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register teal.logger handlers; replace log_info with message #1010

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merged 5 commits into from
Mar 20, 2024
Merged

register teal.logger handlers; replace log_info with message #1010

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9e32c75
register teal.logger handlers; replace log_info with message
pawelru Feb 1, 2024
015c6f8
logger in tests
pawelru Feb 1, 2024
0c67105
Merge branch 'main' into register_handlers
pawelru Mar 11, 2024
4efd779
vbump teal.logger deps
pawelru Mar 20, 2024
3dc9c1b
Merge branch 'main' into register_handlers
pawelru Mar 20, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -45,7 +45,6 @@ Imports:
ggrepel,
grid,
lifecycle (>= 0.2.0),
logger (>= 0.2.0),
methods,
rlistings (>= 0.2.7),
rmarkdown (>= 2.19),
Expand All @@ -58,7 +57,7 @@ Imports:
stats,
teal.code (>= 0.5.0),
teal.data (>= 0.4.0),
teal.logger (>= 0.1.1),
teal.logger (>= 0.1.3.9013),
teal.reporter (>= 0.2.1),
teal.widgets (>= 0.4.0),
tern.gee (>= 0.1.3),
Expand All @@ -68,6 +67,7 @@ Imports:
Suggests:
forcats,
knitr (>= 1.34),
logger (>= 0.2.0),
lubridate (>= 1.7.9),
nestcolor (>= 0.1.0),
styler,
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2 changes: 1 addition & 1 deletion R/tm_a_gee.R
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Expand Up @@ -198,7 +198,7 @@ tm_a_gee <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_a_gee (prototype)")
message("Initializing tm_a_gee (prototype)")

cov_var <- teal.transform::add_no_selected_choices(cov_var, multiple = TRUE)

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2 changes: 1 addition & 1 deletion R/tm_a_mmrm.R
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Expand Up @@ -539,7 +539,7 @@ tm_a_mmrm <- function(label,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args(),
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_a_mmrm")
message("Initializing tm_a_mmrm")
cov_var <- teal.transform::add_no_selected_choices(cov_var, multiple = TRUE)
checkmate::assert_string(label)
checkmate::assert_string(total_label)
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2 changes: 1 addition & 1 deletion R/tm_g_barchart_simple.R
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Expand Up @@ -143,7 +143,7 @@ tm_g_barchart_simple <- function(x = NULL,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_barchart_simple")
message("Initializing tm_g_barchart_simple")
checkmate::assert_string(label)
checkmate::assert_list(plot_options, null.ok = TRUE)
if (length(c(x, fill, x_facet, y_facet)) == 0) {
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2 changes: 1 addition & 1 deletion R/tm_g_ci.R
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Expand Up @@ -275,7 +275,7 @@ tm_g_ci <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_ci")
message("Initializing tm_g_ci")
checkmate::assert_string(label)
stat <- match.arg(stat)
checkmate::assert_class(y_var, classes = "data_extract_spec")
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2 changes: 1 addition & 1 deletion R/tm_g_forest_rsp.R
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Expand Up @@ -335,7 +335,7 @@ tm_g_forest_rsp <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_forest_rsp")
message("Initializing tm_g_forest_rsp")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_g_forest_tte.R
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Expand Up @@ -315,7 +315,7 @@ tm_g_forest_tte <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_forest_tte")
message("Initializing tm_g_forest_tte")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_g_ipp.R
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Expand Up @@ -301,7 +301,7 @@ tm_g_ipp <- function(label,
base_var <- baseline_var # resolves missing argument error
}

logger::log_info("Initializing tm_g_ipp")
message("Initializing tm_g_ipp")
checkmate::assert_class(arm_var, "choices_selected")
checkmate::assert_class(paramcd, "choices_selected")
checkmate::assert_class(id_var, "choices_selected")
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2 changes: 1 addition & 1 deletion R/tm_g_km.R
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Expand Up @@ -326,7 +326,7 @@ tm_g_km <- function(label,
plot_width = NULL,
pre_output = NULL,
post_output = NULL) {
logger::log_info("Initializing tm_g_km")
message("Initializing tm_g_km")

checkmate::assert_string(label)
checkmate::assert_string(dataname)
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2 changes: 1 addition & 1 deletion R/tm_g_lineplot.R
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Expand Up @@ -287,7 +287,7 @@ tm_g_lineplot <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_lineplot")
message("Initializing tm_g_lineplot")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_g_pp_adverse_events.R
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Expand Up @@ -259,7 +259,7 @@ tm_g_pp_adverse_events <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_pp_adverse_events")
message("Initializing tm_g_pp_adverse_events")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_g_pp_patient_timeline.R
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Expand Up @@ -456,7 +456,7 @@ tm_g_pp_patient_timeline <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_pp_patient_timeline")
message("Initializing tm_g_pp_patient_timeline")
checkmate::assert_string(label)
checkmate::assert_string(dataname_adcm)
checkmate::assert_string(dataname_adae)
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2 changes: 1 addition & 1 deletion R/tm_g_pp_therapy.R
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Expand Up @@ -348,7 +348,7 @@ tm_g_pp_therapy <- function(label,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args()) {
logger::log_info("Initializing tm_g_pp_therapy")
message("Initializing tm_g_pp_therapy")
checkmate::assert_class(atirel, "choices_selected", null.ok = TRUE)
checkmate::assert_class(cmdecod, "choices_selected", null.ok = TRUE)
checkmate::assert_class(cmindc, "choices_selected", null.ok = TRUE)
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2 changes: 1 addition & 1 deletion R/tm_g_pp_vitals.R
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Expand Up @@ -278,7 +278,7 @@ tm_g_pp_vitals <- function(label,
aval <- aval_var # resolves missing argument error
}

logger::log_info("Initializing tm_g_pp_vitals")
message("Initializing tm_g_pp_vitals")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_abnormality.R
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Expand Up @@ -327,7 +327,7 @@ tm_t_abnormality <- function(label,
post_output = NULL,
na_level = default_na_str(),
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_abnormality")
message("Initializing tm_t_abnormality")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_abnormality_by_worst_grade.R
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Expand Up @@ -335,7 +335,7 @@ tm_t_abnormality_by_worst_grade <- function(label, # nolint: object_length.
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_abnormality_by_worst_grade")
message("Initializing tm_t_abnormality_by_worst_grade")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_ancova.R
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Expand Up @@ -517,7 +517,7 @@ tm_t_ancova <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_ancova")
message("Initializing tm_t_ancova")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_binary_outcome.R
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Expand Up @@ -444,7 +444,7 @@ tm_t_binary_outcome <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_binary_outcome")
message("Initializing tm_t_binary_outcome")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_coxreg.R
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Expand Up @@ -510,7 +510,7 @@ tm_t_coxreg <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_coxreg")
message("Initializing tm_t_coxreg")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_events.R
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Expand Up @@ -520,7 +520,7 @@ tm_t_events <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_events")
message("Initializing tm_t_events")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_events_by_grade.R
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Expand Up @@ -863,7 +863,7 @@ tm_t_events_by_grade <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_events_by_grade")
message("Initializing tm_t_events_by_grade")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_events_patyear.R
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Expand Up @@ -232,7 +232,7 @@ tm_t_events_patyear <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_events_patyear")
message("Initializing tm_t_events_patyear")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_events_summary.R
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Expand Up @@ -614,7 +614,7 @@ tm_t_events_summary <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_events_summary")
message("Initializing tm_t_events_summary")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_exposure.R
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Expand Up @@ -323,7 +323,7 @@ tm_t_exposure <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_exposure")
message("Initializing tm_t_exposure")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_logistic.R
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Expand Up @@ -294,7 +294,7 @@ tm_t_logistic <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_logistic")
message("Initializing tm_t_logistic")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_mult_events.R
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Expand Up @@ -344,7 +344,7 @@ tm_t_mult_events <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_mult_events")
message("Initializing tm_t_mult_events")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_pp_basic_info.R
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Expand Up @@ -97,7 +97,7 @@ tm_t_pp_basic_info <- function(label,
vars = NULL,
pre_output = NULL,
post_output = NULL) {
logger::log_info("Initializing tm_t_pp_basic_info")
message("Initializing tm_t_pp_basic_info")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(patient_col)
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2 changes: 1 addition & 1 deletion R/tm_t_pp_laboratory.R
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Expand Up @@ -233,7 +233,7 @@ tm_t_pp_laboratory <- function(label,
avalu <- avalu_var # resolves missing argument error
}

logger::log_info("Initializing tm_t_pp_laboratory")
message("Initializing tm_t_pp_laboratory")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_pp_medical_history.R
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Expand Up @@ -137,7 +137,7 @@ tm_t_pp_medical_history <- function(label,
mhdistat = NULL,
pre_output = NULL,
post_output = NULL) {
logger::log_info("Initializing tm_t_pp_medical_history")
message("Initializing tm_t_pp_medical_history")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_pp_prior_medication.R
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Expand Up @@ -125,7 +125,7 @@ tm_t_pp_prior_medication <- function(label,
cmstdy = NULL,
pre_output = NULL,
post_output = NULL) {
logger::log_info("Initializing tm_t_pp_prior_medication")
message("Initializing tm_t_pp_prior_medication")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_shift_by_arm.R
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Expand Up @@ -273,7 +273,7 @@ tm_t_shift_by_arm <- function(label,
base_var <- baseline_var # resolves missing argument error
}

logger::log_info("Initializing tm_t_shift_by_arm")
message("Initializing tm_t_shift_by_arm")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_shift_by_arm_by_worst.R
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Expand Up @@ -284,7 +284,7 @@ tm_t_shift_by_arm_by_worst <- function(label,
base_var <- baseline_var # resolves missing argument error
}

logger::log_info("Initializing tm_t_shift_by_arm_by_worst")
message("Initializing tm_t_shift_by_arm_by_worst")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_shift_by_grade.R
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Expand Up @@ -569,7 +569,7 @@ tm_t_shift_by_grade <- function(label,
na_level = default_na_str(),
code_missing_baseline = FALSE,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_shift_by_grade")
message("Initializing tm_t_shift_by_grade")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_smq.R
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Expand Up @@ -389,7 +389,7 @@ tm_t_smq <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_smq")
message("Initializing tm_t_smq")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_summary.R
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Expand Up @@ -254,7 +254,7 @@ tm_t_summary <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_summary")
message("Initializing tm_t_summary")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_summary_by.R
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Expand Up @@ -392,7 +392,7 @@ tm_t_summary_by <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_summary_by")
message("Initializing tm_t_summary_by")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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2 changes: 1 addition & 1 deletion R/tm_t_tte.R
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Expand Up @@ -489,7 +489,7 @@ tm_t_tte <- function(label,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
logger::log_info("Initializing tm_t_tte")
message("Initializing tm_t_tte")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
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1 change: 1 addition & 0 deletions R/zzz.R
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@@ -1,4 +1,5 @@
.onLoad <- function(libname, pkgname) {
teal.logger::register_logger(namespace = "teal.modules.clinical")
teal.logger::register_handlers("teal.modules.clinical")
tern::set_default_na_str("<Missing>")
}
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