From e218c59ad176d224f59437f3abc0dc1ec28ca895 Mon Sep 17 00:00:00 2001
From: Matthew Fidler <matthew.fidler@gmail.com>
Date: Wed, 18 Sep 2024 11:19:43 -0500
Subject: [PATCH] Update mlxtran and remove file if present

---
 R/equation.R |  1 +
 R/mlxtran.R  | 11 ++++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/equation.R b/R/equation.R
index 534ff0a..32e33d8 100644
--- a/R/equation.R
+++ b/R/equation.R
@@ -301,6 +301,7 @@ mlxTxt <- function(file, retFile=FALSE) {
     .m2 <- c("<MODEL>",
              .lines)
     lapply(.m2, .mlxtranParseItem)
+    .mlxEnv$parsedFile <- TRUE
     if (retFile) return(file)
     .ret <- .mlxtranFinalize(.mlxEnv$lst, equation=TRUE, update=FALSE)
     attr(.ret, "dirn") <- .dirn
diff --git a/R/mlxtran.R b/R/mlxtran.R
index ef4e7c1..1712e8d 100644
--- a/R/mlxtran.R
+++ b/R/mlxtran.R
@@ -11,6 +11,7 @@
   .mlxEnv$lst <- list(mlxtran="")
   .mlxEnv$isDesc <- FALSE
   .mlxEnv$desc <- ""
+  .mlxEnv$parsedFile <- FALSE
 }
 
 #' This parses a single line from something like readLines
@@ -107,7 +108,11 @@
       }
     }
     if (!is.null(.ret$MODEL$LONGITUDINAL)) {
-      .ret$MODEL$LONGITUDINAL$LONGITUDINAL <- .longitudinal(.ret$MODEL$LONGITUDINAL$LONGITUDINAL)
+      .long <- .longitudinal(.ret$MODEL$LONGITUDINAL$LONGITUDINAL)
+      if (.mlxEnv$parsedFile) {
+        .long$file <- NULL
+      }
+      .ret$MODEL$LONGITUDINAL$LONGITUDINAL <- .long
       if (!is.null(.ret$MODEL$LONGITUDINAL$DEFINITION)) {
         .ld <- .longDef(.ret$MODEL$LONGITUDINAL$DEFINITION)
         .monolix2rx$endpointPred <- .getMonolixPreds(.ld)
@@ -178,7 +183,11 @@
   if (!is.null(.mlxEnv$lst$MODEL$LONGITUDINAL)) {
     .long <- .longitudinal(.mlxEnv$lst$MODEL$LONGITUDINAL$LONGITUDINAL)
     .file <- .long$file
+    .mlxEnv$parsedFile <- FALSE
     mlxTxt(.long$file,  retFile=TRUE)
+    if (.mlxEnv$parsedFile) {
+      .minfo(paste0("integrated model file '", .file ,"' into mlxtran object"))
+    }
   }
   .mlxtranFinalize(.mlxEnv$lst, equation=equation, update=update)
 }