remove rplos dependency

DESCRIPTION

@@ -6,7 +6,7 @@ Authors@R: c(
     person("Matthew B.", "Jones", role = "aut", email = "jones@nceas.ucsb.edu", comment=c(ORCID = "0000-0003-0077-4738")),
     person("Maya", "Samet", role = "aut", email = "samet@nceas.ucsb.edu", comment=c(ORCID = "0000-0002-5248-9712"))
     )
-Description: Harvests data package citations from several API sources, including PLOS, Scopus, and Springer.
+Description: Harvests data package citations from several API sources, including PLOS, Scopus, and Springer. This package uses modified functions from `rplos`, which is no longer maintained.
 License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
@@ -17,11 +17,11 @@ Imports:
       jsonlite,
       keyring,
       rcrossref,
-      rplos,
+      solrium,
       stats
 Suggests: 
     covr,
     purrr,
     testthat (>= 3.0.0)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3

NAMESPACE

@@ -11,4 +11,4 @@ export(write_citation_pairs)
 import(dplyr)
 importFrom(curl,curl)
 importFrom(jsonlite,fromJSON)
-importFrom(rplos,searchplos)
+importFrom(stats,complete.cases)

R/citation_search_plos.R

@@ -2,13 +2,13 @@
 #'
 #' This function searches for citations in PLOS. Requests are throttled
 #' at one identifier every 6 seconds so as to not overload the PLOS
-#' API.
+#' API. This function uses modified source code from the `rplos` package, 
+#' which is no longer maintained.
 #'
 #' @param identifiers a vector of identifiers to be searched for
 #'
 #' @return tibble of matching dataset and publication identifiers
 #' @export
-#' @importFrom rplos searchplos
 #' @examples
 #' \dontrun{
 #' identifiers <- c("10.18739/A22274", "10.18739/A2D08X", "10.5063/F1T151VR")
@@ -34,7 +34,7 @@ citation_search_plos <- function(identifiers) {
   # search for identifier
   results <- lapply(identifiers, function(x) {
     Sys.sleep(6)
-    v <- rplos::searchplos(q = x,
+    v <- searchplos(q = x,
                            fl = c("id", "title"),
                            limit = 1000)
     return(v)
@@ -71,3 +71,119 @@ citation_search_plos <- function(identifiers) {
 
   return(plos_results)
 }
+
+#' A Modified Version of rplos::searchplos
+#'
+#' This function is adapted from the searchplos in the `rplos` package, which is no longer maintained.
+#'
+#' @param q Search terms, eg: field:query 
+#' @param fl Fields to return
+#' @param fq Fields to filter query on
+#' @param sort Sort results according to field
+#' @param start Record to start at for pagination
+#' @param limit Number of results to return for pagination
+#' @param sleep Seconds to wait between requests
+#' @param errors One of simple or complete
+#' @param proxy List of args for proxy connection
+#' @param callopts Optional curl options
+#' @param progress Optional logic for progress bar
+#' @param ... Addtl Solr arguments
+searchplos <- function(q = NULL, fl = 'id', fq = NULL, sort = NULL, start = 0,
+                       limit = 10, sleep = 6, errors = "simple", proxy = NULL, callopts = list(), 
+                       progress = NULL, ...) {
+
+    # Make sure limit is a numeric or integer
+    limit <- tryCatch(as.numeric(as.character(limit)), warning=function(e) e)
+    if("warning" %in% class(limit)){
+        stop("limit should be a numeric or integer class value", call. = FALSE)
+    }
+    if(!inherits(limit, "numeric") | is.na(limit))
+        stop("limit should be a numeric or integer class value", call. = FALSE)
+
+    if (is.null(limit)) limit <- 999
+    if (limit == 0) fl <- NULL
+    fl <- paste(fl, collapse = ",")
+
+    args <- list()
+    if (!is.null(fq[[1]])) {
+        if (length(fq) == 1) {
+            args$fq <- fq
+        } else {
+            args <- fq
+            names(args) <- rep("fq",length(args))
+        }
+    }
+    args <- c(args, ploscompact(list(q = q, fl = fl, start = as.integer(start),
+                                     rows = as.integer(limit), sort = sort, wt = 'json')))
+
+    conn_plos <- solrium::SolrClient$new(host = "api.plos.org", path = "search", port = NULL)
+
+    getnum_tmp <- suppressMessages(
+        conn_plos$search(params = list(q = q, fl = fl, rows = 0, wt = "json"))
+    )
+    getnumrecords <- attr(getnum_tmp, "numFound")
+
+    if (getnumrecords > limit) {
+        getnumrecords <- limit
+    } else {
+        getnumrecords <- getnumrecords
+    }
+
+    if (min(getnumrecords, limit) < 1000) {
+        if (!is.null(limit)) args$rows <- limit
+        if (length(args) == 0) args <- NULL
+        jsonout <- suppressMessages(
+            conn_plos$search(params = args, callopts = callopts,
+                             minOptimizedRows = FALSE, progress = progress, ...)
+        )
+        meta <- dplyr::tibble(
+            numFound = attr(jsonout, "numFound"),
+            start = attr(jsonout, "start")
+        )
+        return(list(meta = meta, data = jsonout))
+    } else {
+        byby <- 500
+        getvecs <- seq(from = 0, to = getnumrecords - 1, by = byby)
+        lastnum <- as.numeric(strextract(getnumrecords, "[0-9]{3}$"))
+        if (lastnum == 0)
+            lastnum <- byby
+        if (lastnum > byby) {
+            lastnum <- getnumrecords - getvecs[length(getvecs)]
+        } else {
+            lastnum <- lastnum
+        }
+        getrows <- c(rep(byby, length(getvecs) - 1), lastnum)
+        out <- list()
+        for (i in seq_along(getvecs)) {
+            args$start <- as.integer(getvecs[i])
+            args$rows <- as.integer(getrows[i])
+            if (length(args) == 0) args <- NULL
+            jsonout <- suppressMessages(conn_plos$search(
+                params = ploscompact(list(q = args$q, fl = args$fl, 
+                                          fq = args[names(args) == "fq"],
+                                          sort = args$sort,
+                                          rows = as.integer(args$rows), start = as.integer(args$start),
+                                          wt = "json")), minOptimizedRows = FALSE, callopts = callopts,
+                progress = progress, ...
+            ))
+            out[[i]] <- jsonout
+        }
+        resdf  <- dplyr::bind_rows(out)
+        meta <- dplyr::tibble(
+            numFound = attr(jsonout, "numFound"),
+            start = attr(jsonout, "start")
+        )
+        return(list(meta = meta, data = resdf))
+    }
+}
+#' This function is from the `rplos` package, which is no longer maintained.
+#' @param l a list
+ploscompact <- function(l) Filter(Negate(is.null), l)
+
+#' This function is from the `rplos` package, which is no longer maintained.
+#'
+#' @param str A string
+#' @param pattern A regex pattern
+strextract <- function(str, pattern) {
+    regmatches(str, regexpr(pattern, str))
+}

R/citation_search_springer.R

@@ -10,6 +10,7 @@
 #' @return tibble of matching dataset and publication identifiers
 #' @importFrom jsonlite fromJSON
 #' @importFrom curl curl
+#' @importFrom stats complete.cases
 #' @export
 #' @examples
 #' \dontrun{