Merge pull request #70 from ropensci/I41

start using desc cf #41
ropensci · Apr 9, 2018 · c56c484 · c56c484
2 parents b369b76 + f879691
commit c56c484
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Showing 11 changed files with 91 additions and 97 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -39,6 +39,7 @@ Imports:
     stats,
     stringi,
     readr,
+    desc,
     usethis,
     whisker
 Suggests: testthat,

diff --git a/R/codemeta_description.R b/R/codemeta_description.R
@@ -17,40 +17,39 @@ new_codemeta <- function() {
 codemeta_description <-
   function(f, id = NULL, codemeta = new_codemeta()) {
     if (file.exists(f)) {
-      descr <- cm_read_dcf(f)
+      descr <- desc::desc(f)
     } else {
       return(codemeta)
     }
 
-    if (is.null(descr) || length(descr) == 0) {
-      return(codemeta)
-    }
 
     ## FIXME define an S3 class based on the codemeta list of lists?
     if (is.null(id)) {
-      id <- descr$Package
+      id <- descr$get("Package")
     }
 
     if (is_IRI(id)) {
       codemeta$`@id` <- id
     }
 
-    codemeta$identifier <- descr$Package
-    codemeta$description <- descr$Description
-    codemeta$name <- paste0(descr$Package, ": ", descr$Title)
+    codemeta$identifier <- descr$get("Package")
+    codemeta$description <- descr$get("Description")
+    codemeta$name <- paste0(descr$get("Package"), ": ",
+                            descr$get("Title"))
+
+
+    ## Will later guess these these a la devtools::use_github_links
+    codemeta$codeRepository <- descr$get("URL")
+    codemeta$issueTracker <- descr$get("BugReports")
 
-    ## Will later guess these à la usethis::use_github_links
-    codemeta$codeRepository <- descr$URL
-    codemeta$issueTracker <- descr$BugReports
 
     ## According to crosswalk, codemeta$dateModified and
     ## codemeta$dateCreated are not crosswalked in DESCRIPTION
-    codemeta$datePublished <-
-      descr$Date # probably not avaialable as descr$Date.
+    codemeta$datePublished <- NULL
 
-    codemeta$license <- spdx_license(descr$License)
+    codemeta$license <- spdx_license(descr$get("License"))
 
-    codemeta$version <- descr$Version
+    codemeta$version <- as.character(descr$get_version())
     codemeta$programmingLanguage <-
       list(
         "@type" = "ComputerLanguage",
@@ -64,23 +63,23 @@ codemeta_description <-
     codemeta$runtimePlatform <- R.version.string
 
     if (is.null(codemeta$provider))
-      codemeta$provider <- guess_provider(descr$Package)
-    if ("Authors@R" %in% names(descr)) {
+      codemeta$provider <- guess_provider(descr$get("Package"))
+      authors <- try(descr$get_authors(), silent = TRUE)
+    if (!inherits(authors,'try-error')) {
       codemeta <-
-        parse_people(eval(parse(text = descr$`Authors@R`)), codemeta)
+        parse_people(authors, codemeta)
     } else {
-      codemeta <- parse_people(as.person(descr$Author), codemeta)
-      ## maintainer must come second in case Author list also specifies
-      ## maintainer by role [cre] without email
-      codemeta$maintainer <-
-        person_to_schema(as.person(descr$Maintainer))
+      stop("No correct Authors@R field in DESCRIPTION, please add authors via Authors@R") # nolint
 
     }
 
-    codemeta$softwareSuggestions <- parse_depends(descr$Suggests)
-    codemeta$softwareRequirements <-
-      c(parse_depends(descr$Imports),
-        parse_depends(descr$Depends))
+    dependencies <- descr$get_deps()
+    suggests <- dependencies[dependencies$type == "Suggests",]
+    requirements <- dependencies[dependencies$type %in%
+                                   c("Imports", "Depends"),]
+
+    codemeta$softwareSuggestions <- parse_depends(suggests)
+    codemeta$softwareRequirements <- parse_depends(requirements)
 
 
 

diff --git a/R/create_codemeta.R b/R/create_codemeta.R
@@ -9,7 +9,7 @@
 #' @return a codemeta list object
 #' @export
 #' @examples
-#' cm <- create_codemeta("jsonlite")
+#' cm <- create_codemeta("jqr")
 #' cm$keywords <- list("metadata", "ropensci")
 #' @importFrom jsonlite read_json
 create_codemeta <- function(pkg = ".",

diff --git a/R/parse_citation.R b/R/parse_citation.R
@@ -75,7 +75,7 @@ guess_citation <- function(pkg){
   installed <- installed.packages()
   if(file.exists(file.path(pkg, "inst/CITATION"))){
     bib <- readCitationFile(file.path(pkg, "inst/CITATION"),
-                            meta = cm_read_dcf(file.path(pkg, "DESCRIPTION")))
+                            meta = desc::desc(file.path(pkg, "DESCRIPTION")))
     lapply(bib, parse_citation)
   } else if(pkg %in% installed[,1]){
     bib <- suppressWarnings(citation(pkg)) # don't worry if no date

diff --git a/R/parse_depends.R b/R/parse_depends.R
@@ -1,41 +1,26 @@
 ## internal method for parsing a list of package dependencies into pkg URLs
 
+format_depend <- function(package, version){
+  dep <- list("@type" = "SoftwareApplication",
+              identifier = package,
+              ## FIXME technically the name includes the title
+              name = package)
+
+  ## Add Version if available
+  if (version != "*"){
+    dep$version <- version
+  }
+
+  dep$provider <- guess_provider(package)
 
+  ## implemention could be better, e.g. support versioning
+  #  dep$`@id` <- guess_dep_id(dep)
+  dep
+}
 
 parse_depends <- function(deps) {
-  if (!is.null(deps))
-    str <- strsplit(deps, ",\n*")[[1]]
-  else
-    str <- NULL
-
-  lapply(str, function(str) {
-    #if (length(str) > 1) {
-    #  warning(paste0("package depends", str, "may be multiple packages?"))
-    #}
-
-    pkg <- gsub("\\s*(\\w+)\\s.*", "\\1", str)
-    pkg <- gsub("\\s+", "", pkg)
-
-    dep <- list("@type" = "SoftwareApplication",
-                identifier = pkg,
-                ## FIXME technically the name includes the title
-                name = pkg)
-
-    ## Add Version if available
-    pattern <- "\\s*\\w+\\s+\\([><=]+\\s([1-9.\\-]*)\\)*"
-    version <-  gsub(pattern, "\\1", str)
-    version <-
-      gsub("\\)$", "", version)  ## hack, avoid extraneous ending )
-    has_version  <- grepl(pattern, str)
-    if (has_version)
-      dep$version <- version
-
-    dep$provider <- guess_provider(pkg)
-
-    ## implemention could be better, e.g. support versioning
-    #  dep$`@id` <- guess_dep_id(dep)
-    dep
-  })
+
+  unname(mapply(format_depend, deps$package, deps$version))
 }
 
 

diff --git a/R/utils.R b/R/utils.R
@@ -17,16 +17,6 @@ get_root_path <- function(pkg){
 }
 
 
-## based on devtools::read_dcf
-# https://github.com/r-lib/devtools/blob/50d2dee67922e304f494e2d5ffb1c5e61aa8e860/R/utils.r#L64
-# this is GPL>=2 code
-cm_read_dcf <- function(dcf) {
-
-  fields <- colnames(read.dcf(dcf))
-  as.list(read.dcf(dcf, keep.white = fields)[1, ])
-
-}
-
 ## Like system.file, but pkg can instead be path to package root directory
 get_file <- function(FILE, pkg = "."){
   f <- file.path(pkg, FILE)

diff --git a/codemeta.json b/codemeta.json
@@ -7,7 +7,6 @@
   "identifier": "codemetar",
   "description": "The 'Codemeta' Project defines a 'JSON-LD' format for describing\n  software metadata, as detailed at <https://codemeta.github.io>. This package\n  provides utilities to generate, parse, and modify 'codemeta.json' files \n  automatically for R packages, as well as tools and examples for working with\n  'codemeta.json' 'JSON-LD' more generally.",
   "name": "codemetar: Generate 'CodeMeta' Metadata for R Packages",
-  "issueTracker": "https://github.com/ropensci/codemetar/issues",
   "license": "https://spdx.org/licenses/MIT",
   "version": "0.1.5",
   "programmingLanguage": {
@@ -141,7 +140,7 @@
       "@type": "SoftwareApplication",
       "identifier": "dplyr",
       "name": "dplyr",
-      "version": "0.7.0",
+      "version": ">= 0.7.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -184,11 +183,17 @@
     }
   ],
   "softwareRequirements": [
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "R",
+      "name": "R",
+      "version": ">= 3.0.0"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "jsonlite",
       "name": "jsonlite",
-      "version": "1.3",
+      "version": ">= 1.3",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -263,18 +268,31 @@
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "R",
-      "name": "R",
-      "version": "3.0.0"
+      "identifier": "desc",
+      "name": "desc",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Central R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      }
     }
   ],
-  "codeRepository": "https://github.com/ropensci/codemetar",
   "isPartOf": "https://ropensci.org",
-  "keywords": ["metadata", "codemeta", "ropensci", "citation", "credit", "linked-data"],
+  "keywords": [
+    "metadata",
+    "codemeta",
+    "ropensci",
+    "citation",
+    "credit",
+    "linked-data"
+  ],
   "relatedLink": "https://codemeta.github.io/codemetar",
   "contIntegration": "https://travis-ci.org/ropensci/codemetar",
   "developmentStatus": "active",
   "releaseNotes": "https://github.com/ropensci/codemetar/blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/codemetar/blob/master/README.md",
-  "fileSize": "266.748KB"
+  "fileSize": "266.286KB",
+  "codeRepository": "https://github.com/ropensci/codemetar",
+  "issueTracker": "https://github.com/ropensci/codemetar/issues"
 }
diff --git a/man/codemetar-package.Rd b/man/codemetar-package.Rd
diff --git a/man/create_codemeta.Rd b/man/create_codemeta.Rd
diff --git a/tests/testthat/test-codemeta_description.R b/tests/testthat/test-codemeta_description.R
@@ -7,6 +7,6 @@ testthat::test_that("We can use a preset id", {
 
 testthat::test_that("We can parse plain Authors: & Maintainers: entries", {
   f <- system.file("examples/DESCRIPTION_ex1.dcf", package = "codemetar")
-  codemeta_description(f)
+  expect_error(codemeta_description(f))
 })
 
diff --git a/tests/testthat/test-parse_depends.R b/tests/testthat/test-parse_depends.R
@@ -2,23 +2,24 @@ testthat::context("parse_depends.R")
 
 testthat::test_that("Test the various cases for dependencies", {
 
-  a <- parse_depends(NULL)
-  testthat::expect_length(a, 0)
-  a <- parse_depends(deps = "a4")  # BIOC provider
-  testthat::expect_gt(length(a[[1]]), 1)
-  a <- parse_depends(deps = "httr") # CRAN provider
-  testthat::expect_gt(length(a[[1]]), 1)
-  a <- parse_depends(deps = "R")
-  testthat::expect_equal(a[[1]]$name, "R")
-  a <- parse_depends(deps = "not-a-package")
+  testthat::expect_error(format_depend(NULL))
+  a <- format_depend(package = "a4",
+                     version = "*")  # BIOC provider
+  testthat::expect_equal(a$provider$`@id`, "https://www.bioconductor.org")
+  a <- format_depend(package = "httr",
+                     version = "*") # CRAN provider
+  testthat::expect_equal(a$provider$`@id`, "https://cran.r-project.org")
+  a <- format_depend(package = "R",
+                     version = ">= 3.0.0")
+  testthat::expect_equal(a$name, "R")
 
 })
 
 testthat::test_that("Test the various cases for ids (NOT used currently)", {
 
-  a <- guess_dep_id(parse_depends("a4")[[1]])  # BIOC provider
-  a <- guess_dep_id(parse_depends("httr")[[1]]) # CRAN provider
-  a <- guess_dep_id(parse_depends("R")[[1]])
-  a <- guess_dep_id(parse_depends("not-a-package")[[1]])
+  # a <- guess_dep_id(parse_depends("a4")[[1]])  # BIOC provider
+  # a <- guess_dep_id(parse_depends("httr")[[1]]) # CRAN provider
+  # a <- guess_dep_id(parse_depends("R")[[1]])
+  # a <- guess_dep_id(parse_depends("not-a-package")[[1]])
 
 })
-Original file line number
+Diff line change
@@ Expand Up / @@ -39,6 +39,7 @@ Imports: @@
         stats,
         stringi,
         readr,
+        desc,
         usethis,
         whisker
     Suggests: testthat,
@@ Expand Down @@