dataone: R Interface to the DataONE REST API

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Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.

Author
Matthew B. Jones [aut, cre], Peter Slaughter [aut], Rob Nahf [aut], Carl Boettiger [aut], Chris Jones [aut], Jordan Read [aut], Lauren Walker [aut], Edmund Hart [aut], Scott Chamberlain [aut], Regents of the University of California [cph]
Date of publication
2016-08-30 01:33:34
Maintainer
Matthew B. Jones <jones@nceas.ucsb.edu>
License
Apache License 2.0
Version
2.0.1
URLs

View on CRAN

Man pages

AbstractTableDescriber-class
Base Class for Specific Metadata Parsers
addData
Add a D1Object containing a data object to a DataPackage
archive
Archive an object on a Member Node or Coordinating Node,...
asDataFrame
return the D1Object data as a data.frame.
auth_delete
DELETE a resource with authenticated credentials.
AuthenticationManager
Create an AuthenticationManager object
AuthenticationManager-class
Manage DataONE authentication.
auth_get
GET a resource with authenticated credentials if available.
auth_head
Send a http HEAD request for a resource with authenticated...
auth_post
POST a resource with authenticated credentials.
auth_put
PUT a resource with authenticated credentials.
auth_put_post_delete
POST, PUT, or DELETE a resource with authenticated...
canRead
Test whether the provided subject can read an object.
CertificateManager
Create a CertificateManager object
CertificateManager-class
CertficateManager provides mechanisms to obtain, load,...
CNode
Create a CNode object.
CNode-class
Provides R API to DataONE Coordinating Node services.
convert.csv
Convert a DataFrame to Standard CSV.
createD1Object
Create the Object in the DataONE System
createDataPackage
Create a DataPackage on a DataONE Member Node
createObject
Create an object on a Member Node.
D1Client
The DataONE client class used to downlaod, update and search...
D1Client-class
The D1Client class contains methods that perform high level...
D1Client-initialize
Initialize a D1Client object
d1_errors
This function parses a DataONE service response message for...
d1IdentifierSearch
Query the DataONE Solr endpoint of the Coordinating Node.
D1Node
Create a D1Node object.
D1Node-class
A base class for CNode and MNode.
D1Node-initialize
Initialize a D1Node
D1Object
Create a D1Object instance.
D1Object-class
D1Object (Deprecated) is a representation of a DataObject.
D1Object-initialize
Initialize a D1Object
d1SolrQuery
A method to query the DataONE solr endpoint of the...
data.characterEncoding
CharacterEncoding
data.formatFamily
Data Format
dataone
Search, download and upload data to the DataONE network.
dataone-defunct
Defunct
dataone-deprecated
Deprecated Classes, Methods
data.tableAttributeNames
returns the attribute names
data.tableAttributeOrientation
The Attribute (Header) Orientation
data.tableAttributeStorageTypes
returns the attributes' data storage types
data.tableAttributeTypes
returns the attributes' data types
data.tableFieldDelimiter
Field Delimiter
data.tableMissingValueCodes
returns missing value codes
data.tableQuoteCharacter
Quote Character
data.tableSkipLinesHeader
Number of lines to skip before reading data
describeObject
Efficiently get systemmetadat for an object.
documented.d1Identifiers
Get DataONE identifiers
documented.entityNames
Get the entity names associated with each table
documented.sizes
Get the sizes of the described data tables.
downloadCert
Open the CILogon Certificate download page in the default...
echoCredentials
Echo the credentials used to make the call.
EMLParser
Construct an EML parser object.
EMLParser-class
Handler for Parsing Table Format Details from Metadata
encodeSolr
Encode the input for Solr Queries
encodeUrlPath
Encode the Input for a URL Path Segment.
encodeUrlQuery
Encode the Input for a URL Query Segment.
evaluateAuth
Evaluate DataONE authentication.
generateIdentifier
Get a unique identifier that is generated by the Member Node...
getAuthExpires
Get the expiration date of the current authentication method.
getAuthMethod
Get the current valid authentication mechanism.
getAuthSubject
Get the authentication subject.
getCapabilities
Get the node capabilities description, and store the...
getCert
Get the DataONE X.509 Certificate location.
getCertExpires
Show the date and time when an X.509 certificate expires.
getCertInfo
Get X.509 Certificate information
getCertLocation
Get the file path on disk of the client certificate file.
getChecksum
Get the checksum for the data object associated with the...
getCN
Get the coordinating node associated with this D1Client...
getD1Object
Download a data object from the DataONE Federation.
getData
Get the data content of a D1Object.
getDataObject
Download a data object from the DataONE Federation as a...
getEndpoint
Return the URL endpoint for the DataONE Coordinating Node.
getErrorDescription
Extract an error message from an http response.
getFormat
Get information for a single DataONE object format
getFormatId
Get the FormatId of the D1Object
getIdentifier
Get the Identifier of the D1Object
getMN
Get a member node client based on its node identifier.
getMNode
Get a reference to a node based on its identifier
getMNodeId
Get the member node identifier associated with this D1Client...
getObject
Get the bytes associated with an object on this Node.
getPackage
Download a data package from a member node.
getQueryEngineDescription
Query a node for the list of query engines available on the...
getSystemMetadata
Get the metadata describing system properties associated with...
getToken
Get the value of the DataONE Authentication Token, if one...
getTokenInfo
Get authentication token information
get_user_agent
User agent string
hasReservation
Checks to determine if the supplied subject is the owner of...
isAuthExpired
Check if the currently valid authentication method has...
isAuthorized
Check if an action is authorized for the specified identifier
isAuthValid
Verify authentication for a member node.
isCertExpired
Determine if an X.509 certificate has expired.
listFormats
List all object formats registered in DataONE.
listMemberNodes
List DataONE Member Nodes.
listNodes
Get the list of nodes associated with a CN
listObjects
Retrieve the list of objects that match the search parameters
listQueryEngines
Query a node for the list of query engines available on the...
MNode
Create a MNode object representing a DataONE Member Node...
MNode-class
Provides R API to DataONE Member Node services.
obscureAuth
Temporarity disable DataONE authentication.
obscureCert
Obscure the CILogon Client Certificate
parseCapabilities
Construct a Node, using a passed in capabilities XML
parseSolrResult
Parse Solr output into an R list
ping
Test if a node is online and accepting DataONE requests
query
Search DataONE for data and metadata objects
reserveIdentifier
Reserve a identifier that is unique in the DataONE network.
resolve
Get a list of coordinating nodes holding a given pid.
restoreAuth
Restore authentication (after being disabled with...
restoreCert
Restore the CILogon client certificate by renaming it to its...
setMNodeId
Set the member node identifier to be associated with the...
setObsoletedBy
Set a pid as being obsoleted by another pid
setPublicAccess
Make the object publicly readable.
showAuth
Display all authentication information
showClientSubject
Get DataONE Identity as Stored in the CILogon Certificate.
updateObject
Update an object on a Member Node, by creating a new object...
updateSystemMetadata
Update the system metadata associated with an object.
uploadDataObject
Upload a DataObject to a DataONE member node.
uploadDataPackage
Upload a DataPackage to a DataONE member node.

Files in this package

dataone
dataone/inst
dataone/inst/testfiles
dataone/inst/testfiles/testDataTableParamsDoc-eml-2.1.0.xml
dataone/inst/testfiles/testdoc-eml-2.1.0.xml
dataone/inst/testfiles/sysmeta.xml
dataone/inst/CITATION
dataone/inst/COPYRIGHTS
dataone/inst/extdata
dataone/inst/extdata/sample.csv
dataone/inst/extdata/sample2-eml.xml
dataone/inst/extdata/sample-eml.xml
dataone/inst/doc
dataone/inst/doc/upload-data.R
dataone/inst/doc/download-data.html
dataone/inst/doc/dataone-overview.R
dataone/inst/doc/download-data.Rmd
dataone/inst/doc/dataone-overview.Rmd
dataone/inst/doc/upload-data.Rmd
dataone/inst/doc/upload-data.html
dataone/inst/doc/searching-dataone.Rmd
dataone/inst/doc/searching-dataone.R
dataone/inst/doc/dataone-overview.html
dataone/inst/doc/download-data.R
dataone/inst/doc/searching-dataone.html
dataone/tests
dataone/tests/testthat.R
dataone/tests/testthat
dataone/tests/testthat/test.EMLParser.R
dataone/tests/testthat/test.CertificateManager.R
dataone/tests/testthat/test.CNode.R
dataone/tests/testthat/test.SystemMetadata.R
dataone/tests/testthat/test.MNode.R
dataone/tests/testthat/test.D1Node.R
dataone/tests/testthat/test.AuthenticationManager.R
dataone/tests/testthat/test.auth_request.R
dataone/tests/testthat/test.D1Client.R
dataone/NAMESPACE
dataone/NEWS
dataone/R
dataone/R/CertificateManager.R
dataone/R/AuthenticationManager.R
dataone/R/auth_request.R
dataone/R/MNode.R
dataone/R/D1Node.R
dataone/R/D1Client.R
dataone/R/yyy.R
dataone/R/dataone-package.R
dataone/R/AbstractTableDescriber.R
dataone/R/CNode.R
dataone/R/zzz.R
dataone/R/EMLParser.R
dataone/R/D1Object.R
dataone/vignettes
dataone/vignettes/download-data.Rmd
dataone/vignettes/dataone-overview.Rmd
dataone/vignettes/upload-data.Rmd
dataone/vignettes/download-data_cache
dataone/vignettes/download-data_cache/html
dataone/vignettes/download-data_cache/html/unnamed-chunk-1_66a44dbe59f3fccda904f2c815fa2b24.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-4_6439e2b9d4d7521f258abc450d547191.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-5_c8b332f84be48fca34735139557c38ce.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-1_66a44dbe59f3fccda904f2c815fa2b24.RData
dataone/vignettes/download-data_cache/html/__objects
dataone/vignettes/download-data_cache/html/__globals
dataone/vignettes/download-data_cache/html/unnamed-chunk-5_c8b332f84be48fca34735139557c38ce.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-8_dc0766765f366a50fc944b2895757c23.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-10_2a43bb4137744c85d8bcb71e1ec23e32.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-2_b38fcbdcd904f039400b66c434f6f425.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-10_2a43bb4137744c85d8bcb71e1ec23e32.rdb
dataone/vignettes/download-data_cache/html/__packages
dataone/vignettes/download-data_cache/html/unnamed-chunk-9_b0f9807bcb598084fc89bf192813fd0e.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-7_ffe7157c1fb3492156e7a88f0ec42d58.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-5_c8b332f84be48fca34735139557c38ce.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-6_d9b012bf8434434f29da4582a8cfdb24.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-4_6439e2b9d4d7521f258abc450d547191.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-10_2a43bb4137744c85d8bcb71e1ec23e32.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-6_d9b012bf8434434f29da4582a8cfdb24.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-3_9c74fc00ea9a0aee169317f5541c6572.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-7_ffe7157c1fb3492156e7a88f0ec42d58.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-3_9c74fc00ea9a0aee169317f5541c6572.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-2_b38fcbdcd904f039400b66c434f6f425.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-3_9c74fc00ea9a0aee169317f5541c6572.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-8_dc0766765f366a50fc944b2895757c23.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-4_6439e2b9d4d7521f258abc450d547191.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-6_d9b012bf8434434f29da4582a8cfdb24.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-2_b38fcbdcd904f039400b66c434f6f425.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-9_b0f9807bcb598084fc89bf192813fd0e.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-7_ffe7157c1fb3492156e7a88f0ec42d58.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-8_dc0766765f366a50fc944b2895757c23.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-1_66a44dbe59f3fccda904f2c815fa2b24.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-9_b0f9807bcb598084fc89bf192813fd0e.RData
dataone/vignettes/searching-dataone.Rmd
dataone/README.md
dataone/MD5
dataone/build
dataone/build/vignette.rds
dataone/DESCRIPTION
dataone/man
dataone/man/CNode-class.Rd
dataone/man/createD1Object.Rd
dataone/man/dataone.Rd
dataone/man/listMemberNodes.Rd
dataone/man/data.tableMissingValueCodes.Rd
dataone/man/data.tableQuoteCharacter.Rd
dataone/man/encodeUrlQuery.Rd
dataone/man/convert.csv.Rd
dataone/man/listObjects.Rd
dataone/man/listFormats.Rd
dataone/man/getFormatId.Rd
dataone/man/getMNode.Rd
dataone/man/get_user_agent.Rd
dataone/man/MNode-class.Rd
dataone/man/getDataObject.Rd
dataone/man/getToken.Rd
dataone/man/getCN.Rd
dataone/man/asDataFrame.Rd
dataone/man/data.tableAttributeNames.Rd
dataone/man/data.characterEncoding.Rd
dataone/man/data.tableAttributeOrientation.Rd
dataone/man/listQueryEngines.Rd
dataone/man/data.formatFamily.Rd
dataone/man/auth_post.Rd
dataone/man/updateSystemMetadata.Rd
dataone/man/encodeUrlPath.Rd
dataone/man/getCapabilities.Rd
dataone/man/evaluateAuth.Rd
dataone/man/createDataPackage.Rd
dataone/man/describeObject.Rd
dataone/man/obscureCert.Rd
dataone/man/CNode.Rd
dataone/man/isCertExpired.Rd
dataone/man/showAuth.Rd
dataone/man/CertificateManager.Rd
dataone/man/auth_get.Rd
dataone/man/createObject.Rd
dataone/man/downloadCert.Rd
dataone/man/getIdentifier.Rd
dataone/man/getCertInfo.Rd
dataone/man/setObsoletedBy.Rd
dataone/man/isAuthExpired.Rd
dataone/man/CertificateManager-class.Rd
dataone/man/parseSolrResult.Rd
dataone/man/getEndpoint.Rd
dataone/man/reserveIdentifier.Rd
dataone/man/getChecksum.Rd
dataone/man/D1Client-class.Rd
dataone/man/auth_put_post_delete.Rd
dataone/man/D1Object.Rd
dataone/man/data.tableFieldDelimiter.Rd
dataone/man/getQueryEngineDescription.Rd
dataone/man/D1Client.Rd
dataone/man/encodeSolr.Rd
dataone/man/getCertLocation.Rd
dataone/man/D1Client-initialize.Rd
dataone/man/data.tableSkipLinesHeader.Rd
dataone/man/showClientSubject.Rd
dataone/man/setMNodeId.Rd
dataone/man/documented.sizes.Rd
dataone/man/getSystemMetadata.Rd
dataone/man/D1Node-initialize.Rd
dataone/man/uploadDataPackage.Rd
dataone/man/data.tableAttributeTypes.Rd
dataone/man/isAuthValid.Rd
dataone/man/getTokenInfo.Rd
dataone/man/parseCapabilities.Rd
dataone/man/auth_head.Rd
dataone/man/setPublicAccess.Rd
dataone/man/restoreAuth.Rd
dataone/man/isAuthorized.Rd
dataone/man/MNode.Rd
dataone/man/D1Node-class.Rd
dataone/man/listNodes.Rd
dataone/man/auth_put.Rd
dataone/man/documented.d1Identifiers.Rd
dataone/man/d1SolrQuery.Rd
dataone/man/EMLParser-class.Rd
dataone/man/archive.Rd
dataone/man/resolve.Rd
dataone/man/generateIdentifier.Rd
dataone/man/getErrorDescription.Rd
dataone/man/D1Node.Rd
dataone/man/getCertExpires.Rd
dataone/man/query.Rd
dataone/man/AuthenticationManager.Rd
dataone/man/updateObject.Rd
dataone/man/getAuthExpires.Rd
dataone/man/echoCredentials.Rd
dataone/man/d1IdentifierSearch.Rd
dataone/man/dataone-deprecated.Rd
dataone/man/getAuthSubject.Rd
dataone/man/getCert.Rd
dataone/man/getMN.Rd
dataone/man/uploadDataObject.Rd
dataone/man/canRead.Rd
dataone/man/hasReservation.Rd
dataone/man/EMLParser.Rd
dataone/man/getD1Object.Rd
dataone/man/d1_errors.Rd
dataone/man/addData.Rd
dataone/man/AuthenticationManager-class.Rd
dataone/man/D1Object-class.Rd
dataone/man/data.tableAttributeStorageTypes.Rd
dataone/man/documented.entityNames.Rd
dataone/man/getPackage.Rd
dataone/man/dataone-defunct.Rd
dataone/man/getData.Rd
dataone/man/auth_delete.Rd
dataone/man/getMNodeId.Rd
dataone/man/getFormat.Rd
dataone/man/D1Object-initialize.Rd
dataone/man/getAuthMethod.Rd
dataone/man/ping.Rd
dataone/man/restoreCert.Rd
dataone/man/obscureAuth.Rd
dataone/man/AbstractTableDescriber-class.Rd
dataone/man/getObject.Rd