merge with main

Merge branch 'main' into feat/add-readme-getting-started
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

DESCRIPTION

@@ -20,7 +20,6 @@ Imports:
     glue,
     haven,
     jsonlite,
-    magrittr,
     options,
     purrr,
     R6 (>= 2.4.0),
@@ -47,6 +46,6 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = TRUE)
 RoxygenNote: 7.3.2
-Remotes:  
+Remotes: 
     NovoNordisk-OpenSource/zephyr,
     NovoNordisk-OpenSource/connector.logger

NAMESPACE

@@ -42,7 +42,6 @@ S3method(write_ext,txt)
 S3method(write_ext,xpt)
 S3method(write_ext,yaml)
 S3method(write_ext,yml)
-export("%>%")
 export(connect)
 export(connector)
 export(connector_dbi)
@@ -70,6 +69,5 @@ importFrom(cli,cli_code)
 importFrom(cli,cli_inform)
 importFrom(cli,cli_text)
 importFrom(jsonlite,read_json)
-importFrom(magrittr,"%>%")
 importFrom(options,define_option)
 importFrom(rlang,set_names)

NEWS.md

@@ -1,7 +1,33 @@
+# connector 0.0.4 (2024-12-03)
+
+### Migration:
+-   Migration to public github
+
+### Features:
+-   Update of `create_directory_cnt()`
+-   Added metadata as a parameter in `connect()`
+-   More comprehensive testing
+-   Better integration with [whirl](https://github.com/NovoNordisk-OpenSource/whirl) through [connector.logger](https://github.com/NovoNordisk-OpenSource/connector.logger)
+
+### Other:
+-   Reducing the number of dependencies.
+-   Better messages
+
+# connector 0.0.3 (2024-09-25)
+
+### Breaking Changes:
+-   rename function from `*_cnt` to `cnt_`
+
+### Features:
+-   Nested connectors objects
+-   Use active bindings
+-   User guide added
+
+
 # connector 0.0.2
 
-* Added `connectors` super class
+-   Added `connectors` super class
 
 # connector 0.0.1
 
-* Initial version
+-   Initial version

R/connect.R

@@ -82,7 +82,7 @@ connect <- function(config = "_connector.yml", metadata = NULL, datasource = NUL
   checkmate::assert_logical(logging)
 
   if (!is.list(config)) {
-    if (tools::file_ext(config) %in% c("yml", "yaml")) {
+    if (get_file_ext(config) %in% c("yml", "yaml")) {
       config <- read_file(config, eval.expr = TRUE)
     } else {
       config <- read_file(config)

R/connector.R

@@ -65,7 +65,7 @@ connector <- R6::R6Class(
     #' List available content from the connector. See also [list_content_cnt].
     #' @return A [character] vector of content names
     list_content_cnt = function(...) {
-      self %>%
+      self |>
         list_content_cnt(...)
     },
 
@@ -74,23 +74,23 @@ connector <- R6::R6Class(
     #' @return
     #' R object with the content. For rectangular data a [data.frame].
     read_cnt = function(name, ...) {
-      self %>%
+      self |>
         read_cnt(name, ...)
     },
 
     #' @description
     #' Write content to the connector.See also [write_cnt].
     #' @return `r rd_connector_utils("inv_self")`
     write_cnt = function(x, name, ...) {
-      self %>%
+      self |>
         write_cnt(x, name, ...)
     },
 
     #' @description
     #' Remove or delete content from the connector. See also [remove_cnt].
     #' @return `r rd_connector_utils("inv_self")`
     remove_cnt = function(name, ...) {
-      self %>%
+      self |>
         remove_cnt(name, ...)
     }
   )

R/dbi.R

@@ -70,7 +70,7 @@ connector_dbi <- R6::R6Class(
     #' See also [disconnect_cnt].
     #' @return [invisible] `self`.
     disconnect_cnt = function() {
-      self %>%
+      self |>
         disconnect_cnt()
     },
 
@@ -79,7 +79,7 @@ connector_dbi <- R6::R6Class(
     #' See also [tbl_cnt].
     #' @return A [dplyr::tbl] object.
     tbl_cnt = function(name, ...) {
-      self %>%
+      self |>
         tbl_cnt(name, ...)
     }
   ),

R/dbi_methods.R

@@ -18,7 +18,7 @@
 #' @rdname read_cnt
 #' @export
 read_cnt.connector_dbi <- function(connector_object, name, ...) {
-  connector_object$conn %>%
+  connector_object$conn |>
     DBI::dbReadTable(name = name, ...)
 }
 
@@ -41,7 +41,7 @@ read_cnt.connector_dbi <- function(connector_object, name, ...) {
 #' @rdname write_cnt
 #' @export
 write_cnt.connector_dbi <- function(connector_object, x, name, ...) {
-  connector_object$conn %>%
+  connector_object$conn |>
     DBI::dbWriteTable(name = name, value = x, ...)
   return(invisible(connector_object))
 }
@@ -59,7 +59,7 @@ write_cnt.connector_dbi <- function(connector_object, x, name, ...) {
 #' @rdname list_content_cnt
 #' @export
 list_content_cnt.connector_dbi <- function(connector_object, ...) {
-  connector_object$conn %>%
+  connector_object$conn |>
     DBI::dbListTables(...)
 }
 
@@ -81,7 +81,7 @@ list_content_cnt.connector_dbi <- function(connector_object, ...) {
 #' @rdname remove_cnt
 #' @export
 remove_cnt.connector_dbi <- function(connector_object, name, ...) {
-  connector_object$conn %>%
+  connector_object$conn |>
     DBI::dbRemoveTable(name = name, ...)
   return(invisible(connector_object))
 }
@@ -113,7 +113,7 @@ remove_cnt.connector_dbi <- function(connector_object, name, ...) {
 #' @rdname tbl_cnt
 #' @export
 tbl_cnt.connector_dbi <- function(connector_object, name, ...) {
-  connector_object$conn %>%
+  connector_object$conn |>
     dplyr::tbl(from = name, ...)
 }
 
@@ -133,6 +133,6 @@ tbl_cnt.connector_dbi <- function(connector_object, name, ...) {
 #' @rdname disconnect_cnt
 #' @export
 disconnect_cnt.connector_dbi <- function(connector_object, ...) {
-  connector_object$conn %>%
+  connector_object$conn |>
     DBI::dbDisconnect(...)
 }

R/fs.R

@@ -57,7 +57,7 @@ connector_fs <- R6::R6Class(
     #' See also [download_cnt].
     #' @return [invisible] `file`
     download_cnt = function(name, file = basename(name), ...) {
-      self %>%
+      self |>
         download_cnt(name, file, ...)
     },
 
@@ -66,7 +66,7 @@ connector_fs <- R6::R6Class(
     #' See also [upload_cnt].
     #' @return `r rd_connector_utils("inv_self")`
     upload_cnt = function(file, name = basename(file), ...) {
-      self %>%
+      self |>
         upload_cnt(file, name, ...)
     },
 
@@ -76,7 +76,7 @@ connector_fs <- R6::R6Class(
     #' @param name [character] The name of the directory to create
     #' @return [connector_fs] object of a newly created directory
     create_directory_cnt = function(name, ...) {
-      self %>%
+      self |>
         create_directory_cnt(name, ...)
     },
 
@@ -86,7 +86,7 @@ connector_fs <- R6::R6Class(
     #' @param name [character] The name of the directory to remove
     #' @return `r rd_connector_utils("inv_self")`
     remove_directory_cnt = function(name, ...) {
-      self %>%
+      self |>
         remove_directory_cnt(name, ...)
     }
   ),

R/fs_methods.R

@@ -71,7 +71,7 @@ write_cnt.connector_fs <- function(connector_object, x, name, ...) {
 #' @rdname list_content_cnt
 #' @export
 list_content_cnt.connector_fs <- function(connector_object, ...) {
-  connector_object$path %>%
+  connector_object$path |>
     list.files(...)
 }
 

R/fs_read.R

@@ -10,7 +10,7 @@
 #' @return the result of the reading function
 #' @export
 read_file <- function(path, ...) {
-  find_ext <- tools::file_ext(path)
+  find_ext <- get_file_ext(path)
 
   class(path) <- c(find_ext, class(path))
 

R/fs_write.R

@@ -11,7 +11,7 @@
 #' @return `write_file()`: [invisible()] file.
 #' @export
 write_file <- function(x, file, ...) {
-  find_ext <- tools::file_ext(file) |>
+  find_ext <- get_file_ext(file) |>
     assert_ext("write_ext")
 
   class(file) <- c(find_ext, class(file))

R/utils_fileext.R

@@ -0,0 +1,14 @@
+# Getting file extension
+get_file_ext <- function(file_paths) {
+  vapply(
+    X = file_paths,
+    FUN = function(file_path) {
+      file_name <- basename(file_path)
+      file_parts <- strsplit(file_name, "\\.")[[1]]
+      file_extension <- ifelse(length(file_parts) == 1, "", utils::tail(file_parts, 1))
+      return(file_extension)
+    },
+    FUN.VALUE = character(1),
+    USE.NAMES = FALSE
+  )
+}

R/utils_files.R

@@ -58,14 +58,14 @@ assert_ext <- function(ext, method) {
 #' @importFrom rlang set_names
 #' @noRd
 error_extension <- function() {
-  ext_supp <- supported_fs() %>%
+  ext_supp <- supported_fs() |>
     rlang::set_names("*")
   c(
     "No method found for this extension, please implement your own method
     (to see an example run `connector::example_read_ext()`) or use a supported extension",
     "i" = "Supported extensions are:",
     ext_supp
-  ) %>%
+  ) |>
     cli::cli_abort()
 }
 

dev/connector_config_yaml.qmd

@@ -55,7 +55,7 @@ extract_datasources(yaml_content)
 only_one <- extract_connections(yaml_content)[[1]]
 
 ## Extract fct
-my_backend <- only_one %>%
+my_backend <- only_one |> 
     extract_backends()
 
 #### Create the backend for fs
@@ -124,8 +124,8 @@ connect$sdtm$read("iris")
 
 ## Manipulate a table with the database 
 
-connect$sdtm$tbl("iris")  %>% 
+connect$sdtm$tbl("iris") |>  
     dplyr::filter(Sepal.Length > 5)
 
 
-```
+```

tests/testthat/_snaps/connect.md

@@ -1,7 +1,7 @@
 # Connect datasources to the connections for a yaml file
 
     Code
-      iris_f %>% dplyr::collect()
+      dplyr::collect(iris_f)
     Output
       # A tibble: 118 x 5
          Sepal.Length Sepal.Width Petal.Length Petal.Width Species

tests/testthat/test-connect.R

@@ -7,11 +7,11 @@ test_that("Connect datasources to the connections for a yaml file", {
 
   ## write and read for a system file
   withr::with_options(list(readr.show_col_types = FALSE), {
-    cnts$adam$read_cnt("adsl.csv") %>%
+    cnts$adam$read_cnt("adsl.csv") |>
       expect_s3_class("data.frame")
     expect_error(cnts$adam$read_cnt("do_not_exits.csv"))
 
-    cnts$adam$write_cnt(data.frame(a = 1:10, b = 11:20), "example.csv") %>%
+    cnts$adam$write_cnt(data.frame(a = 1:10, b = 11:20), "example.csv") |>
       expect_no_error()
 
     expect_no_error(cnts$adam$read_cnt("example.csv"))
@@ -26,12 +26,12 @@ test_that("Connect datasources to the connections for a yaml file", {
 
   ## Manipulate a table with the database
 
-  iris_f <- cnts$sdtm$tbl_cnt("iris") %>%
+  iris_f <- cnts$sdtm$tbl_cnt("iris") |>
     dplyr::filter(Sepal.Length > 5)
 
   expect_s3_class(iris_f, "tbl_dbi")
 
-  expect_snapshot(iris_f %>% dplyr::collect())
+  expect_snapshot(dplyr::collect(iris_f))
 })
 
 test_that("Tools for yaml parsinbg", {
@@ -121,9 +121,13 @@ testthat::test_that("Using and uptade metadata", {
 })
 
 test_that("Add logs to connectors object",{
-   # Don't test the logic of connector.logger because it is not the purpose of connector
-   cnts <- connect(yaml_file, logging = TRUE)
 
+  # connector.logger needs to be installed to pass this test - if not available
+  # then skip the test
+  testthat::skip_if_not_installed("connector.logger")
+
+  # Don't test the logic of connector.logger because it is not the purpose of connector
+  cnts <- connect(yaml_file, logging = TRUE)
 
   lapply(cnts, function(x){
     expect_s3_class(x, "connector")