Merge pull request #190 from ropensci/skip-tests

ropensci · Nov 11, 2023 · ccb6c29 · ccb6c29
2 parents 32855b6 + 1a8ed2c
commit ccb6c29
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Showing 14 changed files with 119 additions and 35 deletions.
diff --git a/R/oa2df.R b/R/oa2df.R
@@ -87,6 +87,8 @@ oa2df <- function(data, entity, options = NULL, count_only = FALSE, group_by = N
 #'
 #' @param abstract Logical. If TRUE, the function returns also the abstract of each item.
 #' Defaults to TRUE.
+#' @param pb Progress bar object. If verbose, computed from `oa_progress`.
+#' NULL otherwise.
 #' @inheritParams oa2df
 #'
 #' @return a data.frame.
@@ -131,7 +133,8 @@ oa2df <- function(data, entity, options = NULL, count_only = FALSE, group_by = N
 #'
 #' @export
 #'
-works2df <- function(data, abstract = TRUE, verbose = TRUE) {
+works2df <- function(data, abstract = TRUE, verbose = TRUE,
+                     pb = if (verbose) oa_progress(length(data)) else NULL) {
 
   col_order <- c(
     "id", "display_name", "author", "ab", "publication_date", "relevance_score",
@@ -181,7 +184,6 @@ works2df <- function(data, abstract = TRUE, verbose = TRUE) {
   empty_inst <- empty_list(inst_cols)
 
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   for (i in seq.int(n)) {
@@ -271,7 +273,7 @@ abstract_build <- function(ab) {
 #' It converts bibliographic collection of authors' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of authors' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -306,9 +308,9 @@ abstract_build <- function(ab) {
 #' }
 #'
 #' @export
-authors2df <- function(data, verbose = TRUE) {
+authors2df <- function(data, verbose = TRUE,
+                       pb = if (verbose) oa_progress(length(data)) else NULL) {
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   inst_cols <- c("id", "display_name", "ror", "country_code", "type", "lineage")
@@ -375,7 +377,7 @@ authors2df <- function(data, verbose = TRUE) {
 #' It converts bibliographic collection of institutions' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of institutions' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -403,9 +405,9 @@ authors2df <- function(data, verbose = TRUE) {
 #' }
 #'
 #' @export
-institutions2df <- function(data, verbose = TRUE) {
+institutions2df <- function(data, verbose = TRUE,
+                            pb = if (verbose) oa_progress(length(data)) else NULL) {
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   institution_process <- tibble::tribble(
@@ -476,7 +478,7 @@ institutions2df <- function(data, verbose = TRUE) {
 #' It converts bibliographic collection of venues' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of venues' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -506,10 +508,10 @@ institutions2df <- function(data, verbose = TRUE) {
 #' }
 #'
 #' @export
-venues2df <- function(data, verbose = TRUE) {
+venues2df <- function(data, verbose = TRUE,
+                      pb = if (verbose) oa_progress(length(data)) else NULL) {
 
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
   venue_process <- tibble::tribble(
     ~type, ~field,
@@ -562,7 +564,7 @@ venues2df <- function(data, verbose = TRUE) {
 #' It converts bibliographic collection of concepts' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of concepts' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -592,7 +594,8 @@ venues2df <- function(data, verbose = TRUE) {
 #' }
 #'
 #' @export
-concepts2df <- function(data, verbose = TRUE) {
+concepts2df <- function(data, verbose = TRUE,
+                        pb = if (verbose) oa_progress(length(data)) else NULL) {
 
   concept_process <- tibble::tribble(
     ~type, ~field,
@@ -614,7 +617,6 @@ concepts2df <- function(data, verbose = TRUE) {
   )
 
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   for (i in seq.int(n)) {
@@ -661,7 +663,7 @@ concepts2df <- function(data, verbose = TRUE) {
 #' It converts bibliographic collection of funders' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of funders' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -683,7 +685,8 @@ concepts2df <- function(data, verbose = TRUE) {
 #' }
 #'
 #' @export
-funders2df <- function(data, verbose = TRUE) {
+funders2df <- function(data, verbose = TRUE,
+                       pb = if (verbose) oa_progress(length(data)) else NULL) {
 
   funder_process <- tibble::tribble(
     ~type, ~field,
@@ -707,7 +710,6 @@ funders2df <- function(data, verbose = TRUE) {
   )
 
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   for (i in seq.int(n)) {
@@ -735,7 +737,7 @@ funders2df <- function(data, verbose = TRUE) {
 #' It converts bibliographic collection of sources' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of sources' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -757,7 +759,8 @@ funders2df <- function(data, verbose = TRUE) {
 #' }
 #'
 #' @export
-sources2df <- function(data, verbose = TRUE) {
+sources2df <- function(data, verbose = TRUE,
+                       pb = if (verbose) oa_progress(length(data)) else NULL) {
 
   source_process <- tibble::tribble(
     ~type, ~field,
@@ -791,7 +794,6 @@ sources2df <- function(data, verbose = TRUE) {
   )
 
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   for (i in seq.int(n)) {
@@ -819,7 +821,7 @@ sources2df <- function(data, verbose = TRUE) {
 #' It converts bibliographic collection of publishers' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
 #' The function converts a list of publishers' records obtained using \code{oa_request} into a data frame/tibble.
 #'
-#' @inheritParams oa2df
+#' @inheritParams works2df
 #'
 #' @return a data.frame.
 #'
@@ -841,7 +843,8 @@ sources2df <- function(data, verbose = TRUE) {
 #' }
 #'
 #' @export
-publishers2df <- function(data, verbose = TRUE) {
+publishers2df <- function(data, verbose = TRUE,
+                          pb = if (verbose) oa_progress(length(data)) else NULL) {
 
   publisher_process <- tibble::tribble(
     ~type, ~field,
@@ -867,7 +870,6 @@ publishers2df <- function(data, verbose = TRUE) {
   )
 
   n <- length(data)
-  pb <- oa_progress(n)
   list_df <- vector(mode = "list", length = n)
 
   for (i in seq.int(n)) {

diff --git a/R/oa_fetch.R b/R/oa_fetch.R
@@ -372,10 +372,9 @@ oa_request <- function(query_url,
       "Getting ", n_pages, pg_plural, " of results",
       " with a total of ", n_items, " records..."
     )
+    pb <- oa_progress(n = n_pages, text = "OpenAlex downloading")
   }
 
-  pb <- oa_progress(n = n_pages, text = "OpenAlex downloading")
-
   # Setting items per page
   query_ls[["per-page"]] <- per_page
 

diff --git a/R/oa_ngrams.R b/R/oa_ngrams.R
@@ -67,7 +67,9 @@ oa_ngrams <- function(works_identifier, ...,
       n <- length(query_urls)
 
       #ngrams_failed_template <- data.frame(id = NA, doi = NA, count = NA, ngrams = I(list(NULL)))
-      pb <- oa_progress(n)
+      if (verbose) {
+        pb <- oa_progress(n)
+      }
 
       # Fetch
       if (utils::packageVersion("curl") >= "5") {
@@ -91,7 +93,10 @@ oa_ngrams <- function(works_identifier, ...,
           options("oa_ngrams.message.curlv5" = FALSE)
         }
         # Serial fetch
-        pb_dl <- oa_progress(n, "OpenAlex downloading")
+        if (verbose) {
+          pb_dl <- oa_progress(n, "OpenAlex downloading")
+        }
+
         ngrams_list <- vector("list", n)
         for (i in seq_len(n)) {
           if (verbose) pb_dl$tick()

diff --git a/man/authors2df.Rd b/man/authors2df.Rd
diff --git a/man/concepts2df.Rd b/man/concepts2df.Rd
diff --git a/man/funders2df.Rd b/man/funders2df.Rd
diff --git a/man/institutions2df.Rd b/man/institutions2df.Rd
diff --git a/man/publishers2df.Rd b/man/publishers2df.Rd
diff --git a/man/sources2df.Rd b/man/sources2df.Rd
diff --git a/man/venues2df.Rd b/man/venues2df.Rd