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support #146
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@eblondel
eblondel committed Mar 18, 2024
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263 changes: 178 additions & 85 deletions R/ZenodoRecord.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,12 @@
ZenodoRecord <- R6Class("ZenodoRecord",
inherit = zen4RLogger,
private = list(
allowed_role_types = c("contactperson", "datacollector", "datacurator", "datamanager",
"distributor", "editor", "funder", "hostinginstitution", "producer",
"projectleader", "projectmanager", "projectmember", "registrationagency",
"registrationauthority", "relatedperson", "researcher", "researchgroup",
"rightsholder", "supervisor", "sponsor", "workpackageleader",
"other"),
allowed_relations = c("isCitedBy", "cites", "isSupplementTo", "isSupplementedBy", "isContinuedBy", "continues",
"isDescribedBy", "describes", "hasMetadata", "isMetadataFor", "isNewVersionOf", "isPreviousVersionOf",
"isPartOf", "hasPart", "isReferencedBy", "references", "isDocumentedBy", "documents", "isCompiledBy",
Expand Down Expand Up @@ -321,151 +327,238 @@ ZenodoRecord <- R6Class("ZenodoRecord",
self$metadata$access_conditions <- accessConditions
},

#' @description Add a creator for the record. One approach is to use the \code{firstname} and
#' \code{lastname} arguments, that by default will be concatenated for Zenodo as
#' \code{lastname, firstname}. For more flexibility over this, the \code{name}
#' argument can be directly used.
#' @param firstname creator first name
#' @param lastname creator last name
#' @param name creator name
#' @param affiliation creator affiliation (optional)
#' @param orcid creator ORCID (optional)
#' @param gnd creator GND (optional)
# PERSON OR ORG
#---------------------------------------------------------------------------

#' @description Add a person or organization for the record. For persons, the approach is to use the \code{firstname} and
#' \code{lastname} arguments, that by default will be concatenated for Zenodo as \code{lastname, firstname}.
#' For organizations, use the \code{name} argument.
#' @param firstname person first name
#' @param lastname person last name
#' @param name organization name
#' @param orcid person or organization ORCID (optional)
#' @param gnd person or organization GND (optional)
#' @param isni person or organization ISNI (optional)
#' @param ror person or organization ROR (optional)
#' @param 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
#' @param affiliations person or organization affiliations (optional)
#' @param sandbox Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is \code{FALSE}
#' @param type type of person or org (creators/contributors)
#' @return \code{TRUE} if added, \code{FALSE} otherwise
addCreator = function(firstname, lastname, name = paste(lastname, firstname, sep = ", "),
affiliation = NULL, orcid = NULL, gnd = NULL){
creator <- list(name = name)
if(!is.null(affiliation)) creator <- c(creator, affiliation = affiliation)
if(!is.null(orcid)) creator <- c(creator, orcid = orcid)
if(!is.null(gnd)) creator <- c(creator, gnd = gnd)
if(is.null(self$metadata$creators)) self$metadata$creators <- list()
self$metadata$creators[[length(self$metadata$creators)+1]] <- creator
},

#' @description Removes a creator by a property. The \code{by} parameter should be the name
#' of the creator property ('name' - in the form 'lastname, firstname', 'affiliation',
#' 'orcid' or 'gnd').
#' @param by property used as criterion to remove the creator
#' @param property property value used to remove the creator
#'
#' @note Internal method. Prefer using \code{addCreator} or \code{addContributor}
#'
addPersonOrOrg = function(firstname = NULL, lastname = NULL, name = paste(lastname, firstname, sep = ", "),
orcid = NULL, gnd = NULL, isni = NULL, ror = NULL, role = NULL, affiliations = NULL, sandbox = FALSE,
type){
personOrOrg <- list(
person_or_org = list(
type = if(!is.null(firstname)&&!is.null(lastname)) "personal" else "organizational",
given_name = firstname,
family_name = lastname,
name = name,
identifiers = list()
),
role = NULL,
affiliations = list()
)
#identifiers
if(!is.null(orcid)) personOrOrg$person_or_org$identifiers[[length(personOrOrg$person_or_org$identifiers)+1]] = list(scheme = "orcid", identifier = orcid)
if(!is.null(gnd)) personOrOrg$person_or_org$identifiers[[length(personOrOrg$person_or_org$identifiers)+1]] = list(scheme = "gnd", identifier = gnd)
if(!is.null(isni)) personOrOrg$person_or_org$identifiers[[length(personOrOrg$person_or_org$identifiers)+1]] = list(scheme = "isni", identifier = isni)
if(!is.null(ror)) personOrOrg$person_or_org$identifiers[[length(personOrOrg$person_or_org$identifiers)+1]] = list(scheme = "ror", identifier = ror)

#role
if(!is.null(role)){
if(!(role %in% private$allowed_role_types)){
stop(sprintf("The role type should be one value among values [%s]",
paste(private$allowed_role_types, collapse=",")))
}
personOrOrg$role = role
}

#affiliations
if(!is.null(affiliations)) if(personOrOrg$person_or_org$type == "personal"){
zen = ZenodoManager$new(sandbox = sandbox)
affs = lapply(affiliations, function(affiliation){
zen_affiliation <- zen$getAffiliationById(affiliation)
if(is.null(zen_affiliation)){
warnMsg <- sprintf("Affiliation with id '%s' doesn't exist in Zenodo", affiliation)
self$WARN(errorMsg)
return(NULL)
}
return(list(id = zen_affiliation$id))
})
affs = affs[!sapply(affs,is.null)]
personOrOrg$affiliations = affs
}

if(is.null(self$metadata[[type]])) self$metadata[[type]] <- list()
self$metadata[[type]][[length(self$metadata[[type]])+1]] <- personOrOrg
},

#' @description Removes a person or organization by a property. The \code{by} parameter should be the name
#' of the person or organization property ('name', 'affiliation','orcid','gnd','isni','ror').
#' @param by property used as criterion to remove the person or organization
#' @param property property value used to remove the person or organization
#' @param type type of person or org (creators / contributors)
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeCreator = function(by,property){
#'
#' @note Internal method. Prefer using \code{removeCreator} or \code{removeContributor}
#'
removePersonOrOrg = function(by, property, type){
removed <- FALSE
for(i in 1:length(self$metadata$creators)){
creator <- self$metadata$creators[[i]]
if(creator[[by]]==property){
self$metadata$creators[[i]] <- NULL
for(i in 1:length(self$metadata[[type]])){
personOrOrg <- self$metadata[[type]][[i]]
personOrOrg_map = personOrOrg$person_or_org[names(personOrOrg$person_or_org)!="identifiers"]
if(!is.null(personOrOrg$person_or_org$identifiers)) for(identifier in personOrOrg$person_or_org$identifiers){
personOrOrg_map = c(personOrOrg_map, scheme = identifier$identifier)
names(personOrOrg_map)[names(personOrOrg_map)=="scheme"] = identifier$scheme
}
if(personOrOrg_map[[by]]==property){
self$metadata[[type]][[i]] <- NULL
removed <- TRUE
}
}
return(removed)
},

# CREATORS
#---------------------------------------------------------------------------

#' @description Add a creator for the record. For persons, the approach is to use the \code{firstname} and
#' \code{lastname} arguments, that by default will be concatenated for Zenodo as \code{lastname, firstname}.
#' For organizations, use the \code{name} argument.
#' @param firstname person first name
#' @param lastname person last name
#' @param name organization name
#' @param orcid creator ORCID (optional)
#' @param gnd creator GND (optional)
#' @param isni creator ISNI (optional)
#' @param ror creator ROR (optional)
#' @param 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
#' @param affiliations creator affiliations (optional)
#' @param sandbox Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is \code{FALSE}
#' @return \code{TRUE} if added, \code{FALSE} otherwise
addCreator = function(firstname = NULL, lastname = NULL, name = paste(lastname, firstname, sep = ", "),
orcid = NULL, gnd = NULL, isni = NULL, ror = NULL, role = NULL, affiliations = NULL, sandbox = FALSE){
self$addPersonOrOrg(firstname = firstname, lastname = lastname, name = name,
orcid = orcid, gnd = gnd, isni = isni, ror = ror, role = role, affiliations = affiliations, sandbox = sandbox,
type = "creators")
},

#' @description Removes a creator by name.
#' @param name creator name
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeCreatorByName = function(name){
return(self$removeCreator(by = "name", name))
return(self$removePersonOrOrg(by = "name", name, type = "creators"))
},

#' @description Removes a creator by affiliation.
#' @param affiliation creator affiliation
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeCreatorByAffiliation = function(affiliation){
return(self$removeCreator(by = "affiliation", affiliation))
return(self$removePersonOrOrg(by = "affiliation", affiliation, type = "creators"))
},

#' @description Removes a creator by ORCID.
#' @param orcid creator ORCID
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeCreatorByORCID = function(orcid){
return(self$removeCreator(by = "orcid", orcid))
return(self$removePersonOrOrg(by = "orcid", orcid, type = "creators"))
},

#' @description Removes a creator by GND.
#' @param gnd creator GND
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeCreatorByGND = function(gnd){
return(self$removeCreator(by = "gnd", gnd))
return(self$removePersonOrOrg(by = "gnd", gnd, type = "creators"))
},

#' @description Add a contributor for the record. One approach is to use the \code{firstname} and
#' \code{lastname} arguments, that by default will be concatenated for Zenodo as
#' \code{lastname, firstname}. For more flexibility over this, the \code{name}
#' argument can be directly used.
#' @param firstname contributor first name
#' @param lastname contributor last name
#' @param name contributor name
#' @param type contributor type, among values: ContactPerson,
#' DataCollector, DataCurator, DataManager, Distributor, Editor, Funder, HostingInstitution,
#' Producer, ProjectLeader, ProjectManager, ProjectMember, RegistrationAgency, RegistrationAuthority,
#' RelatedPerson, Researcher, ResearchGroup, RightsHolder, Supervisor, Sponsor, WorkPackageLeader, Other.
#' @param affiliation contributor affiliation (optional)
#' @param orcid contributor orcid (optional)
#' @param gnd contributor gnd (optional)
#' @return \code{TRUE} if added, \code{FALSE} otherwise
addContributor = function(firstname, lastname, name = paste(lastname, firstname, sep = ", "),
type, affiliation = NULL, orcid = NULL, gnd = NULL){
allowedTypes <- c("ContactPerson", "DataCollector", "DataCurator", "DataManager","Distributor",
"Editor", "Funder", "HostingInstitution", "Producer", "ProjectLeader", "ProjectManager",
"ProjectMember", "RegistrationAgency", "RegistrationAuthority", "RelatedPerson",
"Researcher", "ResearchGroup", "RightsHolder","Supervisor", "Sponsor", "WorkPackageLeader", "Other")
if(!(type %in% allowedTypes)){
stop(sprintf("The contributor type should be one value among values [%s]",
paste(allowedTypes, collapse=",")))
}
contributor <- list(name = name, type = type)
if(!is.null(affiliation)) contributor <- c(contributor, affiliation = affiliation)
if(!is.null(orcid)) contributor <- c(contributor, orcid = orcid)
if(!is.null(gnd)) contributor <- c(contributor, gnd = gnd)
if(is.null(self$metadata$contributors)) self$metadata$contributors <- list()
self$metadata$contributors[[length(self$metadata$contributors)+1]] <- contributor
#' @description Removes a creator by ISNI.
#' @param isni creator ISNI
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeCreatorByISNI = function(isni){
return(self$removePersonOrOrg(by = "isni", isni, type = "creators"))
},

#' @description Removes a contributor by a property. The \code{by} parameter should be the name
#' of the contributor property ('name' - in the form 'lastname, firstname', 'affiliation',
#' 'orcid' or 'gnd').
#' \code{FALSE} otherwise.
#' @param by property used as criterion to remove the contributor
#' @param property property value used to remove the contributor
#' @description Removes a creator by ROR.
#' @param ror creator ROR
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributor = function(by,property){
removed <- FALSE
for(i in 1:length(self$metadata$contributors)){
contributor <- self$metadata$contributors[[i]]
if(contributor[[by]]==property){
self$metadata$contributors[[i]] <- NULL
removed <- TRUE
}
}
return(removed)
removeCreatorByROR = function(ror){
return(self$removePersonOrOrg(by = "ror", ror, type = "creators"))
},

# CONTRIBUTORS
#---------------------------------------------------------------------------

#' @description Add a contributor for the record. For persons, the approach is to use the \code{firstname} and
#' \code{lastname} arguments, that by default will be concatenated for Zenodo as \code{lastname, firstname}.
#' For organizations, use the \code{name} argument.
#' @param firstname person first name
#' @param lastname person last name
#' @param name organization name
#' @param orcid contributor ORCID (optional)
#' @param gnd contributor GND (optional)
#' @param isni contributor ISNI (optional)
#' @param ror contributor ROR (optional)
#' @param 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
#' @param affiliations contributor affiliations (optional)
#' @param sandbox Use the Zenodo sandbox infrastructure as basis to control available affiliations. Default is \code{FALSE}
#' @return \code{TRUE} if added, \code{FALSE} otherwise
addContributor = function(firstname = NULL, lastname = NULL, name = paste(lastname, firstname, sep = ", "),
orcid = NULL, gnd = NULL, isni = NULL, ror = NULL, role = NULL, affiliations = NULL, sandbox = FALSE){
self$addPersonOrOrg(firstname = firstname, lastname = lastname, name = name,
orcid = orcid, gnd = gnd, isni = isni, ror = ror, role = role, affiliations = affiliations, sandbox = sandbox,
type = "contributors")
},

#' @description Removes a contributor by name.
#' @param name contributor name
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributorByName = function(name){
return(self$removeContributor(by = "name", name))
return(self$removePersonOrOrg(by = "name", name, type = "contributors"))
},

#' @description Removes a contributor by affiliation.
#' @param affiliation contributor affiliation
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributorByAffiliation = function(affiliation){
return(self$removeContributor(by = "affiliation", affiliation))
return(self$removePersonOrOrg(by = "affiliation", affiliation, type = "contributors"))
},

#' @description Removes a contributor by ORCID.
#' @param orcid contributor ORCID
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributorByORCID = function(orcid){
return(self$removeContributor(by = "orcid", orcid))
return(self$removePersonOrOrg(by = "orcid", orcid, type = "contributors"))
},

#' @description Removes a contributor by GND.
#' @param gnd contributor GND
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributorByGND = function(gnd){
return(self$removeContributor(by = "gnd", gnd))
return(self$removePersonOrOrg(by = "gnd", gnd, type = "contributors"))
},

#' @description Removes a contributor by ISNI.
#' @param isni contributor ISNI
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributorByISNI = function(isni){
return(self$removePersonOrOrg(by = "isni", isni, type = "contributors"))
},

#' @description Removes a contributor by ROR.
#' @param ror contributor ROR
#' @return \code{TRUE} if removed, \code{FALSE} otherwise
removeContributorByROR = function(ror){
return(self$removePersonOrOrg(by = "ror", ror, type = "contributors"))
},

#' @description Set license. The license should be set with the Zenodo id of the license. If not
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