{linter} corrections

ttscience · Feb 8, 2024 · 48b8c75 · 48b8c75
1 parent abcec2a
commit 48b8c75
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Showing 3 changed files with 43 additions and 37 deletions.
diff --git a/R/api_create_study.R b/R/api_create_study.R
@@ -1,6 +1,6 @@
-api__minimization_pocock <- function( # nolint: cyclocomp_linter.
+api__minimization_pocock <- function(
+    # nolint: cyclocomp_linter.
     identifier, name, method, arms, covariates, p, req, res) {
-
   collection <- checkmate::makeAssertCollection()
 
   checkmate::assert(
@@ -18,7 +18,8 @@ api__minimization_pocock <- function( # nolint: cyclocomp_linter.
   checkmate::assert(
     checkmate::check_choice(method, choices = c("range", "var", "sd")),
     .var.name = "method",
-    add = collection)
+    add = collection
+  )
 
   checkmate::assert(
     checkmate::check_list(
@@ -55,43 +56,50 @@ api__minimization_pocock <- function( # nolint: cyclocomp_linter.
         len = 2,
       ),
       .var.name = "covariates1",
-      add = collection)
+      add = collection
+    )
 
     checkmate::assert(
       checkmate::check_names(
         names(c_content),
         permutation.of = c("weight", "levels"),
       ),
       .var.name = "covariates2",
-      add = collection)
+      add = collection
+    )
 
     # check covariate weight
     checkmate::assert(
       checkmate::check_numeric(c_content$weight,
-                               lower = 0,
-                               finite = TRUE,
-                               len = 1,
-                               null.ok = FALSE
+        lower = 0,
+        finite = TRUE,
+        len = 1,
+        null.ok = FALSE
       ),
       .var.name = "weight",
-      add = collection)
+      add = collection
+    )
 
     checkmate::assert(
       checkmate::check_character(c_content$levels,
-                                 min.chars = 1,
-                                 min.len = 2,
-                                 unique = TRUE
+        min.chars = 1,
+        min.len = 2,
+        unique = TRUE
       ),
       .var.name = "levels",
-      add = collection)
+      add = collection
+    )
   }
 
   # check probability
   checkmate::assert(
-    checkmate::check_numeric(p, lower = 0, upper = 1, len = 1,
-                             any.missing = FALSE, null.ok = FALSE),
+    checkmate::check_numeric(p,
+      lower = 0, upper = 1, len = 1,
+      any.missing = FALSE, null.ok = FALSE
+    ),
     .var.name = "p",
-    add = collection)
+    add = collection
+  )
 
 
   if (length(collection$getMessages()) > 0) {

diff --git a/R/api_randomize.R b/R/api_randomize.R
@@ -89,27 +89,25 @@ api__randomize_patient <- function(study_id, current_state, req, res) {
 
   # Dispatch based on randomization method to parse parameters
   params <-
-    switch(
-      method_randomization,
+    switch(method_randomization,
       minimisation_pocock = do.call(
         parse_pocock_parameters, list(db_connection_pool, study_id, current_state)
-        )
+      )
     )
 
   arm_name <-
-    switch(
-      method_randomization,
+    switch(method_randomization,
       minimisation_pocock = do.call(
         unbiased:::randomize_minimisation_pocock, params
-        )
+      )
     )
 
   arm <- dplyr::tbl(db_connection_pool, "arm") |>
     dplyr::filter(study_id == !!study_id & .data$name == arm_name) |>
     dplyr::select("arm_id" = "id", "name", "ratio") |>
     dplyr::collect()
 
-  randomized_patient <-  unbiased:::save_patient(study_id, arm$arm_id)
+  randomized_patient <- unbiased:::save_patient(study_id, arm$arm_id)
 
   if (!is.null(randomized_patient$error)) {
     res$status <- 503

diff --git a/R/db.R b/R/db.R
@@ -139,21 +139,21 @@ create_study <- function(
   r
 }
 
-save_patient <- function(study_id, arm_id){
-
-  r <- tryCatch({
-    randomized_patient <- DBI::dbGetQuery(
-      db_connection_pool,
-      "INSERT INTO patient (arm_id, study_id)
+save_patient <- function(study_id, arm_id) {
+  r <- tryCatch(
+    {
+      randomized_patient <- DBI::dbGetQuery(
+        db_connection_pool,
+        "INSERT INTO patient (arm_id, study_id)
                     VALUES ($1, $2)
                     RETURNING id, arm_id",
-      list(arm_id, study_id)
-    )
-  },
-  error = function(cond) {
-    logger::log_error("Error randomizing patient: {cond}", cond=cond)
-    list(error = conditionMessage(cond))
-  }
+        list(arm_id, study_id)
+      )
+    },
+    error = function(cond) {
+      logger::log_error("Error randomizing patient: {cond}", cond = cond)
+      list(error = conditionMessage(cond))
+    }
   )
 
   return(r)