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#107 style code
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@edgar-manukyan
edgar-manukyan committed Dec 11, 2024
1 parent 59c0072 commit 4ba5d3f
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Showing 2 changed files with 1 addition and 4 deletions.
2 changes: 0 additions & 2 deletions R/generate_code.R
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,6 @@ generate_code <- function(spec, domain, out_dir = ".") {
#' @keywords internal
#'
style_the_code <- function(code_by_topics, domain) {

admiraldev::assert_list_of(code_by_topics, "character")

prefix_f <- paste0(domain, "_template_prefix")
Expand Down Expand Up @@ -296,7 +295,6 @@ remove_last_pipe <- function(code_blocks) {
#' @keywords internal
#'
get_domain_spec <- function(spec, domain) {

admiraldev::assert_data_frame(spec, required_vars = rlang::syms(expected_columns_min()))
admiraldev::assert_character_scalar(domain)

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3 changes: 1 addition & 2 deletions tests/testthat/test-generate_code.R
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ test_that("generate_code works for one topic domain", {
})

test_that("generate_code works for multiple topics domain", {

# nolint start
spec <- tibble::tribble(
~study_number, ~raw_dataset, ~raw_dataset_label, ~raw_variable, ~raw_variable_label, ~raw_variable_ordinal, ~raw_variable_type, ~raw_data_format, ~raw_fmt, ~raw_unk, ~study_specific, ~annotation_ordinal, ~mapping_is_dataset, ~annotation_text, ~target_sdtm_domain, ~target_sdtm_variable, ~target_sdtm_variable_role, ~topic, ~target_sdtm_variable_codelist_code, ~target_sdtm_variable_controlled_terms_or_format, ~target_sdtm_variable_ordinal, ~origin, ~mapping_algorithm, ~entity_sub_algorithm, ~target_hardcoded_value, ~target_term_value, ~target_value, ~target_term_code, ~condition_ordinal, ~condition_group_ordinal, ~condition_add_raw_dat, ~condition_add_tgt_dat, ~condition_left_raw_dataset, ~condition_left_raw_variable, ~condition_left_sdtm_domain, ~condition_left_sdtm_variable, ~condition_operator, ~condition_right_text_value, ~condition_right_sdtm_domain, ~condition_right_sdtm_variable, ~condition_right_raw_dataset, ~condition_right_raw_variable, ~condition_next_logical_operator, ~merge_type, ~merge_left, ~merge_right, ~merge_condition, ~unduplicate_keys, ~groupby_keys, ~target_resource_raw_dataset, ~target_resource_raw_variable,
Expand All @@ -47,7 +46,7 @@ test_that("generate_code works for multiple topics domain", {
"lp_study", "vitals_raw_data", "Vital Signs", "SYS_BP", "Systolic blood pressure", "6", "Text", "3", NA, NA, "FALSE", "2", "FALSE", "VS.VSTEST = 'Systolic Blood Pressure'", "VS", "VSTEST", "Synonym Qualifier", "SYS_BP", "C67153", "(VSTEST)", "8", "Assigned", "hardcode_ct", NA, NA, "Systolic Blood Pressure", "Systolic Blood Pressure", "C25298", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
"lp_study", "vitals_raw_data", "Vital Signs", "SYS_BP", "Systolic blood pressure", "6", "Text", "3", NA, NA, "FALSE", "1", "FALSE", "VS.VSORRES when VS.VSTESTCD = 'SYSBP'", "VS", "VSORRES", "Result Qualifier", "SYS_BP", NA, NA, "12", "CRF", "assign_no_ct", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
"lp_study", "vitals_raw_data", "Vital Signs", "SYS_BP", "Systolic blood pressure", "6", "Text", "3", NA, NA, "FALSE", "3", "FALSE", "VS.VSORRESU = <Fixed Unit>", "VS", "VSORRESU", "Variable Qualifier", "SYS_BP", "C66770", "(VSRESU)", "13", "Assigned", "hardcode_ct", NA, NA, "mmHg", "mmHg", "C49670", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
)
)
# nolint end

# Convert all NA to NA_character_
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