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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.94, Tue Mar 11 21:04:56 2008 UTC
# Line 284  Line 284 
284    
285  # Declare the configuration variables.  # Declare the configuration variables.
286    
287  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
288  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
289                              # standard output                              # standard output
290  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
# Line 296  Line 296 
296  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
297  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
298    
299  =head2 Public Methods  =head2 Tracing Methods
300    
301    =head3 Setups
302    
303        my $count = Tracer::Setups();
304    
305    Return the number of times L</TSetup> has been called.
306    
307    This method allows for the creation of conditional tracing setups where, for example, we
308    may want to set up tracing if nobody else has done it before us.
309    
310    =cut
311    
312    sub Setups {
313        return $SetupCount;
314    }
315    
316  =head3 TSetup  =head3 TSetup
317    
318  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
319    
320  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
321  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 372  Line 387 
387      $SetupCount++;      $SetupCount++;
388  }  }
389    
390  =head3 StandardSetup  =head3 SetLevel
   
 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  
391    
392      ["Sprout", "SproutLoad", "ERDB"]      Tracer::SetLevel($newLevel);
393    
394  This would cause trace messages in the specified three packages to appear in  Modify the trace level. A higher trace level will cause more messages to appear.
 the output. There are two 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.  
395    
396  =over 4  =over 4
397    
398  =item SQL  =item newLevel
   
 Traces SQL commands and activity.  
   
 =item Tracer  
399    
400  Traces error messages and call stacks.  Proposed new trace level.
401    
402  =back  =back
403    
404  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  =cut
 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  
405    
406  Standard tracing is output to the standard output and echoed to the file  sub SetLevel {
407  C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the      $TraceLevel = $_[0];
408  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  
409    
410  The default trace level is 2. To get all messages, specify a trace level of 4.  =head3 ParseTraceDate
 For a genome-by-genome update, use 3.  
411    
412      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl      my $time = Tracer::ParseTraceDate($dateString);
413    
414  would send the trace output to C<traceBruce.log> in the temporary directory.  Convert a date from the trace file into a PERL timestamp.
415    
416  The I<options> parameter is a reference to a hash containing the command-line  =over 4
 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.  
417    
418  You can specify a different default trace level by setting C<$options->{trace}>  =item dateString
 prior to calling this method.  
419    
420  An example at this point would help. Consider, for example, the command-line utility  The date string from the trace file. The format of the string is determined by the
421  C<TransactFeatures>. It accepts a list of positional parameters plus the options  L</Now> method.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
422    
423      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =item RETURN
                         { 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);  
424    
425    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
426    the time string is invalid.
427    
428  The call to C<ParseCommand> specifies the default values for the options and  =back
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
429    
430  The following is a sample command line for C<TransactFeatures>.  =cut
431    
432      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub ParseTraceDate {
433        # Get the parameters.
434        my ($dateString) = @_;
435        # Declare the return variable.
436        my $retVal;
437        # Parse the date.
438        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
439            # Create a time object. Note we need to convert the day, month,
440            # and year to a different base. Years count from 1900, and
441            # the internal month value is relocated to January = 0.
442            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
443        }
444        # Return the result.
445        return $retVal;
446    }
447    
448  Single and double hyphens are equivalent. So, you could also code the  =head3 LogErrors
 above command as  
449    
450      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl      Tracer::LogErrors($fileName);
451    
452  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  Route the standard error output to a log file.
 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<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
453    
454      { trace => 2, sql => 0, safe => 0,  =over 4
       noAlias => 1, start => ' ', tblFiles => 0 }  
455    
456  Use of C<StandardSetup> in this way provides a simple way of performing  =item fileName
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
457    
458  If the C<background> option is specified on the command line, then the  Name of the file to receive the error output.
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
459    
460      -user=Bruce -background  =back
461    
462  then the trace output would go to C<traceBruce.log>, the standard output to  =cut
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
463    
464  The user name is also used as the tracing key for L</Emergency Tracing>.  sub LogErrors {
465  Specifying a value of C<E> for the trace level causes emergency tracing to      # Get the file name.
466  be used instead of custom tracing. If the user name is not specified,      my ($fileName) = @_;
467  the tracing key is taken from the C<Tracing> environment variable. If there      # Open the file as the standard error output.
468  is no value for that variable, the tracing key will be computed from the PID.      open STDERR, '>', $fileName;
469    }
470    
471  Finally, if the special option C<-help> is specified, the option  =head3 Trace
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
472    
473      TransactFeatures -help      Trace($message);
474    
475  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
476    any prior call to B<TSetup>.
477    
478      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =over 4
         -trace    tracing level (default E)  
         -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  
479    
480  The caller has the option of modifying the tracing scheme by placing a value  =item message
 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,  
481    
482      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
483    
484  would set the default trace level to 0 instead of E, while  =back
485    
486      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
487    
488  would set the default to 2, but trace only to the log file, not to the  sub Trace {
489  standard output.      # Get the parameters.
490        my ($message) = @_;
491        # Get the timestamp.
492        my $timeStamp = Now();
493        # Format the message. Note we strip off any line terminators at the end.
494        my $prefix = "[$timeStamp] <$LastCategory>: ";
495        my $formatted = $prefix . Strip($message);
496        # Process according to the destination.
497        if ($Destination eq "TEXT") {
498            # Write the message to the standard output.
499            print "$formatted\n";
500        } elsif ($Destination eq "ERROR") {
501            # Write the message to the error output.
502            print STDERR "$formatted\n";
503        } elsif ($Destination eq "QUEUE") {
504            # Push the message into the queue.
505            push @Queue, "$formatted";
506        } elsif ($Destination eq "HTML") {
507            # Convert the message to HTML and write it to the standard output.
508            my $escapedMessage = CGI::escapeHTML($message);
509            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
510        } elsif ($Destination eq "WARN") {
511           # Emit the message as a warning.
512           warn $message;
513        } elsif ($Destination =~ m/^>>/) {
514            # Write the trace message to an output file.
515            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
516            print TRACING "$formatted\n";
517            close TRACING;
518            # If the Tee flag is on, echo it to the standard output.
519            if ($TeeFlag) {
520                print "$formatted\n";
521            }
522        }
523    }
524    
525  The parameters to this method are as follows.  =head3 T
526    
527  =over 4      my $switch = T($category, $traceLevel);
528    
529  =item categories      or
530    
531  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
532    
533  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
534    is active, else FALSE. If no category is specified, the caller's package name is used.
535    
536  Reference to a hash containing the legal options for the current command mapped  =over 4
 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).  
537    
538  =item parmHelp  =item category
539    
540  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
541  if the user specifies the C<-h> option.  used.
542    
543  =item argv  =item traceLevel
544    
545  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
546    
547  =item RETURN  =item RETURN
548    
549  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 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.  
550    
551  =back  =back
552    
553  =cut  =cut
554    
555  sub StandardSetup {  sub T {
556        # Declare the return variable.
557        my $retVal = 0;
558        # Only proceed if tracing is turned on.
559        if ($Destination ne "NONE") {
560            # Get the parameters.
561            my ($category, $traceLevel) = @_;
562            if (!defined $traceLevel) {
563                # Here we have no category, so we need to get the calling package.
564                # The calling package is normally the first parameter. If it is
565                # omitted, the first parameter will be the tracelevel. So, the
566                # first thing we do is shift the so-called category into the
567                # $traceLevel variable where it belongs.
568                $traceLevel = $category;
569                my ($package, $fileName, $line) = caller;
570                # If there is no calling package, we default to "main".
571                if (!$package) {
572                    $category = "main";
573                } else {
574                    my @cats = split /::/, $package;
575                    $category = $cats[$#cats];
576                }
577            }
578            # Save the category name.
579            $LastCategory = $category;
580            # Convert it to lower case before we hash it.
581            $category = lc $category;
582            # Use the category and tracelevel to compute the result.
583            if (ref $traceLevel) {
584                Confess("Bad trace level.");
585            } elsif (ref $TraceLevel) {
586                Confess("Bad trace config.");
587            }
588            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
589        }
590        # Return the computed result.
591        return $retVal;
592    }
593    
594    =head3 QTrace
595    
596        my $data = QTrace($format);
597    
598    Return the queued trace data in the specified format.
599    
600    =over 4
601    
602    =item format
603    
604    C<html> to format the data as an HTML list, C<text> to format it as straight text.
605    
606    =back
607    
608    =cut
609    
610    sub QTrace {
611        # Get the parameter.
612        my ($format) = @_;
613        # Create the return variable.
614        my $retVal = "";
615        # Only proceed if there is an actual queue.
616        if (@Queue) {
617            # Process according to the format.
618            if ($format =~ m/^HTML$/i) {
619                # Convert the queue into an HTML list.
620                $retVal = "<ul>\n";
621                for my $line (@Queue) {
622                    my $escapedLine = CGI::escapeHTML($line);
623                    $retVal .= "<li>$escapedLine</li>\n";
624                }
625                $retVal .= "</ul>\n";
626            } elsif ($format =~ m/^TEXT$/i) {
627                # Convert the queue into a list of text lines.
628                $retVal = join("\n", @Queue) . "\n";
629            }
630            # Clear the queue.
631            @Queue = ();
632        }
633        # Return the formatted list.
634        return $retVal;
635    }
636    
637    =head3 Confess
638    
639        Confess($message);
640    
641    Trace the call stack and abort the program with the specified message. When used with
642    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
643    So, for example
644    
645        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
646    
647    Will abort the program with a stack trace if the value of C<$recNum> is negative.
648    
649    =over 4
650    
651    =item message
652    
653    Message to include in the trace.
654    
655    =back
656    
657    =cut
658    
659    sub Confess {
660        # Get the parameters.
661        my ($message) = @_;
662        if (! defined($FIG_Config::no_tool_hdr)) {
663            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
664            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
665            # Only proceed if the tool header file is actually present.
666            if (-f $toolHeaderFile) {
667                my @lines = GetFile($toolHeaderFile);
668                Trace("Tool header has " . scalar(@lines) . " lines.");
669            }
670        }
671        # Trace the call stack.
672        Cluck($message);
673        # Abort the program.
674        croak(">>> $message");
675    }
676    
677    =head3 Assert
678    
679        Assert($condition1, $condition2, ... $conditionN);
680    
681    Return TRUE if all the conditions are true. This method can be used in conjunction with
682    the OR operator and the L</Confess> method as a debugging assert.
683    So, for example
684    
685        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
686    
687    Will abort the program with a stack trace if the value of C<$recNum> is negative.
688    
689    =cut
690    sub Assert {
691        my $retVal = 1;
692        LOOP: for my $condition (@_) {
693            if (! $condition) {
694                $retVal = 0;
695                last LOOP;
696            }
697        }
698        return $retVal;
699    }
700    
701    =head3 Cluck
702    
703        Cluck($message);
704    
705    Trace the call stack. Note that for best results, you should qualify the call with a
706    trace condition. For example,
707    
708        Cluck("Starting record parse.") if T(3);
709    
710    will only trace the stack if the trace level for the package is 3 or more.
711    
712    =over 4
713    
714    =item message
715    
716    Message to include in the trace.
717    
718    =back
719    
720    =cut
721    
722    sub Cluck {
723        # Get the parameters.
724        my ($message) = @_;
725        # Trace what's happening.
726        Trace("Stack trace for event: $message");
727        my $confession = longmess($message);
728        # Convert the confession to a series of trace messages. Note we skip any
729        # messages relating to calls into Tracer.
730        for my $line (split /\s*\n/, $confession) {
731            Trace($line) if ($line !~ /Tracer\.pm/);
732        }
733    }
734    
735    =head3 ScriptSetup
736    
737        my ($cgi, $varHash) = ScriptSetup($noTrace);
738    
739    Perform standard tracing and debugging setup for scripts. The value returned is
740    the CGI object followed by a pre-built variable hash. At the end of the script,
741    the client should call L</ScriptFinish> to output the web page.
742    
743    This method calls L</ETracing> to configure tracing, which allows the tracing
744    to be configured via the emergency tracing form on the debugging control panel.
745    Tracing will then be turned on automatically for all programs that use the L</ETracing>
746    method, which includes every program that uses this method or L</StandardSetup>.
747    
748    =over 4
749    
750    =item noTrace (optional)
751    
752    If specified, tracing will be suppressed. This is useful if the script wants to set up
753    tracing manually.
754    
755    =item RETURN
756    
757    Returns a two-element list consisting of a CGI query object and a variable hash for
758    the output page.
759    
760    =back
761    
762    =cut
763    
764    sub ScriptSetup {
765        # Get the parameters.
766        my ($noTrace) = @_;
767        # Get the CGI query object.
768        my $cgi = CGI->new();
769        # Set up tracing if it's not suppressed.
770        ETracing($cgi) unless $noTrace;
771        # Create the variable hash.
772        my $varHash = { results => '' };
773        # Return the query object and variable hash.
774        return ($cgi, $varHash);
775    }
776    
777    =head3 ETracing
778    
779        ETracing($parameter);
780    
781    Set up emergency tracing. Emergency tracing is tracing that is turned
782    on automatically for any program that calls this method. The emergency
783    tracing parameters are stored in a a file identified by a tracing key.
784    If this method is called with a CGI object, then the tracing key is
785    taken from a cookie. If it is called with no parameters, then the tracing
786    key is taken from an environment variable. If it is called with a string,
787    the tracing key is that string.
788    
789    =over 4
790    
791    =item parameter
792    
793    A parameter from which the tracing key is computed. If it is a scalar,
794    that scalar is used as the tracing key. If it is a CGI object, the
795    tracing key is taken from the C<IP> cookie. If it is omitted, the
796    tracing key is taken from the C<TRACING> environment variable. If it
797    is a CGI object and emergency tracing is not on, the C<Trace> and
798    C<TF> parameters will be used to determine the type of tracing.
799    
800    =back
801    
802    =cut
803    
804    sub ETracing {
805        # Get the parameter.
806        my ($parameter) = @_;
807        # Check for CGI mode.
808        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
809        # Default to no tracing except errors.
810        my ($tracing, $dest) = ("0", "WARN");
811        # Check for emergency tracing.
812        my $tkey = EmergencyKey($parameter);
813        my $emergencyFile = EmergencyFileName($tkey);
814        if (-e $emergencyFile) {
815            # We have the file. Read in the data.
816            my @tracing = GetFile($emergencyFile);
817            # Pull off the time limit.
818            my $expire = shift @tracing;
819            # Convert it to seconds.
820            $expire *= 3600;
821            # Check the file data.
822            my $stat = stat($emergencyFile);
823            my ($now) = gettimeofday;
824            if ($now - $stat->mtime > $expire) {
825                # Delete the expired file.
826                unlink $emergencyFile;
827            } else {
828                # Emergency tracing is on. Pull off the destination and
829                # the trace level;
830                $dest = shift @tracing;
831                my $level = shift @tracing;
832                # Convert the destination to a real tracing destination.
833                # temp directory.
834                $dest = EmergencyTracingDest($tkey, $dest);
835                # Insure Tracer is specified.
836                my %moduleHash = map { $_ => 1 } @tracing;
837                $moduleHash{Tracer} = 1;
838                # Set the trace parameter.
839                $tracing = join(" ", $level, sort keys %moduleHash);
840            }
841        } elsif (defined $cgi) {
842            # There's no emergency tracing, but we have a CGI object, so check
843            # for tracing from the form parameters.
844            if ($cgi->param('Trace')) {
845                # Here the user has requested tracing via a form.
846                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
847                $tracing = $cgi->param('Trace') . " Tracer";
848            }
849        }
850        # Setup the tracing we've determined from all the stuff above.
851        TSetup($tracing, $dest);
852        # Check to see if we're a web script.
853        if (defined $cgi) {
854            # Yes we are. Trace the form and environment data.
855            TraceParms($cgi);
856            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
857            # emitted by the script in its raw form.
858            if (T(Raw => 3)) {
859                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
860            }
861        }
862    }
863    
864    =head3 EmergencyFileName
865    
866        my $fileName = Tracer::EmergencyFileName($tkey);
867    
868    Return the emergency tracing file name. This is the file that specifies
869    the tracing information.
870    
871    =over 4
872    
873    =item tkey
874    
875    Tracing key for the current program.
876    
877    =item RETURN
878    
879    Returns the name of the file to contain the emergency tracing information.
880    
881    =back
882    
883    =cut
884    
885    sub EmergencyFileName {
886      # Get the parameters.      # Get the parameters.
887      my ($categories, $options, $parmHelp, @argv) = @_;      my ($tkey) = @_;
888      # Get the default tracing key.      # Compute the emergency tracing file name.
889      my $tkey = EmergencyKey();      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Add the tracing options.  
     if (! exists $options->{trace}) {  
         $options->{trace} = ['2', "tracing level (E for emergency tracing)"];  
890      }      }
891      $options->{sql} = [0, "turn on SQL tracing"];  
892      $options->{help} = [0, "display command-line options"];  =head3 EmergencyFileTarget
893      $options->{user} = [$tkey, "tracing key"];  
894      $options->{background} = [0, "spool standard and error output"];      my $fileName = Tracer::EmergencyFileTarget($tkey);
895      # Create a parsing hash from the options hash. The parsing hash  
896      # contains the default values rather than the default value  Return the emergency tracing target file name. This is the file that receives
897      # and the description. While we're at it, we'll memorize the  the tracing output for file-based tracing.
898      # length of the longest option name.  
899      my $longestName = 0;  =over 4
900      my %parseOptions = ();  
901      for my $key (keys %{$options}) {  =item tkey
902          if (length $key > $longestName) {  
903              $longestName = length $key;  Tracing key for the current program.
904    
905    =item RETURN
906    
907    Returns the name of the file to contain the trace output.
908    
909    =back
910    
911    =cut
912    
913    sub EmergencyFileTarget {
914        # Get the parameters.
915        my ($tkey) = @_;
916        # Compute the emergency tracing file name.
917        return "$FIG_Config::temp/trace$tkey.log";
918          }          }
919          $parseOptions{$key} = $options->{$key}->[0];  
920    =head3 EmergencyTracingDest
921    
922        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
923    
924    This method converts an emergency tracing destination to a real
925    tracing destination. The main difference is that if the
926    destination is C<FILE> or C<APPEND>, we convert it to file
927    output. If the destination is C<DUAL>, we convert it to file
928    and standard output.
929    
930    =over 4
931    
932    =item tkey
933    
934    Tracing key for this environment.
935    
936    =item myDest
937    
938    Destination from the emergency tracing file.
939    
940    =item RETURN
941    
942    Returns a destination that can be passed into L</TSetup>.
943    
944    =back
945    
946    =cut
947    
948    sub EmergencyTracingDest {
949        # Get the parameters.
950        my ($tkey, $myDest) = @_;
951        # Declare the return variable.
952        my $retVal = $myDest;
953        # Process according to the destination value.
954        if ($myDest eq 'FILE') {
955            $retVal = ">" . EmergencyFileTarget($tkey);
956        } elsif ($myDest eq 'APPEND') {
957            $retVal = ">>" . EmergencyFileTarget($tkey);
958        } elsif ($myDest eq 'DUAL') {
959            $retVal = "+>" . EmergencyFileTarget($tkey);
960      }      }
961      # Parse the command line.      # Return the result.
962      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);      return $retVal;
     # 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";  
963      }      }
964      # Now we want to set up tracing. First, we need to know if the user  
965      # wants emergency tracing.  =head3 Emergency
966      if ($retOptions->{trace} eq 'E') {  
967          ETracing($retOptions->{user});      Emergency($key, $hours, $dest, $level, @modules);
968    
969    Turn on emergency tracing. This method is normally invoked over the web from
970    a debugging console, but it can also be called by the C<trace.pl> script.
971    The caller specifies the duration of the emergency in hours, the desired tracing
972    destination, the trace level, and a list of the trace modules to activate.
973    For the length of the duration, when a program in an environment with the
974    specified tracing key active invokes a Sprout CGI script, tracing will be
975    turned on automatically. See L</TSetup> for more about tracing setup and
976    L</ETracing> for more about emergency tracing.
977    
978    =over 4
979    
980    =item tkey
981    
982    The tracing key. This is used to identify the control file and the trace file.
983    
984    =item hours
985    
986    Number of hours to keep emergency tracing alive.
987    
988    =item dest
989    
990    Tracing destination. If no path information is specified for a file
991    destination, it is put in the FIG temporary directory.
992    
993    =item level
994    
995    Tracing level. A higher level means more trace messages.
996    
997    =item modules
998    
999    A list of the tracing modules to activate.
1000    
1001    =back
1002    
1003    =cut
1004    
1005    sub Emergency {
1006        # Get the parameters.
1007        my ($tkey, $hours, $dest, $level, @modules) = @_;
1008        # Create the emergency file.
1009        my $specFile = EmergencyFileName($tkey);
1010        my $outHandle = Open(undef, ">$specFile");
1011        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1012    }
1013    
1014    =head3 EmergencyKey
1015    
1016        my $tkey = EmergencyKey($parameter);
1017    
1018    Return the Key to be used for emergency tracing. This could be an IP address,
1019     a session ID, or a user name, depending on the environment.
1020    
1021    =over 4
1022    
1023    =item parameter
1024    
1025    Parameter defining the method for finding the tracing key. If it is a scalar,
1026    then it is presumed to be the tracing key itself. If it is a CGI object, then
1027    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1028    taken from the C<TRACING> environment variable.
1029    
1030    =item RETURN
1031    
1032    Returns the key to be used for labels in emergency tracing.
1033    
1034    =back
1035    
1036    =cut
1037    
1038    sub EmergencyKey {
1039        # Get the parameters.
1040        my ($parameter) = @_;
1041        # Declare the return variable.
1042        my $retVal;
1043        # Determine the parameter type.
1044        if (! defined $parameter) {
1045            # Here we're supposed to check the environment.
1046            $retVal = $ENV{TRACING};
1047      } else {      } else {
1048          # Here the tracing is controlled from the command line.          my $ptype = ref $parameter;
1049          my @cats = @{$categories};          if ($ptype eq 'CGI') {
1050          if ($retOptions->{sql}) {              # Here we were invoked from a web page. Look for a cookie.
1051              push @cats, "SQL";              $retVal = $parameter->cookie('IP');
1052            } elsif (! $ptype) {
1053                # Here the key was passed in.
1054                $retVal = $parameter;
1055          }          }
         # Add the default categories.  
         push @cats, "Tracer";  
         # 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;  
1056          }          }
1057          # Now we set up the trace mode.      # If no luck finding a key, use the PID.
1058          my $traceMode;      if (! defined $retVal) {
1059          # Verify that we can open a file in the FIG temporary directory.          $retVal = $$;
1060          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";      }
1061          if (open TESTTRACE, ">$traceFileName") {      # Return the result.
1062              # Here we can trace to a file.      return $retVal;
1063              $traceMode = ">$traceFileName";  }
1064              if ($textOKFlag) {  
1065                  # Echo to standard output if the text-OK flag is set.  
1066                  $traceMode = "+$traceMode";  =head3 TraceParms
1067    
1068        Tracer::TraceParms($cgi);
1069    
1070    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1071    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1072    
1073    =over 4
1074    
1075    =item cgi
1076    
1077    CGI query object containing the parameters to trace.
1078    
1079    =back
1080    
1081    =cut
1082    
1083    sub TraceParms {
1084        # Get the parameters.
1085        my ($cgi) = @_;
1086        if (T(CGI => 2)) {
1087            # Here we trace the GET-style URL for the script.
1088            Trace("URL: " . $cgi->url(-relative => 1, -query => 1));
1089        }
1090        if (T(CGI => 3)) {
1091            # Here we want to trace the parameter data.
1092            my @names = $cgi->param;
1093            for my $parmName (sort @names) {
1094                # Note we skip the Trace parameters, which are for our use only.
1095                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1096                    my @values = $cgi->param($parmName);
1097                    Trace("CGI: $parmName = " . join(", ", @values));
1098              }              }
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
             } else {  
                 $traceMode = "WARN";  
1099              }              }
1100            # Display the request method.
1101            my $method = $cgi->request_method();
1102            Trace("Method: $method");
1103          }          }
1104          # Now set up the tracing.      if (T(CGI => 4)) {
1105          TSetup("$traceLevel $cats", $traceMode);          # Here we want the environment data too.
1106            for my $envName (sort keys %ENV) {
1107                Trace("ENV: $envName = $ENV{$envName}");
1108      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{help}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         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] . ")";  
1109              }              }
             print "  $name $desc\n";  
1110          }          }
1111          exit(0);  
1112    =head3 TraceImages
1113    
1114        Tracer::TraceImages($htmlString);
1115    
1116    Trace information about all of an html document's images. The tracing
1117    will be for type "IMG" at level 3. The image's source string
1118    will be displayed. This is generally either the URL of the image or
1119    raw data for the image itself. If the source is too long, only the first 300
1120    characters will be shown at trace level 3. The entire source will be shown,
1121    however, at trace level 4. This method is not very smart, and might catch
1122    Javascript code, but it is still useful when debugging the arcane
1123    behavior of images in multiple browser environments.
1124    
1125    =over 4
1126    
1127    =item htmlString
1128    
1129    HTML text for an outgoing web page.
1130    
1131    =back
1132    
1133    =cut
1134    
1135    sub TraceImages {
1136        # Only proceed if we're at the proper trace level.
1137        if (T(IMG => 3)) {
1138            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1139            # into a variable called "$htmlString". This is because we expect html strings to be
1140            # long, and don't want to copy them any more than we have to.
1141            Trace(length($_[0]) . " characters in web page.");
1142            # Loop through the HTML, culling image tags.
1143            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1144                # Extract the source string and determine whether or not it's too long.
1145                my $srcString = $1;
1146                my $pos = pos($_[0]) - length($srcString);
1147                my $excess = length($srcString) - 300;
1148                # We'll put the display string in here.
1149                my $srcDisplay = $srcString;
1150                # If it's a data string, split it at the comma.
1151                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1152                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1153                # a long string, however, we only show the first 300 characters.
1154                if ($excess > 0 && ! T(IMG => 4)) {
1155                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1156                }
1157                # Output the trace message.
1158                Trace("Image tag at position $pos:\n$srcDisplay");
1159      }      }
     # Trace the options, if applicable.  
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
1160      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
1161  }  }
1162    
 =head3 Setups  
1163    
1164  C<< my $count = Tracer::Setups(); >>  =head3 ScriptFinish
1165    
1166  Return the number of times L</TSetup> has been called.      ScriptFinish($webData, $varHash);
1167    
1168  This method allows for the creation of conditional tracing setups where, for example, we  Output a web page at the end of a script. Either the string to be output or the
1169  may want to set up tracing if nobody else has done it before us.  name of a template file can be specified. If the second parameter is omitted,
1170    it is assumed we have a string to be output; otherwise, it is assumed we have the
1171    name of a template file. The template should have the variable C<DebugData>
1172    specified in any form that invokes a standard script. If debugging mode is turned
1173    on, a form field will be put in that allows the user to enter tracing data.
1174    Trace messages will be placed immediately before the terminal C<BODY> tag in
1175    the output, formatted as a list.
1176    
1177  =cut  A typical standard script would loook like the following.
1178    
1179  sub Setups {      BEGIN {
1180      return $SetupCount;          # Print the HTML header.
1181            print "CONTENT-TYPE: text/html\n\n";
1182  }  }
1183        use Tracer;
1184        use CGI;
1185        use FIG;
1186        # ... more uses ...
1187    
1188  =head3 Open      my ($cgi, $varHash) = ScriptSetup();
1189        eval {
1190            # ... get data from $cgi, put it in $varHash ...
1191        };
1192        if ($@) {
1193            Trace("Script Error: $@") if T(0);
1194        }
1195        ScriptFinish("Html/MyTemplate.html", $varHash);
1196    
1197  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  The idea here is that even if the script fails, you'll see trace messages and
1198    useful output.
1199    
1200  Open a file.  =over 4
1201    
1202  The I<$fileSpec> is essentially the second argument of the PERL C<open>  =item webData
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
1203    
1204      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  A string containing either the full web page to be written to the output or the
1205    name of a template file from which the page is to be constructed. If the name
1206    of a template file is specified, then the second parameter must be present;
1207    otherwise, it must be absent.
1208    
1209  would open for output appended to the specified file, and  =item varHash (optional)
1210    
1211      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  If specified, then a reference to a hash mapping variable names for a template
1212    to their values. The template file will be read into memory, and variable markers
1213    will be replaced by data in this hash reference.
1214    
1215  would open a pipe that sorts the records written and removes duplicates. Note  =back
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
1216    
1217      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
1218    
1219  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub ScriptFinish {
1220  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      # Get the parameters.
1221  failed open will throw an exception and the third parameter will be used to construct      my ($webData, $varHash) = @_;
1222  an error message. If the parameter is omitted, a standard message is constructed      # Check for a template file situation.
1223  using the file spec.      my $outputString;
1224        if (defined $varHash) {
1225            # Here we have a template file. We need to determine the template type.
1226            my $template;
1227            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1228                $template = "$FIG_Config::template_url/$webData";
1229            } else {
1230                $template = "<<$webData";
1231            }
1232            $outputString = PageBuilder::Build($template, $varHash, "Html");
1233        } else {
1234            # Here the user gave us a raw string.
1235            $outputString = $webData;
1236        }
1237        # Check for trace messages.
1238        if ($Destination ne "NONE" && $TraceLevel > 0) {
1239            # We have trace messages, so we want to put them at the end of the body. This
1240            # is either at the end of the whole string or at the beginning of the BODY
1241            # end-tag.
1242            my $pos = length $outputString;
1243            if ($outputString =~ m#</body>#gi) {
1244                $pos = (pos $outputString) - 7;
1245            }
1246            # If the trace messages were queued, we unroll them. Otherwise, we display the
1247            # destination.
1248            my $traceHtml;
1249            if ($Destination eq "QUEUE") {
1250                $traceHtml = QTrace('Html');
1251            } elsif ($Destination =~ /^>>(.+)$/) {
1252                # Here the tracing output it to a file. We code it as a hyperlink so the user
1253                # can copy the file name into the clipboard easily.
1254                my $actualDest = $1;
1255                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1256            } else {
1257                # Here we have one of the special destinations.
1258                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1259            }
1260            substr $outputString, $pos, 0, $traceHtml;
1261        }
1262        # Write the output string.
1263        print $outputString;
1264    }
1265    
1266      Could not open "/usr/spool/news/twitlog"  =head2 Command-Line Utility Methods
1267    
1268  Note that the mode characters are automatically cleaned from the file name.  =head3 SendSMS
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
1269    
1270      Could not open "/usr/spool/news/twitlog": file not found.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1271    
1272  In some versions of PERL the only error message we get is a number, which  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1273  corresponds to the C++ C<errno> value.  user name, password, and API ID for the relevant account in the hash reference variable
1274    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1275    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1276    is C<2561022>, then the FIG_Config file must contain
1277    
1278      Could not open "/usr/spool/news/twitlog": 6.      $phone =  { user => 'BruceTheHumanPet',
1279                    password => 'silly',
1280                    api_id => '2561022' };
1281    
1282  =over 4  The original purpose of this method was to insure Bruce would be notified immediately when the
1283    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1284    when you call this method.
1285    
1286  =item fileHandle  The message ID will be returned if successful, and C<undef> if an error occurs.
1287    
1288  File handle. If this parameter is C<undef>, a file handle will be generated  =over 4
 and returned as the value of this method.  
1289    
1290  =item fileSpec  =item phoneNumber
1291    
1292  File name and mode, as per the PERL C<open> function.  Phone number to receive the message, in international format. A United States phone number
1293    would be prefixed by "1". A British phone number would be prefixed by "44".
1294    
1295  =item message (optional)  =item msg
1296    
1297  Error message to use if the open fails. If omitted, a standard error message  Message to send to the specified phone.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
1298    
1299  =item RETURN  =item RETURN
1300    
1301  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns the message ID if successful, and C<undef> if the message could not be sent.
 open failed.  
1302    
1303  =back  =back
1304    
1305  =cut  =cut
1306    
1307  sub Open {  sub SendSMS {
1308      # Get the parameters.      # Get the parameters.
1309      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1310      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1311      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1312      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1313      if (! $rv) {      if (! defined $FIG_Config::phone) {
1314          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1315          my $sysMessage = $!;      } else {
1316          # See if we need a default message.          # Get the phone data.
1317          if (!$message) {          my $parms = $FIG_Config::phone;
1318              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1319              # filename.          my $url = "http://api.clickatell.com/http/";
1320              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1321              $message = "Could not open \"$fileName\"";          my $ua = LWP::UserAgent->new;
1322            # Request a Clickatell session.
1323            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1324                                         password => $parms->{password},
1325                                         api_id => $parms->{api_id},
1326                                         to => $phoneNumber,
1327                                         text => $msg});
1328            # Check for an error.
1329            if (! $resp->is_success) {
1330                Trace("Alert failed.") if T(1);
1331            } else {
1332                # Get the message ID.
1333                my $rstring = $resp->content;
1334                if ($rstring =~ /^ID:\s+(.*)$/) {
1335                    $retVal = $1;
1336                } else {
1337                    Trace("Phone attempt failed with $rstring") if T(1);
1338          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1339      }      }
     # Return the file handle.  
     return $fileHandle;  
1340  }  }
1341        # Return the result.
1342        return $retVal;
1343    }
1344    
1345    =head3 StandardSetup
1346    
1347  =head3 FindNamePart      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1348    
1349  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  This method performs standard command-line parsing and tracing setup. The return
1350    values are a hash of the command-line options and a list of the positional
1351    parameters. Tracing is automatically set up and the command-line options are
1352    validated.
1353    
1354  Extract the portion of a file specification that contains the file name.  This is a complex method that does a lot of grunt work. The parameters can
1355    be more easily understood, however, once they are examined individually.
1356    
1357  A file specification is the string passed to an C<open> call. It specifies the file  The I<categories> parameter is the most obtuse. It is a reference to a list of
1358  mode and name. In a truly complex situation, it can specify a pipe sequence. This  special-purpose tracing categories. Most tracing categories are PERL package
1359  method assumes that the file name is whatever follows the first angle bracket  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1360  sequence.  So, for example, in the following strings the file name is  B<ERDB>, and B<SproutLoad> packages, you would specify the categories
 C</usr/fig/myfile.txt>.  
1361    
1362      >>/usr/fig/myfile.txt      ["Sprout", "SproutLoad", "ERDB"]
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
1363    
1364  If the method cannot find a file name using its normal methods, it will return the  This would cause trace messages in the specified three packages to appear in
1365  whole incoming string.  the output. There are two special tracing categories that are automatically
1366    handled by this method. In other words, if you used L</TSetup> you would need
1367    to include these categories manually, but if you use this method they are turned
1368    on automatically.
1369    
1370  =over 4  =over 4
1371    
1372  =item fileSpec  =item SQL
1373    
1374  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1375    
1376  =item RETURN  =item Tracer
1377    
1378  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 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.  
1379    
1380  =back  =back
1381    
1382  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1383  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1384  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1385      # Get the parameters.  all tracing at level 3.
     my ($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);  
1386    
1387  is effectively the same as      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1388    
1389      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  Standard tracing is output to the standard output and echoed to the file
1390      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1391    process ID. You can also specify the C<user> parameter to put a user ID
1392    instead of a process ID in the trace file name. So, for example
1393    
1394  Similarly, the following code  The default trace level is 2. To get all messages, specify a trace level of 4.
1395    For a genome-by-genome update, use 3.
1396    
1397      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1398    
1399  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  would send the trace output to C<traceBruce.log> in the temporary directory.
 automatically returns an empty list if the directory fails to open.  
1400    
1401  =over 4  The I<options> parameter is a reference to a hash containing the command-line
1402    options, their default values, and an explanation of what they mean. Command-line
1403    options may be in the form of switches or keywords. In the case of a switch, the
1404    option value is 1 if it is specified and 0 if it is not specified. In the case
1405    of a keyword, the value is separated from the option name by an equal sign. You
1406    can see this last in the command-line example above.
1407    
1408  =item dirName  You can specify a different default trace level by setting C<$options->{trace}>
1409    prior to calling this method.
1410    
1411  Name of the directory to open.  An example at this point would help. Consider, for example, the command-line utility
1412    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1413    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1414    the following code.
1415    
1416  =item filtered      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1417                            { safe => [0, "use database transactions"],
1418                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1419                              start => [' ', "start with this genome"],
1420                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1421                            "<command> <transactionDirectory> <IDfile>",
1422                          @ARGV);
1423    
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
1424    
1425  =item flag  The call to C<ParseCommand> specifies the default values for the options and
1426    stores the actual options in a hash that is returned as C<$options>. The
1427    positional parameters are returned in C<@parameters>.
1428    
1429  TRUE if a failure to open is okay, else FALSE  The following is a sample command line for C<TransactFeatures>.
1430    
1431  =back      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1432    
1433  =cut  Single and double hyphens are equivalent. So, you could also code the
1434  #: Return Type @;  above command as
 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 $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1435    
1436  =head3 SetLevel      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1437    
1438  C<< Tracer::SetLevel($newLevel); >>  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1439    parameters, and would find themselves in I<@parameters> after executing the
1440    above code fragment. The tracing would be set to level 2, and the categories
1441    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1442    and C<DocUtils> was included because it came in within the first parameter
1443    to this method. The I<$options> hash would be
1444    
1445  Modify the trace level. A higher trace level will cause more messages to appear.      { trace => 2, sql => 0, safe => 0,
1446          noAlias => 1, start => ' ', tblFiles => 0 }
1447    
1448  =over 4  Use of C<StandardSetup> in this way provides a simple way of performing
1449    standard tracing setup and command-line parsing. Note that the caller is
1450    not even aware of the command-line switches C<-trace> and C<-sql>, which
1451    are used by this method to control the tracing. If additional tracing features
1452    need to be added in the future, they can be processed by this method without
1453    upsetting the command-line utilities.
1454    
1455  =item newLevel  If the C<background> option is specified on the command line, then the
1456    standard and error outputs will be directed to files in the temporary
1457    directory, using the same suffix as the trace file. So, if the command
1458    line specified
1459    
1460  Proposed new trace level.      -user=Bruce -background
1461    
1462  =back  then the trace output would go to C<traceBruce.log>, the standard output to
1463    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1464    simplify starting a command in the background.
1465    
1466  =cut  The user name is also used as the tracing key for L</Emergency Tracing>.
1467    Specifying a value of C<E> for the trace level causes emergency tracing to
1468    be used instead of custom tracing. If the user name is not specified,
1469    the tracing key is taken from the C<Tracing> environment variable. If there
1470    is no value for that variable, the tracing key will be computed from the PID.
1471    
1472  sub SetLevel {  Finally, if the special option C<-help> is specified, the option
1473      $TraceLevel = $_[0];  names will be traced at level 0 and the program will exit without processing.
1474  }  This provides a limited help capability. For example, if the user enters
1475    
1476  =head3 Now      TransactFeatures -help
1477    
1478  C<< my $string = Tracer::Now(); >>  he would see the following output.
1479    
1480  Return a displayable time stamp containing the local time.      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1481            -trace    tracing level (default E)
1482            -sql      trace SQL commands
1483            -safe     use database transactions
1484            -noAlias  do not expect aliases in CHANGE transactions
1485            -start    start with this genome
1486            -tblFiles output TBL files containing the corrected IDs
1487    
1488  =cut  The caller has the option of modifying the tracing scheme by placing a value
1489    for C<trace> in the incoming options hash. The default value can be overridden,
1490    or the tracing to the standard output can be turned off by suffixing a minus
1491    sign to the trace level. So, for example,
1492    
1493  sub Now {      { trace => [0, "tracing level (default 0)"],
1494      my ($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 $retVal;  
 }  
1495    
1496  # Pad a number to 2 digits.  would set the default trace level to 0 instead of E, while
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1497    
1498  =head3 ParseTraceDate      { trace => ["2-", "tracing level (default 2)"],
1499           ...
1500    
1501  C<< my $time = Tracer::ParseTraceDate($dateString); >>  would set the default to 2, but trace only to the log file, not to the
1502    standard output.
1503    
1504  Convert a date from the trace file into a PERL timestamp.  The parameters to this method are as follows.
1505    
1506  =over 4  =over 4
1507    
1508  =item dateString  =item categories
   
 The date string from the trace file. The format of the string is determined by the  
 L</Now> method.  
   
 =item RETURN  
   
 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  
 the time string is invalid.  
   
 =back  
1509    
1510  =cut  Reference to a list of tracing category names. These should be names of
1511    packages whose internal workings will need to be debugged to get the
1512    command working.
1513    
1514  sub ParseTraceDate {  =item options
     # Get the parameters.  
     my ($dateString) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
     }  
     # Return the result.  
     return $retVal;  
 }  
1515    
1516  =head3 LogErrors  Reference to a hash containing the legal options for the current command mapped
1517    to their default values and descriptions. The user can override the defaults
1518    by specifying the options as command-line switches prefixed by a hyphen.
1519    Tracing-related options may be added to this hash. If the C<-h> option is
1520    specified on the command line, the option descriptions will be used to
1521    explain the options. To turn off tracing to the standard output, add a
1522    minus sign to the value for C<trace> (see above).
1523    
1524  C<< Tracer::LogErrors($fileName); >>  =item parmHelp
1525    
1526  Route the standard error output to a log file.  A string that vaguely describes the positional parameters. This is used
1527    if the user specifies the C<-h> option.
1528    
1529  =over 4  =item argv
1530    
1531  =item fileName  List of command line parameters, including the option switches, which must
1532    precede the positional parameters and be prefixed by a hyphen.
1533    
1534  Name of the file to receive the error output.  =item RETURN
1535    
1536    Returns a list. The first element of the list is the reference to a hash that
1537    maps the command-line option switches to their values. These will either be the
1538    default values or overrides specified on the command line. The remaining
1539    elements of the list are the position parameters, in order.
1540    
1541  =back  =back
1542    
1543  =cut  =cut
1544    
1545  sub LogErrors {  sub StandardSetup {
1546      # Get the file name.      # Get the parameters.
1547      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1548      # Open the file as the standard error output.      # Get the default tracing key.
1549      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1550        # Add the tracing options.
1551        if (! exists $options->{trace}) {
1552            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1553        }
1554        $options->{sql} = [0, "turn on SQL tracing"];
1555        $options->{help} = [0, "display command-line options"];
1556        $options->{user} = [$tkey, "tracing key"];
1557        $options->{background} = [0, "spool standard and error output"];
1558        # Create a parsing hash from the options hash. The parsing hash
1559        # contains the default values rather than the default value
1560        # and the description. While we're at it, we'll memorize the
1561        # length of the longest option name.
1562        my $longestName = 0;
1563        my %parseOptions = ();
1564        for my $key (keys %{$options}) {
1565            if (length $key > $longestName) {
1566                $longestName = length $key;
1567            }
1568            $parseOptions{$key} = $options->{$key}->[0];
1569        }
1570        # Parse the command line.
1571        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1572        # Get the logfile suffix.
1573        my $suffix = $retOptions->{user};
1574        # Check for background mode.
1575        if ($retOptions->{background}) {
1576            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1577            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1578            open STDOUT, ">$outFileName";
1579            open STDERR, ">$errFileName";
1580            # Check for phone support. If we have phone support and a phone number,
1581            # we want to turn it on.
1582            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1583                $retOptions->{phone} = $ENV{PHONE};
1584            }
1585        }
1586        # Now we want to set up tracing. First, we need to know if the user
1587        # wants emergency tracing.
1588        if ($retOptions->{trace} eq 'E') {
1589            ETracing($retOptions->{user});
1590        } else {
1591            # Here the tracing is controlled from the command line.
1592            my @cats = @{$categories};
1593            if ($retOptions->{sql}) {
1594                push @cats, "SQL";
1595            }
1596            # Add the default categories.
1597            push @cats, "Tracer";
1598            # Next, we create the category string by joining the categories.
1599            my $cats = join(" ", @cats);
1600            # Check to determine whether or not the caller wants to turn off tracing
1601            # to the standard output.
1602            my $traceLevel = $retOptions->{trace};
1603            my $textOKFlag = 1;
1604            if ($traceLevel =~ /^(.)-/) {
1605                $traceLevel = $1;
1606                $textOKFlag = 0;
1607            }
1608            # Now we set up the trace mode.
1609            my $traceMode;
1610            # Verify that we can open a file in the FIG temporary directory.
1611            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1612            if (open TESTTRACE, ">$traceFileName") {
1613                # Here we can trace to a file.
1614                $traceMode = ">$traceFileName";
1615                if ($textOKFlag) {
1616                    # Echo to standard output if the text-OK flag is set.
1617                    $traceMode = "+$traceMode";
1618                }
1619                # Close the test file.
1620                close TESTTRACE;
1621            } else {
1622                # Here we can't trace to a file. We trace to the standard output if it's
1623                # okay, and the error log otherwise.
1624                if ($textOKFlag) {
1625                    $traceMode = "TEXT";
1626                } else {
1627                    $traceMode = "WARN";
1628                }
1629            }
1630            # Now set up the tracing.
1631            TSetup("$traceLevel $cats", $traceMode);
1632        }
1633        # Check for the "help" option. If it is specified, dump the command-line
1634        # options and exit the program.
1635        if ($retOptions->{help}) {
1636            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1637            print "$1 [options] $parmHelp\n";
1638            for my $key (sort keys %{$options}) {
1639                my $name = Pad($key, $longestName, 0, ' ');
1640                my $desc = $options->{$key}->[1];
1641                if ($options->{$key}->[0]) {
1642                    $desc .= " (default " . $options->{$key}->[0] . ")";
1643                }
1644                print "  $name $desc\n";
1645            }
1646            exit(0);
1647        }
1648        # Trace the options, if applicable.
1649        if (T(3)) {
1650            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1651            Trace("Selected options: " . join(", ", sort @parms) . ".");
1652        }
1653        # Return the parsed parameters.
1654        return ($retOptions, @retParameters);
1655  }  }
1656    
1657  =head3 ReadOptions  =head3 ReadOptions
1658    
1659  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1660    
1661  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1662  format  format
# Line 1069  Line 1717 
1717    
1718  =head3 GetOptions  =head3 GetOptions
1719    
1720  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1721    
1722  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1723  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 1078  Line 1726 
1726    
1727  Consider the following example.  Consider the following example.
1728    
1729  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1730    
1731  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1732  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1734 
1734  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1735  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1736    
1737  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1738    
1739  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1740    
# Line 1130  Line 1778 
1778    
1779  =head3 MergeOptions  =head3 MergeOptions
1780    
1781  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1782    
1783  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1784  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1149  Line 1797 
1797    
1798  =back  =back
1799    
1800  =cut  =cut
1801    
1802  sub MergeOptions {  sub MergeOptions {
1803      # Get the parameters.      # Get the parameters.
1804      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
1805      # Loop through the defaults.      # Loop through the defaults.
1806      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
1807          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
1808              $table->{$key} = $value;              $table->{$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.");  
1809          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1810      }      }
     # Return the computed result.  
     return $retVal;  
1811  }  }
1812    
1813  =head3 ParseCommand  =head3 ParseCommand
1814    
1815  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1816    
1817  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1818  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1819  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1820  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1821    
1822  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1823    
1824  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1825  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1826    
1827  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1828    
1829  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1830    
1831  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1832    
1833  and C<@arguments> will contain  and C<@arguments> will contain
1834    
1835  C<< apple orange rutabaga >>      apple orange rutabaga
1836    
1837  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1838  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 1886 
1886      return ($optionTable, @retVal);      return ($optionTable, @retVal);
1887  }  }
1888    
 =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 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
1889    
1890  sub Percent {  =head2 File Utility Methods
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
1891    
1892  =head3 GetFile  =head3 GetFile
1893    
1894  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
1895    
1896      or      or
1897    
1898  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1899    
1900  Return the entire contents of a file. In list context, line-ends are removed and  Return the entire contents of a file. In list context, line-ends are removed and
1901  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1661  Line 1945 
1945    
1946  =head3 PutFile  =head3 PutFile
1947    
1948  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
1949    
1950  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
1951    
# Line 1704  Line 1988 
1988      close $handle;      close $handle;
1989  }  }
1990    
1991  =head3 QTrace  =head3 ParseRecord
1992    
1993        my @fields = Tracer::ParseRecord($line);
1994    
1995    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1996    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1997    These will automatically be converted.
1998    
1999  C<< my $data = QTrace($format); >>  =over 4
2000    
2001  Return the queued trace data in the specified format.  =item line
2002    
2003  =over 4  Line of data containing the tab-delimited fields.
2004    
2005  =item format  =item RETURN
2006    
2007  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Returns a list of the fields found in the data line.
2008    
2009  =back  =back
2010    
2011  =cut  =cut
2012    
2013  sub QTrace {  sub ParseRecord {
2014      # Get the parameter.      # Get the parameter.
2015      my ($format) = @_;      my ($line) = @_;
2016      # Create the return variable.      # Remove the trailing new-line, if any.
2017      my $retVal = "";      chomp $line;
2018      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2019      if (@Queue) {      my @retVal = split /\t/, $line;
2020          # Process according to the format.      # Trim and fix the escapes in each piece.
2021          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2022              # Convert the queue into an HTML list.          # Trim leading whitespace.
2023              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2024              for my $line (@Queue) {          # Trim trailing whitespace.
2025                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2026                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2027              }          $value =~ s/\r//g;
2028              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2029          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2030              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2031      }      }
2032      # Return the formatted list.      # Return the result.
2033      return $retVal;      return @retVal;
2034  }  }
2035    
2036  =head3 Confess  =head3 Merge
2037    
2038  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2039    
2040  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2041    
2042  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2043    
2044  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2045    
2046  =over 4  List of scalars to sort and merge.
2047    
2048  =item message  =item RETURN
2049    
2050  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2051    removed.
2052    
2053  =back  =back
2054    
2055  =cut  =cut
2056    
2057  sub Confess {  sub Merge {
2058      # Get the parameters.      # Get the input list in sort order.
2059      my ($message) = @_;      my @inputList = sort @_;
2060      # Trace the call stack.      # Only proceed if the list has at least two elements.
2061      Cluck($message);      if (@inputList > 1) {
2062      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2063      croak(">>> $message");          my $i = 0;
2064            while ($i < @inputList) {
2065                # Get the current entry.
2066                my $thisEntry = $inputList[$i];
2067                # Find out how many elements duplicate the current entry.
2068                my $j = $i + 1;
2069                my $dup1 = $i + 1;
2070                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2071                # If the number is nonzero, splice out the duplicates found.
2072                if ($j > $dup1) {
2073                    splice @inputList, $dup1, $j - $dup1;
2074                }
2075                # Now the element at position $dup1 is different from the element before it
2076                # at position $i. We push $i forward one position and start again.
2077                $i++;
2078            }
2079        }
2080        # Return the merged list.
2081        return @inputList;
2082  }  }
2083    
2084  =head3 Assert  =head3 Open
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
2085    
2086  Return TRUE if all the conditions are true. This method can be used in conjunction with      my $handle = Open($fileHandle, $fileSpec, $message);
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2087    
2088  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Open a file.
2089    
2090  Will abort the program with a stack trace if the value of C<$recNum> is negative.  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2091    function. The mode is specified using Unix-like shell information. So, for
2092    example,
2093    
2094  =cut      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2095    
2096  =head3 Cluck  would open for output appended to the specified file, and
2097    
2098  C<< Cluck($message); >>      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2099    
2100  Trace the call stack. Note that for best results, you should qualify the call with a  would open a pipe that sorts the records written and removes duplicates. Note
2101  trace condition. For example,  the use of file handle syntax in the Open call. To use anonymous file handles,
2102    code as follows.
2103    
2104  C<< Cluck("Starting record parse.") if T(3); >>      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2105    
2106  will only trace the stack if the trace level for the package is 3 or more.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2107    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2108    failed open will throw an exception and the third parameter will be used to construct
2109    an error message. If the parameter is omitted, a standard message is constructed
2110    using the file spec.
2111    
2112  =over 4      Could not open "/usr/spool/news/twitlog"
2113    
2114  =item message  Note that the mode characters are automatically cleaned from the file name.
2115    The actual error message from the file system will be captured and appended to the
2116    message in any case.
2117    
2118  Message to include in the trace.      Could not open "/usr/spool/news/twitlog": file not found.
2119    
2120  =back  In some versions of PERL the only error message we get is a number, which
2121    corresponds to the C++ C<errno> value.
2122    
2123  =cut      Could not open "/usr/spool/news/twitlog": 6.
2124    
2125  sub Cluck {  =over 4
     # 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/);  
     }  
 }  
2126    
2127  =head3 Min  =item fileHandle
2128    
2129  C<< my $min = Min($value1, $value2, ... $valueN); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2130    and returned as the value of this method.
2131    
2132  Return the minimum argument. The arguments are treated as numbers.  =item fileSpec
2133    
2134  =over 4  File name and mode, as per the PERL C<open> function.
2135    
2136  =item $value1, $value2, ... $valueN  =item message (optional)
2137    
2138  List of numbers to compare.  Error message to use if the open fails. If omitted, a standard error message
2139    will be generated. In either case, the error information from the file system
2140    is appended to the message. To specify a conditional open that does not throw
2141    an error if it fails, use C<0>.
2142    
2143  =item RETURN  =item RETURN
2144    
2145  Returns the lowest number in the list.  Returns the name of the file handle assigned to the file, or C<undef> if the
2146    open failed.
2147    
2148  =back  =back
2149    
2150  =cut  =cut
2151    
2152  sub Min {  sub Open {
2153      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2154      my ($retVal, @values) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2155      # Loop through the remaining parameters, looking for the lowest.      # Attempt to open the file.
2156      for my $value (@values) {      my $rv = open $fileHandle, $fileSpec;
2157          if ($value < $retVal) {      # If the open failed, generate an error message.
2158              $retVal = $value;      if (! $rv) {
2159            # Save the system error message.
2160            my $sysMessage = $!;
2161            # See if we need a default message.
2162            if (!$message) {
2163                # Clean any obvious mode characters and leading spaces from the
2164                # filename.
2165                my ($fileName) = FindNamePart($fileSpec);
2166                $message = "Could not open \"$fileName\"";
2167          }          }
2168            # Terminate with an error using the supplied message and the
2169            # error message from the file system.
2170            Confess("$message: $!");
2171      }      }
2172      # Return the minimum found.      # Return the file handle.
2173      return $retVal;      return $fileHandle;
2174  }  }
2175    
2176  =head3 Max  =head3 FindNamePart
2177    
2178  C<< my $max = Max($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2179    
2180  Return the maximum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2181    
2182    A file specification is the string passed to an C<open> call. It specifies the file
2183    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2184    method assumes that the file name is whatever follows the first angle bracket
2185    sequence.  So, for example, in the following strings the file name is
2186    C</usr/fig/myfile.txt>.
2187    
2188        >>/usr/fig/myfile.txt
2189        </usr/fig/myfile.txt
2190        | sort -u > /usr/fig/myfile.txt
2191    
2192    If the method cannot find a file name using its normal methods, it will return the
2193    whole incoming string.
2194    
2195  =over 4  =over 4
2196    
2197  =item $value1, $value2, ... $valueN  =item fileSpec
2198    
2199    File specification string from which the file name is to be extracted.
2200    
2201    =item RETURN
2202    
2203    Returns a three-element list. The first element contains the file name portion of
2204    the specified string, or the whole string if a file name cannot be found via normal
2205    methods. The second element contains the start position of the file name portion and
2206    the third element contains the length.
2207    
2208    =back
2209    
2210    =cut
2211    #: Return Type $;
2212    sub FindNamePart {
2213        # Get the parameters.
2214        my ($fileSpec) = @_;
2215        # Default to the whole input string.
2216        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2217        # Parse out the file name if we can.
2218        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2219            $retVal = $2;
2220            $len = length $retVal;
2221            $pos = (length $fileSpec) - (length $3) - $len;
2222        }
2223        # Return the result.
2224        return ($retVal, $pos, $len);
2225    }
2226    
2227  List of numbers to compare.  =head3 OpenDir
2228    
2229  =item RETURN      my @files = OpenDir($dirName, $filtered, $flag);
2230    
2231  Returns the highest number in the list.  Open a directory and return all the file names. This function essentially performs
2232    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2233    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2234    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2235    filtered out of the return list. If the directory does not open and I<$flag> is not
2236    set, an exception is thrown. So, for example,
2237    
2238  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2239    
2240  =cut  is effectively the same as
2241    
2242  sub Max {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2243      # Get the parameters. Note that we prime the return value with the first parameter.      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     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;  
 }  
2244    
2245  =head3 AddToListMap  Similarly, the following code
2246    
2247  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2248    
2249  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2250  is created for the key. Otherwise, the new value is pushed onto the list.  automatically returns an empty list if the directory fails to open.
2251    
2252  =over 4  =over 4
2253    
2254  =item hash  =item dirName
2255    
2256  Reference to the target hash.  Name of the directory to open.
2257    
2258  =item key  =item filtered
2259    
2260  Key for which the value is to be added.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2261    from the list, else FALSE.
2262    
2263  =item value1, value2, ... valueN  =item flag
2264    
2265  List of values to add to the key's value list.  TRUE if a failure to open is okay, else FALSE
2266    
2267  =back  =back
2268    
2269  =cut  =cut
2270    #: Return Type @;
2271  sub AddToListMap {  sub OpenDir {
2272      # Get the parameters.      # Get the parameters.
2273      my ($hash, $key, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2274      # Process according to whether or not the key already has a value.      # Declare the return variable.
2275      if (! exists $hash->{$key}) {      my @retVal = ();
2276          $hash->{$key} = [@values];      # Open the directory.
2277        if (opendir(my $dirHandle, $dirName)) {
2278            # The directory opened successfully. Get the appropriate list according to the
2279            # strictures of the filter parameter.
2280            if ($filtered) {
2281                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2282      } else {      } else {
2283          push @{$hash->{$key}}, @values;              @retVal = readdir $dirHandle;
2284            }
2285        } elsif (! $flag) {
2286            # Here the directory would not open and it's considered an error.
2287            Confess("Could not open directory $dirName.");
2288      }      }
2289        # Return the result.
2290        return @retVal;
2291  }  }
2292    
 =head3 DebugMode  
2293    
2294  C<< if (Tracer::DebugMode) { ...code... } >>  =head3 Insure
2295    
2296  Return TRUE if debug mode has been turned on, else abort.      Insure($dirName, $chmod);
2297    
2298  Certain CGI scripts are too dangerous to exist in the production  Insure a directory is present.
2299  environment. This method provides a simple way to prevent them  
2300  from working unless they are explicitly turned on by creating a password  =over 4
2301  cookie via the B<SetPassword> script.  If debugging mode  
2302  is not turned on, an error will occur.  =item dirName
2303    
2304    Name of the directory to check. If it does not exist, it will be created.
2305    
2306    =item chmod (optional)
2307    
2308    Security privileges to be given to the directory if it is created.
2309    
2310    =back
2311    
2312  =cut  =cut
2313    
2314  sub DebugMode {  sub Insure {
2315      # Declare the return variable.      my ($dirName, $chmod) = @_;
2316      my $retVal = 0;      if (! -d $dirName) {
2317      # Check the debug configuration.          Trace("Creating $dirName directory.") if T(2);
2318      my $password = CGI::cookie("DebugMode");          eval {
2319      my $encrypted = Digest::MD5::md5_hex($password);              mkpath $dirName;
2320      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {              # If we have permissions specified, set them here.
2321          $retVal = 1;              if (defined($chmod)) {
2322      } else {                  chmod $chmod, $dirName;
2323          # Here debug mode is off, so we generate an error.              }
2324          Confess("Cannot use this facility without logging in.");          };
2325            if ($@) {
2326                Confess("Error creating $dirName: $@");
2327            }
2328      }      }
     # Return the determination indicator.  
     return $retVal;  
2329  }  }
2330    
2331  =head3 Strip  =head3 ChDir
2332    
2333  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2334    
2335  Strip all line terminators off a string. This is necessary when dealing with files  Change to the specified directory.
 that may have been transferred back and forth several times among different  
 operating environments.  
2336    
2337  =over 4  =over 4
2338    
2339  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2340    
2341  The same line of text with all the line-ending characters chopped from the end.  Name of the directory to which we want to change.
2342    
2343  =back  =back
2344    
2345  =cut  =cut
2346    
2347  sub Strip {  sub ChDir {
2348      # Get a copy of the parameter string.      my ($dirName) = @_;
2349      my ($string) = @_;      if (! -d $dirName) {
2350      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2351      # Strip the line terminator characters.      } else {
2352      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2353      # Return the result.          my $okFlag = chdir $dirName;
2354      return $retVal;          if (! $okFlag) {
2355                Confess("Error switching to directory $dirName.");
2356            }
2357        }
2358  }  }
2359    
2360  =head3 Pad  =head3 SetPermissions
2361    
2362  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2363    
2364  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2365  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2366  in the third parameter.  
2367    This method is more vulnerable than most to permission and compatability
2368    problems, so it does internal error recovery.
2369    
2370  =over 4  =over 4
2371    
2372  =item string  =item dirName
2373    
2374  String to be padded.  Name of the directory to process.
2375    
2376  =item len  =item group
2377    
2378  Desired length of the padded string.  Name of the group to be assigned.
2379    
2380  =item left (optional)  =item mask
2381    
2382  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2383    permission bits of any file or directory that does not already have them
2384    set to 1.
2385    
2386  =item padChar (optional)  =item otherMasks
2387    
2388  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2389    one of the patterns, that directory and all its members and subdirectories
2390    will be assigned the new pattern. For example, the following would
2391    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2392    
2393  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2394    
2395  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2396  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2397    
2398        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2399                                                       '^tmp' => 0666);
2400    
2401    Note that the pattern matches are all case-insensitive, and only directory
2402    names are matched, not file names.
2403    
2404  =back  =back
2405    
2406  =cut  =cut
2407    
2408  sub Pad {  sub SetPermissions {
2409      # Get the parameters.      # Get the parameters.
2410      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2411      # Compute the padding character.      # Set up for error recovery.
2412      if (! defined $padChar) {      eval {
2413          $padChar = " ";          # Switch to the specified directory.
2414            ChDir($dirName);
2415            # Get the group ID.
2416            my $gid = getgrnam($group);
2417            # Get the mask for tracing.
2418            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2419            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2420            my $fixCount = 0;
2421            my $lookCount = 0;
2422            # @dirs will be a stack of directories to be processed.
2423            my @dirs = (getcwd());
2424            while (scalar(@dirs) > 0) {
2425                # Get the current directory.
2426                my $dir = pop @dirs;
2427                # Check for a match to one of the specified directory names. To do
2428                # that, we need to pull the individual part of the name off of the
2429                # whole path.
2430                my $simpleName = $dir;
2431                if ($dir =~ m!/([^/]+)$!) {
2432                    $simpleName = $1;
2433                }
2434                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2435                # Search for a match.
2436                my $match = 0;
2437                my $i;
2438                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2439                    my $pattern = $otherMasks[$i];
2440                    if ($simpleName =~ /$pattern/i) {
2441                        $match = 1;
2442                    }
2443                }
2444                # Check for a match. Note we use $i-1 because the loop added 2
2445                # before terminating due to the match.
2446                if ($match && $otherMasks[$i-1] != $mask) {
2447                    # This directory matches one of the incoming patterns, and it's
2448                    # a different mask, so we process it recursively with that mask.
2449                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2450                } else {
2451                    # Here we can process normally. Get all of the non-hidden members.
2452                    my @submems = OpenDir($dir, 1);
2453                    for my $submem (@submems) {
2454                        # Get the full name.
2455                        my $thisMem = "$dir/$submem";
2456                        Trace("Checking member $thisMem.") if T(4);
2457                        $lookCount++;
2458                        if ($lookCount % 1000 == 0) {
2459                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2460                        }
2461                        # Fix the group.
2462                        chown -1, $gid, $thisMem;
2463                        # Insure this member is not a symlink.
2464                        if (! -l $thisMem) {
2465                            # Get its info.
2466                            my $fileInfo = stat $thisMem;
2467                            # Only proceed if we got the info. Otherwise, it's a hard link
2468                            # and we want to skip it anyway.
2469                            if ($fileInfo) {
2470                                my $fileMode = $fileInfo->mode;
2471                                if (($fileMode & $mask) != $mask) {
2472                                    # Fix this member.
2473                                    $fileMode |= $mask;
2474                                    chmod $fileMode, $thisMem;
2475                                    $fixCount++;
2476                                }
2477                                # If it's a subdirectory, stack it.
2478                                if (-d $thisMem) {
2479                                    push @dirs, $thisMem;
2480                                }
2481                            }
2482                        }
2483      }      }
     # 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 .= $pad;  
2484          }          }
2485      }      }
2486      # Return the result.          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2487      return $retVal;      };
2488        # Check for an error.
2489        if ($@) {
2490            Confess("SetPermissions error: $@");
2491  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2492  }  }
2493    
2494  =head3 TICK  =head3 GetLine
   
 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  
2495    
2496      TICK("./protein.cgi")      my @data = Tracer::GetLine($handle);
2497    
2498  it will work correctly in both environments.  Read a line of data from a tab-delimited file.
2499    
2500  =over 4  =over 4
2501    
2502  =item commandString  =item handle
2503    
2504  The command string to pass to the system.  Open file handle from which to read.
2505    
2506  =item RETURN  =item RETURN
2507    
2508  Returns the standard output from the specified command, as a list.  Returns a list of the fields in the record read. The fields are presumed to be
2509    tab-delimited. If we are at the end of the file, then an empty list will be
2510    returned. If an empty line is read, a single list item consisting of a null
2511    string will be returned.
2512    
2513  =back  =back
2514    
2515  =cut  =cut
2516  #: Return Type @;  
2517  sub TICK {  sub GetLine {
2518      # Get the parameters.      # Get the parameters.
2519      my ($commandString) = @_;      my ($handle) = @_;
2520      # Chop off the dot-slash if this is Windows.      # Declare the return variable.
2521      if ($FIG_Config::win_mode) {      my @retVal = ();
2522          $commandString =~ s!^\./!!;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2523        # Read from the file.
2524        my $line = <$handle>;
2525        # Only proceed if we found something.
2526        if (defined $line) {
2527            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2528            # upload control and have a nonstandard EOL combination.
2529            $line =~ s/(\r|\n)+$//;
2530            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2531            if (T(File => 4)) {
2532                my $escapedLine = $line;
2533                $escapedLine =~ s/\n/\\n/g;
2534                $escapedLine =~ s/\r/\\r/g;
2535                $escapedLine =~ s/\t/\\t/g;
2536                Trace("Line read: -->$escapedLine<--");
2537      }      }
2538      # Activate the command and return the result.          # If the line is empty, return a single empty string; otherwise, parse
2539      return `$commandString`;          # it into fields.
2540            if ($line eq "") {
2541                push @retVal, "";
2542            } else {
2543                push @retVal, split /\t/,$line;
2544            }
2545        } else {
2546            # Trace the reason the read failed.
2547            Trace("End of file: $!") if T(File => 3);
2548        }
2549        # Return the result.
2550        return @retVal;
2551  }  }
2552    
2553  =head3 ScriptSetup  =head3 PutLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2554    
2555  Perform standard tracing and debugging setup for scripts. The value returned is      Tracer::PutLine($handle, \@fields, $eol);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2556    
2557  This method calls L</ETracing> to configure tracing, which allows the tracing  Write a line of data to a tab-delimited file. The specified field values will be
2558  to be configured via the emergency tracing form on the debugging control panel.  output in tab-separated form, with a trailing new-line.
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2559    
2560  =over 4  =over 4
2561    
2562  =item noTrace (optional)  =item handle
2563    
2564  If specified, tracing will be suppressed. This is useful if the script wants to set up  Output file handle.
 tracing manually.  
2565    
2566  =item RETURN  =item fields
2567    
2568  Returns a two-element list consisting of a CGI query object and a variable hash for  List of field values.
2569  the output page.  
2570    =item eol (optional)
2571    
2572    End-of-line character (default is "\n").
2573    
2574  =back  =back
2575    
2576  =cut  =cut
2577    
2578  sub ScriptSetup {  sub PutLine {
2579      # Get the parameters.      # Get the parameters.
2580      my ($noTrace) = @_;      my ($handle, $fields, $eol) = @_;
2581      # Get the CGI query object.      # Write the data.
2582      my $cgi = CGI->new();      print $handle join("\t", @{$fields}) . ($eol || "\n");
     # Set up tracing if it's not suppressed.  
     ETracing($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
2583  }  }
2584    
 =head3 ETracing  
   
 C<< ETracing($parameter); >>  
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
2585    
 =cut  
2586    
2587  sub ETracing {  =head2 Other Useful Methods
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
     }  
 }  
2588    
2589  =head3 EmergencyFileName  =head3 ParseParm
2590    
2591  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $listValue = Tracer::ParseParm($string);
2592    
2593  Return the emergency tracing file name. This is the file that specifies  Convert a parameter into a list reference. If the parameter is undefined,
2594  the tracing information.  an undefined value will be returned. Otherwise, it will be parsed as a
2595    comma-separated list of values.
2596    
2597  =over 4  =over 4
2598    
2599  =item tkey  =item string
2600    
2601  Tracing key for the current program.  Incoming string.
2602    
2603  =item RETURN  =item RETURN
2604    
2605  Returns the name of the file to contain the emergency tracing information.  Returns a reference to a list of values, or C<undef> if the incoming value
2606    was undefined.
2607    
2608  =back  =back
2609    
2610  =cut  =cut
2611    
2612  sub EmergencyFileName {  sub ParseParm {
2613      # Get the parameters.      # Get the parameters.
2614      my ($tkey) = @_;      my ($string) = @_;
2615      # Compute the emergency tracing file name.      # Declare the return variable.
2616      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal;
2617        # Check for data.
2618        if (defined $string) {
2619            # We have some, so split it into a list.
2620            $retVal = [ split /\s*,\s*/, $string];
2621        }
2622        # Return the result.
2623        return $retVal;
2624  }  }
2625    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
   
 Return the emergency tracing target file name. This is the file that receives  
 the tracing output for file-based tracing.  
   
 =over 4  
2626    
 =item tkey  
2627    
 Tracing key for the current program.  
2628    
2629  =item RETURN  =head3 Now
2630    
2631  Returns the name of the file to contain the trace output.      my $string = Tracer::Now();
2632    
2633  =back  Return a displayable time stamp containing the local time.
2634    
2635  =cut  =cut
2636    
2637  sub EmergencyFileTarget {  sub Now {
2638      # Get the parameters.      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2639      my ($tkey) = @_;      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2640      # Compute the emergency tracing file name.                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2641      return "$FIG_Config::temp/trace$tkey.log";      return $retVal;
2642    }
2643    
2644    # Pad a number to 2 digits.
2645    sub _p2 {
2646        my ($value) = @_;
2647        $value = "0$value" if ($value < 10);
2648        return $value;
2649  }  }
2650    
2651  =head3 EmergencyTracingDest  =head3 Escape
2652    
2653  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my $codedString = Tracer::Escape($realString);
2654    
2655  This method converts an emergency tracing destination to a real  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2656  tracing destination. The main difference is that if the  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2657  destination is C<FILE> or C<APPEND>, we convert it to file  result is to reverse the effect of L</UnEscape>.
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2658    
2659  =over 4  =over 4
2660    
2661  =item tkey  =item realString
   
 Tracing key for this environment.  
   
 =item myDest  
2662    
2663  Destination from the emergency tracing file.  String to escape.
2664    
2665  =item RETURN  =item RETURN
2666    
2667  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2668    
2669  =back  =back
2670    
2671  =cut  =cut
2672    
2673  sub EmergencyTracingDest {  sub Escape {
2674      # Get the parameters.      # Get the parameter.
2675      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2676      # Declare the return variable.      # Initialize the return variable.
2677      my $retVal = $myDest;      my $retVal = "";
2678      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2679      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2680          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2681      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2682          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2683      } elsif ($myDest eq 'DUAL') {              # itself is in $2. First, move the clear text to the return variable.
2684          $retVal = "+>" . EmergencyFileTarget($tkey);              $retVal .= $1;
2685                # Strip the processed section off the real string.
2686                $realString = substr $realString, (length $2) + (length $1);
2687                # Get the matched character.
2688                my $char = $2;
2689                # If we have a CR, we are done.
2690                if ($char ne "\r") {
2691                    # It's not a CR, so encode the escape sequence.
2692                    $char =~ tr/\t\n/tn/;
2693                    $retVal .= "\\" . $char;
2694                }
2695            } else {
2696                # Here there are no more escape sequences. The rest of the string is
2697                # transferred unmodified.
2698                $retVal .= $realString;
2699                $realString = "";
2700            }
2701      }      }
2702      # Return the result.      # Return the result.
2703      return $retVal;      return $retVal;
2704  }  }
2705    
2706  =head3 Emergency  =head3 UnEscape
2707    
2708  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2709    
2710  Turn on emergency tracing. This method is normally invoked over the web from  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2711  a debugging console, but it can also be called by the C<trace.pl> script.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2712  The caller specifies the duration of the emergency in hours, the desired tracing  be deleted.
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
2713    
2714  =over 4  =over 4
2715    
2716  =item tkey  =item codedString
   
 The tracing key. This is used to identify the control file and the trace file.  
   
 =item hours  
   
 Number of hours to keep emergency tracing alive.  
   
 =item dest  
   
 Tracing destination. If no path information is specified for a file  
 destination, it is put in the FIG temporary directory.  
   
 =item level  
2717    
2718  Tracing level. A higher level means more trace messages.  String to un-escape.
2719    
2720  =item modules  =item RETURN
2721    
2722  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2723    values.
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub Emergency {  sub UnEscape {
2730      # Get the parameters.      # Get the parameter.
2731      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2732      # Create the emergency file.      # Initialize the return variable.
2733      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2734      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2735      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2736            # Loop through the parameter string, looking for escape sequences. We can't do
2737            # translating because it causes problems with the escaped slash. ("\\t" becomes
2738            # "\<tab>" no matter what we do.)
2739            while (length $codedString > 0) {
2740                # Look for the first escape sequence.
2741                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2742                    # Here we found it. The text preceding the sequence is in $1. The sequence
2743                    # itself is in $2. First, move the clear text to the return variable.
2744                    $retVal .= $1;
2745                    $codedString = substr $codedString, (2 + length $1);
2746                    # Get the escape value.
2747                    my $char = $2;
2748                    # If we have a "\r", we are done.
2749                    if ($char ne 'r') {
2750                        # Here it's not an 'r', so we convert it.
2751                        $char =~ tr/\\tn/\\\t\n/;
2752                        $retVal .= $char;
2753                    }
2754                } else {
2755                    # Here there are no more escape sequences. The rest of the string is
2756                    # transferred unmodified.
2757                    $retVal .= $codedString;
2758                    $codedString = "";
2759                }
2760            }
2761        }
2762        # Return the result.
2763        return $retVal;
2764  }  }
2765    
2766  =head3 EmergencyKey  =head3 Percent
2767    
2768  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
2769    
2770  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
2771   a session ID, or a user name, depending on the environment.  is zero, returns zero.
2772    
2773  =over 4  =over 4
2774    
2775  =item parameter  =item number
2776    
2777  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
2778  then it is presumed to be the tracing key itself. If it is a CGI object, then  
2779  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
2780  taken from the C<TRACING> environment variable.  
2781    Percent base.
2782    
2783  =item RETURN  =item RETURN
2784    
2785  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
2786    
2787  =back  =back
2788    
2789  =cut  =cut
2790    
2791  sub EmergencyKey {  sub Percent {
2792      # Get the parameters.      # Get the parameters.
2793      my ($parameter) = @_;      my ($number, $base) = @_;
2794      # Declare the return variable.      # Declare the return variable.
2795      my $retVal;      my $retVal = 0;
2796      # Determine the parameter type.      # Compute the percent.
2797      if (! defined $parameter) {      if ($base != 0) {
2798          # Here we're supposed to check the environment.          $retVal = $number * 100 / $base;
         $retVal = $ENV{TRACING};  
     } else {  
         my $ptype = ref $parameter;  
         if ($ptype eq 'CGI') {  
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2799      }      }
2800      # Return the result.      # Return the result.
2801      return $retVal;      return $retVal;
2802  }  }
2803    
2804    =head3 Min
2805    
2806  =head3 TraceParms      my $min = Min($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
2807    
2808  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Return the minimum argument. The arguments are treated as numbers.
 at level CGI => 4.  
2809    
2810  =over 4  =over 4
2811    
2812  =item cgi  =item $value1, $value2, ... $valueN
2813    
2814  CGI query object containing the parameters to trace.  List of numbers to compare.
2815    
2816    =item RETURN
2817    
2818    Returns the lowest number in the list.
2819    
2820  =back  =back
2821    
2822  =cut  =cut
2823    
2824  sub TraceParms {  sub Min {
2825      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2826      my ($cgi) = @_;      my ($retVal, @values) = @_;
2827      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the lowest.
2828          # Here we want to trace the parameter data.      for my $value (@values) {
2829          my @names = $cgi->param;          if ($value < $retVal) {
2830          for my $parmName (sort @names) {              $retVal = $value;
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
2831  }  }
   
 =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";  
2832      }      }
2833      use Tracer;      # Return the minimum found.
2834      use CGI;      return $retVal;
     use FIG;  
     # ... more uses ...  
   
     my ($cgi, $varHash) = ScriptSetup();  
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
2835      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2836    
2837  The idea here is that even if the script fails, you'll see trace messages and  =head3 Max
2838  useful output.  
2839        my $max = Max($value1, $value2, ... $valueN);
2840    
2841    Return the maximum argument. The arguments are treated as numbers.
2842    
2843  =over 4  =over 4
2844    
2845  =item webData  =item $value1, $value2, ... $valueN
2846    
2847  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2848    
2849  =item varHash (optional)  =item RETURN
2850    
2851  If specified, then a reference to a hash mapping variable names for a template  Returns the highest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2852    
2853  =back  =back
2854    
2855  =cut  =cut
2856    
2857  sub ScriptFinish {  sub Max {
2858      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2859      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
2860      # Check for a template file situation.      # Loop through the remaining parameters, looking for the highest.
2861      my $outputString;      for my $value (@values) {
2862      if (defined $varHash) {          if ($value > $retVal) {
2863          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
2864          }          }
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
2865      }      }
2866      # Check for trace messages.      # Return the maximum found.
2867      if ($Destination ne "NONE" && $TraceLevel > 0) {      return $retVal;
         # 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;  
2868          }          }
2869          # If the trace messages were queued, we unroll them. Otherwise, we display the  
2870          # destination.  =head3 DebugMode
2871          my $traceHtml;  
2872          if ($Destination eq "QUEUE") {      if (Tracer::DebugMode) { ...code... }
2873              $traceHtml = QTrace('Html');  
2874          } elsif ($Destination =~ /^>>(.+)$/) {  Return TRUE if debug mode has been turned on, else abort.
2875              # Here the tracing output it to a file. We code it as a hyperlink so the user  
2876              # can copy the file name into the clipboard easily.  Certain CGI scripts are too dangerous to exist in the production
2877              my $actualDest = $1;  environment. This method provides a simple way to prevent them
2878              $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  from working unless they are explicitly turned on by creating a password
2879    cookie via the B<SetPassword> script.  If debugging mode
2880    is not turned on, an error will occur.
2881    
2882    =cut
2883    
2884    sub DebugMode {
2885        # Declare the return variable.
2886        my $retVal = 0;
2887        # Check the debug configuration.
2888        my $password = CGI::cookie("DebugMode");
2889        my $encrypted = Digest::MD5::md5_hex($password);
2890        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2891            $retVal = 1;
2892          } else {          } else {
2893              # Here we have one of the special destinations.          # Here debug mode is off, so we generate an error.
2894              $traceHtml = "<P>Tracing output type is $Destination.</p>\n";          Confess("Cannot use this facility without logging in.");
         }  
         substr $outputString, $pos, 0, $traceHtml;  
2895      }      }
2896      # Write the output string.      # Return the determination indicator.
2897      print $outputString;      return $retVal;
2898  }  }
2899    
2900  =head3 Insure  =head3 Strip
2901    
2902  C<< Insure($dirName); >>      my $string = Tracer::Strip($line);
2903    
2904  Insure a directory is present.  Strip all line terminators off a string. This is necessary when dealing with files
2905    that may have been transferred back and forth several times among different
2906    operating environments.
2907    
2908  =over 4  =over 4
2909    
2910  =item dirName  =item line
2911    
2912  Name of the directory to check. If it does not exist, it will be created.  Line of text to be stripped.
2913    
2914    =item RETURN
2915    
2916    The same line of text with all the line-ending characters chopped from the end.
2917    
2918  =back  =back
2919    
2920  =cut  =cut
2921    
2922  sub Insure {  sub Strip {
2923      my ($dirName) = @_;      # Get a copy of the parameter string.
2924      if (! -d $dirName) {      my ($string) = @_;
2925          Trace("Creating $dirName directory.") if T(File => 2);      my $retVal = (defined $string ? $string : "");
2926          eval { mkpath $dirName; };      # Strip the line terminator characters.
2927          if ($@) {      $retVal =~ s/(\r|\n)+$//g;
2928              Confess("Error creating $dirName: $@");      # Return the result.
2929          }      return $retVal;
     }  
2930  }  }
2931    
2932  =head3 ChDir  =head3 Pad
2933    
2934  C<< ChDir($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2935    
2936  Change to the specified directory.  Pad a string to a specified length. The pad character will be a
2937    space, and the padding will be on the right side unless specified
2938    in the third parameter.
2939    
2940  =over 4  =over 4
2941    
2942  =item dirName  =item string
2943    
2944  Name of the directory to which we want to change.  String to be padded.
2945    
2946    =item len
2947    
2948    Desired length of the padded string.
2949    
2950    =item left (optional)
2951    
2952    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2953    
2954    =item padChar (optional)
2955    
2956    Character to use for padding. The default is a space.
2957    
2958    =item RETURN
2959    
2960    Returns a copy of the original string with the pad character added to the
2961    specified end so that it achieves the desired length.
2962    
2963  =back  =back
2964    
2965  =cut  =cut
2966    
2967  sub ChDir {  sub Pad {
2968      my ($dirName) = @_;      # Get the parameters.
2969      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
2970          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
2971        if (! defined $padChar) {
2972            $padChar = " ";
2973        }
2974        # Compute the number of spaces needed.
2975        my $needed = $len - length $string;
2976        # Copy the string into the return variable.
2977        my $retVal = $string;
2978        # Only proceed if padding is needed.
2979        if ($needed > 0) {
2980            # Create the pad string.
2981            my $pad = $padChar x $needed;
2982            # Affix it to the return value.
2983            if ($left) {
2984                $retVal = $pad . $retVal;
2985      } else {      } else {
2986          Trace("Changing to directory $dirName.") if T(File => 4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
2987          }          }
2988      }      }
2989        # Return the result.
2990        return $retVal;
2991  }  }
2992    
2993  =head3 SendSMS  =head3 EOF
2994    
2995  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
2996    
2997  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
2998    
2999      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3000                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3001                  api_id => '2561022' };  }
3002    
3003  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3004    
3005  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
3006    
3007  =over 4  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3008    dot-slash (C<./> will be removed. So, for example, if you were doing
3009    
3010  =item phoneNumber      `./protein.cgi`
3011    
3012  Phone number to receive the message, in international format. A United States phone number  from inside a CGI script, it would work fine in Unix, but would issue an error message
3013  would be prefixed by "1". A British phone number would be prefixed by "44".  in Windows complaining that C<'.'> is not a valid command. If instead you code
3014    
3015  =item msg      TICK("./protein.cgi")
3016    
3017  Message to send to the specified phone.  it will work correctly in both environments.
3018    
3019    =over 4
3020    
3021    =item commandString
3022    
3023    The command string to pass to the system.
3024    
3025  =item RETURN  =item RETURN
3026    
3027  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
3028    
3029  =back  =back
3030    
3031  =cut  =cut
3032    #: Return Type @;
3033  sub SendSMS {  sub TICK {
3034      # Get the parameters.      # Get the parameters.
3035      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3036      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3037      my $retVal;      if ($FIG_Config::win_mode) {
3038      # Only proceed if we have phone support.          $commandString =~ s!^\./!!;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
3039      }      }
3040      # Return the result.      # Activate the command and return the result.
3041      return $retVal;      return `$commandString`;
3042  }  }
3043    
3044    
3045  =head3 CommaFormat  =head3 CommaFormat
3046    
3047  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3048    
3049  Insert commas into a number.  Insert commas into a number.
3050    
# Line 2749  Line 3077 
3077      # Return the result.      # Return the result.
3078      return $retVal;      return $retVal;
3079  }  }
 =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);  
3080    
 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(File => 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;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # 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. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($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(File => 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) != $mask) {  
                                 # 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, $fixCount fixed.") if T(File => 2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3081    
3082  =head3 CompareLists  =head3 CompareLists
3083    
3084  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3085    
3086  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3087  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2950  Line 3146 
3146      return ($inserted, $deleted);      return ($inserted, $deleted);
3147  }  }
3148    
 =head3 GetLine  
   
 C<< my @data = Tracer::GetLine($handle); >>  
   
 Read a line of data from a tab-delimited file.  
   
 =over 4  
   
 =item handle  
   
 Open file handle from which to read.  
   
 =item RETURN  
   
 Returns a list of the fields in the record read. The fields are presumed to be  
 tab-delimited. If we are at the end of the file, then an empty list will be  
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
   
 =back  
   
 =cut  
   
 sub GetLine {  
     # Get the parameters.  
     my ($handle) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);  
     # Read from the file.  
     my $line = <$handle>;  
     # Only proceed if we found something.  
     if (defined $line) {  
         # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an  
         # upload control and have a nonstandard EOL combination.  
         $line =~ s/(\r|\n)+$//;  
         # Here we do some fancy tracing to help in debugging complicated EOL marks.  
         if (T(File => 4)) {  
             my $escapedLine = $line;  
             $escapedLine =~ s/\n/\\n/g;  
             $escapedLine =~ s/\r/\\r/g;  
             $escapedLine =~ s/\t/\\t/g;  
             Trace("Line read: -->$escapedLine<--");  
         }  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
     } else {  
         # Trace the reason the read failed.  
         Trace("End of file: $!") if T(File => 3);  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 PutLine  
   
 C<< Tracer::PutLine($handle, \@fields, $eol); >>  
   
 Write a line of data to a tab-delimited file. The specified field values will be  
 output in tab-separated form, with a trailing new-line.  
   
 =over 4  
   
 =item handle  
   
 Output file handle.  
   
 =item fields  
   
 List of field values.  
   
 =item eol (optional)  
   
 End-of-line character (default is "\n").  
   
 =back  
   
 =cut  
   
 sub PutLine {  
     # Get the parameters.  
     my ($handle, $fields, $eol) = @_;  
     # Write the data.  
     print $handle join("\t", @{$fields}) . ($eol || "\n");  
 }  
   
3149  =head3 GenerateURL  =head3 GenerateURL
3150    
3151  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3152    
3153  Generate a GET-style URL for the specified page with the specified parameter  Generate a GET-style URL for the specified page with the specified parameter
3154  names and values. The values will be URL-escaped automatically. So, for  names and values. The values will be URL-escaped automatically. So, for
# Line 3091  Line 3196 
3196    
3197  =head3 ApplyURL  =head3 ApplyURL
3198    
3199  C<< Tracer::ApplyURL($table, $target, $url); >>      Tracer::ApplyURL($table, $target, $url);
3200    
3201  Run through a two-dimensional table (or more accurately, a list of lists), converting the  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3202  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
# Line 3134  Line 3239 
3239    
3240  =head3 CombineURL  =head3 CombineURL
3241    
3242  C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3243    
3244  This method will convert the specified text into HTML hyperlinked to the specified  This method will convert the specified text into HTML hyperlinked to the specified
3245  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
# Line 3175  Line 3280 
3280      return $retVal;      return $retVal;
3281  }  }
3282    
3283    =head3 Cmp
3284    
3285        my $cmp = Tracer::Cmp($a, $b);
3286    
3287    This method performs a universal sort comparison. Each value coming in is
3288    separated into a leading text part and a trailing number part. The text
3289    part is string compared, and if both parts are equal, then the number
3290    parts are compared numerically. A stream of just numbers or a stream of
3291    just strings will sort correctly, and a mixed stream will sort with the
3292    numbers first. Strings with a label and a number will sort in the
3293    expected manner instead of lexically.
3294    
3295    =over 4
3296    
3297    =item a
3298    
3299    First item to compare.
3300    
3301    =item b
3302    
3303    Second item to compare.
3304    
3305    =item RETURN
3306    
3307    Returns a negative number if the first item should sort first (is less), a positive
3308    number if the first item should sort second (is greater), and a zero if the items are
3309    equal.
3310    
3311    =back
3312    
3313    =cut
3314    
3315    sub Cmp {
3316        # Get the parameters.
3317        my ($a, $b) = @_;
3318        # Declare the return value.
3319        my $retVal;
3320        # Check for nulls.
3321        if (! defined($a)) {
3322            $retVal = (! defined($b) ? 0 : -1);
3323        } elsif (! defined($b)) {
3324            $retVal = 1;
3325        } else {
3326            # Here we have two real values. Parse the two strings.
3327            $a =~ /^(\D*)(\d*)$/;
3328            my $aParsed = [$1, $2];
3329            $b =~ /^(\D*)(\d*)$/;
3330            my $bParsed = [$1, $2];
3331            # Compare the string parts.
3332            $retVal = $aParsed->[0] cmp $bParsed->[0];
3333            if (! $retVal) {
3334                $retVal = $aParsed->[1] <=> $bParsed->[1];
3335            }
3336        }
3337        # Return the result.
3338        return $retVal;
3339    }
3340    
3341    
3342  1;  1;

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