datapack: A Flexible Container to Transport and Manipulate Data and Associated Resources

• Author: Matthew B. Jones and Peter Slaughter (NCEAS)
• doi:10.5063/F1QV3JGM
• License: Apache 2
• Package source code on Github
• Submit Bugs and feature requests

The datapack R package provides an abstraction for collating heterogeneous collections of data objects and metadata into a bundle that can be transported and loaded into a single composite file. The methods in this package provide a convenient way to load data from common repositories such as DataONE into the R environment, and to document, serialize, and save data from R to data repositories worldwide.

Installation Notes

The datapack R package requires the R package redland. If you are installing on Ubuntu then the Redland C libraries must be installed before the redland and datapack package can be installed. If you are installing on Mac OS X or Windows then installing these libraries is not required.

The following instructions illustrate how to install datapack and its requirements.

Installing on Mac OS X

On Mac OS X datapack can be installed with the following commands:

install.packages("datapack")
library(datapack)

The datapack R package should be available for use at this point.

Note: if you wish to build the required redland package from source before installing datapack, please see the redland installation instructions.

Installing on Ubuntu

For ubuntu, install the required Redland C libraries by entering the following commands in a terminal window:

sudo apt-get update
sudo apt-get install librdf0 librdf0-dev

Then install the R packages from the R console:

install.packages("datapack")
library(datapack)

The datapack R package should be available for use at this point

Installing on Windows

For windows, the required redland R package is distributed as a binary release, so it is not necessary to install any additional system libraries.

To install the R packages from the R console:

install.packages("datapack")
library(datapack)

Quick Start

See the full manual for documentation, but once installed, the package can be run in R using:

library(datapack)
help("datapack")

Create a DataPackage and add metadata and data DataObjects to it:

library(datapack)
library(uuid)
dp <- new("DataPackage")
mdFile <- system.file("extdata/sample-eml.xml", package="datapack")
mdId <- paste("urn:uuid:", UUIDgenerate(), sep="")
md <- new("DataObject", id=mdId, format="eml://ecoinformatics.org/eml-2.1.0", file=mdFile)
addData(dp, md)

csvfile <- system.file("extdata/sample-data.csv", package="datapack")
sciId <- paste("urn:uuid:", UUIDgenerate(), sep="")
sciObj <- new("DataObject", id=sciId, format="text/csv", filename=csvfile)
dp <- addData(dp, sciObj)
ids <- getIdentifiers(dp)

Add a relationship to the DataPackage that shows that the metadata describes, or "documents", the science data:

dp <- insertRelationship(dp, subjectID=mdId, objectIDs=sciId)
relations <- getRelationships(dp)

Create an Resource Description Framework representation of the relationships in the package:

serializationId <- paste("resourceMap", UUIDgenerate(), sep="")
filePath <- file.path(sprintf("%s/%s.rdf", tempdir(), serializationId))
status <- serializePackage(dp, filePath, id=serializationId, resolveURI="")

Save the DataPackage to a file, using the BagIt packaging format:

bagitFile <- serializeToBagIt(dp) 

Note that the dataone R package can be used to upload a DataPackage to a DataONE Member Node using the uploadDataPackage method. Please see the documentation for the dataone R package, for example:

vignette("upload-data", package="dataone")

Acknowledgements

Work on this package was supported by:

• NSF-ABI grant #1262458 to C. Gries, M. B. Jones, and S. Collins.
• NSF-DATANET grants #0830944 and #1430508 to W. Michener, M. B. Jones, D. Vieglais, S. Allard and P. Cruse
• NSF DIBBS grant #1443062 to T. Habermann and M. B. Jones
• NSF-PLR grant #1546024 to M. B. Jones, S. Baker-Yeboah, J. Dozier, M. Schildhauer, and A. Budden

Additional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.