Merge pull request #114 from haozhu233/master

Added an "Add Crossref Citations" Rstudio addin

DESCRIPTION

@@ -26,9 +26,12 @@ Imports:
     plyr,
     bibtex,
     dplyr (>= 0.5.0),
-    R6
+    R6,
+    shiny,
+    miniUI,
+    stringr
 Suggests:
     testthat,
     knitr,
     covr
-RoxygenNote: 5.0.1.9000
+RoxygenNote: 5.0.1

NAMESPACE

@@ -61,10 +61,30 @@ importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)
 importFrom(methods,as)
 importFrom(methods,is)
+importFrom(miniUI,gadgetTitleBar)
+importFrom(miniUI,miniContentPanel)
+importFrom(miniUI,miniPage)
 importFrom(plyr,ldply)
 importFrom(plyr,llply)
 importFrom(plyr,rbind.fill)
+importFrom(shiny,HTML)
+importFrom(shiny,actionButton)
+importFrom(shiny,dialogViewer)
+importFrom(shiny,fillRow)
+importFrom(shiny,h4)
+importFrom(shiny,htmlOutput)
+importFrom(shiny,observeEvent)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,renderUI)
+importFrom(shiny,req)
+importFrom(shiny,runGadget)
+importFrom(shiny,stopApp)
+importFrom(shiny,textInput)
+importFrom(shiny,uiOutput)
+importFrom(shiny,updateTextInput)
 importFrom(stats,setNames)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_match)
 importFrom(utils,modifyList)
 importFrom(utils,packageVersion)
 importFrom(xml2,read_xml)

R/crAddins.R

@@ -0,0 +1,121 @@
+crAddins <- function() {
+  ui <- miniPage(
+    gadgetTitleBar("Add Crossref Citations"),
+    miniContentPanel(
+      h4("Add a new bibliography entry through Crossref DOI", 
+         class="text-center", style="padding-bottom: 15px;"),
+      fillRow(flex = c(7, 3), height = "45px",
+              uiOutput("cr_input"), uiOutput("add_to_my_citations")),
+      htmlOutput("preview")
+    )
+  )
+
+  server <- function(input, output, session) {
+    output$cr_input <- renderUI({
+      textInput("entered_dois", label = NULL, 
+                placeholder = "Enter a DOI to get started", width = "98%")
+    })
+
+    output$add_to_my_citations <- renderUI({
+      actionButton("add_citations", label = "Add to My Citations",
+                   width = "100%", class="btn-primary")
+    })
+
+    preview_message <- reactiveValues(added = 0, error = 0)
+
+    output$preview <- function(){
+      if(is.null(input$entered_dois))return(NULL)
+      if(input$entered_dois == "" & preview_message$added == 1){return(
+        HTML("<strong style='color:green;'>This citation has been saved ", 
+             "to crossref.bib</strong>")
+      )}
+      if(input$entered_dois == "" & preview_message$error == 1){return(
+        HTML("<strong style='color:red;'>Please make sure you have a valid ", 
+             "Crossref DOI before you save it.</strong>")
+      )}
+      if(substr(input$entered_dois, 1, 3) != "10.")return(NULL)
+      contents <- suppressWarnings(try(cr_cn(dois = input$entered_dois, 
+                         format = "citeproc-json"), silent = TRUE))
+      if(class(contents) == "try-error"){
+        HTML("<strong>Article Not Found.</strong>")
+      }else{
+        HTML(paste0(
+          `if`(is.null(contents$type), NULL, paste0(
+            "<strong>Type:</strong> ", contents$type, "<br>")),
+          `if`(is.null(contents$title), NULL, paste0(
+            "<strong>Title:</strong> ", contents$title, "<br>")),
+          `if`(is.null(contents$author), NULL, 
+              paste0("<strong>Author:</strong> ", 
+                      paste0(paste(contents$author$given, 
+                                   contents$author$family), 
+                             collapse = "; "), "<br>")),
+          `if`(is.null(contents$created), NULL, 
+              paste0("<strong>Time:</strong> ",
+                     contents$created$`date-parts`[1,1], "<br>")),
+          `if`(is.null(contents$publisher), NULL, 
+               paste0("<strong>Publisher:</strong> ",
+                      contents$publisher))
+        ))
+      }
+    }
+
+    parsename <- function(name, isRegx = TRUE){
+      if(isRegx){
+        paste0("\\n\\t", name)
+      }else{
+        paste0("\n\t", name)
+      }
+    } 
+
+    extract_bib <- function(bib, name, regex){
+      regex_full <- paste0(
+        parsename(name), "\\s=\\s", regex
+      )
+      out <- str_match(bib, regex_full)
+      return(out[2])
+    }
+
+    correct_bib <- function(bib){
+      out <- bib
+      if(!str_detect(bib, parsename("author"))){
+        title <- "Untitle"
+        if(str_detect(bib, parsename("title"))){
+          title <- extract_bib(bib, "title", "[^\\w]*(\\w*)")
+        }
+        original <- paste0("\\{.*,", parsename("doi"))
+        if(str_detect(bib, parsename("year"))){
+          year <- extract_bib(bib, "year", "(\\d*)")
+          new <- paste0("\\{", title, "_", year, ",", parsename("doi", F))
+        }else{
+          new <- paste0("\\{", title, ",", parsename("doi", F))
+        }
+        out <- sub(original, new, bib)
+      }
+      return(out)
+    }
+
+    observeEvent(input$add_citations, {
+      bib_to_write <- suppressWarnings(try(cr_cn(dois = input$entered_dois),
+                                           silent = TRUE))
+      if(class(bib_to_write) != "try-error"){
+        if(!"crossref.bib" %in% list.files()){file.create("crossref.bib")}
+        bib_to_write <- correct_bib(bib_to_write)
+        write(paste0(bib_to_write, "\n"), "crossref.bib", append = T)
+        updateTextInput(session, "entered_dois", value = "")
+        preview_message$added <- 1
+        preview_message$error <- 0
+      }else{
+        updateTextInput(session, "entered_dois", value = "")
+        preview_message$added <- 0
+        preview_message$error <- 1
+      }
+    })
+
+    observeEvent(input$done, {
+      invisible(stopApp())
+    })
+  }
+
+  viewer <- dialogViewer("Add Crossref Citations", width = 600, height = 800)
+  runGadget(ui, server, viewer = viewer)
+}

R/rcrossref-package.R

@@ -50,6 +50,11 @@
 #' write_disk accept http_status parse_url add_headers config user_agent
 #' @importFrom jsonlite toJSON fromJSON
 #' @importFrom plyr rbind.fill llply ldply
+#' @importFrom shiny h4 fillRow htmlOutput renderUI textInput actionButton req
+#' HTML observeEvent updateTextInput stopApp dialogViewer runGadget uiOutput
+#' reactiveValues
+#' @importFrom miniUI miniPage gadgetTitleBar miniContentPanel
+#' @importFrom stringr str_detect str_match
 #' @name rcrossref-package
 #' @aliases rcrossref
 #' @docType package

inst/rstudio/addins.dcf

@@ -0,0 +1,4 @@
+Name: Add Crossref Citations
+Description: Add a new bibliography entry through Crossref DOI
+Binding: crAddins
+Interactive: true