CLI tool and SDK for interacting with the PubWeb platform
Project description
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 |
Project details
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