dandi-cli-docker

Containerized DANDI CLI wrapper for downloading or uploading a file with environment variable flags.

Build

docker build -t dandi-cli-env .

The Dockerfile installs a temporary compiler toolchain because some platforms do not have prebuilt wheels for all DANDI dependencies, such as numcodecs.

Download

DANDI's documented download command is just dandi download <url>. This container keeps that shape and passes DANDI_URL directly to the CLI.

docker run --rm \
  -e DANDI_ACTION=download \
  -e DANDI_URL="DANDI:000023" \
  -e OUTPUT_DIR=/output \
  -v "$PWD/data:/output" \
  dandi-cli-env

DANDI_URL can be a DANDI identifier, API URL, web URL, or dandi:// URL that the DANDI CLI supports.

Upload

Upload mode follows the EMBER/DANDI staging flow: download the draft Dandiset, organize files from INPUT_DIR, validate the staged Dandiset, then upload to the ember-dandi instance.

docker run --rm \
  -e DANDI_ACTION=upload \
  -e DATASET_ID=000123 \
  -e DANDI_API_KEY="$DANDI_API_KEY" \
  -e INPUT_DIR=/input \
  -v "$PWD/source_folder:/input:ro" \
  dandi-cli-env

The upload command run inside the container is equivalent to:

dandi download "https://dandi.emberarchive.org/dandiset/<DATASET_ID>/draft"
cd "<DATASET_ID>"
dandi organize "$INPUT_DIR" -f dry
dandi organize "$INPUT_DIR"
dandi validate .
dandi upload -i ember-dandi

Environment Variables

Variable	Default	Description
DANDI_ACTION	unset	Required. Must be download or upload.
DANDI_URL	unset	URL or identifier passed to dandi download. Required for downloads.
OUTPUT_DIR	/output	Directory where downloads are saved.
DATASET_ID	unset	Dandiset identifier used to download the draft Dandiset before upload. DANDISET_ID is also accepted.
DANDISET_URL	https://dandi.emberarchive.org/dandiset/<DATASET_ID>/draft	Draft Dandiset URL used during upload staging.
INPUT_DIR	/input	Mounted source folder passed to dandi organize during upload.
UPLOAD_WORK_DIR	/work	Temporary staging directory for the downloaded draft Dandiset.
DANDI_API_KEY	unset	DANDI API token. Required for uploads. The entrypoint maps this to the instance-specific variable, such as EMBER_DANDI_API_KEY for ember-dandi.
DANDI_INSTANCE	ember-dandi	Instance passed to dandi upload -i.