incorporate June's comments and ready to remove simple_rapply

R/oa2df.R

@@ -8,6 +8,10 @@
 #' The argument can be one of c("works", "authors", "venues", "institutions", "concepts").
 #' @param abstract Logical. If TRUE, the function returns also the abstract of each item.
 #' Ignored if entity is different from "works". Defaults to TRUE.
+#' @param verbose Logical.
+#' If TRUE, print information about the dataframe conversion process.
+#' Defaults to TRUE.
+#'
 #' @inheritParams oa_query
 #' @inheritParams oa_request
 #' @return A tibble/dataframe result of the original OpenAlex result list.
@@ -187,10 +191,10 @@ works2df <- function(data, abstract = TRUE, verbose = TRUE) {
 
     if (!is.null(paper$primary_location)) {
       so_info <- paper$primary_location["source"]
-      so_info <- if (is.na(so_info)) NA else so_info[[1]]
-
+      so_info <- if (length(so_info[[1]]) == 0) NA else so_info[[1]]
+      venue_info <- replace_w_na(paper$primary_location[venue_cols])
       venue <- setNames(
-        c(paper$primary_location[venue_cols], so_info[so_cols]),
+        c(venue_info, so_info[so_cols]),
         c(names(venue_cols), names(so_cols))
       )
     }
@@ -208,12 +212,11 @@ works2df <- function(data, abstract = TRUE, verbose = TRUE) {
           }
           first_inst <- prepend(first_inst, "institution")
           aff_raw <- list(au_affiliation_raw = l$raw_affiliation_string[1])
-          l_author <- l_author <- if (length(l$author) > 0) {
-            prepend(l$author, "au")
+          l_author <- if (length(l$author) > 0) {
+            prepend(replace_w_na(l$author), "au")
           } else {
             empty_list(c("au_id", "au_display_name", "au_orcid"))
           }
-
           c(l_author, l["author_position"], aff_raw, first_inst)
         }), "rbind_df"
       )
@@ -223,8 +226,9 @@ works2df <- function(data, abstract = TRUE, verbose = TRUE) {
     if (!is.null(paper$abstract_inverted_index) && abstract) {
       ab <- abstract_build(paper$abstract_inverted_index)
     }
+    paper_biblio <- replace_w_na(paper$biblio) # TODO replace sapply with something else
 
-    out_ls <- c(sim_fields, venue, paper$biblio, list(author = author, ab = ab))
+    out_ls <- c(sim_fields, venue, paper_biblio, list(author = author, ab = ab))
     out_ls[sapply(out_ls, is.null)] <- NULL
     list_df[[i]] <- out_ls
   }
@@ -337,7 +341,7 @@ authors2df <- function(data, verbose = TRUE) {
       }
       sub_affiliation <- prepend(sub_affiliation, "affiliation")
     }
-
+    sub_affiliation <- replace_w_na(sub_affiliation)
     list_df[[i]] <- c(sim_fields, sub_affiliation)
   }
 
@@ -729,6 +733,7 @@ funders2df <- function(data, verbose = TRUE) {
   }
 
   out_df <- rbind_oa_ls(list_df)
+  out_df
 }
 
 
@@ -819,6 +824,7 @@ sources2df <- function(data, verbose = TRUE) {
   }
 
   out_df <- rbind_oa_ls(list_df)
+  out_df
 }
 
 
@@ -901,6 +907,7 @@ publishers2df <- function(data, verbose = TRUE) {
   }
 
   out_df <- rbind_oa_ls(list_df)
+  out_df
 }
 
 

R/utils.R

@@ -10,6 +10,10 @@ simple_rapply <- function(x, fn, ...) {
 
 `%||%` <- function(x, y) if (is.null(x)) y else x
 
+replace_w_na <- function(x){
+  lapply(x, `%||%`, y = NA)
+}
+
 subs_na <- function(x, type = c("row_df", "col_df", "flat", "rbind_df", "identical"), prefix = NULL) {
   type <- match.arg(type)
   if (length(x) == 0) {
@@ -21,10 +25,11 @@ subs_na <- function(x, type = c("row_df", "col_df", "flat", "rbind_df", "identic
   }
 
   out <- switch(type,
-    row_df = as.data.frame(x),
+    row_df = as.data.frame(replace_w_na(x)),
     col_df = tibble::enframe(unlist(x)),
     flat = unlist(x),
-    rbind_df = do.call(rbind.data.frame, x)
+    rbind_df = do.call(rbind.data.frame, lapply(x, replace_w_na)
+    )
   )
 
   if (!is.null(prefix)) {

tests/testthat/test-oa_fetch.R

@@ -332,3 +332,29 @@ test_that("oa_fetch works for publishers", {
   expect_true(nrow(s) > 100)
 })
 
+test_that("oa_fetch works with 1 identifier", {
+  w <- oa_fetch(identifier = "W3046863325") # Work
+  a <- oa_fetch(identifier = "A1969205032") # Author
+  i <- oa_fetch(identifier = "I4200000001") # Institution
+  f <- oa_fetch(identifier = "F4320332161") # Funder
+  p <- oa_fetch(identifier = "P4310311775") # Publisher
+  s <- oa_fetch(identifier = "S1983995261") # Source
+  co <- oa_fetch(identifier = "C2522767166") # Concept
+
+  expect_s3_class(w, "data.frame")
+  expect_s3_class(a, "data.frame")
+  expect_s3_class(i, "data.frame")
+  expect_s3_class(f, "data.frame")
+  expect_s3_class(p, "data.frame")
+  expect_s3_class(s, "data.frame")
+  expect_s3_class(co, "data.frame")
+
+  expect_equal(dim(w), c(1, 30))
+  expect_equal(dim(a), c(1, 15))
+  expect_equal(dim(i), c(1, 21))
+  expect_equal(dim(f), c(1, 17))
+  expect_equal(dim(p), c(1, 19))
+  expect_equal(dim(s), c(1, 26))
+  expect_equal(dim(co), c(1, 16))
+
+})