pubweb 0.3.7

CLI tool and SDK for interacting with the PubWeb platform

PubWeb Client

A Python 3.8+ library for the PubWeb platform.

Installation

You can install PubWeb using pip

pip install pubweb

or by cloning the repo and running

python setup.py install

Usage

CLI Usage

Run pubweb-cli configure to configure your login credentials.

Specify the --interactive flag to gather the command arguments interactively.

Example:

$ pubweb-cli upload --interactive
? What project is this dataset associated with?  Test project
? Enter the full path of the data directory  /shared/biodata/test
? Please confirm that you wish to upload 20 files (0.630 GB)  Yes
? What type of files?  Illumina Sequencing Run
? What is the name of this dataset?  test
? Enter a description of the dataset (optional)

Listing datasets:

Usage: pubweb-cli list_datasets [OPTIONS]

  List available datasets

Options:
  --project TEXT         ID of the project
  --interactive          Gather arguments interactively
  --help                 Show this message and exit.

Downloading a dataset:

Usage: pubweb-cli download [OPTIONS]

  Download dataset files

Options:
  --project TEXT         Name or ID of the project
  --dataset TEXT         ID of the dataset
  --data-directory TEXT  Directory to store the files
  --interactive          Gather arguments interactively
  --help                 Show this message and exit.

Uploading a dataset:

Usage: pubweb-cli upload [OPTIONS]

  Upload and create a dataset

Options:
  --name TEXT             Name of the dataset
  --description TEXT      Description of the dataset (optional)
  --project TEXT          Name or ID of the project
  --process TEXT          Name or ID of the ingest process
  --data-directory TEXT   Directory you wish to upload
  --interactive           Gather arguments interactively
  --use-third-party-tool  Use third party tool for upload (Generate manifest and one-time upload authentication token)
  --help                  Show this message and exit.

SDK Usage

Sample	Description
01_Intro	Authenticating and installing
02_Uploading_a_dataset
03_Downloading_a_dataset
04_Interacting_with_files
05_Analyzing_a_dataset
06_Using_references	Managing reference data