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Joyent Manta R Software Development Kit
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Update README.md

Windows OpenSSL version bump
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README.md

mantaRSDK

Joyent Manta R Software Development Kit 0.8.1

System Requirements

To use this you need a working Manta account, Unix/Linux/Windows R v3.0 or up, as well as environment variables set for Manta use, and openSSL installed and working.

If you have the Node.js Manta Command Line Tools working on a Unix/Linux platform, this should work as is.

Windows has specific requirements, detailed below.

Getting Started with Manta

1) Create a Joyent Cloud account at http://www.joyent.com

2) Create a private/public ssh key pair using the Joyent web console, as prompted when you sign up. Copy and save the value of your SSH key id which will look something like this:
91:b4:d2:34:f1:b8:3c:1b:11:d1:b7:6c:e4:3c:4e:01

3.1) UNIX (WINDOWS - skip ahead and do steps 3.3 - 3.5 ) Put the private key file and public key files into a .ssh directory located in your home directory/folder. Private key is named 'id_rsa' and public key is named 'id_rsa.pub'

mantaRSDK will look for the Unix SSH key pair here:

~/.ssh/id_rsa
~/.ssh/id_rsa.pub

3.2) UNIX: ENVIRONMENT VARIABLES add these lines to ~/.bashrc or ~/.bash_profile with a text editor, substituting your username.

export MANTA_URL=https://us-east.manta.joyent.com
export MANTA_USER=yourusername
export MANTA_KEY_ID=91:b4:d2:34:f1:b8:3c:1b:11:d1:b7:6c:e4:3c:4e:01 

then source the appropriate file:

source ~/.bash_profile  
source ~/.bashrc

3.3) WINDOWS: Put the Joyent generated private key file and public key files into a .ssh directory located in your home directory/folder. Private key is named 'id_rsa' and public key is named 'id_rsa.pub'.

Windows -SSH key pair should be in your account folder "youraccount":

C:\Users\youraccount\.ssh\id_rsa
C:\Users\youraccount\.ssh\id_rsa.pub

3.4) WINDOWS - Install the free Windows 64 bit version of OpenSSL from http://slproweb.com/download/Win64OpenSSL-1_0_1j.exe . Make note of the folder path for openssl.exe to add to your system PATH in the next step.

3.5) WINDOWS - Environment Variables and PATH Set the environment variables from an administrator account as follows: Run a command prompt as administrator. Click on "Start" button, type cmd, right click on cmd program icon and select "Run as administrator". Launch System Properies by issuing the command "start sysdm.cpl". From the System Properties dialogue box, select tab "Advanced" then button at the bottom "Environment Variables..." Use the Environment Variables dialogue box to add in these three, supplying your own values for MANTA_KEY_ID and MANTA_USER:

Variable        Value
MANTA_KEY_ID    91:b4:d2:34:f1:b8:3c:1b:11:de:b7:6c:e4:3c:4e:01
MANTA_URL       https://us-east-manta.joyent.com
MANTA_USER      yourusername

Edit the User variable 'PATH' by clicking on "Edit", hit the END key on your keyboard and type ";" then the full openssl.exe path you got from step 3.4) so it is added to the end of the Path like this:

...;C:\bin\OpenSSL-Win64\bin

Click the Environment Variables dialogue box "OK" button and then the "Systems Properties" "OK" button.

4) UNIX/LINUX/WINDOWS Optional (and useful for debugging your SSH key install). Download and install Node.js at http://nodejs.org/download. Install the Node.js package called "manta" with the command "npm install -g manta" from a shell or command prompt. Try the command 'mput to see if you can put a simple text file on manta and list your manta directory as follows:

Unix or Windows command line prompt:

echo "hello manta" > hello.txt
mput -f hello.txt ~~/stor
mls

If this is not working, check to see your enviroment variables are set with the command "env | grep MANTA" on Unix, or "set" on Windows.

Once you have Manta working from the command line you are ready to install mantaRSDK into R:

Installing the mantaRSDK package in R

mantaRSDK Installation

The mantaRSDK uses install_github() which requires the Rtools package:

http://cran.r-project.org/bin/windows/Rtools

Testing From R

Install:

install.packages("devtools")
library(devtools)
install_github("Rbunyan", username="joyent")
install_github("mantaRSDK", username="joyent")

Test:

library(mantaRSDK)
?mantaRSDK
mantaWhoami(all=TRUE)
mantaLs.l()
mantaSetwd.public()
mattaGetwd()
# Work through Examples in these key Help pages
?mantaSetwd
?mantaMkdir
?mantaPut
?mantaGet
?mantaSave.ws
?mantaJob.launch

Remove:

library(mantaRSDK)
detach(package:mantaRSDK, unload=TRUE)

mantaRSDK Functions

Manta Account Management

     mantaAccount() mantaWhoami() mantaGetLimits() mantaSetLimits()

Manta Hierarchical Directory Operations

     mantaGetwd() mantaSetwd() mantaSetwd.jobs() mantaSetwd.public()
     mantaSetwd.reports() mantaSetwd.stor() mantaSetwd.ws()
     mantaMkdir() mantaRmdir() mantaLs() mantaLs.du() mantaLs.l()
     mantaLs.n() mantaLs.paths() mantaLs.url() mantaFind()
     mantaFind.du() mantaFind.l() mantaFind.n() mantaFind.sizepath()
     mantaFind.sizes() mantaFind.url()

Manta Object Store Operations

     mantaExists() mantaPut() mantaGet() mantaCat() mantaRm()
     mantaSnapln() mantaDump() mantaSource() mantaSave() mantaLoad()
     mantaSave.ws() mantaLoad.ws()

Manta Compute Job Operations

     mantaJob.setup() mantaMap() mantaReduce() mantaJob.launch()
     mantaJob.status() mantaJob.done() mantaJob.cancel()
     mantaJob.errors() mantaJob.errors.stderr() mantaJob.failures()
     mantaJob.inputs() mantaJob.outputs() mantaJob.outputs.cat()
     mantaJobs() mantaJobs.running() mantaJobs.tail()

Exposed Low Level Calls

     mantaAttempt() mantaXfer() mantaSave.image()

Useful Bunyan Debug/Log Utilities

     bunyanSetLog() bunyanBuffer() bunyanTraceback()

More Function Detail

Manta Account Management

     mantaAccount()

Changes current Manta account information.

     mantaWhoami()

Report the active Manta account settings.

     mantaGetLimits()

Returns Manta durability level, connection timeouts and limits currently active.

     mantaSetLimits()

Sets Manta durability level, connection timeouts and limits currently active.

Manta Hierarchical Directory Operations

     mantaGetwd()

Gets Manta working directory.

     mantaSetwd()
     mantaSetwd.public()
     mantaSetwd.stor()
     mantaSetwd.ws()
     mantaSetwd.jobs()
     mantaSetwd.reports()

Sets Manta working directory. Dotted forms are top-level (public, stor, jobs, reports) or workspace (as set by mantaSave.ws).

     mantaMkdir()

Makes a Manta subdirectory, optionally with parent directories.

     mantaRmdir()

Removes a Manta subdirectory.

     mantaLs()
     mantaLs.du()
     mantaLs.l()
     mantaLs.n()
     mantaLs.paths()
     mantaLs.url()

Lists, searches, filters, sorts and formats Manta directory listings. Dotted forms alter the format of the output. Numerical values are returned by n (number) and du (disk used).

     mantaFind()
     mantaFind.du()
     mantaFind.l()
     mantaFind.n()
     mantaFind.sizepath()
     mantaFind.sizes()
     mantaFind.url()

Recursive find tool for retrieving matching objects/subdirs from Manta hierarchy. Dotted forms alter the format of the output. Numerical values are returned by n (number) and du (disk used).

Manta Object Store Operations

     mantaExists()

Tests to see if a Manta object or subdirectory exists.

     mantaPut()

Uploads file(s) (vectorized), or raw R buffer data to Manta Storage Service.

     mantaGet()

Downloads Manta object(s) (vectorized) specified to file(s) or buffer.

     mantaCat()

Retrieves object from Manta and uses cat() to print contents to the R console.

     mantaRm()

Removes specified Manta object, optionally recursive.

     mantaSnapln()

Makes a Snaplink - combination snapshot and symbolic link.

     mantaDump()

Uses dump() to upload text parsable R data to Manta Storage Service.

     mantaSource()

Downloads specified Manta object and applies source() to parse R code file.

     mantaSave()

Uploads R data to Manta Storage Service using R function save().

     mantaLoad()

Downloads specified Manta object containing R data and uses R function load().

     mantaSave.ws()

Saves R workspace to Manta R workspace directory with an audit trail of backups.

     mantaLoad.ws()

Loads last current R workspace from Manta R workspace directory.

Manta Compute Job Operations

     mantaJob.setup()
     mantaMap()
     mantaReduce()

Constructors for R format Manta Job including name, and UNIX command line tasks as defined by mantaMap(), and/or mantaReduce() functions.

     mantaJob.launch()

Submits list of input Manta objects and R format Manta Job specification, runs job optionally polls job status. Returns job status.

     mantaJob.cancel()

Sends Manta a cancel message to stop running job.

     mantaJob.status()

Returns JSON Manta job status data given Manta job identifier.

     mantaJob.done()

Checks or polls status of a Manta job. Returns done or not as logical.

     mantaJob.errors()

Returns JSON Manta error messages given Manta job identifier.

     mantaJob.errors.stderr()

Retrieves JSON errors given Manta job identifier, then retrieves each stderr message archived on Manta (if any) and uses mantaCat() to print contents of stderr to the console.

     mantaJob.failures()

Returns list of failures given Manta job identifier.

     mantaJob.inputs()

Returns list of input Manta objects given Manta job identifier.

     mantaJob.outputs()

Returns list of output Manta objects given Manta job identifier.

     mantaJob.outputs.cat()

Retrieves list of Manta output objects given Manta job identifier, then retrieves each object from Manta and uses cat() to print contents to the R console.

     mantaJobs()

Lists all Manta job identifiers, sorted by time.

     mantaJobs.running()

Lists identifiers of any running Manta jobs.

     mantaJobs.tail()

Returns identifier of last run Manta job identifier, or from offset n up from end of list.

Exposed Low Level Calls

     mantaAttempt()

raw REST API Manta Caller with exception handling, used by many functions.

     mantaXfer()

raw REST API Manta Caller for mantaPut() mantaGet() and related data transfer routines.

     mantaSave.image()

Workspace Upload function that calls R save.image(); used by mantaSave.ws().

Useful Bunyan Debug/Log Utilities

     bunyanSetLog()

Starts bunyan JSON message logging at supplied logging threshold to file or memory buffer.

     bunyanBuffer()

Returns memory buffer.

     bunyanTraceback()

Get messages from memory after last bunyanSetpoint

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