PEPHubClient

PEPHubClient is a tool to provide Python API and CLI for PEPhub.

Documentation: https://pep.databio.org

Source Code: https://github.com/pepkit/pephubclient

Installation

To install pepdbagent use this command:

pip install pephubclient

or install the latest version from the GitHub repository:

pip install git+https://github.com/pepkit/pephubclient.git

pephubclient features:

1. push (upload) projects)
2. pull (download projects)

Additionally, our client supports pephub authorization. The authorization process is based on pephub device authorization protocol. To upload projects or to download private projects, user must be authorized through pephub.

If you want to use your own pephub instance, you can specify it by setting the PEPHUB_BASE_URL environment variable. e.g. export PEPHUB_BASE_URL=https://pephub.databio.org/ (This is the original pephub instance)

To login, use the login argument; to logout, use logout.

login accepts two optional arguments:

• --token — register a JWT token directly, skipping the browser device-code flow.
• --url — base URL of the pephub instance to authenticate against (overrides PEPHUB_BASE_URL for this login).

e.g. phc login --token <JWT> --url https://pephub.databio.org/

Credentials are cached in $PH_HOME/jwt.toml, which stores both the token and its base URL. PH_HOME defaults to ~/.pephubclient/; set the PH_HOME environment variable to use a different directory.

$ phc --help
                                                                                                                   
 Usage: pephubclient [OPTIONS] COMMAND [ARGS]...                                                                   
                                                                                                                   
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --version             -v                                                                                        │
│ --install-completion            Install completion for the current shell.                                       │
│ --show-completion               Show completion for the current shell, to copy it or customize the              │
│                                 installation.                                                                   │
│ --help                          Show this message and exit.                                                     │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ login               Login to PEPhub                                                                             │
│ logout              Logout                                                                                      │
│ pull                Download and save project locally.                                                          │
│ push                Upload/update project in PEPhub                                                             │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

$ phc pull --help
                                                                                                                   
 Usage: pephubclient pull [OPTIONS] PROJECT_REGISTRY_PATH                                                          
                                                                                                                   
 Download and save project locally.                                                                                
                                                                                                                   
╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *    project_registry_path      TEXT  [default: None] [required]                                                │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --force    --no-force      Overwrite project if it exists. [default: no-force]                                  │
│ --help                     Show this message and exit.                                                          │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

$ phc push --help
                                                                                                                   
 Usage: pephubclient push [OPTIONS] CFG                                                                            
                                                                                                                   
 Upload/update project in PEPhub                                                                                   
                                                                                                                   
╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *    cfg      TEXT  Project config file (YAML) or sample table (CSV/TSV)with one row per sample to constitute   │
│                     project                                                                                     │
│                     [default: None]                                                                             │
│                     [required]                                                                                  │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --namespace                        TEXT  Project namespace [default: None] [required]                        │
│ *  --name                             TEXT  Project name [default: None] [required]                             │
│    --tag                              TEXT  Project tag [default: None]                                         │
│    --force         --no-force               Force push to the database. Use it to update, or upload project.    │
│                                             [default: no-force]                                                 │
│    --is-private    --no-is-private          Upload project as private. [default: no-is-private]                 │
│    --help                                   Show this message and exit.                                         │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯