Merge pull request #36 from ropensci/rc_0_3_1

Author: bwiernik

.Rbuildignore

@@ -17,3 +17,4 @@ citeproc_json_from_rorcid.json
 appveyor.yml
 ^LICENSE\.md$
 vignettes/handlr.Rmd
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.3.1
+Date: 2025-03-03 19:19:14 UTC
+SHA: 49db50362a6ac3f96b7de40542cba633ea9edfc8

DESCRIPTION

@@ -5,17 +5,19 @@ Description: Converts among many citation formats, including 'BibTeX',
     'Citation File Format'. A low level 'R6' class is provided, as well
     as stand-alone functions for each citation format for both read
     and write.
-Version: 0.3.0
+Version: 0.3.1
 License: MIT + file LICENSE
 Authors@R: c(
-    person("Scott", "Chamberlain", role = c("aut", "cre"),
+    person("Scott", "Chamberlain", role = c("aut"),
     email = "[email protected]",
     comment = c(ORCID = "0000-0003-1444-9135")),
+    person("Brenton M.", "Wiernik", role = c("aut", "cre"),
+    email = "[email protected]",
+    comment = c(ORCID = "0000-0001-9560-6336")),
     person("Thierry", "Onkelinx", email = "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0001-8804-4216"))
     )
-URL: https://github.com/ropensci/handlr (devel), 
-    https://docs.ropensci.org/handlr/ (docs)
+URL: https://github.com/ropensci/handlr, https://docs.ropensci.org/handlr/
 BugReports: https://github.com/ropensci/handlr/issues
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
@@ -32,7 +34,7 @@ Suggests:
     jsonld,
     data.table,
     bibtex
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 X-schema.org-applicationCategory: Metadata
 X-schema.org-keywords: doi, metadata, citation, bibtex, Crossref, Crosscite, Codemeta, RIS, Citeproc, RDF, XML, JSON
 X-schema.org-isPartOf: https://ropensci.org

NEWS.md

@@ -1,3 +1,12 @@
+handlr 0.3.1
+============
+
+### MINOR IMPROVEMENTS
+
+* Update maintainer to Brenton M. Wiernik.
+* Improved support for Citation File Format (CFF) and codemeta.json
+
+
 handlr 0.3.0
 ============
 

R/a_types.R

@@ -1,5 +1,5 @@
 #' cff references types
-#' @references http://bit.ly/2PRK1Vt
+#' @references https://bit.ly/2PRK1Vt
 #' @details cff citation format types for references
 #' @name cff_reference_types
 #' @docType data

R/codemeta_writer.R

@@ -1,10 +1,10 @@
 #' codemeta writer
-#' 
+#'
 #' @export
 #' @param z an object of class `handl`; see [handl] for more
-#' @param auto_unbox (logical) automatically "unbox" all atomic 
+#' @param auto_unbox (logical) automatically "unbox" all atomic
 #' vectors of length 1 (default: `TRUE`). passed to [jsonlite::toJSON()]
-#' @param pretty (logical) adds indentation whitespace to JSON output 
+#' @param pretty (logical) adds indentation whitespace to JSON output
 #' (default: `TRUE`), passed to [jsonlite::toJSON()]
 #' @param ... further params passed to [jsonlite::toJSON()]
 #' @return an object of class `json`
@@ -16,8 +16,8 @@
 #' (z <- bibtex_reader(x))
 #' codemeta_writer(z)
 #' }
-#' 
-#' # many citeproc to schema 
+#'
+#' # many citeproc to schema
 #' z <- system.file('extdata/citeproc-many.json', package = "handlr")
 #' w <- citeproc_reader(x = z)
 #' codemeta_writer(w)
@@ -26,7 +26,7 @@ codemeta_writer <- function(z, auto_unbox = TRUE, pretty = TRUE, ...) {
   assert(z, "handl")
   stopifnot(length(z) > 0)
   w <- if (attr(z, "many") %||% FALSE) {
-    lapply(z, codemeta_write_one) 
+    lapply(z, codemeta_write_one)
   } else {
     codemeta_write_one(z)
   }
@@ -42,7 +42,7 @@ codemeta_write_one <- function(z) {
     "codeRepository" = z$b_url,
     "title" = z$title,
     "agents" = z$author,
-    "description" = parse_attributes(z$description, 
+    "description" = parse_attributes(z$description,
       content = "text", first = TRUE),
     "version" = z$software_version,
     # FIXME: not sure what's going on here
@@ -54,4 +54,4 @@ codemeta_write_one <- function(z) {
   ))
 }
 
-cm_urls <- c("http://purl.org/codemeta/2.0", "http://schema.org")
+cm_urls <- c("https://purl.org/codemeta/2.0", "https://schema.org")

R/doi_utils.R

@@ -6,8 +6,8 @@ doi_resolver <- "https://doi.org"
 # validate_doi: should extract DOI if it's in a URL
 # validate_doi(doi = "10.1371/journal.pone.0025995") # valid
 # validate_doi(doi = "10/journal.pone.0025995") # invalid
-# validate_doi(doi = "http://dx.doi.org/10.5063/F1M61H5X") # valid url
-# validate_doi(doi = "http://dx.doi.org/30.5063/F1M61H5X") # invalid url
+# validate_doi(doi = "https://doi.org/10.5063/F1M61H5X") # valid url
+# validate_doi(doi = "https://doi.org/30.5063/F1M61H5X") # invalid url
 validate_doi <- function(doi) {
   # doi <- grep(doi_pattern, doi, perl = TRUE, value = TRUE)
   doi <- regmatches(doi, regexpr(doi_pattern, doi, perl=TRUE))
@@ -39,8 +39,8 @@ normalize_doi <- function(doi) {
   file.path(doi_resolver, doi_str)
 }
 
-# is_url_doi("http://doi.org/10.1371/journal.pone.0025995")
-# doi_from_url(url = "http://doi.org/10.1371/journal.pone.0025995")
+# is_url_doi("https://doi.org/10.1371/journal.pone.0025995")
+# doi_from_url(url = "https://doi.org/10.1371/journal.pone.0025995")
 doi_from_url <- function(url) {
   if (is_url_doi(url)) {
     df <- urltools::url_parse(url)

R/handlr-package.r

@@ -1,31 +1,31 @@
 #' **Citation format converter**
-#' 
+#'
 #' A tool for converting among citation formats
-#' 
+#'
 #' @section supported readers:
-#' 
+#'
 #' - citeproc
 #' - ris
 #' - bibtex (requires suggested package `bibtex`)
 #' - codemeta
 #' - cff
-#' 
+#'
 #' @section supported writers:
-#' 
+#'
 #' - citeproc
 #' - ris
 #' - bibtex
 #' - schema.org
 #' - rdfxml (requires suggested package `jsonld`)
 #' - codemeta
 #' - cff
-#' 
+#'
 #' @section links for citation formats:
-#' 
+#'
 #' - citeproc: <https://en.wikipedia.org/wiki/CiteProc>
 #' - codemeta: <https://codemeta.github.io/>
 #' - ris: <https://en.wikipedia.org/wiki/RIS_(file_format)>
-#' - bibtex: <http://www.bibtex.org/>
+#' - bibtex: <https://www.bibtex.org/>
 #' - schema.org: <https://schema.org/>
 #' - rdfxml: <https://en.wikipedia.org/wiki/RDF/XML>
 #' - cff: <https://citation-file-format.github.io/>
@@ -38,5 +38,5 @@
 #' @name handlr-package
 #' @aliases handlr
 #' @author Scott Chamberlain \email{sckott@@protonmail.com}
-#' @docType package
-NULL
+#' @keywords internal
+"_PACKAGE"

R/schema_org_writer.R

@@ -1,10 +1,10 @@
 #' Schema org writer
-#' 
+#'
 #' @export
 #' @param z an object of class `handl`; see [handl] for more
-#' @param auto_unbox (logical) automatically "unbox" all atomic 
+#' @param auto_unbox (logical) automatically "unbox" all atomic
 #' vectors of length 1 (default: `TRUE`). passed to [jsonlite::toJSON()]
-#' @param pretty (logical) adds indentation whitespace to JSON output 
+#' @param pretty (logical) adds indentation whitespace to JSON output
 #' (default: `TRUE`), passed to [jsonlite::toJSON()]
 #' @param ... further params passed to [jsonlite::toJSON()]
 #' @return an object of class `json`
@@ -17,8 +17,8 @@
 #' schema_org_writer(tmp)
 #' schema_org_writer(tmp, pretty = FALSE)
 #' }
-#' 
-#' # many citeproc to schema 
+#'
+#' # many citeproc to schema
 #' z <- system.file('extdata/citeproc-many.json', package = "handlr")
 #' w <- citeproc_reader(x = z)
 #' schema_org_writer(w)
@@ -32,23 +32,23 @@ schema_org_writer <- function(z, auto_unbox = TRUE, pretty = TRUE, ...) {
 
 schema_hsh <- function(x) {
   ccp(list(
-    "@context" = if (!is.null(x$id)) "http://schema.org" else NULL,
+    "@context" = if (!is.null(x$id)) "https://schema.org" else NULL,
     "@type" = x$type,
     "@id" = x$id,
-    "identifier" = to_schema_org_identifier(x$id, 
+    "identifier" = to_schema_org_identifier(x$id,
       ccp(list(alternate_identifier = x$alternate_identifier %||% NULL))),
     "url" = x$b_url,
     "additionalType" = x$additional_type,
     "name" = parse_attributes(x$title, content = "text", first = TRUE),
     "author" = to_schema_org(x$author),
     "editor" = to_schema_org(x$editor),
-    "description" = 
+    "description" =
       parse_attributes(x$description, content = "text", first = TRUE),
     "license" = unlist(ccp(lapply(x$license, function(l) l$id))),
     "version" = x$software_version,
-    "keywords" = if (!is.null(x$keywords)) 
-      paste0(lapply(x$keywords, function(k) 
-        parse_attributes(k, content = "text", first = TRUE)), 
+    "keywords" = if (!is.null(x$keywords))
+      paste0(lapply(x$keywords, function(k)
+        parse_attributes(k, content = "text", first = TRUE)),
       collapse = ", ") else NULL,
     "inLanguage" = x$language %||% NULL,
     "contentSize" = x$content_size %||% NULL,
@@ -60,7 +60,7 @@ schema_hsh <- function(x) {
     "pageEnd" = x$last_page %||% NULL,
     "spatialCoverage" = x$spatial_coverage %||% NULL,
     "sameAs" = to_schema_org(x$is_identical_to),
-    "isPartOf" = if (x$type == "Dataset") NULL else 
+    "isPartOf" = if (x$type == "Dataset") NULL else
       to_schema_org_container(x$is_part_of, list(
         container_title = x$container_title, type = x$type)),
     "hasPart" = to_schema_org(x$has_part),
@@ -70,13 +70,13 @@ schema_hsh <- function(x) {
     "@reverse" = x$reverse.presence,
     "contentUrl" = x$content_url %||% NULL,
     "schemaVersion" = x$schema_version %||% NULL,
-    "includedInDataCatalog" = if (x$type == "Dataset") 
-      to_schema_org_container(x$is_part_of, 
+    "includedInDataCatalog" = if (x$type == "Dataset")
+      to_schema_org_container(x$is_part_of,
         list(container_title = x$container_title, type = x$type)) else NULL,
-    "publisher" = if (!is.null(x$publisher)) 
+    "publisher" = if (!is.null(x$publisher))
       list("@type" = "Organization", "name" = x$publisher) else NULL,
     "funding" = to_schema_org(x$funding),
-    "provider" = if (!is.null(x$service_provider)) 
+    "provider" = if (!is.null(x$service_provider))
       list("@type" = "Organization", "name" = x$service_provider) else NULL
   ))
 }
@@ -109,7 +109,7 @@ wrap_list <- function(m) {
 }
 
 to_schema_org_identifier <- function(element, options = list()) {
-  ident <- list( 
+  ident <- list(
     "@type" = "PropertyValue",
     propertyID = if (!is.null(normalize_doi(element))) "doi" else "url",
     value = element

R/translations.R

@@ -1,17 +1,17 @@
 # from https://github.com/datacite/bolognese/blob/master/lib/bolognese/utils.rb
 
 LICENSE_NAMES <- list(
-  "http://creativecommons.org/publicdomain/zero/1.0/" = 
+  "https://creativecommons.org/publicdomain/zero/1.0/" = 
     "Public Domain (CC0 1.0)",
-  "http://creativecommons.org/licenses/by/3.0/" = 
+  "https://creativecommons.org/licenses/by/3.0/" = 
     "Creative Commons Attribution 3.0 (CC-BY 3.0)",
-  "http://creativecommons.org/licenses/by/4.0/" = 
+  "https://creativecommons.org/licenses/by/4.0/" = 
     "Creative Commons Attribution 4.0 (CC-BY 4.0)",
-  "http://creativecommons.org/licenses/by-nc/4.0/" = 
+  "https://creativecommons.org/licenses/by-nc/4.0/" = 
     "Creative Commons Attribution Noncommercial 4.0 (CC-BY-NC 4.0)",
-  "http://creativecommons.org/licenses/by-sa/4.0/" = 
+  "https://creativecommons.org/licenses/by-sa/4.0/" = 
     "Creative Commons Attribution Share Alike 4.0 (CC-BY-SA 4.0)",
-  "http://creativecommons.org/licenses/by-nc-nd/4.0/" = 
+  "https://creativecommons.org/licenses/by-nc-nd/4.0/" = 
     "Creative Commons Attribution Noncommercial No Derivatives 4.0 (CC-BY-NC-ND 4.0)"
 )