Data to Discovery The iPlant Collaborative Community Cyberinfrastructure for Life Science Nirav Merchant ([email protected]) iPlant / University.

Data to Discovery

The iPlant Collaborative Community Cyberinfrastructure for Life Science

Nirav Merchant ([email protected])iPlant / University of Arizona

Introduction to iPlant Science API

Data to Discovery

Topic Coverage

• API: What why and ….who cares• Why do we need API’s• Connecting parts of iPlant with API• Hands on work with API– Login/get tokens– See your files– Submit a tasks (on Docker)– Inspect results– Play with commands on your own

Data to Discovery

The iPlant Collaborative: Vision

www.iPlantCollaborative.org

Enable life science researchers and educators touse and extend cyberinfrastructure

Data to Discovery

iPlant: Layer Cake

Data to Discovery

iPlant Architectural Motivation • We strive to be the CI Lego blocks• Danish 'leg godt' - 'play well’• Also translates as 'I put together' in

Latin• If a solution is not available you can

craft your own using iPlant CI components

Data to Discovery

API’s are everywhere• API = Application Programming

Interface• We will focus on web API (and what is

that ?)• They help others do creative things

with your applications/platform (without you having to build it for them)

• You will find the used in your phone to your TV and everywhere in between (facebook, google or any company providing service)

• It is the window into their platform (but with monkey/safety bars)

Data to Discovery

So how do you use Web API’s ?

• Use the same protocol as web url’s i.e http

• Everything is called as a URL• We call that REST interface• RES What ?• Things that do not fit on a url are

provided as JSON• J What ? • You have to know some basic

scripting or programming to benefit from it

Data to Discovery

Why did iPlant build API ?

Data Store

Computing Options

HPC

Cloud

HTC

Security

Data to Discovery

Really why did you build it ?

• More people sharing applications/pipelines

• Not enough resources available at authors home institution/lab to share analysis with world

• HPC was not a web friendly world• Lab with HPC access wanted web

interfaces (like DE)• No one else was building generic CI

API• We want people to extend our

platform

Data to Discovery

Your tool box

• Command line access on a linux, mac or PC

• cURL http://curl.haxx.se/download.html

• Text editor• Familiarity with shell (say what ?)• http://agaveapi.co/• Lots of patience (level = Sage)• Creativity !

Data to Discovery

Prepare you environment

• If you do not have a mac or linux box with curl and bash, please ssh using UA netid to:research.u.arizona.edu

• Go to http://agaveapi.co/ • We will explore the live docs (say

what)(Documentation | REST API DOCS)http://agaveapi.co/live-docs/

• Log into iPlant DE using your browser (de.iplantc.org)

Data to Discovery

Some terminology

• Tokens• Keys• Secrets• Agave-cli (you will like it)• Template (read some json and visit

DE)

• Now lets review Agav-cli options (in bin dir) and jump to live docs

Data to Discovery

Hands on Steps

• ssh research.u.arizona.edu or use your own mac, linux box

• bash• git clone https://bitbucket.org/taccaci/foundation-cli.git

agave-cli

• export PATH=$PATH:`pwd`/agave-cli/bin

• tenants-init choose iplant

• clients-create -N cli-demo -S

• files-list <your login>

• jobs-template -AV demo-pyplot-demo-advanced-0.1.0u1 > submit.json

• edit submit.json to "line" and remove .0 for size

• jobs-submit -V -W -F submit.json