Adds access to Zotero group libraries via BBT. Resolves #9

.gitignore

@@ -2,5 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
-
-*.Rproj
+*.Rproj
+.DS_Store

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: citr
 Type: Package
 Title: 'RStudio' Add-in to Insert Markdown Citations
-Description: Functions and an 'RStudio' add-in that search a 'BibTeX'-file to create and
+Description: Functions and an 'RStudio' add-in that search a 'Bib(La)TeX'-file to create and
   insert formatted Markdown citations into the current document.
-Version: 0.2.0.9047
-Date: 2016-9-20
+Version: 0.2.0.9055
+Date: 2017-12-17
 Authors@R: c(
   person("Frederik", "Aust", email = "frederik.aust@uni-koeln.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4900-788X")),
   person("Yihui", "Xie", role = "ctb")
@@ -22,9 +22,11 @@ Imports:
   assertthat (>= 0.1),
   methods (>= 3.0.0),
   curl (>= 1.1),
+  httr (>= 1.3.1),
   stringi (>= 1.1.2)
 Suggests:
   testthat (>= 1.0.2)
 License: MIT + file LICENSE
+Encoding: UTF-8
 LazyData: TRUE
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1.9000

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2016
-COPYRIGHT HOLDER: Frederik Aust
+COPYRIGHT HOLDER: Frederik Aust

R/insert_citation.R

@@ -32,6 +32,7 @@
 insert_citation <- function(
   bib_file = getOption("citr.bibliography_path")
   , use_betterbiblatex = getOption("citr.use_betterbiblatex")
+  , betterbiblatex_format = getOption("citr.betterbiblatex_format")
   , encoding = getOption("citr.encoding")
 ) {
   assert_that(is.character(bib_file))
@@ -45,6 +46,11 @@ insert_citation <- function(
   } else stop("The use of this addin requires RStudio 0.99.796 or newer (your version is ", rstudioapi::versionInfo()$version, ").")
 
   betterbiblatex <- betterbiblatex_available()
+  if(betterbiblatex) {
+    bbt_libraries <- query_bbt_libraries()
+    bbt_libraries_options <- unlist(bbt_libraries[, "name"])
+    names(bbt_libraries_options) <- unlist(bbt_libraries[, "name"])
+  }
 
   # Get bibliography files from YAML front matter if available
   ## Let's hope this doesn't cause too much trouble; this is a lot more sofisticated in rmarkdown, but the functions are not exported.
@@ -119,7 +125,7 @@ insert_citation <- function(
       stableColumnLayout(
         selectizeInput(
           "selected_key"
-          , choices = c(`No references found` = "")
+          , choices = c("No references found" = "")
           , label = ""
           , width = 700
           , multiple = TRUE
@@ -137,13 +143,14 @@ insert_citation <- function(
       hr(),
       uiOutput("bib_file"),
       uiOutput("zotero_status"),
-      uiOutput("read_error")
+      uiOutput("read_error"),
+      uiOutput("bbt_libraries")
     )
   )
 
   server <- function(input, output, session) {
 
-    reactive_variables <- reactiveValues(reload_bib = "init", use_betterbiblatex = use_betterbiblatex) # Set initial value
+    reactive_variables <- reactiveValues(reload_bib = "init", use_betterbiblatex = use_betterbiblatex, zotero_options = FALSE) # Set initial value
 
     # Zotero use
     observeEvent(input$disconnect_zotero, {
@@ -164,12 +171,18 @@ insert_citation <- function(
       reactive_variables$reload_bib <- paste0(sample(letters, 100, replace = TRUE), collapse = "") # Do stuff to trigger reload_bib reactive
     })
 
+    observeEvent(input$zotero_toggle_options, {
+      reactive_variables$zotero_options <- !reactive_variables$zotero_options
+    })
+
     output$zotero_status <- renderUI({
       if(betterbiblatex) {
         if(reactive_variables$use_betterbiblatex) {
           helpText(
             "Connected to Zotero."
-            , actionLink("discard_cache", "Reload database")
+            , actionLink("discard_cache", if(length(bibliography()) == 0) "Load libraries" else "Reload libraries")
+            , "|"
+            , actionLink("zotero_toggle_options", if(!reactive_variables$zotero_options) "Select group libraries" else "Hide group libraries")
             , "|"
             , actionLink("disconnect_zotero", "Disconnect")
           )
@@ -182,6 +195,20 @@ insert_citation <- function(
       }
     })
 
+    output$bbt_libraries <- renderUI({
+      if(betterbiblatex) {
+        if(length(bbt_libraries_options) > 1 && reactive_variables$use_betterbiblatex && reactive_variables$zotero_options) {
+          checkboxGroupInput(
+            "zotero_groups"
+            , label = NULL
+            , choices = as.list(bbt_libraries_options)
+            , selected = bbt_libraries_options[!bbt_libraries_options %in% c(getOption("citr.exclude_betterbiblatex_library"), "citr_dummy")]
+            , inline = TRUE
+          )
+        } else NULL
+      }
+    })
+
     output$bib_file <- renderUI({
       if(is.null(yaml_bib_file)) {
         div(
@@ -238,19 +265,39 @@ insert_citation <- function(
         is.null(getOption("citr.bibliography_cache")) || (is.character(getOption("citr.bibliography_cache")) && grepl("^Error: ", getOption("citr.bibliography_cache"))) #||
         # (!is.null(yaml_bib_file) && !isTRUE(all.equal(absolute_yaml_bib_file, getOption("citr.bibliography_path"))))
       ) {
-        withProgress({
+        shiny::withProgress({
           if(betterbiblatex && reactive_variables$use_betterbiblatex) {
 
             if(!is.null(input$update_bib)) options(citr.bibliography_path = input$update_bib)
-            current_bib <- load_betterbiblatex_bib(encoding)
+
+            if(reactive_variables$reload_bib == "init") {
+              current_bib <- c()
+            } else {
+              exclude_betterbiblatex_library <- c(bbt_libraries_options[!bbt_libraries_options %in% input$zotero_groups], "citr_dummy")
+
+              options("citr.exclude_betterbiblatex_library" = exclude_betterbiblatex_library)
+
+              if(!all(bbt_libraries_options %in% exclude_betterbiblatex_library)) {
+                current_bib <- load_betterbiblatex_bib(
+                  encoding = encoding
+                  , betterbiblatex_format = betterbiblatex_format
+                  , exclude_betterbiblatex_library = exclude_betterbiblatex_library
+                  , increment_progress = TRUE
+                )
+              } else {
+                current_bib <- c()
+              }
+            }
 
           } else {
             if(is.null(yaml_bib_file)) { # Use specified bibliography
 
               if(!is.null(input$read_bib)) {
                 options(citr.bibliography_path = input$read_bib)
+                setProgress(detail = input$read_bib)
                 current_bib <- tryCatch(RefManageR::ReadBib(file = input$read_bib, check = FALSE, .Encoding = encoding), error = error_handler)
               } else {
+                setProgress(detail = getOption("citr.bibliography_path"))
                 current_bib <- tryCatch(RefManageR::ReadBib(file = getOption("citr.bibliography_path"), check = FALSE, .Encoding = encoding), error = error_handler)
               }
 
@@ -259,9 +306,14 @@ insert_citation <- function(
               options(citr.bibliography_path = absolute_yaml_bib_file)
 
               if(length(yaml_bib_file) == 1) {
+                setProgress(detail = basename(absolute_yaml_bib_file))
                 current_bib <- tryCatch(RefManageR::ReadBib(file = absolute_yaml_bib_file, check = FALSE, .Encoding = encoding), error = error_handler)
               } else {
-                bibs <- lapply(absolute_yaml_bib_file, function(file) tryCatch(RefManageR::ReadBib(file, check = FALSE, .Encoding = encoding), error = error_handler))
+                bibs <- lapply(absolute_yaml_bib_file, function(file) {
+                  setProgress(detail = basename(file))
+                  tryCatch(RefManageR::ReadBib(file, check = FALSE, .Encoding = encoding), error = error_handler)
+                  shiny::incProgress(1/length(absolute_yaml_bib_file))
+                  })
 
                 ## Merge if multiple bib files were imported succesfully
                 not_found <- sapply(bibs, is.null)
@@ -270,7 +322,7 @@ insert_citation <- function(
               }
             }
           }
-        }, message = "Loading bibliography...")
+        }, message = "Loading Zotero libraries...")
 
         ## Cache bibliography
         options(citr.bibliography_cache = current_bib)
@@ -290,9 +342,10 @@ insert_citation <- function(
         citation_keys <- citation_keys[order(current_references)]
         names(citation_keys) <- current_references[order(current_references)]
 
-        updateSelectInput(session, "selected_key", choices = c(`Search terms` = "", citation_keys), label = "")
+        updateSelectInput(session, "selected_key", choices = c("Search terms" = "", citation_keys), label = "")
       } else {
-        updateSelectInput(session, "selected_key", c(`.bib-file(s) not found` = ""), label = "")
+        selected_key_default <- if(betterbiblatex && reactive_variables$use_betterbiblatex) c("No citations found. (Re-)Load Zotero libraries." = "") else c(".bib-file(s) not found" = "")
+        updateSelectInput(session, "selected_key", selected_key_default, label = "")
       }
     })
 

R/md_cite_zotero.R

@@ -3,7 +3,6 @@
 #' Look up entries in Zotero database and insert citation in Markdown format.
 #'
 #' @param in_paren Logical. Determines if citation is in parentheses.
-#' @param bib_file Character. Path to Bib(La)TeX-file. See details.
 #'
 #' @details The path to the Bib(La)TeX-file can be set in the global options and is set to
 #'    \code{references.bib} when the package is loaded. Once the path is changed in the
@@ -17,14 +16,13 @@
 #'
 #' @examples
 #' \dontrun{
-#'   md_cite_zotero(bib_file = "references.bib")
+#'   md_cite_zotero()
 #' }
 #'
 #' @import assertthat
 
 md_cite_zotero <- function(
   in_paren = TRUE
-  , bib_file = options("citr.bibliography_path")
 ) {
   if(!betterbiblatex_available()) stop("Could not connect to Zotero's Better-BibTeX extension. Is Zotero up and running?")
   assert_that(is.flag(in_paren))

R/onload.R

@@ -3,7 +3,9 @@
   op_citr <- list(
     citr.bibliography_path = "./references.bib"
     , citr.bibliography_cache = NULL
+    , citr.betterbiblatex_format = "bibtex"
     , citr.use_betterbiblatex = TRUE
+    , citr.exclude_betterbiblatex_library = NULL
     , citr.parent_documents = c("index.Rmd", "master.Rmd")
     , citr.encoding = "UTF-8"
   )

R/query_bib.R

@@ -8,8 +8,10 @@
 #' @param cache Logical. If \code{cache = TRUE} cached bibliography is used, if available. If
 #'    \code{cache = FALSE} bibliography is re-imported on every function call.
 #' @param use_betterbiblatex Logical. If \code{use_betterbiblatex = TRUE} references are imported from Zotero/Juris-M.
+#' @param betterbiblatex_format Charcter. Bibliography format to export from Zotero/Juris-M. Can be either \code{"bibtex"} or \code{"biblatex"}. Ignored if \code{use_betterbiblatex = FALSE}.
 #'    Requires that the \href{https://github.com/retorquere/zotero-better-bibtex}{Better Bib(La)TeX} is installed and
 #'    Zotero/Juris-M is running.
+#' @param exclude_betterbiblatex_library Character. A vector of Zotero/Juris-M library names not to query.
 #' @param encoding Character. Encoding of the Bib(La)TeX-file.
 #'
 #' @details The path to the BibTeX-file can be set in the global options and is set to
@@ -28,6 +30,8 @@ query_bib <- function(
   , bib_file = getOption("citr.bibliography_path")
   , cache = TRUE
   , use_betterbiblatex = getOption("citr.use_betterbiblatex")
+  , betterbiblatex_format = getOption("citr.betterbiblatex_format")
+  , exclude_betterbiblatex_library = getOption("citr.exclude_betterbiblatex_library")
   , encoding = getOption("citr.encoding")
 ) {
   assert_that(is.string(x))
@@ -37,12 +41,16 @@ query_bib <- function(
   if(use_betterbiblatex && !betterbiblatex_available()) {
     message("Could not connect to Zotero's Better-BibTeX extension; importing references from", bib_file, ". Is Zotero up and running?")
   }
+  assert_that(is.string(betterbiblatex_format))
+  if(!betterbiblatex_format %in% c("bibtex", "biblatex")) stop("Bibliography format not supported. Use either 'bibtex'  or 'biblatex'.")
+  assert_that(is.string(encoding))
 
   # Use cached bibliography, if available
   if(is.null(getOption("citr.bibliography_cache")) || !cache) {
 
     if(use_betterbiblatex & betterbiblatex_available()) {
-      bib <- load_betterbiblatex_bib(encoding)
+      cat("Connecting to Zotero...\n")
+      bib <- load_betterbiblatex_bib(encoding, betterbiblatex_format, exclude_betterbiblatex_library)
     } else {
       bib <- RefManageR::ReadBib(file = bib_file, check = FALSE, .Encoding = encoding)
     }
@@ -127,38 +135,82 @@ betterbiblatex_available <- function() {
   )
 }
 
-load_betterbiblatex_bib <- function(encoding) {
+load_betterbiblatex_bib <- function(encoding, betterbiblatex_format = "bibtex", exclude_betterbiblatex_library = NULL, increment_progress = FALSE) {
+
+  bib <- c()
+  bbt_libraries <- query_bbt_libraries()
+
+  if(is.null(bbt_libraries)) {
+    betterbibtex_url <- paste0("http://localhost:23119/better-bibtex/library?library.", betterbiblatex_format)
+    bib <- import_bbt_piecewise(bib, betterbibtex_url, encoding, increment_progress)
+  } else {
+    betterbibtex_baseurl <- "http://localhost:23119/better-bibtex/library?/"
+    bbt_libraries <- bbt_libraries[!unlist(bbt_libraries[, "name"] %in% exclude_betterbiblatex_library), , drop = FALSE]
+    group_library_id <- unlist(bbt_libraries[, "id"])
+
+    for(bib_i in group_library_id) {
+      betterbibtex_url_i <- paste0(betterbibtex_baseurl, bib_i, "/library.", betterbiblatex_format)
+      group_library_name_i <- unlist(bbt_libraries[unlist(bbt_libraries[, "id"]) == bib_i, "name"])
+      if(increment_progress) {
+        setProgress(detail = paste0("\n'", group_library_name_i[[1]], "'"))
+      } else {
+        cat("Importing '", group_library_name_i, "'...\n", sep = "")
+      }
+
+      bib <- import_bbt_piecewise(
+        bib
+        , betterbibtex_url_i
+        , encoding
+        , increment_progress = increment_progress
+        , progress_share = 1 / length(group_library_id)
+      )
+    }
+  }
+
+  class(bib) <- c("BibEntry", "bibentry")
+  bib
+}
 
-  # library("httr")
-  # bb_response <- POST(
-  #   bb_library_url
-  #   , add_headers("Content-Type" = "application/json")
-  #   , body = '{"jsonrpc": "2.0", "method": "libraries" }'
-  #   , encode = "json"
-  # )
-  #
-  # headers(bb_response)$`x-zotero-version`
-  # do.call(rbind, content(bb_response)$result)
 
-  betterbibtex_url <- "http://localhost:23119/better-bibtex/library?library.biblatex"
-  betterbibtex_bib <- rawToChar(curl::curl_fetch_memory(url = betterbibtex_url)$content)
-  betterbibtex_bib <- strsplit(betterbibtex_bib, "@comment\\{jabref-meta")[[1]][1] # Remove jab-ref comments
-  betterbibtex_entries <- strsplit(gsub("(@\\w+\\{)", "~!citr!~\\1", betterbibtex_bib), "~!citr!~" )[[1]]
+import_bbt_piecewise <- function(x, location, encoding, increment_progress, progress_share = 1) {
+  betterbibtex_bib_i <- rawToChar(curl::curl_fetch_memory(url = location)$content)
+  betterbibtex_bib_i <- strsplit(betterbibtex_bib_i, "@comment\\{jabref-meta")[[1]][1] # Remove jab-ref comments
+  betterbibtex_entries_i <- strsplit(gsub("(@\\w+\\{)", "~!citr!~\\1", betterbibtex_bib_i), "~!citr!~" )[[1]]
 
   # Create and read multiple biblatex files because bibtex::read.bib does not work with large files
-  bib <- c()
-  no_batches <- length(betterbibtex_entries) %/% 100 + 1
+  no_batches <- length(betterbibtex_entries_i) %/% 100 + 1
 
-  for(i in seq_len(no_batches)) {
+  for(j in seq_len(no_batches)) {
     tmp_bib_file <- paste0(paste(sample(c(letters, LETTERS, 0:9), size = 32, replace = TRUE), collapse = ""), ".bib")
 
-    writeLines(betterbibtex_entries[((i-1) * 100 + 1):min(i * 100, length(betterbibtex_entries))], con = file(tmp_bib_file, encoding = encoding))
-    bib <- c(bib, RefManageR::ReadBib(file = tmp_bib_file, check = FALSE))
+    tmp_con <- file(tmp_bib_file, encoding = encoding)
+    writeLines(betterbibtex_entries_i[((j-1) * 100 + 1):min(j * 100, length(betterbibtex_entries_i))], con = tmp_con)
+    close(tmp_con)
+
+    x <- c(x, RefManageR::ReadBib(file = tmp_bib_file, check = FALSE, .Encoding = encoding))
     file.remove(tmp_bib_file)
+
+    if(increment_progress) shiny::incProgress((1 / no_batches) * progress_share)
   }
 
-  try(on.exit(file.remove(tmp_bib_file)))
+  try(on.exit(suppressWarnings(file.remove(tmp_bib_file))), silent = TRUE)
+  x
+}
 
-  class(bib) <- c("BibEntry", "bibentry")
-  bib
+
+query_bbt_libraries <- function(x) {
+  # If installed BBT is >= 5.0.50 use JSON-RPC to qurey library IDs
+  bbt_json_response <- httr::POST(
+    "http://localhost:23119/better-bibtex/json-rpc"
+    , httr::add_headers("Content-Type" = "application/json")
+    , body = '{"jsonrpc": "2.0", "method": "user.groups" }'
+    , encode = "json"
+  )
+
+  if(any(grepl("No endpoint found", httr::content(bbt_json_response)))) {
+    NULL
+  } else {
+    do.call(rbind, httr::content(bbt_json_response)$result)
+  }
 }
+

inst/rstudio/addins.dcf

@@ -1,4 +1,4 @@
 Name: Insert citations
 Description: Inserts Markdown citations
 Binding: insert_citation
-Interactive: true
+Interactive: true