In uva-bi-sdad/dc.vdoe.sol.scores: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(echo = TRUE)

Load dataset json template and dataset yml

dataset_metadata <- jsonlite::read_json("dataset-metadata.json")
yml_metadata <- rmarkdown::yaml_front_matter(here::here("data-raw/dataset_create.Rmd"))

Set title

dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[1]]$value <- yml_metadata$dataset$citation$title

Set description

dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[5]]$value[[1]]$dsDescriptionValue$value <- yml_metadata$dataset$citation$dsDescriptionValue

Set subject

dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[6]]$value[[1]] <- yml_metadata$dataset$citation$subject

Set production date

dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[2]]$value[[1]] <- yml_metadata$dataset$citation$productionDate

Set authors

## Remove existing author entries
dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[3]]$value <- NULL
## Add author entries
num_yml_authors <- length(yml_metadata$dataset$citation$author)
for (i in 1:num_yml_authors) {
  dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[3]]$value[[i]] <-
    list(
      authorName = list(
        value = yml_metadata$dataset$citation$author[[i]]$authorName,
        typeClass = "primitive",
        multiple = FALSE,
        typeName = "authorName"
      ),
      authorAffiliation = list(
        value = yml_metadata$dataset$citation$author[[i]]$authorAffiliation,
        typeClass = "primitive",
        multiple = FALSE,
        typeName = "authorAffiliation"
      )
    )
}

Set contact

## Remove existing contact entries
dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[4]]$value <- NULL
## Add contact entries
num_yml_contacts <- length(yml_metadata$dataset$citation$datasetContact)
for (i in 1:num_yml_contacts) {
  dataset_metadata$datasetVersion$metadataBlocks$citation$fields[[4]]$value[[i]] <-
    list(
      datasetContactName = list(
        value = yml_metadata$dataset$citation$datasetContact[[i]]$datasetContactName,
        typeClass = "primitive",
        multiple = FALSE,
        typeName = "datasetContactName"
      ),
      datasetContactEmail = list(
        value = yml_metadata$dataset$citation$datasetContact[[i]]$datasetContactEmail,
        typeClass = "primitive",
        multiple = FALSE,
        typeName = "datasetContactEmail"
      )
    )
}

Set geographic coverage

## Remove existing geographic coverage entries
dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[1]]$value <- NULL
## Add geographic coverage entries
nms <- names(yml_metadata$dataset$geospatial$geographicCoverage)

if ("country" %in% nms) {
  dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[1]]$value[[1]]$country <-
    list(
      typeName = "country",
      multiple = FALSE,
      typeClass = "controlledVocabulary",
      value = yml_metadata$dataset$geospatial$geographicCoverage$country
    )
}
if ("state" %in% nms) {
  dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[1]]$value[[1]]$state <- 
    list(
      typeName = "state",
      multiple = FALSE,
      typeClass = "primitive",
      value = yml_metadata$dataset$geospatial$geographicCoverage$state
  )
}
if ("city" %in% nms) {
  dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[1]]$value[[1]]$city <- 
    list(
      typeName = "city",
      multiple = FALSE,
      typeClass = "primitive",
      value = yml_metadata$dataset$geospatial$geographicCoverage$city
  )
}
if ("otherGeographicCoverage" %in% nms) {
  dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[1]]$value[[1]]$otherGeographicCoverage <- 
    list(
      typeName = "otherGeographicCoverage",
      multiple = FALSE,
      typeClass = "primitive",
      value = yml_metadata$dataset$geospatial$geographicCoverage$otherGeographicCoverage
  )
}

Set geographic unit

## Remove existing geographic unit entries
dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[2]]$value <- NULL
## Add geographic unit entries
geo_unit_l <- as.list(yml_metadata$dataset$geospatial$geographicUnit)
dataset_metadata$datasetVersion$metadataBlocks$geospatial$fields[[2]]$value <- geo_unit_l

Create or update dataverse dataset

if (exists("data/dataset_doi")) {
  dataset_doi <- readLines(here::here("data/dataset_doi"))[1]

  if (is.na(dataset_doi)) {
    ## Create dataset
    ds_info <- dataverse::create_dataset(
      dataverse = "biocomplexity",
      body = dataset_metadata,
      key = Sys.getenv("DATAVERSE_KEY"),
      server = Sys.getenv("DATAVERSE_SERVER")
    )

    ## Save dataset DOI to data
    writeLines(ds_info$data$persistentId, here::here("data/dataset_doi"))
  } else {
    dataverse::update_dataset(
      dataset = dataset_doi,
      body = dataset_metadata,
      key = Sys.getenv("DATAVERSE_KEY"),
      server = Sys.getenv("DATAVERSE_SERVER")
    )
  }
}