feat: remove datanames from shinyttests2

insightsengineering · Nov 5, 2024 · 0335c66 · 0335c66
1 parent 7d12d67
commit 0335c66
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Showing 36 changed files with 130 additions and 230 deletions.
diff --git a/tests/testthat/test-shinytest2-tm_a_gee.R b/tests/testthat/test-shinytest2-tm_a_gee.R
@@ -15,9 +15,7 @@ app_driver_tm_a_gee <- function() {
       ) %>%
       droplevels()
   })
-  datanames <- c("ADSL", "ADQS")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_a_mmrm.R b/tests/testthat/test-shinytest2-tm_a_mmrm.R
@@ -1,4 +1,4 @@
-app_driver_tm_a_mmrm <- function(fit_model = TRUE) { # nolint: object_length.
+app_driver_tm_a_mmrm <- function(fit_model = TRUE) {
   arm_ref_comp <- list(
     ARMCD = list(
       ref = "ARM B",
@@ -20,10 +20,7 @@ app_driver_tm_a_mmrm <- function(fit_model = TRUE) { # nolint: object_length.
           as.factor() #' making consecutive numeric factor
       )
   })
-
-  datanames <- c("ADSL", "ADQS")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   arm_var <- choices_selected(c("ARM", "ARMCD"), "ARM")
 

diff --git a/tests/testthat/test-shinytest2-tm_g_barchart_simple.R b/tests/testthat/test-shinytest2-tm_g_barchart_simple.R
@@ -10,10 +10,7 @@ app_driver_tm_g_barchart_simple <- function() { # nolint: object_length.
       !((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X"))
     )
   })
-
-  datanames <- c("ADSL", "ADAE")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_g_ci.R b/tests/testthat/test-shinytest2-tm_g_ci.R
@@ -4,8 +4,8 @@ app_driver_tm_g_ci <- function() {
     ADSL <- teal.data::rADSL
     ADLB <- teal.data::rADLB
   })
-  teal.data::datanames(data) <- c("ADSL", "ADLB")
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[c("ADSL", "ADLB")]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
+
   init_teal_app_driver(
     data = data,
     modules = tm_g_ci(

diff --git a/tests/testthat/test-shinytest2-tm_g_forest_rsp.R b/tests/testthat/test-shinytest2-tm_g_forest_rsp.R
@@ -1,18 +1,14 @@
 app_driver_tm_g_forest_rsp <- function() {
-  data <- teal.data::teal_data() %>%
-    within({
-      library(dplyr)
-      library(tern)
-      ADSL <- teal.data::rADSL
-      ADRS <- teal.data::rADRS %>%
-        mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
-        with_label("Character Result/Finding") %>%
-        filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
-    })
-
-  datanames <- c("ADSL", "ADRS")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  data <- within(teal.data::teal_data(), {
+    library(dplyr)
+    library(tern)
+    ADSL <- teal.data::rADSL
+    ADRS <- teal.data::rADRS %>%
+      mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
+      with_label("Character Result/Finding") %>%
+      filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+  })
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   arm_ref_comp <- list(
     ARM = list(

diff --git a/tests/testthat/test-shinytest2-tm_g_forest_tte.R b/tests/testthat/test-shinytest2-tm_g_forest_tte.R
@@ -1,13 +1,10 @@
-app_driver_tm_g_forest_tte <- function() { # nolint: object_length.
+app_driver_tm_g_forest_tte <- function() {
   data <- within(teal.data::teal_data(), {
     ADSL <- teal.modules.clinical::tmc_ex_adsl
     ADSL$RACE <- with_label(droplevels(ADSL$RACE), "Race")
     ADTTE <- teal.modules.clinical::tmc_ex_adtte
   })
-
-  datanames <- c("ADSL", "ADTTE")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   arm_ref_comp <- list(
     ARM = list(

diff --git a/tests/testthat/test-shinytest2-tm_g_ipp.R b/tests/testthat/test-shinytest2-tm_g_ipp.R
@@ -1,20 +1,16 @@
 app_driver_tm_g_ipp <- function() {
-  data <- teal.data::teal_data() %>%
-    within({
-      library(dplyr)
-      library(tern)
-      ADSL <- teal.data::rADSL %>%
-        slice(1:20) %>%
-        df_explicit_na()
-      ADLB <- teal.data::rADLB %>%
-        filter(USUBJID %in% ADSL$USUBJID) %>%
-        df_explicit_na() %>%
-        filter(AVISIT != "SCREENING")
-    })
-
-  datanames <- c("ADSL", "ADLB")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  data <- within(teal.data::teal_data(), {
+    library(dplyr)
+    library(tern)
+    ADSL <- teal.data::rADSL %>%
+      slice(1:20) %>%
+      df_explicit_na()
+    ADLB <- teal.data::rADLB %>%
+      filter(USUBJID %in% ADSL$USUBJID) %>%
+      df_explicit_na() %>%
+      filter(AVISIT != "SCREENING")
+  })
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_g_km.R b/tests/testthat/test-shinytest2-tm_g_km.R
@@ -1,18 +1,14 @@
 app_driver_tm_g_km <- function() {
-  data <- teal.data::teal_data() %>%
-    within({
-      library(dplyr)
-      ADSL <- tmc_ex_adsl
-      ADTTE <- tmc_ex_adtte %>%
-        rename(
-          VALUE_UNIT = AVALU,
-          ANALYSIS_VAL = AVAL,
-          CENSORING = CNSR
-        )
-    })
-
-  datanames <- c("ADSL", "ADTTE")
-  teal.data::datanames(data) <- datanames
+  data <- within(teal.data::teal_data(), {
+    library(dplyr)
+    ADSL <- tmc_ex_adsl
+    ADTTE <- tmc_ex_adtte %>%
+      rename(
+        VALUE_UNIT = AVALU,
+        ANALYSIS_VAL = AVAL,
+        CENSORING = CNSR
+      )
+  })
   teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
 
   arm_ref_comp <- list(

diff --git a/tests/testthat/test-shinytest2-tm_g_lineplot.R b/tests/testthat/test-shinytest2-tm_g_lineplot.R
@@ -8,10 +8,7 @@ app_driver_tm_g_lineplot <- function() {
       AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min)
     )
   })
-
-  datanames <- c("ADSL", "ADLB")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_g_pp_adverse_events.R b/tests/testthat/test-shinytest2-tm_g_pp_adverse_events.R
@@ -1,15 +1,12 @@
-app_driver_tm_g_pp_adverse_events <- function() { # nolint: object_length
-  data <- teal.data::teal_data() |> within({
+app_driver_tm_g_pp_adverse_events <- function() { # nolint: object_length.
+  data <- within(teal.data::teal_data(), {
     library(nestcolor)
     library(dplyr)
 
     ADAE <- teal.data::rADAE
     ADSL <- teal.data::rADSL %>% filter(USUBJID %in% ADAE$USUBJID)
   })
-
-  teal.data::datanames(data) <- c("ADAE", "ADSL")
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[c("ADAE", "ADSL")]
-
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_g_pp_patient_timeline.R b/tests/testthat/test-shinytest2-tm_g_pp_patient_timeline.R
@@ -1,4 +1,4 @@
-app_driver_tm_g_pp_patient_timeline <- function() { # nolint object_length
+app_driver_tm_g_pp_patient_timeline <- function() { # nolint object_length.
   data <- teal.data::teal_data()
   data <- within(data, {
     library(dplyr)
@@ -21,12 +21,11 @@ app_driver_tm_g_pp_patient_timeline <- function() { # nolint object_length
   })
 
   adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
-  teal.data::datanames(data) <- c("ADSL", "ADAE", "ADCM")
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[c("ADSL", "ADAE", "ADCM")]
+
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
   teal.data::join_keys(data)["ADCM", "ADCM"] <- adcm_keys
   teal.data::join_keys(data)["ADAE", "ADCM"] <- c("STUDYID", "USUBJID")
 
-
   init_teal_app_driver(
     data = data,
     modules = tm_g_pp_patient_timeline(

diff --git a/tests/testthat/test-shinytest2-tm_g_pp_therapy.R b/tests/testthat/test-shinytest2-tm_g_pp_therapy.R
@@ -1,4 +1,4 @@
-app_driver_tm_g_pp_therapy <- function() { # nolint: object_length.
+app_driver_tm_g_pp_therapy <- function() {
   data <- within(teal.data::teal_data(), {
     ADCM <- teal.modules.clinical::tmc_ex_adcm
     ADSL <- dplyr::filter(
@@ -23,10 +23,8 @@ app_driver_tm_g_pp_therapy <- function() { # nolint: object_length.
   })
 
   adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
-  datanames <- c("ADSL", "ADCM")
 
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
   teal.data::join_keys(data)["ADCM", "ADCM"] <- adcm_keys
 
   init_teal_app_driver(
@@ -144,7 +142,7 @@ testthat::test_that(
 # Test changing selection ------------------------------------
 
 # Check if a new selection of input changes the plot and table without any validation errors.
-test_different_selection <- function(input_name, input_id, new_value) { # nolint object_length
+test_different_selection <- function(input_name, input_id, new_value) {
   testthat::test_that(
     sprintf(
       "e2e - tm_g_pp_therapy: Selection of %s changes the plot and table without any validation errors.",

diff --git a/tests/testthat/test-shinytest2-tm_g_pp_vitals.R b/tests/testthat/test-shinytest2-tm_g_pp_vitals.R
@@ -1,13 +1,9 @@
 app_driver_tm_g_pp_vitals <- function() {
-  data <- teal.data::teal_data() %>%
-    within({
-      ADSL <- teal.data::rADSL
-      ADVS <- teal.data::rADVS
-    })
-
-  datanames <- c("ADSL", "ADVS")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  data <- within(teal.data::teal_data(), {
+    ADSL <- teal.data::rADSL
+    ADVS <- teal.data::rADVS
+  })
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_t_abnormality.R b/tests/testthat/test-shinytest2-tm_t_abnormality.R
@@ -12,9 +12,7 @@ app_driver_tm_t_abnormality <- function() {
         ) %>% with_label("On Treatment Record Flag")
       )
   })
-  datanames <- c("ADSL", "ADLB")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R b/tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R
@@ -1,16 +1,12 @@
-app_driver_tm_t_abnormality_by_worst_grade <- function() { # nolint: object_length
-  data <- teal.data::teal_data() %>%
-    within({
-      library(dplyr)
+app_driver_tm_t_abnormality_by_worst_grade <- function() { # nolint: object_length.
+  data <- within(teal.data::teal_data(), {
+    library(dplyr)
 
-      ADSL <- teal.data::rADSL
-      ADLB <- teal.data::rADLB %>%
-        filter(!AVISIT %in% c("SCREENING", "BASELINE"))
-    })
-
-  datanames <- c("ADSL", "ADLB")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+    ADSL <- teal.data::rADSL
+    ADLB <- teal.data::rADLB %>%
+      filter(!AVISIT %in% c("SCREENING", "BASELINE"))
+  })
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_t_ancova.R b/tests/testthat/test-shinytest2-tm_t_ancova.R
@@ -1,13 +1,9 @@
 app_driver_tm_t_ancova <- function() {
-  data <- teal.data::teal_data() %>%
-    within({
-      ADSL <- tmc_ex_adsl
-      ADQS <- tmc_ex_adqs
-    })
-
-  datanames <- c("ADSL", "ADQS")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  data <- within(teal.data::teal_data(), {
+    ADSL <- tmc_ex_adsl
+    ADQS <- tmc_ex_adqs
+  })
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   arm_ref_comp <- list(
     ARM = list(

diff --git a/tests/testthat/test-shinytest2-tm_t_binary_outcome.R b/tests/testthat/test-shinytest2-tm_t_binary_outcome.R
@@ -1,19 +1,15 @@
 app_driver_tm_t_binary_outcome <- function() {
-  data <- teal.data::teal_data() %>%
-    within({
-      library(dplyr)
-      ADSL <- teal.data::rADSL
-      ADRS <- teal.data::rADRS %>%
-        mutate(
-          AVALC = d_onco_rsp_label(AVALC) %>%
-            with_label("Character Result/Finding")
-        ) %>%
-        filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
-    })
-
-  datanames <- c("ADSL", "ADRS")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  data <- within(teal.data::teal_data(), {
+    library(dplyr)
+    ADSL <- teal.data::rADSL
+    ADRS <- teal.data::rADRS %>%
+      mutate(
+        AVALC = d_onco_rsp_label(AVALC) %>%
+          with_label("Character Result/Finding")
+      ) %>%
+      filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+  })
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   arm_ref_comp <- list(
     ARMCD = list(ref = "ARM B", comp = c("ARM A", "ARM C")),

diff --git a/tests/testthat/test-shinytest2-tm_t_coxreg.R b/tests/testthat/test-shinytest2-tm_t_coxreg.R
@@ -5,9 +5,7 @@ app_driver_tm_t_coxreg <- function() {
     ADSL <- teal.data::rADSL
     ADTTE <- teal.data::rADTTE
   })
-  datanames <- c("ADSL", "ADTTE")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   arm_ref_comp <- list(
     ACTARMCD = list(

diff --git a/tests/testthat/test-shinytest2-tm_t_events.R b/tests/testthat/test-shinytest2-tm_t_events.R
@@ -4,9 +4,7 @@ app_driver_tm_t_events <- function() {
     ADSL <- teal.data::rADSL
     ADAE <- teal.data::rADAE
   })
-  datanames <- c("ADSL", "ADAE")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_t_events_by_grade.R b/tests/testthat/test-shinytest2-tm_t_events_by_grade.R
@@ -1,18 +1,15 @@
-app_driver_tm_t_events_by_grade <- function() { # nolint: object_length
+app_driver_tm_t_events_by_grade <- function() { # nolint: object_length.
   data <- teal.data::teal_data()
   data <- within(data, {
     library(dplyr)
 
     ADSL <- teal.data::rADSL
-    lbls_adae <- col_labels(teal.data::rADAE)
+    .lbls_adae <- col_labels(teal.data::rADAE)
     ADAE <- teal.data::rADAE %>%
       mutate_if(is.character, as.factor)
-    col_labels(ADAE) <- lbls_adae
+    col_labels(ADAE) <- .lbls_adae
   })
-
-  datanames <- c("ADSL", "ADAE")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,

diff --git a/tests/testthat/test-shinytest2-tm_t_events_patyear.R b/tests/testthat/test-shinytest2-tm_t_events_patyear.R
@@ -8,10 +8,7 @@ app_driver_tm_t_events_patyear <- function() {
       mutate(is_event = CNSR == 0) %>%
       mutate(n_events = as.integer(is_event))
   })
-
-  datanames <- c("ADSL", "ADAETTE")
-  teal.data::datanames(data) <- datanames
-  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]
 
   init_teal_app_driver(
     data = data,