Fixed #11: validation of heat map ranges

R/GCAT/R/GCAT.main.R

@@ -141,6 +141,17 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
         exception("", "time.input is NA.")
     }
   
+  # Check heatmap ranges
+  for (range1 in list(lagRange, totalRange, totalODRange, specRange)) {
+    if (!identical(range1,NA)) {
+      range1.string = paste(range1,collapse="-")
+      if (length(range1) != 2) exception("",paste("Heat map range must contain 2 values.  Bad range:", range1.string))
+      if (!all(is.finite(range1))) exception("",paste("Heat map range must be numeric and finite.  Bad range:", range1.string))
+      if (!all(range1 >= 0)) exception("",paste("Heat map range must be positive.  Bad range:", range1.string))
+      if (range1[1] >= range1[2]) exception("",paste("Heat map range max must be > min.  Bad range:", range1.string))
+    }
+  }
+  
     # MB: Now add.constant will always be 0.
     # No need to check.
     #if (add.constant < 0)

R/GCAT/inst/extdata/heatmap_tests/test_heatmap_limits.R

@@ -11,13 +11,6 @@ INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv"
 library(GCAT)
 setwd(INPUT.DIR)
 time.input=1/3600
-# - do not specify parameter ranges
-out1 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,   
-                         out.dir = OUTPUT.DIR.1, graphic.dir = OUTPUT.DIR.1, 
-                         add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
-                         use.linear.param=F, use.loess=F, smooth.param=0.1,
-                         points.to.remove = integer(), remove.jumps = F, time.input=time.input,
-                         silent = F, verbose = T, return.fit = T, overview.jpgs = T)
 
 # - do specify parameter ranges
 out2 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,   
@@ -28,5 +21,13 @@ out2 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file
                          silent = F, verbose = T, return.fit = T, overview.jpgs = T,
                          lagRange = c(0,3), totalRange = c(0.2,0.82), totalODRange = c(0.06,1), specRange = c(0.04,0.13))
 
+# - do not specify parameter ranges
+out1 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,   
+                          out.dir = OUTPUT.DIR.1, graphic.dir = OUTPUT.DIR.1, 
+                          add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
+                          use.linear.param=F, use.loess=F, smooth.param=0.1,
+                          points.to.remove = integer(), remove.jumps = F, time.input=time.input,
+                          silent = F, verbose = T, return.fit = T, overview.jpgs = T)
+
 #  Verify that specifying parameter ranges did not affect any computations except for how the heat maps are drawn
 all.equal(out1,out2)

Rails/app/models/assay.rb

@@ -97,10 +97,21 @@ class Assay
   #validates :plate_dimensions_column, :numericality => { :only_integer => true, :greater_than => 0}
   #validates :plate_dimensions_row, :numericality => { :only_integer => true, :greater_than => 0 }
   
-  #validate inoculation timepoint
+  # (7) validate inoculation timepoint
   validates :start_index, :numericality => { :only_integer => true, :greater_than => 0}
   
-  
+  # (8) validate heatmap ranges
+#validates_numericality_of :blank_value_input,:if => :user_input?,  :message => '- Invalid OD blank value. Please Enter A Real Number.'
+  validates_numericality_of :totg_min, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :totg_max, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :totg_OD_min, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :totg_OD_max, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :specg_min, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :specg_max, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :lagT_min, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+  validates_numericality_of :lagT_max, :if => :user_input?, :allow_blank => true, :greater_than_or_equal_to => 0, :message => '- Please Enter a positive real number.'
+
+
   def initialize(attributes = {})
     attributes.each do |name, value|
       send("#{name}=", value)