Upload
louisa-riley
View
216
Download
0
Embed Size (px)
Citation preview
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 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
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