From 38c8a091de31babd4c486c75b94cc5512fe78c67 Mon Sep 17 00:00:00 2001
From: Lukas Wallrich <lukas.wallrich@gmail.com>
Date: Fri, 5 Jul 2024 14:41:59 +0100
Subject: [PATCH] Fix url issue and RIS export

---
 R/export.R | 22 +++-------------------
 R/import.R |  8 +++++++-
 2 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/R/export.R b/R/export.R
index f14823dd..8cdbacc3 100644
--- a/R/export.R
+++ b/R/export.R
@@ -75,28 +75,12 @@ export_ris <- function(citations, filename = "citations.ris", source_field = "DB
 
   if (tolower(tools::file_ext(filename)) != "ris") warning("Function saves a RIS file, so filename should (usually) end in .ris. For now, name is used as provided.")
 
-  if (!is.null(source_field) && source_field %in% names(citations)) {
-    citations <- citations %>% dplyr::rename(cite_source_include = .data[[source_field]])
-  }
-
-  if (!is.null(label_field) && label_field %in% names(citations)) {
-    citations <- citations %>% dplyr::rename(cite_label_include = .data[[label_field]])
-  }
-
-  if (!is.null(string_field) && string_field %in% names(citations)) {
-    citations <- citations %>% dplyr::rename(cite_string_include = .data[[string_field]])
-  }
-
-  select_cols <- c("source_type", "duplicate_id") %in% names(citations)
-  citations <- citations %>%
-    dplyr::select(c("source_type", "duplicate_id")[select_cols], dplyr::everything(), -tidyselect::any_of(c("cite_source", "cite_string", "cite_label", "record_id")))
-
   synthesisr_codes <- dplyr::bind_rows(
     tibble::tribble(
       ~code, ~field, ~ris_synthesisr,
-      source_field, "cite_source_include", TRUE,
-      string_field, "cite_string_include", TRUE,
-      label_field, "cite_label_include", TRUE,
+      source_field, "cite_source", TRUE,
+      string_field, "cite_string", TRUE,
+      label_field, "cite_label", TRUE,
       "C1", "duplicate_id", TRUE,
       "C2", "record_ids", TRUE
     ),
diff --git a/R/import.R b/R/import.R
index 869dc30d..c363644c 100644
--- a/R/import.R
+++ b/R/import.R
@@ -137,9 +137,15 @@ read_citations <- function(files = NULL,
     message(paste0(utils::capture.output(report), collapse = "\n"))
   }
 
-  ref_list %>%
+  refs <- ref_list %>%
     purrr::map(tibble::as_tibble) %>%
     purrr::reduce(dplyr::bind_rows)
+  
+  missing_fields <- setdiff(key_fields, colnames(refs))
+  refs[missing_fields] <- NA
+
+  refs
+  
 }