-
Notifications
You must be signed in to change notification settings - Fork 14
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
add config_metadata_dataverse.json workflow example
- Loading branch information
Showing
3 changed files
with
166 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| #handle_entities_zenodo | ||
| handle_entities_zenodo <- function(handler, source, config, handle = TRUE){ | ||
|
|
||
| if(!requireNamespace("zen4R", quietly = TRUE)){ | ||
| stop("The Dataverse handler requires the 'zen4R' package") | ||
| } | ||
|
|
||
| ZENODO <- config$software$input$zenodo | ||
| if(is.null(ZENODO)){ | ||
| stop("There is no Zenodo input software configured to handle entities from Dataverse") | ||
| } | ||
| ZENODO_CONFIG <- config$software$input$zenodo_config | ||
|
|
||
| results <- zen4R::getDepositions(q = source) | ||
| if(length(results)==0) return(list()) | ||
|
|
||
| entities <- lapply(1:length(results), function(i){ | ||
| result <- results[[i]] | ||
| config$logger.info(sprintf("Creating entity (%s out of %s) from Zenodo deposit/record with DOI '%s'", i, nrow(results), ds_doi)) | ||
|
|
||
| #create entity | ||
| entity <- geoflow::geoflow_entity$new() | ||
| #entity Identifier | ||
| entity$setIdentifier("doi", result$doi) | ||
| #semantic identifier | ||
| identifiers = result$metadata$related_identifiers[sapply(result$metadata$related_identifiers, function(x){x$scheme == "urn" && x$relation == "isIdenticalTo"})] | ||
| if(length(identifiers)>0){ | ||
| identifier = identifiers[[1]]$identifier | ||
| entity$setIdentifier("id", substr(identifier, 5,nchar(identifier))) | ||
| } | ||
|
|
||
| #entity Date | ||
| if(!is.null(result$created)) entity$addDate(dateType = "creation", date = str_to_posix(result$created)) | ||
| if(!is.null(result$modified)) entity$addDate(dateType = "lastUpdate", date = str_to_posix(result$modified)) | ||
| if(!is.null(result$metadata$publication_date)) entity$addDate(dateType = "publication", date = str_to_posix(result$metadata$publication_date)) | ||
| if(!is.null(result$metadata$embargo_date)) entity$addDate(dateType = "embargo", date = str_to_posix(result$metadata$embargo_date)) | ||
|
|
||
| #entity common metadata | ||
| #entity Type | ||
| entity$setType(key = "generic", result$metadata$upload_type) | ||
| #entity Title | ||
| entity$setTitle("title", result$metadata$title) | ||
| #entity Description | ||
| entity$setDescription("abstract", result$metadata$description) | ||
| #entity subjects (one single theme subject feed with keywords - freetext - and zenodo "subjects") | ||
| subj <- geoflow::geoflow_subject$new() | ||
| subj$setKey("theme") | ||
| subj$setName("General") | ||
| for(kwd in result$metadata$keywords){ | ||
| keyword = geoflow_keyword$new() | ||
| keyword$setName(kwd) | ||
| subj$addKeyword(keyword) | ||
| } | ||
| for(sbj in result$metadata$subjects){ | ||
| keyword = geoflow_keyword$new() | ||
| keyword$setName(sbj$term) | ||
| keyword$setUri(sbj$identifier) | ||
| subj$addKeyword(keyword) | ||
| } | ||
| entity$addSubject(subj) | ||
|
|
||
| #entity Contacts/roles | ||
| #pointOfContact | ||
| datasetContacts <- citation$fields[citation$fields$typeName == "datasetContact",]$value | ||
| for(datasetContact in datasetContacts){ | ||
| datasetContactNames <- unlist(strsplit(datasetContact$datasetContactName$value," ")) | ||
| poc <- geoflow::geoflow_contact$new() | ||
| poc$setIdentifier(key = "id", datasetContact$datasetContactEmail$value) | ||
| poc$setFirstName(datasetContactNames[1]) | ||
| poc$setLastName(datasetContactNames[2]) | ||
| poc$setRole("pointOfContact") | ||
| entity$addContact(poc) | ||
| #metadata | ||
| meta <- poc$clone() | ||
| meta$setRole("metadata") | ||
| entity$addContact(meta) | ||
| } | ||
| #creator(s) | ||
| creators <- result$metadata$creators | ||
| for(creator in creators){ | ||
| creatorNames <- unlist(strsplit(creator$name, ", ")) | ||
| creator_c <- geoflow::geoflow_contact$new() | ||
| creator_c$setFirstName(authorNames[2]) | ||
| creator_c$setLastName(authorNames[1]) | ||
| if(!is.null(creator$affiliation)) creator_c$setOrganizationName(creator$affiliation) | ||
| if(!is.null(creator$orcid)) creator_c$setIdentifier("orcid", creator$orcid) | ||
| if(!is.null(creator$gnd)) creator_c$setIdentifier("gnd", creator$gnd) | ||
| creator_c$setRole("creator") | ||
| entity$addContact(creator_c) | ||
| } | ||
| #contributor(s) | ||
| contribs <- result$metadata$contributors | ||
| for(contrib in contribs){ | ||
| contribNames <- unlist(strsplit(contrib$name, ", ")) | ||
| contrib_c <- geoflow::geoflow_contact$new() | ||
| contrib_c$setFirstName(contribNames[2]) | ||
| contrib_c$setLastName(contribNames[1]) | ||
| if(!is.null(contrib$affiliation)) contrib_c$setOrganizationName(contrib$affiliation) | ||
| if(!is.null(contrib$orcid)) contrib_c$setIdentifier("orcid", contrib$orcid) | ||
| if(!is.null(contrib$gnd)) contrib_c$setIdentifier("gnd", contrib$gnd) | ||
| contrib_c$setRole("contributor") | ||
| entity$addContact(contrib_c) | ||
| } | ||
| #relations | ||
| #references | ||
| if(length(result$metadata$references)>0){ | ||
| for(reference in result$metadata$references){ | ||
| ref_rel = geoflow_relation$new() | ||
| ref_rel$setKey("ref") | ||
| ref_rel$setName(reference) | ||
| entity$addRelation(ref_rel) | ||
| } | ||
| } | ||
| #grants | ||
| if(length(result$metadata$grants)>0){ | ||
| for(grant in result$metadata$grants){ | ||
| grant_rel = geoflow_relation$new() | ||
| grant_rel$setKey("grant") | ||
| grant_rel$setName(grant$id) | ||
| entity$addRelation(grant_rel) | ||
| } | ||
| } | ||
|
|
||
| #license / terms of use | ||
| rights <- geoflow::geoflow_right$new() | ||
| if(!is.null(result$metadata$license)) { | ||
| rights$setKey("license") | ||
| rights$setValues(ds$license) | ||
| entity$addRight(rights) | ||
| } | ||
| if(result$metadata$access_right != "open"){ | ||
| access_rights = geoflow::geoflow_right$new() | ||
| access_rights$setKey("accessRight") | ||
| access_rights$setValues(result$metadata$access_right) | ||
| entity$addRight(access_rights) | ||
| } | ||
|
|
||
| #entity SpatialCoverage | ||
| #entity TemporalCoverage | ||
|
|
||
| #data | ||
| if(length(result$files)>0){ | ||
| data <- geoflow::geoflow_data$new() | ||
| data$setAccess("zenodo") | ||
| data$source <- lapply(1:length(result$files), function(i){ | ||
| z_file <- result$files[[i]] | ||
| z_filename <- z_file$filename | ||
| attr(z_filename, "uri") <- result$doi | ||
| return(z_filename) | ||
| }) | ||
| data$upload <- TRUE | ||
| entity$setData(data) | ||
| } | ||
| return(entity) | ||
| }) | ||
|
|
||
|
|
||
| return(entities) | ||
| } |