Merge pull request #133 from IQSS/dev

For CRAN 0.3.14

.Rbuildignore

@@ -6,6 +6,7 @@ man-roxygen/*
 ^README\.Rmd$
 ^README\.html$
 ^CONTRIBUTING\.md$
+tests/.*_ghaction.R
 ^vignettes/figure$
 ^vignettes/figure/.+$
 \.Rmd2$

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

@@ -3,7 +3,6 @@
 on:
   schedule:
     - cron: "20 3 * * *" # Run every morning at 3:20am UTC
-    # - cron: "7 1 * * *" # Run every morning at 1:07am UTC (~8pm central)
 
 name: R-CMD-check-daily
 
@@ -13,9 +12,11 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: "always"
       - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
@@ -55,6 +56,13 @@ jobs:
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Test live dataverse in vignettes
+        run: |
+          devtools::load_all()
+          source("tests/B-search_ghaction.R")
+          source("tests/C-download_ghaction.R")
+        shell: Rscript {0}
+
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}

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

@@ -4,12 +4,9 @@ on:
   push:
     branches:
       - dev
-      # - main
-      # - master
-  # pull_request:
-  #   branches:
-  #     - main
-  #     - master
+  pull_request:
+    branches:
+      - main
 
 name: R-CMD-check-dev
 
@@ -19,32 +16,32 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
-      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          cache: "always"
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
       - name: Check
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Test live dataverse in vignettes
+        run: |
+          devtools::load_all()
+          source("tests/B-search_ghaction.R")
+          source("tests/C-download_ghaction.R")
         shell: Rscript {0}
 
       - name: Test coverage

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

@@ -5,16 +5,9 @@
 # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
-  push:
-    branches:
-      - main
-      - master
-      # - dev
-
   pull_request:
     branches:
       - main
-      - master
 
 name: R-CMD-check-thorough
 
@@ -43,7 +36,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         id: install-r
@@ -52,6 +45,8 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: "always"
       - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Restore R package cache
@@ -91,6 +86,13 @@ jobs:
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Test live dataverse in vignettes
+        run: |
+          devtools::load_all()
+          source("tests/B-search_ghaction.R")
+          source("tests/C-download_ghaction.R")
+        shell: Rscript {0}
+
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: dataverse
-Version: 0.3.13
+Version: 0.3.14
 Title: Client for Dataverse 4+ Repositories
 Authors@R:
    c(person(given = "Shiro", 
@@ -32,7 +32,12 @@ Authors@R:
             role = "ctb"),
      person(given = "Edward", 
             family = "Jee", 
-            role = "ctb"))
+            role = "ctb"),
+     person(given = "Johannes", 
+            family = "Gruber",
+            role = c("ctb"),
+            email = "[email protected]",
+            comment = c(ORCID = "0000-0001-9177-1772")))
 Imports:
     checkmate,
     httr,
@@ -59,6 +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: 7.2.0
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3

NAMESPACE

@@ -38,6 +38,10 @@ export(get_file_by_doi)
 export(get_file_by_id)
 export(get_file_by_name)
 export(get_file_metadata)
+export(get_url)
+export(get_url_by_doi)
+export(get_url_by_id)
+export(get_url_by_name)
 export(get_user_key)
 export(initiate_sword_dataset)
 export(list_datasets)

NEWS.md

@@ -1,5 +1,11 @@
 # dataverse
 
+# CHANGES in dataverse 0.3.14
+
+* Improve recommendation for rdata loading (#107, #127)
+* `get_file_by_*()` can now return the download URL to be used in external functions or programs, useful for large files (#128, implemented in #129 @JBGruber and @kuriwaki)
+* Removes remote resource from vignette and move them to ghactions (#131)
+
 # CHANGES in dataverse 0.3.12 and 0.3.13
 
 * Update expired token (#123)

R/add_dataset_file.R

@@ -59,17 +59,17 @@
 #' }
 #' @export
 add_dataset_file <-
-function(file,
-         dataset,
-         description = NULL,
-         key = Sys.getenv("DATAVERSE_KEY"),
-         server = Sys.getenv("DATAVERSE_SERVER"),
-         ...) {
+  function(file,
+           dataset,
+           description = NULL,
+           key = Sys.getenv("DATAVERSE_KEY"),
+           server = Sys.getenv("DATAVERSE_SERVER"),
+           ...) {
     dataset <- dataset_id(dataset, key = key, server = server, ...)
 
     bod2 <- list(forceReplace = force)
     if (!is.null(description)) {
-        bod2$description <- description
+      bod2$description <- description
     }
     jsondata <- as.character(jsonlite::toJSON(bod2, auto_unbox = TRUE))
 
@@ -81,44 +81,48 @@ function(file,
     httr::stop_for_status(r, task = httr::content(r)$message)
     out <- jsonlite::fromJSON(httr::content(r, "text", encoding = "UTF-8"))
     out$data$files$dataFile$id[1L]
-}
+  }
 
 #' @rdname add_dataset_file
 #' @export
 update_dataset_file <-
-function(file,
-         dataset = NULL,
-         id,
-         description = NULL,
-         force = TRUE,
-         key = Sys.getenv("DATAVERSE_KEY"),
-         server = Sys.getenv("DATAVERSE_SERVER"),
-         ...) {
+  function(file,
+           dataset = NULL,
+           id,
+           description = NULL,
+           force = TRUE,
+           key = Sys.getenv("DATAVERSE_KEY"),
+           server = Sys.getenv("DATAVERSE_SERVER"),
+           ...) {
     dataset <- dataset_id(dataset, key = key, server = server, ...)
 
     # get file ID from 'dataset'
     if (!is.numeric(id)) {
-        if (inherits(id, "dataverse_file")) {
-            id <- get_fileid(id, key = key, server = server)
-        } else if (is.null(dataset)) {
-            stop("When 'id' is a character string, dataset must be specified. Or, use a global fileid instead.")
-        } else {
-            id <- get_fileid(dataset, id, key = key, server = server, ...)
-        }
+      if (inherits(id, "dataverse_file")) {
+        id <- get_fileid(id, key = key, server = server)
+      } else if (is.null(dataset)) {
+        stop("When 'id' is a character string, dataset must be specified. Or, use a global fileid instead.")
+      } else {
+        id <- get_fileid(dataset, id, key = key, server = server, ...)
+      }
     }
 
     bod2 <- list(forceReplace = force)
     if (!is.null(description)) {
-        bod2$description <- description
+      bod2$description <- description
     }
     jsondata <- as.character(jsonlite::toJSON(bod2, auto_unbox = TRUE))
 
     u <- paste0(api_url(server), "files/", id, "/replace")
-    r <- httr::POST(u, httr::add_headers("X-Dataverse-key" = key), ...,
+    r <- httr::POST(u,
+                    httr::add_headers("X-Dataverse-key" = key), ...,
                     body = list(file = httr::upload_file(file),
                                 jsonData = jsondata
-                                ),
+                    ),
                     encode = "multipart")
     httr::stop_for_status(r, task = httr::content(r)$message)
-    structure(jsonlite::fromJSON(httr::content(r, as = "text", encoding = "UTF-8"), simplifyDataFrame = FALSE)$data$files[[1L]], class = "dataverse_file")
-}
+    structure(jsonlite::fromJSON(
+      httr::content(r, as = "text", encoding = "UTF-8"),
+      simplifyDataFrame = FALSE)$data$files[[1L]], class = "dataverse_file"
+    )
+  }

R/get_dataframe.R

@@ -84,15 +84,13 @@
 #'
 #' # 3. RData files are read in by `base::load()` but cannot be assigned to an
 #' # object name. The following shows two possible ways to read in such files.
+#' # First, the RData object can be loaded to the environment without object assignment.
 #'
-#' # First, without relying on `get_dataframe_*`, write as a binary file:
-#' as_binary <- get_file_by_doi(
-#'  filedoi = "doi:10.70122/FK2/PPIAXE/5VPXKE",
-#'  server = "demo.dataverse.org")
-#'
-#' temp <- tempdir()
-#' writeBin(as_binary, path(temp, "county.RData"))
-#' load(path(temp, "county.RData"))
+#' get_dataframe_by_doi(
+#'   filedoi = "10.70122/FK2/PPIAXE/X2FC5V",
+#'   server = "demo.dataverse.org",
+#'   original = TRUE,
+#'   .f = function(x) load(x, envir = .GlobalEnv))
 #'
 #' # If you are certain each RData contains only one object, one could define a
 #' # custom function used in https://stackoverflow.com/a/34926943
@@ -151,7 +149,7 @@ get_dataframe_by_id <- function(
   }
 
   # READ raw data
-  raw <- get_file(file = fileid, original = original, ...)
+  raw <- get_file(file = fileid, original = original, return_url = FALSE, ...)
 
   # save to temp and then read it in with supplied function
   if (!is.null(.f)) {

R/get_file.R

@@ -85,6 +85,7 @@ get_file <- function(
   dataset       = NULL,
   format        = c("original", "bundle"),
   vars          = NULL,
+  return_url    = FALSE,
   key           = Sys.getenv("DATAVERSE_KEY"),
   server        = Sys.getenv("DATAVERSE_SERVER"),
   original      = TRUE,
@@ -124,6 +125,7 @@ get_file <- function(
         key         = key,
         server      = server,
         original    = original,
+        return_url  = return_url,
         ...
       )
     }
@@ -148,6 +150,7 @@ get_file_by_name <- function(
   dataset,
   format        = c("original", "bundle"),
   vars          = NULL,
+  return_url    = FALSE,
   key           = Sys.getenv("DATAVERSE_KEY"),
   server        = Sys.getenv("DATAVERSE_SERVER"),
   original      = TRUE,
@@ -171,6 +174,7 @@ get_file_by_name <- function(
     key         = key,
     server      = server,
     original    = original,
+    return_url  = return_url,
     ...
   )
 }