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Setting up your environment

Preparing to use Docker

First, open two UNIX terminal windows, each with access to Docker. The way you do this varies by platform:

  1. If you are on Mac or Windows and using Kitematic, click the [DOCKER CLI] button two times.
  2. If you are on Mac or Windows using Docker Toolbox, click the Docker Quickstart Terminal icon twice to launch the two windows
  3. If you are on Linux with Docker installed natively, open a terminal session. Make sure you are able to access Docker by typing docker images
  4. If you are on Mac or Linux using a VM to run Linux, follow Linux-native instructions entirely within the VM

Launching an Agave CLI container

Choose one (but not both) of your Docker-enabled terminal sessions. Enter the following text exactly:

docker run -it --rm=true -v $HOME/.agave:/root/.agave -v $HOME:/home -w /home iplantc/agave-cli bash

This launches a container running the latest release of the iPlant flavor of the agave-cli. It mounts Agave's local "cache" directory and also mounts your local home directory under /home inside the container. Check the contents of /home to verify that you can see your own files and folders.

media/agave-cli-window.png

Note: You should have two windows open that resemble this image

Set up your Agave environment

In your agave-cli window, run the following command: auth-check. If you get an error Please run /usr/local/agave-cli/... then do the following:

# Set up the CLI to point to iPlant
tenants-init -t iplantc.org
# Create an OAuth2 API client at iPlant.
# You will be prompted for your iPlant username and password
clients-create -S -N "dib_0923" -D "Workshop client"
# Create and cache an Agave API access token
# You will be prompted for your iPlant password
auth-tokens-create -S

If you do not get an error from auth-check, please run auth-tokens-refresh -S before proceeding with the next parts of the workshop.

Retrieving your AWS credentials

The iPlant team has created a set of credentials for each workshop attendee and stored it in the Agave document store. In the next steps, you will retrieve that information yo can use it later. If you have your own AWS credentials you'd prefer to use, talk to the instructors and we'll get you set up.

Query the iPlant Agave metadata service

In the agave-cli window, enter the following command, substituting IPLANT_USERNAME with your own iPlant username. Pay careful attention to the use of single and double quotes!

metadata-list -v -Q '{"name":"iplant-aws.dib-0923.IPLANT_USERNAME"}'

You should get a response back that looks like this (abbreviated) JSON document:

[
{
    "_links": {
        "self": {
            "href": "https://agave.iplantc.org/meta/v2/data/0001442525546151-e0bd34dffff8de6-0001-012"
        }
    },
    "associationIds": [],
    "created": "2015-09-17T16:32:26.151-05:00",
    "internalUsername": null,
    "lastUpdated": "2015-09-17T16:32:26.151-05:00",
    "name": "iplant-aws.dib-0923.IPLANT_USERNAME",
    "owner": "vaughn",
    "schemaId": null,
    "uuid": "0001442525546151-e0bd34dffff8de6-0001-012",
    "value": {
        "apikeys": {
            "key": "AMWIM3BEAT3BEAWT3BEA",
            "secret": "yfP3ylcmq6Syp6Syp6VPIjHxCT5v66VPIjHOTxXa"
        }
    }}]

This document contains every detail you need to interact with iPlant's AWS account. Let's take a minute to learn how to pull key bits out for use in scripting. We will use the jq parser, which is installed by default in the iPlant agave-cli image.

Change into /home in the container, then pipe the document out to a file.

cd /home && metadata-list -v -Q '{"name":"iplant-aws.dib-0923.IPLANT_USERNAME"}' > my-aws-creds.json

The JSON file my-aws-creds.json contains an array consisting of one object with several keys. Some of those keys have children. Here's how to use jq to extract the iam_user, which is your AWS username, from the document:

jq -r .[0].value.identity.iam_user my-aws-creds.json

You should get back IPLANT_USERNAME.iplantc.org

Exercises:

  1. Find your AWS key and secret
  2. Find the name of the S3 bucket you have been assigned
  3. Find out who is the owner of the JSON document that was shared with you
  4. What is the uuid of the document?
  5. Bonus: Use metadata-pems-list UUID to find out if anyone else has read permission on this document

Check out the workshop material from Github

The iPlant team has prepared several useful utility files and scripts to help with the objectives of the workshop. In the agave-cli window:

  1. cd /home
  2. check out the repository git clone https://github.com/iPlantCollaborativeOpenSource/Advanced_iPlant.git
  3. cd Advanced_iPlant

You will be working out of this directory exclusively for the rest of the workshop.

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