHIR Patient resource with a Bloom Filter identifier can be found here
• A transaction Bundle containing demo data based on a FHIR Patient resource with a DIC pseudonym identifier can be found here

Central Research Repository (CRR) Configuration

Prerequisite

• The hapi-fhir-client-5.1.0.jar has to be installed as a regular DSF BPE plugin by dropping the jar file into the folder /opt/bpe/app/plugin.
  Make sure the file is readable by the bpe, for example by executing:

  sudo chmod 440 hapi-fhir-client-5.1.0.jar
  sudo chown root:bpe hapi-fhir-client-5.1.0.jar
  

Download Process Plugin

• Add the codex-process-data-transfer-0.4.0.jar to the folder /opt/bpe/process.
  Make sure the file is readable by the bpe user or group, for example by executing:

  sudo chmod 440 codex-process-data-transfer-0.4.0.jar
  sudo chown codex-process-data-transfer-0.4.0.jar
  

Configuration

The following list highlights environment variables that can be set in the /opt/bpe/docker-compose.yml file. See Configuration Parameters v0.4.0 for a full list of all options.

CRR private-key:

• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_CRR_PRIVATE_KEY

Generate a key-pair using:

• openssl genrsa -out keypair.pem 4096
• openssl rsa -in keypair.pem -pubout -out crr_public-key.pem
• openssl pkcs8 -topk8 -inform PEM -outform PEM -nocrypt -in keypair.pem -out crr_private-key.pem

CRR GECCO FHIR repository:

• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_BASE_URL
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_BASICAUTH_USERNAME
• DE_NETZWERK_UNIVERSITAETSMEDIZIN_CODEX_GECCO_SERVER_BASICAUTH_PASSWORD_FILE

Process exclude config:

• ORG_HIGHMED_DSF_BPE_PROCESS_EXCLUDED: wwwnetzwerk-universitaetsmedizinde_dataTrigger/0.4.0,wwwnetzwerk-universitaetsmedizinde_dataSend/0.4.0,wwwnetzwerk-universitaetsmedizinde_dataTranslate/0.4.0
  The processes trigger, send and translate are not needed at the central research repository (CRR).