IQSS · kuriwaki · Oct 4, 2024 · Sep 14, 2024 · Sep 14, 2024 · Sep 15, 2024
diff --git a/DESCRIPTION b/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
diff --git a/NAMESPACE b/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)

diff --git a/R/SWORD_files.R b/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)

diff --git a/R/dataverse-package.R b/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"
diff --git a/R/utils.R b/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"]]
 }

diff --git a/man/dataverse.Rd b/man/dataverse.Rd
diff --git a/tests/testthat/tests-dataset_metadata.R b/tests/testthat/tests-dataset_metadata.R
@@ -22,6 +22,12 @@ test_that("check versions format", {
   ds_index  <- which(sapply(contents, function(x) x$identifier) == "FK2/HXJVJU")
   actual    <- dataset_versions(contents[[ds_index]])
 
-  expect_length(actual[[1]], 17L)
+  expected_names <- c(
+    "citationDate", "createTime", "datasetId", "datasetPersistentId",
+    "fileAccessRequest", "files", "id", "lastUpdateTime", "latestVersionPublishingState",
+    "license", "metadataBlocks", "publicationDate", "releaseTime",
+    "storageIdentifier", "UNF", "versionMinorNumber", "versionNumber",
+    "versionState")
+  expect_setequal(names(actual[[1]]), expected_names)
   expect_s3_class(actual[[2]], "dataverse_dataset_version")
 })
diff --git a/tests/testthat/tests-get_dataframe-dataframe-basketball.R b/tests/testthat/tests-get_dataframe-dataframe-basketball.R
@@ -10,7 +10,9 @@ test_that("roster-by-name", {
   actual <-
     get_dataframe_by_name(
       filename = expected_ds$roster$label , # A value like "roster-bulls-1996.tab",
-      dataset  = dirname(expected_ds$roster$dataFile$persistentId)#, # A value like "doi:10.70122/FK2/HXJVJU",
+      dataset  = dirname(expected_ds$roster$dataFile$persistentId),#, # A value like "doi:10.70122/FK2/HXJVJU",
+      # quieten readr::read_tsv during test
+      .f = function(...) readr::read_tsv(..., show_col_types = FALSE)
     )
 
   expect_equal(actual, expected_file)
@@ -24,7 +26,9 @@ test_that("roster-by-doi", {
 
   actual <-
     get_dataframe_by_doi(
-      filedoi  = expected_ds$roster$dataFile$persistentId # A value like "doi:10.70122/FK2/HXJVJU/SA3Z2V",
+      filedoi  = expected_ds$roster$dataFile$persistentId, # A value like "doi:10.70122/FK2/HXJVJU/SA3Z2V",
+      # quieten readr::read_tsv during test
+      .f = function(...) readr::read_tsv(..., show_col_types = FALSE)
     )
 
   expect_equal(actual, expected_file)
@@ -38,7 +42,9 @@ test_that("roster-by-id", {
 
   actual <-
     get_dataframe_by_id(
-      fileid   = expected_ds$roster$dataFile$id # A value like 1734005
+      fileid   = expected_ds$roster$dataFile$id, # A value like 1734005
+      # quieten readr::read_tsv during test
+      .f = function(...) readr::read_tsv(..., show_col_types = FALSE)
     )
 
   expect_equal(actual, expected_file)

diff --git a/tests/testthat/tests-get_dataset.R b/tests/testthat/tests-get_dataset.R
@@ -10,8 +10,15 @@ test_that("download tab from DOI and filename", {
   actual    <- get_dataset(contents[[ds_index]])
   files     <- actual$files
   expected_dv <- retrieve_info_dataverse("expected-dataverse.yml")
+  expected_names <- c(
+    "citationDate", "createTime", "datasetId",
+    "datasetPersistentId", "fileAccessRequest", "files", "id",
+    "lastUpdateTime", "latestVersionPublishingState", "license",
+    "metadataBlocks", "publicationDate", "releaseTime",
+    "storageIdentifier", "UNF", "versionMinorNumber",
+    "versionNumber", "versionState")
 
-  expect_length(actual                      , 17L)
+  expect_setequal(names(actual)             , expected_names)
   expect_equal(actual$id                    , 182158L)
   expect_equal(actual$datasetId             , 1734004L)
   expect_equal(actual$datasetPersistentId   , "doi:10.70122/FK2/HXJVJU")

diff --git a/tests/testthat/tests-search.R b/tests/testthat/tests-search.R
@@ -1,34 +1,34 @@
 test_that("simple search query", {
   testthat::skip_on_cran()
-  expect_true(is.data.frame(dataverse_search("Gary King", key = "", server = "dataverse.harvard.edu")))
+  expect_true(is.data.frame(dataverse_search("Gary King", key = "", server = "dataverse.harvard.edu", verbose = FALSE)))
 })
 
 test_that("named argument search", {
   testthat::skip_on_cran()
-  expect_true(is.data.frame(dataverse_search(author = "Gary King", title = "Ecological Inference", key = "", server = "dataverse.harvard.edu")))
+  expect_true(is.data.frame(dataverse_search(author = "Gary King", title = "Ecological Inference", key = "", server = "dataverse.harvard.edu", verbose = FALSE)))
 })
 
 test_that("simple search w/type argument", {
   testthat::skip_on_cran()
-  expect_true(is.data.frame(dataverse_search(author = "Gary King", type = "dataset", key = "", server = "dataverse.harvard.edu")))
+  expect_true(is.data.frame(dataverse_search(author = "Gary King", type = "dataset", key = "", server = "dataverse.harvard.edu", verbose = FALSE)))
 })
 
 test_that("date range search using fq", {
   testthat::skip_on_cran()
-  expect_true(is.data.frame(dataverse_search("*", fq = "dateSort:[2018-01-01T00:00:00Z+TO+2019-01-01T00:00:00Z]", type = "dataset", key = "", server = "dataverse.harvard.edu")))
+  expect_true(is.data.frame(dataverse_search("*", fq = "dateSort:[2018-01-01T00:00:00Z+TO+2019-01-01T00:00:00Z]", type = "dataset", key = "", server = "dataverse.harvard.edu", verbose = FALSE)))
 })
 
 test_that("publication year using fq", {
   testthat::skip_on_cran()
-  expect_true(is.data.frame(dataverse_search("*", fq = "publicationDate:2018", type = "dataset", key = "", server = "dataverse.harvard.edu")))
+  expect_true(is.data.frame(dataverse_search("*", fq = "publicationDate:2018", type = "dataset", key = "", server = "dataverse.harvard.edu", verbose = FALSE)))
 })
 
 test_that("filter dataverses by subject using fq", {
   testthat::skip_on_cran()
-  expect_true(is.data.frame(dataverse_search("*", fq = "subject_ss:Social+Sciences", type = "dataverse", key = "", server = "dataverse.harvard.edu")))
+  expect_true(is.data.frame(dataverse_search("*", fq = "subject_ss:Social+Sciences", type = "dataverse", key = "", server = "dataverse.harvard.edu", verbose = FALSE)))
 })
 
 test_that("empty fq search", {
   testthat::skip_on_cran()
-  expect_length(dataverse_search("*", fq = "dateSort:[2019-02-01T00:00:00Z+TO+2019-01-01T00:00:00Z]", type = "dataset", key = "", server = "dataverse.harvard.edu"), 0)
+  expect_length(dataverse_search("*", fq = "dateSort:[2019-02-01T00:00:00Z+TO+2019-01-01T00:00:00Z]", type = "dataset", key = "", server = "dataverse.harvard.edu", verbose = FALSE), 0)
 })