bibtex_core_data no comma after doi field

[aterhorst]

Hi. I picked up an issue. The bibtext_core_data function appears to leave out comma after doi field. I create an entry using the scopus_id as my object identifier in abstract_retrieval.

[muschellij2]

PRs are welcome, thanks!

On Wed, Dec 8, 2021 at 6:09 PM Andrew Terhorst @.***> wrote:

The bibtext_core_data function appears to leave out comma after doi entry.

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-- Best, John

[aterhorst]

# load libraries

require(tidyverse)
require(bib2df)
require(rscopus)

# import bibtext file used in thesis

phd_bib <- bib2df::bib2df("clean_bib.bib") %>%
  select(title = TITLE, key = BIBTEXKEY, author_list = AUTHOR) %>%
  rownames_to_column(var = "entry_no")

# scopus query

set_api_key(Sys.getenv("ELSEVIER_KEY"))
have_api_key()

# create empty bibtex file

fn <- "fixed_bib.bib"
cat("", file = fn) 

# loop through raw bibtex file

for(i in 1:nrow(phd_bib)){
  skip_to_next <- FALSE
  tryCatch({
    message('\r', i, '/', nrow(phd_bib), appendLF = FALSE)

    # define search string
    search_string <- paste("TITLE (\"", phd_bib$title[i],"\")")

    # execute search
    search <- scopus_search(
      verbose = F,
      query = search_string,
      view = "COMPLETE",
      count = 1,
      max_count = 1,
      wait_time = 0.5,
      http = "https://api.elsevier.com/content/search/scopus")

    # extract scopus_id
    result <- gen_entries_to_df(search[["entries"]])$df %>%
      select(scopus_id = `dc:identifier`) %>%
      mutate(scopus_id = str_remove(scopus_id, "SCOPUS_ID:"))

    # pull bibtex entry
    entry <- abstract_retrieval(result$scopus_id, identifier = "scopus", verbose = F)
    bib <- bibtex_core_data(entry)

    # append to bibtex file
    cat(bib, file = fn, append = T)
    cat("\n", file =fn, append = T)}, error = function(e) { skip_to_next <<- TRUE })
if(skip_to_next) { next }
}

[aterhorst]

clean_bib.bib.zip

[muschellij2]

Got it. I’ll happily review a pull request for the fix

On Wed, Dec 8, 2021 at 6:56 PM Andrew Terhorst @.***> wrote:

clean_bib.bib.zip https://github.com/muschellij2/rscopus/files/7681192/clean_bib.bib.zip

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Reply to this email directly, view it on GitHub https://github.com/muschellij2/rscopus/issues/44#issuecomment-989322676, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIGPLSQ6NZH57QYSMEUK5DUP7WB7ANCNFSM5JU7U3DA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Best, John

[aterhorst]

My work around is to add a comma before "abstract =" using find and replace.

[muschellij2]

As there is no reproducible example, closing.