Merge pull request #114 from nlmixr2/113-na-babelmixr2

Fix the `NA` runCommand that doesn't work as advertised
nlmixr2 · Aug 11, 2024 · bd453c2 · bd453c2
2 parents ee03d62 + 216d1f3
commit bd453c2
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Showing 4 changed files with 115 additions and 13 deletions.
diff --git a/R/monolixNlmixr2est.R b/R/monolixNlmixr2est.R
@@ -137,6 +137,9 @@
   cmd <- rxode2::rxGetControl(ui, "runCommand", "")
   if (is.character(cmd)) {
     cmd <- .monolixRunCommand
+  } else if (is.na(cmd)) {
+    .minfo("run Monolix manually and rerun nlmixr()")
+    return(NULL)
   } else if (!is.function(cmd)) {
     stop("invalid value for monolixControl(runCommand=)",
          call.=FALSE)
@@ -231,6 +234,7 @@
   .mlxtran <- .ui$monolixMlxtranFile
   .runLock <- .ui$monolixRunLock
 
+  .cmd <- rxode2::rxGetControl(.ui, "runCommand", "")
   if (file.exists(.qs)) {
     .minfo("load saved nlmixr2 object")
     .ret <- qs::qread(.qs)
@@ -258,9 +262,11 @@
       return(invisible())
     }
     .runLS <- FALSE
-    .cmd <- rxode2::rxGetControl(.ui, "runCommand", "")
     if (!identical(.cmd, "")) {
       .monolixRunner(ui=.ui)
+      if (is.na(.cmd)) {
+        return(invisible())
+      }
     } else {
       if (.hasLixoftConnectors()) {
         .x <- try(lixoftConnectors::loadProject(.mlxtran), silent=TRUE)
@@ -282,6 +288,10 @@
       }
     }
   } else {
+    if (is.na(.cmd)) {
+      .minfo(paste0("leaving alone monolix files because '", .model, "' is present"))
+      return(invisible())
+    }
     .minfo(paste0("assuming monolix is running because '", .model, "' is present"))
   }
   if (!dir.exists(.exportPath)) {

diff --git a/R/nonmemNlmixr2est.R b/R/nonmemNlmixr2est.R
@@ -207,13 +207,11 @@
               quote=FALSE)
     .minfo("done")
   }
-  if (!rxode2::rxGetControl(.ui, "run", TRUE)) {
+  .cmd <- rxode2::rxGetControl(.ui, "runCommand", "")
+  if (!rxode2::rxGetControl(.ui, "run", TRUE) ||
+        is.na(.cmd)) {
     .minfo("only exported NONMEM control stream/data")
-    return(invisible())
-  }
-  if (is.na(rxode2::rxGetControl(.ui, "runCommand", ""))) {
-    .minfo("not running NONMEM")
-    return(.ui)
+    return(invisible(.ui))
   }
   if (!file.exists(file.path(.exportPath, .ui$nonmemXml))) {
     print(file.path(.exportPath, .ui$nonmemXml))

diff --git a/tests/testthat/test-monolix.R b/tests/testthat/test-monolix.R
@@ -85,7 +85,7 @@ if (FALSE) {
                                                           low=NA_real_, hi=NA_real_)),
                  NULL)
   })
-  
+
 }
 
 
@@ -267,3 +267,47 @@ test_that("monolix dsl", {
   .ee(.rxToM("add.sd"), "add__sd")
 
 })
+
+test_that("monolix model creation without running", {
+  withr::with_tempdir({
+
+    one.cmt <- function() {
+      ini({
+        tka <- 0.45 ; label("Ka")
+        tcl <- log(c(0, 2.7, 100)) ; label("Log Cl")
+        tv <- 3.45; label("log V")
+        cl.wt <- 0
+        v.wt <- 0
+        eta.ka ~ 0.6
+        eta.cl ~ 0.3
+        eta.v ~ 0.1
+        add.sd <- 0.7
+      })
+      model({
+        ka <- exp(tka + eta.ka)
+        cl <- exp(tcl + eta.cl + WT * cl.wt)
+        v <- exp(tv + eta.v)+ WT ^ 2 * v.wt
+        d/dt(depot) <- -depot*ka
+        d/dt(central) <- depot*ka - cl*central/v
+        cp <-central/v
+        cp ~ add(add.sd)
+      })
+    }
+
+    files <- c("monolixTest-monolix.csv", "monolixTest-monolix.mlxtran",
+               "monolixTest-monolix.md5", "monolixTest-monolix.txt")
+
+    nlmixr2(one.cmt, nlmixr2data::theo_sd, "monolix",
+            monolixControl(runCommand=NA, modelName="monolixTest"))
+
+    lapply(files, function(f) { expect_true(file.exists(f)) })
+
+    nlmixr2(one.cmt, nlmixr2data::theo_sd, "monolix",
+            monolixControl(runCommand=NA, modelName="monolixTest"))
+    lapply(files, function(f) {
+      expect_true(file.exists(f))
+      unlink(f)
+    })
+
+  })
+})
diff --git a/tests/testthat/test-nonmem.R b/tests/testthat/test-nonmem.R
@@ -125,6 +125,7 @@ withr::with_tempdir({
     })
 
     test_that("NONMEM dsl, full model", {
+
       one.cmt <- function() {
         ini({
           tka <- 0.45 ; label("Ka")
@@ -145,16 +146,18 @@ withr::with_tempdir({
           cp ~ add(add.sd)
         })
       }
+
       expect_message(
-        ui <-
           nlmixr(
             one.cmt, data=nlmixr2data::Oral_1CPT, est="nonmem",
             control=nonmemControl(runCommand=NA)
           ),
-        regexp="not running NONMEM"
+        regexp="only exported NONMEM"
       )
+
       expect_s3_class(ui, "rxUi")
       expect_type(ui$nonmemModel, "character")
+
       expect_equal(
         ui$nonmemModel,
         paste(
@@ -223,6 +226,7 @@ withr::with_tempdir({
           collapse="\n"
         )
       )
+
     })
 
     # pk.turnover.emax3 <- function() {
@@ -600,13 +604,13 @@ withr::with_tempdir({
           d/dt(A_tr2) = KTR * A_tr1 - KTR * A_tr2;
           d/dt(A_tr3) = KTR * A_tr2 - KTR * A_tr3;
           d/dt(A_circ) = KTR * A_tr3 - KTR * A_circ;
-          
+
           CIRC ~ prop(prop.err)
         })
       }
-      
+
       w <- wbc()
-      
+
       expect_equal(
         w$nonmemErrF,
         paste(c(
@@ -761,3 +765,49 @@ withr::with_tempdir({
     })
   })
 })
+
+
+test_that("nonmem model creation without running", {
+  withr::with_tempdir({
+
+    one.cmt <- function() {
+      ini({
+        tka <- 0.45 ; label("Ka")
+        tcl <- log(c(0, 2.7, 100)) ; label("Log Cl")
+        tv <- 3.45; label("log V")
+        cl.wt <- 0
+        v.wt <- 0
+        eta.ka ~ 0.6
+        eta.cl ~ 0.3
+        eta.v ~ 0.1
+        add.sd <- 0.7
+      })
+      model({
+        ka <- exp(tka + eta.ka)
+        cl <- exp(tcl + eta.cl + WT * cl.wt)
+        v <- exp(tv + eta.v)+ WT ^ 2 * v.wt
+        d/dt(depot) <- -depot*ka
+        d/dt(central) <- depot*ka - cl*central/v
+        cp <-central/v
+        cp ~ add(add.sd)
+      })
+    }
+
+    files <- c("nonmemTest.csv", "nonmemTest.md5", "nonmemTest.nmctl")
+
+    nlmixr2(one.cmt, nlmixr2data::theo_sd, "nonmem",
+            nonmemControl(runCommand=NA, modelName="nonmemTest"))
+
+    lapply(files, function(f) { expect_true(file.exists(file.path("nonmemTest-nonmem", f))) })
+
+    nlmixr2(one.cmt, nlmixr2data::theo_sd, "nonmem",
+            nonmemControl(runCommand=NA, modelName="nonmemTest"))
+
+    lapply(files, function(f) {
+      expect_true(file.exists(file.path("nonmemTest-nonmem", f)))
+      unlink(file.path("nonmemTest-nonmem", f))
+    })
+    unlink("nonmemTest-nonmem", recursive = TRUE)
+
+  })
+})