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support #387 testing back Zenodo action based on new Zenodo API
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@eblondel
eblondel committed May 15, 2024
1 parent eaf54b8 commit 5c62e77
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2 changes: 2 additions & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,8 @@ Suggests:
d4storagehub4R,
rmarkdown,
dataverse
Remotes:
eblondel/zen4R
License: MIT + file LICENSE
URL: https://github.com/r-geoflow/geoflow
BugReports: https://github.com/r-geoflow/geoflow
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5 changes: 2 additions & 3 deletions doc/Summary_metadata.csv
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Expand Up @@ -22,9 +22,7 @@
"Date","edition",,,"x",,,,,,,,
"Date","embargo",,,,,,,,"x",,,
"Type","generic",,,"x",,,,,"x",,"x",
"Type","zenodoUploadType",,,,,,,,"x",,,
"Type","zenodoPublicationType",,,,,,,,"x",,,
"Type","zenodoImageType",,,,,,,,"x",,,
"Type","zenodoResourceType",,,,,,,,"x",,,
"Language",,,,"x",,,,,,"x",,
"SpatialCoverage","ewkt",,,"x",,,,"x",,,,
"SpatialCoverage","wkt",,,"x",,,,"x",,,,
Expand All @@ -48,6 +46,7 @@
"Rights","license","x","x","x",,,,,"x","x",,"x"
"Rights","accessRight",,,,,,,,"x",,,
"Rights","accessConditions",,,,,,,,"x",,,
"Rights","embargoReason",,,,,,,,"x",,,
"Provenance","statement","x","x","x",,,,,,,,
"Provenance","process","x","x","x",,,,,,,,
"Format","ressource",,,"x",,,,,,,,
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164 changes: 91 additions & 73 deletions inst/actions/zen4R_deposit_record.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ function(action, entity, config){
#if nothing is found, we use the default get depositions by identifier, used if no DOI is specified
#this approach is possible because the Zenodo record has a related identifier as URN, specified when
#creating the record. For existing record we also check the presence of the URN as related identifier
#e.g. urn:my-metadata-identifier
#e.g. my-metadata-identifier
deposits <- NULL
if(!is.null(entity$identifiers[["doi"]])){
#TODO review if getting deposit with concept DOI we don't inherit bucket link for doing file upload with new API
Expand All @@ -68,10 +68,9 @@ function(action, entity, config){
related_identifiers <- deposit$metadata$related_identifiers
if(!is.null(related_identifiers)){
for(related_identifier in related_identifiers){
if(startsWith(related_identifier$identifier,"urn")){
related_id <- unlist(strsplit(related_identifier$identifier, "urn:"))[2]
if(related_id == entity$identifiers[["id"]] &
related_identifier$relation == "isIdenticalTo"){
if(related_identifier$scheme == "urn"){
if(related_identifier$identifier == entity$identifiers[["id"]] &
related_identifier$relation_type$id == "isidenticalto"){
zenodo_metadata <<- deposit
break
}
Expand All @@ -86,23 +85,34 @@ function(action, entity, config){

#action to perform: create empty record or update existing record
update <- FALSE
record_state <- NULL
record_status <- NULL
if(is.null(zenodo_metadata)){
config$logger.info(sprintf("Zenodo: No existing Zenodo record with related identifier '%s'", paste0("urn:",entity$identifiers[["id"]])))
config$logger.info(sprintf("Zenodo: No existing Zenodo record with related identifier '%s'", entity$identifiers[["id"]]))
config$logger.info("Zenodo: creating a new deposit empty record")
zenodo_metadata <- ZENODO$createEmptyRecord()
reserveDOI = TRUE
if(!is.null(entity$identifiers[["doi"]])) if(regexpr("zenodo", entity$identifiers[["doi"]])<0){
reserveDOI = FALSE
}
zenodo_metadata <- ZENODO$createEmptyRecord(reserveDOI = reserveDOI)
if("bucket" %in% names(zenodo_metadata$links)){
entity$addResource("zenodo_bucket", zenodo_metadata$links$bucket) #attempt to keep bucket since zenodo seems not to retrieve always bucket link
}
zenodo_metadata$addRelatedIdentifier("isIdenticalTo", paste("urn", entity$identifiers[["id"]], sep=":"))
record_state <- zenodo_metadata$state
zenodo_metadata$addRelatedIdentifier(
identifier = entity$identifiers[["id"]],
scheme = "urn",
relation_type = "isidenticalto"
)
record_status <- zenodo_metadata$status
}else{
config$logger.info(sprintf("Zenodo: Existing record with related identifier '%s'", paste0("urn:",entity$identifiers[["id"]])))
config$logger.info(sprintf("Zenodo: Existing record with related identifier '%s' (URN scheme)", entity$identifiers[["id"]]))
update <- TRUE
record_state <- zenodo_metadata$state
record_status <- zenodo_metadata$status

#case of submitted records and 'edition' strategy, need to unlock record
if(zenodo_metadata$state == "done" && strategy == "edition"){
#case of published records and 'edition' strategy, need to unlock record
if(record_status == "published" &&
zenodo_metadata$is_published &&
!zenodo_metadata$is_draft &&
strategy == "edition"){
config$logger.info(sprintf("Zenodo: record '%s' already published. Need to unlock it for edition", zenodo_metadata$id))
unlocked_rec <- ZENODO$editRecord(zenodo_metadata$id)
if(is(unlocked_rec, "ZenodoRecord")){
Expand All @@ -116,7 +126,7 @@ function(action, entity, config){
}
}

doi <- zenodo_metadata$metadata$prereserve_doi$doi
doi <- zenodo_metadata$pids$doi$identifier

#if entity already comes with a DOI, we set it (this might be a preset DOI from Zenodo or elsewhere)
if(!is.null(entity$identifiers[["doi"]])){
Expand All @@ -138,20 +148,20 @@ function(action, entity, config){
}
#basic record description
zenodo_metadata$setTitle(entity$titles[["title"]])
if(!is.null(entity$titles[["alternative"]])){
zenodo_metadata$addAdditionalTitle(entity$titles[["alternative"]], type = "alternative-title")
}
zenodo_metadata$setDescription(entity$descriptions[["abstract"]])
zenodo_metadata$setNotes(entity$descriptions[["info"]])

if(!is.null(entity$descriptions[["info"]])){
zenodo_metadata$addAdditionalDescription(entity$descriptions[["info"]], type = "technical-info")
}

#keywords (free text) & subjects
zenodo_metadata$metadata$keywords <- list()
zenodo_metadata$metadata$subjects <- list()
for(subject in entity$subjects){
for(kwd in subject$keywords){
kwd_name <- kwd$name
kwd_uri <- kwd$uri
if(is.null(kwd_uri))
zenodo_metadata$addKeyword(kwd_name)
else
zenodo_metadata$addSubject(kwd_name, kwd_uri)
zenodo_metadata$addSubject(kwd$name)
}
}

Expand All @@ -164,20 +174,19 @@ function(action, entity, config){
if(!is.null(edition)){
zenodo_metadata$setVersion(edition)
}
#upload type
#TODO think on how to map upload types between Dublin core, ISO/OGC metadata, Zenodo
if(!is.null(entity$types[["generic"]])) zenodo_metadata$setUploadType(tolower(entity$types[["generic"]]))
if(!is.null(entity$types[["zenodoUploadType"]])) zenodo_metadata$setUploadType(entity$types[["zenodoUploadType"]])
#resource type
#TODO think on how to map resource types between Dublin core, ISO/OGC metadata, Zenodo
if(!is.null(entity$types[["generic"]])) zenodo_metadata$setResourceType(tolower(entity$types[["generic"]]))
if(!is.null(entity$types[["zenodoResourceType"]])) zenodo_metadata$setResourceType(entity$types[["zenodoResourceType"]])

#publication type
if(zenodo_metadata$metadata$upload_type == "publication"){
if(!is.null(entity$types[["zenodoPublicationType"]]))
zenodo_metadata$setPublicationType(entity$types[["zenodoPublicationType"]])
}
#image type
if(zenodo_metadata$metadata$upload_type == "image"){
if(!is.null(entity$types[["zenodoImageType"]]))
zenodo_metadata$setImageType(entity$types[["zenodoImageType"]])
#publisher
if(length(entity$contacts)>0){
publisher <- "Zenodo"
publishers <- entity$contacts[sapply(entity$contacts, function(x){x$role == "publisher"})]
if(length(publishers)>0){
publisher = publishers[[1]]$organizationName #we assume publisher is an organization
}
zenodo_metadata$setPublisher(publisher)
}

#creators
Expand All @@ -204,14 +213,14 @@ function(action, entity, config){
if(is.na(contact$firstName) || is.na(contact$lastName)){
zenodo_metadata$addCreator(
name = contact$organizationName,
affiliation = contact$organizationName,
affiliations = contact$organizationName,
orcid = orcid
)
}else{
zenodo_metadata$addCreator(
firstname = contact$firstName,
lastname = contact$lastName,
affiliation = contact$organizationName,
affiliations = contact$organizationName,
orcid = orcid
)
}
Expand All @@ -225,8 +234,8 @@ function(action, entity, config){
licenses <- entity$rights[sapply(entity$rights, function(x){tolower(x$key) == "license"})]
if(length(licenses)>0){
license <- licenses[[1]]$values[[1]]
accepted_licenses <- ZENODO$getLicenses()$id
if(license %in% accepted_licenses){
the_license <- ZENODO$getLicenseById(license)
if(!is.null(the_license)){
zenodo_metadata$setLicense(license, sandbox = ZENODO$sandbox)
}else{
config$logger.warn(sprintf("Zenodo :license specified (%s) in entity doesn't match Zenodo accepted list of licenses. license %s ignored!",
Expand All @@ -236,35 +245,44 @@ function(action, entity, config){
}

# AccessRight
# Access right with the following values: 'open','embargoed', 'restricted','closed'
zenodo_metadata$setAccessPolicyRecord("public") #always the case for Zenodo (at least for now)
# Access right with the following values: 'public','restricted'
if(length(entity$rights)>0){
accessRights <- entity$rights[sapply(entity$rights, function(x){tolower(x$key) == "accessright"})]
config$logger.info(sprintf("accessRight: '%s'", accessRights))
if(length(accessRights)>0){
accessRight <- accessRights[[1]]$values[[1]]
config$logger.info(sprintf("accessRight Value: '%s'", accessRight))
zenodo_metadata$setAccessRight(accessRight)
if ("embargoed" %in% accessRight) {
config$logger.info(sprintf("Embargoed! Looking for embargoed date..."))
embargoDates <- entity$dates[sapply(entity$dates, function(date){date$key == "embargo"})]
embargoDate <- if(length(embargoDates)>0) embargoDates[[1]]$value else config$logger.error(sprintf("Zenodo: 'embargo' not set in entity$dates whereas 'embargoed' is set in entity$rights. Please check your entities !"))
zenodo_metadata$setEmbargoDate(embargoDate)
zenodo_metadata$setAccessPolicyFiles(accessRight)
if(accessRight == "restricted"){
#manage embargo
embargoDates <- entity$dates[sapply(entity$dates, function(date){date$key == "embargo"})]
if(length(embargoDates)>0){
embargoDate = embargoDates[[1]]$value
config$logger.info(sprintf("Setting embargo date '%s'", embargoDate))
embargoReason = ""
embargoReasons = entity$rights[sapply(entity$rights, function(x){tolower(x$key) == "embargoreason"})]
if(length(embargoReasons)>0){
embargoReason = embargoReasons[[1]]$values[[1]]
config$logger.info(sprintf("Setting embargo reason: %s", embargoReason))
}
else if ("restricted" %in% accessRight) {
config$logger.info(sprintf("Restricted! :/ :/ Looking for accessConditions..."))
accessConditions <- entity$rights[sapply(entity$rights, function(x){tolower(x$key) == "accessconditions"})][[1]]$values[[1]]
zenodo_metadata$setAccessConditions(accessConditions)
zenodo_metadata$setAccessPolicyEmbargo(active = TRUE, until = as.Date(embargoDate), reason = embargoReason)
}
#access conditions
#TODO to review if available through new Zeonod API
# accessConditions <- entity$rights[sapply(entity$rights, function(x){tolower(x$key) == "accessconditions"})]
# if(length(accessConditions)>0){
# zenodo_metadata$setAccessConditions(accessConditions[[1]]$values[[1]])
# }
}
}else{
config$logger.info(sprintf("Zenodo: accessRight specified in entity not available. accessRight will be set to public!"))
zenodo_metadata$setAccessPolicyFiles("public")
}
else{
config$logger.info(sprintf("Zenodo: accessRight specified in entity not available. accessRight will be set to open!"))
zenodo_metadata$setAccessRight("open")
}
}else{
config$logger.info(sprintf("Zenodo: Rights is empty. accessRight will be set to public!"))
zenodo_metadata$setAccessPolicyFiles("public")
}
else{
config$logger.info(sprintf("Zenodo: Rights is empty. accessRight will be set to open!"))
zenodo_metadata$setAccessRight("open")
}

#references
if(length(entity$relations)>0){
Expand All @@ -290,17 +308,18 @@ function(action, entity, config){
}

#communities
if(length(communities)>0){
zenodo_metadata$metadata$communities <- list()
for(community in communities) if(!is.na(community)) zenodo_metadata$addCommunity(community, sandbox = ZENODO$sandbox)
}
#TODO to analyze if this can be done with new Zenodo API
# if(length(communities)>0){
# zenodo_metadata$metadata$communities <- list()
# for(community in communities) if(!is.na(community)) zenodo_metadata$addCommunity(community, sandbox = ZENODO$sandbox)
# }
}else{
config$logger.info("Skipping update of Zenodo record metadata (option 'update_metadata' FALSE)")
}

#file uploads (for new or edited records)
#note: for new versions this is managed directly with ZENODO$depositRecordVersion
if(depositWithFiles & (!update | (update & update_files)) & record_state == "unsubmitted"){
if(depositWithFiles & (!update | (update & update_files)) & record_status == "draft" & zenodo_metadata$is_draft){
if(deleteOldFiles & !skipDataDownload){
config$logger.info("Zenodo: deleting old files...")
zen_files <- ZENODO$getFiles(zenodo_metadata$id)
Expand Down Expand Up @@ -375,10 +394,9 @@ function(action, entity, config){
}
}
config$logger.info(sprintf("Deposit record with id '%s' - publish = %s", zenodo_metadata$id, tolower(as.character(publish))))
out <- switch(record_state,
"unsubmitted" = ZENODO$depositRecord(zenodo_metadata, publish = publish),
"inprogress" = ZENODO$depositRecord(zenodo_metadata, publish = publish),
"done" = {
out <- switch(record_status,
"draft" = ZENODO$depositRecord(zenodo_metadata, publish = publish),
"published" = {
switch(strategy,
"edition" = ZENODO$depositRecord(zenodo_metadata, publish = publish),
"newversion" = {
Expand Down Expand Up @@ -417,21 +435,21 @@ function(action, entity, config){
}

#we set the (prereserved) doi to the entity in question
doi_to_save <- try(out$metadata$prereserve_doi$doi, silent = TRUE)
if(is(doi_to_save, "try-error")) doi_to_save <- entity$identifiers[["doi"]]
config$logger.info(sprintf("Setting DOI '%s' to save and export for record",out$metadata$prereserve_doi$doi))
doi_to_save <- out$pids$doi$identifier
if(!is.null(entity$identifiers[["doi"]])) doi_to_save <- entity$identifiers[["doi"]]
config$logger.info(sprintf("Setting DOI '%s' to save and export for record",doi_to_save))
for(i in 1:length(config$metadata$content$entities)){
ent <- config$metadata$content$entities[[i]]
if(ent$identifiers[["id"]]==entity$identifiers[["id"]]){
if(regexpr("zenodo", doi)>0){
config$metadata$content$entities[[i]]$identifiers[["zenodo_doi_to_save"]] <- out$metadata$prereserve_doi$doi
config$metadata$content$entities[[i]]$identifiers[["zenodo_doi_to_save"]] <- out$getDOI()
config$metadata$content$entities[[i]]$identifiers[["zenodo_conceptdoi_to_save"]] <- out$getConceptDOI()
config$metadata$content$entities[[i]]$setStatus("zenodo", ifelse(publish, "published", "draft"))
}
break;
}
}
entity$identifiers[["zenodo_doi_to_save"]] <- out$metadata$prereserve_doi$doi
entity$identifiers[["zenodo_doi_to_save"]] <- out$getDOI()
entity$identifiers[["zenodo_conceptdoi_to_save"]] <- out$getConceptDOI()
entity$setStatus("zenodo", ifelse(publish, "published", "draft"))

Expand Down
5 changes: 4 additions & 1 deletion inst/extdata/workflows/config_metadata_gsheets_zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,10 @@
"logos": [
"https://via.placeholder.com/300x150.png/09f/fff?text=geoflow"
],
"mode": "entity"
"mode": "entity",
"options": {
"skipEnrichWithDatatypes": true
}
},
"metadata": {
"entities": [
Expand Down
1 change: 1 addition & 0 deletions tests/testthat/test_config_metadata_gsheets_zenodo.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ test_that("debug",{
expect_equal(names(DEBUG), c("config", "entity"))
expect_is(DEBUG$config, "list")
expect_is(DEBUG$entity, "geoflow_entity")
closeWorkflow(DEBUG$config)
})

#execute
Expand Down

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