Pseudonymize FHIR🔥 resources from and to MongoDB databases
This is a command line tool to run pseudonymization / anonymization on FHIR resources via the FHIR® Pseudonymizer. It currently supports reading from a MongoDB database. Data from all collections are send to the FHIR pseudonymization service and written back to a target database and its collections accordingly.
The project name is the only required command line flag to provide when running the tool.
It is used by convention as a suffix to determine the source database (idat_fhir_[project]).
The target database name is set to psn_fhir_[project].
Configuration properties are set via a YAML file which defaults to app.yaml.
Usage:
pseudonymous [flags]
Flags:
-c, --config string config file (default is ./app.yaml)
-h, --help help for pseudonymous
-p, --project string project name (required)Binary releases and docker images are available under releases.
| Name | Default | Description |
|---|---|---|
app.log-level |
info | Log level (error,warn,info,debug) |
app.concurrency |
5 | Number of concurrent threads |
gpas.url |
URL to the gPAS service for auto-creating pseudonymization domains | |
fhir.provider.mongodb.connection |
mongodb://localhost | MongoDB connection string |
fhir.provider.mongodb.batch-size |
5000 | Batch size when reading data from the source database |
fhir.pseudonymizer.url |
http://localhost:5000/fhir | FHIR® Pseudonymizer endpoint |
fhir.pseudonymizer.retry.count |
10 | Retry count |
fhir.pseudonymizer.retry.timeout |
10 | Retry timeout |
fhir.pseudonymizer.retry.wait |
5 | Retry wait between retries |
fhir.pseudonymizer.retry.max-wait |
20 | Retry maximum wait |
Override configuration properties by providing environment variables with their respective names.
Upper case env variables are supported as well as underscores (_) instead of . and -.