Merge pull request #136 from mtmorgan/code-cleanup

Code cleanup

.github/workflows/R-CMD-check-dev.yaml

@@ -12,7 +12,7 @@ name: R-CMD-check-dev
 
 jobs:
   R-CMD-check-dev:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:

DESCRIPTION

@@ -64,6 +64,6 @@ URL: https://iqss.github.io/dataverse-client-r/, https://dataverse.org/, https:/
 BugReports: https://github.com/iqss/dataverse-client-r/issues
 VignetteBuilder: knitr
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3

NAMESPACE

@@ -1,5 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(create_zip,character)
+S3method(create_zip,data.frame)
+S3method(create_zip,list)
+S3method(dataset_id,character)
+S3method(dataset_id,dataverse_dataset)
+S3method(dataset_id,default)
+S3method(dataverse_id,character)
+S3method(dataverse_id,dataverse)
+S3method(get_fileid,character)
+S3method(get_fileid,dataverse_file)
+S3method(get_fileid,numeric)
 S3method(print,dataset_atom)
 S3method(print,dataset_statement)
 S3method(print,dataverse)

R/SWORD_files.R

@@ -1,6 +1,7 @@
 create_zip <- function(x, ...) {
     UseMethod("create_zip", x)
 }
+#' @export
 create_zip.character <- function(x, ...) {
     f <- file.exists(x)
     if (any(!f)) {
@@ -11,6 +12,7 @@ create_zip.character <- function(x, ...) {
         return(tmp)
     }
 }
+#' @export
 create_zip.data.frame <- function(x, ...) {
     tmpdf <- tempfile(fileext = ".zip")
     on.exit(file.remove(tmpdf), add = TRUE)
@@ -19,6 +21,7 @@ create_zip.data.frame <- function(x, ...) {
     stopifnot(!utils::zip(tmp, tmpdf))
     return(tmp)
 }
+#' @export
 create_zip.list <- function(x, ...) {
     tmpdf <- sapply(seq_along(x), tempfile(fileext = ".zip"))
     on.exit(file.remove(tmpdf), add = TRUE)

R/dataverse-package.R

@@ -1,4 +1,3 @@
-#' @docType package
 #' @name dataverse
 #' @title Client for Dataverse Repositories
 #' @description Provides access to Dataverse 4+ APIs, enabling data search, retrieval, and deposit.
@@ -27,4 +26,4 @@
 #'
 #'  \href{https://dataverse.harvard.edu/}{Harvard IQSS Dataverse}
 #'
-NULL
+"_PACKAGE"

R/print.R

@@ -54,10 +54,17 @@ print.dataverse_dataset <- function(x, ...) {
             cat("Release Date: ", x$releaseTime, "\n", sep = "")
         }
         if ("license" %in% names(x)) {
-            cat("License: ", x$license, "\n", sep = "")
+            if (is.list(x$license)) {
+                ## Dataverse >= 5.10
+                license <- x$license$name
+            } else {
+                ## legacy
+                license <- x$name
+            }
+            cat("License: ", license,"\n", sep = "")
         }
         if ("files" %in% names(x)) {
-            n <- length(x$files)
+            n <- NROW(x$files)
             cat(n, ngettext(n, " File:", " Files:"), "\n", sep = "")
             print(x$files[c("label", "version", "id", "contentType")])
         }

R/utils.R

@@ -5,9 +5,11 @@ dataverse_id <- function(x, ...) {
 dataverse_id.default <- function(x, ...) {
   x
 }
+#' @export
 dataverse_id.character <- function(x, ...) {
   get_dataverse(x, ..., check = FALSE)$id
 }
+#' @export
 dataverse_id.dataverse <- function(x, ...) {
   x$id
 }
@@ -16,9 +18,11 @@ dataverse_id.dataverse <- function(x, ...) {
 dataset_id <- function(x, ...) {
   UseMethod("dataset_id", x)
 }
+#' @export
 dataset_id.default <- function(x, ...) {
   x
 }
+#' @export
 dataset_id.character <- function(x, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
   x <- prepend_doi(x)
   u <- paste0(api_url(server), "datasets/:persistentId?persistentId=", x)
@@ -28,6 +32,7 @@ dataset_id.character <- function(x, key = Sys.getenv("DATAVERSE_KEY"), server =
                 })
   jsonlite::fromJSON(httr::content(r, as = "text", encoding = "UTF-8"))[["data"]][["id"]]
 }
+#' @export
 dataset_id.dataverse_dataset <- function(x, ...) {
   x$id
 }
@@ -37,6 +42,7 @@ get_fileid <- function(x, ...) {
   UseMethod("get_fileid", x)
 }
 
+#' @export
 get_fileid.numeric <- function(x, file, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
   files <- dataset_files(x, key = key, server = server, ...)
   ids <- unlist(lapply(files, function(x) x[["datafile"]][["id"]]))
@@ -57,6 +63,7 @@ get_fileid.numeric <- function(x, file, key = Sys.getenv("DATAVERSE_KEY"), serve
   id
 }
 
+#' @export
 get_fileid.character <- function(x, file, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
   files <- dataset_files(prepend_doi(x), key = key, server = server, ...)
   ids <- unlist(lapply(files, function(x) x[["dataFile"]][["id"]]))
@@ -77,6 +84,7 @@ get_fileid.character <- function(x, file, key = Sys.getenv("DATAVERSE_KEY"), ser
   id
 }
 
+#' @export
 get_fileid.dataverse_file <- function(x, ...) {
   x[["dataFile"]][["id"]]
 }

man-roxygen/ds.R

@@ -1,3 +1,3 @@
 #' @param dataset A character specifying a persistent identification ID for a dataset,
-#'  for example `"doi:10.70122/FK2/HXJVJU"`. Alternatively, an object of class
+#'  for example `"10.70122/FK2/HXJVJU"`. Alternatively, an object of class
 #'  \dQuote{dataverse_dataset} obtained by `dataverse_contents()`.

man-roxygen/envvars.R

@@ -7,5 +7,5 @@
 #'   most major. The server can be defined each time within a function, or it can
 #'   be set as a default via an environment variable. To set a default, run
 #'   `Sys.setenv("DATAVERSE_SERVER" = "dataverse.harvard.edu")`
-#'   or add `DATAVERSE_SERVER = "dataverse.harvard.edu` in one's `.Renviron`
+#'   or add `DATAVERSE_SERVER = "dataverse.harvard.edu"` in one's `.Renviron`
 #'   file (`usethis::edit_r_environ()`), with the appropriate domain as its value.