add support for OSF repositories

also update rendering to handle the option

for details see codecheckers/register#25

Author: nuest

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.0.0.9008
+Version: 0.0.0.9009
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",
@@ -15,7 +15,16 @@ Authors@R:
 Description: This contains helper functions for CODECHECKERS (<https://codecheck.org.uk>).
 License: MIT + file LICENSE
 Depends: R (>= 4.0.0), gh, R.cache, parsedate
-Imports: yaml, xtable, stringr, rmarkdown, knitr, jsonlite, assertthat, rorcid
+Imports: 
+    yaml,
+    xtable,
+    stringr,
+    rmarkdown,
+    knitr,
+    jsonlite,
+    assertthat,
+    rorcid,
+    osfr
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1

NAMESPACE

@@ -21,6 +21,9 @@ importFrom(R.cache,addMemoization)
 importFrom(R.cache,getCacheRootPath)
 importFrom(gh,gh)
 importFrom(knitr,kable)
+importFrom(osfr,osf_download)
+importFrom(osfr,osf_ls_files)
+importFrom(osfr,osf_retrieve_node)
 importFrom(parsedate,parse_date)
 importFrom(rmarkdown,render)
 importFrom(rorcid,check_dois)

R/configuration.R

@@ -1,36 +1,118 @@
+#' Retrieve a codecheck.yml file from a remote repository
+#' 
+#' @author Daniel Nüst
+#' @param x the repo specification
+get_codecheck_yml_uncached <- function(x) {
+  spec <- parse_repository_spec(x)
+  
+  result <- switch (spec[["type"]],
+    "github" = get_codecheck_yml_github(spec[["repo"]]),
+    "osf" = get_codecheck_yml_osf(spec[["repo"]])
+  )
+  
+  return(result)
+}
+
+#' Retrieve a codecheck.yml file from a GitHub repository
+#' 
 #' @author Daniel Nüst
 #' @importFrom gh gh
-get_codecheck_yml_uncached <- function(repo) {
-  repo_files <- gh::gh("GET /repos/codecheckers/:repo/contents/",
-                       repo = repo,
+#' @param x the org/repo to download the file from
+get_codecheck_yml_github <- function(x) {
+  org_repo <- strsplit(x, "/", fixed = TRUE)[[1]]
+  
+  if (length(org_repo) != 2) {
+    stop("Incomplete repo specification for type 'github', need 'org/repo' but have '", x, "'")
+  }
+  
+  repo_files <- gh::gh("GET /repos/:org/:repo/contents/",
+                       org = org_repo[[1]],
+                       repo = org_repo[[2]],
                        .accept = "application/vnd.github.VERSION.raw")
   repo_file_names <- sapply(repo_files, "[[", "name")
 
   if ("codecheck.yml" %in% repo_file_names) {
     config_file_response <- gh::gh(
-      "GET /repos/codecheckers/:repo/contents/:file",
-      repo = repo,
+      "GET /repos/:org/:repo/contents/:file",
+      org = org_repo[[1]],
+      repo = org_repo[[2]],
       file = "codecheck.yml",
       .accept = "application/vnd.github.VERSION.raw")
     config_file <- yaml::read_yaml(text = config_file_response$message)
     return(config_file)
   } else {
+    warning("codecheck.yml not found in list of repository files for ", x)
+    return(NULL)
+  }
+}
+
+#' Retrieve a codecheck.yml file from an OSF project
+#' 
+#' @author Daniel Nüst
+#' @param x the OSF id (5 characters)
+#' @importFrom osfr osf_retrieve_node osf_ls_files osf_download
+get_codecheck_yml_osf <- function(x) {
+  repo <- osfr::osf_retrieve_node(x)
+  repo_files <- osfr::osf_ls_files(repo, pattern = "codecheck.yml")
+  
+  if (nrow(repo_files) == 1) {
+    temp_dir <- tempdir()
+    osfr::osf_download(repo_files, path = temp_dir)
+    local_file <- file.path(temp_dir, "codecheck.yml")
+    config_file <- yaml::read_yaml(file = local_file)
+    file.remove(local_file)
+    return(config_file)
+  } else {
+    warning("codecheck.yml not found in list of repository files for https://osf.io/", x)
     return(NULL)
   }
 }
 
+#' Parse the repository specification in the column "Repo" in the register CSV file
+#' 
+#' Based roughly on [`remotes::parse_one_extra`](https://github.com/r-lib/remotes/blob/master/R/deps.R#L519)
+#' 
+#' Supported variants:
+#' 
+#' - `osf::ABC12`
+#' - `github::codecheckers/Piccolo-2020`
+#' 
+#' @author Daniel Nüst
+#' @param x the repository specification to parse
+#' @return a named character vector with the items `type` and `repo`
+parse_repository_spec <- function(x) {
+  pieces <- strsplit(x, "::", fixed = TRUE)[[1]]
+  
+  #if (length(pieces) == 1) {
+    #type <- "github"
+    #repo <- paste0("codecheckers/", pieces)
+  #} else
+  if (length(pieces) == 2) {
+    type <- pieces[1]
+    repo <- pieces[2]
+  } else {
+    stop("Malformed repository specification '", x, "'")
+  }
+  
+  if (! type %in% c("github", "osf")) {
+    stop("Unsupported repository type '", type, "'")
+  }
+  
+  return(c(type = type, repo = repo))
+}
+
 get_codecheck_yml_cached <- R.cache::addMemoization(get_codecheck_yml_uncached)
 
 #' Get the CODECHECK configuration file from a repository
 #' 
-#' @param repo Repository in the codecheckers organisation on GitHub
+#' @param x Repository in the codecheckers organisation on GitHub
 #' 
 #' @author Daniel Nüst
 #' @importFrom R.cache addMemoization
 #' 
 #' @export
-get_codecheck_yml <- function(repo) {
-  configuration <- get_codecheck_yml_cached(repo)
+get_codecheck_yml <- function(x) {
+  configuration <- get_codecheck_yml_cached(x)
   return(configuration)
 }
 

R/register.R

@@ -64,13 +64,23 @@ register_render <- function(register = read.csv("register.csv", as.is = TRUE),
 
   # turn repositories into links for table rendering
   register_table$Repository <- sapply(X = register$Repository,
-                                 FUN = function(repository_name) {
-                                   if (!is.na(repository_name)) {
-                                     urrl <- paste0("https://github.com/codecheckers/",
-                                                    repository_name)
-                                     paste0("[", repository_name, "](", urrl, ")")
+                                 FUN = function(repository) {
+                                   spec <- parse_repository_spec(repository)
+                                   
+                                   if (!is.na(spec)) {
+                                     urrl <- "#"
+                                     
+                                     if (spec[["type"]] == "github") {
+                                       urrl <- paste0("https://github.com/", spec[["repo"]])
+                                       paste0("[", spec[["repo"]], "](", urrl, ")")
+                                     } else if (spec[["type"]] == "osf") {
+                                       urrl <- paste0("https://osf.io/", spec[["repo"]])
+                                       paste0("[", spec[["repo"]], "](", urrl, ")")
+                                     } else {
+                                       repository
+                                     }
                                    } else {
-                                     repository_name
+                                     repository
                                    }
                                  })
 
@@ -133,11 +143,14 @@ register_render <- function(register = read.csv("register.csv", as.is = TRUE),
     register_table$`Paper reference` <- stringr::str_trim(references)
     register_table$`Repository Link` <- sapply(
       X = register$Repository,
-      FUN = function(repository_name) {
-        if (!is.na(repository_name)) {
-          paste0("https://github.com/codecheckers/", repository_name)
+      FUN = function(repository) {
+        spec <- parse_repository_spec(repository)
+        if (spec[["type"]] == "github") {
+          paste0("https://github.com/", spec[["repo"]])
+        } else if (spec[["type"]] == "osf") {
+          paste0("https://osf.io/", spec[["repo"]])
         } else {
-          NA
+          repository
         }
       }
     )
@@ -168,12 +181,16 @@ register_render <- function(register = read.csv("register.csv", as.is = TRUE),
 #' - Does the repo have a LICENSE?
 #' 
 #' @param register A `data.frame` with all required information for the register's view
+#' @param from The first register entry to check
+#' @param to The last register entry to check
 #' 
 #' @author Daniel Nüst
 #' @importFrom gh gh
 #' @export
-register_check <- function(register = read.csv("register.csv", as.is = TRUE)) {
-  for (i in seq_len(nrow(register))) {
+register_check <- function(register = read.csv("register.csv", as.is = TRUE),
+                           from = 1,
+                           to = nrow(register)) {
+  for (i in seq(from = from, to = to)) {
     cat("Checking", toString(register[i, ]), "\n")
     entry <- register[i, ]
 

inst/tinytest/test_codecheck_yml_retrieval.R

@@ -0,0 +1,20 @@
+tinytest::using(ttdo)
+
+# Invalid or unsupported ----
+expect_error(get_codecheck_yml("unsupported::repo/spec"),
+             pattern = "Unsupported repository type 'unsupported")
+expect_error(get_codecheck_yml("github::not_org_and_repo"),
+             pattern = "Incomplete repo specification for type 'github'(.*)'not_org_and_repo'")
+
+expect_warning(get_codecheck_yml("github::codecheckers/register"),
+               pattern = "codecheck.yml not found in(.*)codecheckers/register")
+expect_warning(get_codecheck_yml("osf::6K5FH"),
+               pattern = "codecheck.yml not found in(.*)https://osf.io/6K5FH")
+
+# GitHub ----
+expect_silent({ piccolo <- get_codecheck_yml("github::codecheckers/Piccolo-2020") })
+expect_equal(piccolo$report, "http://doi.org/10.5281/zenodo.3674056")
+
+# OSF ----
+expect_silent({ agile <- get_codecheck_yml("osf::5SVMT") })
+expect_equal(agile$report, "https://doi.org/10.17605/OSF.IO/5SVMT")