From 41117529b000796a24f0181b29fb809ea6232005 Mon Sep 17 00:00:00 2001
From: pchelle <chelle.pierre@gmail.com>
Date: Fri, 6 Sep 2024 08:59:09 -0400
Subject: [PATCH 1/3] Fixes #1274 Prevent crash of 0 simulated values in log
 scale

Provides a warning for such a case
---
 R/messages.R                              | 7 +++++++
 R/qualification-comparison-time-profile.R | 9 ++++++++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/R/messages.R b/R/messages.R
index ae259216..d85bf693 100644
--- a/R/messages.R
+++ b/R/messages.R
@@ -296,6 +296,13 @@ messages <- list(
       paste0(highlight(unique(values)), collapse = "', '"), "'."
     )
   },
+  warningLogScaleIssue = function(output) {
+    paste0(
+      "Plot scale is logarithmic, however all values from simulated output '", 
+      highlight(output), "' were 0."
+    )
+  },
+  
   #----- Info messages ----
   runStarting = function(runName, subRun = NULL) {
     if (is.null(subRun)) {
diff --git a/R/qualification-comparison-time-profile.R b/R/qualification-comparison-time-profile.R
index f2b62196..dde3edd4 100644
--- a/R/qualification-comparison-time-profile.R
+++ b/R/qualification-comparison-time-profile.R
@@ -124,7 +124,14 @@ addOutputToComparisonTimeProfile <- function(outputMapping, simulationDuration,
     molWeight = molWeight
   )
   simulatedValues <- simulatedValues[selectedTimeValues]
-
+  logScaleIssue <- all(simulatedValues == 0, isIncluded(axesProperties$y$scale, "log")) 
+  if(logScaleIssue){
+    warning(messages$warningLogScaleIssue(outputMapping$Output), call. = FALSE)
+    # Set the first value to 1 to avoid log scale issue
+    # Since this only affect one value, no line will plotted
+    simulatedValues[1] <- 1
+  }
+  
   # Add simulated values to plot
   plotObject <- tlf::addLine(
     x = simulatedTime,

From 180cd68a754db23b22786215346b938e60b65a23 Mon Sep 17 00:00:00 2001
From: pchelle <chelle.pierre@gmail.com>
Date: Fri, 6 Sep 2024 10:14:40 -0400
Subject: [PATCH 2/3] Remove the curve and legend if values are all <=0

---
 R/qualification-comparison-time-profile.R | 31 ++++++++++++-----------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/R/qualification-comparison-time-profile.R b/R/qualification-comparison-time-profile.R
index dde3edd4..d2daaebe 100644
--- a/R/qualification-comparison-time-profile.R
+++ b/R/qualification-comparison-time-profile.R
@@ -124,25 +124,26 @@ addOutputToComparisonTimeProfile <- function(outputMapping, simulationDuration,
     molWeight = molWeight
   )
   simulatedValues <- simulatedValues[selectedTimeValues]
-  logScaleIssue <- all(simulatedValues == 0, isIncluded(axesProperties$y$scale, "log")) 
+  # If issues with log scale due to all zeros or negative values
+  # Warn and do not plot the data
+  logScaleIssue <- all(simulatedValues <= 0, isIncluded(axesProperties$y$scale, "log")) 
   if(logScaleIssue){
     warning(messages$warningLogScaleIssue(outputMapping$Output), call. = FALSE)
-    # Set the first value to 1 to avoid log scale issue
-    # Since this only affect one value, no line will plotted
-    simulatedValues[1] <- 1
   }
   
-  # Add simulated values to plot
-  plotObject <- tlf::addLine(
-    x = simulatedTime,
-    y = simulatedValues,
-    caption = prettyCaption(paste(outputMapping$Caption, "Simulated Data"), plotObject),
-    linetype = tlfLinetype(outputMapping$LineStyle),
-    color = outputMapping$Color,
-    size = outputMapping$Size,
-    plotObject = plotObject
-  )
-
+  if(!logScaleIssue){
+    # Add simulated values to plot
+    plotObject <- tlf::addLine(
+      x = simulatedTime,
+      y = simulatedValues,
+      caption = prettyCaption(paste(outputMapping$Caption, "Simulated Data"), plotObject),
+      linetype = tlfLinetype(outputMapping$LineStyle),
+      color = outputMapping$Color,
+      size = outputMapping$Size,
+      plotObject = plotObject
+    )
+  }
+  
   # Loop on each observed dataset in OutputMappings
   for (observedDataSet in outputMapping$ObservedData) {
     # Get data and meta data of observed results

From 5a12cf9397fc635d164200217abd03cefe1bd51b Mon Sep 17 00:00:00 2001
From: pchelle <chelle.pierre@gmail.com>
Date: Fri, 6 Sep 2024 10:16:01 -0400
Subject: [PATCH 3/3] Update message for <=0

---
 R/messages.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/messages.R b/R/messages.R
index d85bf693..a77128de 100644
--- a/R/messages.R
+++ b/R/messages.R
@@ -299,7 +299,7 @@ messages <- list(
   warningLogScaleIssue = function(output) {
     paste0(
       "Plot scale is logarithmic, however all values from simulated output '", 
-      highlight(output), "' were 0."
+      highlight(output), "' were lower or equal to 0."
     )
   },