Plans for the next major release (v3)

[chgl]

• [ ] Default to using the much faster System.Text.Json-based FHIR parser and remove the option to unset it
• [ ] For backwards-compatibility reasons back when only gPAS was supported as a pseudonymization service, we've defaulted PseudonymizationService to gPAS. In the next version, this should be set to None. Possibly log a warning/error if the anonymization.yaml uses a pseudonymize method but no backend is defined at startup.
• [ ] Instead of vendoring the Tools-for-health-data-anonymization, use the provided Nuget package (https://github.com/microsoft/Tools-for-Health-Data-Anonymization/issues/74). This might require additional effort to get our custom processors to work.
• [ ] remove the gPAS__Version setting, defaulting it to 2023 in the hopes that the published FHIR endpoint is now stable enough.
• [ ] remove Jaeger tracing support. Using only OTEL from now on.
• [ ] move metrics config inside a Metrics.Enabled and Metrics.Port complex type

[Hanrepo]

Could you add the certificate path as an environment variable? We had problems because of SSL to connect gPAS server.

[chgl]

@Hanrepo sure! If you have a self-signed certificate you should be able to just mount it inside the container's /etc/ssl/certs/ directory. That's not specific to this app. There's also SSL_CERT_FILE and SSL_CERT_DIR from the internal openssl used that should work.

[Hanrepo]

Thank you for your prompt response. I'm facing another issue while configuring the anonymization.yaml settings. I attempted to pseudonymize birthdates with

• path: Patient.birthDate method: generalize cases: $this.replaceMatches('(?\d{2,4})-(?\d{1,2})-(?\d{1,2})\b', '${year}-${month}') base the guidelines from FHIR-anonymization.md. However, it seems like it's not working. Could you please assist me with this?

[chgl]

Looks like GitHub is messing up the formatting a bit, but I believe what you want is:

fhirVersion: R4
fhirPathRules:
  - path: Patient.birthDate
    method: generalize
    cases:
      "$this": "$this.toString().replaceMatches('(?<year>\\\\d{2,4})-(?<month>\\\\d{2})-(?<day>\\\\d{2})\\\\b', '${year}-${month}')"
    otherValues: redact

You're running into the intricacies of YAML string escaping unfortunately - so \\d becomes \\\\d. An alternative syntax would be [0-9]{2,4}. It also seems like the example in the docs is missing a closing ) and toString() seems to be required as well.

I've added a snapshot test for this config as an example https://github.com/miracum/fhir-pseudonymizer/pull/103.

[Hanrepo]

hi, we meet a new problem, "Failed to create CoreCLR, HRESULT: 0x8007000E", by setting mem_limit: 4g in Compose.yaml still not help.

---

` #version: '3' services: pseudonymizer: image: ghcr.io/miracum/fhir-pseudonymizer:v2.20.0 ports:

• "8089:8080" environment: PseudonymizationService: "gPAS" UseSystemTextJsonFhirSerializer: "true" AnonymizationEngineConfigPath: "/etc/anonymization.yaml" gPASURL: "" gPASVersion: "2023.1.0" gPASAuthBasicUsername: "" gPASAuthBasicPassword: "" SSL_CERT_FILE: "/etc/certs/nginx-selfsigned.crt" SSL_KEY_FILE: "/etc/certs/nginx-selfsigned.key"

  volumes:

  • /opt/fhir-pseudonymizer-master/anonymization.yaml:/etc/anonymization.yaml
  • /opt/fhir-pseudonymizer-master/certs/nginx-selfsigned.crt:/etc/certs/ngi>
    • /opt/fhir-pseudonymizer-master/certs/nginx-selfsigned.key:/etc/certs/ngi> command: --sslcert /certs/nginx-selfsigned.crt --sslkey /certs/nginx-selfsigned.key networks:
    • mynet mem_limit: 4g memswap_limit: 4g

networks: mynet: external: true name:

'

.yaml sieht so aus.

[chgl]

Not sure the mem_limit is still used in current compose versions. It should use the deploy: section instead: https://docs.docker.com/compose/compose-file/deploy/#memory - you can check whether the limits were set using docker stats. If your machine has a lot of CPUs, you might want to limit the available CPUs as well: each one increases the size of required memory by the application. It might be easier to create a dedicated issue for better tracking in the future :).