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#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

package Tracer;

    require Exporter;
    @ISA = ('Exporter');
    @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);
    @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
    use strict;
    use Carp qw(longmess croak);
    use CGI;
    use Cwd;
    use FIG_Config;
    use PageBuilder;
    use Digest::MD5;
    use File::Basename;
    use File::Path;
    use File::stat;

=head1 Tracing and Debugging Helpers

=head2 Introduction

This package provides simple tracing for debugging and reporting purposes. To use it simply call the
L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace
message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself
has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace
level is less than or equal to this package's trace level and whose category is activated will
be written. Thus, a higher trace level on a message indicates that the message
is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will
appear. To generate a trace message, use the following syntax.

C<< Trace($message) if T(errors => 4); >>

This statement will produce a trace message if the trace level is 4 or more and the C<errors>
category is active. Note that the special category C<main> is always active, so

C<< Trace($message) if T(main => 4); >>

will trace if the trace level is 4 or more.

If the category name is the same as the package name, all you need is the number. So, if the
following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
active and the trace level is 2 or more.

C<< Trace($message) if T(2); >>

To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list
of category names, and a set of options. The trace level and list of category names are
specified as a space-delimited string. Thus

C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>

sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
specifies that messages should be output as HTML paragraphs.

To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
level 3 and writes the output to the standard error output. This sort of thing might be
useful in a CGI environment.

C<< TSetup('3 *', 'WARN'); >>

In addition to HTML and file output for trace messages, you can specify that the trace messages
be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
is useful if you are building a web page. Instead of having the trace messages interspersed with
the page output, they can be gathered together and displayed at the end of the page. This makes
it easier to debug page formatting problems.

Finally, you can specify that all trace messages be emitted as warnings.

The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
Thus, debugging information is available and easily retrieved even when the application is
being used out in the field.

There is no hard and fast rule on how to use trace levels. The following is therefore only
a suggestion.

=over 4

=item Error 0

Message indicates an error that may lead to incorrect results or that has stopped the
application entirely.

=item Warning 1

Message indicates something that is unexpected but that probably did not interfere
with program execution.

=item Notice 2

Message indicates the beginning or end of a major task.

=item Information 3

Message indicates a subtask. In the FIG system, a subtask generally relates to a single
genome. This would be a big loop that is not expected to execute more than 500 times or so.

=item Detail 4

Message indicates a low-level loop iteration.

=back

=cut

# Declare the configuration variables.

my $Destination = "NONE";   # Description of where to send the trace output.
my $TeeFlag = 0;            # TRUE if output is going to a file and to the
                            # standard output
my %Categories = ( main => 1 );
                            # hash of active category names
my $TraceLevel = 0;         # trace level; a higher trace level produces more
                            # messages
my @Queue = ();             # queued list of trace messages.
my $LastCategory = "main";  # name of the last category interrogated
my $SetupCount = 0;         # number of times TSetup called
my $AllTrace = 0;           # TRUE if we are tracing all categories.

=head2 Public Methods

=head3 TSetup

C<< TSetup($categoryList, $target); >>

This method is used to specify the trace options. The options are stored as package data
and interrogated by the L</Trace> and L</T> methods.

=over 4

=item categoryList

A string specifying the trace level and the categories to be traced, separated by spaces.
The trace level must come first.

=item target

The destination for the trace output. To send the trace output to a file, specify the file
name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
symbol with a C<+> to echo output to a file AND to the standard output. In addition to
sending the trace messages to a file, you can specify a special destination. C<HTML> will
cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
cause trace messages to be emitted as warnings using the B<warn> directive.  C<NONE> will
cause tracing to be suppressed.

=back

=cut

sub TSetup {
    # Get the parameters.
    my ($categoryList, $target) = @_;
    # Parse the category list.
    my @categoryData = split /\s+/, $categoryList;
    # Extract the trace level.
    $TraceLevel = shift @categoryData;
    # Presume category-based tracing until we learn otherwise.
    $AllTrace = 0;
    # Build the category hash. Note that if we find a "*", we turn on non-category
    # tracing. We must also clear away any pre-existing data.
    %Categories = ( main => 1 );
    for my $category (@categoryData) {
        if ($category eq '*') {
            $AllTrace = 1;
        } else {
            $Categories{lc $category} = 1;
        }
    }
    # Now we need to process the destination information. The most important special
    # cases are the single ">", which requires we clear the file first, and the
    # "+" prefix which indicates a double echo.
    if ($target =~ m/^\+?>>?/) {
        if ($target =~ m/^\+/) {
            $TeeFlag = 1;
            $target = substr($target, 1);
        }
        if ($target =~ m/^>[^>]/) {
            open TRACEFILE, $target;
            print TRACEFILE Now() . " Tracing initialized.\n";
            close TRACEFILE;
            $Destination = ">$target";
        } else {
            $Destination = $target;
        }
    } else {
        $Destination = uc($target);
    }
    # Increment the setup counter.
    $SetupCount++;
}

=head3 StandardSetup

C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>

This method performs standard command-line parsing and tracing setup. The return
values are a hash of the command-line options and a list of the positional
parameters. Tracing is automatically set up and the command-line options are
validated.

This is a complex method that does a lot of grunt work. The parameters can
be more easily understood, however, once they are examined individually.

The I<categories> parameter is the most obtuse. It is a reference to a list of
special-purpose tracing categories. Most tracing categories are PERL package
names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
B<ERDB>, and B<SproutLoad> packages, you would specify the categories

    ["Sprout", "SproutLoad", "ERDB"]

This would cause trace messages in the specified three packages to appear in
the output. There are threer special tracing categories that are automatically
handled by this method. In other words, if you used L</TSetup> you would need
to include these categories manually, but if you use this method they are turned
on automatically.

=over 4

=item FIG

Turns on trace messages inside the B<FIG> package.

=item SQL

Traces SQL commands and activity.

=item Tracer

Traces error messages and call stacks.

=back

C<SQL> is only turned on if the C<-sql> option is specified in the command line.
The trace level is specified using the C<-trace> command-line option. For example,
the following command line for C<TransactFeatures> turns on SQL tracing and runs
all tracing at level 3.

    TransactFeatures -trace=3 -sql register ../xacts IDs.tbl

Standard tracing is output to the standard output and echoed to the file
C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
process ID. You can also specify the C<user> parameter to put a user ID
instead of a process ID in the trace file name. So, for example

The default trace level is 2. To get all messages, specify a trace level of 4.
For a genome-by-genome update, use 3.

    TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl

would send the trace output to C<traceBruce.log> in the temporary directory.

The I<options> parameter is a reference to a hash containing the command-line
options, their default values, and an explanation of what they mean. Command-line
options may be in the form of switches or keywords. In the case of a switch, the
option value is 1 if it is specified and 0 if it is not specified. In the case
of a keyword, the value is separated from the option name by an equal sign. You
can see this last in the command-line example above.

You can specify a different default trace level by setting C<$options->{trace}>
prior to calling this method.

An example at this point would help. Consider, for example, the command-line utility
C<TransactFeatures>. It accepts a list of positional parameters plus the options
C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
the following code.

    my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
                        { safe => [0, "use database transactions"],
                          noAlias => [0, "do not expect aliases in CHANGE transactions"],
                          start => [' ', "start with this genome"],
                          tblFiles => [0, "output TBL files containing the corrected IDs"] },
                        "command transactionDirectory IDfile",
                      @ARGV);


The call to C<ParseCommand> specifies the default values for the options and
stores the actual options in a hash that is returned as C<$options>. The
positional parameters are returned in C<@parameters>. 

The following is a sample command line for C<TransactFeatures>.

    TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl

In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
parameters, and would find themselves in I<@parameters> after executing the
above code fragment. The tracing would be set to level 2, and the categories
would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
and C<DocUtils> was included because it came in within the first parameter
to this method. The I<$options> hash would be

    { trace => 2, sql => 0, safe => 0,
      noAlias => 1, start => ' ', tblFiles => 0 }

Use of C<StandardSetup> in this way provides a simple way of performing
standard tracing setup and command-line parsing. Note that the caller is
not even aware of the command-line switches C<-trace> and C<-sql>, which
are used by this method to control the tracing. If additional tracing features
need to be added in the future, they can be processed by this method without
upsetting the command-line utilities.

If the C<background> option is specified on the command line, then the
standard and error outputs will be directed to files in the temporary
directory, using the same suffix as the trace file. So, if the command
line specified

    -user=Bruce -background

then the trace output would go to C<traceBruce.log>, the standard output to
C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
simplify starting a command in the background.

Finally, if the special option C<-h> is specified, the option names will
be traced at level 0 and the program will exit without processing.
This provides a limited help capability. For example, if the user enters

    TransactFeatures -h

he would see the following output.

    TransactFeatures [options] command transactionDirectory IDfile
        -trace    tracing level (default 2)
        -sql      trace SQL commands
        -safe     use database transactions
        -noAlias  do not expect aliases in CHANGE transactions
        -start    start with this genome
        -tblFiles output TBL files containing the corrected IDs

The caller has the option of modifying the tracing scheme by placing a value
for C<trace> in the incoming options hash. The default value can be overridden,
or the tracing to the standard output can be turned off by suffixing a minus
sign to the trace level. So, for example, 

    { trace => [0, "tracing level (default 0)"],
       ...

would set the default trace level to 0 instead of 2, while

    { trace => ["2-", "tracing level (default 2)"],
       ...

would leave the default at 2, but trace only to the log file, not to the
standard output.

The parameters to this method are as follows.

=over 4

=item categories

Reference to a list of tracing category names. These should be names of
packages whose internal workings will need to be debugged to get the
command working.

=item options

Reference to a hash containing the legal options for the current command mapped
to their default values and descriptions. The user can override the defaults
by specifying the options as command-line switches prefixed by a hyphen.
Tracing-related options may be added to this hash. If the C<-h> option is
specified on the command line, the option descriptions will be used to
explain the options. To turn off tracing to the standard output, add a
minus sign to the value for C<trace> (see above).

=item parmHelp

A string that vaguely describes the positional parameters. This is used
if the user specifies the C<-h> option.

=item argv

List of command line parameters, including the option switches, which must
precede the positional parameters and be prefixed by a hyphen.

=item RETURN

Returns a list. The first element of the list is the reference to a hash that
maps the command-line option switches to their values. These will either be the
default values or overrides specified on the command line. The remaining
elements of the list are the position parameters, in order.

=back

=cut

sub StandardSetup {
    # Get the parameters.
    my ($categories, $options, $parmHelp, @argv) = @_;
    # Add the tracing options.
    if (! exists $options->{trace}) {
        $options->{trace} = [2, "tracing level"];
    }
    $options->{sql} = [0, "turn on SQL tracing"];
    $options->{h} = [0, "display command-line options"];
    $options->{user} = [$$, "trace log file name suffix"];
    $options->{background} = [0, "spool standard and error output"];
    # Create a parsing hash from the options hash. The parsing hash
    # contains the default values rather than the default value
    # and the description. While we're at it, we'll memorize the
    # length of the longest option name.
    my $longestName = 0;
    my %parseOptions = ();
    for my $key (keys %{$options}) {
        if (length $key > $longestName) {
            $longestName = length $key;
        }
        $parseOptions{$key} = $options->{$key}->[0];
    }
    # Parse the command line.
    my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
    # Get the logfile suffix.
    my $suffix = $retOptions->{user};
    # Check for background mode.
    if ($retOptions->{background}) {
        my $outFileName = "$FIG_Config::temp/out$suffix.log";
        my $errFileName = "$FIG_Config::temp/err$suffix.log";
        open STDOUT, ">$outFileName";
        open STDERR, ">$errFileName";
    }
    # Now we want to set up tracing. First, we need to know if SQL is to
    # be traced.
    my @cats = @{$categories};
    if ($retOptions->{sql}) {
        push @cats, "SQL";
    }
    # Add the default categories.
    push @cats, "Tracer", "FIG";
    # Next, we create the category string by joining the categories.
    my $cats = join(" ", @cats);
    # Check to determine whether or not the caller wants to turn off tracing
    # to the standard output.
    my $traceLevel = $retOptions->{trace};
    my $textOKFlag = 1;
    if ($traceLevel =~ /^(.)-/) {
        $traceLevel = $1;
        $textOKFlag = 0;
    }
    # Now we set up the trace mode.
    my $traceMode;
    # Verify that we can open a file in the FIG temporary directory.
    my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
    if (open TESTTRACE, ">$traceFileName") {
        # Here we can trace to a file.
        $traceMode = ">$traceFileName";
        if ($textOKFlag) {
            # Echo to standard output if the text-OK flag is set.
            $traceMode = "+$traceMode";
        }
        # Close the test file.
        close TESTTRACE;
    } else {
        # Here we can't trace to a file. We trace to the standard output if it's
        # okay, and the error log otherwise.
        if ($textOKFlag) {
            $traceMode = "TEXT";
        } else {
            $traceMode = "WARN";
        }
    }
    # Now set up the tracing.
    TSetup("$traceLevel $cats", $traceMode);
    # Check for the "h" option. If it is specified, dump the command-line
    # options and exit the program.
    if ($retOptions->{h}) {
        $0 =~ m#[/\\](\w+)(\.pl)?$#i;
        Trace("$1 [options] $parmHelp") if T(0);
        for my $key (sort keys %{$options}) {
            my $name = Pad($key, $longestName, 0, ' ');
            my $desc = $options->{$key}->[1];
            if ($options->{$key}->[0]) {
                $desc .= " (default " . $options->{$key}->[0] . ")";
            }
            Trace("  $name $desc") if T(0);
        }
        exit(0);
    }
    # Return the parsed parameters.
    return ($retOptions, @retParameters);
}

=head3 Setups

C<< my $count = Tracer::Setups(); >>

Return the number of times L</TSetup> has been called.

This method allows for the creation of conditional tracing setups where, for example, we
may want to set up tracing if nobody else has done it before us.

=cut

sub Setups {
    return $SetupCount;
}

=head3 Open

C<< my $handle = Open($fileHandle, $fileSpec, $message); >>

Open a file.

The I<$fileSpec> is essentially the second argument of the PERL C<open>
function. The mode is specified using Unix-like shell information. So, for
example,

    Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");

would open for output appended to the specified file, and

    Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");

would open a pipe that sorts the records written and removes duplicates. Note
the use of file handle syntax in the Open call. To use anonymous file handles,
code as follows.

    my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");

The I<$message> parameter is used if the open fails. If it is set to C<0>, then
the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
failed open will throw an exception and the third parameter will be used to construct
an error message. If the parameter is omitted, a standard message is constructed
using the file spec.

    Could not open "/usr/spool/news/twitlog"

Note that the mode characters are automatically cleaned from the file name.
The actual error message from the file system will be captured and appended to the
message in any case.

    Could not open "/usr/spool/news/twitlog": file not found.

In some versions of PERL the only error message we get is a number, which
corresponds to the C++ C<errno> value.

    Could not open "/usr/spool/news/twitlog": 6.

=over 4

=item fileHandle

File handle. If this parameter is C<undef>, a file handle will be generated
and returned as the value of this method.

=item fileSpec

File name and mode, as per the PERL C<open> function.

=item message (optional)

Error message to use if the open fails. If omitted, a standard error message
will be generated. In either case, the error information from the file system
is appended to the message. To specify a conditional open that does not throw
an error if it fails, use C<0>.

=item RETURN

Returns the name of the file handle assigned to the file, or C<undef> if the
open failed.

=back

=cut

sub Open {
    # Get the parameters.
    my ($fileHandle, $fileSpec, $message) = @_;
    # Attempt to open the file.
    my $rv = open $fileHandle, $fileSpec;
    # If the open failed, generate an error message.
    if (! $rv) {
        # Save the system error message.
        my $sysMessage = $!;
        # See if we need a default message.
        if (!$message) {
            # Clean any obvious mode characters and leading spaces from the
            # filename.
            my ($fileName) = FindNamePart($fileSpec);
            $message = "Could not open \"$fileName\"";
        }
        # Terminate with an error using the supplied message and the
        # error message from the file system.
        Confess("$message: $!");
    }
    # Return the file handle.
    return $fileHandle;
}

=head3 FindNamePart

C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>

Extract the portion of a file specification that contains the file name.

A file specification is the string passed to an C<open> call. It specifies the file
mode and name. In a truly complex situation, it can specify a pipe sequence. This
method assumes that the file name is whatever follows the first angle bracket
sequence.  So, for example, in the following strings the file name is
C</usr/fig/myfile.txt>.

    >>/usr/fig/myfile.txt
    </usr/fig/myfile.txt
    | sort -u > /usr/fig/myfile.txt

If the method cannot find a file name using its normal methods, it will return the
whole incoming string.

=over 4

=item fileSpec

File specification string from which the file name is to be extracted.

=item RETURN

Returns a three-element list. The first element contains the file name portion of
the specified string, or the whole string if a file name cannot be found via normal
methods. The second element contains the start position of the file name portion and
the third element contains the length.

=back

=cut
#: Return Type $;
sub FindNamePart {
    # Get the parameters.
    my ($fileSpec) = @_;
    # Default to the whole input string.
    my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
    # Parse out the file name if we can.
    if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
        $retVal = $2;
        $len = length $retVal;
        $pos = (length $fileSpec) - (length $3) - $len;
    }
    # Return the result.
    return ($retVal, $pos, $len);
}

=head3 OpenDir

C<< my @files = OpenDir($dirName, $filtered, $flag); >>

Open a directory and return all the file names. This function essentially performs
the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
filtered out of the return list. If the directory does not open and I<$flag> is not
set, an exception is thrown. So, for example,

    my @files = OpenDir("/Volumes/fig/contigs", 1);

is effectively the same as

    opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
    my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);

Similarly, the following code

    my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);

Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
automatically returns an empty list if the directory fails to open.

=over 4

=item dirName

Name of the directory to open.

=item filtered

TRUE if files whose names begin with a period (C<.>) should be automatically removed
from the list, else FALSE.

=item flag

TRUE if a failure to open is okay, else FALSE

=back

=cut
#: Return Type @;
sub OpenDir {
    # Get the parameters.
    my ($dirName, $filtered, $flag) = @_;
    # Declare the return variable.
    my @retVal = ();
    # Open the directory.
    if (opendir(my $dirHandle, $dirName)) {
        # The directory opened successfully. Get the appropriate list according to the
        # strictures of the filter parameter.
        if ($filtered) {
            @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
        } else {
            @retVal = readdir $dirHandle;
        }
    } elsif (! $flag) {
        # Here the directory would not open and it's considered an error.
        Confess("Could not open directory $dirName.");
    }
    # Return the result.
    return @retVal;
}

=head3 SetLevel

C<< Tracer::SetLevel($newLevel); >>

Modify the trace level. A higher trace level will cause more messages to appear.

=over 4

=item newLevel

Proposed new trace level.

=back

=cut

sub SetLevel {
    $TraceLevel = $_[0];
}

=head3 Now

C<< my $string = Tracer::Now(); >>

Return a displayable time stamp containing the local time.

=cut

sub Now {
    my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
    my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
                 _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
    return $retVal;
}

# Pad a number to 2 digits.
sub _p2 {
    my ($value) = @_;
    $value = "0$value" if ($value < 10);
    return $value;
}

=head3 LogErrors

C<< Tracer::LogErrors($fileName); >>

Route the standard error output to a log file.

=over 4

=item fileName

Name of the file to receive the error output.

=back

=cut

sub LogErrors {
    # Get the file name.
    my ($fileName) = @_;
    # Open the file as the standard error output.
    open STDERR, '>', $fileName;
}

=head3 ReadOptions

C<< my %options = Tracer::ReadOptions($fileName); >>

Read a set of options from a file. Each option is encoded in a line of text that has the
format

I<optionName>C<=>I<optionValue>C<; >I<comment>

The option name must consist entirely of letters, digits, and the punctuation characters
C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
character is a semi-colon will be ignored. The return hash will map each option name to
the corresponding option value.

=over 4

=item fileName

Name of the file containing the option data.

=item RETURN

Returns a hash mapping the option names specified in the file to their corresponding option
value.

=back

=cut

sub ReadOptions {
    # Get the parameters.
    my ($fileName) = @_;
    # Open the file.
    (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
    # Count the number of records read.
    my ($records, $comments) = 0;
    # Create the return hash.
    my %retVal = ();
    # Loop through the file, accumulating key-value pairs.
    while (my $line = <CONFIGFILE>) {
        # Denote we've read a line.
        $records++;
        # Determine the line type.
        if ($line =~ /^\s*[\n\r]/) {
            # A blank line is a comment.
            $comments++;
        } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
            # Here we have an option assignment.
            retVal{$1} = $2;
        } elsif ($line =~ /^\s*;/) {
            # Here we have a text comment.
            $comments++;
        } else {
            # Here we have an invalid line.
            Trace("Invalid option statement in record $records.") if T(0);
        }
    }
    # Return the hash created.
    return %retVal;
}

=head3 GetOptions

C<< Tracer::GetOptions(\%defaults, \%options); >>

Merge a specified set of options into a table of defaults. This method takes two hash references
as input and uses the data from the second to update the first. If the second does not exist,
there will be no effect. An error will be thrown if one of the entries in the second hash does not
exist in the first.

Consider the following example.

C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>

In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as

C<< {databaseType => 'Oracle'} >>

an error will occur because the B<databaseType> option does not exist.

=over 4

=item defaults

Table of default option values.

=item options

Table of overrides, if any.

=item RETURN

Returns a reference to the default table passed in as the first parameter.

=back

=cut

sub GetOptions {
    # Get the parameters.
    my ($defaults, $options) = @_;
    # Check for overrides.
    if ($options) {
        # Loop through the overrides.
        while (my ($option, $setting) = each %{$options}) {
            # Insure this override exists.
            if (!exists $defaults->{$option}) {
                croak "Unrecognized option $option encountered.";
            } else {
                # Apply the override.
                $defaults->{$option} = $setting;
            }
        }
    }
    # Return the merged table.
    return $defaults;
}

=head3 MergeOptions

C<< Tracer::MergeOptions(\%table, \%defaults); >>

Merge default values into a hash table. This method looks at the key-value pairs in the
second (default) hash, and if a matching key is not found in the first hash, the default
pair is copied in. The process is similar to L</GetOptions>, but there is no error-
checking and no return value.

=over 4

=item table

Hash table to be updated with the default values.

=item defaults

Default values to be merged into the first hash table if they are not already present.

=back

=cut

sub MergeOptions {
    # Get the parameters.
    my ($table, $defaults) = @_;
    # Loop through the defaults.
    while (my ($key, $value) = each %{$defaults}) {
        if (!exists $table->{$key}) {
            $table->{$key} = $value;
        }
    }
}

=head3 Trace

C<< Trace($message); >>

Write a trace message to the target location specified in L</TSetup>. If there has not been
any prior call to B<TSetup>.

=over 4

=item message

Message to write.

=back

=cut

sub Trace {
    # Get the parameters.
    my ($message) = @_;
    # Get the timestamp.
    my $timeStamp = Now();
    # Format the message. Note we strip off any line terminators at the end.
    my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);
    # Process according to the destination.
    if ($Destination eq "TEXT") {
        # Write the message to the standard output.
        print "$formatted\n";
    } elsif ($Destination eq "ERROR") {
        # Write the message to the error output.
        print STDERR "$formatted\n";
    } elsif ($Destination eq "QUEUE") {
        # Push the message into the queue.
        push @Queue, "$formatted";
    } elsif ($Destination eq "HTML") {
        # Convert the message to HTML and write it to the standard output.
        my $escapedMessage = CGI::escapeHTML($message);
        print "<p>$formatted</p>\n";
    } elsif ($Destination eq "WARN") {
       # Emit the message as a warning.
       warn $message;
    } elsif ($Destination =~ m/^>>/) {
        # Write the trace message to an output file.
        (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
        print TRACING "$formatted\n";
        close TRACING;
        # If the Tee flag is on, echo it to the standard output.
        if ($TeeFlag) {
            print "$formatted\n";
        }
    }
}

=head3 T

C<< my $switch = T($category, $traceLevel); >>

    or

C<< my $switch = T($traceLevel); >>

Return TRUE if the trace level is at or above a specified value and the specified category
is active, else FALSE. If no category is specified, the caller's package name is used.

=over 4

=item category

Category to which the message belongs. If not specified, the caller's package name is
used.

=item traceLevel

Relevant tracing level.

=item RETURN

TRUE if a message at the specified trace level would appear in the trace, else FALSE.

=back

=cut

sub T {
    # Declare the return variable.
    my $retVal = 0;
    # Only proceed if tracing is turned on.
    if ($Destination ne "NONE") {
        # Get the parameters.
        my ($category, $traceLevel) = @_;
        if (!defined $traceLevel) {
            # Here we have no category, so we need to get the calling package.
            # The calling package is normally the first parameter. If it is
            # omitted, the first parameter will be the tracelevel. So, the
            # first thing we do is shift the so-called category into the
            # $traceLevel variable where it belongs.
            $traceLevel = $category;
            my ($package, $fileName, $line) = caller;
            # If there is no calling package, we default to "main".
            if (!$package) {
                $category = "main";
            } else {
                $category = $package;
            }
        }
        # Save the category name.
        $LastCategory = $category;
        # Convert it to lower case before we hash it.
        $category = lc $category;
        # Use the category and tracelevel to compute the result.
        if (ref $traceLevel) {
            Confess("Bad trace level.");
        } elsif (ref $TraceLevel) {
            Confess("Bad trace config.");
        }
        $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
    }
    # Return the computed result.
    return $retVal;
}

=head3 ParseCommand

C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>

Parse a command line consisting of a list of parameters. The initial parameters may be option
specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
off and merged into a table of default options. The remainder of the command line is
returned as a list of positional arguments. For example, consider the following invocation.

C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>

In this case, the list @words will be treated as a command line. There are two options available,
B<errors> and B<logFile>. If @words has the following format

C<< -logFile=error.log apple orange rutabaga >>

then at the end of the invocation, C<$options> will be

C<< { errors => 0, logFile => 'error.log' } >>

and C<@arguments> will contain

C<< apple orange rutabaga >>

The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
support for quote characters.

=over 4

=item optionTable

Table of default options.

=item inputList

List of words on the command line.

=item RETURN

Returns a reference to the option table and a list of the positional arguments.

=back

=cut

sub ParseCommand {
    # Get the parameters.
    my ($optionTable, @inputList) = @_;
    # Process any options in the input list.
    my %overrides = ();
    while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
        # Get the current option.
        my $arg = shift @inputList;
        # Pull out the option name.
        $arg =~ /^-([^=]*)/g;
        my $name = $1;
        # Check for an option value.
        if ($arg =~ /\G=(.*)$/g) {
            # Here we have a value for the option.
            $overrides{$name} = UnEscape($1);
        } else {
            # Here there is no value, so we use 1.
            $overrides{$name} = 1;
        }
    }
    # Merge the options into the defaults.
    GetOptions($optionTable, \%overrides);
    # Translate the remaining parameters.
    my @retVal = ();
    for my $inputParm (@inputList) {
        push @retVal, UnEscape($inputParm);
    }
    # Return the results.
    return ($optionTable, @retVal);
}

=head3 Escape

C<< my $codedString = Tracer::Escape($realString); >>

Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
result is to reverse the effect of L</UnEscape>.

=over 4

=item realString

String to escape.

=item RETURN

Escaped equivalent of the real string.

=back

=cut

sub Escape {
    # Get the parameter.
    my ($realString) = @_;
    # Initialize the return variable.
    my $retVal = "";
    # Loop through the parameter string, looking for sequences to escape.
    while (length $realString > 0) {
        # Look for the first sequence to escape.
        if ($realString =~ /^(.*?)([\n\t\r\\])/) {
            # Here we found it. The text preceding the sequence is in $1. The sequence
            # itself is in $2. First, move the clear text to the return variable.
            $retVal .= $1;
            # Strip the processed section off the real string.
            $realString = substr $realString, (length $2) + (length $1);
            # Get the matched character.
            my $char = $2;
            # If we have a CR, we are done.
            if ($char ne "\r") {
                # It's not a CR, so encode the escape sequence.
                $char =~ tr/\t\n/tn/;
                $retVal .= "\\" . $char;
            }
        } else {
            # Here there are no more escape sequences. The rest of the string is
            # transferred unmodified.
            $retVal .= $realString;
            $realString = "";
        }
    }
    # Return the result.
    return $retVal;
}

=head3 UnEscape

C<< my $realString = Tracer::UnEscape($codedString); >>

Replace escape sequences with their actual equivalents. C<\t> will be replaced by
a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
be deleted.

=over 4

=item codedString

String to un-escape.

=item RETURN

Returns a copy of the original string with the escape sequences converted to their actual
values.

=back

=cut

sub UnEscape {
    # Get the parameter.
    my ($codedString) = @_;
    # Initialize the return variable.
    my $retVal = "";
    # Only proceed if the incoming string is nonempty.
    if (defined $codedString) {
        # Loop through the parameter string, looking for escape sequences. We can't do
        # translating because it causes problems with the escaped slash. ("\\t" becomes
        # "\<tab>" no matter what we do.)
        while (length $codedString > 0) {
            # Look for the first escape sequence.
            if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
                # Here we found it. The text preceding the sequence is in $1. The sequence
                # itself is in $2. First, move the clear text to the return variable.
                $retVal .= $1;
                $codedString = substr $codedString, (2 + length $1);
                # Get the escape value.
                my $char = $2;
                # If we have a "\r", we are done.
                if ($char ne 'r') {
                    # Here it's not an 'r', so we convert it.
                    $char =~ tr/\\tn/\\\t\n/;
                    $retVal .= $char;
                }
            } else {
                # Here there are no more escape sequences. The rest of the string is
                # transferred unmodified.
                $retVal .= $codedString;
                $codedString = "";
            }
        }
    }
    # Return the result.
    return $retVal;
}

=head3 ParseRecord

C<< my @fields = Tracer::ParseRecord($line); >>

Parse a tab-delimited data line. The data line is split into field values. Embedded tab
and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
These will automatically be converted.

=over 4

=item line

Line of data containing the tab-delimited fields.

=item RETURN

Returns a list of the fields found in the data line.

=back

=cut

sub ParseRecord {
    # Get the parameter.
    my ($line) = @_;
    # Remove the trailing new-line, if any.
    chomp $line;
    # Split the line read into pieces using the tab character.
    my @retVal = split /\t/, $line;
    # Trim and fix the escapes in each piece.
    for my $value (@retVal) {
        # Trim leading whitespace.
        $value =~ s/^\s+//;
        # Trim trailing whitespace.
        $value =~ s/\s+$//;
        # Delete the carriage returns.
        $value =~ s/\r//g;
        # Convert the escapes into their real values.
        $value =~ s/\\t/"\t"/ge;
        $value =~ s/\\n/"\n"/ge;
    }
    # Return the result.
    return @retVal;
}

=head3 Merge

C<< my @mergedList = Tracer::Merge(@inputList); >>

Sort a list of strings and remove duplicates.

=over 4

=item inputList

List of scalars to sort and merge.

=item RETURN

Returns a list containing the same elements sorted in ascending order with duplicates
removed.

=back

=cut

sub Merge {
    # Get the input list in sort order.
    my @inputList = sort @_;
    # Only proceed if the list has at least two elements.
    if (@inputList > 1) {
        # Now we want to move through the list splicing out duplicates.
        my $i = 0;
        while ($i < @inputList) {
            # Get the current entry.
            my $thisEntry = $inputList[$i];
            # Find out how many elements duplicate the current entry.
            my $j = $i + 1;
            my $dup1 = $i + 1;
            while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
            # If the number is nonzero, splice out the duplicates found.
            if ($j > $dup1) {
                splice @inputList, $dup1, $j - $dup1;
            }
            # Now the element at position $dup1 is different from the element before it
            # at position $i. We push $i forward one position and start again.
            $i++;
        }
    }
    # Return the merged list.
    return @inputList;
}

=head3 GetFile

C<< my @fileContents = Tracer::GetFile($fileName); >>

    or

C<< my $fileContents = Tracer::GetFile($fileName); >>

Return the entire contents of a file. In list context, line-ends are removed and
each line is a list element. In scalar context, line-ends are replaced by C<\n>.

=over 4

=item fileName

Name of the file to read.

=item RETURN

In a list context, returns the entire file as a list with the line terminators removed.
In a scalar context, returns the entire file as a string. If an error occurs opening
the file, an empty list will be returned.

=back

=cut

sub GetFile {
    # Get the parameters.
    my ($fileName) = @_;
    # Declare the return variable.
    my @retVal = ();
    # Open the file for input.
    my $ok = open INPUTFILE, "<$fileName";
    if (!$ok) {
        # If we had an error, trace it. We will automatically return a null value.
        Trace("Could not open \"$fileName\" for input: $!") if T(0);
    } else {
        # Read the whole file into the return variable, stripping off any terminator
        # characters.
        my $lineCount = 0;
        while (my $line = <INPUTFILE>) {
            $lineCount++;
            $line = Strip($line);
            push @retVal, $line;
        }
        # Close it.
        close INPUTFILE;
        my $actualLines = @retVal;
    }
    # Return the file's contents in the desired format.
    if (wantarray) {
        return @retVal;
    } else {
        return join "\n", @retVal;
    }
}

=head3 QTrace

C<< my $data = QTrace($format); >>

Return the queued trace data in the specified format.

=over 4

=item format

C<html> to format the data as an HTML list, C<text> to format it as straight text.

=back

=cut

sub QTrace {
    # Get the parameter.
    my ($format) = @_;
    # Create the return variable.
    my $retVal = "";
    # Only proceed if there is an actual queue.
    if (@Queue) {
        # Process according to the format.
        if ($format =~ m/^HTML$/i) {
            # Convert the queue into an HTML list.
            $retVal = "<ul>\n";
            for my $line (@Queue) {
                my $escapedLine = CGI::escapeHTML($line);
                $retVal .= "<li>$escapedLine</li>\n";
            }
            $retVal .= "</ul>\n";
        } elsif ($format =~ m/^TEXT$/i) {
            # Convert the queue into a list of text lines.
            $retVal = join("\n", @Queue) . "\n";
        }
        # Clear the queue.
        @Queue = ();
    }
    # Return the formatted list.
    return $retVal;
}

=head3 Confess

C<< Confess($message); >>

Trace the call stack and abort the program with the specified message. When used with
the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
So, for example

C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>

Will abort the program with a stack trace if the value of C<$recNum> is negative.

=over 4

=item message

Message to include in the trace.

=back

=cut

sub Confess {
    # Get the parameters.
    my ($message) = @_;
    # Trace the call stack.
    Cluck($message);
    # Abort the program.
    croak(">>> $message");
}

=head3 Assert

C<< Assert($condition1, $condition2, ... $conditionN); >>

Return TRUE if all the conditions are true. This method can be used in conjunction with
the OR operator and the L</Confess> method as a debugging assert.
So, for example

C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>

Will abort the program with a stack trace if the value of C<$recNum> is negative.

=cut
sub Assert {
    my $retVal = 1;
    LOOP: for my $condition (@_) {
        if (! $condition) {
            $retVal = 0;
            last LOOP;
        }
    }
    return $retVal;
}

=head3 Cluck

C<< Cluck($message); >>

Trace the call stack. Note that for best results, you should qualify the call with a
trace condition. For example,

C<< Cluck("Starting record parse.") if T(3); >>

will only trace the stack if the trace level for the package is 3 or more.

=over 4

=item message

Message to include in the trace.

=back

=cut

sub Cluck {
    # Get the parameters.
    my ($message) = @_;
    # Trace what's happening.
    Trace("Stack trace for event: $message");
    my $confession = longmess($message);
    # Convert the confession to a series of trace messages. Note we skip any
    # messages relating to calls into Tracer.
    for my $line (split /\s*\n/, $confession) {
        Trace($line) if ($line !~ /Tracer\.pm/);
    }
}

=head3 Min

C<< my $min = Min($value1, $value2, ... $valueN); >>

Return the minimum argument. The arguments are treated as numbers.

=over 4

=item $value1, $value2, ... $valueN

List of numbers to compare.

=item RETURN

Returns the lowest number in the list.

=back

=cut

sub Min {
    # Get the parameters. Note that we prime the return value with the first parameter.
    my ($retVal, @values) = @_;
    # Loop through the remaining parameters, looking for the lowest.
    for my $value (@values) {
        if ($value < $retVal) {
            $retVal = $value;
        }
    }
    # Return the minimum found.
    return $retVal;
}

=head3 Max

C<< my $max = Max($value1, $value2, ... $valueN); >>

Return the maximum argument. The arguments are treated as numbers.

=over 4

=item $value1, $value2, ... $valueN

List of numbers to compare.

=item RETURN

Returns the highest number in the list.

=back

=cut

sub Max {
    # Get the parameters. Note that we prime the return value with the first parameter.
    my ($retVal, @values) = @_;
    # Loop through the remaining parameters, looking for the highest.
    for my $value (@values) {
        if ($value > $retVal) {
            $retVal = $value;
        }
    }
    # Return the maximum found.
    return $retVal;
}

=head3 AddToListMap

C<< Tracer::AddToListMap(\%hash, $key, $value); >>

Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
is created for the key. Otherwise, the new value is pushed onto the list.

=over 4

=item hash

Reference to the target hash.

=item key

Key for which the value is to be added.

=item value

Value to add to the key's value list.

=back

=cut

sub AddToListMap {
    # Get the parameters.
    my ($hash, $key, $value) = @_;
    # Process according to whether or not the key already has a value.
    if (! exists $hash->{$key}) {
        $hash->{$key} = [$value];
    } else {
        push @{$hash->{$key}}, $value;
    }
}

=head3 DebugMode

C<< if (Tracer::DebugMode) { ...code... } >>

Return TRUE if debug mode has been turned on, else output an error
page and return FALSE.

Certain CGI scripts are too dangerous to exist in the production
environment. This method provides a simple way to prevent them
from working unless they are explicitly turned on by creating a password
cookie via the B<SetPassword> script.  If debugging mode
is not turned on, an error web page will be output directing the
user to enter in the correct password.

=cut

sub DebugMode {
    # Declare the return variable.
    my $retVal = 0;
    # Check the debug configuration.
    my $password = CGI::cookie("DebugMode");
    my $encrypted = Digest::MD5::md5_hex($password);
    if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
        $retVal = 1;
    } else {
        # Here debug mode is off, so we generate an error page.
        my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");
        print $pageString;
    }
    # Return the determination indicator.
    return $retVal;
}

=head3 Strip

C<< my $string = Tracer::Strip($line); >>

Strip all line terminators off a string. This is necessary when dealing with files
that may have been transferred back and forth several times among different
operating environments.

=over 4

=item line

Line of text to be stripped.

=item RETURN

The same line of text with all the line-ending characters chopped from the end.

=back

=cut

sub Strip {
    # Get a copy of the parameter string.
    my ($string) = @_;
    my $retVal = (defined $string ? $string : "");
    # Strip the line terminator characters.
    $retVal =~ s/(\r|\n)+$//g;
    # Return the result.
    return $retVal;
}

=head3 Pad

C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>

Pad a string to a specified length. The pad character will be a
space, and the padding will be on the right side unless specified
in the third parameter.

=over 4

=item string

String to be padded.

=item len

Desired length of the padded string.

=item left (optional)

TRUE if the string is to be left-padded; otherwise it will be padded on the right.

=item padChar (optional)

Character to use for padding. The default is a space.

=item RETURN

Returns a copy of the original string with the pad character added to the
specified end so that it achieves the desired length.

=back

=cut

sub Pad {
    # Get the parameters.
    my ($string, $len, $left, $padChar) = @_;
    # Compute the padding character.
    if (! defined $padChar) {
        $padChar = " ";
    }
    # Compute the number of spaces needed.
    my $needed = $len - length $string;
    # Copy the string into the return variable.
    my $retVal = $string;
    # Only proceed if padding is needed.
    if ($needed > 0) {
        # Create the pad string.
        my $pad = $padChar x $needed;
        # Affix it to the return value.
        if ($left) {
            $retVal = $pad . $retVal;
        } else {
            $retVal .= $pad;
        }
    }
    # Return the result.
    return $retVal;
}

=head3 EOF

This is a constant that is lexically greater than any useful string.

=cut

sub EOF {
    return "\xFF\xFF\xFF\xFF\xFF";
}

=head3 TICK

C<< my @results = TICK($commandString); >>

Perform a back-tick operation on a command. If this is a Windows environment, any leading
dot-slash (C<./> will be removed. So, for example, if you were doing

    `./protein.cgi`

from inside a CGI script, it would work fine in Unix, but would issue an error message
in Windows complaining that C<'.'> is not a valid command. If instead you code

    TICK("./protein.cgi")

it will work correctly in both environments.

=over 4

=item commandString

The command string to pass to the system.

=item RETURN

Returns the standard output from the specified command, as a list.

=back

=cut
#: Return Type @;
sub TICK {
    # Get the parameters.
    my ($commandString) = @_;
    # Chop off the dot-slash if this is Windows.
    if ($FIG_Config::win_mode) {
        $commandString =~ s!^\./!!;
    }
    # Activate the command and return the result.
    return `$commandString`;
}

=head3 ScriptSetup

C<< my ($query, $varHash) = ScriptSetup(); >>

Perform standard tracing and debugging setup for scripts. The value returned is
the CGI object followed by a pre-built variable hash.

The C<Trace> query parameter is used to determine whether or not tracing is active and
which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
the C<CGI> trace module will trace parameter and environment information. Parameters are
traced at level 3 and environment variables at level 4. At the end of the script, the
client should call L</ScriptFinish> to output the web page.

=cut

sub ScriptSetup {
    # Get the CGI query object.
    my $query = CGI->new();
    # Check for tracing. Set it up if the user asked for it.
    if ($query->param('Trace')) {
        # Set up tracing to be queued for display at the bottom of the web page.
        TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
        # Trace the parameter and environment data.
        if (T(CGI => 3)) {
            # Here we want to trace the parameter data.
            my @names = $query->param;
            for my $parmName (sort @names) {
                # Note we skip "Trace", which is for our use only.
                if ($parmName ne 'Trace') {
                    my @values = $query->param($parmName);
                    Trace("CGI: $parmName = " . join(", ", @values));
                }
            }
        }
        if (T(CGI => 4)) {
            # Here we want the environment data too.
            for my $envName (sort keys %ENV) {
                Trace("ENV: $envName = $ENV{$envName}");
            }
        }
    } else {
        # Here tracing is to be turned off. All we allow is errors traced into the
        # error log.
        TSetup("0", "WARN");
    }
    # Create the variable hash.
    my $varHash = { DebugData => '' };
    # If we're in DEBUG mode, set up the debug mode data for forms.
    if (Tracer::DebugMode) {
        $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
    }
    # Return the query object and variable hash.
    return ($query, $varHash);
}

=head3 ScriptFinish

C<< ScriptFinish($webData, $varHash); >>

Output a web page at the end of a script. Either the string to be output or the
name of a template file can be specified. If the second parameter is omitted,
it is assumed we have a string to be output; otherwise, it is assumed we have the
name of a template file. The template should have the variable C<DebugData>
specified in any form that invokes a standard script. If debugging mode is turned
on, a form field will be put in that allows the user to enter tracing data.
Trace messages will be placed immediately before the terminal C<BODY> tag in
the output, formatted as a list.

A typical standard script would loook like the following.

    BEGIN {
        # Print the HTML header.
        print "CONTENT-TYPE: text/html\n\n";
    }
    use Tracer;
    use CGI;
    use FIG;
    # ... more uses ...
    
    my ($query, $varHash) = ScriptSetup();
    eval {
        # ... get data from $query, put it in $varHash ...
    };
    if ($@) {
        Trace("Script Error: $@") if T(0);
    }
    ScriptFinish("Html/MyTemplate.html", $varHash);

The idea here is that even if the script fails, you'll see trace messages and
useful output.

=over 4

=item webData

A string containing either the full web page to be written to the output or the
name of a template file from which the page is to be constructed. If the name
of a template file is specified, then the second parameter must be present;
otherwise, it must be absent.

=item varHash (optional)

If specified, then a reference to a hash mapping variable names for a template
to their values. The template file will be read into memory, and variable markers
will be replaced by data in this hash reference.

=back

=cut

sub ScriptFinish {
    # Get the parameters.
    my ($webData, $varHash) = @_;
    # Check for a template file situation.
    my $outputString;
    if (defined $varHash) {
        # Here we have a template file. We need to apply the variables to the template.
        $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
    } else {
        # Here the user gave us a raw string.
        $outputString = $webData;
    }
    # Check for trace messages.
    if ($Destination eq "QUEUE") {
        # We have trace messages, so we want to put them at the end of the body. This
        # is either at the end of the whole string or at the beginning of the BODY
        # end-tag.
        my $pos = length $outputString;
        if ($outputString =~ m#</body>#gi) {
            $pos = (pos $outputString) - 7;
        }
        substr $outputString, $pos, 0, QTrace('Html');
    }
    # Write the output string.
    print $outputString;
}

=head3 Insure

C<< Insure($dirName); >>

Insure a directory is present.

=over 4

=item dirName

Name of the directory to check. If it does not exist, it will be created.

=back

=cut

sub Insure {
    my ($dirName) = @_;
    if (! -d $dirName) {
        Trace("Creating $dirName directory.") if T(2);
        eval { mkpath $dirName; };
        if ($@) {
            Confess("Error creating $dirName: $@");
        }
    }
}

=head3 ChDir

C<< ChDir($dirName); >>

Change to the specified directory.

=over 4

=item dirName

Name of the directory to which we want to change.

=back

=cut

sub ChDir {
    my ($dirName) = @_;
    if (! -d $dirName) {
        Confess("Cannot change to directory $dirName: no such directory.");
    } else {
        Trace("Changing to directory $dirName.") if T(4);
        my $okFlag = chdir $dirName;
        if (! $okFlag) {
            Confess("Error switching to directory $dirName.");
        }
    }
}

=head3 SetPermissions

C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>

Set the permissions for a directory and all the files and folders inside it.
In addition, the group ownership will be changed to the specified value.

This method is more vulnerable than most to permission and compatability
problems, so it does internal error recovery.

=over 4

=item dirName

Name of the directory to process.

=item group

Name of the group to be assigned.

=item mask

Permission mask. Bits that are C<1> in this mask will be ORed into the
permission bits of any file or directory that does not already have them
set to 1.

=item otherMasks

Map of search patterns to permission masks. If a directory name matches
one of the patterns, that directory and all its members and subdirectories
will be assigned the new pattern. For example, the following would
assign 01664 to most files, but would use 01777 for directories named C<tmp>.

    Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);

The list is ordered, so the following would use 0777 for C<tmp1> and
0666 for C<tmp>, C<tmp2>, or C<tmp3>.

    Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
                                                   '^tmp' => 0666);

Note that the pattern matches are all case-insensitive, and only directory
names are matched, not file names.

=back

=cut

sub SetPermissions {
    # Get the parameters.
    my ($dirName, $group, $mask, @otherMasks) = @_;
    # Set up for error recovery.
    eval {
        # Switch to the specified directory.
        ChDir($dirName);
        # Get the group ID.
        my $gid = getgrnam($group);
        # Get the mask for tracing.
        my $traceMask = sprintf("%04o", $mask) . "($mask)";
        Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
        my $fixCount = 0;
        my $lookCount = 0;
        # @dirs will be a stack of directories to be processed.
        my @dirs = (getcwd());
        while (scalar(@dirs) > 0) {
            # Get the current directory.
            my $dir = pop @dirs;
            # Check for a match to one of the specified directory names. To do
            # that, we need to pull the individual part of the name off of the
            # whole path.
            my $simpleName = $dir;
            if ($dir =~ m!/(.+)$!) {
                $simpleName = $1;
            }
            # Search for a match.
            my $match = 0;
            my $i;
            for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
                my $pattern = $otherMasks[$i];
                if ($simpleName =~ /$pattern/i) {
                    $match = 1;
                }
            }
            # Check for a match.
            if ($match && $otherMasks[$i+1] != $mask) {
                # This directory matches one of the incoming patterns, and it's
                # a different mask, so we process it recursively with that mask.
                SetPermissions($dir, $group, $otherMasks[$i+1], @otherMasks);
            } else {
                # Here we can process normally. Get all of the non-hidden members.
                my @submems = OpenDir($dir, 1);
                for my $submem (@submems) {
                    # Get the full name.
                    my $thisMem = "$dir/$submem";
                    Trace("Checking member $thisMem.") if T(4);
                    $lookCount++;
                    if ($lookCount % 1000 == 0) {
                        Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
                    }
                    # Fix the group.
                    chown -1, $gid, $thisMem;
                    # Insure this member is not a symlink.
                    if (! -l $thisMem) {
                        # Get its info.
                        my $fileInfo = stat $thisMem;
                        # Only proceed if we got the info. Otherwise, it's a hard link
                        # and we want to skip it anyway.
                        if ($fileInfo) {
                            my $fileMode = $fileInfo->mode;
                            if (($fileMode & $mask) == 0) {
                                # Fix this member.
                                $fileMode |= $mask;
                                chmod $fileMode, $thisMem;
                                $fixCount++;
                            }
                            # If it's a subdirectory, stack it.
                            if (-d $thisMem) {
                                push @dirs, $thisMem;
                            }
                        }
                    }
                }
            }
        }
        Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
    };
    # Check for an error.
    if ($@) {
        Confess("SetPermissions error: $@");
    }
}

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