provenance, RDF

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dataset
 Title: Create Data Frames that are Easier to Exchange and Reuse
-Version: 0.3.4
-Date: 2024-12-23
+Version: 0.3.4001
+Date: 2024-12-24
 DOI: 10.32614/CRAN.package.dataset
 Language: en-US
 Authors@R: 
@@ -33,13 +33,15 @@ Imports:
     labelled,
     methods,
     pillar,
+    RefManageR,
     rlang,
     tibble,
     utils,
     vctrs (>= 0.5.2)
 RoxygenNote: 7.3.2
 Suggests: 
     knitr,
+    rdflib,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0)

NAMESPACE

@@ -60,6 +60,7 @@ export(dataset_title)
 export(dataset_to_triples)
 export(defined)
 export(definition_attribute)
+export(describe)
 export(description)
 export(dublincore)
 export(geolocation)
@@ -97,6 +98,7 @@ export(xsd_convert)
 import(methods)
 import(pillar)
 import(vctrs)
+importFrom(RefManageR,BibEntry)
 importFrom(assertthat,assert_that)
 importFrom(cli,cat_line)
 importFrom(haven,as_factor)

R/agent.R

@@ -0,0 +1,121 @@
+
+
+#' @keywords internal
+`agent<-` <- function(x,  value) {
+
+  return_type <- NULL
+
+  if ("dataset_bibentry" %in% names(attributes(x))) {
+    dataset_bibentry <- get_bibentry(x)
+    return_type <- "dataset"
+  } else if (inherits(x, "dublincore")) {
+    dataset_bibentry  <- x
+    return_type <- "dublincore"
+  } else if (inherits(x, "datacite")) {
+    dataset_bibentry <- x
+    return_type <- "datacite"
+  } else {
+    stop("Error: agent(x)<- x must be a dataset_df, a dublincore or a datacite object.")
+  }
+
+  assertthat::assert_that(all(inherits(value, "person")),
+                                   msg = "Error: agent(x) <- value: value must be a vector of utils::persons.")
+
+  creators   <- ifelse(is.null(dataset_bibentry$author), ":tba", dataset_bibentry$author)
+  publishers <- ifelse(is.null(dataset_bibentry$publisher), ":unas", dataset_bibentry$publisher)
+  contributors <- ifelse(is.null(dataset_bibentry$contributor), ":unas", dataset_bibentry$contributor)
+
+  get_creator <- function(x) {
+    if (!is.null(x$role)) ifelse("cre" %in% x$role, TRUE, FALSE) else FALSE
+  }
+
+  get_author <- function(x) {
+    if (!is.null(x$role)) ifelse("aut" %in% x$role, TRUE, FALSE) else FALSE
+  }
+
+  get_publisher <- function(x) {
+    if (!is.null(x$role)) ifelse("pbl" %in% x$role, TRUE, FALSE) else FALSE
+  }
+
+  is_creator <- vapply(value, get_creator, logical(1))
+  is_author  <- vapply(value, get_creator, logical(1))
+  is_publisher <- vapply(value, get_publisher, logical(1))
+
+
+  new_creators     <- c(value[is_creator], value[is_author[!is_creator]])
+  new_publishers   <- c(value[is_publisher])
+  new_contributors <- c(value[!value %in% c(creators, publishers)])
+
+  creators     <- ifelse(length(new_creators)>0, new_creators, creators)
+  publishers   <- ifelse(length(new_publishers)>0, new_publishers, publishers)
+  contributors <- ifelse(length(new_creators)>0, new_contributors, contributors)
+
+  dataset_bibentry$author      <- ifelse(length(new_creators)>0, new_creators, dataset_bibentry[[1]]$author)
+  dataset_bibentry$contributor <- contributors
+  dataset_bibentry$publisher   <- publishers
+
+  if ( return_type %in% c("datacite", "dublincore")) {
+    dataset_bibentry
+  } else if ( return_type == "dataset") {
+    attr(x, "dataset_bibentry") <- dataset_bibentry
+    invisible(x)
+  }
+}
+
+#' @keywords internal
+agent <- function(x) {
+
+  if(inherits(x, "dataset_df")) {
+    dataset_bibentry <- get_bibentry(x)
+  } else if(inherits(x, "datacite")) {
+       dataset_bibentry <- x
+       creators   <- ifelse(is.null(dataset_bibentry$author), ":tba", dataset_bibentry$author)
+       publishers <- ifelse(is.null(dataset_bibentry$publisher), ":unas", dataset_bibentry$publisher)
+       contributors <- ifelse(is.null(dataset_bibentry$contributor), ":unas", dataset_bibentry$contributor)
+
+  } else if (inherits(x, "dublincore")) {
+    dataset_bibentry <- x
+    creators   <- ifelse(is.null(dataset_bibentry$author), ":tba", dataset_bibentry$author)
+    publishers <- ifelse(is.null(dataset_bibentry$publisher), ":unas", dataset_bibentry$publisher)
+    contributors <- ifelse(is.null(dataset_bibentry$contributor), ":unas", dataset_bibentry$contributor)
+    } else if ( all(inherits(x, "person"))) {
+      contributors <- x
+      publishers <- x
+      creators <- x
+    return_type <- "persons_vector"
+  } else {
+    stop("Error: agent(x)<- x must be a dataset_df, a vector of persons, a dublincore or datacite object.")
+  }
+
+  get_creator <- function(x) {
+    if (!is.null(x$role)) ifelse("cre" %in% x$role, TRUE, FALSE) else FALSE
+  }
+
+  get_author <- function(x) {
+    if (!is.null(x$role)) ifelse("aut" %in% x$role, TRUE, FALSE) else FALSE
+  }
+
+  get_publisher <- function(x) {
+    if (!is.null(x$role)) ifelse("pbl" %in% x$role, TRUE, FALSE) else FALSE
+  }
+
+  is_creator <- vapply(creators, get_creator, logical(1))
+  is_author  <- vapply(creators, get_creator, logical(1))
+  is_publisher  <- vapply(creators, get_publisher, logical(1))
+
+  new_creators     <- c(creators[is_creator], creators[is_author[!is_creator]])
+  new_contributors <- c(contributors[!contributors %in% c(creators, publishers)])
+  new_publishers <- publishers[is_publisher]
+
+  creators     <- if(length(new_creators)>0)   creators <- new_creators
+  contributors <- if(length(new_contributors)>0)   contributors <- new_contributors
+  publishers  <-  if(length(new_publishers)>0) publishers <- new_publishers
+
+
+
+  list(creators = creators,
+       contributors = contributors,
+       publishers = publishers)
+
+}
+

R/as_dublincore.R

@@ -0,0 +1,164 @@
+#' @rdname dublincore
+#' @param type For \code{as_dublincore}, any of \code{"bibentry", "dataset_df", "list", "ntriples"}.
+#' @param ... Optional parameters to add to a \code{dublincore} object.
+#' \code{author=person("Jane", "Doe")} adds an author to the citation
+#' object if \code{type="dataset"}.
+#' @export
+as_dublincore <- function(x, type = "bibentry", ...) {
+
+  citation_author <- person(NULL, NULL)
+
+  is_person <- function(p) ifelse (inherits(p, "person"), TRUE, FALSE)
+
+  arguments <- list(...)
+
+  if (!is.null(arguments$author)) {
+    if ( is_person(arguments$author))  {
+      citation_author <- arguments$author
+    } else {
+      stop("as_dublincore(x, ..., author = ): author must be created with utils::person().")
+    }
+  }
+
+  if (! type %in% c("bibentry", "list", "dataset_df", "ntriples")) {
+    warning_message <- "as_dublincore(ds, type=...) type cannot be "
+    warning(warning_message, type, ". Reverting to 'bibentry'.")
+    type <- 'bibentry'
+  }
+
+  dataset_bibentry     <- get_bibentry(x)
+  dataset_title   <- dataset_bibentry$title
+  dataset_creator <- dataset_bibentry$author
+
+  if (! is_person(dataset_creator)) {
+    stop('attr(x, "dataset_bibentry")$author is not a person object.')
+  }
+
+  if (!is.null(dataset_bibentry$year)) {
+    if(is.null(dataset_bibentry$dataset_date)) {
+      dataset_date <- as.character(dataset_bibentry$year)
+    } else {
+      dataset_date <- as.character(dataset_bibentry$date)
+    }
+  } else if (!is.null(dataset_bibentry$date)) {
+    dataset_date <- dataset_bibentry$date
+  } else {
+    dataset_date <- ":tba"
+  }
+
+  dataset_relation <- ifelse (is.null(dataset_bibentry$relation), ":unas", as.character(dataset_bibentry$relation))
+  dataset_identifier <- ifelse (is.null(dataset_bibentry$identifier), ":tba", as.character(dataset_bibentry$identifier))
+  dataset_version <- ifelse (is.null(dataset_bibentry$version), ":unas", as.character(dataset_bibentry$version))
+  dataset_description <- ifelse (is.null(dataset_bibentry$description), ":unas", as.character(dataset_bibentry$description))
+  dataset_language <- ifelse (is.null(dataset_bibentry$language), ":unas", as.character(dataset_bibentry$language))
+  dataset_format <- ifelse (is.null(dataset_bibentry$format), ":tba", as.character(dataset_bibentry$format))
+  dataset_rights <- ifelse (is.null(dataset_bibentry$rights), ":tba", as.character(dataset_bibentry$rights))
+  dataset_coverage  <- ifelse (is.null(dataset_bibentry$coverage), ":unas", as.character(dataset_bibentry$coverage))
+  datasource <- ifelse (is.null(dataset_bibentry$datasource), ":unas", as.character(dataset_bibentry$datasource))
+  dataset_contributor <- ifelse (is.null(dataset_bibentry$contributor), "", as.character(dataset_bibentry$contributor))
+  dataset_subject   <- ifelse (is.null(dataset_bibentry$subject), "", as.character(dataset_bibentry$subject))
+  dataset_publisher <- ifelse (is.null(dataset_bibentry$publisher), "", as.character(dataset_bibentry$publisher))
+
+  properties <- c(length(dataset_title),
+                  length(as.character(dataset_creator)),
+                  length(dataset_identifier),
+                  length(dataset_publisher),
+                  length(dataset_subject),
+                  length("DCMITYPE:Dataset"),
+                  length(dataset_contributor),
+                  length(dataset_date),
+                  length(dataset_language),
+                  length(dataset_relation),
+                  length(dataset_format),
+                  length(dataset_rights),
+                  length(datasource),
+                  length(dataset_description),
+                  length(dataset_coverage)
+  )
+
+  if (type == "bibentry") {
+    new_dublincore(title       = dataset_title,
+                   creator     = dataset_creator,
+                   identifier  = dataset_identifier,
+                   publisher   = dataset_publisher,
+                   subject     = dataset_subject,
+                   type = "DCMITYPE:Dataset",
+                   contributor = dataset_contributor,
+                   publication_date = dataset_date,
+                   language    = dataset_language,
+                   relation    = dataset_relation,
+                   format      = dataset_format,
+                   rights      = dataset_rights,
+                   datasource  = datasource,
+                   description = dataset_description,
+                   coverage    = dataset_coverage)
+  } else if (type== "list") {
+    if (dataset_contributor == "") dataset_contributor <- NULL
+    if (dataset_subject == "") dataset_subject <- NULL
+
+    list(title=dataset_title,
+         creator=dataset_creator,
+         identifier = dataset_identifier,
+         publisher = dataset_publisher,
+         subject = dataset_subject,
+         type = "DCMITYPE:Dataset",
+         contributor = dataset_contributor,
+         date = dataset_date,
+         language = dataset_language,
+         relation = dataset_relation,
+         format = dataset_format,
+         rights = dataset_rights,
+         datasource = datasource,
+         description = dataset_description,
+         coverage = dataset_coverage)
+  } else if ( type  == "dataset_df") {
+    assertthat::assert_that(
+      all(properties)==1, msg= "In as_dublincore() not all properties have a length 1 to export into datataset (data.frame)."
+    )
+    dataset_df(
+      data.frame(title = dataset_title,
+                 creator = as.character(dataset_creator),
+                 identifier = dataset_identifier,
+                 publisher = dataset_publisher,
+                 subject = dataset_subject,
+                 type = "DCMITYPE:Dataset",
+                 contributor = dataset_contributor,
+                 date = dataset_date,
+                 language = dataset_language,
+                 relation = dataset_relation,
+                 format = dataset_format,
+                 rights = dataset_rights,
+                 datasource = datasource,
+                 description = dataset_description,
+                 coverage = dataset_coverage),
+      reference = list(
+        title = paste0("The Dublin Core Metadata of `", dataset_bibentry$title, "'"),
+        author = citation_author,
+        year = substr(as.character(Sys.Date()),1,4)
+
+      ))
+  } else if (type=="ntriples") {
+    dclist <- list(title=dataset_title,
+                   creator=dataset_creator,
+                   identifier = dataset_identifier,
+                   publisher = dataset_publisher,
+                   subject = dataset_subject,
+                   type = "DCMITYPE:Dataset",
+                   contributor = dataset_contributor,
+                   date = dataset_date,
+                   language = dataset_language,
+                   relation = dataset_relation,
+                   format = dataset_format,
+                   rights = dataset_rights,
+                   datasource = datasource,
+                   description = dataset_description,
+                   coverage = dataset_coverage)
+
+    if ( dataset_identifier == ":tba") {
+      dataset_id <- "http:/example.com/dataset_tba/"
+    } else {
+      dataset_id <- dataset_identifier
+    }
+    dublincore_to_triples(dclist=dclist, dataset_id=dataset_id)
+  }
+}