Open chgl opened 1 year ago
Could you add the certificate path as an environment variable? We had problems because of SSL to connect gPAS server.
@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.
Thank you for your prompt response. I'm facing another issue while configuring the anonymization.yaml settings. I attempted to pseudonymize birthdates with
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.
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:
networks: mynet: external: true name:
.yaml sieht so aus.
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 :).
System.Text.Json
-based FHIR parser and remove the option to unset itgPAS
was supported as a pseudonymization service, we've defaultedPseudonymizationService
togPAS
. In the next version, this should be set toNone
. Possibly log a warning/error if the anonymization.yaml uses apseudonymize
method but no backend is defined at startup.gPAS__Version
setting, defaulting it to 2023 in the hopes that the published FHIR endpoint is now stable enough.Metrics.Enabled
andMetrics.Port
complex type