update tests/testthat/test-read_from_dhis2_helpers.R

R/read_from_fingertips-helpers.R

@@ -43,13 +43,7 @@ get_fingertips_metadata <- function() {
 #' @keywords internal
 #' @noRd
 #'
-get_ind_id_from_ind_name <- function(metadata =
-                                       list(indicator_profile_domain =
-                                              fingertipsR::indicators(),
-                                            indicator_ids_names      =
-                                              fingertipsR::indicators_unique(),
-                                            area_type                =
-                                              fingertipsR::area_types()),
+get_ind_id_from_ind_name <- function(metadata,
                                      indicator_name = "Pupil absence") {
   checkmate::assert_list(metadata,
                          len = 3L, null.ok = FALSE,
@@ -110,13 +104,7 @@ get_ind_id_from_ind_name <- function(metadata =
 #' @keywords internal
 #' @noRd
 #'
-get_ind_id_from_domain_id <- function(metadata =
-                                        list(indicator_profile_domain =
-                                               fingertipsR::indicators(),
-                                             indicator_ids_names      =
-                                               fingertipsR::indicators_unique(),
-                                             area_type                =
-                                               fingertipsR::area_types()),
+get_ind_id_from_domain_id <- function(metadata,
                                       domain_id      = 1000041L,
                                       indicator_name = NULL) {
   checkmate::assert_list(metadata,
@@ -185,14 +173,7 @@ get_ind_id_from_domain_id <- function(metadata =
 #' @keywords internal
 #' @noRd
 #'
-get_ind_id_from_domain_name <- function(metadata =
-                                          list(indicator_profile_domain =
-                                                 fingertipsR::indicators(),
-                                               indicator_ids_names      =
-                                                 fingertipsR::indicators_unique(), # nolint: line_length_linter
-                                               fingertipsR::indicators_unique(), # nolint: line_length_linter
-                                               area_type                =
-                                                 fingertipsR::area_types()),
+get_ind_id_from_domain_name <- function(metadata,
                                         domain_name    = "B. Wider determinants of health", # nolint: line_length_linter
                                         indicator_name = NULL) {
   checkmate::assert_list(metadata,
@@ -268,14 +249,8 @@ get_ind_id_from_domain_name <- function(metadata =
 #' }
 #' @keywords internal
 #' @noRd
-get_profile_name <- function(metadata =
-                               list(indicator_profile_domain =
-                                      fingertipsR::indicators(),
-                                    indicator_ids_names      =
-                                      fingertipsR::indicators_unique(),
-                                    area_type                =
-                                      fingertipsR::area_types()),
-                             profile_id = 19L,
+get_profile_name <- function(metadata,
+                             profile_id   = 19L,
                              profile_name = "Public Health Outcomes Framework") { # nolint: line_length_linter
   checkmate::assert_list(metadata,
                          len = 3L, null.ok = FALSE,
@@ -333,13 +308,7 @@ get_profile_name <- function(metadata =
 #' }
 #' @keywords internal
 #' @noRd
-get_ind_id_from_profile <- function(metadata =
-                                      list(indicator_profile_domain =
-                                             fingertipsR::indicators(),
-                                           indicator_ids_names      =
-                                             fingertipsR::indicators_unique(),
-                                           area_type                =
-                                             fingertipsR::area_types()),
+get_ind_id_from_profile <- function(metadata,
                                     domain_id      = NULL,
                                     domain_name    = NULL,
                                     indicator_name = NULL,
@@ -410,8 +379,7 @@ get_ind_id_from_profile <- function(metadata =
 #' }
 #' @keywords internal
 #' @noRd
-fingertips_subset_rows <- function(data = readepi(profile_id   = 19L,
-                                                  area_type_id = 202L)[["data"]], # nolint: line_length_linter
+fingertips_subset_rows <- function(data,
                                    records     = c("E92000001", "E12000002",
                                                    "E12000009"),
                                    id_col_name = "AreaCode") {
@@ -459,8 +427,7 @@ fingertips_subset_rows <- function(data = readepi(profile_id   = 19L,
 #' }
 #' @keywords internal
 #' @noRd
-fingertips_subset_columns <- function(data   = readepi(profile_id   = 19L,
-                                                       area_type_id = 202L)[["data"]], # nolint: line_length_linter
+fingertips_subset_columns <- function(data,
                                       fields = c("IndicatorID", "AreaCode",
                                                  "Age", "Value")) {
   checkmate::assert_data_frame(data,

R/read_servers.R

@@ -108,8 +108,8 @@ sql_server_read_data <- function(dbms          = "MySQL",
 
   # separate the srcs
   attributes <- identify_tables_and_queries(src = src, tables = tables)
-  queries <- attributes[["queries"]]
-  src     <- attributes[["tables"]]
+  queries    <- attributes[["queries"]]
+  src        <- attributes[["tables"]]
 
   # fetch data from queries
   if (length(queries) > 0L) {

R/read_servers_helpers.R

@@ -64,7 +64,7 @@ connect_to_server <- function(dbms          = "MySQL",
 #' @param query the SQL query
 #' @param tables the list of all tables from the database
 #'
-#' @return a `character` with the identified tables name(s) from the SQL query
+#' @return a `character` with the extracted table name(s) from the SQL query
 #'
 #' @examples
 #' \dontrun{
@@ -175,7 +175,7 @@ fetch_data_from_query <- function(src           = "select author_id, name, last_
 #' @param port the server port ID
 #'
 #' @return a `list` of 1 or more elements of type `data.frame` where every
-#'    element contains the subset of the data from the corresponding table.
+#'    element contains the subset of the data from the corresponding table
 #' @examples
 #' \dontrun{
 #' result <- sql_select_data(
@@ -273,7 +273,7 @@ sql_select_data <- function(table_names   = "author",
 #' @param id_position the id position
 #'
 #' @returns a `list` of 2 elements of type `character` and `numeric`
-#'    corresponding to the ID column name and position.
+#'    corresponding to the ID column name and position
 #' @keywords internal
 #' @noRd
 get_id_column_name <- function(id_col_name = c("author_id", "rfam_acc"),
@@ -313,7 +313,7 @@ get_id_column_name <- function(id_col_name = c("author_id", "rfam_acc"),
 #' @param port the server port ID
 #'
 #' @return an object of type `data.frame` with the entire dataset fetched from
-#'    the specified table.
+#'    the specified table
 #'
 #' @examples
 #' \dontrun{
@@ -447,7 +447,7 @@ sql_select_records_and_fields <- function(table          = "author",
 #' @param from the table name
 #' @param driver_name the name of the MS driver
 #'
-#' @return prints the first 5 rows of the specified table.
+#' @return prints the first 5 rows of the specified table
 #'
 #' @examples
 #' \dontrun{

tests/testthat/test-read_from_dhis2_helpers.R

@@ -17,7 +17,6 @@ httptest::with_mock_api({
 test_that("dhis2_login fails as expected", {
   testthat::skip_on_cran()
   testthat::skip_if_offline()
-  testthat::skip_if_not_installed("httptest")
   expect_error(
     dhis2_login(
       base_url  = file.path("test", "play.dhis2.org", "dev"),
@@ -52,7 +51,7 @@ test_that("dhis2_subset_fields fails as expected", {
   testthat::skip_on_cran()
   testthat::skip_if_offline()
   data <- readepi(
-    credentials_file = system.file("extdata", "test.ini", package = "readepi"),
+    credentials_file  = system.file("extdata", "test.ini", package = "readepi"),
     data_source        = "https://play.dhis2.org/dev",
     dataset            = "pBOMPrpg1QX,BfMAe6Itzgt",
     organisation_unit  = "DiszpKrYNg8",

tests/testthat/test-read_from_fingertips-helpers.R

@@ -467,13 +467,13 @@ httptest::with_mock_api({
     testthat::skip_on_cran()
     testthat::skip_if_offline()
     res <- get_profile_name(
-      profile_id   = 19L,
-      profile_name = "Public Health Outcomes Framework",
       metadata = list(
         indicator_profile_domain = fingertipsR::indicators(),
-        indicator_ids_names      = fingertipsR::indicators_unique(),
-        area_type                = fingertipsR::area_types()
-      )
+        indicator_ids_names = fingertipsR::indicators_unique(),
+        area_type = fingertipsR::area_types()
+      ),
+      profile_id = 19L,
+      profile_name = "Public Health Outcomes Framework"
     )
     expect_type(res, "list")
     expect_length(res, 2L)