pubweb 0.5.0

CLI tool 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 repository and running:

python setup.py install

Set Up

Run a one-time configuration of your login credentials in the command line using:

pubweb-cli configure

This will ask you to select an authentication method. If you are a member of Fred Hutch or the University of Washington, select the default method which will give you a link to use to log through the browser. If you are not a member of those institutions, select the non-institutional authentication method and enter your Data Portal username and password into the command line when prompted.

Command Line Usage

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.

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.

Interactive Commands

When running a command, you can 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)
? How would you like to upload or download your data? PubWeb CLI

Python Usage

See the following set of Jupyter notebooks that contain examples on the following topics:

Jupyter Notebook	Topic
Introduction	Installing and authenticating
Uploading a dataset	Uploading data
Downloading a dataset	Downloading data
Interacting with a dataset	Calling data and reading into tables
Analyzing a dataset	Running analysis pipelines
Using references	Managing reference data

R Usage

Jupyter Notebook	Topic
Downloading a dataset in R	Reading data with R

Advanced Usage

Supported environment variables

Name	Description	Default
PW_HOME	Local configuration directory	~/.pubweb
PW_BASE_URL	Base URL of the data portal	data-portal.io

Configuration

The pubweb-cli configure command creates a file in PW_HOME called config.ini.

You can set the base_url property in the config file rather than using the environment variable.

[General]
base_url = data-portal.io