From a199ab76c853f5153fc14f47e56d5a58a8e20911 Mon Sep 17 00:00:00 2001
From: Jeanette Clark <jclark@nceas.ucsb.edu>
Date: Thu, 15 Aug 2024 17:18:50 +0000
Subject: [PATCH] make the write citations function more robust

---
 R/write_citation_pairs.R | 120 +++++++++++++++++++++------------------
 1 file changed, 65 insertions(+), 55 deletions(-)

diff --git a/R/write_citation_pairs.R b/R/write_citation_pairs.R
index 5093a02..b2dd2ab 100644
--- a/R/write_citation_pairs.R
+++ b/R/write_citation_pairs.R
@@ -13,59 +13,69 @@
 #' }
 
 write_citation_pairs <- function(citation_list, path) {
-  if (any(!(c("article_id", "dataset_id") %in% names(citation_list)))) {
-    stop(
-      .call = FALSE,
-      "citations_list data.frame does not contain variables article_id and/or dataset_id"
-    )
-  }
-  
-  # write list of citations to bib format
-  bib <-
-    rcrossref::cr_cn(dois = citation_list$article_id, format = "bibtex")
-  
-  t <- tempfile()
-  writeLines(unlist(bib), t)
-  
-  # import as a dataframe
-  df <- bib2df::bib2df(t)
-  
-  # assign article_id to data.frame
-  df$dataset_id <- citation_list$dataset_id
-  
-  # rename for database ingest
-  cit_full <- df %>%
-    dplyr::rename(
-      target_id = .data$dataset_id,
-      source_id = .data$DOI,
-      source_url = .data$URL,
-      origin = .data$AUTHOR,
-      title = .data$TITLE,
-      publisher = .data$PUBLISHER,
-      journal = .data$JOURNAL,
-      volume = .data$VOLUME,
-      page = .data$PAGES,
-      year_of_publishing = .data$YEAR
-    ) %>%
-    dplyr::select(
-      .data$target_id,
-      .data$source_id,
-      .data$source_url,
-      .data$origin,
-      .data$title,
-      .data$publisher,
-      .data$journal,
-      .data$volume,
-      .data$page,
-      .data$year_of_publishing
-    ) %>%
-    dplyr::mutate(
-      id = NA,
-      report = NA,
-      metadata = NA,
-      link_publication_date = Sys.Date()
-    ) #%>%
-  #dplyr::mutate(publisher = ifelse(.data$publisher == "Elsevier {BV", "Elsevier", "Copernicus"))
-  
-  jsonlite::write_json(cit_full, path)
+    if (any(!(c("article_id", "dataset_id") %in% names(citation_list)))) {
+        stop(
+            .call = FALSE,
+            "citations_list data.frame does not contain variables article_id and/or dataset_id"
+        )
+    }
+    
+    # write list of citations to bib format
+    bib_full <- c()
+    for (i in 1:nrow(citation_list)){
+        bib <- tryCatch({
+            trimws(rcrossref::cr_cn(dois = citation_list$article_id[i], format = "bibtex"))
+        }, error = function(e) {
+            paste0("@article{ERROR, title={", conditionMessage(e), "}, volume={ERROR}, ISSN={ERROR}, url={ERROR}, DOI={", citation_list$article_id[i], "}, number={ERROR}, journal={ERROR}, publisher={ERROR}, author={ERROR}, year={1900}, month=dec, pages={ERROR} }\n")
+        }, warning = function(w) {
+            paste0("@article{WARNING, title={", conditionMessage(w), "}, volume={WARNING}, ISSN={WARNING}, url={WARNING}, DOI={", citation_list$article_id[i], "}, number={WARNING}, journal={WARNING}, publisher={WARNING}, author={WARNING}, year={1900}, month=dec, pages={WARNING} }\n")
+        })
+        bib_full <- paste(bib_full, bib, sep = "\n")
+    }
+    
+    
+    t <- tempfile()
+    writeLines(bib_full, t)
+    
+    # import as a dataframe
+    df <- bib2df::bib2df(t)
+    
+    # assign article_id to data.frame
+    df$dataset_id <- citation_list$dataset_id
+    
+    # rename for database ingest
+    cit_full <- df %>%
+        dplyr::rename(
+            target_id = .data$dataset_id,
+            source_id = .data$DOI,
+            source_url = .data$URL,
+            origin = .data$AUTHOR,
+            title = .data$TITLE,
+            publisher = .data$PUBLISHER,
+            journal = .data$JOURNAL,
+            volume = .data$VOLUME,
+            page = .data$PAGES,
+            year_of_publishing = .data$YEAR
+        ) %>%
+        dplyr::select(
+            .data$target_id,
+            .data$source_id,
+            .data$source_url,
+            .data$origin,
+            .data$title,
+            .data$publisher,
+            .data$journal,
+            .data$volume,
+            .data$page,
+            .data$year_of_publishing
+        ) %>%
+        dplyr::mutate(
+            id = NA,
+            report = NA,
+            metadata = NA,
+            link_publication_date = Sys.Date()
+        ) #%>%
+    #dplyr::mutate(publisher = ifelse(.data$publisher == "Elsevier {BV", "Elsevier", "Copernicus"))
+    
+    jsonlite::write_json(cit_full, path)
 }