Package 'zen4R'

Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload and download of files.
Authors: Emmanuel Blondel [aut, cre] , Julien Barde [ctb] , Stephen Eglen [ctb] , Hans Van Calster [ctb] , Floris Vanderhaeghe [ctb] , Jemma Stachelek [ctb]
Maintainer: Emmanuel Blondel <[email protected]>
License: MIT + file LICENSE
Version: 0.10
Built: 2024-11-13 05:15:01 UTC
Source: https://github.com/eblondel/zen4r

Help Index

download_zenodo

Description

download_zenodo allows to download archives attached to a Zenodo record, identified by its DOI or concept DOI.

Usage

download_zenodo(
  doi,
  path = ".",
  files = list(),
  sandbox = FALSE,
  logger = NULL,
  quiet = FALSE,
  ...
)

Arguments

doi

a Zenodo DOI or concept DOI
path

the target directory where to download files
files

subset of filenames to restrain to download. If ignored, all files will be downloaded.
sandbox

Use the sandbox infrastructure. Default is FALSE
logger

a logger to print Zenodo API-related messages. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)
quiet

Logical (FALSE by default). Do you want to suppress informative messages (not warnings)?
...

any other arguments for parallel downloading (more information at ZenodoRecord, downloadFiles() documentation)

Examples

## Not run: 
 #simple download (sequential)   
 download_zenodo("10.5281/zenodo.2547036")
 
 library(parallel)
 #download files as parallel using a cluster approach (for both Unix/Win systems)
 download_zenodo("10.5281/zenodo.2547036", 
   parallel = TRUE, parallel_handler = parLapply, cl = makeCluster(2))
 
 #download files as parallel using mclapply (for Unix systems)
 download_zenodo("10.5281/zenodo.2547036",
   parallel = TRUE, parallel_handler = mclapply, mc.cores = 2)

## End(Not run)

export_zenodo

Description

export_zenodo allows to export a Zenodo record, identified by its DOI or concept DOI, using one of the export formats supported by Zenodo.

Usage

export_zenodo(
  doi,
  filename,
  format,
  append_format = TRUE,
  sandbox = FALSE,
  logger = NULL
)

Arguments

doi

a Zenodo DOI or concept DOI
filename

a base file name (without file extension) to export to.
format

a valid Zenodo export format among the following: BibTeX, CSL, DataCite, DublinCore, DCAT, JSON, JSON-LD, GeoJSON, MARCXML.
append_format

wether format name has to be appended to the filename. Default is TRUE (for backward compatibility reasons). Set it to FALSE if you want to use only the filename.
sandbox

Use the sandbox infrastructure. Default is FALSE
logger

a logger to print Zenodo API-related messages. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Value

the exported file name (with extension)

Examples

## Not run: 
 export_zenodo("10.5281/zenodo.2547036", filename = "test", format = "BibTeX", append_format = F)

## End(Not run)

get_licenses

Description

get_licenses allows to list all licenses supported by Zenodo.

Usage

get_licenses(pretty = TRUE, sandbox = FALSE)

Arguments

pretty

output delivered as data.frame
sandbox

Use the sandbox infrastructure. Default is FALSE

Value

the licenses as list or data.frame

Examples

## Not run: 
 get_licenses(pretty = TRUE)

## End(Not run)

get_versions

Description

get_versions allows to execute a workflow

Usage

get_versions(doi, sandbox = FALSE, logger = NULL)

Arguments

doi

a Zenodo DOI or concept DOI
sandbox

Use the sandbox infrastructure. Default is FALSE
logger

a logger to print messages. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Value

an object of class data.frame giving the record versions including date, version number and version-specific DOI.

Examples

## Not run: 
get_versions("10.5281/zenodo.2547036")

## End(Not run)

get_zenodo

Description

get_zenodo allows to get a Zenodo record, identified by its DOI or concept DOI.

Usage

get_zenodo(doi, sandbox = FALSE, logger = NULL)

Arguments

doi

a Zenodo DOI or concept DOI
sandbox

Use the sandbox infrastructure. Default is FALSE
logger

a logger to print messages. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Value

an object of class data.frame giving the record versions including date, version number and version-specific DOI.

object of class ZenodoRecord

Examples

## Not run: 
 get_zenodo("10.5281/zenodo.2547036")

## End(Not run)

Interface to 'Zenodo' REST API

Description

Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo', upload and download of files.

Author(s)

Emmanuel Blondel [email protected]

See Also

Useful links:

zen4RLogger

Description

zen4RLogger

zen4RLogger

Format

R6Class object.

Value

Object of R6Class for modelling a simple logger

Public fields

verbose.info

logger info status

verbose.debug

logger debug status

loggerType

Logger type, either "INFO", "DEBUG" or NULL (if no logger)

Methods

Public methods

Method logger()

internal logger function for the Zenodo manager

Usage
zen4RLogger$logger(type, text)
Arguments
type

logger message type, "INFO", "WARN", or "ERROR"

text

log message

Method INFO()

internal INFO logger function

Usage
zen4RLogger$INFO(text)
Arguments
text

log message

Method WARN()

internal WARN logger function

Usage
zen4RLogger$WARN(text)
Arguments
text

log message

Method ERROR()

internal ERROR logger function

Usage
zen4RLogger$ERROR(text)
Arguments
text

log message

Method new()

initialize the Zenodo logger

Usage
zen4RLogger$new(logger = NULL)
Arguments
logger

logger type NULL, 'INFO', or 'DEBUG'

Method getClassName()

Get object class name

Usage
zen4RLogger$getClassName()
Returns

the class name, object of class character

Method getClass()

Get object class

Usage
zen4RLogger$getClass()
Returns

the class, object of class R6

Method clone()

The objects of this class are cloneable with this method.

Usage
zen4RLogger$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Logger class used internally by zen4R

zenodo_pat

Description

Get Zenodo personal access token, looking in env var 'ZENODO_PAT'

Usage

zenodo_pat(quiet = TRUE)

Arguments

quiet

Hide log message, default is TRUE

ZenodoManager

Description

ZenodoManager

ZenodoManager

Format

R6Class object.

Value

Object of R6Class for modelling an ZenodoManager

Super class

zen4R::zen4RLogger -> ZenodoManager

Public fields

sandbox

Zenodo manager sandbox status, TRUE if we interact with Sandbox infra

anonymous

Zenodo manager anonymous status, TRUE when no token is specified

Methods

Public methods

Inherited methods

Method new()

initializes the Zenodo Manager

Usage
ZenodoManager$new(
  url = "https://zenodo.org/api",
  token = zenodo_pat(),
  sandbox = FALSE,
  logger = NULL,
  keyring_backend = "env"
)
Arguments
url

Zenodo API URL. By default, the url is set to "https://zenodo.org/api". For tests, the Zenodo sandbox API URL can be used: https://sandbox.zenodo.org/api

token

the user token. By default an attempt will be made to retrieve token using zenodo_pat

sandbox

Indicates if the Zenodo sandbox platform should be used. Default is FALSE

logger

logger type. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

keyring_backend

The keyring backend used to store user token. The keyring_backend can be set to use a different backend for storing the Zenodo token with keyring (Default value is 'env').

Method getToken()

Get user token

Usage
ZenodoManager$getToken()
Returns

the token, object of class character

Method getLanguages()

Get Languages supported by Zenodo.

Usage
ZenodoManager$getLanguages(pretty = TRUE)
Arguments
pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of languages as data.frame. Set pretty = FALSE to get the raw list of languages

Returns

list of languages as data.frame or list

Method getLanguageById()

Get language by Id.

Usage
ZenodoManager$getLanguageById(id)
Arguments
id

license id

Returns

the license

Method getLicenses()

Get Licenses supported by Zenodo.

Usage
ZenodoManager$getLicenses(pretty = TRUE)
Arguments
pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of licenses as data.frame. Set pretty = FALSE to get the raw list of licenses.

Returns

list of licenses as data.frame or list

Method getLicenseById()

Get license by Id.

Usage
ZenodoManager$getLicenseById(id)
Arguments
id

license id

Returns

the license

Method getResourceTypes()

Get Resource types supported by Zenodo.

Usage
ZenodoManager$getResourceTypes(pretty = TRUE)
Arguments
pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of resource types as data.frame. Set pretty = FALSE to get the raw list of resource types

Returns

list of resource types as data.frame or list

Method getResourceTypeById()

Get resource type by Id.

Usage
ZenodoManager$getResourceTypeById(id)
Arguments
id

resource type id

Returns

the resource type

Method getCommunities()

Get Communities supported by Zenodo.

Usage
ZenodoManager$getCommunities(pretty = TRUE, q = "", size = 500)
Arguments
pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of communities as data.frame. Set pretty = FALSE to get the raw list of communities

q

an ElasticSearch compliant query, object of class character. Default is emtpy. Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently, not all communities can be listed from Zenodo, a query has to be specified.

size

number of communities to be returned. By default equal to 500

Returns

list of communities as data.frame or list

Method getCommunityById()

Get community by Id.

Usage
ZenodoManager$getCommunityById(id)
Arguments
id

community id

Returns

the community

Method submitRecordToCommunities()

Submit a published record to one or more community

Usage
ZenodoManager$submitRecordToCommunities(
  record,
  communities = list(),
  message = NULL
)
Arguments
record

an object of class ZenodoRecord

communities

communities to which the record will be submitted

message

message to send to the community curator(s), either a text or a named list for each community in case a community-specific message should be sent

Returns

a submission object of class list, or NULL if nothing was submitted

Method removeRecordFromCommunities()

Remove a record from one or more community

Usage
ZenodoManager$removeRecordFromCommunities(record, communities = list())
Arguments
record

an object of class ZenodoRecord

communities

communities to which the record will be submitted

Returns

TRUE if removed, FALSE otherwise

Method getRecordCommunities()

Get record communities

Usage
ZenodoManager$getRecordCommunities(record)
Arguments
record

object of class ZenodoRecord

Returns

the list of communities in which the record was included

Method createReviewRequest()

Creates a record review request in a community

Usage
ZenodoManager$createReviewRequest(record, community)
Arguments
record

an object of class ZenodoRecord

community

a community to which the record is submitted for review and publication

Returns

a review request object of class list, or NULL if nothing was submitted

Method getReviewRequest()

Get a record review request

Usage
ZenodoManager$getReviewRequest(record)
Arguments
record

an object of class ZenodoRecord

Returns

a review request object of class list, or NULL if nothing exists

Method deleteReviewRequest()

Deletes a review request

Usage
ZenodoManager$deleteReviewRequest(record)
Arguments
record

an object of class ZenodoRecord

Returns

TRUE if deleted, FALSE otherwise

Method submitRecordForReview()

Submits a record for review. Prior to this submission, a community has to be selected for a record. This is done by using the method createReviewRequest(record, community).

Usage
ZenodoManager$submitRecordForReview(recordId, message = NULL)
Arguments
recordId

the ID of a Zenodo record

message

message content for the submission. Optional

Returns

TRUE if submitted, FALSE otherwise

Method getGrants()

Get Grants supported by Zenodo. DEPRECATED: replaced by getAwards

Usage
ZenodoManager$getGrants(q = "", pretty = TRUE, size = 500)
Arguments
q

an ElasticSearch compliant query, object of class character. Default is emtpy. Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently, not all grants can be listed from Zenodo, a query has to be specified.

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of grants as data.frame. Set pretty = FALSE to get the raw list of grants

size

number of grants to be returned. By default equal to 500.

Returns

list of grants as data.frame or list

Method getAwards()

Get Awards supported by Zenodo.

Usage
ZenodoManager$getAwards(q = "", pretty = TRUE, size = 500)
Arguments
q

an ElasticSearch compliant query, object of class character. Default is emtpy. Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently, not all awards can be listed from Zenodo, a query has to be specified.

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of awards as data.frame. Set pretty = FALSE to get the raw list of awards

size

number of awards to be returned. By default equal to 500.

Returns

list of awards as data.frame or list

Method getGrantsByName()

Get grants by name. DEPRECATED: replaced by getAwardByName

Usage
ZenodoManager$getGrantsByName(name, pretty = TRUE)
Arguments
name

name

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of grants as data.frame. Set pretty = FALSE to get the raw list of grants

Returns

list of grants as data.frame or list

Method getAwardsByName()

Get awards by name.

Usage
ZenodoManager$getAwardsByName(name, pretty = TRUE)
Arguments
name

name

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of awards as data.frame. Set pretty = FALSE to get the raw list of awards

Returns

list of awards as data.frame or list

Method getGrantById()

Get grant by Id.DEPRECATED: replaced by getAwardById

Usage
ZenodoManager$getGrantById(id)
Arguments
id

grant id

Returns

the grant

Method getAwardById()

Get award by Id.

Usage
ZenodoManager$getAwardById(id)
Arguments
id

award id

Returns

the award

Method getAffiliations()

Get Affiliations supported by Zenodo.

Usage
ZenodoManager$getAffiliations(q = "", pretty = TRUE, size = 500)
Arguments
q

an ElasticSearch compliant query, object of class character. Default is emtpy. Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently, not all affiliations can be listed from Zenodo, a query has to be specified.

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of affiliations as data.frame. Set pretty = FALSE to get the raw list of affiliations

size

number of affiliations to be returned. By default equal to 500.

Returns

list of affiliations as data.frame or list

Method getAffiliationByName()

Get affiliations by name.

Usage
ZenodoManager$getAffiliationByName(name, pretty = TRUE)
Arguments
name

name

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of affiliations as data.frame. Set pretty = FALSE to get the raw list of affiliations

Returns

list of affiliations as data.frame or list

Method getAffiliationById()

Get affiliation by Id.

Usage
ZenodoManager$getAffiliationById(id)
Arguments
id

affiliation id

Returns

the affiliation

Method getFunders()

Get Funders supported by Zenodo based on a query.

Usage
ZenodoManager$getFunders(q = "", pretty = TRUE, size = 500)
Arguments
q

an ElasticSearch compliant query, object of class character. Default is emtpy. Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently, not all funders can be listed from Zenodo, a query has to be specified.

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of funders as data.frame. Set pretty = FALSE to get the raw list of funders

size

number of funders to be returned. By default equal to 500

Returns

list of funders as data.frame or list

Method getFundersByName()

Get funders by name.

Usage
ZenodoManager$getFundersByName(name, pretty = TRUE)
Arguments
name

name

pretty

Prettify the output. By default the argument pretty is set to TRUE which will returns the list of funders as data.frame. Set pretty = FALSE to get the raw list of funders

Returns

list of funders as data.frame or list

Method getFunderById()

Get funder by Id.

Usage
ZenodoManager$getFunderById(id)
Arguments
id

funder id

Returns

the funder

Method getDepositions()

Get the list of Zenodo records deposited in your Zenodo workspace (user records). By default the list of depositions will be returned by page with a size of 10 results per page (default size of the Zenodo API). The parameter q allows to specify an ElasticSearch-compliant query to filter depositions (default query is empty to retrieve all records). The argument all_versions, if set to TRUE allows to get all versions of records as part of the depositions list. The argument exact specifies that an exact matching is wished, in which case paginated search will be disabled (only the first search page will be returned). Examples of ElasticSearch queries for Zenodo can be found at https://help.zenodo.org/guides/search/.

Usage
ZenodoManager$getDepositions(
  q = "",
  size = 10,
  all_versions = FALSE,
  exact = TRUE,
  quiet = FALSE
)
Arguments
q

Elastic-Search-compliant query, as object of class character. Default is ""

size

number of depositions to be retrieved per request (paginated). Default is 10

all_versions

object of class logical indicating if all versions of deposits have to be retrieved. Default is FALSE

exact

object of class logical indicating if exact matching has to be applied. Default is TRUE

quiet

object of class logical indicating if logs have to skipped. Default is FALSE

Returns

a list of ZenodoRecord

Method getDepositionByConceptDOI()

Get a Zenodo deposition record by concept DOI (generic DOI common to all deposition record versions).

Usage
ZenodoManager$getDepositionByConceptDOI(conceptdoi)
Arguments
conceptdoi

the concept DOI, object of class character

Returns

an object of class ZenodoRecord if record does exist, NULL otherwise

Method getDepositionByDOI()

Get a Zenodo deposition record by DOI.

Usage
ZenodoManager$getDepositionByDOI(doi)
Arguments
doi

the DOI, object of class character

Returns

an object of class ZenodoRecord if record does exist, NULL otherwise

Method getDepositionById()

Get a Zenodo deposition record by ID.

Usage
ZenodoManager$getDepositionById(recid)
Arguments
recid

the record ID, object of class character

Returns

an object of class ZenodoRecord if record does exist, NULL otherwise

Method getDepositionByConceptId()

Get a Zenodo deposition record by concept ID.

Usage
ZenodoManager$getDepositionByConceptId(conceptrecid)
Arguments
conceptrecid

the record concept ID, object of class character

Returns

an object of class ZenodoRecord if record does exist, NULL otherwise

Method depositRecord()

Deposits a record on Zenodo.

Usage
ZenodoManager$depositRecord(record, reserveDOI = TRUE, publish = FALSE)
Arguments
record

the record to deposit, object of class ZenodoRecord

reserveDOI

reserve DOI. By default TRUE

publish

object of class logical indicating if record has to be published (default FALSE). Can be set to TRUE (to use CAUTIOUSLY, only if you want to publish your record)

Returns

object of class ZenodoRecord

Method reserveDOI()

Reserves a DOI for a deposition (draft record)

Usage
ZenodoManager$reserveDOI(record)
Arguments
record

the record to deposit, object of class ZenodoRecord

Returns

object of class ZenodoRecord

Method deleteDOI()

Reserves a DOI for a deposition (draft record)

Usage
ZenodoManager$deleteDOI(record)
Arguments
record

the record for which DOI has to be deleted, object of class ZenodoRecord

Returns

object of class ZenodoRecord

Method depositRecordVersion()

Deposits a record version on Zenodo.

Usage
ZenodoManager$depositRecordVersion(
  record,
  delete_latest_files = TRUE,
  files = list(),
  publish = FALSE
)
Arguments
record

the record version to deposit, object of class ZenodoRecord

delete_latest_files

object of class logical indicating if latest files have to be deleted. Default is TRUE

files

a list of files to be uploaded with the new record version

publish

object of class logical indicating if record has to be published (default FALSE)

Returns

TRUE if deposited (and eventually published), FALSE otherwise

Method deleteRecord()

Deletes a record given its ID

Usage
ZenodoManager$deleteRecord(recordId)
Arguments
recordId

the ID of the record to be deleted

Returns

TRUE if deleted, FALSE otherwise

Method deleteRecordByDOI()

Deletes a record by DOI

Usage
ZenodoManager$deleteRecordByDOI(doi)
Arguments
doi

the DOI of the record to be deleted

Returns

TRUE if deleted, FALSE otherwise

Method deleteRecords()

Deletes all Zenodo deposited (unpublished) records. The parameter q allows to specify an ElasticSearch-compliant query to filter depositions (default query is empty to retrieve all records). Examples of ElasticSearch queries for Zenodo can be found at https://help.zenodo.org/guides/search/.

Usage
ZenodoManager$deleteRecords(q = "", size = 10)
Arguments
q

an ElasticSearch compliant query, object of class character

size

number of records to be passed to $getDepositions method

Returns

TRUE if all records have been deleted, FALSE otherwise

Method createEmptyRecord()

Creates an empty record in the Zenodo deposit. Returns the record newly created in Zenodo, as an object of class ZenodoRecord with an assigned identifier.

Usage
ZenodoManager$createEmptyRecord(reserveDOI = TRUE)
Arguments
reserveDOI

reserve DOI. By default TRUE

Returns

an object of class ZenodoRecord

Method editRecord()

Unlocks a record already submitted. Required to edit metadata of a Zenodo record already published.

Usage
ZenodoManager$editRecord(recordId)
Arguments
recordId

the ID of the record to unlock and set in editing mode.

Returns

an object of class ZenodoRecord

Method discardChanges()

Discards changes on a Zenodo record. Deleting a draft for an unpublished record will remove the draft and associated files from the system. Deleting a draft for a published record will remove the draft but not the published record.

Usage
ZenodoManager$discardChanges(recordId)
Arguments
recordId

the ID of the record for which changes have to be discarded.

Returns

an object of class ZenodoRecord

Method publishRecord()

Publishes a Zenodo record.

Usage
ZenodoManager$publishRecord(recordId)
Arguments
recordId

the ID of the record to be published.

Returns

an object of class ZenodoRecord

Method getFiles()

Get list of files attached to a Zenodo record.

Usage
ZenodoManager$getFiles(recordId)
Arguments
recordId

the ID of the record.

Returns

list of files

Method getFile()

Get a file record metadata.

Usage
ZenodoManager$getFile(recordId, filename)
Arguments
recordId

the ID of the record.

filename

filename

Returns

the file metadata

Method startFileUpload()

Start a file upload. The method will create a key for the file to be uploaded This method is essentially for internal purpose, and is called directly in uploadFile for user convenience and for backward compatibility with the legacy Zenodo API.

Usage
ZenodoManager$startFileUpload(path, recordId)
Arguments
path

Local path of the file

recordId

ID of the record

Method completeFileUpload()

Completes a file upload. The method will complete a file upload through a commit operation This method is essentially for internal purpose, and is called directly in uploadFile for user convenience and for backward compatibility with the legacy Zenodo API.

Usage
ZenodoManager$completeFileUpload(path, recordId)
Arguments
path

Local path of the file

recordId

ID of the record

Method uploadFile()

Uploads a file to a Zenodo record. With the new Zenodo Invenio RDM API, this method internally calls startFileUpload to create a file record (with a filename key) at start, followed by the actual file content upload. At this stage, the file upload is in "pending" status. At the end, the function calls completeFileUpload to commit the file which status becomes "completed".

Usage
ZenodoManager$uploadFile(path, record = NULL)
Arguments
path

Local path of the file

record

object of class ZenodoRecord

Method deleteFile()

Deletes a file for a record. With the new Zenodo Invenio RDM API, if a file is deleted although its status was pending, only the upload content is deleted, and the file upload record (identified by a filename key) is kept. If the status was completed (with a file commit), the file record is deleted.

Usage
ZenodoManager$deleteFile(recordId, filename)
Arguments
recordId

ID of the record

filename

name of the file to be deleted

Method getRecords()

Get the list of Zenodo records. By defaut the list of records will be returned by page with a size of 10 results per page (default size of the Zenodo API). The parameter q allows to specify an ElasticSearch-compliant query to filter depositions (default query is empty to retrieve all records). The argument all_versions, if set to TRUE allows to get all versions of records as part of the depositions list. The argument exact specifies that an exact matching is wished, in which case paginated search will be disabled (only the first search page will be returned). Examples of ElasticSearch queries for Zenodo can be found at https://help.zenodo.org/guides/search/.

Usage
ZenodoManager$getRecords(q = "", size = 10, all_versions = FALSE, exact = TRUE)
Arguments
q

Elastic-Search-compliant query, as object of class character. Default is ""

size

number of records to be retrieved per request (paginated). Default is 10

all_versions

object of class logical indicating if all versions of records have to be retrieved. Default is FALSE

exact

object of class logical indicating if exact matching has to be applied. Default is TRUE

quiet

object of class logical indicating if logs have to skipped. Default is FALSE

Returns

a list of ZenodoRecord

Method getRecordByConceptDOI()

Get Record by concept DOI

Usage
ZenodoManager$getRecordByConceptDOI(conceptdoi)
Arguments
conceptdoi

the concept DOI

Returns

a object of class ZenodoRecord

Method getRecordByDOI()

Get Record by DOI

Usage
ZenodoManager$getRecordByDOI(doi)
Arguments
doi

the DOI

Returns

a object of class ZenodoRecord

Method getRecordById()

Get Record by ID

Usage
ZenodoManager$getRecordById(recid)
Arguments
recid

the record ID

Returns

a object of class ZenodoRecord

Method getRecordByConceptId()

Get Record by concept ID

Usage
ZenodoManager$getRecordByConceptId(conceptrecid)
Arguments
conceptrecid

the concept ID

Returns

a object of class ZenodoRecord

Method getRequests()

Search requests

Usage
ZenodoManager$getRequests(q = "", sort = "bestmatch", size = 10)
Arguments
q

Search query used to filter results based on ElasticSearch's query string syntax. e.g. https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-query-string-query.html#query-string-syntax

sort

Sort search results. Built-in options are "bestmatch", "name", "newest", "oldest" (default: "bestmatch" or "newest").

size

number of records to be retrieved per request (paginated). Default is 10

Returns

a list of ZenodoRecord

Method getRequest()

Get a request

Usage
ZenodoManager$getRequest(request_id)
Arguments
request_id

the request ID

Returns

the request list object, NULL otherwise

Method isActionableRequest()

Checks if the request can be subject to an operation (accept, decline, cancel) depending on its status. To be subject to an operation, a request should not be closed or expired

Usage
ZenodoManager$isActionableRequest(request_id)
Arguments
request_id

the request ID

Returns

TRUE if

Method acceptRequest()

Accepts a request

Usage
ZenodoManager$acceptRequest(request_id, message = NULL)
Arguments
request_id

the request ID

message

optional message reason for acceptance

Returns

TRUE if accepted, FALSE otherwise

Method declineRequest()

Declines a request

Usage
ZenodoManager$declineRequest(request_id, message = NULL)
Arguments
request_id

the request ID

message

optional message reason for declination

Returns

TRUE if declined, FALSE otherwise

Method cancelRequest()

Cancels a request

Usage
ZenodoManager$cancelRequest(request_id, message = NULL)
Arguments
request_id

the request ID

message

optional message reason for cancelation

Returns

TRUE if canceled, FALSE otherwise

Method clone()

The objects of this class are cloneable with this method.

Usage
ZenodoManager$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Main user class to be used with zen4R

Author(s)

Emmanuel Blondel <[email protected]>

Examples

## Not run: 
  ZENODO <- ZenodoManager$new(
     url = "https://sandbox.zenodo.org/api",
     token = "<your_token>",
     logger = "INFO"
  )
  
  #create (deposit) an empty record
  newRec <- ZENODO$createEmptyRecord()
  
  #create and fill a local (not yet deposited) record
  myrec <- ZenodoRecord$new()
  myrec$setTitle("my R package")
  myrec$setDescription("A description of my R package")
  myrec$setUploadType("software")
  myrec$addCreator(
    firstname = "John", lastname = "Doe",
    affiliation = "Independent", orcid = "0000-0000-0000-0000"
   )
  myrec$setLicense("mit")
  myrec$setAccessRight("open")
  myrec$setDOI("mydoi") #use this method if your DOI has been assigned elsewhere, outside Zenodo
  
  #deposit the record 
  myrec <- ZENODO$depositRecord(myrec)
  
  #publish a record (with caution!!)
  #this method will PUBLISH the deposition done earlier
  ZENODO$publishRecord(myrec$id)
  #With even more caution the publication can be done with a shortcut argument at deposit time
  ZENODO$depositRecord(myrec, publish = TRUE)
  
  #delete a record (by id)
  #this methods only works for unpublished deposits 
  #(if a record is published, it cannot be deleted anymore!)
  ZENODO$deleteRecord(myrec$id)
  
  #HOW TO UPLOAD FILES to a deposit
  
  #upload a file
  ZENODO$uploadFile("path/to/your/file", record = myrec)
  
  #list files
  zen_files <- ZENODO$getFiles(myrec$id)
  
  #delete a file?
  ZENODO$deleteFile(myrec$id, zen_files[[1]]$filename)

## End(Not run)

ZenodoRecord

Description

ZenodoRecord

ZenodoRecord

Format

R6Class object.

Value

Object of R6Class for modelling an ZenodoRecord

Super class

zen4R::zen4RLogger -> ZenodoRecord

Public fields

created

record creation date

updated

record update date

revision_id

revision id

is_draft

is draft

is_published

is published

status

record status

versions

versions

access

access policies

files

list of files associated to the record

id

record id

links

list of links associated to the record

metadata

metadata elements associated to the record

parent

parent record

pids

pids

stats

stats

Methods

Public methods

Inherited methods

Method new()

method is used to instantiate a ZenodoRecord

Usage
ZenodoRecord$new(obj = NULL, logger = "INFO")
Arguments
obj

an optional list object to create the record

logger

a logger to print log messages. It can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Method getStats()

Get record statistics

Usage
ZenodoRecord$getStats()
Returns

statistics as data.frame

Method getId()

Get the record Id

Usage
ZenodoRecord$getId()
Returns

the Id, object of class character

Method getParentId()

Get the parent record Id

Usage
ZenodoRecord$getParentId()
Returns

the parent Id, object of class character

Method getConceptId()

Get the concept record Id

Usage
ZenodoRecord$getConceptId()
Returns

the concept Id, object of class character

Method setDOI()

Set the DOI. This method can be used if a DOI has been already assigned outside Zenodo.

Usage
ZenodoRecord$setDOI(doi, provider = NULL, client = NULL)
Arguments
doi

DOI to set for the record

provider

DOI provider

client

DOI client

Method getDOI()

Get the record DOI.

Usage
ZenodoRecord$getDOI()
Returns

the DOI, object of class character

Method getConceptDOI()

Get the concept (generic) DOI. The concept DOI is a generic DOI common to all versions of a Zenodo record.

Usage
ZenodoRecord$getConceptDOI()
Returns

the concept DOI, object of class character

Method setAccessPolicyRecord()

Set the access policy for record, among values "public" (default) or "restricted" In Zenodo, in principle, the access policy 'restricted' is not available for records.

Usage
ZenodoRecord$setAccessPolicyRecord(access = c("public", "restricted"))
Arguments
access

access policy ('public' or 'restricted')

Method setAccessPolicyFiles()

Set the access policy for files, among values "public" (default) or "restricted"

Usage
ZenodoRecord$setAccessPolicyFiles(access = c("public", "restricted"))
Arguments
access

access policy ('public' or 'restricted')

Method setAccessPolicyEmbargo()

Set access policy embargo options

Usage
ZenodoRecord$setAccessPolicyEmbargo(active = FALSE, until = NULL, reason = "")
Arguments
active

whether embargo is active or not. Default is FALSE

until

embargo date, object of class Date. Default is NULL. Must be provided if embargo is active

reason

embargo reason, object of class character. Default is an empty string

Method setResourceType()

Set the resource type (mandatory).

Usage
ZenodoRecord$setResourceType(resourceType)
Arguments
resourceType

record resource type

Method setUploadType()

Set the upload type (mandatory). Deprecated since zen4R 1.0

Usage
ZenodoRecord$setUploadType(uploadType)
Arguments
uploadType

record upload type among the following values: 'publication', 'poster', 'presentation', 'dataset', 'image', 'video', 'software', 'lesson', 'physicalobject', 'other'

Method setPublicationType()

Set the publication type (mandatory if upload type is 'publication'). Deprecated since zen4R 1.0

Usage
ZenodoRecord$setPublicationType(publicationType)
Arguments
publicationType

record publication type among the following values: 'annotationcollection', 'book', 'section', 'conferencepaper', 'datamanagementplan', 'article', 'patent', 'preprint', 'deliverable', 'milestone', 'proposal', 'report', 'softwaredocumentation', 'taxonomictreatment', 'technicalnote', 'thesis', 'workingpaper', 'other'

Method setImageType()

Set the image type (mandatory if image type is 'image'). Deprecated since zen4R 1.0

Usage
ZenodoRecord$setImageType(imageType)
Arguments
imageType

record publication type among the following values: 'figure','plot', 'drawing','diagram','photo', or 'other'

Method setPublisher()

Set the publisher

Usage
ZenodoRecord$setPublisher(publisher)
Arguments
publisher

publisher object of class character

Method setPublicationDate()

Set the publication date. For more information on the accepted format, please check https://inveniordm.docs.cern.ch/reference/metadata/#publication-date-1

Usage
ZenodoRecord$setPublicationDate(publicationDate)
Arguments
publicationDate

object of class character

Method addDate()

Add date

Usage
ZenodoRecord$addDate(date, type, description = NULL)
Arguments
date

date

type

type of date, among following values: 'accepted', 'available', 'collected', 'copyrighted', 'created', 'issued', 'other', 'submitted', 'updated', 'valid', 'withdrawn'

description

free text, specific information about the date

Method removeDate()

Remove a date

Usage
ZenodoRecord$removeDate(date, type)
Arguments
date

the date to remove

type

the date type of the date to be removed

Returns

TRUE if removed, FALSE otherwise

Method setTitle()

Set the record title.

Usage
ZenodoRecord$setTitle(title)
Arguments
title

object of class character

Method addAdditionalTitle()

Add additional record title

Usage
ZenodoRecord$addAdditionalTitle(title, type, lang = "eng")
Arguments
title

title free text

type

type of title, among following values: alternative-title, subtitle, translated-title, other

lang

language id

Returns

TRUE if added, FALSE otherwise

Method removeAdditionalTitle()

Removes additional record title.

Usage
ZenodoRecord$removeAdditionalTitle(title, type, lang = "eng")
Arguments
title

title free text

type

type of title, among following values: abstract, methods, series-information, table-of-contents, technical-info, other

lang

language id

Returns

TRUE if removed, FALSE otherwise

Method setDescription()

Set the record description

Usage
ZenodoRecord$setDescription(description)
Arguments
description

object of class character

Method addAdditionalDescription()

Add additional record description

Usage
ZenodoRecord$addAdditionalDescription(description, type, lang = "eng")
Arguments
description

description free text

type

type of description, among following values: abstract, methods, series-information, table-of-contents, technical-info, other

lang

language id

Returns

TRUE if added, FALSE otherwise

Method removeAdditionalDescription()

Removes additional record description

Usage
ZenodoRecord$removeAdditionalDescription(description, type, lang = "eng")
Arguments
description

description free text

type

type of description, among following values: abstract, methods, series-information, table-of-contents, technical-info, other

lang

language id

Returns

TRUE if removed, FALSE otherwise

Method addPersonOrOrg()

Add a person or organization for the record. For persons, the approach is to use the firstname and lastname arguments, that by default will be concatenated for Zenodo as lastname, firstname. For organizations, use the name argument.

Usage
ZenodoRecord$addPersonOrOrg(
  firstname = NULL,
  lastname = NULL,
  name = paste(lastname, firstname, sep = ", "),
  orcid = NULL,
  gnd = NULL,
  isni = NULL,
  ror = NULL,
  role = NULL,
  affiliations = NULL,
  sandbox = FALSE,
  type
)
Arguments
firstname

person first name

lastname

person last name

name

organization name

orcid

person or organization ORCID (optional)

gnd

person or organization GND (optional)

isni

person or organization ISNI (optional)

ror

person or organization ROR (optional)

role

role, values among: contactperson, datacollector, datacurator, datamanager, distributor, editor, funder, hostinginstitution, producer, projectleader, projectmanager, projectmember, registrationagency, registrationauthority, relatedperson, researcher, researchgroup, rightsholder, supervisor, sponsor, workpackageleader, other

affiliations

person or organization affiliations (optional)

sandbox

Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is FALSE

type

type of person or org (creators/contributors)

Returns

TRUE if added, FALSE otherwise

Method removePersonOrOrg()

Removes a person or organization by a property. The by parameter should be the name of the person or organization property ('name', 'affiliation','orcid','gnd','isni','ror').

Usage
ZenodoRecord$removePersonOrOrg(by, property, type)
Arguments
by

property used as criterion to remove the person or organization

property

property value used to remove the person or organization

type

type of person or org (creators / contributors)

Returns

TRUE if removed, FALSE otherwise

Method addCreator()

Add a creator for the record. For persons, the approach is to use the firstname and lastname arguments, that by default will be concatenated for Zenodo as lastname, firstname. For organizations, use the name argument.

Usage
ZenodoRecord$addCreator(
  firstname = NULL,
  lastname = NULL,
  name = paste(lastname, firstname, sep = ", "),
  orcid = NULL,
  gnd = NULL,
  isni = NULL,
  ror = NULL,
  role = NULL,
  affiliations = NULL,
  sandbox = FALSE
)
Arguments
firstname

person first name

lastname

person last name

name

organization name

orcid

creator ORCID (optional)

gnd

creator GND (optional)

isni

creator ISNI (optional)

ror

creator ROR (optional)

role

role, values among: contactperson, datacollector, datacurator, datamanager, distributor, editor, funder, hostinginstitution, producer, projectleader, projectmanager, projectmember, registrationagency, registrationauthority, relatedperson, researcher, researchgroup, rightsholder, supervisor, sponsor, workpackageleader, other

affiliations

creator affiliations (optional)

sandbox

Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is FALSE

Returns

TRUE if added, FALSE otherwise

Method removeCreatorByName()

Removes a creator by name.

Usage
ZenodoRecord$removeCreatorByName(name)
Arguments
name

creator name

Returns

TRUE if removed, FALSE otherwise

Method removeCreatorByAffiliation()

Removes a creator by affiliation.

Usage
ZenodoRecord$removeCreatorByAffiliation(affiliation)
Arguments
affiliation

creator affiliation

Returns

TRUE if removed, FALSE otherwise

Method removeCreatorByORCID()

Removes a creator by ORCID.

Usage
ZenodoRecord$removeCreatorByORCID(orcid)
Arguments
orcid

creator ORCID

Returns

TRUE if removed, FALSE otherwise

Method removeCreatorByGND()

Removes a creator by GND.

Usage
ZenodoRecord$removeCreatorByGND(gnd)
Arguments
gnd

creator GND

Returns

TRUE if removed, FALSE otherwise

Method removeCreatorByISNI()

Removes a creator by ISNI.

Usage
ZenodoRecord$removeCreatorByISNI(isni)
Arguments
isni

creator ISNI

Returns

TRUE if removed, FALSE otherwise

Method removeCreatorByROR()

Removes a creator by ROR.

Usage
ZenodoRecord$removeCreatorByROR(ror)
Arguments
ror

creator ROR

Returns

TRUE if removed, FALSE otherwise

Method addContributor()

Add a contributor for the record. For persons, the approach is to use the firstname and lastname arguments, that by default will be concatenated for Zenodo as lastname, firstname. For organizations, use the name argument.

Usage
ZenodoRecord$addContributor(
  firstname = NULL,
  lastname = NULL,
  name = paste(lastname, firstname, sep = ", "),
  orcid = NULL,
  gnd = NULL,
  isni = NULL,
  ror = NULL,
  role = NULL,
  affiliations = NULL,
  sandbox = FALSE
)
Arguments
firstname

person first name

lastname

person last name

name

organization name

orcid

contributor ORCID (optional)

gnd

contributor GND (optional)

isni

contributor ISNI (optional)

ror

contributor ROR (optional)

role

role, values among: contactperson, datacollector, datacurator, datamanager, distributor, editor, funder, hostinginstitution, producer, projectleader, projectmanager, projectmember, registrationagency, registrationauthority, relatedperson, researcher, researchgroup, rightsholder, supervisor, sponsor, workpackageleader, other

affiliations

contributor affiliations (optional)

sandbox

Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is FALSE

Returns

TRUE if added, FALSE otherwise

Method removeContributorByName()

Removes a contributor by name.

Usage
ZenodoRecord$removeContributorByName(name)
Arguments
name

contributor name

Returns

TRUE if removed, FALSE otherwise

Method removeContributorByAffiliation()

Removes a contributor by affiliation.

Usage
ZenodoRecord$removeContributorByAffiliation(affiliation)
Arguments
affiliation

contributor affiliation

Returns

TRUE if removed, FALSE otherwise

Method removeContributorByORCID()

Removes a contributor by ORCID.

Usage
ZenodoRecord$removeContributorByORCID(orcid)
Arguments
orcid

contributor ORCID

Returns

TRUE if removed, FALSE otherwise

Method removeContributorByGND()

Removes a contributor by GND.

Usage
ZenodoRecord$removeContributorByGND(gnd)
Arguments
gnd

contributor GND

Returns

TRUE if removed, FALSE otherwise

Method removeContributorByISNI()

Removes a contributor by ISNI.

Usage
ZenodoRecord$removeContributorByISNI(isni)
Arguments
isni

contributor ISNI

Returns

TRUE if removed, FALSE otherwise

Method removeContributorByROR()

Removes a contributor by ROR.

Usage
ZenodoRecord$removeContributorByROR(ror)
Arguments
ror

contributor ROR

Returns

TRUE if removed, FALSE otherwise

Method addRight()

Add right/license. Please see https://inveniordm.docs.cern.ch/reference/metadata/#rights-licenses-0-n

Usage
ZenodoRecord$addRight(
  id = NULL,
  title = NULL,
  description = NULL,
  link = NULL,
  sandbox = FALSE
)
Arguments
id

license id

title

license title

description

a multi-lingual list

link

license link

sandbox

Use the Zenodo sandbox infrastructure as basis to control available licenses. Default is FALSE

Method setLicense()

Set license. The license should be set with the Zenodo id of the license. If not recognized by Zenodo, the function will return an error. The list of licenses can fetched with the ZenodoManager and the function $getLicenses().

Usage
ZenodoRecord$setLicense(licenseId, sandbox = FALSE)
Arguments
licenseId

a license Id

sandbox

Use the Zenodo sandbox infrastructure as basis to control available licenses. Default is FALSE

Returns

TRUE if set, FALSE otherwise

Method setVersion()

Set record version.

Usage
ZenodoRecord$setVersion(version)
Arguments
version

the record version to set

Method addLanguage()

Adds a language.

Usage
ZenodoRecord$addLanguage(language)
Arguments
language

ISO 639-2 or 639-3 code

Method setLanguage()

Set the language

Usage
ZenodoRecord$setLanguage(language)
Arguments
language

ISO 639-2 or 639-3 code

Method addRelatedIdentifier()

Adds a related identifier with a given scheme and relation type.

Usage
ZenodoRecord$addRelatedIdentifier(
  identifier,
  scheme,
  relation_type,
  resource_type = NULL
)
Arguments
identifier

identifier

scheme

scheme among following values: ark, arxiv, bibcode, doi, ean13, eissn, handle, igsn, isbn, issn, istc, lissn, lsid, pubmed id, purl, upc, url, urn, w3id

relation_type

relation type among following values: iscitedby, cites, issupplementto, issupplementedby, iscontinuedby, continues, isdescribedby, describes, hasmetadata, ismetadatafor, isnewversionof, ispreviousversionof, ispartof, haspart, isreferencedby, references, isdocumentedby, documents, iscompiledby, compiles, isvariantformof, isoriginalformof, isidenticalto, isalternateidentifier, isreviewedby, reviews, isderivedfrom, issourceof, requires, isrequiredby, isobsoletedby, obsoletes

resource_type

optional resource type

Returns

TRUE if added, FALSE otherwise

Method removeRelatedIdentifier()

Removes a related identifier with a given scheme/relation_type

Usage
ZenodoRecord$removeRelatedIdentifier(identifier, scheme, relation_type)
Arguments
identifier

identifier

scheme

scheme among following values: ark, arxiv, bibcode, doi, ean13, eissn, handle, igsn, isbn, issn, istc, lissn, lsid, pubmed id, purl, upc, url, urn, w3id

relation_type

relation type among following values: iscitedby, cites, issupplementto, issupplementedby, iscontinuedby, continues, isdescribedby, describes, hasmetadata, ismetadatafor, isnewversionof, ispreviousversionof, ispartof, haspart, isreferencedby, references, isdocumentedby, documents, iscompiledby, compiles, isvariantformof, isoriginalformof, isidenticalto, isalternateidentifier, isreviewedby, reviews, isderivedfrom, issourceof, requires, isrequiredby, isobsoletedby, obsoletes

Returns

TRUE if removed, FALSE otherwise

Method setReferences()

Set references

Usage
ZenodoRecord$setReferences(references)
Arguments
references

a vector or list of references to set for the record

Method addReference()

Add a reference

Usage
ZenodoRecord$addReference(reference)
Arguments
reference

the reference to add

Returns

TRUE if added, FALSE otherwise

Method removeReference()

Remove a reference

Usage
ZenodoRecord$removeReference(reference)
Arguments
reference

the reference to remove

Returns

TRUE if removed, FALSE otherwise

Method setSubjects()

Set subjects

Usage
ZenodoRecord$setSubjects(subjects)
Arguments
subjects

a vector or list of subjects to set for the record

Method setKeywords()

Set keywords

Usage
ZenodoRecord$setKeywords(keywords)
Arguments
keywords

a vector or list of keywords to set for the record

Method addSubject()

Add a subject

Usage
ZenodoRecord$addSubject(subject)
Arguments
subject

the subject to add

Returns

TRUE if added, FALSE otherwise

Method addKeyword()

Add a keyword

Usage
ZenodoRecord$addKeyword(keyword)
Arguments
keyword

the keyword to add

Returns

TRUE if added, FALSE otherwise

Method removeSubject()

Remove a subject

Usage
ZenodoRecord$removeSubject(subject)
Arguments
subject

the subject to remove

Returns

TRUE if removed, FALSE otherwise

Method removeKeyword()

Remove a keyword

Usage
ZenodoRecord$removeKeyword(keyword)
Arguments
keyword

the keyword to remove

Returns

TRUE if removed, FALSE otherwise

Method setNotes()

Set notes. HTML is not allowed

Usage
ZenodoRecord$setNotes(notes)
Arguments
notes

object of class character

Method addFunding()

Adds funding. Used internally, prefer using addGrant instead.

Usage
ZenodoRecord$addFunding(funder = NULL, grant = NULL, sandbox = FALSE)
Arguments
funder

funder id or name

grant

grant id or title

sandbox

Use the Zenodo sandbox infrastructure as basis to control available grants. Default is FALSE

Method addGrant()

Adds a grant to the record metadata.

Usage
ZenodoRecord$addGrant(grant, sandbox = FALSE)
Arguments
grant

grant to add. The grant should be set with the id of the grant. If not recognized by Zenodo, the function will return an warning only. The list of grants can fetched with the ZenodoManager and the function $getAwards().

sandbox

Use the Zenodo sandbox infrastructure as basis to control available grants. Default is FALSE

Returns

TRUE if added, FALSE otherwise

Method setGrants()

Set a vector of character strings identifying grants

Usage
ZenodoRecord$setGrants(grants, sandbox = FALSE)
Arguments
grants

a vector or list of grants Values should among known grants The list of grants can fetched with the ZenodoManager and the function $getAwards(). Each grant should be set with the Zenodo id of the grant If not recognized by Zenodo, the function will raise a warning only.

sandbox

Use the Zenodo sandbox infrastructure as basis to control available grants. Default is FALSE

Method removeGrant()

Removes a grant from the record metadata.

Usage
ZenodoRecord$removeGrant(grant)
Arguments
grant

grant to remove. The grant should be set with the Zenodo id of the grant

Returns

TRUE if removed, FALSE otherwise

Method setJournalTitle()

Set Journal title to the record metadata

Usage
ZenodoRecord$setJournalTitle(title)
Arguments
title

a title, object of class character

Method setJournalVolume()

Set Journal volume to the record metadata

Usage
ZenodoRecord$setJournalVolume(volume)
Arguments
volume

a volume

Method setJournalIssue()

Set Journal issue to the record metadata

Usage
ZenodoRecord$setJournalIssue(issue)
Arguments
issue

an issue

Method setJournalPages()

Set Journal pages to the record metadata

Usage
ZenodoRecord$setJournalPages(pages)
Arguments
pages

number of pages

Method setConferenceTitle()

Set conference title to the record metadata

Usage
ZenodoRecord$setConferenceTitle(title)
Arguments
title

conference title, object of class character

Method setConferenceAcronym()

Set conference acronym to the record metadata

Usage
ZenodoRecord$setConferenceAcronym(acronym)
Arguments
acronym

conference acronym, object of class character

Method setConferenceDates()

Set conference dates to the record metadata

Usage
ZenodoRecord$setConferenceDates(dates)
Arguments
dates

conference dates, object of class character

Method setConferencePlace()

Set conference place to the record metadata

Usage
ZenodoRecord$setConferencePlace(place)
Arguments
place

conference place, object of class character

Method setConferenceUrl()

Set conference url to the record metadata

Usage
ZenodoRecord$setConferenceUrl(url)
Arguments
url

conference url, object of class character

Method setConferenceSession()

Set conference session to the record metadata

Usage
ZenodoRecord$setConferenceSession(session)
Arguments
session

conference session, object of class character

Method setConferenceSessionPart()

Set conference session part to the record metadata

Usage
ZenodoRecord$setConferenceSessionPart(part)
Arguments
part

conference session part, object of class character

Method setImprintPublisher()

Set imprint publisher to the record metadata

Usage
ZenodoRecord$setImprintPublisher(publisher)
Arguments
publisher

the publisher, object of class character

Method setImprintISBN()

Set imprint ISBN to the record metadata

Usage
ZenodoRecord$setImprintISBN(isbn)
Arguments
isbn

the ISBN, object of class character

Method setImprintPlace()

Set imprint place to the record metadata

Usage
ZenodoRecord$setImprintPlace(place)
Arguments
place

the place, object of class character

Method setPartofTitle()

Set title to which record is part of

Usage
ZenodoRecord$setPartofTitle(title)
Arguments
title

the title, object of class character

Method setPartofPages()

Set pages to which record is part of

Usage
ZenodoRecord$setPartofPages(pages)
Arguments
pages

the pages, object of class character

Method setThesisUniversity()

Set thesis university

Usage
ZenodoRecord$setThesisUniversity(university)
Arguments
university

the university, object of class character

Method addThesisSupervisor()

Adds thesis supervisor

Usage
ZenodoRecord$addThesisSupervisor(
  firstname,
  lastname,
  affiliation = NULL,
  orcid = NULL,
  gnd = NULL
)
Arguments
firstname

supervisor first name

lastname

supervisor last name

affiliation

supervisor affiliation (optional)

orcid

supervisor ORCID (optional)

gnd

supervisor GND (optional)

Method removeThesisSupervisor()

Removes a thesis supervisor by a property. The by parameter should be the name of the thesis supervisor property ('name' - in the form 'lastname, firstname', 'affiliation', 'orcid' or 'gnd').

Usage
ZenodoRecord$removeThesisSupervisor(by, property)
Arguments
by

property used as criterion to remove the thesis supervisor

property

property value used to remove the thesis supervisor

Returns

TRUE if removed, FALSE otherwise

Method removeThesisSupervisorByName()

Removes a thesis supervisor by name.

Usage
ZenodoRecord$removeThesisSupervisorByName(name)
Arguments
name

thesis supervisor name

Returns

TRUE if removed, FALSE otherwise

Method removeThesisSupervisorByAffiliation()

Removes a thesis supervisor by affiliation

Usage
ZenodoRecord$removeThesisSupervisorByAffiliation(affiliation)
Arguments
affiliation

thesis supervisor affiliation

Returns

TRUE if removed, FALSE otherwise

Method removeThesisSupervisorByORCID()

Removes a thesis supervisor by ORCID

Usage
ZenodoRecord$removeThesisSupervisorByORCID(orcid)
Arguments
orcid

thesis supervisor ORCID

Returns

TRUE if removed, FALSE otherwise

Method removeThesisSupervisorByGND()

Removes a thesis supervisor by GND

Usage
ZenodoRecord$removeThesisSupervisorByGND(gnd)
Arguments
gnd

thesis supervisor GND

Returns

TRUE if removed, FALSE otherwise

Method addLocation()

Adds a location to the record metadata.

Usage
ZenodoRecord$addLocation(place, description = NULL, lat = NULL, lon = NULL)
Arguments
place

place (required)

description

description

lat

latitude

lon

longitude

Method removeLocation()

Removes a grant from the record metadata.

Usage
ZenodoRecord$removeLocation(place)
Arguments
place

place (required)

Returns

TRUE if removed, FALSE otherwise

Method exportAs()

Exports record to a file by format.

Usage
ZenodoRecord$exportAs(format, filename, append_format = TRUE)
Arguments
format

the export format to use. Possibles values are: BibTeX, CSL, DataCite, DublinCore, DCAT, JSON, JSON-LD, GeoJSON, MARCXML

filename

the target filename (without extension)

append_format

wether format name has to be appended to the filename. Default is TRUE (for backward compatibility reasons). Set it to FALSE if you want to use only the filename.

Returns

the writen file name (with extension)

Method exportAsBibTeX()

Exports record as BibTeX

Usage
ZenodoRecord$exportAsBibTeX(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsCSL()

Exports record as CSL

Usage
ZenodoRecord$exportAsCSL(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsDataCite()

Exports record as DataCite

Usage
ZenodoRecord$exportAsDataCite(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsDublinCore()

Exports record as DublinCore

Usage
ZenodoRecord$exportAsDublinCore(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsDCAT()

Exports record as DCAT

Usage
ZenodoRecord$exportAsDCAT(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsJSON()

Exports record as JSON

Usage
ZenodoRecord$exportAsJSON(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsJSONLD()

Exports record as JSONLD

Usage
ZenodoRecord$exportAsJSONLD(filename)
Arguments
filename

the target filename (without extension)

Method exportAsGeoJSON()

Exports record as GeoJSON

Usage
ZenodoRecord$exportAsGeoJSON(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsMARCXML()

Exports record as MARCXML

Usage
ZenodoRecord$exportAsMARCXML(filename)
Arguments
filename

the target filename (without extension)

Returns

the writen file name (with extension)

Method exportAsAllFormats()

Exports record in all Zenodo record export formats. This function will create one file per Zenodo metadata formats.

Usage
ZenodoRecord$exportAsAllFormats(filename)
Arguments
filename

the target filename (without extension)

Method listFiles()

list files attached to the record

Usage
ZenodoRecord$listFiles(pretty = TRUE)
Arguments
pretty

whether a pretty output (data.frame) should be returned (default TRUE), otherwise the raw list of files is returned.

Returns

the files, as data.frame or list

Method downloadFiles()

Downloads files attached to the record

Usage
ZenodoRecord$downloadFiles(
  path = ".",
  files = list(),
  parallel = FALSE,
  parallel_handler = NULL,
  cl = NULL,
  quiet = FALSE,
  overwrite = TRUE,
  timeout = 60,
  ...
)
Arguments
path

target download path (by default it will be the current working directory)

files

(list of) file(s) to download. If not specified, by default all files will be downloaded.

parallel

whether download has to be done in parallel using the chosen parallel_handler. Default is FALSE

parallel_handler

The parallel handler to use eg. mclapply. To use a different parallel handler (such as eg parLapply or parSapply), specify its function in parallel_handler argument. For cluster-based parallel download, this is the way to proceed. In that case, the cluster should be created earlier by the user with makeCluster and passed as cl argument. After downloading all files, the cluster will be stopped automatically.

cl

an optional cluster for cluster-based parallel handlers

quiet

(default is FALSE) can be set to suppress informative messages (not warnings).

overwrite

(default is TRUE) can be set to FALSE to avoid re-downloading existing files.

timeout

(default is 60s) see download.file.

...

arguments inherited from parallel::mclapply or the custom parallel_handler can be added (eg. mc.cores for mclapply)

Method print()

Prints a ZenodoRecord

Usage
ZenodoRecord$print(..., format = "internal", depth = 1)
Arguments
...

any other parameter. Not used

format

format to use for printing. By default, internal uses an zen4R internal printing method. Other methods available are those supported by Zenodo for record export, and can be used only if the record has already been published (with a DOI). Attemps to print using a Zenodo export format for a record will raise a warning message and revert to "internal" format

depth

an internal depth parameter for indentation of print statements, in case of listing or recursive use of print

Method toDCEntry()

Maps to an atom4R DCEntry. Note: applies only to published records.

Usage
ZenodoRecord$toDCEntry()
Returns

an object of class DCEntry

Method getFirstDOI()

Get DOI of the first record version.

Usage
ZenodoRecord$getFirstDOI()
Returns

the first DOI, object of class character

Method getLastDOI()

Get DOI of the latest record version.

Usage
ZenodoRecord$getLastDOI()
Returns

the last DOI, object of class character

Method getVersions()

Get record versions with creation/publication date, version (ordering number) and DOI.

Usage
ZenodoRecord$getVersions()
Returns

a data.frame with the record versions

Method clone()

The objects of this class are cloneable with this method.

Usage
ZenodoRecord$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Internal method. Prefer using addCreator or addContributor

Internal method. Prefer using removeCreator or removeContributor

See examples in download_zenodo utility function.

Author(s)

Emmanuel Blondel <[email protected]>

ZenodoRequest

Description

ZenodoRequest

ZenodoRequest

Format

R6Class object.

Value

Object of R6Class for modelling a generic Zenodo request

Super class

zen4R::zen4RLogger -> ZenodoRequest

Methods

Public methods

Inherited methods

Method new()

Initializes a ZenodoRequest

Usage
ZenodoRequest$new(
  url,
  type,
  request,
  data = NULL,
  file = NULL,
  progress = FALSE,
  accept = "application/vnd.inveniordm.v1+json",
  token,
  logger = NULL,
  ...
)
Arguments
url

request URL

type

Type of request: 'GET', 'POST', 'PUT', 'DELETE'

request

the method request

data

payload (optional)

file

to be uploaded (optional)

progress

whether a progress status has to be displayed for download/upload

accept

accept header. Default is "application/vnd.inveniordm.v1+json"

token

user token

logger

the logger type

...

any other arg

Method execute()

Executes the request

Usage
ZenodoRequest$execute()

Method getRequest()

Get request

Usage
ZenodoRequest$getRequest()

Method getRequestHeaders()

Get request headers

Usage
ZenodoRequest$getRequestHeaders()

Method getStatus()

Get request status

Usage
ZenodoRequest$getStatus()

Method getResponse()

Get request response

Usage
ZenodoRequest$getResponse()

Method getException()

Get request exception

Usage
ZenodoRequest$getException()

Method getResult()

Get request result

Usage
ZenodoRequest$getResult()

Method setResult()

Set request result

Usage
ZenodoRequest$setResult(result)
Arguments
result

result to be set

Method clone()

The objects of this class are cloneable with this method.

Usage
ZenodoRequest$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Abstract class used internally by zen4R

Author(s)

Emmanuel Blondel <[email protected]>