PEPHubClient is a tool to provide Python API and CLI for PEPhub.
Documentation: https://pep.databio.org
Source Code: https://github.com/pepkit/pephubclient
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
push(upload) projects)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 PEPHUB_BASE_URL environment variable.
e.g. export PEPHUB_BASE_URL=https://pephub.databio.org/ (This is original pephub instance)
To login, use the login argument; to logout, use logout.
$ 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. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯