Merge branch 'feat/GLOB-12083' into 'develop'

Fix all requests from CRAN manual review

See merge request r-stack/sevenbridges2!86

.Rbuildignore

@@ -1,6 +1,7 @@
 ^.*\.Rproj$
 ^.covrignore
 ^CRAN-SUBMISSION$
+^LICENSE\.md$
 ^\.DS_Store$
 ^\.Rproj\.user$
 ^\.github$

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.1.0
-Date: 2024-01-16 17:25:52 UTC
-SHA: 4f3005d57e8525dc00ee25f3da32b3932d05df8c
+Date: 2024-02-02 14:55:17 UTC
+SHA: 27fa8f5ee3169d24c65b3cf68722829c51341730

DESCRIPTION

@@ -1,17 +1,18 @@
 Package: sevenbridges2
 Type: Package
-Title: Seven Bridges Platform API Client in R
+Title: The 'Seven Bridges Platform' API Client
 Version: 0.1.0
 Authors@R: c(
-    person("Marija", "Jovanovic", email = "[email protected]", role = c("aut", "cre")),
+    person("Marija", "Gacic", email = "[email protected]", role = c("aut", "cre")),
     person("Marko", "Trifunovic", email = "[email protected]", role = c("aut")),
     person("Vladimir", "Obucina", email = "[email protected]", role = c("aut")),
-    person("Seven Bridges Genomics Inc.", role = c("cph", "fnd"))
+    person("Velsera", role = c("cph", "fnd"))
     )
-Maintainer: Marija Jovanovic <[email protected]>
-Description: R client and utilities for Seven Bridges platform API, from Cancer
-    Genomics Cloud to other Seven Bridges supported platforms.
-License: Apache License 2.0 | file LICENSE
+Maintainer: Marija Gacic <[email protected]>
+Description: R client and utilities for 'Seven Bridges Platform' API, from 'Cancer Genomics Cloud' 
+    to other 'Seven Bridges' supported platforms. API documentation is hosted publicly 
+    at <https://docs.sevenbridges.com/docs/the-api>.
+License: Apache License 2.0
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr

NEWS.md

@@ -1,5 +1,3 @@
 # sevenbridges2 0.1.0
 
-# sevenbridges2 0.0.1
-
 * Initial CRAN submission.

R/class-file.R

@@ -771,10 +771,10 @@ File <- R6::R6Class(
     #'                    )
     #'
     #'  # Download file object
-    #'  file_object$download()
+    #'  file_object$download(directory_path = ".")
     #' }
     #'
-    download = function(directory_path = getwd(),
+    download = function(directory_path,
                         filename = self$name,
                         method = "curl",
                         # nolint start
@@ -786,8 +786,12 @@ File <- R6::R6Class(
         self$url <- self$get_download_url()
       }
 
-      # check if directory exists
-      check_download_path(directory_path, filename)
+      if (is_missing(directory_path)) {
+        rlang::abort("Please, provide directory path where to download your file.") # nolint
+      } else {
+        # check if directory exists
+        check_download_path(directory_path, filename)
+      }
 
       # check retry parameters
       check_retry_params(retry_count, parameter_to_validate = "count")
@@ -833,12 +837,12 @@ File <- R6::R6Class(
             }
             # wait for 5 seconds before new attemt - print the countdown message
             for (seconds_left in retry_timeout:1) {
-              cat(glue::glue_col("Retrying in {green {seconds_left}} seconds...", "\r")) # nolint
+              rlang::inform(glue::glue_col("Retrying in {green {seconds_left}} seconds...", "\r")) # nolint
               Sys.sleep(1)
             }
 
             # print a blank line to clear the countdown message
-            cat("\r", "                              ", "\r")
+            rlang::inform(glue::glue("\r", "                              ", "\r")) # nolint
           }
         )
       }

R/class-files.R

@@ -243,6 +243,7 @@ Files <- R6::R6Class(
     #'
     #' @importFrom checkmate assert_list
     #' @importFrom glue glue_col
+    #' @importFrom rlang inform
     #'
     #' @examples
     #' \dontrun{
@@ -288,22 +289,13 @@ Files <- R6::R6Class(
         )
         element <- setNames(list(element), names(res[i]))
         result <- append(result, element)
-        cat(
-          glue::glue_col("{blue  Original file id: }
-                           {names(res[i])}"),
-          "\n"
+        rlang::inform(
+          glue::glue_col(
+            "{blue  Original file id:} {names(res[i])}", "\n",
+            "{blue  Copied file id:} {res[[i]]$new_file_id}", "\n",
+            "{blue  Copied file name:} {res[[i]]$new_file_name}", "\n"
+          )
         )
-        cat(
-          glue::glue_col("{blue  Copied file id: }
-                           {res[[i]]$new_file_id}"),
-          "\n"
-        )
-        cat(
-          glue::glue_col("{blue  Copied file name: }
-                           {res[[i]]$new_file_name}"),
-          "\n"
-        )
-        cat("\n")
       }
       invisible(result)
     }, # nocov end

R/class-project.R

@@ -123,9 +123,12 @@ Project <- R6::R6Class(
     #' }
     #'
     print = function() {
-      cat(glue::glue_col("{blue  Project name: } {self$name}"), "\n") # nocov
-      cat(glue::glue_col("{blue  Project id: } {self$id}"), "\n") # nocov
-    },
+      # nocov start
+      rlang::inform(glue::glue_col(
+        "{blue  Project name: } {self$name} ", "\n",
+        "{blue  Project id: } {self$id} ", "\n"
+      ))
+    }, # nocov end
 
     # Print Project object in detail ------------------------------------------
     #' @description Detailed print method for Project class.

README.md

@@ -136,6 +136,6 @@ Contributors should sign the [Seven Bridges Contributor Agreement](https://secur
 
 ## Copyright
 
-© 2023 Seven Bridges Genomics, Inc. All rights reserved.
+© 2024 Velsera, Inc. All rights reserved.
 
-This project is licensed under the terms of the [Apache License 2.0](LICENSE).
+This project is licensed under the terms of the Apache License 2.0.

cran-comments.md

@@ -12,3 +12,12 @@ This is a resubmission. In this version I have:
 * Updated classes documentation to meet styling and formatting policies.
 
 * Updated DESCRIPTION file.
+
+* Added API reference url in description of DESCRIPTION file.
+
+* Removed License file and its reference in DESCRIPTION since we don't have 
+  additional restrictions to the license.
+
+* Replaced usage of cat() with rlang's inform function.
+
+* Updated tests to not use getwd() function.