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Tutorial Setup

This tutorial assumes you have some basic knowledge of the concepts and usage of bagit, bdbag, and minid. If not, click on the appropriate link(s) for additional information.

The following tutorial setup steps are common to all of the tutorials in this guide.

  1. Ensure that you have the prerequisites installed in your environment.
  2. Install the software.
  3. Configure the software so that your own efforts are consistent with what is presented in the tutorials.

Prerequisites

  • Python 2.7 or higher
  • The following Python modules: setuptools, pip, wheel. It is recommended to upgrade these modules even if they are already present. The following command can be used: 
    pip install --upgrade pip setuptools wheel
  • Optional: For uploading to AWS S3, you first need to install awscli, which you can install via pip. Additionally, you need a valid AWS user account and need to know your aws_access_key_id and aws_secret_access_key_id. Once you have these, run aws configure and enter the keys at the prompts. Finally, create a bucket where you will upload your files. You can do this via either awscli or the AWS S3 Web Browser GUI.

Note: When using pip install commands, it may be necessary to use sudo on Unix and Mac systems if you are modifying the system Python installation. Alternatively, you can pass the --user flag to pip install in order to use the Python user install directory for your platform.

Installation

Use pip to install bdbag version 1.4.1 or greater, and minid version 1.3.0 or greater from PyPi:

pip install --upgrade 'bdbag>=1.4.1'
pip install --upgrade 'minid>=1.3.0'

Next, check that the correct versions were installed:

nih-commons:mdarcy[~] bdbag --version
1.4.1
nih-commons:mdarcy[~] minid --version
1.3.0

Finally, use minid to register yourself as a user with the minid server. Check your email for the server reponse which will contain a code that you will need to create and update minid identifiers.

nih-commons:mdarcy[~] minid --register_user --email mdarcy@not-my-real-email.org --name mdarcy --orcid 0000-0003-2280-917X
2018-06-06 23:14:06,959 - INFO - Registering new user "mdarcy" with email "mdarcy@not-my-real-email.org" and orcid "0000-0003-2280-917X"

Configuration

Once you have bdbag and minid installed, there are a couple of recommended configuration steps that you can perform that will save you from having to pass the same parameters repeatedly when using the CLI or equivalent API functions.

First, modify the ~/.bdbag/bdbag.json (or %userprofile%\.bdbag\bdbag.json on Windows) configuration file and add key-value pairs such as Source-Organization, Contact-Name, Contact-Email, Contact-Orcid to the bag_metadata element of the configuration. Note that none of these elements are required, however if you want them to be automatically populated in the bag-info.txt metadata of bags you create, it is a good idea to add them now.

nih-commons:mdarcy[~] cat ./.bdbag/bdbag.json
{
  "bag_config": {
    "bag_algorithms": [
      "md5"
    ],
    "bag_metadata": {
      "BagIt-Profile-Identifier": "https://raw.githubusercontent.com/fair-research/bdbag/master/profiles/bdbag-profile.json",
      "Contact-Name": "mdarcy",
      "Contact-Orcid": "0000-0003-2280-917X"
    },
    "bag_processes": 1
  },
  "identifier_resolvers": [
    "n2t.net",
    "identifiers.org"
  ]
}

Next, add your minid user information to the ~/.minid/minid-config.cfg file:

nih-commons:mdarcy[~] cat .minid/minid-config.cfg
[general]
minid_server: http://minid.bd2k.org/minid
username: mdarcy
email: mdarcy@not-my-real-email.org
orcid: 0000-0003-2280-917X
code: e4506f64-9090-451f-ab4e-1192705dd89f

You're all set!

Ready to continue to Tutorial #1?