minimal parsing of sys dependencies thanks to @jeroen cf #147

DESCRIPTION

@@ -28,10 +28,15 @@ Authors@R:
              role = "ctb"),
       person(given = "Noam",
              family = "Ross",
-             role = "ctb"),
+             role = "ctb",
+             comment=c(ORCID = "0000-0002-2136-0000")),
       person(given = "Arfon",
              family = "Smith",
-             role = "ctb"))
+             role = "ctb"),
+      person(given = "Jeroen", 
+             family = "Ooms", 
+             role = "ctb",
+             comment = c(ORCID = "0000-0002-4035-0289")))
 Description: The 'Codemeta' Project defines a 'JSON-LD' format for describing
   software metadata, as detailed at <https://codemeta.github.io>. This package
   provides utilities to generate, parse, and modify 'codemeta.json' files 

R/codemeta_description.R

@@ -122,7 +122,9 @@ codemeta_description <-
 
     codemeta$softwareSuggestions <- parse_depends(suggests)
     codemeta$softwareRequirements <- parse_depends(requirements)
-
+    codemeta$softwareRequirements <- c(codemeta$softwareRequirements,
+                                       parse_sys_reqs(descr$get("Package"),
+                                                      descr$get("SystemRequirements")))
 
 
     ## add any additional codemeta terms found in the DESCRIPTION metadata

R/parse_depends.R

@@ -77,3 +77,22 @@ add_remote_to_dep <- function(package, remotes){
     remote_provider
   }
 }
+
+
+# helper to get system dependencies
+get_sys_links <- function(pkg, description = ""){
+  out1 <- jsonlite::fromJSON(sprintf("https://sysreqs.r-hub.io/pkg/%s", pkg), simplifyVector = FALSE)
+  out2 <- jsonlite::fromJSON(sprintf("https://sysreqs.r-hub.io/map/%s", curl::curl_escape(description)), simplifyVector = FALSE)
+  sysreqs <- unique(c(sapply(out1, names), sapply(out2, names)))
+  sprintf("https://sysreqs.r-hub.io/get/%s", sysreqs)
+}
+
+format_sys_req <- function(url){
+  list("@type" = "SoftwareApplication",
+       identifier = url)
+}
+
+parse_sys_reqs <- function(pkg, sys_reqs){
+  urls <- get_sys_links(pkg, description = sys_reqs)
+  purrr::map(urls, format_sys_req)
+}

codemeta.json

@@ -64,12 +64,19 @@
     {
       "@type": "Person",
       "givenName": "Noam",
-      "familyName": "Ross"
+      "familyName": "Ross",
+      "@id": "https://orcid.org/0000-0002-2136-0000"
     },
     {
       "@type": "Person",
       "givenName": "Arfon",
       "familyName": "Smith"
+    },
+    {
+      "@type": "Person",
+      "givenName": "Jeroen",
+      "familyName": "Ooms",
+      "@id": "https://orcid.org/0000-0002-4035-0289"
     }
   ],
   "copyrightHolder": [
@@ -422,7 +429,7 @@
   "keywords": ["metadata", "codemeta", "ropensci", "citation", "credit", "linked-data", "json-ld"],
   "releaseNotes": "https://github.com/ropensci/codemetar/blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/codemetar/blob/master/README.md",
-  "fileSize": "277.352KB",
+  "fileSize": "278.447KB",
   "contIntegration": [
     "https://travis-ci.org/ropensci/codemetar",
     "https://ci.appveyor.com/project/cboettig/codemetar/branch/master",

inst/examples/DESCRIPTION_sysreqs

@@ -0,0 +1,79 @@
+Package: codemetar
+Type: Package
+Title: Generate 'CodeMeta' Metadata for R Packages
+Version: 0.1.6
+Authors@R:
+    c(person(given = "Carl",
+             family = "Boettiger",
+             role = c("aut", "cre", "cph"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-1642-628X")),
+      person(given = "Anna",
+             family = "Krystalli",
+             role = c("rev", "ctb"),
+             comment = c(ORCID = "0000-0002-2378-4915")),
+      person(given = "Toph",
+             family = "Allen",
+             role = "rev",
+             comment = c(ORCID = "0000-0003-4580-091X")),
+      person(given = "Maëlle",
+             family = "Salmon",
+             role = c("ctb", "aut"),
+             comment = c(ORCID = "0000-0002-2815-0399")),
+      person(given = "rOpenSci",
+             role = "fnd",
+             comment = "https://ropensci.org/"),
+      person(given = "Katrin",
+             family = "Leinweber",
+             role = "ctb"),
+      person(given = "Noam",
+             family = "Ross",
+             role = "ctb"),
+      person(given = "Arfon",
+             family = "Smith",
+             role = "ctb"))
+Description: The 'Codemeta' Project defines a 'JSON-LD' format for describing
+  software metadata, as detailed at <https://codemeta.github.io>. This package
+  provides utilities to generate, parse, and modify 'codemeta.json' files
+  automatically for R packages, as well as tools and examples for working with
+  'codemeta.json' 'JSON-LD' more generally.
+License: GPL-3
+URL: https://github.com/ropensci/codemetar, https://ropensci.github.io/codemetar
+BugReports: https://github.com/ropensci/codemetar/issues
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1.9000
+Depends: R (>= 3.0.0)
+Imports:
+    jsonlite (>= 1.3),
+    jsonld,
+    git2r,
+    devtools,
+    memoise,
+    methods,
+    stats,
+    stringi,
+    readr,
+    desc,
+    usethis,
+    whisker,
+    tibble,
+    crul,
+    gh,
+    stringr,
+    sessioninfo,
+    purrr
+Suggests:
+    testthat,
+    jsonvalidate,
+    covr,
+    knitr,
+    rmarkdown,
+    magrittr,
+    xml2,
+    dplyr (>= 0.7.0),
+    printr
+SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or libmagick++-dev (deb)
+VignetteBuilder: knitr
+X-schema.org-keywords: metadata, codemeta, ropensci, citation, credit, linked-data
+X-schema.org-isPartOf: https://ropensci.org

tests/testthat/test-parse_depends.R

@@ -42,3 +42,10 @@ testthat::test_that("Test the various cases for ids (NOT used currently)", {
   # a <- guess_dep_id(parse_depends("not-a-package")[[1]])
 
 })
+
+testthat::test_that("Sys requirements", {
+  f <- system.file("examples/DESCRIPTION_sysreqs", package = "codemetar")
+  descr <- codemeta_description(f)
+  testthat::expect_equal(descr$softwareRequirements[[22]]$identifier,
+                         "https://sysreqs.r-hub.io/get/imagemagick")
+})