calypr-cli

calypr-cli is Calypr's command-line client for working with Gen3-style data commons from a terminal. It combines the standard data transfer flows with operator-oriented surfaces for permissions, collaborators, and portal configuration.

What It Does

The CLI currently groups into four main areas:

Command group	Purpose
configure, auth	Store credentials, create named profiles, and check connectivity
upload*, download*, retry-upload	Transfer files to and from supported backends
collaborators	Manage collaboration requests and approvals
permissions, portal	Operator workflows for Arborist-backed permissions and Gecko-backed portal config

Most commands require a configured --profile, and the default backend is gen3.

Operator Surfaces

Two command groups are specific to the Calypr fork rather than the legacy data transfer client:

Command group	Supported surface	Deliberate non-goals
permissions	Public Gen3 /authz routes exposed through revproxy	Raw Arborist catalog/admin CRUD and arbitrary policy mutation
portal	Public /gecko routes exposed through revproxy	Backend-only Gecko paths and undocumented admin-only flows

Detailed operator docs live here:

• permissions CLI guide
• portal CLI guide
• developer docs

Install And Build

The repo keeps a root main package, so the primary local build path is the repo root:

go build .

To install the current checkout:

go install .

There is also a compatibility entrypoint under ./cmd/calypr-cli if you need a subdirectory main package explicitly:

go build ./cmd/calypr-cli

Common Setup

Configure a profile with credentials and an API endpoint:

calypr-cli configure \
  --profile=myprofile \
  --cred=/path/to/credentials.json \
  --apiendpoint=https://example.com

Check the resulting profile or auth state:

calypr-cli auth --profile=myprofile

Upload Behavior

calypr-cli supports the newer Gen3 object management upload flow via the --use-shepherd=true configure flag. When enabled, uploads attempt that API first and fall back to the older Fence/Indexd path if needed.

Example:

calypr-cli configure \
  --profile=myprofile \
  --cred=/path/to/credentials.json \
  --apiendpoint=https://example.com \
  --use-shepherd=true

Uploads can also attach public file object metadata with --metadata. The CLI looks for a sibling file named [filename]_metadata.json.

Example:

calypr-cli upload \
  --profile=myprofile \
  --upload-path=/path/to/myfile.bam \
  --metadata

Metadata file shape:

{
  "authz": ["/example/authz/resource"],
  "aliases": ["example_alias"],
  "metadata": {
    "any": {
      "arbitrary": ["json", "metadata"]
    }
  }
}

The authz list may be required by the target commons. The metadata in this file is public-facing and should not contain sensitive content.