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getopt = function (spec=NULL,opt=commandArgs(TRUE),command=strsplit(commandArgs(FALSE)[4],"=")[[1]][2],usage=FALSE,debug=FALSE) {
# notes on naming convention:
# 1. an "option" is one of the shell-split input strings
# 2. a "flag" is a subclass of "option". a "flag" can be defined as having
# no "argument" (see below), a required "argument", or an optional
# "argument".
# 3. an "argument" is a subclass of "option", and is the value associated
# with a flag.
# 4. a "long flag" is a subclass of flag, and begins with the string "--".
# if the "long flag" has an associated "argument", it may be delimited from
# the "long flag" by either an "=", or may be the subsequent "option".
# 5. a "short flag" is a subclass of flag, and begins with the string "-".
# if a "short flag" has an associated "argument", it is the subsequent
# "option". "short flags" may be bundled together, sharing a single leading
# "-", but only the final "short flag" is able to have a corresponding
# "argument".
#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=no argument, 1=required argument, 2=optional
# argument
#
# column 4: mode of argument. one of "logical", "integer", "double",
# "complex", "character"
#
# column 5 (optional): description of option.
#
# littler compatibility - map argv vector to opt
if (exists("argv", where = .GlobalEnv, inherits = FALSE)) {
opt = get("argv", envir = .GlobalEnv);
}
ncol=4;
maxcol=6;
col.long.name = 1;
col.short.name = 2;
col.has.argument = 3;
col.mode = 4;
col.description = 5;
flag.no.argument = 0;
flag.required.argument = 1;
flag.optional.argument = 2;
result = list();
result$ARGS = vector(mode="character");
#no spec. fail.
if ( is.null(spec) ) {
stop('argument "spec" must be non-null.');
#spec is not a matrix. attempt to coerce, if possible. issue a warning.
} else if ( !is.matrix(spec) ) {
if ( length(spec)/4 == as.integer(length(spec)/4) ) {
warning('argument "spec" was coerced to a 4-column (row-major) matrix. use a matrix to prevent the coercion');
spec = matrix( spec, ncol=ncol, byrow=TRUE );
} else {
stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.');
}
#spec is a matrix, but it has too few columns.
} else if ( dim(spec)[2] < ncol ) {
stop(paste('"spec" should have at least ",ncol," columns.',sep=''));
#spec is a matrix, but it has too many columns.
} else if ( dim(spec)[2] > maxcol ) {
stop(paste('"spec" should have no more than ",maxcol," columns.',sep=''));
#spec is a matrix, and it has some optional columns.
} else if ( dim(spec)[2] != ncol ) {
ncol = dim(spec)[2];
}
#sanity check. make sure long names are unique, and short names are unique.
if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) {
stop(paste('redundant long names for flags (column ',col.long.name,').',sep=''));
}
if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) {
stop(paste('redundant short names for flags (column ',col.short.name,').',sep=''));
}
# if usage=TRUE, don't process opt, but generate a usage string from the data in spec
if ( usage ) {
ret = '';
ret = paste(ret,"Usage: ",command,sep='');
for ( j in 1:(dim(spec))[1] ) {
ret = paste(ret,' [-[-',spec[j,col.long.name],'|',spec[j,col.short.name],']',sep='');
if (spec[j,col.has.argument] == flag.no.argument) {
ret = paste(ret,']',sep='');
} else if (spec[j,col.has.argument] == flag.required.argument) {
ret = paste(ret,' <',spec[j,col.mode],'>]',sep='');
} else if (spec[j,col.has.argument] == flag.optional.argument) {
ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep='');
}
}
# include usage strings
if ( ncol >= 5 ) {
max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]])));
ret = paste(ret,"\n",sep='');
for (j in 1:(dim(spec))[1] ) {
ret = paste(ret,sprintf(paste(" -%s|--%-",max.long,"s %s\n",sep=''),
spec[j,col.short.name],spec[j,col.long.name],spec[j,col.description]
),sep='');
}
}
else {
ret = paste(ret,"\n",sep='');
}
return(ret);
}
#XXX check spec validity here. e.g. column three should be convertible to integer
i = 1;
while ( i <= length(opt) ) {
if ( debug ) print(paste("processing",opt[i]));
current.flag = 0; #XXX use NA
optstring = opt[i];
#long flag
if ( substr(optstring, 1, 2) == '--' ) {
if ( debug ) print(paste(" long option:",opt[i]));
optstring = substring(optstring,3);
this.flag = NA;
this.argument = NA;
kv = strsplit(optstring, '=')[[1]];
if ( !is.na(kv[2]) ) {
this.flag = kv[1];
this.argument = kv[2];
} else {
this.flag = optstring;
}
rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE );
#long flag is invalid, matches no options
if ( length(rowmatch) == 0 ) {
stop(paste('long flag "', this.flag, '" is invalid', sep=''));
#long flag is ambiguous, matches too many options
} else if ( length(rowmatch) > 1 ) {
stop(paste('long flag "', this.flag, '" is ambiguous', sep=''));
}
#if we have an argument
if ( !is.na(this.argument) ) {
#if we can't accept the argument, bail out
if ( spec[rowmatch, col.has.argument] == flag.no.argument ) {
stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));
#otherwise assign the argument to the flag
} else {
storage.mode(this.argument) = spec[rowmatch, col.mode];
result[spec[rowmatch, col.long.name]] = this.argument;
i = i + 1;
next;
}
#otherwise, we don't have an argument
} else {
#if we require an argument, bail out
###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
### stop(paste('long flag "', this.flag, '" requires an argument', sep=''));
#long flag has no attached argument. set flag as present. set current.flag so we can peek ahead later and consume the argument if it's there
###} else {
result[spec[rowmatch, col.long.name]] = TRUE;
current.flag = rowmatch;
###}
}
#short flag(s)
} else if ( substr(optstring, 1, 1) == '-' ) {
if ( debug ) print(paste(" short option:",opt[i]));
these.flags = strsplit(optstring,'')[[1]];
done = FALSE;
for ( j in 2:length(these.flags) ) {
this.flag = these.flags[j];
rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );
#short flag is invalid, matches no options
if ( length(rowmatch) == 0 ) {
stop(paste('short flag "', this.flag, '" is invalid', sep=''));
#short flag is ambiguous, matches too many options
} else if ( length(rowmatch) > 1 ) {
stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));
#short flag has an argument, but is not the last in a compound flag string
} else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));
#short flag has no argument, flag it as present
} else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
result[spec[rowmatch, col.long.name]] = TRUE;
done = TRUE;
#can't definitively process this flag yet, need to see if next option is an argument or not
} else {
result[spec[rowmatch, col.long.name]] = TRUE;
current.flag = rowmatch;
done = FALSE;
}
}
if ( done ) {
i = i + 1;
next;
}
}
#invalid opt
if ( current.flag == 0 ) {
stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
#TBD support for positional args
#if ( debug ) print(paste('"', optstring, '" not a valid option. It is appended to getopt(...)$ARGS', sep=''));
#result$ARGS = append(result$ARGS, optstring);
# some dangling flag, handle it
} else if ( current.flag > 0 ) {
if ( debug ) print(' dangling flag');
if ( length(opt) > i ) {
peek.optstring = opt[i + 1];
if ( debug ) print(paste(' peeking ahead at: "',peek.optstring,'"',sep=''));
#got an argument. attach it, increment the index, and move on to the next option. we don't allow arguments beginning with '-' UNLESS
#specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals).
if ( substr(peek.optstring, 1, 1) != '-' |
#match negative double
( substr(peek.optstring, 1, 1) == '-'
& regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
& spec[current.flag, col.mode]== 'double'
) |
#match negative integer
( substr(peek.optstring, 1, 1) == '-'
& regexpr('^-[0123456789]+$',peek.optstring) > 0
& spec[current.flag, col.mode]== 'integer'
)
) {
if ( debug ) print(paste(' consuming argument *',peek.optstring,'*',sep=''));
storage.mode(peek.optstring) = spec[current.flag, col.mode];
result[spec[current.flag, col.long.name]] = peek.optstring;
i = i + 1;
#a lone dash
} else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
if ( debug ) print(' consuming "lone dash" argument');
storage.mode(peek.optstring) = spec[current.flag, col.mode];
result[spec[current.flag, col.long.name]] = peek.optstring;
i = i + 1;
#no argument
} else {
if ( debug ) print(' no argument!');
#if we require an argument, bail out
if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
stop(paste('flag "', this.flag, '" requires an argument', sep=''));
#otherwise set flag as present.
} else if (
spec[current.flag, col.has.argument] == flag.optional.argument |
spec[current.flag, col.has.argument] == flag.no.argument
) {
x = TRUE;
storage.mode(x) = spec[current.flag, col.mode];
result[spec[current.flag, col.long.name]] = x;
} else {
stop("this should never happen (1). please inform the author.");
}
}
#trailing flag without required argument
} else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
stop(paste('flag "', this.flag, '" requires an argument', sep=''));
#trailing flag without optional argument
} else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
x = TRUE;
storage.mode(x) = spec[current.flag, col.mode];
result[spec[current.flag, col.long.name]] = x;
#trailing flag without argument
} else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
x = TRUE;
storage.mode(x) = spec[current.flag, col.mode];
result[spec[current.flag, col.long.name]] = x;
} else {
stop("this should never happen (2). please inform the author.");
}
#no dangling flag, nothing to do.
} else {
}
i = i+1;
}
return(result);
}
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