--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/charts.r	Fri Apr 25 20:09:09 2014 -0400
@@ -0,0 +1,459 @@
+#!/usr/bin/Rscript
+
+#' Returns file name of calling Rscript
+#'
+#' \code{get_Rscript_filename} returns the file name of calling Rscript 
+#' @return A string with the filename of the calling script.
+#'      If not found (i.e. you are in a interactive session) returns NA.
+#'
+#' @export
+get_Rscript_filename <- function() {
+    prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1])
+    if( .Platform$OS.type == "windows") { 
+        prog <- gsub("\\\\", "\\\\\\\\", prog)
+    }
+    prog
+}
+
+#' Recursively sorts a list
+#'
+#' \code{sort_list} returns a sorted list
+#' @param unsorted_list A list.
+#' @return A sorted list.
+#' @export
+sort_list <- function(unsorted_list) {
+    for(ii in seq(along=unsorted_list)) {
+        if(is.list(unsorted_list[[ii]])) {
+            unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]])
+        }
+    }
+    unsorted_list[sort(names(unsorted_list))] 
+}
+
+#' #!/path/to/Rscript
+#' library('getopt');
+#' #get options, using the spec as defined by the enclosed list.
+#' #we read the options from the default: commandArgs(TRUE).
+#' spec = matrix(c(
+#'   'verbose', 'v', 2, "integer",
+#'   'help'   , 'h', 0, "logical",
+#'   'count'  , 'c', 1, "integer",
+#'   'mean'   , 'm', 1, "double",
+#'   'sd'     , 's', 1, "double"
+#' ), byrow=TRUE, ncol=4);
+#' opt = getopt(spec);
+#' 
+#' # if help was asked for print a friendly message 
+#' # and exit with a non-zero error code
+#' if ( !is.null(opt$help) ) {
+#'   cat(getopt(spec, usage=TRUE));
+#'   q(status=1);
+#' }
+#' 
+#' #set some reasonable defaults for the options that are needed,
+#' #but were not specified.
+#' if ( is.null(opt$mean    ) ) { opt$mean    = 0     }
+#' if ( is.null(opt$sd      ) ) { opt$sd      = 1     }
+#' if ( is.null(opt$count   ) ) { opt$count   = 10    }
+#' if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }
+#' 
+#' #print some progress messages to stderr, if requested.
+#' if ( opt$verbose ) { write("writing...",stderr()); }
+#' 
+#' #do some operation based on user input.
+#' cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n"));
+#' cat("\n");
+#' 
+#' #signal success and exit.
+#' #q(status=0);
+getopt = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) {
+
+  # 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=''));
+  }
+  # convert numeric type to double type
+  spec[,4] <- gsub("numeric", "double", spec[,4])
+
+  # 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 = paste(kv[-1], collapse="=");
+      } 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 ) {
+        # check if there is an exact match and use that
+        rowmatch = which(this.flag == spec[,col.long.name])
+        if(length(rowmatch) == 0) {
+          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(paste("This should never happen.",
+              "Is your spec argument correct?  Maybe you forgot to set",
+              "ncol=4, byrow=TRUE in your matrix call?"));
+	  }
+        }
+      #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);
+}
+
+# convert multi parameter string (i.e. key1: value, key2: value, ...) to object
+split <- function(argument){
+    # process parameter string
+    options <- list()
+    list <- gsub("\\s","", argument)
+    list <- strsplit(list, ",")
+    if (length(list) > 0) {
+        list <- list[[1]]
+        for (entry in list) {
+            pair <- strsplit(entry, ":")
+            if (length(pair) > 0) {
+                pair <- pair[[1]]
+                if (length(pair) == 2) {
+                    options[[pair[1]]] <- pair[2]
+                }
+            }
+        }
+    }
+    return(options)
+}
+
+# get options, using the spec as defined by the enclosed list.
+spec = matrix(c(
+    'workdir',  'w', 1, 'character', 'Work directory',
+    'module',   'm', 1, 'character', 'Module name',
+    'input',    'i', 1, 'character', 'Input tabular file',
+    'columns',  'c', 1, 'character', 'Columns string',
+    'settings', 's', 1, 'character', 'Settings string',
+    'output',   'o', 1, 'character', 'Output tabular file',
+    'help',     'h', 0, '',          'Help',
+    'verbose',  'v', 0, '',          'Verbose'
+), byrow=TRUE, ncol=5);
+opt = getopt(spec);
+
+# show help
+if ( !is.null(opt$help) ||
+    is.null(opt$module) ||
+    is.null(opt$input) ||
+    is.null(opt$columns) ||
+    is.null(opt$output)) {
+    cat(getopt(spec, usage=TRUE))
+    q(status=1);
+}
+
+# read columns/settings
+columns = split(opt$columns)
+settings = split(opt$settings)
+
+# read table
+table <- read.table(opt$input)
+
+# identify module file
+module_file = paste(opt$workdir, opt$module, '.r', sep='')
+
+# source module
+source(module_file)
+
+# run module
+l = wrapper (table, columns, settings)
+
+# header
+header_title <- '# title - Chart Utilities (charts)'
+header_date <- paste('# date -', Sys.time(), sep=' ')
+header_module <- paste('# module -', opt$module, sep=' ')
+header_settings <- paste('# settings -', opt$settings, sep=' ')
+header_columns <- paste('# columns -', opt$columns, sep=' ')
+
+# fill gaps
+if (length(l) > 0) {
+    # print details
+    if (!is.null(opt$verbose)) {
+        print ('Columns:')
+        print (columns)
+        print ('Settings:')
+        print (settings)
+        print ('Result:')
+        print (l)
+    }
+
+    # create output file
+    output <- file(opt$output, open='wt')
+    
+    # write header
+    writeLines('#', output)
+    writeLines(header_title, output)
+    writeLines(header_date, output)
+    writeLines(header_module, output)
+    writeLines(header_settings, output)
+    writeLines(header_columns, output)
+    writeLines('#', output)
+    
+    # write table
+    write.table(l, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
+    
+    # close file
+    close(output)
+} else {
+    print ('Columns:')
+    print (columns)
+    print ('Settings:')
+    print (settings)
+    print ('No output generated.')
+}
\ No newline at end of file