view GetOptions.R @ 0:8c5de60b3c04 draft

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# Created on 25 sep. 2012

# @author: Alban Ott
# @copyright: IGM ebio.igmors.u-psud.fr
# @licence: GPL v3
#

# Il est interdit de mettre ARGUMENT comme argument long
# spec contains at least 4 columns, as many as 5 columns.
#
# column 1: long name of flag
#
# column 2: short name of flag
#
# column 3: argument flag.  0=without argument, 1=with argument
#
# column 4: mode of argument.  one of "logical", "integer", "double",
# "complex", "character", "" for arguments without value (return logical)
#
# column 5 (optional): description of ARGUMENT.
#


RetreiveAndDestroy=function(opt,root,stem,regexp,SearchNames,Out,isValue,NbFound,StockNames){
	Bool=lapply(paste(root,SearchNames,stem,sep=""),grepl,opt)
	names(Bool)=StockNames
	Pos=lapply(Bool,which)
	names(Pos)=StockNames
	disable=c()
	for (i in StockNames){
		nbmatch=length(Pos[[i]])
		if(nbmatch>0){
			NbFound[[i]]=NbFound[[i]]+nbmatch
			disable=c(disable,-1*Pos[[i]])
			if(is.null(Out[[i]])){
				if(isValue[[i]]!=0){
					if(regexp=="next"){
						Out[[i]]=opt[Pos[[i]]+1]
						disable=c(disable,-1*(Pos[[i]]+1))
					}else{
						Out[[i]]=sub(regexp,"\\1",opt[Pos[[i]]])
					}
				}else{
					Out[[i]]=TRUE
				}
			}else{
				if(isValue[[i]]!=0){
					if(regexp=="next"){
						Out[[i]]=c(Out[[i]],opt[Pos[[i]]+1])
						disable=c(disable,-1*(Pos[[i]]+1))
					}else{
						Out[[i]]=c(Out[[i]],sub(regexp,"\\1",opt[Pos[[i]]]))
					}
				}else{
					Out[[i]]=c(Out[[i]],TRUE)
				}
			}
		}
	}
	if(length(disable)>0){
		opt=opt[disable]
	}
	Out[["ARGUMENT"]]=list()
	Out[["ARGUMENT"]][["opt"]]=opt
	Out[["ARGUMENT"]][["NbFound"]]=NbFound
	return(Out)
}

getopt = function (spec=NULL,opt=commandArgs()) {
	
	FindArgs=which(opt=="--args")
	if(length(FindArgs)!=1){
		stop(length(FindArgs)," --args found where 1 expected.",call.=F)
	}
	ExecName=sub("--file=","",opt[FindArgs-1])
	
	if(FindArgs<length(opt)){
		opt=opt[(FindArgs+1):length(opt)]
	}else{
		opt=""
	}
	
	
	min.columns=5
	colNames=c("LongName","ShortName","Flag","Mod","Default")
	max.columns=6
	DimSpec=dim(spec)
	if(DimSpec[2]>min.columns){
		colNames=c(colNames,"Description")
	}
	
	if(is.null(spec) | !is.matrix(spec) | (DimSpec[2]<min.columns | DimSpec[2]>max.columns)){
		stop('argument "spec" is required and must be a matrix with 4|5 columns.',call.=F)
	}
	colnames(spec)=colNames
	
	spec=as.data.frame(spec,stringsAsFactors=F)
	#spec validation
	if(length(unique(c(spec$ShortName,"ARGUMENT","args")))!=DimSpec[1]+2 | length(unique(spec$LongName))!=DimSpec[1]){
		stop('Long|Short names for flags must be unique (Long name : "ARGUMENT" and "args" forbidden).',
				"\n","List of duplicated :",
				"\n","Short: ",paste(spec$ShortName[duplicated(c(spec$ShortName,"ARGUMENT","args"))],collapse=" "),
				"\n","Long:  ",paste(spec$ShortName[duplicated(spec$LongName)],collapse=" "),call.=F)
	}
	if(length(which(nchar(spec$ShortName)>1))!=0){
		stop('Short names flags can\'t be longer than 1 character.')
	}
	
	
	#initialize 
	Out=list()
	Short2Long=list()
	NbFound=list()
	isValue=list()
	for (i in 1:DimSpec[1]){
		Short2Long[[spec$ShortName[i]]]=spec$LongName[i]
		NbFound[[spec$LongName[i]]]=0
		isValue[[spec$LongName[i]]]=spec$Flag[i]
	}
	
	#Map, retreive and suppress ARGUMENTs and arguments
	#Value ARGUMENT --example=value
	Out=RetreiveAndDestroy(opt,"^--","=.+$",".+=(.+)$",spec$LongName,Out,isValue,NbFound,spec$LongName)
	opt=Out[["ARGUMENT"]][["opt"]]
	NbFound=Out[["ARGUMENT"]][["NbFound"]]
	Out[["ARGUMENT"]]=NULL
	#boolean ARGUMENT --example
	Out=RetreiveAndDestroy(opt,"^--","$","$",spec$LongName,Out,isValue,NbFound,spec$LongName)
	opt=Out[["ARGUMENT"]][["opt"]]
	NbFound=Out[["ARGUMENT"]][["NbFound"]]
	Out[["ARGUMENT"]]=NULL
	#short name ARGUMENT -t value OR boolean -t
	Out=RetreiveAndDestroy(opt,"^-","$","next",spec$ShortName,Out,isValue,NbFound,spec$LongName)
	opt=Out[["ARGUMENT"]][["opt"]]
	NbFound=Out[["ARGUMENT"]][["NbFound"]]
	Out[["ARGUMENT"]]=NULL
	#Warn about non mapped ARGUMENTs
	if(length(opt)>0){
		PosUnkArg=which(grepl("^-",opt))
		if(length(PosUnkArg)){
			message("Error, argument unreconized :","\n",paste(opt[PosUnkArg],collapse="\n"),"\n\n")
		}
		if(length(PosUnkArg)>0){
			opt=opt[PosUnkArg*-1]
		}
	}
	#Arguments
	Out[["ARGUMENT"]]=opt
	
	#Validation of ARGUMENTs
	for(i in 1:DimSpec[1]){
		if(spec$Flag[i]=="0"){#verify boolean arguments
			NbValue=length(Out[[spec$LongName[i]]])
			if(NbValue>1){
				message("Warning : ",spec$LongName[i]," found ",NbValue," times")
			}
		}
		if(length(Out[[spec$LongName[i]]])==0){
			Out[[spec$LongName[i]]]=spec$Default[i]
		}
		library("methods")
		Out[[spec$LongName[i]]]=as(Out[[spec$LongName[i]]],spec$Mod[i])
	}
	
	return(Out)
}

# column 3: argument flag.  0=no argument, 1=required argument, 2=optional argument