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inst/shiny-examples/citationchaser/mixed_id_wrapper.R

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+#' Wrapper for multiple input ID types
+#' 
+#' @description A wrapper function allowing the searching of multiple different 
+#' identifiers at once.
+#' @param input a dataframe with one column containing the record identifiers, 
+#' and a second column detailing the type of ID (must be one of the following: 
+#' 'doi', 'pmid', 'opmcid', 'coreid', 'magid', or 'lens_id'.)
+#' @param search The type of search to be run, whether looking up citations 
+#' to populate the input table ('input'), or references for backward 
+#' citation chasing ('references'), citing articles for forward citation 
+#' chasing ('citations') or both references and citations ('both').
+#' @param token The lens.org API access token.
+#' @return A list of three outputs: a data-table for presentation in the Shiny 
+#' app, an RIS (text) file containing all citations, and a dataframe with the 
+#' full JSON output from the lens.org API query.
+#' @examples 
+#' \dontrun{
+#' ids <- c('10.1007/978-3-642-37048-9_13', 
+#'          '10.1111/sum.12030', 
+#'          '10.5194/bg-13-3619-2016', 
+#'          '10.1016/j.agee.2012.09.006',
+#'          '32652585',
+#'          '32706299')
+#' type <- c('doi', 
+#'           'doi', 
+#'           'doi', 
+#'           'doi', 
+#'           'pmid', 
+#'           'pmid')
+#' input <- data.frame(ids, type)
+#' test1 <- get_refs_mixed(input, search = 'input', token = token)
+#' test2 <- get_refs_mixed(input, search = 'references', token = token)
+#' }
+get_refs_mixed <- function(input,
+                           search,
+                           token){
+
+  #split input data by ID type
+  #doi <- split(input, input$type)$doi
+  #pmid <- split(input, input$type)$pmid
+  #pmcid <- split(input, input$type)$pmcid
+  #core <- split(input, input$type)$core
+  #magid <- split(input, input$type)$magid
+  #lens <- split(input, input$type)$lens
+
+  #for each ID type, run a lookup
+  #for input
+  if(search == 'input'){
+    #create blank outputs
+    display <- data.table::data.table(NULL)
+    ris <- ''
+    df <- data.frame()
+
+    #dois
+    if(('doi' %in% input$type) == TRUE){
+      data_doi <- split(input, input$type)$doi
+      id_list_doi <- as.vector(data_doi[,1])
+      intermediate_doi <- get_citation(id_list_doi, type = 'doi', token = token)
+      display_doi <- tryCatch(intermediate_doi$display, error = function(cond){return(NULL)})
+      ris_doi <- tryCatch(intermediate_doi$ris, error = function(cond){return(NULL)})
+      df_doi <- tryCatch(intermediate_doi$df, error = function(cond){return(NULL)})
+      print('DOIs searched')
+    } else {
+      display_doi <- NULL
+      ris_doi <- NULL
+      df_doi <- NULL
+    }
+
+    #pmid
+    if(('pmid' %in% input$type) == TRUE){
+      data_pmid <- split(input, input$type)$pmid
+      id_list_pmid <- as.vector(data_pmid[,1])
+      intermediate_pmid <- get_citation(id_list_pmid, type = 'pmid', token = token)
+      display_pmid <- tryCatch(intermediate_pmid$display, error = function(cond){return(NULL)})
+      ris_pmid <- tryCatch(intermediate_pmid$ris, error = function(cond){return(NULL)})
+      df_pmid <- tryCatch(intermediate_pmid$df, error = function(cond){return(NULL)})
+      print('PMIDs searched')
+    } else {
+      display_pmid <- NULL
+      ris_pmid <- NULL
+      df_pmid <- NULL
+    }
+
+    #pmcid
+    if(('pmcid' %in% input$type) == TRUE){
+      data_pmcid <- split(input, input$type)$pmcid
+      id_list_pmcid <- as.vector(data_pmcid[,1])
+      intermediate_pmcid <- get_citation(id_list_pmcid, type = 'pmcid', token = token)
+      display_pmcid <- tryCatch(intermediate_pmcid$display, error = function(cond){return(NULL)})
+      ris_pmcid <- tryCatch(intermediate_pmcid$ris, error = function(cond){return(NULL)})
+      df_pmcid <- tryCatch(intermediate_pmcid$df, error = function(cond){return(NULL)})
+      print('PMIDs searched')
+    } else {
+      display_pmcid <- NULL
+      ris_pmcid <- NULL
+      df_pmcid <- NULL
+    }
+
+    #magid
+    if(('magid' %in% input$type) == TRUE){
+      data_magid <- split(input, input$type)$magid
+      id_list_magid <- as.vector(data_magid[,1])
+      intermediate_magid <- get_citation(id_list_magid, type = 'magid', token = token)
+      display_magid <- tryCatch(intermediate_magid$display, error = function(cond){return(NULL)})
+      ris_magid <- tryCatch(intermediate_magid$ris, error = function(cond){return(NULL)})
+      df_magid <- tryCatch(intermediate_magid$df, error = function(cond){return(NULL)})
+      print('MAGIDs searched')
+    } else {
+      display_magid <- NULL
+      ris_magid <- NULL
+      df_magid <- NULL
+    }
+
+    #coreid
+    if(('coreid' %in% input$type) == TRUE){
+      data_coreid <- split(input, input$type)$coreid
+      id_list_coreid <- as.vector(data_coreid[,1])
+      intermediate_coreid <- get_citation(id_list_coreid, type = 'coreid', token = token)
+      display_coreid <- tryCatch(intermediate_coreid$display, error = function(cond){return(NULL)})
+      ris_coreid <- tryCatch(intermediate_coreid$ris, error = function(cond){return(NULL)})
+      df_coreid <- tryCatch(intermediate_coreid$df, error = function(cond){return(NULL)})
+      print('COREIDs searched')
+    } else {
+      display_coreid <- NULL
+      ris_coreid <- NULL
+      df_coreid <- NULL
+    }
+
+    #lensid
+    if(('lens_id' %in% input$type) == TRUE){
+      data_lens_id <- split(input, input$type)$lens_id
+      id_list_lens_id <- as.vector(data_lens_id[,1])
+      intermediate_lens_id <- get_citation(id_list_lens_id, type = 'lens_id', token = token)
+      display_lens_id <- tryCatch(intermediate_lens_id$display, error = function(cond){return(NULL)})
+      ris_lens_id <- tryCatch(intermediate_lens_id$ris, error = function(cond){return(NULL)})
+      df_lens_id <- tryCatch(intermediate_lens_id$df, error = function(cond){return(NULL)})
+      print('LENSIDs searched')
+    } else {
+      display_lens_id <- NULL
+      ris_lens_id <- NULL
+      df_lens_id <- NULL
+    }
+
+    #combine list outputs
+    display <- dplyr::bind_rows(display_doi, 
+                                display_pmid, 
+                                display_pmcid, 
+                                display_magid, 
+                                display_coreid, 
+                                display_lens_id)
+    ris <- paste(ris_doi, 
+                 ris_pmid, 
+                 ris_pmcid, 
+                 ris_magid, 
+                 ris_coreid, 
+                 ris_lens_id, 
+                 sep = '\n\n')
+    df <- dplyr::bind_rows(df_doi, 
+                           df_pmid, 
+                           df_pmcid, 
+                           df_magid, 
+                           df_coreid, 
+                           df_lens_id)
+
+    return(list(display = display, ris = ris, df = df))
+  } else {
+
+    #create blank outputs
+    display <- data.table::data.table(NULL)
+    ris <- ''
+    df <- data.frame()
+
+    #dois
+    if(('doi' %in% input$type) == TRUE){
+      data_doi <- split(input, input$type)$doi
+      id_list_doi <- as.vector(data_doi[,1])
+      intermediate_doi <- get_refs(id_list_doi, type = 'doi', get_records = search, token = token)
+      display_doi <- tryCatch(intermediate_doi$display, error = function(cond){return(NULL)})
+      ris_doi <- tryCatch(intermediate_doi$ris, error = function(cond){return(NULL)})
+      df_doi <- tryCatch(intermediate_doi$df, error = function(cond){return(NULL)})
+    } else {
+      display_doi <- NULL
+      ris_doi <- NULL
+      df_doi <- NULL
+    }
+
+    #pmid
+    if(('pmid' %in% input$type) == TRUE){
+      data_pmid <- split(input, input$type)$pmid
+      id_list_pmid <- as.vector(data_pmid[,1])
+      intermediate_pmid <- get_refs(id_list_pmid, type = 'pmid', get_records = search, token = token)
+      display_pmid <- tryCatch(intermediate_pmid$display, error = function(cond){return(NULL)})
+      ris_pmid <- tryCatch(intermediate_pmid$ris, error = function(cond){return(NULL)})
+      df_pmid <- tryCatch(intermediate_pmid$df, error = function(cond){return(NULL)})
+    } else {
+      display_pmid <- NULL
+      ris_pmid <- NULL
+      df_pmid <- NULL
+    }
+
+    #pmcid
+    if(('pmcid' %in% input$type) == TRUE){
+      data_pmcid <- split(input, input$type)$pmcid
+      id_list_pmcid <- as.vector(data_pmcid[,1])
+      intermediate_pmcid <- get_refs(id_list_pmcid, type = 'pmcid', get_records = search, token = token)
+      display_pmcid <- tryCatch(intermediate_pmcid$display, error = function(cond){return(NULL)})
+      ris_pmcid <- tryCatch(intermediate_pmcid$ris, error = function(cond){return(NULL)})
+      df_pmcid <- tryCatch(intermediate_pmcid$df, error = function(cond){return(NULL)})
+    } else {
+      display_pmcid <- NULL
+      ris_pmcid <- NULL
+      df_pmcid <- NULL
+    }
+
+    #magid
+    if(('magid' %in% input$type) == TRUE){
+      data_magid <- split(input, input$type)$magid
+      id_list_magid <- as.vector(data_magid[,1])
+      intermediate_magid <- get_refs(id_list_magid, type = 'magid', get_records = search, token = token)
+      display_magid <- tryCatch(intermediate_magid$display, error = function(cond){return(NULL)})
+      ris_magid <- tryCatch(intermediate_magid$ris, error = function(cond){return(NULL)})
+      df_magid <- tryCatch(intermediate_magid$df, error = function(cond){return(NULL)})
+    } else {
+      display_magid <- NULL
+      ris_magid <- NULL
+      df_magid <- NULL
+    }
+
+    #coreid
+    if(('coreid' %in% input$type) == TRUE){
+      data_coreid <- split(input, input$type)$coreid
+      id_list_coreid <- as.vector(data_coreid[,1])
+      intermediate_coreid <- get_refs(id_list_coreid, type = 'coreid', get_records = search, token = token)
+      display_coreid <- tryCatch(intermediate_coreid$display, error = function(cond){return(NULL)})
+      ris_coreid <- tryCatch(intermediate_coreid$ris, error = function(cond){return(NULL)})
+      df_coreid <- tryCatch(intermediate_coreid$df, error = function(cond){return(NULL)})
+    } else {
+      display_coreid <- NULL
+      ris_coreid <- NULL
+      df_coreid <- NULL
+    }
+
+    #lensid
+    if(('lens_id' %in% input$type) == TRUE){
+      data_lens_id <- split(input, input$type)$lens_id
+      id_list_lens_id <- as.vector(data_lens_id[,1])
+      intermediate_lens_id <- get_refs(id_list_lens_id, type = 'lens_id', get_records = search, token = token)
+      display_lens_id <- tryCatch(intermediate_lens_id$display, error = function(cond){return(NULL)})
+      ris_lens_id <- tryCatch(intermediate_lens_id$ris, error = function(cond){return(NULL)})
+      df_lens_id <- tryCatch(intermediate_lens_id$df, error = function(cond){return(NULL)})
+    } else {
+      display_lens_id <- NULL
+      ris_lens_id <- NULL
+      df_lens_id <- NULL
+    }
+
+    #combine list outputs
+    display <- dplyr::bind_rows(display_doi, 
+                                display_pmid, 
+                                display_pmcid, 
+                                display_magid, 
+                                display_coreid, 
+                                display_lens_id)
+    ris <- paste(ris_doi, 
+                 ris_pmid, 
+                 ris_pmcid, 
+                 ris_magid, 
+                 ris_coreid, 
+                 ris_lens_id, 
+                 sep = '\n\n')
+    df <- dplyr::bind_rows(df_doi, 
+                           df_pmid, 
+                           df_pmcid, 
+                           df_magid, 
+                           df_coreid, 
+                           df_lens_id)
+
+    return(list(display = display, ris = ris, df = df))
+
+  }
+
+}
+