R Interface to the DataONE REST API

Documentation for package ‘dataone’ version 2.2.2

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-- A --

AbstractTableDescriber-class	Base Class for Specific Metadata Parsers
addData-method	Add a D1Object containing a data object to a DataPackage
archive	Archive an object on a Member Node or Coordinating Node, which hides it from casual searches.
archive-method	Archive an object on a Member Node or Coordinating Node, which hides it from casual searches.
asDataFrame	return the D1Object data as a data.frame.
asDataFrame-method	return the D1Object data as a data.frame.
AuthenticationManager	Create an AuthenticationManager object
AuthenticationManager-class	Manage DataONE authentication.
AuthenticationManager-method	Create an AuthenticationManager object
auth_delete	DELETE a resource with authenticated credentials.
auth_get	GET a resource with authenticated credentials if available.
auth_head	Send a http HEAD request for a resource with authenticated credentials if available.
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 credentials.

-- C --

canRead-method	Test whether the provided subject can read an object.
CertificateManager	Create a CertificateManager object
CertificateManager-class	CertficateManager provides mechanisms to obtain, load, verify, and display X509 certificates.
CertificateManager-method	Create a CertificateManager object
CNode	Create a CNode object.
CNode-class	Provides R API to DataONE Coordinating Node services.
CNode-method	Create a CNode object.
convert.csv	Convert a DataFrame to Standard CSV.
convert.csv-method	Convert a DataFrame to Standard CSV.
createD1Object	Create the Object in the DataONE System
createD1Object-method	Create the Object in the DataONE System
createDataPackage	Create a DataPackage on a DataONE Member Node
createDataPackage-method	Create a DataPackage on a DataONE Member Node
createObject	Create an object on a Member Node.
createObject-method	Create an object on a Member Node.

-- D --

D1Client	The DataONE client class used to download, update and search for data in the DataONE network.
D1Client-class	The D1Client class contains methods that perform high level DataONE tasks
D1Client-initialize	Initialize a D1Client object
D1Client-method	The DataONE client class used to download, update and search for data in the DataONE network.
d1IdentifierSearch	Query the DataONE Solr endpoint of the Coordinating Node.
d1IdentifierSearch-method	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
D1Node-method	Create a D1Node object.
D1Object	Create a D1Object instance.
D1Object-class	D1Object (Defunct) is a representation of a DataObject.
D1Object-initialize	Initialize a D1Object
d1SolrQuery	A method to query the DataONE solr endpoint of the Coordinating Node.
d1SolrQuery-method	A method to query the DataONE solr endpoint of the Coordinating Node.
d1_errors	This function parses a DataONE service response message for errors, and extracts and prints error information.
data.characterEncoding	CharacterEncoding
data.characterEncoding-method	CharacterEncoding
data.formatFamily	Data Format
data.formatFamily-method	Data Format
data.tableAttributeNames	returns the attribute names
data.tableAttributeNames-method	returns the attribute names
data.tableAttributeOrientation	The Attribute (Header) Orientation
data.tableAttributeOrientation-method	The Attribute (Header) Orientation
data.tableAttributeStorageTypes	returns the attributes' data storage types
data.tableAttributeStorageTypes-method	returns the attributes' data storage types
data.tableAttributeTypes	returns the attributes' data types
data.tableAttributeTypes-method	returns the attributes' data types
data.tableFieldDelimiter	Field Delimiter
data.tableFieldDelimiter-method	Field Delimiter
data.tableMissingValueCodes	returns missing value codes
data.tableMissingValueCodes-method	returns missing value codes
data.tableQuoteCharacter	Quote Character
data.tableQuoteCharacter-method	Quote Character
data.tableSkipLinesHeader	Number of lines to skip before reading data
data.tableSkipLinesHeader-method	Number of lines to skip before reading data
dataone	Search, download and upload data to the DataONE network.
describeObject	Efficiently get systemmetadata for an object.
describeObject-method	Efficiently get systemmetadata for an object.
documented.d1Identifiers	Get DataONE identifiers
documented.d1Identifiers-method	Get DataONE identifiers
documented.entityNames	Get the entity names associated with each table
documented.entityNames-method	Get the entity names associated with each table
documented.sizes	Get the sizes of the described data tables.
documented.sizes-method	Get the sizes of the described data tables.
downloadCert	Open the CILogon Certificate download page in the default browser.
downloadCert-method	Open the CILogon Certificate download page in the default browser.
downloadObject	Download an object from the DataONE Federation to Disk.
downloadObject-method	Download an object from the DataONE Federation to Disk.

-- E --

echoCredentials	Echo the credentials used to make the call.
echoCredentials-method	Echo the credentials used to make the call.
EMLParser	Construct an EML parser object.
EMLParser-class	Handler for Parsing Table Format Details from Metadata
EMLParser-method	Construct an EML parser object.
encodeSolr	Encode the input for Solr Queries
encodeSolr-method	Encode the input for Solr Queries
encodeUrlPath	Encode the Input for a URL Path Segment.
encodeUrlPath-method	Encode the Input for a URL Path Segment.
encodeUrlQuery	Encode the Input for a URL Query Segment.
encodeUrlQuery-method	Encode the Input for a URL Query Segment.
enerateIdentifier	Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.
evaluateAuth	Evaluate DataONE authentication.
evaluateAuth-method	Evaluate DataONE authentication.

-- G --

generateIdentifier	Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.
generateIdentifier-method	Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.
getAuthExpires	Get the expiration date of the current authentication method.
getAuthExpires-method	Get the expiration date of the current authentication method.
getAuthMethod	Get the current valid authentication mechanism.
getAuthMethod-method	Get the current valid authentication mechanism.
getAuthSubject	Get the authentication subject.
getAuthSubject-method	Get the authentication subject.
getCapabilities	Get the node capabilities description, and store the information in the MNode.
getCapabilities-method	Get the node capabilities description, and store the information in the MNode.
getCert	Get the DataONE X.509 Certificate location.
getCert-method	Get the DataONE X.509 Certificate location.
getCertExpires	Show the date and time when an X.509 certificate expires.
getCertExpires-method	Show the date and time when an X.509 certificate expires.
getCertInfo	Get X.509 Certificate information
getCertInfo-method	Get X.509 Certificate information
getCertLocation	Get the file path on disk of the client certificate file.
getCertLocation-method	Get the file path on disk of the client certificate file.
getChecksum	Get the checksum for the data object associated with the specified pid.
getChecksum-method	Get the checksum for the data object associated with the specified pid.
getCN	Get the coordinating node associated with this D1Client object.
getCN-method	Get the coordinating node associated with this D1Client object.
getD1Object	Download a data object from the DataONE Federation.
getD1Object-method	Download a data object from the DataONE Federation.
getData-method	Get the data content of a D1Object.
getDataObject	Download a file (and it's associated system metadata) from the DataONE Federation as a DataObject.
getDataObject-method	Download a file (and it's associated system metadata) from the DataONE Federation as a DataObject.
getDataPackage	Download data from the DataONE Federation as a DataPackage.
getDataPackage-method	Download data from the DataONE Federation as a DataPackage.
getEndpoint	Return the URL endpoint for the DataONE Coordinating Node.
getEndpoint-method	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
getFormat-method	Get information for a single DataONE object format
getFormatId-method	Get the FormatId of the D1Object
getIdentifier-method	Get the Identifier of the D1Object
getMetadataMember	Get the DataObject containing package metadata
getMetadataMember-method	Get the DataObject containing package metadata
getMN	Get a member node client based on its node identifier.
getMN-method	Get a member node client based on its node identifier.
getMNode	Get a reference to a node based on its identifier
getMNode-method	Get a reference to a node based on its identifier
getMNodeId	Get the member node identifier associated with this D1Client object..
getMNodeId-method	Get the member node identifier associated with this D1Client object..
getObject	Get the bytes associated with an object on this Node.
getObject-method	Get the bytes associated with an object on this Node.
getPackage	Download a data package from a member node.
getPackage-method	Download a data package from a member node.
getQueryEngineDescription	Query a node for the list of query engines available on the node
getQueryEngineDescription-method	Query a node for the list of query engines available on the node
getSystemMetadata	Get the metadata describing system properties associated with an object on this Node.
getSystemMetadata-method	Get the metadata describing system properties associated with an object on this Node.
getToken	Get the value of the DataONE Authentication Token, if one exists.
getToken-method	Get the value of the DataONE Authentication Token, if one exists.
getTokenInfo	Get authentication token information
getTokenInfo-method	Get authentication token information
get_user_agent	User agent string

-- H --

hasReservation	Checks to determine if the supplied subject is the owner of the reservation of id.
hasReservation-method	Checks to determine if the supplied subject is the owner of the reservation of id.

-- I --

initialize-method	Initialize a D1Client object
initialize-method	Initialize a D1Node
initialize-method	Initialize a D1Object
isAuthExpired	Check if the currently valid authentication method has reached the expiration time.
isAuthExpired-method	Check if the currently valid authentication method has reached the expiration time.
isAuthorized	Check if an action is authorized for the specified identifier
isAuthorized-method	Check if an action is authorized for the specified identifier
isAuthValid	Verify authentication for a member node.
isAuthValid-method	Verify authentication for a member node.
isCertExpired	Determine if an X.509 certificate has expired.
isCertExpired-method	Determine if an X.509 certificate has expired.

-- L --

listFormats	List all object formats registered in DataONE.
listFormats-method	List all object formats registered in DataONE.
listMemberNodes	List DataONE Member Nodes.
listMemberNodes-method	List DataONE Member Nodes.
listNodes	Get the list of nodes associated with a CN
listNodes-method	Get the list of nodes associated with a CN
listObjects	Retrieve the list of objects that match the search parameters
listObjects-method	Retrieve the list of objects that match the search parameters
listQueryEngines	Query a node for the list of query engines available on the node
listQueryEngines-method	Query a node for the list of query engines available on the node

-- M --

MNode	Create a MNode object representing a DataONE Member Node repository.
MNode-class	Provides R API to DataONE Member Node services.
MNode-method	Create a MNode object representing a DataONE Member Node repository.

-- O --

obscureAuth	Temporarily disable DataONE authentication.
obscureAuth-method	Temporarily disable DataONE authentication.
obscureCert	Obscure the CILogon Client Certificate
obscureCert-method	Obscure the CILogon Client Certificate

-- P --

parseCapabilities	Construct a Node, using a passed in capabilities XML
parseCapabilities-method	Construct a Node, using a passed in capabilities XML
parseSolrResult	Parse Solr output into an R list
parseSolrResult-method	Parse Solr output into an R list
ping	Test if a node is online and accepting DataONE requests
ping-method	Test if a node is online and accepting DataONE requests

-- Q --

query	Search DataONE for data and metadata objects
query-method	Search DataONE for data and metadata objects

-- R --

reserveIdentifier	Reserve a identifier that is unique in the DataONE network.
reserveIdentifier-method	Reserve a identifier that is unique in the DataONE network.
resolve	Get a list of coordinating nodes holding a given pid.
resolve-method	Get a list of coordinating nodes holding a given pid.
restoreAuth	Restore authentication (after being disabled with 'obscureAuth').
restoreAuth-method	Restore authentication (after being disabled with 'obscureAuth').
restoreCert	Restore the CILogon client certificate by renaming it to its original location
restoreCert-method	Restore the CILogon client certificate by renaming it to its original location

-- S --

setMNodeId	Set the member node identifier to be associated with the D1Client object.
setMNodeId-method	Set the member node identifier to be associated with the D1Client object.
setObsoletedBy	Set a pid as being obsoleted by another pid
setObsoletedBy-method	Set a pid as being obsoleted by another pid
setPublicAccess-method	Make the object publicly readable.
showAuth	Display all authentication information
showAuth-method	Display all authentication information
showClientSubject	Get DataONE Identity as Stored in the CILogon Certificate.
showClientSubject-method	Get DataONE Identity as Stored in the CILogon Certificate.

-- U --

updateObject	Update an object on a Member Node, by creating a new object that replaces an original.
updateObject-method	Update an object on a Member Node, by creating a new object that replaces an original.
updateSystemMetadata	Update the system metadata associated with an object.
updateSystemMetadata-method	Update the system metadata associated with an object.
uploadDataObject	Upload a DataObject to a DataONE member node.
uploadDataObject-method	Upload a DataObject to a DataONE member node.
uploadDataPackage	Upload a DataPackage to a DataONE member node.
uploadDataPackage-method	Upload a DataPackage to a DataONE member node.