Merge pull request #26 from DataONEorg/develop

Fix bug in issue 24 and add argument checking for issue 25
DataONEorg · Apr 23, 2021 · 9a9ae0e · 9a9ae0e
2 parents 9953752 + 07dfc52
commit 9a9ae0e
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Showing 6 changed files with 15 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: scythe
 Title: Harvest and register data package citations 
-Version: 0.9.0
+Version: 0.9.1
 Authors@R: c(
     person("Jeanette", "Clark", role = c("aut", "cre"), email = "jeanetteclark@nceas.ucsb.edu", comment=c(ORCID = "0000-0003-4703-1974")),
     person("Matthew B.", "Jones", role = "aut", email = "jones@nceas.ucsb.edu", comment=c(ORCID = "0000-0003-0077-4738")),

diff --git a/R/citation_search.R b/R/citation_search.R
@@ -13,6 +13,10 @@
 citation_search <- function(identifiers,
                             sources = c("plos", "scopus", "springer")) {
 
+  if(!("character" %in% class(identifiers))){
+    stop("Identifiers must be a character vector.")
+  }
+
   # run the 'citation_search_*' function for each source
   for (source in sources) {
     search_function <- paste0(source, " <- citation_search_", source, "(identifiers)")

diff --git a/R/citation_search_plos.R b/R/citation_search_plos.R
@@ -52,6 +52,7 @@ citation_search_plos <- function(identifiers) {
     plos_results <- do.call(rbind, plos_results)
     names(plos_results)[which(names(plos_results) == "id")] <- "article_id"
     names(plos_results)[which(names(plos_results) == "title")] <- "article_title"
+    plos_results <- plos_results[complete.cases(plos_results), ]
 
     return(plos_results)
 }
diff --git a/R/citation_search_scopus.R b/R/citation_search_scopus.R
@@ -14,7 +14,7 @@
 #' }
 citation_search_scopus <- function(identifiers) {
 
-    check_identifiers(identifiers)
+    identifiers <- check_identifiers(identifiers)
 
     if (length(identifiers) > 8){
         message(paste0("Your result will take ~", length(identifiers)/9 ," seconds to return, since this function is rate limited to 9 calls per second."))
@@ -25,7 +25,8 @@ citation_search_scopus <- function(identifiers) {
         warning("Skipping Scopus search due to missing API key. Set an API key using scythe_set_key() to include Scopus results.")
         return()
     }
-    identifiers_enc <- utils::URLencode(identifiers, reserved = TRUE)
+    identifiers_enc <- lapply(identifiers, utils::URLencode, reserved = TRUE)
+    identifiers_enc <- unlist(identifiers_enc)
     results <- list()
     for (i in 1:length(identifiers_enc)) {
         Sys.sleep(0.12)

diff --git a/R/citation_search_springer.R b/R/citation_search_springer.R
@@ -29,7 +29,8 @@ citation_search_springer <- function(identifiers) {
         return()
     }
 
-    identifiers_enc <- utils::URLencode(identifiers, reserved = T)
+    identifiers_enc <- lapply(identifiers, utils::URLencode, reserved = TRUE)
+    identifiers_enc <- unlist(identifiers_enc)
 
     results <- list()
     for (i in 1:length(identifiers_enc)) {
@@ -69,6 +70,9 @@ citation_search_springer <- function(identifiers) {
 
     # remove doi: prefix for consistency
     springer_results$article_id <- gsub("doi:", "", springer_results$article_id)
+
+    # drop NA results
+    springer_results <- springer_results[complete.cases(springer_results), ]
 
     return(springer_results)
 

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ including Scopus, PLOS, and Springer.
 ### Released version
 
 ```
-remotes::install_github("DataONEorg/scythe@v0.9.0")
+remotes::install_github("DataONEorg/scythe@v0.9.1")
 ```
 
 The *scythe* R package should be available for use at this point.