Tweaks

ppernot · Jul 21, 2022 · 9f6d163 · 9f6d163
1 parent 8b6c4ba
commit 9f6d163
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Showing 3 changed files with 21 additions and 17 deletions.
diff --git a/server_files/neutralsEdit.R b/server_files/neutralsEdit.R
@@ -94,20 +94,19 @@ shiny::observeEvent(
     # Make copy of source directory
     neutralsOrigDir = file.path(neutralsSource,neutralsOrigVersion())
     neutralsCopyDir = file.path(neutralsSource,neutralsCopyVersion())
-    if(!dir.exists(neutralsCopyDir))
-      dir.create(neutralsCopyDir)
-    files = list.files(path=neutralsOrigDir)
-    for(file in files)
+    if(!dir.exists(neutralsCopyDir)) {
       file.copy(
         from = file.path(neutralsOrigDir,file),
         to   = file.path(neutralsCopyDir,file),
-        overwrite = TRUE
+        recursive = TRUE
       )
-    id = shiny::showNotification(
-      h4(paste0('Created version: ', neutralsCopyVersion())),
-      closeButton = FALSE,
-      duration = 5
-    )
+      id = shiny::showNotification(
+        h4(paste0('Created new version: ', neutralsCopyVersion())),
+        closeButton = FALSE,
+        duration = 5
+      )
+    }
+
     # Save modified file to target version
     data = isolate(input$ace)
     writeLines(
@@ -119,5 +118,6 @@ shiny::observeEvent(
       closeButton = FALSE,
       duration = 5
     )
+
   }
 )
diff --git a/server_files/neutralsParse.R b/server_files/neutralsParse.R
@@ -33,6 +33,10 @@ observeEvent(
   {
     req(neutralsVersion())
 
+    pasteNoNA = function(x) {
+      paste(x[!is.na(x)],collapse=" ")
+    }
+
     nbReac = 0
     reactants = products = params = type = orig = notes = list()
 
@@ -41,7 +45,7 @@ observeEvent(
           file = file.path(neutralsSource,neutralsVersion(),filename),
           header = FALSE
         )
-        comments = apply(scheme, 1, function(x) paste(x[15:length(x)],collapse=" "))
+        comments = apply(scheme, 1, function(x) pasteNoNA(x[15:length(x)]))
         scheme  = t(apply(scheme, 1, function(x) gsub(" ", "", x)))
         for (i in 1:nrow(scheme)) {
           if(substr(scheme[i,1],1,1)=='#') next
@@ -63,7 +67,7 @@ observeEvent(
           file = file.path(neutralsSource,neutralsVersion(),filename),
           header = FALSE
         )
-        comments = apply(scheme, 1, function(x) paste(x[25:length(x)],collapse=" "))
+        comments = apply(scheme, 1, function(x) pasteNoNA(x[25:length(x)]))
         scheme  = t(apply(scheme, 1, function(x) gsub(" ", "", x)))
         for (i in 1:nrow(scheme)) {
           if(substr(scheme[i,1],1,1)=='#') next
@@ -86,7 +90,7 @@ observeEvent(
           file = file.path(neutralsSource,neutralsVersion(),filename),
           header = FALSE
         )
-        comments = apply(scheme, 1, function(x) paste(x[15:length(x)],collapse=" "))
+        comments = apply(scheme, 1, function(x) pasteNoNA(x[15:length(x)]))
         scheme  = t(apply(scheme, 1, function(x) gsub(" ", "", x)))
         for (i in 1:nrow(scheme)) {
           if(substr(scheme[i,1],1,1)=='#') next
@@ -109,7 +113,7 @@ observeEvent(
           file = file.path(neutralsSource,neutralsVersion(),filename),
           header = FALSE
         )
-        comments = apply(scheme, 1, function(x) paste(x[25:length(x)],collapse=" "))
+        comments = apply(scheme, 1, function(x) pasteNoNA(x[25:length(x)]))
         scheme  = t(apply(scheme, 1, function(x) gsub(" ", "", x)))
         for (i in 1:nrow(scheme)) {
           if(substr(scheme[i,1],1,1)=='#') next
@@ -135,7 +139,7 @@ observeEvent(
           header = FALSE,
           stringsAsFactors = FALSE
         )
-        comments = apply(scheme, 1, function(x) paste(x[25:length(x)],collapse=" "))
+        comments = apply(scheme, 1, function(x) pasteNoNA(x[25:length(x)]))
         scheme  = t(apply(scheme, 1, function(x) gsub(" ", "", x)))
         for (i in 1:nrow(scheme)) {
           if(substr(scheme[i,1],1,1)=='#') next

diff --git a/server_files/neutralsSample.R b/server_files/neutralsSample.R
@@ -243,7 +243,7 @@ output$plotRate = renderPlot({
 
   par(
     mfrow = c(1, 2),
-    mar = c(3,3,8,2),
+    mar = c(3,3,9,2),
     mgp = gPars$mgp,
     tcl = gPars$tcl,
     lwd = gPars$lwd,
@@ -273,7 +273,7 @@ output$plotRate = renderPlot({
       side = 3,
       cex = 1.5,
       adj = 0,
-      line = 7,
+      line = 8,
       padj = 1,
       col = gPars$cols[1]
     )