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: | 2024-10-14 05:33:21 UTC |
Source: | https://github.com/eblondel/zen4r |
download_zenodo
allows to download archives attached to a Zenodo
record, identified by its DOI or concept DOI.
download_zenodo( doi, path = ".", files = list(), sandbox = FALSE, logger = NULL, quiet = FALSE, ... )
download_zenodo( doi, path = ".", files = list(), sandbox = FALSE, logger = NULL, quiet = FALSE, ... )
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 |
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 ( |
... |
any other arguments for parallel downloading (more information at
ZenodoRecord, |
## 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)
## 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
allows to export a Zenodo record, identified by its
DOI or concept DOI, using one of the export formats supported by Zenodo.
export_zenodo( doi, filename, format, append_format = TRUE, sandbox = FALSE, logger = NULL )
export_zenodo( doi, filename, format, append_format = TRUE, sandbox = FALSE, logger = NULL )
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 |
sandbox |
Use the sandbox infrastructure. Default is |
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) |
the exported file name (with extension)
## Not run: export_zenodo("10.5281/zenodo.2547036", filename = "test", format = "BibTeX", append_format = F) ## End(Not run)
## Not run: export_zenodo("10.5281/zenodo.2547036", filename = "test", format = "BibTeX", append_format = F) ## End(Not run)
get_licenses
allows to list all licenses supported by Zenodo.
get_licenses(pretty = TRUE, sandbox = FALSE)
get_licenses(pretty = TRUE, sandbox = FALSE)
pretty |
output delivered as |
sandbox |
Use the sandbox infrastructure. Default is |
the licenses as list
or data.frame
## Not run: get_licenses(pretty = TRUE) ## End(Not run)
## Not run: get_licenses(pretty = TRUE) ## End(Not run)
get_versions
allows to execute a workflow
get_versions(doi, sandbox = FALSE, logger = NULL)
get_versions(doi, sandbox = FALSE, logger = NULL)
doi |
a Zenodo DOI or concept DOI |
sandbox |
Use the sandbox infrastructure. Default is |
logger |
a logger to print messages. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs) |
an object of class data.frame
giving the record versions
including date, version number and version-specific DOI.
## Not run: get_versions("10.5281/zenodo.2547036") ## End(Not run)
## Not run: get_versions("10.5281/zenodo.2547036") ## End(Not run)
get_zenodo
allows to get a Zenodo record, identified by
its DOI or concept DOI.
get_zenodo(doi, sandbox = FALSE, logger = NULL)
get_zenodo(doi, sandbox = FALSE, logger = NULL)
doi |
a Zenodo DOI or concept DOI |
sandbox |
Use the sandbox infrastructure. Default is |
logger |
a logger to print messages. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs) |
an object of class data.frame
giving the record versions
including date, version number and version-specific DOI.
object of class ZenodoRecord
## Not run: get_zenodo("10.5281/zenodo.2547036") ## End(Not run)
## Not run: get_zenodo("10.5281/zenodo.2547036") ## End(Not run)
Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo', upload and download of files.
Emmanuel Blondel [email protected]
Useful links:
zen4RLogger
zen4RLogger
R6Class
object.
Object of R6Class
for modelling a simple logger
verbose.info
logger info status
verbose.debug
logger debug status
loggerType
Logger type, either "INFO", "DEBUG" or NULL (if no logger)
logger()
internal logger function for the Zenodo manager
zen4RLogger$logger(type, text)
type
logger message type, "INFO", "WARN", or "ERROR"
text
log message
INFO()
internal INFO logger function
zen4RLogger$INFO(text)
text
log message
WARN()
internal WARN logger function
zen4RLogger$WARN(text)
text
log message
ERROR()
internal ERROR logger function
zen4RLogger$ERROR(text)
text
log message
new()
initialize the Zenodo logger
zen4RLogger$new(logger = NULL)
logger
logger type NULL, 'INFO', or 'DEBUG'
getClassName()
Get object class name
zen4RLogger$getClassName()
the class name, object of class character
getClass()
Get object class
zen4RLogger$getClass()
the class, object of class R6
clone()
The objects of this class are cloneable with this method.
zen4RLogger$clone(deep = FALSE)
deep
Whether to make a deep clone.
Logger class used internally by zen4R
Get Zenodo personal access token, looking in env var 'ZENODO_PAT'
zenodo_pat(quiet = TRUE)
zenodo_pat(quiet = TRUE)
quiet |
Hide log message, default is |
ZenodoManager
ZenodoManager
R6Class
object.
Object of R6Class
for modelling an ZenodoManager
zen4R::zen4RLogger
-> ZenodoManager
sandbox
Zenodo manager sandbox status, TRUE
if we interact with Sandbox infra
anonymous
Zenodo manager anonymous status, TRUE
when no token is specified
new()
initializes the Zenodo Manager
ZenodoManager$new( url = "https://zenodo.org/api", token = zenodo_pat(), sandbox = FALSE, logger = NULL, keyring_backend = "env" )
url
Zenodo API URL. By default, the url is set to "https://zenodo.org/api". For tests, the Zenodo sandbox API URL can be used: https://sandbox.zenodo.org/api
token
the user token. By default an attempt will be made to retrieve token using zenodo_pat
sandbox
Indicates if the Zenodo sandbox platform should be used. Default is FALSE
logger
logger type. The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)
keyring_backend
The keyring backend used to store user token. The keyring_backend
can be set to use a different backend for storing the Zenodo token with keyring (Default value is 'env').
getToken()
Get user token
ZenodoManager$getToken()
the token, object of class character
getLanguages()
Get Languages supported by Zenodo.
ZenodoManager$getLanguages(pretty = TRUE)
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of languages as data.frame
.
Set pretty = FALSE
to get the raw list of languages
list of languages as data.frame
or list
getLanguageById()
Get language by Id.
ZenodoManager$getLanguageById(id)
id
license id
the license
getLicenses()
Get Licenses supported by Zenodo.
ZenodoManager$getLicenses(pretty = TRUE)
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of licenses as data.frame
.
Set pretty = FALSE
to get the raw list of licenses.
list of licenses as data.frame
or list
getLicenseById()
Get license by Id.
ZenodoManager$getLicenseById(id)
id
license id
the license
getResourceTypes()
Get Resource types supported by Zenodo.
ZenodoManager$getResourceTypes(pretty = TRUE)
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of resource types as data.frame
.
Set pretty = FALSE
to get the raw list of resource types
list of resource types as data.frame
or list
getResourceTypeById()
Get resource type by Id.
ZenodoManager$getResourceTypeById(id)
id
resource type id
the resource type
getCommunities()
Get Communities supported by Zenodo.
ZenodoManager$getCommunities(pretty = TRUE, q = "", size = 500)
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of communities as data.frame
.
Set pretty = FALSE
to get the raw list of communities
q
an ElasticSearch compliant query, object of class character
. Default is emtpy.
Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently,
not all communities can be listed from Zenodo, a query has to be specified.
size
number of communities to be returned. By default equal to 500
list of communities as data.frame
or list
getCommunityById()
Get community by Id.
ZenodoManager$getCommunityById(id)
id
community id
the community
submitRecordToCommunities()
Submit a published record to one or more community
ZenodoManager$submitRecordToCommunities( record, communities = list(), message = NULL )
record
an object of class ZenodoRecord
communities
communities to which the record will be submitted
message
message to send to the community curator(s), either a text or a named list for each community in case a community-specific message should be sent
a submission object of class list
, or NULL if nothing was submitted
removeRecordFromCommunities()
Remove a record from one or more community
ZenodoManager$removeRecordFromCommunities(record, communities = list())
record
an object of class ZenodoRecord
communities
communities to which the record will be submitted
TRUE
if removed, FALSE
otherwise
getRecordCommunities()
Get record communities
ZenodoManager$getRecordCommunities(record)
record
object of class ZenodoRecord
the list of communities in which the record was included
createReviewRequest()
Creates a record review request in a community
ZenodoManager$createReviewRequest(record, community)
record
an object of class ZenodoRecord
community
a community to which the record is submitted for review and publication
a review request object of class list
, or NULL if nothing was submitted
getReviewRequest()
Get a record review request
ZenodoManager$getReviewRequest(record)
record
an object of class ZenodoRecord
a review request object of class list
, or NULL if nothing exists
deleteReviewRequest()
Deletes a review request
ZenodoManager$deleteReviewRequest(record)
record
an object of class ZenodoRecord
TRUE
if deleted, FALSE
otherwise
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)
.
ZenodoManager$submitRecordForReview(recordId, message = NULL)
recordId
the ID of a Zenodo record
message
message content for the submission. Optional
TRUE
if submitted, FALSE
otherwise
getGrants()
Get Grants supported by Zenodo. DEPRECATED: replaced by getAwards
ZenodoManager$getGrants(q = "", pretty = TRUE, size = 500)
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.
list of grants as data.frame
or list
getAwards()
Get Awards supported by Zenodo.
ZenodoManager$getAwards(q = "", pretty = TRUE, size = 500)
q
an ElasticSearch compliant query, object of class character
. Default is emtpy.
Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently,
not all awards can be listed from Zenodo, a query has to be specified.
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of awards as data.frame
.
Set pretty = FALSE
to get the raw list of awards
size
number of awards to be returned. By default equal to 500.
list of awards as data.frame
or list
getGrantsByName()
Get grants by name. DEPRECATED: replaced by getAwardByName
ZenodoManager$getGrantsByName(name, pretty = TRUE)
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
list of grants as data.frame
or list
getAwardsByName()
Get awards by name.
ZenodoManager$getAwardsByName(name, pretty = TRUE)
name
name
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of awards as data.frame
.
Set pretty = FALSE
to get the raw list of awards
list of awards as data.frame
or list
getGrantById()
Get grant by Id.DEPRECATED: replaced by getAwardById
ZenodoManager$getGrantById(id)
id
grant id
the grant
getAwardById()
Get award by Id.
ZenodoManager$getAwardById(id)
id
award id
the award
getAffiliations()
Get Affiliations supported by Zenodo.
ZenodoManager$getAffiliations(q = "", pretty = TRUE, size = 500)
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.
list of affiliations as data.frame
or list
getAffiliationByName()
Get affiliations by name.
ZenodoManager$getAffiliationByName(name, pretty = TRUE)
name
name
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of affiliations as data.frame
.
Set pretty = FALSE
to get the raw list of affiliations
list of affiliations as data.frame
or list
getAffiliationById()
Get affiliation by Id.
ZenodoManager$getAffiliationById(id)
id
affiliation id
the affiliation
getFunders()
Get Funders supported by Zenodo based on a query.
ZenodoManager$getFunders(q = "", pretty = TRUE, size = 500)
q
an ElasticSearch compliant query, object of class character
. Default is emtpy.
Note that the Zenodo API restrains a maximum number of 10,000 records to be retrieved. Consequently,
not all funders can be listed from Zenodo, a query has to be specified.
pretty
Prettify the output. By default the argument pretty
is set to
TRUE
which will returns the list of funders as data.frame
.
Set pretty = FALSE
to get the raw list of funders
size
number of funders to be returned. By default equal to 500
list of funders as data.frame
or list
getFundersByName()
Get funders by name.
ZenodoManager$getFundersByName(name, pretty = TRUE)
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
list of funders as data.frame
or list
getFunderById()
Get funder by Id.
ZenodoManager$getFunderById(id)
id
funder id
the funder
getDepositions()
Get the list of Zenodo records deposited in your Zenodo workspace (user records). By default
the list of depositions will be returned by page with a size of 10 results per page (default size of
the Zenodo API). The parameter q
allows to specify an ElasticSearch-compliant query to filter
depositions (default query is empty to retrieve all records). The argument all_versions
, if set
to TRUE allows to get all versions of records as part of the depositions list. The argument exact
specifies that an exact matching is wished, in which case paginated search will be disabled (only the first
search page will be returned).
Examples of ElasticSearch queries for Zenodo can be found at https://help.zenodo.org/guides/search/.
ZenodoManager$getDepositions( q = "", size = 10, all_versions = FALSE, exact = TRUE, quiet = FALSE )
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
a list of ZenodoRecord
getDepositionByConceptDOI()
Get a Zenodo deposition record by concept DOI (generic DOI common to all deposition record versions).
ZenodoManager$getDepositionByConceptDOI(conceptdoi)
conceptdoi
the concept DOI, object of class character
an object of class ZenodoRecord
if record does exist, NULL otherwise
getDepositionByDOI()
Get a Zenodo deposition record by DOI.
ZenodoManager$getDepositionByDOI(doi)
doi
the DOI, object of class character
an object of class ZenodoRecord
if record does exist, NULL otherwise
getDepositionById()
Get a Zenodo deposition record by ID.
ZenodoManager$getDepositionById(recid)
recid
the record ID, object of class character
an object of class ZenodoRecord
if record does exist, NULL otherwise
getDepositionByConceptId()
Get a Zenodo deposition record by concept ID.
ZenodoManager$getDepositionByConceptId(conceptrecid)
conceptrecid
the record concept ID, object of class character
an object of class ZenodoRecord
if record does exist, NULL otherwise
depositRecord()
Deposits a record on Zenodo.
ZenodoManager$depositRecord(record, reserveDOI = TRUE, publish = FALSE)
record
the record to deposit, object of class ZenodoRecord
reserveDOI
reserve DOI. By default TRUE
publish
object of class logical
indicating if record has to be published (default FALSE
).
Can be set to TRUE
(to use CAUTIOUSLY, only if you want to publish your record)
object of class ZenodoRecord
reserveDOI()
Reserves a DOI for a deposition (draft record)
ZenodoManager$reserveDOI(record)
record
the record to deposit, object of class ZenodoRecord
object of class ZenodoRecord
deleteDOI()
Reserves a DOI for a deposition (draft record)
ZenodoManager$deleteDOI(record)
record
the record for which DOI has to be deleted, object of class ZenodoRecord
object of class ZenodoRecord
depositRecordVersion()
Deposits a record version on Zenodo.
ZenodoManager$depositRecordVersion( record, delete_latest_files = TRUE, files = list(), publish = FALSE )
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
)
TRUE
if deposited (and eventually published), FALSE
otherwise
deleteRecord()
Deletes a record given its ID
ZenodoManager$deleteRecord(recordId)
recordId
the ID of the record to be deleted
TRUE
if deleted, FALSE
otherwise
deleteRecordByDOI()
Deletes a record by DOI
ZenodoManager$deleteRecordByDOI(doi)
doi
the DOI of the record to be deleted
TRUE
if deleted, FALSE
otherwise
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/.
ZenodoManager$deleteRecords(q = "", size = 10)
q
an ElasticSearch compliant query, object of class character
size
number of records to be passed to $getDepositions
method
TRUE
if all records have been deleted, FALSE
otherwise
createEmptyRecord()
Creates an empty record in the Zenodo deposit. Returns the record
newly created in Zenodo, as an object of class ZenodoRecord
with an
assigned identifier.
ZenodoManager$createEmptyRecord(reserveDOI = TRUE)
reserveDOI
reserve DOI. By default TRUE
an object of class ZenodoRecord
editRecord()
Unlocks a record already submitted. Required to edit metadata of a Zenodo record already published.
ZenodoManager$editRecord(recordId)
recordId
the ID of the record to unlock and set in editing mode.
an object of class ZenodoRecord
discardChanges()
Discards changes on a Zenodo record. Deleting a draft for an unpublished record will remove the draft and associated files from the system. Deleting a draft for a published record will remove the draft but not the published record.
ZenodoManager$discardChanges(recordId)
recordId
the ID of the record for which changes have to be discarded.
an object of class ZenodoRecord
publishRecord()
Publishes a Zenodo record.
ZenodoManager$publishRecord(recordId)
recordId
the ID of the record to be published.
an object of class ZenodoRecord
getFiles()
Get list of files attached to a Zenodo record.
ZenodoManager$getFiles(recordId)
recordId
the ID of the record.
list of files
getFile()
Get a file record metadata.
ZenodoManager$getFile(recordId, filename)
recordId
the ID of the record.
filename
filename
the file metadata
startFileUpload()
Start a file upload. The method will create a key for the file to be uploaded
This method is essentially for internal purpose, and is called directly in uploadFile
for user convenience and for backward compatibility with the legacy Zenodo API.
ZenodoManager$startFileUpload(path, recordId)
path
Local path of the file
recordId
ID of the record
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.
ZenodoManager$completeFileUpload(path, recordId)
path
Local path of the file
recordId
ID of the record
uploadFile()
Uploads a file to a Zenodo record. With the new Zenodo Invenio RDM API, this method
internally calls startFileUpload
to create a file record (with a filename key) at start, followed
by the actual file content upload. At this stage, the file upload is in "pending" status. At the end,
the function calls completeFileUpload
to commit the file which status becomes "completed".
ZenodoManager$uploadFile(path, record = NULL)
path
Local path of the file
record
object of class ZenodoRecord
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.
ZenodoManager$deleteFile(recordId, filename)
recordId
ID of the record
filename
name of the file to be deleted
getRecords()
Get the list of Zenodo records. By defaut the list of records will be returned by
page with a size of 10 results per page (default size of the Zenodo API). The parameter
q
allows to specify an ElasticSearch-compliant query to filter depositions
(default query is empty to retrieve all records). The argument all_versions
,
if set to TRUE allows to get all versions of records as part of the depositions list.
The argument exact
specifies that an exact matching is wished, in which case
paginated search will be disabled (only the first search page will be returned).
Examples of ElasticSearch queries for Zenodo can be found at https://help.zenodo.org/guides/search/.
ZenodoManager$getRecords(q = "", size = 10, all_versions = FALSE, exact = TRUE)
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
a list of ZenodoRecord
getRecordByConceptDOI()
Get Record by concept DOI
ZenodoManager$getRecordByConceptDOI(conceptdoi)
conceptdoi
the concept DOI
a object of class ZenodoRecord
getRecordByDOI()
Get Record by DOI
ZenodoManager$getRecordByDOI(doi)
doi
the DOI
a object of class ZenodoRecord
getRecordById()
Get Record by ID
ZenodoManager$getRecordById(recid)
recid
the record ID
a object of class ZenodoRecord
getRecordByConceptId()
Get Record by concept ID
ZenodoManager$getRecordByConceptId(conceptrecid)
conceptrecid
the concept ID
a object of class ZenodoRecord
getRequests()
Search requests
ZenodoManager$getRequests(q = "", sort = "bestmatch", size = 10)
q
Search query used to filter results based on ElasticSearch's query string syntax. e.g. https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-query-string-query.html#query-string-syntax
sort
Sort search results. Built-in options are "bestmatch", "name", "newest", "oldest" (default: "bestmatch" or "newest").
size
number of records to be retrieved per request (paginated). Default is 10
a list of ZenodoRecord
getRequest()
Get a request
ZenodoManager$getRequest(request_id)
request_id
the request ID
the request list
object, NULL otherwise
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
ZenodoManager$isActionableRequest(request_id)
request_id
the request ID
TRUE
if
acceptRequest()
Accepts a request
ZenodoManager$acceptRequest(request_id, message = NULL)
request_id
the request ID
message
optional message reason for acceptance
TRUE
if accepted, FALSE
otherwise
declineRequest()
Declines a request
ZenodoManager$declineRequest(request_id, message = NULL)
request_id
the request ID
message
optional message reason for declination
TRUE
if declined, FALSE
otherwise
cancelRequest()
Cancels a request
ZenodoManager$cancelRequest(request_id, message = NULL)
request_id
the request ID
message
optional message reason for cancelation
TRUE
if canceled, FALSE
otherwise
clone()
The objects of this class are cloneable with this method.
ZenodoManager$clone(deep = FALSE)
deep
Whether to make a deep clone.
Main user class to be used with zen4R
Emmanuel Blondel <[email protected]>
## Not run: ZENODO <- ZenodoManager$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]]$filename) ## End(Not run)
## Not run: ZENODO <- ZenodoManager$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]]$filename) ## End(Not run)
ZenodoRecord
ZenodoRecord
R6Class
object.
Object of R6Class
for modelling an ZenodoRecord
zen4R::zen4RLogger
-> ZenodoRecord
created
record creation date
updated
record update date
revision_id
revision id
is_draft
is draft
is_published
is published
status
record status
versions
versions
access
access policies
files
list of files associated to the record
id
record id
links
list of links associated to the record
metadata
metadata elements associated to the record
parent
parent record
pids
pids
stats
stats
new()
method is used to instantiate a ZenodoRecord
ZenodoRecord$new(obj = NULL, logger = "INFO")
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)
getStats()
Get record statistics
ZenodoRecord$getStats()
statistics as data.frame
getId()
Get the record Id
ZenodoRecord$getId()
the Id, object of class character
getParentId()
Get the parent record Id
ZenodoRecord$getParentId()
the parent Id, object of class character
getConceptId()
Get the concept record Id
ZenodoRecord$getConceptId()
the concept Id, object of class character
setDOI()
Set the DOI. This method can be used if a DOI has been already assigned outside Zenodo.
ZenodoRecord$setDOI(doi, provider = NULL, client = NULL)
doi
DOI to set for the record
provider
DOI provider
client
DOI client
getDOI()
Get the record DOI.
ZenodoRecord$getDOI()
the DOI, object of class character
getConceptDOI()
Get the concept (generic) DOI. The concept DOI is a generic DOI common to all versions of a Zenodo record.
ZenodoRecord$getConceptDOI()
the concept DOI, object of class character
setAccessPolicyRecord()
Set the access policy for record, among values "public" (default) or "restricted" In Zenodo, in principle, the access policy 'restricted' is not available for records.
ZenodoRecord$setAccessPolicyRecord(access = c("public", "restricted"))
access
access policy ('public' or 'restricted')
setAccessPolicyFiles()
Set the access policy for files, among values "public" (default) or "restricted"
ZenodoRecord$setAccessPolicyFiles(access = c("public", "restricted"))
access
access policy ('public' or 'restricted')
setAccessPolicyEmbargo()
Set access policy embargo options
ZenodoRecord$setAccessPolicyEmbargo(active = FALSE, until = NULL, reason = "")
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
setResourceType()
Set the resource type (mandatory).
ZenodoRecord$setResourceType(resourceType)
resourceType
record resource type
setUploadType()
Set the upload type (mandatory). Deprecated since zen4R 1.0
ZenodoRecord$setUploadType(uploadType)
uploadType
record upload type among the following values: 'publication', 'poster', 'presentation', 'dataset', 'image', 'video', 'software', 'lesson', 'physicalobject', 'other'
setPublicationType()
Set the publication type (mandatory if upload type is 'publication'). Deprecated since zen4R 1.0
ZenodoRecord$setPublicationType(publicationType)
publicationType
record publication type among the following values: 'annotationcollection', 'book', 'section', 'conferencepaper', 'datamanagementplan', 'article', 'patent', 'preprint', 'deliverable', 'milestone', 'proposal', 'report', 'softwaredocumentation', 'taxonomictreatment', 'technicalnote', 'thesis', 'workingpaper', 'other'
setImageType()
Set the image type (mandatory if image type is 'image'). Deprecated since zen4R 1.0
ZenodoRecord$setImageType(imageType)
imageType
record publication type among the following values: 'figure','plot', 'drawing','diagram','photo', or 'other'
setPublisher()
Set the publisher
ZenodoRecord$setPublisher(publisher)
publisher
publisher object of class character
setPublicationDate()
Set the publication date. For more information on the accepted format, please check https://inveniordm.docs.cern.ch/reference/metadata/#publication-date-1
ZenodoRecord$setPublicationDate(publicationDate)
publicationDate
object of class character
addDate()
Add date
ZenodoRecord$addDate(date, type, description = NULL)
date
date
type
type of date, among following values: 'accepted', 'available', 'collected', 'copyrighted', 'created', 'issued', 'other', 'submitted', 'updated', 'valid', 'withdrawn'
description
free text, specific information about the date
removeDate()
Remove a date
ZenodoRecord$removeDate(date, type)
date
the date to remove
type
the date type of the date to be removed
TRUE
if removed, FALSE
otherwise
setTitle()
Set the record title.
ZenodoRecord$setTitle(title)
title
object of class character
addAdditionalTitle()
Add additional record title
ZenodoRecord$addAdditionalTitle(title, type, lang = "eng")
title
title free text
type
type of title, among following values: alternative-title, subtitle, translated-title, other
lang
language id
TRUE
if added, FALSE
otherwise
removeAdditionalTitle()
Removes additional record title.
ZenodoRecord$removeAdditionalTitle(title, type, lang = "eng")
title
title free text
type
type of title, among following values: abstract, methods, series-information, table-of-contents, technical-info, other
lang
language id
TRUE
if removed, FALSE
otherwise
setDescription()
Set the record description
ZenodoRecord$setDescription(description)
description
object of class character
addAdditionalDescription()
Add additional record description
ZenodoRecord$addAdditionalDescription(description, type, lang = "eng")
description
description free text
type
type of description, among following values: abstract, methods, series-information, table-of-contents, technical-info, other
lang
language id
TRUE
if added, FALSE
otherwise
removeAdditionalDescription()
Removes additional record description
ZenodoRecord$removeAdditionalDescription(description, type, lang = "eng")
description
description free text
type
type of description, among following values: abstract, methods, series-information, table-of-contents, technical-info, other
lang
language id
TRUE
if removed, FALSE
otherwise
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.
ZenodoRecord$addPersonOrOrg( firstname = NULL, lastname = NULL, name = paste(lastname, firstname, sep = ", "), orcid = NULL, gnd = NULL, isni = NULL, ror = NULL, role = NULL, affiliations = NULL, sandbox = FALSE, type )
firstname
person first name
lastname
person last name
name
organization name
orcid
person or organization ORCID (optional)
gnd
person or organization GND (optional)
isni
person or organization ISNI (optional)
ror
person or organization ROR (optional)
role
role, values among: contactperson, datacollector, datacurator, datamanager, distributor, editor, funder, hostinginstitution, producer, projectleader, projectmanager, projectmember, registrationagency, registrationauthority, relatedperson, researcher, researchgroup, rightsholder, supervisor, sponsor, workpackageleader, other
affiliations
person or organization affiliations (optional)
sandbox
Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is FALSE
type
type of person or org (creators/contributors)
TRUE
if added, FALSE
otherwise
removePersonOrOrg()
Removes a person or organization by a property. The by
parameter should be the name
of the person or organization property ('name', 'affiliation','orcid','gnd','isni','ror').
ZenodoRecord$removePersonOrOrg(by, property, type)
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)
TRUE
if removed, FALSE
otherwise
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.
ZenodoRecord$addCreator( firstname = NULL, lastname = NULL, name = paste(lastname, firstname, sep = ", "), orcid = NULL, gnd = NULL, isni = NULL, ror = NULL, role = NULL, affiliations = NULL, sandbox = FALSE )
firstname
person first name
lastname
person last name
name
organization name
orcid
creator ORCID (optional)
gnd
creator GND (optional)
isni
creator ISNI (optional)
ror
creator ROR (optional)
role
role, values among: contactperson, datacollector, datacurator, datamanager, distributor, editor, funder, hostinginstitution, producer, projectleader, projectmanager, projectmember, registrationagency, registrationauthority, relatedperson, researcher, researchgroup, rightsholder, supervisor, sponsor, workpackageleader, other
affiliations
creator affiliations (optional)
sandbox
Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is FALSE
TRUE
if added, FALSE
otherwise
removeCreatorByName()
Removes a creator by name.
ZenodoRecord$removeCreatorByName(name)
name
creator name
TRUE
if removed, FALSE
otherwise
removeCreatorByAffiliation()
Removes a creator by affiliation.
ZenodoRecord$removeCreatorByAffiliation(affiliation)
affiliation
creator affiliation
TRUE
if removed, FALSE
otherwise
removeCreatorByORCID()
Removes a creator by ORCID.
ZenodoRecord$removeCreatorByORCID(orcid)
orcid
creator ORCID
TRUE
if removed, FALSE
otherwise
removeCreatorByGND()
Removes a creator by GND.
ZenodoRecord$removeCreatorByGND(gnd)
gnd
creator GND
TRUE
if removed, FALSE
otherwise
removeCreatorByISNI()
Removes a creator by ISNI.
ZenodoRecord$removeCreatorByISNI(isni)
isni
creator ISNI
TRUE
if removed, FALSE
otherwise
removeCreatorByROR()
Removes a creator by ROR.
ZenodoRecord$removeCreatorByROR(ror)
ror
creator ROR
TRUE
if removed, FALSE
otherwise
addContributor()
Add a contributor for the record. For persons, the approach is to use the firstname
and
lastname
arguments, that by default will be concatenated for Zenodo as lastname, firstname
.
For organizations, use the name
argument.
ZenodoRecord$addContributor( firstname = NULL, lastname = NULL, name = paste(lastname, firstname, sep = ", "), orcid = NULL, gnd = NULL, isni = NULL, ror = NULL, role = NULL, affiliations = NULL, sandbox = FALSE )
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
TRUE
if added, FALSE
otherwise
removeContributorByName()
Removes a contributor by name.
ZenodoRecord$removeContributorByName(name)
name
contributor name
TRUE
if removed, FALSE
otherwise
removeContributorByAffiliation()
Removes a contributor by affiliation.
ZenodoRecord$removeContributorByAffiliation(affiliation)
affiliation
contributor affiliation
TRUE
if removed, FALSE
otherwise
removeContributorByORCID()
Removes a contributor by ORCID.
ZenodoRecord$removeContributorByORCID(orcid)
orcid
contributor ORCID
TRUE
if removed, FALSE
otherwise
removeContributorByGND()
Removes a contributor by GND.
ZenodoRecord$removeContributorByGND(gnd)
gnd
contributor GND
TRUE
if removed, FALSE
otherwise
removeContributorByISNI()
Removes a contributor by ISNI.
ZenodoRecord$removeContributorByISNI(isni)
isni
contributor ISNI
TRUE
if removed, FALSE
otherwise
removeContributorByROR()
Removes a contributor by ROR.
ZenodoRecord$removeContributorByROR(ror)
ror
contributor ROR
TRUE
if removed, FALSE
otherwise
addRight()
Add right/license. Please see https://inveniordm.docs.cern.ch/reference/metadata/#rights-licenses-0-n
ZenodoRecord$addRight( id = NULL, title = NULL, description = NULL, link = NULL, sandbox = FALSE )
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
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 $getLicenses()
.
ZenodoRecord$setLicense(licenseId, sandbox = FALSE)
licenseId
a license Id
sandbox
Use the Zenodo sandbox infrastructure as basis to control available licenses. Default is FALSE
TRUE
if set, FALSE
otherwise
setVersion()
Set record version.
ZenodoRecord$setVersion(version)
version
the record version to set
addLanguage()
Adds a language.
ZenodoRecord$addLanguage(language)
language
ISO 639-2 or 639-3 code
setLanguage()
Set the language
ZenodoRecord$setLanguage(language)
language
ISO 639-2 or 639-3 code
addRelatedIdentifier()
Adds a related identifier with a given scheme and relation type.
ZenodoRecord$addRelatedIdentifier( identifier, scheme, relation_type, resource_type = NULL )
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
TRUE
if added, FALSE
otherwise
removeRelatedIdentifier()
Removes a related identifier with a given scheme/relation_type
ZenodoRecord$removeRelatedIdentifier(identifier, scheme, relation_type)
identifier
identifier
scheme
scheme among following values: ark, arxiv, bibcode, doi, ean13, eissn, handle, igsn, isbn, issn, istc, lissn, lsid, pubmed id, purl, upc, url, urn, w3id
relation_type
relation type among following values: iscitedby, cites, issupplementto, issupplementedby, iscontinuedby, continues, isdescribedby, describes, hasmetadata, ismetadatafor, isnewversionof, ispreviousversionof, ispartof, haspart, isreferencedby, references, isdocumentedby, documents, iscompiledby, compiles, isvariantformof, isoriginalformof, isidenticalto, isalternateidentifier, isreviewedby, reviews, isderivedfrom, issourceof, requires, isrequiredby, isobsoletedby, obsoletes
TRUE
if removed, FALSE
otherwise
setReferences()
Set references
ZenodoRecord$setReferences(references)
references
a vector or list of references to set for the record
addReference()
Add a reference
ZenodoRecord$addReference(reference)
reference
the reference to add
TRUE
if added, FALSE
otherwise
removeReference()
Remove a reference
ZenodoRecord$removeReference(reference)
reference
the reference to remove
TRUE
if removed, FALSE
otherwise
setSubjects()
Set subjects
ZenodoRecord$setSubjects(subjects)
subjects
a vector or list of subjects to set for the record
setKeywords()
Set keywords
ZenodoRecord$setKeywords(keywords)
keywords
a vector or list of keywords to set for the record
addSubject()
Add a subject
ZenodoRecord$addSubject(subject)
subject
the subject to add
TRUE
if added, FALSE
otherwise
addKeyword()
Add a keyword
ZenodoRecord$addKeyword(keyword)
keyword
the keyword to add
TRUE
if added, FALSE
otherwise
removeSubject()
Remove a subject
ZenodoRecord$removeSubject(subject)
subject
the subject to remove
TRUE
if removed, FALSE
otherwise
removeKeyword()
Remove a keyword
ZenodoRecord$removeKeyword(keyword)
keyword
the keyword to remove
TRUE
if removed, FALSE
otherwise
setNotes()
Set notes. HTML is not allowed
ZenodoRecord$setNotes(notes)
notes
object of class character
addFunding()
Adds funding. Used internally, prefer using addGrant
instead.
ZenodoRecord$addFunding(funder = NULL, grant = NULL, sandbox = FALSE)
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
addGrant()
Adds a grant to the record metadata.
ZenodoRecord$addGrant(grant, sandbox = FALSE)
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 $getAwards()
.
sandbox
Use the Zenodo sandbox infrastructure as basis to control available grants. Default is FALSE
TRUE
if added, FALSE
otherwise
setGrants()
Set a vector of character strings identifying grants
ZenodoRecord$setGrants(grants, sandbox = FALSE)
grants
a vector or list of grants Values should among known grants The list of grants can
fetched with the ZenodoManager
and the function $getAwards()
. Each grant should be set with
the Zenodo id of the grant If not recognized by Zenodo, the function will raise a warning only.
sandbox
Use the Zenodo sandbox infrastructure as basis to control available grants. Default is FALSE
removeGrant()
Removes a grant from the record metadata.
ZenodoRecord$removeGrant(grant)
grant
grant to remove. The grant should be set with the Zenodo id of the grant
TRUE
if removed, FALSE
otherwise
setJournalTitle()
Set Journal title to the record metadata
ZenodoRecord$setJournalTitle(title)
title
a title, object of class character
setJournalVolume()
Set Journal volume to the record metadata
ZenodoRecord$setJournalVolume(volume)
volume
a volume
setJournalIssue()
Set Journal issue to the record metadata
ZenodoRecord$setJournalIssue(issue)
issue
an issue
setJournalPages()
Set Journal pages to the record metadata
ZenodoRecord$setJournalPages(pages)
pages
number of pages
setConferenceTitle()
Set conference title to the record metadata
ZenodoRecord$setConferenceTitle(title)
title
conference title, object of class character
setConferenceAcronym()
Set conference acronym to the record metadata
ZenodoRecord$setConferenceAcronym(acronym)
acronym
conference acronym, object of class character
setConferenceDates()
Set conference dates to the record metadata
ZenodoRecord$setConferenceDates(dates)
dates
conference dates, object of class character
setConferencePlace()
Set conference place to the record metadata
ZenodoRecord$setConferencePlace(place)
place
conference place, object of class character
setConferenceUrl()
Set conference url to the record metadata
ZenodoRecord$setConferenceUrl(url)
url
conference url, object of class character
setConferenceSession()
Set conference session to the record metadata
ZenodoRecord$setConferenceSession(session)
session
conference session, object of class character
setConferenceSessionPart()
Set conference session part to the record metadata
ZenodoRecord$setConferenceSessionPart(part)
part
conference session part, object of class character
setImprintPublisher()
Set imprint publisher to the record metadata
ZenodoRecord$setImprintPublisher(publisher)
publisher
the publisher, object of class character
setImprintISBN()
Set imprint ISBN to the record metadata
ZenodoRecord$setImprintISBN(isbn)
isbn
the ISBN, object of class character
setImprintPlace()
Set imprint place to the record metadata
ZenodoRecord$setImprintPlace(place)
place
the place, object of class character
setPartofTitle()
Set title to which record is part of
ZenodoRecord$setPartofTitle(title)
title
the title, object of class character
setPartofPages()
Set pages to which record is part of
ZenodoRecord$setPartofPages(pages)
pages
the pages, object of class character
setThesisUniversity()
Set thesis university
ZenodoRecord$setThesisUniversity(university)
university
the university, object of class character
addThesisSupervisor()
Adds thesis supervisor
ZenodoRecord$addThesisSupervisor( firstname, lastname, affiliation = NULL, orcid = NULL, gnd = NULL )
firstname
supervisor first name
lastname
supervisor last name
affiliation
supervisor affiliation (optional)
orcid
supervisor ORCID (optional)
gnd
supervisor GND (optional)
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').
ZenodoRecord$removeThesisSupervisor(by, property)
by
property used as criterion to remove the thesis supervisor
property
property value used to remove the thesis supervisor
TRUE
if removed, FALSE
otherwise
removeThesisSupervisorByName()
Removes a thesis supervisor by name.
ZenodoRecord$removeThesisSupervisorByName(name)
name
thesis supervisor name
TRUE
if removed, FALSE
otherwise
removeThesisSupervisorByAffiliation()
Removes a thesis supervisor by affiliation
ZenodoRecord$removeThesisSupervisorByAffiliation(affiliation)
affiliation
thesis supervisor affiliation
TRUE
if removed, FALSE
otherwise
removeThesisSupervisorByORCID()
Removes a thesis supervisor by ORCID
ZenodoRecord$removeThesisSupervisorByORCID(orcid)
orcid
thesis supervisor ORCID
TRUE
if removed, FALSE
otherwise
removeThesisSupervisorByGND()
Removes a thesis supervisor by GND
ZenodoRecord$removeThesisSupervisorByGND(gnd)
gnd
thesis supervisor GND
TRUE
if removed, FALSE
otherwise
addLocation()
Adds a location to the record metadata.
ZenodoRecord$addLocation(place, description = NULL, lat = NULL, lon = NULL)
place
place (required)
description
description
lat
latitude
lon
longitude
removeLocation()
Removes a grant from the record metadata.
ZenodoRecord$removeLocation(place)
place
place (required)
TRUE
if removed, FALSE
otherwise
exportAs()
Exports record to a file by format.
ZenodoRecord$exportAs(format, filename, append_format = TRUE)
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
.
the writen file name (with extension)
exportAsBibTeX()
Exports record as BibTeX
ZenodoRecord$exportAsBibTeX(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsCSL()
Exports record as CSL
ZenodoRecord$exportAsCSL(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsDataCite()
Exports record as DataCite
ZenodoRecord$exportAsDataCite(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsDublinCore()
Exports record as DublinCore
ZenodoRecord$exportAsDublinCore(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsDCAT()
Exports record as DCAT
ZenodoRecord$exportAsDCAT(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsJSON()
Exports record as JSON
ZenodoRecord$exportAsJSON(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsJSONLD()
Exports record as JSONLD
ZenodoRecord$exportAsJSONLD(filename)
filename
the target filename (without extension)
exportAsGeoJSON()
Exports record as GeoJSON
ZenodoRecord$exportAsGeoJSON(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsMARCXML()
Exports record as MARCXML
ZenodoRecord$exportAsMARCXML(filename)
filename
the target filename (without extension)
the writen file name (with extension)
exportAsAllFormats()
Exports record in all Zenodo record export formats. This function will create one file per Zenodo metadata formats.
ZenodoRecord$exportAsAllFormats(filename)
filename
the target filename (without extension)
listFiles()
list files attached to the record
ZenodoRecord$listFiles(pretty = TRUE)
pretty
whether a pretty output (data.frame
) should be returned (default TRUE
), otherwise
the raw list of files is returned.
the files, as data.frame
or list
downloadFiles()
Downloads files attached to the record
ZenodoRecord$downloadFiles( path = ".", files = list(), parallel = FALSE, parallel_handler = NULL, cl = NULL, quiet = FALSE, overwrite = TRUE, timeout = 60, ... )
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
)
print()
Prints a ZenodoRecord
ZenodoRecord$print(..., format = "internal", depth = 1)
...
any other parameter. Not used
format
format to use for printing. By default, internal
uses an zen4R internal
printing method. Other methods available are those supported by Zenodo for record export, and can be used
only if the record has already been published (with a DOI). Attemps to print using a Zenodo export format
for a record will raise a warning message and revert to "internal" format
depth
an internal depth parameter for indentation of print statements, in case of listing or recursive use of print
toDCEntry()
Maps to an atom4R DCEntry. Note: applies only to published records.
ZenodoRecord$toDCEntry()
an object of class DCEntry
getFirstDOI()
Get DOI of the first record version.
ZenodoRecord$getFirstDOI()
the first DOI, object of class character
getLastDOI()
Get DOI of the latest record version.
ZenodoRecord$getLastDOI()
the last DOI, object of class character
getVersions()
Get record versions with creation/publication date, version (ordering number) and DOI.
ZenodoRecord$getVersions()
a data.frame
with the record versions
clone()
The objects of this class are cloneable with this method.
ZenodoRecord$clone(deep = FALSE)
deep
Whether to make a deep clone.
Internal method. Prefer using addCreator
or addContributor
Internal method. Prefer using removeCreator
or removeContributor
See examples in download_zenodo
utility function.
Emmanuel Blondel <[email protected]>
ZenodoRequest
ZenodoRequest
R6Class
object.
Object of R6Class
for modelling a generic Zenodo request
zen4R::zen4RLogger
-> ZenodoRequest
new()
Initializes a ZenodoRequest
ZenodoRequest$new( url, type, request, data = NULL, file = NULL, progress = FALSE, accept = "application/vnd.inveniordm.v1+json", token, logger = NULL, ... )
url
request URL
type
Type of request: 'GET', 'POST', 'PUT', 'DELETE'
request
the method request
data
payload (optional)
file
to be uploaded (optional)
progress
whether a progress status has to be displayed for download/upload
accept
accept header. Default is "application/vnd.inveniordm.v1+json"
token
user token
logger
the logger type
...
any other arg
execute()
Executes the request
ZenodoRequest$execute()
getRequest()
Get request
ZenodoRequest$getRequest()
getRequestHeaders()
Get request headers
ZenodoRequest$getRequestHeaders()
getStatus()
Get request status
ZenodoRequest$getStatus()
getResponse()
Get request response
ZenodoRequest$getResponse()
getException()
Get request exception
ZenodoRequest$getException()
getResult()
Get request result
ZenodoRequest$getResult()
setResult()
Set request result
ZenodoRequest$setResult(result)
result
result to be set
clone()
The objects of this class are cloneable with this method.
ZenodoRequest$clone(deep = FALSE)
deep
Whether to make a deep clone.
Abstract class used internally by zen4R
Emmanuel Blondel <[email protected]>