fix order variable. Closes #8

NAMESPACE

@@ -41,6 +41,7 @@ importFrom(glue,glue_collapse)
 importFrom(graphics,stem)
 importFrom(janitor,make_clean_names)
 importFrom(magrittr,"%>%")
+importFrom(magrittr,extract2)
 importFrom(purrr,map)
 importFrom(purrr,map2_chr)
 importFrom(purrr,map_chr)
@@ -52,6 +53,7 @@ importFrom(stringr,str_extract)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(tidyselect,all_of)
+importFrom(tidyselect,any_of)
 importFrom(tm,stemDocument)
 importFrom(utils,capture.output)
 importFrom(utils,packageVersion)

R/order.R

@@ -46,16 +46,18 @@ xportr_order <- function(.df, metacore, domain = NULL, verbose = getOption("xpor
   }
 
   # Grabs vars from Spec and inputted dataset
-  vars_in_spec_ds <- metadata[[variable_name]]
+  vars_in_spec_ds <- metadata[, c(variable_name, order_name)] %>%
+    arrange(!!sym(order_name)) %>%
+    extract2(variable_name)
 
+  vars_in_spec_ds <- vars_in_spec_ds[!is.na(vars_in_spec_ds)]
   # Grabs all variables from Spec file and orders accordingly
   ord_vars <- .df %>% 
-    select(all_of(vars_in_spec_ds)) %>%
-    arrange(!!sym(order_name))
+    select(any_of(vars_in_spec_ds))
 
   # Variables not in Spec file - will be moved to the end
   drop_vars <- .df %>% 
-    select(!all_of(vars_in_spec_ds))
+    select(!any_of(vars_in_spec_ds))
 
   # Used in warning message for how many vars have been moved
   moved_vars <- nrow(drop_vars)

R/xportr-package.R

@@ -11,14 +11,15 @@
 #' @importFrom glue glue glue_collapse
 #' @importFrom cli cli_alert_info cli_h2 cli_alert_success cli_alert_info
 #'   cli_div cli_alert_success cli_text cli_h2
-#' @importFrom tidyselect all_of
+#' @importFrom tidyselect all_of any_of
 #' @importFrom utils capture.output str tail packageVersion
 #' @importFrom stringr str_detect str_extract str_replace str_replace_all
 #' @importFrom readr parse_number
 #' @importFrom purrr map_chr map2_chr
 #' @importFrom janitor make_clean_names
 #' @importFrom tm stemDocument
 #' @importFrom graphics stem
+#' @importFrom magrittr extract2
 "_PACKAGE"
 
 globalVariables(c("abbr_parsed", "abbr_stem", "adj_orig", "adj_parsed", "col_pos", "dict_varname",

tests/testthat/test-var-order.R

@@ -1,44 +1,30 @@
 # library(dplyr)
-# library(haven)
-# library(testthat)
+suppressWarnings({
+  library(haven)
+  library(readxl)
+})
+
 # 
 # #context("xportr_seq correctly order dataset according to spec")
-# 
-# test_that("Variables are correctly grabbed from the Spec file", {
-#   
-#   spec_manual <- c("STUDYID", "USUBJID","SUBJID","SITEID","AGE","SEX","RACE","ACOUNTRY","FASFL","ITTFL")
-#   
-#   spec_xportr <- get_spec_col_names("ADAE", tab_model="ADAM", 
-#                                     path_to_spec = "~/xportr/inst/specs", vendor = "GSK")[1:10]
-#   
-#   expect_equal(spec_manual, spec_xportr)
-# })
-# 
-# 
-# test_that("Variable are ordered correctly", {
-#   
-#   ADAE <- read_sas("~/xptr/inst/extdata/adae.sas7bdat")
-#   
-#   ADAE_xportr <- xportr_ord("ADAE", ADAE, tab_model = "ADAM", 
-#                             path_to_spec = "~/xportr/inst/specs", 
-#                             vendor = "GSK", verbose = FALSE,
-#                             msg_var_order = TRUE)
-#   
-#   vars_in_spec_ds <- c("STUDYID","SITEID", "USUBJID","SUBJID", "TRT01A", "TRT01AN",
-#                        "AETERM", "AEDECOD","AESOC","AGE","SEX","RACE","SAFFL","ASTDT",
-#                        "ASTTM","AENDT","ADURC","AEACN","AESER","AEOUT", "AEREL","ATOXGR", 
-#                        "ATOXGRN","AFTRTSTC")
-#   
-#   # Grabs all variables from Spec file and orders accordingly
-#   seq_vars <- ADAE %>% 
-#     select(all_of(vars_in_spec_ds)) 
-#   
-#   # Variables not in Spec file - will be moved to the end
-#   drop_vars <- ADAE %>% 
-#     select(!all_of(vars_in_spec_ds))
-#   
-#   ADAE_manual <- bind_cols(seq_vars, drop_vars)
-#   
-#   expect_equal(ADAE_xportr, ADAE_manual)
-# })
-# 
+#
+
+test_that("Variable are ordered correctly", {
+
+  ADAE <- read_sas(system.file("extdata", "adae.sas7bdat", package = "xportr"))
+  met <- read_excel(system.file("specs", "ADaM_spec.xlsx", package = "xportr"), 3)
+
+  withr::with_options(
+    list(xportr.order_name = "Order", xportr.variable_name = "Variable"), {
+      ADAE_xportr <- xportr_order(ADAE, metacore = met, "ADAE", verbose = "none")
+    }
+  )
+
+  after_names <- c("STUDYID", "USUBJID", "AEDECOD", "AESOC", "AETERM", "AESER", 
+                   "ASTDT", "AENDT", "ATOXGR", "TRT01A", "TRT01AN", "SAFFL", "SUBJID", 
+                   "WEIGHTBL", "SEX", "AGE", "AGEU", "RACE", "SITEID", "RACEN", 
+                   "ASTTM", "ADURC", "AEACN", "AEOUT", "AEREL", "ATOXGRN", "AFTRTSTC", 
+                   "AEWDFL")
+
+  expect_equal(names(ADAE_xportr), after_names)
+})
+