Citation meta problem ... potential solution (#241)

* Add tempdir() to avoid to writing guess_other_metadata() into the parent directory.

* + swap the default
+ updating the roxygen docs

* + Add myself as a ctb in DESCRIPTION

* + mention of changes in NEWS.md
+ linking this PR

* Address #240 and avoid pre-commit hook without user consent

* Correct link in NEWS.md #240

* Modify the way the file size is calculated.

+ Amend guess_fileSize() in guess_other_metadata.R as proposed #239
+ Update tests
+ Drop dependency to 'pkgbuild'
+ Add NEWS in NEWS.md

* Modify the way the file size is calculated.

+ Amend guess_fileSize() in guess_other_metadata.R as proposed #239
+ Update tests
+ Drop dependency to 'pkgbuild'
+ Update documentation in 'write_codemeta()'
+ Upddate corresponding Rd-files
+ Add NEWS in NEWS.md

* Address #238

+ Add NEWS

* Update tests and add CITATION_ex2 #241

NEWS.md

@@ -10,6 +10,8 @@
 * `write_codemeta()`: the default of argument `use_git_hook` is now `FALSE` to avoid an 
 unwanted alteration of the user's git environment [issue #240](https://github.com/ropensci/codemetar/issues/240).
 * Package dependency to 'pkgbuild' has been dropped.
+* `write_codemeta()` does not crash anymore if the `CITATION` file contains a line `citation(auto = meta)` [Issue #238](https://github.com/ropensci/codemetar/issues/238).
+
 
 # codemetar 0.1.7 2018-12
 

R/parse_citation.R

@@ -32,7 +32,6 @@ parse_citation <- function(bib) {
 ## so would need to include schema.org context
 
 bibentry_to_schema_field <- function(bibtype) {
-
   switch(
     bibtype,
     "Article" = "ScholarlyArticle",
@@ -159,11 +158,40 @@ guess_citation <- function(pkg) {
 # read_citation_with_encoding --------------------------------------------------
 read_citation_with_encoding <- function(citation_file, encoding = NA)
 {
-  meta <- if (! is.na(encoding)) {
-
+  meta <- if (!is.na(encoding)) {
     list(Encoding = encoding)
 
   } # else NULL implicitly
 
-  utils::readCitationFile(citation_file, meta = meta)
+  ## try to read citation file
+  citation <- try(utils::readCitationFile(citation_file, meta = meta), silent = TRUE)
+
+  ## if this fails for a very specific reason, namely a line similar to
+  ## citation(auto = meta), this line gets removed and we continue working
+  ## with a temporary CITATION file
+  if(inherits(citation, "try-error")){
+    if(grepl(pattern = "Error in.+?auto", citation[1])){
+      ## >> (1) read original CITATION file
+      temp_citation <-
+        readLines(
+          con = citation_file,
+          encoding = if (!is.na(encoding)) encoding else "unknown")
+
+      ## >> (2) remove citation(auto = meta)
+      repl_id <- which(grepl(
+        pattern = "citation\\s*\\(auto\\s*=\\s*meta\\s*\\)",
+        x = temp_citation
+        ))
+      temp_citation <- temp_citation[-repl_id]
+
+      ## >> (3) write new temporary citation file
+      temp_file <- tempfile()
+      writeLines(temp_citation, temp_file)
+
+      ## >> (4) apply extraction
+      citation <- utils::readCitationFile(temp_file, meta = meta)
+    }
+  }
+
+  return(citation)
 }

inst/examples/CITATION_ex2

@@ -0,0 +1,28 @@
+citation(auto = meta)
+bibentry(bibtype = "Article",
+         header = "To cite RNeXML in publications, please use:",
+         title = "{RNeXML}: {A} Package for Reading and Writing Richly Annotated Phylogenetic, Character, and Trait Data in {R}",
+         journal = "Methods in Ecology and Evolution",
+         author = c(
+             person("Carl", "Boettiger"),
+             person("Scott", "Chamberlain"),
+             person("Rutger", "Vos"),
+             person("Hilmar", "Lapp")),
+         year = 2016,
+         volume = 7,
+         pages = "352--357",
+         doi = "10.1111/2041-210X.12469")
+
+bibentry(bibtype = "Article",
+         header = "To cite RNeXML in publications, please use:",
+         title = "{RNeXML}: {A} Package for Reading and Writing Richly Annotated Phylogenetic, Character, and Trait Data in {R}",
+         journal = "Methods in Ecology and Evolution",
+         author = c(
+             person("Carl", "Boettiger"),
+             person("Scott", "Chamberlain"),
+             person("Rutger", "Vos"),
+             person("Hilmar", "Lapp")),
+         year = 2016,
+         volume = 7,
+         pages = "352--357",
+         doi = "https://doi.org/10.1111/2041-210X.12469")

tests/testthat/test-parse_citation.R

@@ -1,6 +1,5 @@
 testthat::context("parse citation")
 
-
 testthat::test_that("We can parse bibentry citations into schema.org",{
 
   bib <- citation("knitr") # Manual, Book, Incollection
@@ -14,7 +13,6 @@ testthat::test_that("We can parse bibentry citations into schema.org",{
 })
 
 testthat::test_that("We can parse citations", {
-
   ## installed package
   a <- guess_citation("knitr")
 
@@ -32,3 +30,7 @@ testthat::test_that("We can use encoding", {
   testthat::expect_silent(parse_citation(bib))
 })
 
+testthat::test_that("Test citation with encoding and citation line", {
+  f <- system.file("examples/CITATION_ex2", package = "codemetar")
+  testthat::expect_s3_class(read_citation_with_encoding(f), "citation")
+})