Skip to main content

Add HTTP read only dataset support to dtool

Project description

PyPi package Travis CI build status (Linux) Code Coverage

Features

  • Publish dtool datasets by making them accessible via HTTP(S)
  • Interact with dtool datasets over HTTP(S)
  • Copy a dataset over HTTP(S)

Installation

To install the dtool-http package.

cd dtool-http
python setup.py install

Usage

To publish a dataset hosted in Amazon S3 or Microsoft Azure Storage use the dtool_publish_dataset command line utility:

$ dtool_publish_dataset azure://jicinformatics/c58038a4-3a54-425e-9087-144d0733387f
Dataset accessible at: https://jicinformatics.blob.core.windows.net/c58038a4-3a54-425e-9087-144d0733387f

To show the descriptive metadata of the published dataset:

$ dtool readme show https://jicinformatics.blob.core.windows.net/c58038a4-3a54-425e-9087-144d0733387f
---
description: Enterobacteria phage lambda, complete genome
creation_date: 2018-02-06
accession: NC_001416.1
link: https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1
reference: |
  Nucleotide [Internet]. Bethesda (MD):
  National Library of Medicine (US),
  National Center for Biotechnology Information; [1988] - .
  Accession No. NC_001416.1, Enterobacteria phage lambda, complete genome
  [cited 2018 Feb 06]
  Available from: https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1

To copy the dataset to local disk:

$ dtool copy https://jicinformatics.blob.core.windows.net/c58038a4-3a54-425e-9087-144d0733387f ~/my_datasets
Dataset copied to:
file:///Users/olssont/my_datasets/lamda-phage-genome

Serving a directory of datasets over HTTP

There is a simple utility for serving datasets in a directory over HTTP called dtool_serve_direcotry. This is mainly useful for testing purposes.

Usage:

$ dtool_serve_directory ~/my_datasets

The default port used is 8081. To show the descriptive metadata in the README one can use dtool:

$ dtool readme show http://localhost:8081/lamda-phage-genome
---
description: Enterobacteria phage lambda, complete genome
creation_date: 2018-02-06
accession: NC_001416.1
link: https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1
reference: |
  Nucleotide [Internet]. Bethesda (MD):
  National Library of Medicine (US),
  National Center for Biotechnology Information; [1988] - .
  Accession No. NC_001416.1, Enterobacteria phage lambda, complete genome
  [cited 2018 Feb 06]
  Available from: https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
dtool-http-0.2.1.tar.gz (5.6 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page