Metadata-Version: 2.1
Name: pubweb
Version: 0.5.0
Summary: CLI tool for interacting with the PubWeb platform
Home-page: https://github.com/FredHutch/PubWeb-client
Author: Fred Hutch
Author-email: hutchdatacore@fredhutch.org
License: MIT
Description: # PubWeb Client
        
        [![Build Python package](https://github.com/FredHutch/PubWeb-client/actions/workflows/package.yml/badge.svg)](https://github.com/FredHutch/PubWeb-client/actions/workflows/package.yml)
        [![Lint and run tests](https://github.com/FredHutch/PubWeb-client/actions/workflows/lint.yml/badge.svg)](https://github.com/FredHutch/PubWeb-client/actions/workflows/lint.yml)
        ![](https://img.shields.io/pypi/v/pubweb.svg)
        
        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:
        ```bash
        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:
        ```bash
        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:
        ```bash
        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:
        
        ```bash
        $ 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](samples/Getting_started.ipynb)                      | Installing and authenticating        |
        | [Uploading a dataset](samples/Uploading_a_dataset.ipynb)           | Uploading data                       |
        | [Downloading a dataset](samples/Downloading_a_dataset.ipynb)       | Downloading data                     |
        | [Interacting with a dataset](samples/Interacting_with_files.ipynb) | Calling data and reading into tables |
        | [Analyzing a dataset](samples/Analyzing_a_dataset.ipynb)           | Running analysis pipelines           |
        | [Using references](samples/Using_references.ipynb)                 | Managing reference data              |
        
        ## R Usage
        
        | Jupyter Notebook                                    | Topic               |
        |-----------------------------------------------------|---------------------|
        | [Downloading a dataset in R](samples/Using-R.ipynb) | 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. 
        
        ```ini
        [General]
        base_url = data-portal.io
        ```
Platform: UNKNOWN
Description-Content-Type: text/markdown
