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DukeDSClient CircleCI Coverage Status

This command line program (ddd) will allow you to upload, download, and manage projects in the DHTS Storage as a Service. Previously there was a ddsclient command line tool that is now deprecated.

For help email [email protected].

Requirements

NOTE: When installing Python on Windows be sure to check the Add Python to PATH checkbox. This will avoid a problem where pip3 and/or dds cannot be found.

Installation:

DukeDSClient can be installed using the pip3 command line program.

To install or upgrade DukeDSClient from a Terminal or Command Prompt run the following:

pip3 install --upgrade DukeDSClient

The above commmand will install the latest version of DukeDSClient from PyPI.

If you receive a permission denied error it may be due to you not having superuser or administrative privileges on your machine. You can run pip3 with the --user scheme or create a virtual environment to work around this limitation. Please see the tutorial on installing packages for more details.

Storage Setup

Before you can use the ddd command line tool you must create a File System (container) at https://azurestorage.duhs.duke.edu/.

Config file setup.

DukeDSClient requires a config file at ~/.ddsclient containing settings used to access the backing storge. Minimally the config file must contain two fields:

  • azure_storage_account - Azure storage account that contains your Azure container
  • azure_container_name - Azure container where your projects(top level folders) will exist.

The simplest way to find these two values is from the URL field for your File System (container) at https://azurestorage.duhs.duke.edu/.

For example if the URL field is https://mylab.dfs.core.windows.net/sequencing-data the azure_storage_account field should be mylab and the azure_container_name should be sequencing-data.

The config file is in YAML format so for the above example the contents should be:

azure_storage_account: mylab
azure_container_name: sequencing-data

Delivery Config

If you wish to use the deliver command you must add a delivery_token field to the config file. Email [email protected] for help getting this token.

Usage:

See general help screen:

ddd -h

See help screen for a particular command:

ddd <command> -h

All commands take the form:

ddd <command> <arguments...>

Upload:

ddd upload -p <ProjectName> <Folders/Files...>

This will create a project with the name ProjectName in the duke data service for your user if one doesn't exist. It will then upload the Folders and it's contents to that project. Any items that already exist with the same hash will not be uploaded.

Example: Upload a folder named 'results' to new or existing project named 'Analyzed Mouse RNA':

ddd upload -p 'Analyzed Mouse RNA' results

Download:

ddd download -p <ProjectName> [Folder]

This will download the contents of ProjectName into the specified folder. Currently it requires the directory be empty or not exist. It will create Folder if it doesn't exist. If Folder is not specified it will use the name of the project with spaces translated to '_'.

Example: Download the contents of project named 'Mouse RNA' into '/tmp/mouserna' :

ddd download -p 'Mouse RNA' /tmp/mouserna

Downloading to a file share

To download a project onto a file share (such as a CIFS share) specify a path within the share for the Folder to download directly there.

Developer:

Install dependencies:

pip install -r devRequirements.txt

Setup pre-commit hook:

ln pre-commit.sh .git/hooks/pre-commit

Run linter/style checker:

flake8 --ignore E501 ddsc/

Run the tests

python setup.py test