R Interface to the DataONE REST API


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Documentation for package ‘dataone’ version 2.2.1

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A C D E G H I L M O P Q R S U

-- 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.