Return 0-row dfs for 0 obs citable downloads

R/finbif_occurrence_load.R

@@ -313,7 +313,7 @@ finbif_occurrence_load <- function(
  )
 
  facts_df <- structure(
- try(read_finbif_tsv(fb_records_obj), silent = TRUE),
+ read_finbif_tsv(fb_records_obj),
  facts = facts[[ftype]],
  fact_type = ftype,
  id = id,
@@ -909,9 +909,15 @@ dt_read <- function(fb_occurrence_obj) {
 
  }
 
- cols <- do.call(data.table::fread, args)
+ cols <- rownames(sysdata("cite_file_vars"))
 
- cols <- names(cols)
+ if (file.exists(args[["input"]])) {
+
+ cols <- do.call(data.table::fread, args)
+
+ cols <- names(cols)
+
+ }
 
  cols <- make.names(cols)
 
@@ -1012,7 +1018,13 @@ dt_read <- function(fb_occurrence_obj) {
 
  args[["header"]] <- FALSE
 
- df <- do.call(data.table::fread, args)
+ df <- structure(vector("list", length(args_select)), class = "data.frame")
+
+ if (file.exists(args[["input"]])) {
+
+ df <- do.call(data.table::fread, args)
+
+ }
 
  names(df) <- cols[args_select]
 
@@ -1059,10 +1071,12 @@ rd_read <- function(fb_occurrence_obj) {
 
  connection_obj <- list(file = file, tsv = tsv, mode = "")
 
+ con <- open_tsv_connection(connection_obj)
+
  quote <- ""
 
  df <- utils::read.delim(
- open_tsv_connection(connection_obj),
+ con,
  nrows = 1L,
  na.strings = "",
  quote = quote,
@@ -1087,14 +1101,12 @@ rd_read <- function(fb_occurrence_obj) {
 
  n <- as.integer(fb_occurrence_obj[["n"]])
 
- if (identical(n, 0L)) {
+ if (identical(n, 0L) || inherits(con, "textConnection")) {
 
  df <- df[0L, ]
 
  } else {
 
- connection_obj <- list(file = file, tsv = tsv, mode = "")
-
  df <- utils::read.delim(
  open_tsv_connection(connection_obj),
  header = FALSE,
@@ -1194,7 +1206,7 @@ spread_facts <- function(facts) {
 
  drop_facts_na <- attr(facts, "drop_facts_na", TRUE)
 
- if (inherits(facts, "try-error")) {
+ if (identical(nrow(facts), 0L)) {
 
  facts <- data.frame(
  Parent = NA_character_,
@@ -1510,20 +1522,39 @@ nlines <- function(fb_occurrence_obj) {
 }
 
 #' @noRd
+#' @importFrom utils unzip
 
 open_tsv_connection <- function(connection_obj) {
 
  file <- connection_obj[["file"]]
 
  mode <- connection_obj[["mode"]]
 
+ tsv <- connection_obj[["tsv"]]
+
  nchars <- nchar(file)
 
- switch(
- substring(file, nchars - 3L, nchars),
- .tsv = file(file, mode),
- unz(file, connection_obj[["tsv"]], mode)
- )
+ ext <- substring(file, nchars - 3L, nchars)
+
+ if (identical(ext, ".tsv")) {
+
+ file(file, mode)
+
+ } else if (tsv %in% utils::unzip(file, list = TRUE)[["Name"]]) {
+
+ unz(file, tsv, mode)
+
+ } else {
+
+ vars <- sysdata("cite_file_vars")
+
+ vars <- rownames(vars)
+
+ vars <- paste0(vars, collapse = "\t")
+
+ textConnection(vars)
+
+ }
 
 }
 

tests/testthat/test-finbif_occurrence_load.R

@@ -303,3 +303,14 @@ test_that(
 
  }
 )
+
+test_that(
+ "reading a zip file with no tsv does not trigger an error", {
+
+ expect_s3_class(
+ open_tsv_connection(list(file = "HBF.6968.zip", tsv = "none")),
+ "textConnection"
+ )
+
+ }
+)