Trouble with CLI bulk-import

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Jonathan Reeder

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Feb 16, 2026, 12:31:13 PM (yesterday) Feb 16
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Hi all, I'm trying to import the MIMIC-IV dataset into a FHIR server I'm hosting locally.

I'm running the HAPI FHIR server and a postgres server in a docker container. I'm able to successfully launch the server, but of course it's empty to start.

I'm using the following command to attempt to bulk import the MIMIC<resource>.ndjson.gz files:

./hapi-fhir-cli bulk-import --port 0 --fhir-version r4 --target-base http://localhost:8080/fhir --source-directory /mnt/share/MIMIC-FHIR --batch-size 100

The cli tool runs and says that it detects 30 files (correct). But it fails with an "HTTP 400 Invalid request: The FHIR endpoint on this server does not know how to handle POST operation[$import] with parameters [[]]"

I have bulk_import_enabled: true in my application.yaml

The parameters being empty seems like it may be a problem. I'm wondering why it's not able to build the correct parameters based on the .ndjson.gz files containing FHIR resources?

I appreciate any help.
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