bib_converter_biblatex.R

# Need to do one of these for books, code, etcx.
# description -------------------------------------------------------------

# Export as Better BibTex

# Code for converting exported bibtex file into format that:
# 1) is read into Academic and 2) the pdfs are renamed after being copied
# into the relevant folder
# TODO: not all abstracts being read (may be that some are called "summary")
# TODO: "strings cannot contain newlines" error in some abstracts
# TODO: is there a way to automate the copy paste of files into folder?

# http://www.pik-potsdam.de/~pichler/blog/post/set-this-up/setting-up-this-site/

#' @title bibtex_2academic
#' @description import publications from a bibtex file to a hugo-academic website
#' @author Lorenzo Busetto, phD (2017) <lbusett@gmail.com>
#' @modified Peter Paul Pichler (2019) <pichler@pik-potsdam.de>


# load libraries  ---------------------------------------------------------

library(RefManageR)
library(tidyverse)
library(anytime)
library(tibble)


# load data ---------------------------------------------------------------


# Read in the file
bibfile<-"./publications/EMB_publications/EMB_publications.bib"

# select destination folder -----------------------------------------------


# Identify the folder in which publications are kept
outfold<-"./publications/articles"

abstract = TRUE
overwrite = TRUE

# Import the bibtex file and convert to data.frame
mypubs   <- ReadBib(bibfile, check = "warn", .Encoding = "UTF-8") %>%
  as.data.frame() %>%
  rownames_to_column() %>% # retain rownames (as labels for bibtex re-export)
  mutate_all(funs(str_remove_all(.,"[{}\"]"))) %>%   ### remove {}" from bibtext entries
  mutate_all(funs(str_replace_all(.,'\\\\%', '%'))) ### some replace double escaped % for markdown


# mypubs$rowname<-gsub("_","-",mypubs$rowname)
# mypubs$rowname<-paste("pub",nrow(mypubs),sep="_")

# bt first neeed to convert from better biblatex format 
# mypubs$year<-str_split_i(mypubs$date,"-", 1)
mypubs$date<-mypubs$year
mypubs$journal
mypubs <-mypubs %>% 
  mutate(journal = case_when(
    journal == "QUANTITATIVE SCIENCE STUDIES" ~ "Quantiative Science Studies",
    journal == "BIOTROPICA" ~ "Biotropica",
    .default = as.character(journal)))

mypubs$jrnl_short<-gsub(" ","_",tolower(mypubs$journal))


mypubs<-mypubs %>% rowid_to_column() 
mypubs$rowname=paste(mypubs$jrnl_short,mypubs$year,mypubs$rowid,sep="_")


# make bibtype the name of the type column (default for WriteBib)
if (has_name(mypubs, "document_type") & !(has_name(mypubs, "bibtype"))) {
  mypubs <- mypubs %>% rename(bibtype = document_type)
}

# create a function which populates the md template based on the info
# about a publication
# x<-mypubs[3,]
# x<-mypubs[85,]
# x[85,]
x<-mypubs





create_qmd <- function(x) {
  
  #
  # foldername <- paste(x[["date"]], x[["title"]] %>%
  #                       str_replace_all(fixed(" "), "_") %>%
  #                       str_remove_all(fixed(":")) %>%
  #                       str_sub(1, 20), sep = "_")
  #
  # define a date and create filename by using the rowname for each article
  foldername <- x[["rowname"]]
  
  folder = paste0(outfold, "/", foldername)
  sapply(folder, dir.create)
  
  # dir.create(file.path(outfold, foldername), showWarnings = TRUE)
  filename = "index.qmd"
  # start writing
  outsubfold = paste(outfold, foldername, sep="/")
  
  if (!file.exists(file.path(outsubfold, filename)) | overwrite) {
    fileConn <- file.path(outsubfold, filename)
    write("---", fileConn)
    # write(fileConn)
    
    # Title 
    write(paste0("title: \"", x[["title"]], "\""), fileConn, append = T)
    # Year
    write(paste0("date: \"", x[["year"]], "\""), fileConn, append = T)
    
    # Authors. Comma separated list, e.g. `["Bob Smith", "David Jones"]`.
    auth_hugo <- str_replace_all(x["author"], " and ", "\", \"")
    auth_hugo <- stringi::stri_trans_general(auth_hugo, "latin-ascii")
    write(paste0("author: [\"", auth_hugo,"\"]"), fileConn, append = T)
    
    # Journal
    publication <- x[["journal"]]
    x[["publication"]] <- x[["journal"]]
    if (is.na(x[["journal"]])==FALSE) {
      write(paste0("publication: \"", x[["journal"]], "\""), fileConn, append = T)
    } else {
      write("publication: ", fileConn, append = T)
    }
    # 
    # if (!is.na(x[["volume"]])==TRUE) {
    #   volume<-x[["volume"]]
    # } else {
    #   volume<-"volume: 'No volume'"
    # }
    # 
    # 
    x[is.na(x)] <- "none"
    
    # Volume
    
    x[["volume"]]<-str_replace(x[["volume"]], "n/a", "")
    # write(paste0("volume: \"", x[["volume"]], "\""), fileConn, append = T)
    
    
    
    if (is.na(x[["volume"]])==FALSE) {
      write(paste0("volume: \"", x[["volume"]], "\""), fileConn, append = T)
    } else {
      write("volume: ", fileConn, append = T)
    }
    # 
    # 
    # Number
    if ((is.na(x[["number"]]))==FALSE) {
      write(paste0("number: \"", x[["number"]], "\""), fileConn, append = T)
    } else {
      write("number: 'No number'", fileConn, append = T)
    }
    
    # Pages
    x[["pages"]]<-gsub("--","-",x[["pages"]])
    
    if ((is.na(x[["pages"]]))==FALSE) {
      write(paste0("pages: \"", x[["pages"]], "\""), fileConn, append = T)
    } else {
      write("pages: ", fileConn, append = T)
    }
    
    
    # DOI
    if ((is.na(x[["doi"]]))==FALSE) {
      write(paste0("doi: \"", x[["doi"]], "\""), fileConn, append = T)
    } else {
      write("doi: ", fileConn, append = T)
    }
    
    
    # Abstract and optional shortened version.
    x[["abstract"]]<-gsub("&gt;",">",x[["abstract"]])
    x[["abstract"]]<-gsub("\\\\","",x[["abstract"]])
    
    
    
    if ((is.na(x[["abstract"]]))==FALSE) {
      write(paste0("abstract: \"", x[["abstract"]], "\""), fileConn, append = T)
    } else {
      write("abstract: ", fileConn, append = T)
    }
    
    # Categories Comma separated list, e.g. `["term1", "term2"]`.
    # x<-x %>% re name(keywords1=keywords,
    #                 keywords2=`keywords-plus`) %>% 
    #   mutate(keywords2=tolower(keywords2)) %>% 
    #   relocate(keywords2,.after=keywords1)
    # 
    # 
    x[["keywords-plus"]]<-str_replace_all(x[["keywords-plus"]], c("[;]"=","))
    x[["keywords-plus"]]<-tolower(x[["keywords-plus"]])
    x[["keywords"]]<-paste0(x[["keywords-plus"]],x[["keywords"]], sep = ",")
    x[["keywords"]]<-str_replace_all(x[["keywords"]], c("NA,"=""))
    x[["keywords"]]<-str_replace_all(x[["keywords"]], c("NA"=""))
    x[["keywords"]]<-str_replace_all(x[["keywords"]], c("[//*]"=","))
    x[["keywords"]]<-str_replace_all(x[["keywords"]], "[/*]", ",")
    x[["keywords"]]<-str_replace_all(x[["keywords"]], "[:]", "-")
    # x[["keywords"]]<-str_replace_all(x[["keywords"]], "[ //n]", "")
    x[["keywords"]]<- stringi::stri_trans_general(x[["keywords"]], "latin-ascii")
    
    if ((is.na(x[["keywords"]]))==TRUE) {
      write("categories: ", fileConn, append = T)
    } else {
      write("categories: ", fileConn, append = T)
      kw<-as.data.frame(x[["keywords"]])
      
      names(kw)<-"kw"
      cat_hugo<-kw %>% separate_longer_delim(kw, delim = ",")
      cat_hugo$prefix<-'  - '
      cat_hugo$kw<-paste0(cat_hugo$prefix,cat_hugo$kw,sep="")
      write(cat_hugo$kw,fileConn, append = T)
      # write(paste0("categories: ", kw,""),fileConn, append = T)
      # for(i in 1:nrow(cat_hugo)) {
      #   write(cat("  - ", cat_hugo$kw[i], "\n"), fileConn, append = T)
      # }
      # write("\n", fileConn, append = T)
    }
    # write(paste0("categories: "), fileConn, append = T)
    # write(cat_hugo, fileConn, append = T)
    
    write("url: ", fileConn, append = T)
    
    # # URL
    # if ((is.na(x[["url"]]))==FALSE) {
    #   write(paste0("url: \"", x[["url"]], "\""), fileConn, append = T)
    # } else {
    #   write("url: \"\"", fileConn, append = T)
    # }
    # Publication type. Legend:
    # 0 = Uncategorized, 1 = Conference paper, 2 = Journal article
    # 3 = Manuscript, 4 = Report, 5 = Book,  6 = Book section
    # write(paste0("type: \"", x[["bibtype"]],"\""),
    #       fileConn, append = T)
    
    
    pdf_folder <- x[["file"]]
    pdf_folder<-as_tibble(pdf_folder) 
    
    pdf_info<-pdf_folder %>% 
      separate(value,c("value","folder"),extra="drop") %>% 
      mutate(value=paste("./publications/articles/files",folder,"*.pdf",sep = "/")) %>% 
      replace_na(list(folder="missing"))
    pdf_folder<-as.vector(pdf_info$value)
    folder<-as.vector(pdf_info$folder)
    
    
    
    # write(paste0("full_citation: \"", publication,"\""), fileConn, append = T)
    
    # write(paste0("categories: \"", "TBD\""), fileConn, append = T)
    
    
    
    
    
    # Image
    write(paste0("image: featured.png"),fileConn, append = T)
    # Preprint
    write("url_preprint: \"\"", fileConn, append = T)
    # Code
    write("url_code: \"\"", fileConn, append = T)
    # Data set
    write("url_dataset: \"\"", fileConn, append = T)
    
    
    
    # OTHER STUFF
    
    # keywords<-x[["keywords"]] 
    # keywords <- str_replace_all(x["keywords"], ",", "\", \"")
    # keywords <- stringi::stri_trans_general(keywords, "latin-ascii")
    # write(paste0("keywords = [\"", keywords,"\"]"), fileConn, append = T)
    
    # write("image_preview: \"\"", fileConn, append = T)
    
    # write("selected: false", fileConn, append = T)
    
    # write("projects = []", fileConn, append = T)
    
    # write("tags: []", fileConn, append = T)
    
    # write("url_project: \"\"", fileConn, append = T)
    
    # write("url_slides: \"\"", fileConn, append = T)
    
    # write("url_video: \"\"", fileConn, append = T)
    
    # write("url_poster: \"\"", fileConn, append = T)
    
    # write("url_source: \"\"", fileConn, append = T)
    
    # toc: false
    
    # title-block-style: none
    
    # write("highlight = true", fileConn, append = T)
    
    current.folder <-paste("./publications/EMB_publications/files/",folder,"/",sep = "")
    new.folder <- paste("./publications/articles",foldername,"",sep="/")
    
    # find the files that you want
    list.of.files <- list.files(current.folder)
    new_name<-str_split(list.of.files," - ", n = 3)
    new_name<-unlist(new_name)
    new_name<-paste(new_name[1],new_name[2])
    new_name<-gsub(" ", "_",new_name)
    new_name<-gsub("[.]", "",new_name)
    new_name<-paste(new_name,".pdf",sep="")
    file.rename(from = (paste(current.folder,
                              (list.files(current.folder)),sep="/")), 
                to = (paste(current.folder,new_name,sep="/")))
    
    # copy the files to the new folder
    file.copy(paste(current.folder,"/",new_name,sep=""), new.folder)
    
    
    write(paste0("bib: './articles/", x[["rowname"]],"/cite.bib'",sep="",collapse="|"),fileConn, append = T)
    write(paste0("pdf: './articles/",  x[["rowname"]],"/",new_name,"'",sep="",collapse="|"),fileConn, append = T)
    
    write("---", fileConn, append = T)
    
    
  }
  
  # convert entry back to data frame
  df_entry = as.data.frame(as.list(x), stringsAsFactors=FALSE) %>%
    column_to_rownames("rowname")
  
  # write cite.bib file to outsubfolder
  WriteBib(as.BibEntry(df_entry[1,]), paste(outsubfold, "cite.bib", sep="/"))
  
  
  
  # Move the pdf files
  # identify the folders
  
  
  # '", pdf_folder,"'",sep=""),fileConn, append = T)
  
}
# apply the "create_qmd" function over the publications list to generate
# the different "qmd" files.
# x<-mypubs


# run it ------------------------------------------------------------------



apply(mypubs, FUN = function(x) create_qmd(x), MARGIN = 1)
# }


# # To rename the pdfs
# # directory<-"./EMB_publications/files"
# path = "./publications/articles/"
# folder_names<-list.files(path)
# file_paths<-paste(path,folder_names,sep="")
# directory<-as.data.frame(directory)
# list.files(file_paths) # only file name
# list.files(file_paths, full.names=TRUE) # full path
# old_file_names<-list.files(file_paths, full.names=TRUE) # full path


# DO I NEED THIS?
# 
# # get only the ones that are pdf
# old_file_names<-Filter(function(x) str_detect(x, "pdf$"), old_file_names)
# pathsplit<-str_split(old_file_names, "/", simplify = TRUE)
# new_file_names<-paste(pathsplit[,1],pathsplit[,2],pathsplit[,3],pathsplit[,4],pathsplit[,4],sep="/")
# new_file_names<-paste(new_file_names,".pdf",sep="")
# file.rename(old_file_names,new_file_names)











#
#
#   #
#   # new_name_fcn <- function(x) {
#   #   new_name<-paste(x, list.files(x),sep="/")
#   #   return(new_name)
#   # }
#   #
#   # library(purrr)
#   # x <- nrow(directory)
#   #  <- map(1:x, paste(directory, list.files[.directory,sep="/"))
#   #
#   # file_names_new<-new_name_fcn(directory)
#   # new_name_fcn(x)<-paste(x, list.files(x),sep="/")
#   # file_names_new<-sapply(directory,new_name_fcn)
#   directory<-directory[10]
#   file_names_old<-list.files(directory)
#   file_names_new <- paste0(folder_names,".pdf")
#   file.rename(
#     paste0(directory,file_names_old,sep="/"),       # Rename files
#               paste0(directory[10], "/",file_names_new[10])
#
#   file.rename("./EMB_publications/files/3739/3739.pdf",
#               "./EMB_publications/files/3739/Araujo_etal_2013_PlantEcology.pdf")


# # option 2 ----------------------------------------------------------------
#
# #
# # NOT AS COOL
#
# # https://amirdjv.netlify.app/post/converting-bibtex-files-to-md-files/
# # https://github.com/petzi53/bib2academic
# devtools::install_github("petzi53/bib2academic")
# library(bib2academic)
# library(bibtex)
# bib2acad(bibfile = "./EMB_publications/EMB_publications.bib", copybib = TRUE, abstract = TRUE,overwrite = FALSE)
#
# bib2acad(
#   paste(
#     getwd(),
#     "./EMB_publications.bib",
#     sep = "/"),
#   copybib = TRUE, abstract = TRUE, overwrite = TRUE)
#
# bibFiles <- list.files("my-bib-folder", full.names = TRUE)
# mdFiles <- list.files("my-md-folder", full.names = TRUE)
#
#
# file.copy(from = bibFiles, to = "static/files/citations/")
# file.copy(from = mdFiles, to = "content/publication/")
#
# blogdown::serve_site()
# #
# #
# #