Plans for the next major release (v3) about fhir-pseudonymizer HOT 6 OPEN

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 #103.

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

from fhir-pseudonymizer.

@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.

from fhir-pseudonymizer.

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?

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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"
  gPAS__URL: ""
  gPAS__Version: "2023.1.0"
  gPAS__Auth__Basic__Username: ""
  gPAS__Auth__Basic__Password: ""
  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.

from fhir-pseudonymizer.

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 :).

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