Downloading data using API

[Donovan Parks]

Hello,

I'm having some trouble download data from IMG through the provided API. Specifically, I'm trying to download the data for the honey bee project at:

http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=HoneyBeecolony

I can successfully log-in to JGI and generate a cookie with:

curl -s https://signon.jgi.doe.gov/signon/create --data-ascii login=m...@gmail.com\&password=password -b cookies -c cookies > /dev/null

After this, I can grab the XML file describing the organisms download tree with:

curl -s -o HoneyBeecolony.xml "http://genome.jgi.doe.gov/ext-api/downloads/get-directory?organism=HoneyBeecolony" -b cookies &> /dev/null

Looking in the XML file, I can find the file I want:

<file label="European and Africanized bee gut microbiome from the USDA-ARS Beltsville Bee Research Center: Honey Bee colony" filename="3300000267.tar.gz" size="160 MB" timestamp="Thu Apr 11 19:36:51 PDT 2013" url="/ext-api/downloads/get_tape_file?blocking=true&amp;url=/HoneyBeecolony/download/_JAMO/52904c40067c013e2b067554/3300000267.tar.gz" project="403942" md5="df26a556ac7836b1252bc6666a469b46" />

I have not been able to download this file though. I have tried:

curl -s -o HoneyBeecolony.tar.gz http://genome.jgi.doe.gov/HoneyBeecolony/download/_JAMO/52904c40067c013e2b067554/3300000267.tar.gz -b cookies

This downloads a 'page not found' message from the server. I've also tried:

curl -s -o HoneyBeecolony.tar.gz 'http://genome.jgi.doe.gov/ext-api/downloads/get_tape_file?blocking=true&url=/HoneyBeecolony/download/_JAMO/52904c40067c013e2b067554/3300000267.tar.gz' -b cookies -c cookies

This also downloads an HTML file indicating a server side error. What is the correct URL?

Thanks for any and all advice.

Regards,

Donovan

[Ken Chu]

The jgi portal is not a IMG tool 

Please use their Comments/Question link (lcoated at the bottom of their home page, http://genome.jgi.doe.gov/) about their API.