From 64c62809b39590845189b64c7b8ca4bf04f9e1a4 Mon Sep 17 00:00:00 2001
From: Richard Hanna <HANNAR1@EMAIL.CHOP.EDU>
Date: Fri, 8 Mar 2024 13:58:17 -0500
Subject: [PATCH] Move convert_mixed_instrument to distill fx

---
 R/clean_redcap_long.R            | 28 +++++++++++++++++++---------
 man/distill_repeat_table_long.Rd | 10 +++++++++-
 2 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/R/clean_redcap_long.R b/R/clean_redcap_long.R
index a2b55f7f..f2fb1b5f 100644
--- a/R/clean_redcap_long.R
+++ b/R/clean_redcap_long.R
@@ -82,7 +82,7 @@ clean_redcap_long <- function(db_data_long,
     mixed_structure_ref <- data.frame()
 
     if (allow_mixed_structure) {
-      # Retrieve mixed structure fields and forms
+      # Retrieve mixed structure fields and forms in reference df
       mixed_structure_ref <- get_mixed_structure_fields(db_data_long) %>%
         filter(.data$rep_and_nonrep & !str_ends(.data$field_name, "_form_complete")) %>%
         left_join(db_metadata_long %>% select(.data$field_name, .data$form_name),
@@ -91,14 +91,11 @@ clean_redcap_long <- function(db_data_long,
 
       # Update if project actually has mixed structure
       has_mixed_structure_forms <- nrow(mixed_structure_ref) > 0
-
       # Convert mixed instruments to mixed structure format
-      if (has_mixed_structure_forms) {
-        db_data_long <- convert_mixed_instrument(db_data_long, mixed_structure_ref)
-      }
     } else {
-      # Throw error if mixed structure detected and not allowed
-      check_repeat_and_nonrepeat(db_data_long)
+      if (!has_mixed_structure_forms) {
+        check_repeat_and_nonrepeat(db_data_long)
+      }
     }
 
     repeated_forms_tibble <- tibble(
@@ -109,7 +106,9 @@ clean_redcap_long <- function(db_data_long,
           .x,
           db_data_long,
           db_metadata_long,
-          linked_arms
+          linked_arms,
+          has_mixed_structure_forms = has_mixed_structure_forms,
+          mixed_structure_ref = mixed_structure_ref
         )
       ),
       structure = case_when(
@@ -268,13 +267,19 @@ distill_nonrepeat_table_long <- function(form_name,
 #' \code{REDCapR::redcap_metadata_read()$data}
 #' @param linked_arms Output of \code{link_arms}, linking instruments to REDCap
 #' events/arms
+#' @param has_mixed_structure Whether the instrument under evaluation has a mixed
+#' structure. Default `FALSE`.
+#' @param name mixed_structure_ref A mixed structure reference dataframe supplied
+#' by `get_mixed_structure_fields()`.
 #'
 #' @keywords internal
 
 distill_repeat_table_long <- function(form_name,
                                       db_data_long,
                                       db_metadata_long,
-                                      linked_arms) {
+                                      linked_arms,
+                                      has_mixed_structure_forms = FALSE,
+                                      mixed_structure_ref = NULL) {
   has_repeat_forms <- "redcap_repeat_instance" %in% names(db_data_long)
 
   my_record_id <- names(db_data_long)[1]
@@ -308,6 +313,11 @@ distill_repeat_table_long <- function(form_name,
     my_fields <- c(my_fields, "redcap_data_access_group")
   }
 
+  # If has mixed structure, convert form
+  if (has_mixed_structure_forms) {
+    db_data_long <- convert_mixed_instrument(db_data_long, mixed_structure_ref %>% filter(form_name == my_form))
+  }
+
   # Setup data for loop redcap_arm linking
   db_data_long <- db_data_long %>%
     add_partial_keys(var = .data$redcap_event_name) %>%
diff --git a/man/distill_repeat_table_long.Rd b/man/distill_repeat_table_long.Rd
index 814abbcb..6cecc0fc 100644
--- a/man/distill_repeat_table_long.Rd
+++ b/man/distill_repeat_table_long.Rd
@@ -8,7 +8,9 @@ distill_repeat_table_long(
   form_name,
   db_data_long,
   db_metadata_long,
-  linked_arms
+  linked_arms,
+  has_mixed_structure_forms = FALSE,
+  mixed_structure_ref = NULL
 )
 }
 \arguments{
@@ -23,6 +25,12 @@ REDCap metadata.}
 
 \item{linked_arms}{Output of \code{link_arms}, linking instruments to REDCap
 events/arms}
+
+\item{has_mixed_structure}{Whether the instrument under evaluation has a mixed
+structure. Default \code{FALSE}.}
+
+\item{name}{mixed_structure_ref A mixed structure reference dataframe supplied
+by \code{get_mixed_structure_fields()}.}
 }
 \value{
 A \code{tibble} of all data related to a specified \code{form_name}