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Allow bbt_update_bib() to ingest multiple Rmd files with potentially shared .bib files #52

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Allow bbt_update_bib() to ingest multiple Rmd files with potentially shared .bib files #52

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7244b97
update 2025-03-08 08:02:17.902535
OPECHEESE Mar 8, 2025
5eb2cce
update 2025-03-08 08:02:41.504833
OPECHEESE Mar 8, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
RoxygenNote: 7.3.2
Imports:
httr,
rstudioapi,
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61 changes: 42 additions & 19 deletions R/update.R
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Expand Up @@ -4,36 +4,59 @@
#' This function takes an RMarkdown file location and a bibliography file
#' as inputs and updates the bibliography file.
#'
#' @param path_rmd The path to the RMarkdown file.
#' @param path_bib The path to the bibliography file.
#' @param path_rmd The path to the RMarkdown file(s).
#' @param path_bib Optionally, the path to the bibliography file.
#' The default value `NULL`uses `bbt_guess_bib_file()` to detect the path from
#' the 'YAML' front matter of `path_rmd`.
#' @param encoding Passed to [rmarkdown::yaml_front_matter()]
#' @param quiet Use `TRUE` to suppress message on successful write.
#' @inheritParams bbt_write_bib
#'
#' @return `path_bib`, invisibly
#' @export
bbt_update_bib <- function(path_rmd,
path_bib = bbt_guess_bib_file(path_rmd),
path_bib = NULL,
ignore = character(0),
translator = bbt_guess_translator(path_bib),
translator = NULL,
library_id = getOption("rbbt.default.library_id", 1),
overwrite = TRUE, filter = identity, quiet = FALSE) {
keys <- bbt_detect_citations(path_rmd)
bbt_write_bib(
path = path_bib,
keys = keys,
ignore = ignore,
translator = translator,
overwrite = overwrite,
filter = filter
)

if (!quiet) {
references <- if (length(keys) != 1) "references" else "reference"
message(sprintf("Wrote %d %s to '%s'", length(keys), references, path_bib))
# Extract citations from all rmds
keys_list <- lapply(path_rmd, bbt_detect_citations)
# If no bib path given, guess from files. Otherwise, repeat given bib path
if(is.null(path_bib)){
path_bib <- sapply(path_rmd, bbt_guess_bib_file)
} else {
path_bib <- rep(path_bib, length(keys_list))
}

invisible(path_bib)
# Preallocate list and name it
keys_per_bib <- vector("list", length = length(unique(path_bib)))
names(keys_per_bib) <- unique(path_bib)
# Get keys from all documents per unique bib file
for(thisb in names(keys_per_bib)){
keys_per_bib[[thisb]] <- unique(do.call(c, keys_list[path_bib == thisb]))
}
# If no translator given, guess from files. Otherwise, repeat given translator
if(is.null(translator)){
translator <- sapply(names(keys_per_bib), bbt_guess_translator)
} else {
translator <- rep(translator, length(keys_list))
}
# Write files and report status messages
out_file <- sapply(seq_along(keys_per_bib), function(i){
fl <- bbt_write_bib(
path = names(keys_per_bib)[i],
keys = keys_per_bib[[i]],
ignore = ignore,
translator = translator[i],
overwrite = overwrite,
filter = filter
)
if (!quiet) {
message(sprintf("Wrote %d %s to '%s'", length(keys_per_bib[[1]]), c("reference", "references")[(length(keys_per_bib[[1]]) > 1)+1L], names(keys_per_bib)[1]))
}
fl
})
return(invisible(out_file))
}

#' @rdname bbt_update_bib
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10 changes: 6 additions & 4 deletions man/bbt_update_bib.Rd
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1 change: 1 addition & 0 deletions rbbt.Rproj
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@@ -1,4 +1,5 @@
Version: 1.0
ProjectId: 5ad6e129-6c23-4b55-902b-135693439039

RestoreWorkspace: No
SaveWorkspace: No
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