Release 4.8.0.0

GLUE.r

@@ -30,6 +30,8 @@ OD<-paste(DSSATD, OutputD, sep="");
 GD<-paste(DSSATD, GenotypeD, sep="");
 
 eval(parse(text=paste("ModelRunIndicatorPath='",OD,"/ModelRunIndicator.txt'",sep = ''))); 
+glueWarningLogFile <- file.path(OD, "GlueWarning.txt");
+glueExcludedModelListFile <- file.path(WD, "GlueExcludedModels.csv");
 ##Path of the model run indicator file, which indicates which component of GLUE is finished so far.
 
 
@@ -115,6 +117,17 @@ LineSplit = unlist(strsplit(DSSATPro[LineNo]," "))
 ModelSelect = LineSplit[length(LineSplit)]
 write(c("Model Name =",ModelSelect), file = ModelRunIndicatorPath, ncolumns=2, append = T);
 
+# Check is model is in the exclusion list
+eval(parse(text=paste("excludedFile<-readLines('",glueExcludedModelListFile,"',n=-1)",sep = '')));
+excludedFile.df <- read.table(textConnection(excludedFile[-c(1,2)]),header=F, sep=",")
+colnames(excludedFile.df) <- unlist(strsplit(sub("@", "", excludedFile[2]), split = ","))
+if (substr(ModelSelect,1,5) %in% excludedFile.df[,"MODEL"]) {
+  errorMsg <- paste0("Currently model ", ModelSelect, " is not supported by GLUE, please modify the DSSATPRO.v48 file to change to other model for crop ", CropName, ".")
+  write(errorMsg, file = glueWarningLogFile, ncolumns=1, append = T);
+  # stop(errorMsg)
+  q()
+}
+
 # Get the genotype file name
 GenotypeFilePath<-GD;
 CurrentGenotypeFile<-paste0(GD, "/",CropName,substr(ModelSelect,3,8),".CUL")
@@ -209,14 +222,13 @@ write(c("Parameter property:",CulFile ), file = ModelRunIndicatorPath, append =
 
 # convert text to dataframe
 CulFile.df = paste0(substr(CulFile,1,6), substr(CulFile,30,nchar(CulFile)[1]))
-header = unlist(strsplit(CulFile.df[2]," "))
-header = header[-which(nchar(header)<1)]
+header = unlist(strsplit(CulFile.df[2],split="(\\s|\\|)+"))
+header = header[which(nchar(header)>0)]
 CulData = read.table(textConnection(CulFile.df[-c(1,2)]),header=F)
 colnames(CulData) = header
 
-Cali = unlist(strsplit(CulFile[1],"                "))
-
-Cali.reshape = paste(Cali[1],"placeholder",Cali[2],sep = " ")
+Cali = unlist(strsplit(CulFile[1],"\\s+"))
+Cali.reshape = paste(c(Cali[1],"placeholder", Cali[2:length(Cali)]), sep=" ", collapse = " ")
 Cali.df = read.table(textConnection(Cali.reshape),header = F)
 colnames(Cali.df) = header
 CulData = rbind(CulData,Cali.df)

GenotypeChange.r

@@ -12,8 +12,8 @@ OldLine<-GenotypeFile[LineNumber];#Get the line according to the line number.
 
 R<-RunNumber;#Get what parameter set will be used to change the genotype file.
 
-if (CropName != "SC")
-{
+# if (CropName != "SC")
+# {
   ParameterStep<-6;
   ValuePosition1<-(38-ParameterStep);
   ValuePosition2<-(42-ParameterStep);
@@ -52,59 +52,59 @@ if (CropName != "SC")
   }
 
   GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
-} else
-{
-  ParameterStep<-15;
-
-  #chp modified
-  ValuePosition1<-(47-ParameterStep); #The initial starting point was 42, but it was changed to 46 since "EXPNO" was added by Cheryl recently.
-  ValuePosition2<-(61-ParameterStep); #The initial ending point was 47, but it is 51 now.
-
-  for (i in 1:TotalParameterNumber)
-  {
-  ValuePosition1<-ValuePosition1+ParameterStep;
-  ValuePosition2<-ValuePosition2+ParameterStep;
-
-  eval(parse(text = paste("Parameter<-RandomMatrix[R,",i,"]",sep = '')));
-
-  if(Parameter>=0 & Parameter<10)
-  {
-  ParameterFormat<-sprintf('%1.3f', Parameter);
-  } else if (Parameter>=10 & Parameter<100)
-  {
-  ParameterFormat<-sprintf('%2.2f', Parameter);
-
-  # chp added extra format statement for values between 100 and 1000
-  } else if (Parameter>=100 & Parameter<1000)
-  {
-  ParameterFormat<-sprintf('%3.1f', Parameter);
-  } else
-
-  # chp - how to get format xxxx. (with nothing past the ".") ?
-  {
-  ParameterFormat<-sprintf('%4.0f', Parameter);
-  }
-
-  ##chp
-  #print(ParameterFormat);
-  #print (" ");
-
-  substr(OldLine, ValuePosition1, ValuePosition2)<-'      ';# Delete initial values.
-  substr(OldLine, ValuePosition1, ValuePosition2)<-ParameterFormat;
-
- }
-
-  GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
-
-  eval(parse(text=paste('ECOFilePath="',GD,'/SCCAN048.ECO"',sep = '')));
-  ReadLine<-readLines(ECOFilePath, n=-1)
-  ECOFile<-as.character(ReadLine);
-  #Get the ECO file from the Genotype directory.
-
-  eval(parse(text=paste("NewECOFilePath='",OD,"/SCCAN048.ECO'",sep = '')));
-  write(ECOFile, file=NewECOFilePath);
-  #Save the ECO file in the GLWork directory. 
-}
+# } else
+# {
+#   ParameterStep<-15;
+# 
+#   #chp modified
+#   ValuePosition1<-(47-ParameterStep); #The initial starting point was 42, but it was changed to 46 since "EXPNO" was added by Cheryl recently.
+#   ValuePosition2<-(61-ParameterStep); #The initial ending point was 47, but it is 51 now.
+# 
+#   for (i in 1:TotalParameterNumber)
+#   {
+#   ValuePosition1<-ValuePosition1+ParameterStep;
+#   ValuePosition2<-ValuePosition2+ParameterStep;
+# 
+#   eval(parse(text = paste("Parameter<-RandomMatrix[R,",i,"]",sep = '')));
+# 
+#   if(Parameter>=0 & Parameter<10)
+#   {
+#   ParameterFormat<-sprintf('%1.3f', Parameter);
+#   } else if (Parameter>=10 & Parameter<100)
+#   {
+#   ParameterFormat<-sprintf('%2.2f', Parameter);
+#   
+#   # chp added extra format statement for values between 100 and 1000
+#   } else if (Parameter>=100 & Parameter<1000)
+#   {
+#   ParameterFormat<-sprintf('%3.1f', Parameter);
+#   } else
+#   
+#   # chp - how to get format xxxx. (with nothing past the ".") ?
+#   {
+#   ParameterFormat<-sprintf('%4.0f', Parameter);
+#   }
+# 
+#   ##chp
+#   #print(ParameterFormat);
+#   #print (" ");
+#   
+#   substr(OldLine, ValuePosition1, ValuePosition2)<-'      ';# Delete initial values.
+#   substr(OldLine, ValuePosition1, ValuePosition2)<-ParameterFormat;
+#   
+#  }
+# 
+#   GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
+#   
+#   eval(parse(text=paste('ECOFilePath="',GD,'/SCCAN048.ECO"',sep = '')));
+#   ReadLine<-readLines(ECOFilePath, n=-1)
+#   ECOFile<-as.character(ReadLine);
+#   #Get the ECO file from the Genotype directory.
+#   
+#   eval(parse(text=paste("NewECOFilePath='",OD,"/SCCAN048.ECO'",sep = '')));
+#   write(ECOFile, file=NewECOFilePath);
+#   #Save the ECO file in the GLWork directory. 
+# }
 
 eval(parse(text=paste("NewGenotypeFilePath='",OD,"/",GenotypeFileName,".CUL'",sep = '')));
 write(GenotypeFile, file=NewGenotypeFilePath);

GlueExcludedModels.csv

@@ -0,0 +1,11 @@
+*Simulation/Crop Models,,
+@MODEL,CROP,Description
+PRFRM,PO,FORAGE-Perennial peanut
+SCCAN,SC,CANEGRO-Sugarcane
+SCCSP,SC,CASUPRO-Sugarcane
+SCSAM,SC,SAMUCA-Sugarcane
+PRFRM,BM,FORAGE-Bermudagrass
+PRFRM,BR,FORAGE-Brachiaria
+PRFRM,BH,FORAGE-Bahiagrass
+PRFRM,AL,FORAGE-Alfalfa
+SUOIL,SU,OILCROP-Sunflower