orcid_citations fxn added

.gitignore

@@ -2,4 +2,5 @@
 .DS_Store
 .Rproj.user
 inst/ignore/auth.R
+inst/ignore/issn_title_collect.R
 .httr-oauth

.travis.yml

@@ -2,6 +2,11 @@ language: r
 sudo: false
 cache: packages
 
+addons:
+  apt:
+    packages:
+      - libv8-dev
+
 matrix:
   include:
     - os: linux

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Interface to the 'Orcid.org' API
 Description: Client for the 'Orcid.org' API (<https://orcid.org/>).
     Functions included for searching for people, searching by 'DOI',
     and searching by 'Orcid' 'ID'.
-Version: 0.4.3.9110
+Version: 0.4.3.9113
 Authors@R: 
     c(person(given = "Scott",
              family = "Chamberlain",
@@ -30,7 +30,9 @@ Imports:
     data.table
 Suggests:
     testthat,
-    knitr
+    knitr,
+    rcrossref,
+    handlr
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr
 X-schema.org-applicationCategory: Literature

NAMESPACE

@@ -21,6 +21,7 @@ export(orcid_activities)
 export(orcid_address)
 export(orcid_auth)
 export(orcid_bio)
+export(orcid_citations)
 export(orcid_doi)
 export(orcid_educations)
 export(orcid_email)
@@ -40,6 +41,7 @@ export(works)
 importFrom(crul,HttpClient)
 importFrom(fauxpas,find_error_class)
 importFrom(fauxpas,http)
+importFrom(handlr,HandlrClient)
 importFrom(httr,add_headers)
 importFrom(httr,oauth2.0_token)
 importFrom(httr,oauth_app)

R/orcid_citations.R

@@ -0,0 +1,169 @@
+#' Get citations
+#'
+#' @export
+#' @param orcid (character) Orcid identifier(s) of the form 
+#' XXXX-XXXX-XXXX-XXXX. required.
+#' @param put_code (character/integer) one or more put codes. up to 
+#' 50. optional
+#' @param cr_format Used in Crossref queries only. Name of the format. One of 
+#' "rdf-xml", "turtle",
+#' "citeproc-json", "citeproc-json-ish", "text", "ris", "bibtex" (default), 
+#' "crossref-xml", "datacite-xml","bibentry", or "crossref-tdm". The format 
+#' "citeproc-json-ish" is a format that is not quite proper citeproc-json.
+#' passed to `rcrossref::cr_cn`. The special "citeproc2bibtex" value asks
+#' for citeproc-json from Crossref, then converts it into bibtex format 
+#' using [handlr::HandlrClient]
+#' @param cr_style Used in Crossref queries only. A CSL style (for text 
+#' format only). See ‘get_styles()’ for options. Default: apa. 
+#' passed to `rcrossref::cr_cn`
+#' @param cr_locale Used in Crossref queries only. Language locale. 
+#' See [Sys.getlocale], passed to `rcrossref::cr_cn`
+#' @param ... Curl options passed on to [crul::HttpClient]
+#' @template deets
+#' @details This function is focused on getting citations only.
+#' You can get all citations for an ORCID, or for certain works
+#' using a PUT code, or for many PUT codes.
+#' 
+#' We attempt to get citations via Crossref using \pkg{rcrossref} 
+#' whenever possible as they are the most flexible and don't have as 
+#' many mistakes in the text. If there is no DOI, we fetch the 
+#' citation from ORCID.
+#' 
+#' Right now we get JSON citations back. We'd like to support bibtex
+#' format. DOI.org supports this but not ORCID.
+#'
+#' @return data.frame, with the columns:
+#' 
+#' - put: ORCID PUT code, identifying the work identifier in ORCID's records
+#' - id: the external identifier
+#' - id_type: the type of external identifier
+#' - format: the citation format retrieved
+#' - citation: the citation as JSON
+#' 
+#' @examples \dontrun{
+#' (res <- orcid_citations(orcid = "0000-0002-9341-7985"))
+#' (res2 <- orcid_citations(orcid = "0000-0002-1642-628X"))
+#' (res2 <- orcid_citations(orcid = c("0000-0002-9341-7985", "0000-0002-1642-628X")))
+#' 
+#' # get individual works
+#' ## a single put code
+#' (a <- orcid_citations(orcid = "0000-0002-9341-7985", put_code = 5011717))
+#' ## many put codes
+#' (b <- orcid_citations(orcid = "0000-0002-9341-7985", 
+#'    put_code = c(5011717, 15536016)))
+#' 
+#' # request other formats, Crossref only
+#' orcid_citations(orcid = "0000-0002-9341-7985", cr_format = "turtle")
+#' 
+#' # parse citation data if you wish
+#' # for parsing bibtex can use bibtex package or others
+#' (res <- orcid_citations(orcid = "0000-0002-9341-7985"))
+#' lapply(res[res$format == "csl-json", "citation"][[1]], jsonlite::fromJSON)
+#' 
+#' # lots of citations
+#' orcid_citations(orcid = "0000-0001-8642-6325")
+#' 
+#' # example with no external identifier, returns NA's
+#' orcid_citations(orcid = "0000-0001-8642-6325", 26222265)
+#' }
+orcid_citations <- function(orcid, put_code = NULL, cr_format = "bibtex", 
+  cr_style = "apa", cr_locale = "en-US", ...) {
+
+  if (!is.null(put_code)) {
+    if (length(orcid) > 1) {
+      stop("if 'put_code' is given, 'orcid' must be length 1")
+    }
+  }
+
+  tmp <- orcid_works(orcid, put_code)
+
+  dat <- if (!is.null(put_code)) {
+    list(list(tmp[[1]]$works))
+  } else {
+    lapply(tmp, function(w) split(w$works, w$works$`put-code`))
+  }
+
+  if (length(orcid) > 1) {
+    Map(function(a, b) each_orcid(a, b, put_code, cr_format, cr_style, cr_locale), 
+      dat, orcid, ...) 
+  } else {
+    # each_orcid(dat[[1]], orcid, put_code, cr_format, cr_style, cr_locale, ...)
+    do_all(dat[[1]], orcid, put_code, cr_format, cr_style, cr_locale)
+  }
+}
+
+each_orcid <- function(m, orcid, put_code, cr_format, cr_style, cr_locale, ...) {
+  cites <- plyr::llply(m, function(z) {
+    # fix for whenever > 1 put code to make column names more useable
+    if (all(grepl("work", names(z)))) {
+      names(z) <- gsub("^work\\.", "", names(z))
+    }
+    pc <- z$`put-code`
+    if (!is.null(put_code)) {
+      if (length(put_code) == 1) {
+        df <- z$`external-ids`$`external-id`[[1]]
+        process_cites(df, pc, orcid, cr_format, cr_style, cr_locale, ...)
+      } else {
+        df <- z$`external-ids`
+        Map(process_cites, df, pc, orcid = orcid, cr_format = cr_format, 
+          cr_style = cr_style, cr_locale = cr_locale, ...)
+      } 
+    } else {
+      df <- z$`external-ids.external-id`[[1]]
+      process_cites(df, pc, orcid, cr_format, cr_style, cr_locale, ...)
+    }
+  }, .inform = TRUE)
+  # unnest if no names at top level
+  if (is.null(names(cites[[1]])) && length(cites[[1]]) > 1) cites <- unlist(cites, FALSE)
+  # combine
+  as_dt(cites)
+}
+
+process_cites <- function(df, pc, orcid, cr_format, cr_style, cr_locale, ...) {
+  if (length(df) == 0) {
+    return(list(put = pc, id = NA_character_, id_type = NA_character_, 
+      format = NA_character_, citation = ""))
+  }
+  if ("doi" %in% df$`external-id-type`) {
+    id <- df[df$`external-id-type` %in% "doi", "external-id-value"]
+    type <- "doi"
+    if (cr_format == "citeproc2bibtex") {
+      chkpkg('handlr')
+      cr_format = "citeproc-json"
+      fmat <- "bibtex"
+      ct <- cite_doi(id, cr_format, cr_style, cr_locale, ...) %||% ""
+      cli <- handlr::HandlrClient$new(x = ct)
+      cli$read("citeproc")
+      ct <- paste0(cli$write("bibtex"), collapse = "\n")
+    } else {
+      fmat <- cr_format
+      ct <- cite_doi(id, cr_format, cr_style, cr_locale, ...) %||% ""
+    }
+  } else {
+    id <- df[df$`external-id-type` %in% "eid", "external-id-value"]
+    type <- "eid"
+    fmat <- 'csl-json'
+    ct <- cite_put(orcid, pc, ...) %||% ""
+  }
+  list(put = pc, id = id, id_type = type, format = fmat, citation = ct)
+}
+
+chkpkg <- function(x) {
+  if (!requireNamespace(x, quietly = TRUE)) {
+    stop("Please install ", x, call. = FALSE)
+  } else {
+    invisible(TRUE)
+  }
+}
+
+cite_doi <- function(x, cr_format = "bibtex", cr_style = "apa", cr_locale = "en-US", ...) {
+  chkpkg('rcrossref')
+  rcrossref::cr_cn(x, format = cr_format, style = cr_style, locale = cr_locale, raw = TRUE, ...)
+}
+
+cite_put <- function(orcid, pc, ...) {
+  orcid_prof_helper(orcid, file.path("work", pc), 
+    ctype = "application/vnd.citationstyles.csl+json", 
+    # ctype = "application/x-bibtex", 
+    parse = FALSE, ...)
+}

R/rorcid-package.R

@@ -50,6 +50,7 @@
 #' @importFrom crul HttpClient
 #' @importFrom fauxpas http find_error_class
 #' @importFrom jsonlite fromJSON
+#' @importFrom handlr HandlrClient
 #' @name rorcid-package
 #' @docType package
 #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com}
@@ -66,6 +67,13 @@ NULL
 
 #' Lookup vector for journal titles by ISSN
 #' 
+#' named vector of journal titles. the values are journal titles and 
+#' the names are ISSN's.
+#' 
+#' length: 57,968
+#' 
+#' data collected on 2018-06-13 from Crossref
+#' 
 #' @name issn_title
 #' @docType data
 #' @keywords data

R/zzz.R

@@ -102,10 +102,10 @@ pluck <- function(x, name, type) {
 
 pop <- function(x, name) x[ !names(x) %in% name ]
 
-orcid_prof_helper <- function(x, path, ctype = ojson, ...) {
+orcid_prof_helper <- function(x, path, ctype = ojson, parse = TRUE, ...) {
   url2 <- file.path(orcid_base(), x, path)
   out <- orc_GET(url2, ctype = ctype, ...)
-  switch_parser(ctype, out)
+  if (parse) switch_parser(ctype, out) else out
 }
 
 switch_parser <- function(ctype, x) {