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revision 1.79, Thu Nov 9 21:12:46 2006 UTC revision 1.93, Tue Feb 5 02:17:29 2008 UTC
# Line 186  Line 186 
186  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187  will be configured automatically.  will be configured automatically.
188    
189    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192  =head3 Debugging Control Panel  =head3 Debugging Control Panel
193    
194  The debugging control panel provides several tools to assist in development of  The debugging control panel provides several tools to assist in development of
# Line 293  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 369  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.  
405    
406      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  sub SetLevel {
407        $TraceLevel = $_[0];
408    }
409    
410  Standard tracing is output to the standard output and echoed to the file  =head3 ParseTraceDate
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
411    
412  The default trace level is 2. To get all messages, specify a trace level of 4.      my $time = Tracer::ParseTraceDate($dateString);
 For a genome-by-genome update, use 3.  
413    
414      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  Convert a date from the trace file into a PERL timestamp.
415    
416  would send the trace output to C<traceBruce.log> in the temporary directory.  =over 4
417    
418  The I<options> parameter is a reference to a hash containing the command-line  =item dateString
 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.  
419    
420  You can specify a different default trace level by setting C<$options->{trace}>  The date string from the trace file. The format of the string is determined by the
421  prior to calling this method.  L</Now> method.
422    
423  An example at this point would help. Consider, for example, the command-line utility  =item RETURN
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
424    
425      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
426                          { safe => [0, "use database transactions"],  the time string is invalid.
                           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);  
427    
428    =back
429    
430  The call to C<ParseCommand> specifies the default values for the options and  =cut
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
431    
432  The following is a sample command line for C<TransactFeatures>.  sub ParseTraceDate {
433        # Get the parameters.
434        my ($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 $retVal;
446    }
447    
448      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
449    
450  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 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<$options> hash would be  
451    
452      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
453    
454  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
455    
456  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
457    
458      -user=Bruce -background  Name of the file to receive the error output.
459    
460  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
461    
462  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
463    
464  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
465  be traced at level 0 and the program will exit without processing.      # Get the file name.
466  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
467        # Open the file as the standard error output.
468        open STDERR, '>', $fileName;
469    }
470    
471      TransactFeatures -h  =head3 Trace
472    
473  he would see the following output.      Trace($message);
474    
475      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
476          -trace    tracing level (default E)  any prior call to B<TSetup>.
         -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  
477    
478  The caller has the option of modifying the tracing scheme by placing a value  =over 4
 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,  
479    
480      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
481    
482  would set the default trace level to 0 instead of E, while  Message to write.
483    
484      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
485    
486  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
487    
488  The parameters to this method are as follows.  sub Trace {
489        # 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  =over 4  =head3 T
526    
527  =item categories      my $switch = T($category, $traceLevel);
528    
529  Reference to a list of tracing category names. These should be names of      or
 packages whose internal workings will need to be debugged to get the  
 command working.  
530    
531  =item options      my $switch = T($traceLevel);
532    
533  Reference to a hash containing the legal options for the current command mapped  Return TRUE if the trace level is at or above a specified value and the specified category
534  to their default values and descriptions. The user can override the defaults  is active, else FALSE. If no category is specified, the caller's package name is used.
 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).  
535    
536  =item parmHelp  =over 4
537    
538  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
539    
540  =item argv  Category to which the message belongs. If not specified, the caller's package name is
541    used.
542    
543  List of command line parameters, including the option switches, which must  =item traceLevel
544  precede the positional parameters and be prefixed by a hyphen.  
545    Relevant tracing level.
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.      # Get the parameters.
561      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
562      # Get the default tracing key.          if (!defined $traceLevel) {
563      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
564      # Add the tracing options.              # The calling package is normally the first parameter. If it is
565      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
566          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
567      }              # $traceLevel variable where it belongs.
568      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
569      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
570      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
571      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
572      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
573      } else {      } else {
574          # Here the tracing is controlled from the command line.                  my @cats = split /::/, $package;
575          my @cats = @{$categories};                  $category = $cats[$#cats];
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # 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;  
576          }          }
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
577              }              }
578              # Close the test file.          # Save the category name.
579              close TESTTRACE;          $LastCategory = $category;
580          } else {          # Convert it to lower case before we hash it.
581              # Here we can't trace to a file. We trace to the standard output if it's          $category = lc $category;
582              # okay, and the error log otherwise.          # Use the category and tracelevel to compute the result.
583              if ($textOKFlag) {          if (ref $traceLevel) {
584                  $traceMode = "TEXT";              Confess("Bad trace level.");
585              } else {          } elsif (ref $TraceLevel) {
586                  $traceMode = "WARN";              Confess("Bad trace config.");
587              }              }
588            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
589          }          }
590          # Now set up the tracing.      # Return the computed result.
591          TSetup("$traceLevel $cats", $traceMode);      return $retVal;
592      }      }
593      # Check for the "h" option. If it is specified, dump the command-line  
594      # options and exit the program.  =head3 QTrace
595      if ($retOptions->{h}) {  
596          $0 =~ m#[/\\](\w+)(\.pl)?$#i;      my $data = QTrace($format);
597          print "$1 [options] $parmHelp\n";  
598          for my $key (sort keys %{$options}) {  Return the queued trace data in the specified format.
599              my $name = Pad($key, $longestName, 0, ' ');  
600              my $desc = $options->{$key}->[1];  =over 4
601              if ($options->{$key}->[0]) {  
602                  $desc .= " (default " . $options->{$key}->[0] . ")";  =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              print "  $name $desc\n";              $retVal .= "</ul>\n";
626            } elsif ($format =~ m/^TEXT$/i) {
627                # Convert the queue into a list of text lines.
628                $retVal = join("\n", @Queue) . "\n";
629          }          }
630          exit(0);          # Clear the queue.
631            @Queue = ();
632      }      }
633      # Return the parsed parameters.      # Return the formatted list.
634      return ($retOptions, @retParameters);      return $retVal;
635  }  }
636    
637  =head3 Setups  =head3 Confess
638    
639  C<< my $count = Tracer::Setups(); >>      Confess($message);
640    
641  Return the number of times L</TSetup> has been called.  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  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
646  may want to set up tracing if nobody else has done it before us.  
647    Will abort the program with a stack trace if the value of C<$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  =cut
658    
659  sub Setups {  sub Confess {
660      return $SetupCount;      # Get the parameters.
661        my ($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 Open  =head3 Assert
678    
679  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      Assert($condition1, $condition2, ... $conditionN);
680    
681  Open a file.  Return TRUE if all the conditions are true. This method can be used in conjunction with
682    the OR operator and the L</Confess> method as a debugging assert.
683    So, for example
684    
685  The I<$fileSpec> is essentially the second argument of the PERL C<open>      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
686    
687      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Will abort the program with a stack trace if the value of C<$recNum> is negative.
688    
689  would open for output appended to the specified file, and  =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 $retVal;
699    }
700    
701      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =head3 Cluck
702    
703  would open a pipe that sorts the records written and removes duplicates. Note      Cluck($message);
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
704    
705      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Trace the call stack. Note that for best results, you should qualify the call with a
706    trace condition. For example,
707    
708  The I<$message> parameter is used if the open fails. If it is set to C<0>, then      Cluck("Starting record parse.") if T(3);
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
709    
710      Could not open "/usr/spool/news/twitlog"  will only trace the stack if the trace level for the package is 3 or more.
711    
712  Note that the mode characters are automatically cleaned from the file name.  =over 4
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
713    
714      Could not open "/usr/spool/news/twitlog": file not found.  =item message
715    
716  In some versions of PERL the only error message we get is a number, which  Message to include in the trace.
 corresponds to the C++ C<errno> value.  
717    
718      Could not open "/usr/spool/news/twitlog": 6.  =back
719    
720  =over 4  =cut
721    
722  =item fileHandle  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 ($line !~ /Tracer\.pm/);
732        }
733    }
734    
735  File handle. If this parameter is C<undef>, a file handle will be generated  =head3 ScriptSetup
 and returned as the value of this method.  
736    
737  =item fileSpec      my ($cgi, $varHash) = ScriptSetup($noTrace);
738    
739  File name and mode, as per the PERL C<open> function.  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  =item message (optional)  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  Error message to use if the open fails. If omitted, a standard error message  =over 4
749  will be generated. In either case, the error information from the file system  
750  is appended to the message. To specify a conditional open that does not throw  =item noTrace (optional)
751  an error if it fails, use C<0>.  
752    If specified, tracing will be suppressed. This is useful if the script wants to set up
753    tracing manually.
754    
755  =item RETURN  =item RETURN
756    
757  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns a two-element list consisting of a CGI query object and a variable hash for
758  open failed.  the output page.
759    
760  =back  =back
761    
762  =cut  =cut
763    
764  sub Open {  sub ScriptSetup {
765      # Get the parameters.      # Get the parameters.
766      my ($fileHandle, $fileSpec, $message) = @_;      my ($noTrace) = @_;
767      # Attempt to open the file.      # Get the CGI query object.
768      my $rv = open $fileHandle, $fileSpec;      my $cgi = CGI->new();
769      # If the open failed, generate an error message.      # Set up tracing if it's not suppressed.
770      if (! $rv) {      ETracing($cgi) unless $noTrace;
771          # Save the system error message.      # Create the variable hash.
772          my $sysMessage = $!;      my $varHash = { results => '' };
773          # See if we need a default message.      # Return the query object and variable hash.
774          if (!$message) {      return ($cgi, $varHash);
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
         }  
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
     }  
     # Return the file handle.  
     return $fileHandle;  
775  }  }
776    
777  =head3 FindNamePart  =head3 ETracing
778    
779  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      ETracing($parameter);
780    
781  Extract the portion of a file specification that contains the file name.  Set up emergency tracing. Emergency tracing is tracing that is turned
782    on automatically for any program that calls this method. The emergency
783    tracing parameters are stored in a a file identified by a tracing key.
784    If this method is called with a CGI object, then the tracing key is
785    taken from a cookie. If it is called with no parameters, then the tracing
786    key is taken from an environment variable. If it is called with a string,
787    the tracing key is that string.
788    
789  A file specification is the string passed to an C<open> call. It specifies the file  =over 4
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
790    
791      >>/usr/fig/myfile.txt  =item parameter
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
792    
793  If the method cannot find a file name using its normal methods, it will return the  A parameter from which the tracing key is computed. If it is a scalar,
794  whole incoming string.  that scalar is used as the tracing key. If it is a CGI object, the
795    tracing key is taken from the C<IP> cookie. If it is omitted, the
796    tracing key is taken from the C<TRACING> environment variable. If it
797    is a CGI object and emergency tracing is not on, the C<Trace> and
798    C<TF> parameters will be used to determine the type of tracing.
799    
800    =back
801    
802    =cut
803    
804    sub ETracing {
805        # Get the parameter.
806        my ($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        # If we're a web script, trace the parameter and environment data.
853        if (defined $cgi) {
854            TraceParms($cgi);
855        }
856    }
857    
858    =head3 EmergencyFileName
859    
860        my $fileName = Tracer::EmergencyFileName($tkey);
861    
862    Return the emergency tracing file name. This is the file that specifies
863    the tracing information.
864    
865  =over 4  =over 4
866    
867  =item fileSpec  =item tkey
868    
869  File specification string from which the file name is to be extracted.  Tracing key for the current program.
870    
871  =item RETURN  =item RETURN
872    
873  Returns a three-element list. The first element contains the file name portion of  Returns the name of the file to contain the emergency tracing information.
 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.  
874    
875  =back  =back
876    
877  =cut  =cut
878  #: Return Type $;  
879  sub FindNamePart {  sub EmergencyFileName {
880      # Get the parameters.      # Get the parameters.
881      my ($fileSpec) = @_;      my ($tkey) = @_;
882      # Default to the whole input string.      # Compute the emergency tracing file name.
883      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      return "$FIG_Config::temp/Emergency$tkey.txt";
     # 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);  
884  }  }
885    
886  =head3 OpenDir  =head3 EmergencyFileTarget
887    
888  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
889    
890  Open a directory and return all the file names. This function essentially performs  Return the emergency tracing target file name. This is the file that receives
891  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the tracing output for file-based tracing.
 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,  
892    
893      my @files = OpenDir("/Volumes/fig/contigs", 1);  =over 4
894    
895  is effectively the same as  =item tkey
896    
897      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  Tracing key for the current program.
898      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
899    =item RETURN
900    
901    Returns the name of the file to contain the trace output.
902    
903    =back
904    
905    =cut
906    
907    sub EmergencyFileTarget {
908        # Get the parameters.
909        my ($tkey) = @_;
910        # Compute the emergency tracing file name.
911        return "$FIG_Config::temp/trace$tkey.log";
912    }
913    
914  Similarly, the following code  =head3 EmergencyTracingDest
915    
916      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
917    
918  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method converts an emergency tracing destination to a real
919  automatically returns an empty list if the directory fails to open.  tracing destination. The main difference is that if the
920    destination is C<FILE> or C<APPEND>, we convert it to file
921    output. If the destination is C<DUAL>, we convert it to file
922    and standard output.
923    
924  =over 4  =over 4
925    
926  =item dirName  =item tkey
927    
928  Name of the directory to open.  Tracing key for this environment.
929    
930  =item filtered  =item myDest
931    
932  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Destination from the emergency tracing file.
 from the list, else FALSE.  
933    
934  =item flag  =item RETURN
935    
936  TRUE if a failure to open is okay, else FALSE  Returns a destination that can be passed into L</TSetup>.
937    
938  =back  =back
939    
940  =cut  =cut
941  #: Return Type @;  
942  sub OpenDir {  sub EmergencyTracingDest {
943      # Get the parameters.      # Get the parameters.
944      my ($dirName, $filtered, $flag) = @_;      my ($tkey, $myDest) = @_;
945      # Declare the return variable.      # Declare the return variable.
946      my @retVal = ();      my $retVal = $myDest;
947      # Open the directory.      # Process according to the destination value.
948      if (opendir(my $dirHandle, $dirName)) {      if ($myDest eq 'FILE') {
949          # The directory opened successfully. Get the appropriate list according to the          $retVal = ">" . EmergencyFileTarget($tkey);
950          # strictures of the filter parameter.      } elsif ($myDest eq 'APPEND') {
951          if ($filtered) {          $retVal = ">>" . EmergencyFileTarget($tkey);
952              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      } elsif ($myDest eq 'DUAL') {
953          } else {          $retVal = "+>" . EmergencyFileTarget($tkey);
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
954      }      }
955      # Return the result.      # Return the result.
956      return @retVal;      return $retVal;
957  }  }
958    
959  =head3 SetLevel  =head3 Emergency
960    
961  C<< Tracer::SetLevel($newLevel); >>      Emergency($key, $hours, $dest, $level, @modules);
962    
963  Modify the trace level. A higher trace level will cause more messages to appear.  Turn on emergency tracing. This method is normally invoked over the web from
964    a debugging console, but it can also be called by the C<trace.pl> script.
965    The caller specifies the duration of the emergency in hours, the desired tracing
966    destination, the trace level, and a list of the trace modules to activate.
967    For the length of the duration, when a program in an environment with the
968    specified tracing key active invokes a Sprout CGI script, tracing will be
969    turned on automatically. See L</TSetup> for more about tracing setup and
970    L</ETracing> for more about emergency tracing.
971    
972  =over 4  =over 4
973    
974  =item newLevel  =item tkey
975    
976  Proposed new trace level.  The tracing key. This is used to identify the control file and the trace file.
977    
978  =back  =item hours
979    
980  =cut  Number of hours to keep emergency tracing alive.
981    
982  sub SetLevel {  =item dest
     $TraceLevel = $_[0];  
 }  
983    
984  =head3 Now  Tracing destination. If no path information is specified for a file
985    destination, it is put in the FIG temporary directory.
986    
987  C<< my $string = Tracer::Now(); >>  =item level
988    
989  Return a displayable time stamp containing the local time.  Tracing level. A higher level means more trace messages.
990    
991  =cut  =item modules
992    
993  sub Now {  A list of the tracing modules to activate.
     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;  
 }  
994    
995  # Pad a number to 2 digits.  =back
996  sub _p2 {  
997      my ($value) = @_;  =cut
998      $value = "0$value" if ($value < 10);  
999      return $value;  sub Emergency {
1000        # Get the parameters.
1001        my ($tkey, $hours, $dest, $level, @modules) = @_;
1002        # Create the emergency file.
1003        my $specFile = EmergencyFileName($tkey);
1004        my $outHandle = Open(undef, ">$specFile");
1005        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1006  }  }
1007    
1008  =head3 ParseTraceDate  =head3 EmergencyKey
1009    
1010  C<< my $time = Tracer::ParseTraceDate($dateString); >>      my $tkey = EmergencyKey($parameter);
1011    
1012  Convert a date from the trace file into a PERL timestamp.  Return the Key to be used for emergency tracing. This could be an IP address,
1013     a session ID, or a user name, depending on the environment.
1014    
1015  =over 4  =over 4
1016    
1017  =item dateString  =item parameter
1018    
1019  The date string from the trace file. The format of the string is determined by the  Parameter defining the method for finding the tracing key. If it is a scalar,
1020  L</Now> method.  then it is presumed to be the tracing key itself. If it is a CGI object, then
1021    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1022    taken from the C<TRACING> environment variable.
1023    
1024  =item RETURN  =item RETURN
1025    
1026  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns the key to be used for labels in emergency tracing.
 the time string is invalid.  
1027    
1028  =back  =back
1029    
1030  =cut  =cut
1031    
1032  sub ParseTraceDate {  sub EmergencyKey {
1033      # Get the parameters.      # Get the parameters.
1034      my ($dateString) = @_;      my ($parameter) = @_;
1035      # Declare the return variable.      # Declare the return variable.
1036      my $retVal;      my $retVal;
1037      # Parse the date.      # Determine the parameter type.
1038      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      if (! defined $parameter) {
1039          # Create a time object. Note we need to convert the day, month,          # Here we're supposed to check the environment.
1040          # and year to a different base. Years count from 1900, and          $retVal = $ENV{TRACING};
1041          # the internal month value is relocated to January = 0.      } else {
1042          $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);          my $ptype = ref $parameter;
1043            if ($ptype eq 'CGI') {
1044                # Here we were invoked from a web page. Look for a cookie.
1045                $retVal = $parameter->cookie('IP');
1046            } elsif (! $ptype) {
1047                # Here the key was passed in.
1048                $retVal = $parameter;
1049            }
1050        }
1051        # If no luck finding a key, use the PID.
1052        if (! defined $retVal) {
1053            $retVal = $$;
1054      }      }
1055      # Return the result.      # Return the result.
1056      return $retVal;      return $retVal;
1057  }  }
1058    
 =head3 LogErrors  
1059    
1060  C<< Tracer::LogErrors($fileName); >>  =head3 TraceParms
1061    
1062        Tracer::TraceParms($cgi);
1063    
1064  Route the standard error output to a log file.  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1065    at level CGI => 4.
1066    
1067  =over 4  =over 4
1068    
1069  =item fileName  =item cgi
1070    
1071  Name of the file to receive the error output.  CGI query object containing the parameters to trace.
1072    
1073  =back  =back
1074    
1075  =cut  =cut
1076    
1077  sub LogErrors {  sub TraceParms {
1078      # Get the file name.      # Get the parameters.
1079      my ($fileName) = @_;      my ($cgi) = @_;
1080      # Open the file as the standard error output.      if (T(CGI => 3)) {
1081      open STDERR, '>', $fileName;          # Here we want to trace the parameter data.
1082            my @names = $cgi->param;
1083            for my $parmName (sort @names) {
1084                # Note we skip the Trace parameters, which are for our use only.
1085                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1086                    my @values = $cgi->param($parmName);
1087                    Trace("CGI: $parmName = " . join(", ", @values));
1088                }
1089            }
1090            # Display the request method.
1091            my $method = $cgi->request_method();
1092            Trace("Method: $method");
1093        }
1094        if (T(CGI => 4)) {
1095            # Here we want the environment data too.
1096            for my $envName (sort keys %ENV) {
1097                Trace("ENV: $envName = $ENV{$envName}");
1098            }
1099        }
1100  }  }
1101    
1102  =head3 ReadOptions  =head3 ScriptFinish
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1103    
1104  I<optionName>C<=>I<optionValue>C<; >I<comment>      ScriptFinish($webData, $varHash);
1105    
1106  The option name must consist entirely of letters, digits, and the punctuation characters  Output a web page at the end of a script. Either the string to be output or the
1107  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  name of a template file can be specified. If the second parameter is omitted,
1108  character is a semi-colon will be ignored. The return hash will map each option name to  it is assumed we have a string to be output; otherwise, it is assumed we have the
1109  the corresponding option value.  name of a template file. The template should have the variable C<DebugData>
1110    specified in any form that invokes a standard script. If debugging mode is turned
1111    on, a form field will be put in that allows the user to enter tracing data.
1112    Trace messages will be placed immediately before the terminal C<BODY> tag in
1113    the output, formatted as a list.
1114    
1115  =over 4  A typical standard script would loook like the following.
1116    
1117  =item fileName      BEGIN {
1118            # Print the HTML header.
1119            print "CONTENT-TYPE: text/html\n\n";
1120        }
1121        use Tracer;
1122        use CGI;
1123        use FIG;
1124        # ... more uses ...
1125    
1126  Name of the file containing the option data.      my ($cgi, $varHash) = ScriptSetup();
1127        eval {
1128            # ... get data from $cgi, put it in $varHash ...
1129        };
1130        if ($@) {
1131            Trace("Script Error: $@") if T(0);
1132        }
1133        ScriptFinish("Html/MyTemplate.html", $varHash);
1134    
1135  =item RETURN  The idea here is that even if the script fails, you'll see trace messages and
1136    useful output.
1137    
1138  Returns a hash mapping the option names specified in the file to their corresponding option  =over 4
 value.  
1139    
1140  =back  =item webData
1141    
1142  =cut  A string containing either the full web page to be written to the output or the
1143    name of a template file from which the page is to be constructed. If the name
1144    of a template file is specified, then the second parameter must be present;
1145    otherwise, it must be absent.
1146    
1147  sub ReadOptions {  =item varHash (optional)
1148      # Get the parameters.  
1149      my ($fileName) = @_;  If specified, then a reference to a hash mapping variable names for a template
1150      # Open the file.  to their values. The template file will be read into memory, and variable markers
1151      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");  will be replaced by data in this hash reference.
1152      # Count the number of records read.  
1153      my ($records, $comments) = 0;  =back
1154      # Create the return hash.  
1155      my %retVal = ();  =cut
1156      # Loop through the file, accumulating key-value pairs.  
1157      while (my $line = <CONFIGFILE>) {  sub ScriptFinish {
1158          # Denote we've read a line.      # Get the parameters.
1159          $records++;      my ($webData, $varHash) = @_;
1160          # Determine the line type.      # Check for a template file situation.
1161          if ($line =~ /^\s*[\n\r]/) {      my $outputString;
1162              # A blank line is a comment.      if (defined $varHash) {
1163              $comments++;          # Here we have a template file. We need to determine the template type.
1164          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {          my $template;
1165              # Here we have an option assignment.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1166              retVal{$1} = $2;              $template = "$FIG_Config::template_url/$webData";
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
1167          } else {          } else {
1168              # Here we have an invalid line.              $template = "<<$webData";
             Trace("Invalid option statement in record $records.") if T(0);  
1169          }          }
1170            $outputString = PageBuilder::Build($template, $varHash, "Html");
1171        } else {
1172            # Here the user gave us a raw string.
1173            $outputString = $webData;
1174      }      }
1175      # Return the hash created.      # Check for trace messages.
1176      return %retVal;      if ($Destination ne "NONE" && $TraceLevel > 0) {
1177            # We have trace messages, so we want to put them at the end of the body. This
1178            # is either at the end of the whole string or at the beginning of the BODY
1179            # end-tag.
1180            my $pos = length $outputString;
1181            if ($outputString =~ m#</body>#gi) {
1182                $pos = (pos $outputString) - 7;
1183            }
1184            # If the trace messages were queued, we unroll them. Otherwise, we display the
1185            # destination.
1186            my $traceHtml;
1187            if ($Destination eq "QUEUE") {
1188                $traceHtml = QTrace('Html');
1189            } elsif ($Destination =~ /^>>(.+)$/) {
1190                # Here the tracing output it to a file. We code it as a hyperlink so the user
1191                # can copy the file name into the clipboard easily.
1192                my $actualDest = $1;
1193                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1194            } else {
1195                # Here we have one of the special destinations.
1196                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1197            }
1198            substr $outputString, $pos, 0, $traceHtml;
1199        }
1200        # Write the output string.
1201        print $outputString;
1202  }  }
1203    
1204  =head3 GetOptions  =head2 Command-Line Utility Methods
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
1205    
1206  Merge a specified set of options into a table of defaults. This method takes two hash references  =head3 SendSMS
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
1207    
1208  Consider the following example.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1209    
1210  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1211    user name, password, and API ID for the relevant account in the hash reference variable
1212    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1213    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1214    is C<2561022>, then the FIG_Config file must contain
1215    
1216  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and      $phone =  { user => 'BruceTheHumanPet',
1217  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of                  password => 'silly',
1218  B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and                  api_id => '2561022' };
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1219    
1220  C<< {databaseType => 'Oracle'} >>  The original purpose of this method was to insure Bruce would be notified immediately when the
1221    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1222    when you call this method.
1223    
1224  an error will occur because the B<databaseType> option does not exist.  The message ID will be returned if successful, and C<undef> if an error occurs.
1225    
1226  =over 4  =over 4
1227    
1228  =item defaults  =item phoneNumber
1229    
1230  Table of default option values.  Phone number to receive the message, in international format. A United States phone number
1231    would be prefixed by "1". A British phone number would be prefixed by "44".
1232    
1233  =item options  =item msg
1234    
1235  Table of overrides, if any.  Message to send to the specified phone.
1236    
1237  =item RETURN  =item RETURN
1238    
1239  Returns a reference to the default table passed in as the first parameter.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1240    
1241  =back  =back
1242    
1243  =cut  =cut
1244    
1245  sub GetOptions {  sub SendSMS {
1246      # Get the parameters.      # Get the parameters.
1247      my ($defaults, $options) = @_;      my ($phoneNumber, $msg) = @_;
1248      # Check for overrides.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1249      if ($options) {      my $retVal;
1250          # Loop through the overrides.      # Only proceed if we have phone support.
1251          while (my ($option, $setting) = each %{$options}) {      if (! defined $FIG_Config::phone) {
1252              # Insure this override exists.          Trace("Phone support not present in FIG_Config.") if T(1);
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
1253              } else {              } else {
1254                  # Apply the override.          # Get the phone data.
1255                  $defaults->{$option} = $setting;          my $parms = $FIG_Config::phone;
1256            # Get the Clickatell URL.
1257            my $url = "http://api.clickatell.com/http/";
1258            # Create the user agent.
1259            my $ua = LWP::UserAgent->new;
1260            # Request a Clickatell session.
1261            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1262                                         password => $parms->{password},
1263                                         api_id => $parms->{api_id},
1264                                         to => $phoneNumber,
1265                                         text => $msg});
1266            # Check for an error.
1267            if (! $resp->is_success) {
1268                Trace("Alert failed.") if T(1);
1269            } else {
1270                # Get the message ID.
1271                my $rstring = $resp->content;
1272                if ($rstring =~ /^ID:\s+(.*)$/) {
1273                    $retVal = $1;
1274                } else {
1275                    Trace("Phone attempt failed with $rstring") if T(1);
1276              }              }
1277          }          }
1278      }      }
1279      # Return the merged table.      # Return the result.
1280      return $defaults;      return $retVal;
1281  }  }
1282    
1283  =head3 MergeOptions  =head3 StandardSetup
1284    
1285  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1286    
1287  Merge default values into a hash table. This method looks at the key-value pairs in the  This method performs standard command-line parsing and tracing setup. The return
1288  second (default) hash, and if a matching key is not found in the first hash, the default  values are a hash of the command-line options and a list of the positional
1289  pair is copied in. The process is similar to L</GetOptions>, but there is no error-  parameters. Tracing is automatically set up and the command-line options are
1290  checking and no return value.  validated.
1291    
1292    This is a complex method that does a lot of grunt work. The parameters can
1293    be more easily understood, however, once they are examined individually.
1294    
1295    The I<categories> parameter is the most obtuse. It is a reference to a list of
1296    special-purpose tracing categories. Most tracing categories are PERL package
1297    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1298    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1299    
1300        ["Sprout", "SproutLoad", "ERDB"]
1301    
1302    This would cause trace messages in the specified three packages to appear in
1303    the output. There are two special tracing categories that are automatically
1304    handled by this method. In other words, if you used L</TSetup> you would need
1305    to include these categories manually, but if you use this method they are turned
1306    on automatically.
1307    
1308  =over 4  =over 4
1309    
1310  =item table  =item SQL
1311    
1312  Hash table to be updated with the default values.  Traces SQL commands and activity.
1313    
1314  =item defaults  =item Tracer
1315    
1316  Default values to be merged into the first hash table if they are not already present.  Traces error messages and call stacks.
1317    
1318  =back  =back
1319    
1320  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1321    The trace level is specified using the C<-trace> command-line option. For example,
1322    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1323    all tracing at level 3.
1324    
1325  sub MergeOptions {      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
     # Get the parameters.  
     my ($table, $defaults) = @_;  
     # Loop through the defaults.  
     while (my ($key, $value) = each %{$defaults}) {  
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
     }  
 }  
1326    
1327  =head3 Trace  Standard tracing is output to the standard output and echoed to the file
1328    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1329    process ID. You can also specify the C<user> parameter to put a user ID
1330    instead of a process ID in the trace file name. So, for example
1331    
1332  C<< Trace($message); >>  The default trace level is 2. To get all messages, specify a trace level of 4.
1333    For a genome-by-genome update, use 3.
1334    
1335  Write a trace message to the target location specified in L</TSetup>. If there has not been      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
 any prior call to B<TSetup>.  
1336    
1337  =over 4  would send the trace output to C<traceBruce.log> in the temporary directory.
1338    
1339  =item message  The I<options> parameter is a reference to a hash containing the command-line
1340    options, their default values, and an explanation of what they mean. Command-line
1341    options may be in the form of switches or keywords. In the case of a switch, the
1342    option value is 1 if it is specified and 0 if it is not specified. In the case
1343    of a keyword, the value is separated from the option name by an equal sign. You
1344    can see this last in the command-line example above.
1345    
1346  Message to write.  You can specify a different default trace level by setting C<$options->{trace}>
1347    prior to calling this method.
1348    
1349  =back  An example at this point would help. Consider, for example, the command-line utility
1350    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1351    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1352    the following code.
1353    
1354  =cut      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1355                            { safe => [0, "use database transactions"],
1356                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1357                              start => [' ', "start with this genome"],
1358                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1359                            "<command> <transactionDirectory> <IDfile>",
1360                          @ARGV);
1361    
 sub Trace {  
     # Get the parameters.  
     my ($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";  
         }  
     }  
 }  
1362    
1363  =head3 T  The call to C<ParseCommand> specifies the default values for the options and
1364    stores the actual options in a hash that is returned as C<$options>. The
1365    positional parameters are returned in C<@parameters>.
1366    
1367  C<< my $switch = T($category, $traceLevel); >>  The following is a sample command line for C<TransactFeatures>.
1368    
1369      or      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1370    
1371  C<< my $switch = T($traceLevel); >>  Single and double hyphens are equivalent. So, you could also code the
1372    above command as
1373    
1374  Return TRUE if the trace level is at or above a specified value and the specified category      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
 is active, else FALSE. If no category is specified, the caller's package name is used.  
1375    
1376  =over 4  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1377    parameters, and would find themselves in I<@parameters> after executing the
1378    above code fragment. The tracing would be set to level 2, and the categories
1379    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1380    and C<DocUtils> was included because it came in within the first parameter
1381    to this method. The I<$options> hash would be
1382    
1383  =item category      { trace => 2, sql => 0, safe => 0,
1384          noAlias => 1, start => ' ', tblFiles => 0 }
1385    
1386  Category to which the message belongs. If not specified, the caller's package name is  Use of C<StandardSetup> in this way provides a simple way of performing
1387  used.  standard tracing setup and command-line parsing. Note that the caller is
1388    not even aware of the command-line switches C<-trace> and C<-sql>, which
1389    are used by this method to control the tracing. If additional tracing features
1390    need to be added in the future, they can be processed by this method without
1391    upsetting the command-line utilities.
1392    
1393  =item traceLevel  If the C<background> option is specified on the command line, then the
1394    standard and error outputs will be directed to files in the temporary
1395    directory, using the same suffix as the trace file. So, if the command
1396    line specified
1397    
1398  Relevant tracing level.      -user=Bruce -background
1399    
1400  =item RETURN  then the trace output would go to C<traceBruce.log>, the standard output to
1401    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1402    simplify starting a command in the background.
1403    
1404  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  The user name is also used as the tracing key for L</Emergency Tracing>.
1405    Specifying a value of C<E> for the trace level causes emergency tracing to
1406    be used instead of custom tracing. If the user name is not specified,
1407    the tracing key is taken from the C<Tracing> environment variable. If there
1408    is no value for that variable, the tracing key will be computed from the PID.
1409    
1410  =back  Finally, if the special option C<-help> is specified, the option
1411    names will be traced at level 0 and the program will exit without processing.
1412    This provides a limited help capability. For example, if the user enters
1413    
1414  =cut      TransactFeatures -help
1415    
1416  sub T {  he would see the following output.
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
     }  
     # Return the computed result.  
     return $retVal;  
 }  
1417    
1418  =head3 ParseCommand      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1419            -trace    tracing level (default E)
1420            -sql      trace SQL commands
1421            -safe     use database transactions
1422            -noAlias  do not expect aliases in CHANGE transactions
1423            -start    start with this genome
1424            -tblFiles output TBL files containing the corrected IDs
1425    
1426  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  The caller has the option of modifying the tracing scheme by placing a value
1427    for C<trace> in the incoming options hash. The default value can be overridden,
1428    or the tracing to the standard output can be turned off by suffixing a minus
1429    sign to the trace level. So, for example,
1430    
1431  Parse a command line consisting of a list of parameters. The initial parameters may be option      { trace => [0, "tracing level (default 0)"],
1432  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped         ...
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
1433    
1434  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  would set the default trace level to 0 instead of E, while
1435    
1436  In this case, the list @words will be treated as a command line. There are two options available,      { trace => ["2-", "tracing level (default 2)"],
1437  B<errors> and B<logFile>. If @words has the following format         ...
1438    
1439  C<< -logFile=error.log apple orange rutabaga >>  would set the default to 2, but trace only to the log file, not to the
1440    standard output.
1441    
1442  then at the end of the invocation, C<$options> will be  The parameters to this method are as follows.
1443    
1444  C<< { errors => 0, logFile => 'error.log' } >>  =over 4
1445    
1446  and C<@arguments> will contain  =item categories
1447    
1448  C<< apple orange rutabaga >>  Reference to a list of tracing category names. These should be names of
1449    packages whose internal workings will need to be debugged to get the
1450    command working.
1451    
1452  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =item options
 support for quote characters.  
1453    
1454  =over 4  Reference to a hash containing the legal options for the current command mapped
1455    to their default values and descriptions. The user can override the defaults
1456    by specifying the options as command-line switches prefixed by a hyphen.
1457    Tracing-related options may be added to this hash. If the C<-h> option is
1458    specified on the command line, the option descriptions will be used to
1459    explain the options. To turn off tracing to the standard output, add a
1460    minus sign to the value for C<trace> (see above).
1461    
1462  =item optionTable  =item parmHelp
1463    
1464  Table of default options.  A string that vaguely describes the positional parameters. This is used
1465    if the user specifies the C<-h> option.
1466    
1467  =item inputList  =item argv
1468    
1469  List of words on the command line.  List of command line parameters, including the option switches, which must
1470    precede the positional parameters and be prefixed by a hyphen.
1471    
1472  =item RETURN  =item RETURN
1473    
1474  Returns a reference to the option table and a list of the positional arguments.  Returns a list. The first element of the list is the reference to a hash that
1475    maps the command-line option switches to their values. These will either be the
1476    default values or overrides specified on the command line. The remaining
1477    elements of the list are the position parameters, in order.
1478    
1479  =back  =back
1480    
1481  =cut  =cut
1482    
1483  sub ParseCommand {  sub StandardSetup {
1484      # Get the parameters.      # Get the parameters.
1485      my ($optionTable, @inputList) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1486      # Process any options in the input list.      # Get the default tracing key.
1487      my %overrides = ();      my $tkey = EmergencyKey();
1488      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Add the tracing options.
1489          # Get the current option.      if (! exists $options->{trace}) {
1490          my $arg = shift @inputList;          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1491          # Pull out the option name.      }
1492          $arg =~ /^-([^=]*)/g;      $options->{sql} = [0, "turn on SQL tracing"];
1493          my $name = $1;      $options->{help} = [0, "display command-line options"];
1494          # Check for an option value.      $options->{user} = [$tkey, "tracing key"];
1495          if ($arg =~ /\G=(.*)$/g) {      $options->{background} = [0, "spool standard and error output"];
1496              # Here we have a value for the option.      # Create a parsing hash from the options hash. The parsing hash
1497              $overrides{$name} = UnEscape($1);      # contains the default values rather than the default value
1498        # and the description. While we're at it, we'll memorize the
1499        # length of the longest option name.
1500        my $longestName = 0;
1501        my %parseOptions = ();
1502        for my $key (keys %{$options}) {
1503            if (length $key > $longestName) {
1504                $longestName = length $key;
1505            }
1506            $parseOptions{$key} = $options->{$key}->[0];
1507        }
1508        # Parse the command line.
1509        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1510        # Get the logfile suffix.
1511        my $suffix = $retOptions->{user};
1512        # Check for background mode.
1513        if ($retOptions->{background}) {
1514            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1515            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1516            open STDOUT, ">$outFileName";
1517            open STDERR, ">$errFileName";
1518            # Check for phone support. If we have phone support and a phone number,
1519            # we want to turn it on.
1520            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1521                $retOptions->{phone} = $ENV{PHONE};
1522            }
1523        }
1524        # Now we want to set up tracing. First, we need to know if the user
1525        # wants emergency tracing.
1526        if ($retOptions->{trace} eq 'E') {
1527            ETracing($retOptions->{user});
1528          } else {          } else {
1529              # Here there is no value, so we use 1.          # Here the tracing is controlled from the command line.
1530              $overrides{$name} = 1;          my @cats = @{$categories};
1531            if ($retOptions->{sql}) {
1532                push @cats, "SQL";
1533          }          }
1534            # Add the default categories.
1535            push @cats, "Tracer";
1536            # Next, we create the category string by joining the categories.
1537            my $cats = join(" ", @cats);
1538            # Check to determine whether or not the caller wants to turn off tracing
1539            # to the standard output.
1540            my $traceLevel = $retOptions->{trace};
1541            my $textOKFlag = 1;
1542            if ($traceLevel =~ /^(.)-/) {
1543                $traceLevel = $1;
1544                $textOKFlag = 0;
1545      }      }
1546      # Merge the options into the defaults.          # Now we set up the trace mode.
1547      GetOptions($optionTable, \%overrides);          my $traceMode;
1548      # Translate the remaining parameters.          # Verify that we can open a file in the FIG temporary directory.
1549      my @retVal = ();          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1550      for my $inputParm (@inputList) {          if (open TESTTRACE, ">$traceFileName") {
1551          push @retVal, UnEscape($inputParm);              # Here we can trace to a file.
1552                $traceMode = ">$traceFileName";
1553                if ($textOKFlag) {
1554                    # Echo to standard output if the text-OK flag is set.
1555                    $traceMode = "+$traceMode";
1556      }      }
1557      # Return the results.              # Close the test file.
1558      return ($optionTable, @retVal);              close TESTTRACE;
1559            } else {
1560                # Here we can't trace to a file. We trace to the standard output if it's
1561                # okay, and the error log otherwise.
1562                if ($textOKFlag) {
1563                    $traceMode = "TEXT";
1564                } else {
1565                    $traceMode = "WARN";
1566                }
1567            }
1568            # Now set up the tracing.
1569            TSetup("$traceLevel $cats", $traceMode);
1570        }
1571        # Check for the "help" option. If it is specified, dump the command-line
1572        # options and exit the program.
1573        if ($retOptions->{help}) {
1574            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1575            print "$1 [options] $parmHelp\n";
1576            for my $key (sort keys %{$options}) {
1577                my $name = Pad($key, $longestName, 0, ' ');
1578                my $desc = $options->{$key}->[1];
1579                if ($options->{$key}->[0]) {
1580                    $desc .= " (default " . $options->{$key}->[0] . ")";
1581                }
1582                print "  $name $desc\n";
1583            }
1584            exit(0);
1585        }
1586        # Trace the options, if applicable.
1587        if (T(3)) {
1588            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1589            Trace("Selected options: " . join(", ", sort @parms) . ".");
1590        }
1591        # Return the parsed parameters.
1592        return ($retOptions, @retParameters);
1593  }  }
1594    
1595  =head3 Escape  =head3 ReadOptions
1596    
1597        my %options = Tracer::ReadOptions($fileName);
1598    
1599    Read a set of options from a file. Each option is encoded in a line of text that has the
1600    format
1601    
1602  C<< my $codedString = Tracer::Escape($realString); >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1603    
1604  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  The option name must consist entirely of letters, digits, and the punctuation characters
1605  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1606  result is to reverse the effect of L</UnEscape>.  character is a semi-colon will be ignored. The return hash will map each option name to
1607    the corresponding option value.
1608    
1609  =over 4  =over 4
1610    
1611  =item realString  =item fileName
1612    
1613  String to escape.  Name of the file containing the option data.
1614    
1615  =item RETURN  =item RETURN
1616    
1617  Escaped equivalent of the real string.  Returns a hash mapping the option names specified in the file to their corresponding option
1618    value.
1619    
1620  =back  =back
1621    
1622  =cut  =cut
1623    
1624  sub Escape {  sub ReadOptions {
1625      # Get the parameter.      # Get the parameters.
1626      my ($realString) = @_;      my ($fileName) = @_;
1627      # Initialize the return variable.      # Open the file.
1628      my $retVal = "";      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1629      # Loop through the parameter string, looking for sequences to escape.      # Count the number of records read.
1630      while (length $realString > 0) {      my ($records, $comments) = 0;
1631          # Look for the first sequence to escape.      # Create the return hash.
1632          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      my %retVal = ();
1633              # Here we found it. The text preceding the sequence is in $1. The sequence      # Loop through the file, accumulating key-value pairs.
1634              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <CONFIGFILE>) {
1635              $retVal .= $1;          # Denote we've read a line.
1636              # Strip the processed section off the real string.          $records++;
1637              $realString = substr $realString, (length $2) + (length $1);          # Determine the line type.
1638              # Get the matched character.          if ($line =~ /^\s*[\n\r]/) {
1639              my $char = $2;              # A blank line is a comment.
1640              # If we have a CR, we are done.              $comments++;
1641              if ($char ne "\r") {          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1642                  # It's not a CR, so encode the escape sequence.              # Here we have an option assignment.
1643                  $char =~ tr/\t\n/tn/;              retVal{$1} = $2;
1644                  $retVal .= "\\" . $char;          } elsif ($line =~ /^\s*;/) {
1645              }              # Here we have a text comment.
1646                $comments++;
1647          } else {          } else {
1648              # Here there are no more escape sequences. The rest of the string is              # Here we have an invalid line.
1649              # transferred unmodified.              Trace("Invalid option statement in record $records.") if T(0);
             $retVal .= $realString;  
             $realString = "";  
1650          }          }
1651      }      }
1652      # Return the result.      # Return the hash created.
1653      return $retVal;      return %retVal;
1654  }  }
1655    
1656  =head3 UnEscape  =head3 GetOptions
1657    
1658  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::GetOptions(\%defaults, \%options);
1659    
1660  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Merge a specified set of options into a table of defaults. This method takes two hash references
1661  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  as input and uses the data from the second to update the first. If the second does not exist,
1662  be deleted.  there will be no effect. An error will be thrown if one of the entries in the second hash does not
1663    exist in the first.
1664    
1665    Consider the following example.
1666    
1667        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1668    
1669    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1670    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1671    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1672    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1673    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1674    
1675        {databaseType => 'Oracle'}
1676    
1677    an error will occur because the B<databaseType> option does not exist.
1678    
1679  =over 4  =over 4
1680    
1681  =item codedString  =item defaults
1682    
1683  String to un-escape.  Table of default option values.
1684    
1685    =item options
1686    
1687    Table of overrides, if any.
1688    
1689  =item RETURN  =item RETURN
1690    
1691  Returns a copy of the original string with the escape sequences converted to their actual  Returns a reference to the default table passed in as the first parameter.
 values.  
1692    
1693  =back  =back
1694    
1695  =cut  =cut
1696    
1697  sub UnEscape {  sub GetOptions {
1698      # Get the parameter.      # Get the parameters.
1699      my ($codedString) = @_;      my ($defaults, $options) = @_;
1700      # Initialize the return variable.      # Check for overrides.
1701      my $retVal = "";      if ($options) {
1702      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1703      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1704          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1705          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1706          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
         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;  
                 }  
1707              } else {              } else {
1708                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1709                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
1710              }              }
1711          }          }
1712      }      }
1713      # Return the result.      # Return the merged table.
1714      return $retVal;      return $defaults;
1715  }  }
1716    
1717  =head3 ParseRecord  =head3 MergeOptions
1718    
1719  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1720    
1721  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Merge default values into a hash table. This method looks at the key-value pairs in the
1722  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  second (default) hash, and if a matching key is not found in the first hash, the default
1723  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1724    checking and no return value.
1725    
1726  =over 4  =over 4
1727    
1728  =item line  =item table
1729    
1730  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
1731    
1732  =item RETURN  =item defaults
1733    
1734  Returns a list of the fields found in the data line.  Default values to be merged into the first hash table if they are not already present.
1735    
1736  =back  =back
1737    
1738  =cut  =cut
1739    
1740  sub ParseRecord {  sub MergeOptions {
1741      # Get the parameter.      # Get the parameters.
1742      my ($line) = @_;      my ($table, $defaults) = @_;
1743      # Remove the trailing new-line, if any.      # Loop through the defaults.
1744      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
1745      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
1746      my @retVal = split /\t/, $line;              $table->{$key} = $value;
1747      # 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;  
1748      }      }
     # Return the result.  
     return @retVal;  
1749  }  }
1750    
1751  =head3 Merge  =head3 ParseCommand
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
1752    
1753  =item inputList      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1754    
1755  List of scalars to sort and merge.  Parse a command line consisting of a list of parameters. The initial parameters may be option
1756    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1757    off and merged into a table of default options. The remainder of the command line is
1758    returned as a list of positional arguments. For example, consider the following invocation.
1759    
1760  =item RETURN      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1761    
1762  Returns a list containing the same elements sorted in ascending order with duplicates  In this case, the list @words will be treated as a command line and there are two options available,
1763  removed.  B<errors> and B<logFile>. If @words has the following format
1764    
1765  =back      -logFile=error.log apple orange rutabaga
1766    
1767  =cut  then at the end of the invocation, C<$options> will be
1768    
1769  sub Merge {      { errors => 0, logFile => 'error.log' }
     # 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;  
 }  
1770    
1771  =head3 Percent  and C<@arguments> will contain
1772    
1773  C<< my $percent = Tracer::Percent($number, $base); >>      apple orange rutabaga
1774    
1775  Returns the percent of the base represented by the given number. If the base  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1776  is zero, returns zero.  support for quote characters. Options can be specified with single or double hyphens.
1777    
1778  =over 4  =over 4
1779    
1780  =item number  =item optionTable
1781    
1782  Percent numerator.  Table of default options.
1783    
1784  =item base  =item inputList
1785    
1786  Percent base.  List of words on the command line.
1787    
1788  =item RETURN  =item RETURN
1789    
1790  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1791    
1792  =back  =back
1793    
1794  =cut  =cut
1795    
1796  sub Percent {  sub ParseCommand {
1797      # Get the parameters.      # Get the parameters.
1798      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1799      # Declare the return variable.      # Process any options in the input list.
1800      my $retVal = 0;      my %overrides = ();
1801      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1802      if ($base != 0) {          # Get the current option.
1803          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
1804            # Pull out the option name.
1805            $arg =~ /^--?([^=]*)/g;
1806            my $name = $1;
1807            # Check for an option value.
1808            if ($arg =~ /\G=(.*)$/g) {
1809                # Here we have a value for the option.
1810                $overrides{$name} = UnEscape($1);
1811            } else {
1812                # Here there is no value, so we use 1.
1813                $overrides{$name} = 1;
1814      }      }
1815      # Return the result.      }
1816      return $retVal;      # Merge the options into the defaults.
1817        GetOptions($optionTable, \%overrides);
1818        # Translate the remaining parameters.
1819        my @retVal = ();
1820        for my $inputParm (@inputList) {
1821            push @retVal, UnEscape($inputParm);
1822        }
1823        # Return the results.
1824        return ($optionTable, @retVal);
1825  }  }
1826    
1827    
1828    =head2 File Utility Methods
1829    
1830  =head3 GetFile  =head3 GetFile
1831    
1832  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
1833    
1834      or      or
1835    
1836  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1837    
1838  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
1839  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 1648  Line 1883 
1883    
1884  =head3 PutFile  =head3 PutFile
1885    
1886  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
1887    
1888  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
1889    
# Line 1691  Line 1926 
1926      close $handle;      close $handle;
1927  }  }
1928    
1929  =head3 QTrace  =head3 ParseRecord
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
   
 =head3 Confess  
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
1930    
1931  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @fields = Tracer::ParseRecord($line);
1932    
1933  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1934    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1935    These will automatically be converted.
1936    
1937  =over 4  =over 4
1938    
1939  =item message  =item line
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Confess {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
   
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
   
 =head3 Cluck  
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
1940    
1941  =over 4  Line of data containing the tab-delimited fields.
1942    
1943  =item message  =item RETURN
1944    
1945  Message to include in the trace.  Returns a list of the fields found in the data line.
1946    
1947  =back  =back
1948    
1949  =cut  =cut
1950    
1951  sub Cluck {  sub ParseRecord {
1952      # Get the parameters.      # Get the parameter.
1953      my ($message) = @_;      my ($line) = @_;
1954      # Trace what's happening.      # Remove the trailing new-line, if any.
1955      Trace("Stack trace for event: $message");      chomp $line;
1956      my $confession = longmess($message);      # Split the line read into pieces using the tab character.
1957      # Convert the confession to a series of trace messages. Note we skip any      my @retVal = split /\t/, $line;
1958      # messages relating to calls into Tracer.      # Trim and fix the escapes in each piece.
1959      for my $line (split /\s*\n/, $confession) {      for my $value (@retVal) {
1960          Trace($line) if ($line !~ /Tracer\.pm/);          # Trim leading whitespace.
1961            $value =~ s/^\s+//;
1962            # Trim trailing whitespace.
1963            $value =~ s/\s+$//;
1964            # Delete the carriage returns.
1965            $value =~ s/\r//g;
1966            # Convert the escapes into their real values.
1967            $value =~ s/\\t/"\t"/ge;
1968            $value =~ s/\\n/"\n"/ge;
1969      }      }
1970        # Return the result.
1971        return @retVal;
1972  }  }
1973    
1974  =head3 Min  =head3 Merge
1975    
1976  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @mergedList = Tracer::Merge(@inputList);
1977    
1978  Return the minimum argument. The arguments are treated as numbers.  Sort a list of strings and remove duplicates.
1979    
1980  =over 4  =over 4
1981    
1982  =item $value1, $value2, ... $valueN  =item inputList
1983    
1984  List of numbers to compare.  List of scalars to sort and merge.
1985    
1986  =item RETURN  =item RETURN
1987    
1988  Returns the lowest number in the list.  Returns a list containing the same elements sorted in ascending order with duplicates
1989    removed.
1990    
1991  =back  =back
1992    
1993  =cut  =cut
1994    
1995  sub Min {  sub Merge {
1996      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the input list in sort order.
1997      my ($retVal, @values) = @_;      my @inputList = sort @_;
1998      # Loop through the remaining parameters, looking for the lowest.      # Only proceed if the list has at least two elements.
1999      for my $value (@values) {      if (@inputList > 1) {
2000          if ($value < $retVal) {          # Now we want to move through the list splicing out duplicates.
2001              $retVal = $value;          my $i = 0;
2002            while ($i < @inputList) {
2003                # Get the current entry.
2004                my $thisEntry = $inputList[$i];
2005                # Find out how many elements duplicate the current entry.
2006                my $j = $i + 1;
2007                my $dup1 = $i + 1;
2008                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2009                # If the number is nonzero, splice out the duplicates found.
2010                if ($j > $dup1) {
2011                    splice @inputList, $dup1, $j - $dup1;
2012                }
2013                # Now the element at position $dup1 is different from the element before it
2014                # at position $i. We push $i forward one position and start again.
2015                $i++;
2016          }          }
2017      }      }
2018      # Return the minimum found.      # Return the merged list.
2019      return $retVal;      return @inputList;
2020  }  }
2021    
2022  =head3 Max  =head3 Open
2023    
2024  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2025    
2026  Return the maximum argument. The arguments are treated as numbers.  Open a file.
2027    
2028  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2029    function. The mode is specified using Unix-like shell information. So, for
2030    example,
2031    
2032  =item $value1, $value2, ... $valueN      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2033    
2034  List of numbers to compare.  would open for output appended to the specified file, and
2035    
2036  =item RETURN      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2037    
2038  Returns the highest number in the list.  would open a pipe that sorts the records written and removes duplicates. Note
2039    the use of file handle syntax in the Open call. To use anonymous file handles,
2040    code as follows.
2041    
2042  =back      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2043    
2044  =cut  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2045    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2046    failed open will throw an exception and the third parameter will be used to construct
2047    an error message. If the parameter is omitted, a standard message is constructed
2048    using the file spec.
2049    
2050  sub Max {      Could not open "/usr/spool/news/twitlog"
2051      # Get the parameters. Note that we prime the return value with the first parameter.  
2052      my ($retVal, @values) = @_;  Note that the mode characters are automatically cleaned from the file name.
2053      # Loop through the remaining parameters, looking for the highest.  The actual error message from the file system will be captured and appended to the
2054      for my $value (@values) {  message in any case.
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
 }  
2055    
2056  =head3 AddToListMap      Could not open "/usr/spool/news/twitlog": file not found.
2057    
2058  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  In some versions of PERL the only error message we get is a number, which
2059    corresponds to the C++ C<errno> value.
2060    
2061  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list      Could not open "/usr/spool/news/twitlog": 6.
 is created for the key. Otherwise, the new value is pushed onto the list.  
2062    
2063  =over 4  =over 4
2064    
2065  =item hash  =item fileHandle
2066    
2067    File handle. If this parameter is C<undef>, a file handle will be generated
2068    and returned as the value of this method.
2069    
2070    =item fileSpec
2071    
2072  Reference to the target hash.  File name and mode, as per the PERL C<open> function.
2073    
2074  =item key  =item message (optional)
2075    
2076  Key for which the value is to be added.  Error message to use if the open fails. If omitted, a standard error message
2077    will be generated. In either case, the error information from the file system
2078    is appended to the message. To specify a conditional open that does not throw
2079    an error if it fails, use C<0>.
2080    
2081  =item value1, value2, ... valueN  =item RETURN
2082    
2083  List of values to add to the key's value list.  Returns the name of the file handle assigned to the file, or C<undef> if the
2084    open failed.
2085    
2086  =back  =back
2087    
2088  =cut  =cut
2089    
2090  sub AddToListMap {  sub Open {
2091      # Get the parameters.      # Get the parameters.
2092      my ($hash, $key, @values) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2093      # Process according to whether or not the key already has a value.      # Attempt to open the file.
2094      if (! exists $hash->{$key}) {      my $rv = open $fileHandle, $fileSpec;
2095          $hash->{$key} = [@values];      # If the open failed, generate an error message.
2096      } else {      if (! $rv) {
2097          push @{$hash->{$key}}, @values;          # Save the system error message.
2098            my $sysMessage = $!;
2099            # See if we need a default message.
2100            if (!$message) {
2101                # Clean any obvious mode characters and leading spaces from the
2102                # filename.
2103                my ($fileName) = FindNamePart($fileSpec);
2104                $message = "Could not open \"$fileName\"";
2105      }      }
2106            # Terminate with an error using the supplied message and the
2107            # error message from the file system.
2108            Confess("$message: $!");
2109        }
2110        # Return the file handle.
2111        return $fileHandle;
2112  }  }
2113    
2114  =head3 DebugMode  =head3 FindNamePart
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else abort.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2115    
2116  =cut      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2117    
2118  sub DebugMode {  Extract the portion of a file specification that contains the file name.
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error.  
         Confess("Cannot use this facility without logging in.");  
     }  
     # Return the determination indicator.  
     return $retVal;  
 }  
2119    
2120  =head3 Strip  A file specification is the string passed to an C<open> call. It specifies the file
2121    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2122    method assumes that the file name is whatever follows the first angle bracket
2123    sequence.  So, for example, in the following strings the file name is
2124    C</usr/fig/myfile.txt>.
2125    
2126  C<< my $string = Tracer::Strip($line); >>      >>/usr/fig/myfile.txt
2127        </usr/fig/myfile.txt
2128        | sort -u > /usr/fig/myfile.txt
2129    
2130  Strip all line terminators off a string. This is necessary when dealing with files  If the method cannot find a file name using its normal methods, it will return the
2131  that may have been transferred back and forth several times among different  whole incoming string.
 operating environments.  
2132    
2133  =over 4  =over 4
2134    
2135  =item line  =item fileSpec
2136    
2137  Line of text to be stripped.  File specification string from which the file name is to be extracted.
2138    
2139  =item RETURN  =item RETURN
2140    
2141  The same line of text with all the line-ending characters chopped from the end.  Returns a three-element list. The first element contains the file name portion of
2142    the specified string, or the whole string if a file name cannot be found via normal
2143    methods. The second element contains the start position of the file name portion and
2144    the third element contains the length.
2145    
2146  =back  =back
2147    
2148  =cut  =cut
2149    #: Return Type $;
2150  sub Strip {  sub FindNamePart {
2151      # Get a copy of the parameter string.      # Get the parameters.
2152      my ($string) = @_;      my ($fileSpec) = @_;
2153      my $retVal = (defined $string ? $string : "");      # Default to the whole input string.
2154      # Strip the line terminator characters.      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2155      $retVal =~ s/(\r|\n)+$//g;      # Parse out the file name if we can.
2156        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2157            $retVal = $2;
2158            $len = length $retVal;
2159            $pos = (length $fileSpec) - (length $3) - $len;
2160        }
2161      # Return the result.      # Return the result.
2162      return $retVal;      return ($retVal, $pos, $len);
2163  }  }
2164    
2165  =head3 Pad  =head3 OpenDir
2166    
2167  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @files = OpenDir($dirName, $filtered, $flag);
2168    
2169  Pad a string to a specified length. The pad character will be a  Open a directory and return all the file names. This function essentially performs
2170  space, and the padding will be on the right side unless specified  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2171  in the third parameter.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2172    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2173    filtered out of the return list. If the directory does not open and I<$flag> is not
2174    set, an exception is thrown. So, for example,
2175    
2176  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
2177    
2178  =item string  is effectively the same as
2179    
2180  String to be padded.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2181        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2182    
2183  =item len  Similarly, the following code
2184    
2185  Desired length of the padded string.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2186    
2187  =item left (optional)  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2188    automatically returns an empty list if the directory fails to open.
2189    
2190  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =over 4
2191    
2192  =item padChar (optional)  =item dirName
2193    
2194  Character to use for padding. The default is a space.  Name of the directory to open.
2195    
2196  =item RETURN  =item filtered
2197    
2198  Returns a copy of the original string with the pad character added to the  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2199  specified end so that it achieves the desired length.  from the list, else FALSE.
2200    
2201    =item flag
2202    
2203    TRUE if a failure to open is okay, else FALSE
2204    
2205  =back  =back
2206    
2207  =cut  =cut
2208    #: Return Type @;
2209  sub Pad {  sub OpenDir {
2210      # Get the parameters.      # Get the parameters.
2211      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $filtered, $flag) = @_;
2212      # Compute the padding character.      # Declare the return variable.
2213      if (! defined $padChar) {      my @retVal = ();
2214          $padChar = " ";      # Open the directory.
2215      }      if (opendir(my $dirHandle, $dirName)) {
2216      # Compute the number of spaces needed.          # The directory opened successfully. Get the appropriate list according to the
2217      my $needed = $len - length $string;          # strictures of the filter parameter.
2218      # Copy the string into the return variable.          if ($filtered) {
2219      my $retVal = $string;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2220          } else {          } else {
2221              $retVal .= $pad;              @retVal = readdir $dirHandle;
2222          }          }
2223        } elsif (! $flag) {
2224            # Here the directory would not open and it's considered an error.
2225            Confess("Could not open directory $dirName.");
2226      }      }
2227      # Return the result.      # Return the result.
2228      return $retVal;      return @retVal;
2229  }  }
2230    
 =head3 EOF  
2231    
2232  This is a constant that is lexically greater than any useful string.  =head3 Insure
2233    
2234  =cut      Insure($dirName, $chmod);
2235    
2236  sub EOF {  Insure a directory is present.
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2237    
2238  =head3 TICK  =over 4
2239    
2240  C<< my @results = TICK($commandString); >>  =item dirName
2241    
2242  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Name of the directory to check. If it does not exist, it will be created.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2243    
2244      `./protein.cgi`  =item chmod (optional)
2245    
2246  from inside a CGI script, it would work fine in Unix, but would issue an error message  Security privileges to be given to the directory if it is created.
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2247    
2248      TICK("./protein.cgi")  =back
2249    
2250  it will work correctly in both environments.  =cut
2251    
2252  =over 4  sub Insure {
2253        my ($dirName, $chmod) = @_;
2254        if (! -d $dirName) {
2255            Trace("Creating $dirName directory.") if T(2);
2256            eval {
2257                mkpath $dirName;
2258                # If we have permissions specified, set them here.
2259                if (defined($chmod)) {
2260                    chmod $chmod, $dirName;
2261                }
2262            };
2263            if ($@) {
2264                Confess("Error creating $dirName: $@");
2265            }
2266        }
2267    }
2268    
2269  =item commandString  =head3 ChDir
2270    
2271  The command string to pass to the system.      ChDir($dirName);
2272    
2273  =item RETURN  Change to the specified directory.
2274    
2275  Returns the standard output from the specified command, as a list.  =over 4
2276    
2277    =item dirName
2278    
2279    Name of the directory to which we want to change.
2280    
2281  =back  =back
2282    
2283  =cut  =cut
2284  #: Return Type @;  
2285  sub TICK {  sub ChDir {
2286      # Get the parameters.      my ($dirName) = @_;
2287      my ($commandString) = @_;      if (! -d $dirName) {
2288      # Chop off the dot-slash if this is Windows.          Confess("Cannot change to directory $dirName: no such directory.");
2289      if ($FIG_Config::win_mode) {      } else {
2290          $commandString =~ s!^\./!!;          Trace("Changing to directory $dirName.") if T(File => 4);
2291            my $okFlag = chdir $dirName;
2292            if (! $okFlag) {
2293                Confess("Error switching to directory $dirName.");
2294            }
2295      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2296  }  }
2297    
2298  =head3 ScriptSetup  =head3 SetPermissions
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2299    
2300  Perform standard tracing and debugging setup for scripts. The value returned is      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 the CGI object followed by a pre-built variable hash.  
2301    
2302  The C<Trace> form parameter is used to determine whether or not tracing is active and  Set the permissions for a directory and all the files and folders inside it.
2303  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  In addition, the group ownership will be changed to the specified value.
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2304    
2305  In some situations, it is not practical to invoke tracing via form parameters. For this  This method is more vulnerable than most to permission and compatability
2306  situation, you can turn on emergency tracing from the debugging control panel.  problems, so it does internal error recovery.
 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>.  
2307    
2308  =over 4  =over 4
2309    
2310  =item noTrace (optional)  =item dirName
   
 If specified, tracing will be suppressed. This is useful if the script wants to set up  
 tracing manually.  
2311    
2312  =item RETURN  Name of the directory to process.
2313    
2314  Returns a two-element list consisting of a CGI query object and a variable hash for  =item group
 the output page.  
2315    
2316  =back  Name of the group to be assigned.
2317    
2318  =cut  =item mask
2319    
2320  sub ScriptSetup {  Permission mask. Bits that are C<1> in this mask will be ORed into the
2321      # Get the parameters.  permission bits of any file or directory that does not already have them
2322      my ($noTrace) = @_;  set to 1.
     # Get the CGI query object.  
     my $cgi = CGI->new();  
     # Set up tracing if it's not suppressed.  
     ETracing($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
 }  
2323    
2324  =head3 ETracing  =item otherMasks
2325    
2326  C<< ETracing($parameter); >>  Map of search patterns to permission masks. If a directory name matches
2327    one of the patterns, that directory and all its members and subdirectories
2328    will be assigned the new pattern. For example, the following would
2329    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2330    
2331  Set up emergency tracing. Emergency tracing is tracing that is turned      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
 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.  
2332    
2333  =over 4  The list is ordered, so the following would use 0777 for C<tmp1> and
2334    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2335    
2336  =item parameter      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2337                                                       '^tmp' => 0666);
2338    
2339  A parameter from which the tracing key is computed. If it is a scalar,  Note that the pattern matches are all case-insensitive, and only directory
2340  that scalar is used as the tracing key. If it is a CGI object, the  names are matched, not file names.
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
2341    
2342  =back  =back
2343    
2344  =cut  =cut
2345    
2346  sub ETracing {  sub SetPermissions {
2347      # Get the parameter.      # Get the parameters.
2348      my ($parameter) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2349      # Check for CGI mode.      # Set up for error recovery.
2350      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);      eval {
2351      # Default to no tracing except errors.          # Switch to the specified directory.
2352      my ($tracing, $dest) = ("0", "WARN");          ChDir($dirName);
2353      # Check for emergency tracing.          # Get the group ID.
2354      my $tkey = EmergencyKey($parameter);          my $gid = getgrnam($group);
2355      my $emergencyFile = EmergencyFileName($tkey);          # Get the mask for tracing.
2356      if (-e $emergencyFile) {          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2357          # We have the file. Read in the data.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2358          my @tracing = GetFile($emergencyFile);          my $fixCount = 0;
2359          # Pull off the time limit.          my $lookCount = 0;
2360          my $expire = shift @tracing;          # @dirs will be a stack of directories to be processed.
2361          # Convert it to seconds.          my @dirs = (getcwd());
2362          $expire *= 3600;          while (scalar(@dirs) > 0) {
2363          # Check the file data.              # Get the current directory.
2364          my $stat = stat($emergencyFile);              my $dir = pop @dirs;
2365          my ($now) = gettimeofday;              # Check for a match to one of the specified directory names. To do
2366          if ($now - $stat->mtime > $expire) {              # that, we need to pull the individual part of the name off of the
2367              # Delete the expired file.              # whole path.
2368              unlink $emergencyFile;              my $simpleName = $dir;
2369                if ($dir =~ m!/([^/]+)$!) {
2370                    $simpleName = $1;
2371                }
2372                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2373                # Search for a match.
2374                my $match = 0;
2375                my $i;
2376                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2377                    my $pattern = $otherMasks[$i];
2378                    if ($simpleName =~ /$pattern/i) {
2379                        $match = 1;
2380                    }
2381                }
2382                # Check for a match. Note we use $i-1 because the loop added 2
2383                # before terminating due to the match.
2384                if ($match && $otherMasks[$i-1] != $mask) {
2385                    # This directory matches one of the incoming patterns, and it's
2386                    # a different mask, so we process it recursively with that mask.
2387                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2388          } else {          } else {
2389              # Emergency tracing is on. Pull off the destination and                  # Here we can process normally. Get all of the non-hidden members.
2390              # the trace level;                  my @submems = OpenDir($dir, 1);
2391              $dest = shift @tracing;                  for my $submem (@submems) {
2392              my $level = shift @tracing;                      # Get the full name.
2393              # Convert the destination to a real tracing destination.                      my $thisMem = "$dir/$submem";
2394              # temp directory.                      Trace("Checking member $thisMem.") if T(4);
2395              $dest = EmergencyTracingDest($tkey, $dest);                      $lookCount++;
2396              # Insure Tracer is specified.                      if ($lookCount % 1000 == 0) {
2397              my %moduleHash = map { $_ => 1 } @tracing;                          Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2398              $moduleHash{Tracer} = 1;                      }
2399              # Set the trace parameter.                      # Fix the group.
2400              $tracing = join(" ", $level, sort keys %moduleHash);                      chown -1, $gid, $thisMem;
2401                        # Insure this member is not a symlink.
2402                        if (! -l $thisMem) {
2403                            # Get its info.
2404                            my $fileInfo = stat $thisMem;
2405                            # Only proceed if we got the info. Otherwise, it's a hard link
2406                            # and we want to skip it anyway.
2407                            if ($fileInfo) {
2408                                my $fileMode = $fileInfo->mode;
2409                                if (($fileMode & $mask) != $mask) {
2410                                    # Fix this member.
2411                                    $fileMode |= $mask;
2412                                    chmod $fileMode, $thisMem;
2413                                    $fixCount++;
2414                                }
2415                                # If it's a subdirectory, stack it.
2416                                if (-d $thisMem) {
2417                                    push @dirs, $thisMem;
2418                                }
2419          }          }
     } 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";  
2420          }          }
2421      }      }
2422      # Setup the tracing we've determined from all the stuff above.              }
2423      TSetup($tracing, $dest);          }
2424      # If we're a web script, trace the parameter and environment data.          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2425      if (defined $cgi) {      };
2426          TraceParms($cgi);      # Check for an error.
2427        if ($@) {
2428            Confess("SetPermissions error: $@");
2429      }      }
2430  }  }
2431    
2432  =head3 EmergencyFileName  =head3 GetLine
2433    
2434  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my @data = Tracer::GetLine($handle);
2435    
2436  Return the emergency tracing file name. This is the file that specifies  Read a line of data from a tab-delimited file.
 the tracing information.  
2437    
2438  =over 4  =over 4
2439    
2440  =item tkey  =item handle
2441    
2442  Tracing key for the current program.  Open file handle from which to read.
2443    
2444  =item RETURN  =item RETURN
2445    
2446  Returns the name of the file to contain the emergency tracing information.  Returns a list of the fields in the record read. The fields are presumed to be
2447    tab-delimited. If we are at the end of the file, then an empty list will be
2448    returned. If an empty line is read, a single list item consisting of a null
2449    string will be returned.
2450    
2451  =back  =back
2452    
2453  =cut  =cut
2454    
2455  sub EmergencyFileName {  sub GetLine {
2456      # Get the parameters.      # Get the parameters.
2457      my ($tkey) = @_;      my ($handle) = @_;
2458      # Compute the emergency tracing file name.      # Declare the return variable.
2459      return "$FIG_Config::temp/Emergency$tkey.txt";      my @retVal = ();
2460        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2461        # Read from the file.
2462        my $line = <$handle>;
2463        # Only proceed if we found something.
2464        if (defined $line) {
2465            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2466            # upload control and have a nonstandard EOL combination.
2467            $line =~ s/(\r|\n)+$//;
2468            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2469            if (T(File => 4)) {
2470                my $escapedLine = $line;
2471                $escapedLine =~ s/\n/\\n/g;
2472                $escapedLine =~ s/\r/\\r/g;
2473                $escapedLine =~ s/\t/\\t/g;
2474                Trace("Line read: -->$escapedLine<--");
2475            }
2476            # If the line is empty, return a single empty string; otherwise, parse
2477            # it into fields.
2478            if ($line eq "") {
2479                push @retVal, "";
2480            } else {
2481                push @retVal, split /\t/,$line;
2482            }
2483        } else {
2484            # Trace the reason the read failed.
2485            Trace("End of file: $!") if T(File => 3);
2486        }
2487        # Return the result.
2488        return @retVal;
2489  }  }
2490    
2491  =head3 EmergencyFileTarget  =head3 PutLine
2492    
2493  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2494    
2495  Return the emergency tracing target file name. This is the file that receives  Write a line of data to a tab-delimited file. The specified field values will be
2496  the tracing output for file-based tracing.  output in tab-separated form, with a trailing new-line.
2497    
2498  =over 4  =over 4
2499    
2500  =item tkey  =item handle
2501    
2502  Tracing key for the current program.  Output file handle.
2503    
2504  =item RETURN  =item fields
2505    
2506  Returns the name of the file to contain the trace output.  List of field values.
2507    
2508    =item eol (optional)
2509    
2510    End-of-line character (default is "\n").
2511    
2512  =back  =back
2513    
2514  =cut  =cut
2515    
2516  sub EmergencyFileTarget {  sub PutLine {
2517      # Get the parameters.      # Get the parameters.
2518      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2519      # Compute the emergency tracing file name.      # Write the data.
2520      return "$FIG_Config::temp/trace$tkey.log";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2521  }  }
2522    
 =head3 EmergencyTracingDest  
2523    
 C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  
2524    
2525  This method converts an emergency tracing destination to a real  =head2 Other Useful Methods
2526  tracing destination. The main difference is that if the  
2527  destination is C<FILE> or C<APPEND>, we convert it to file  =head3 ParseParm
 output.  
2528    
2529  =over 4      my $listValue = Tracer::ParseParm($string);
2530    
2531  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2532    an undefined value will be returned. Otherwise, it will be parsed as a
2533    comma-separated list of values.
2534    
2535  Tracing key for this environment.  =over 4
2536    
2537  =item myDest  =item string
2538    
2539  Destination from the emergency tracing file.  Incoming string.
2540    
2541  =item RETURN  =item RETURN
2542    
2543  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2544    was undefined.
2545    
2546  =back  =back
2547    
2548  =cut  =cut
2549    
2550  sub EmergencyTracingDest {  sub ParseParm {
2551      # Get the parameters.      # Get the parameters.
2552      my ($tkey, $myDest) = @_;      my ($string) = @_;
2553      # Declare the return variable.      # Declare the return variable.
2554      my $retVal;      my $retVal;
2555      # Process according to the destination value.      # Check for data.
2556      if ($myDest eq 'FILE') {      if (defined $string) {
2557          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2558      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } else {  
         $retVal = $myDest;  
2559      }      }
2560      # Return the result.      # Return the result.
2561      return $retVal;      return $retVal;
2562  }  }
2563    
 =head3 Emergency  
2564    
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
2565    
 Turn on emergency tracing. This method can only be invoked over the web and is  
 should not be called if debug mode is off. The caller specifies the duration of the  
 emergency in hours, the desired tracing 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.  
2566    
2567  =over 4  =head3 Now
2568    
2569  =item tkey      my $string = Tracer::Now();
2570    
2571  The tracing key. This is used to identify the control file and the trace file.  Return a displayable time stamp containing the local time.
2572    
2573  =item hours  =cut
2574    
2575  Number of hours to keep emergency tracing alive.  sub Now {
2576        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2577        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2578                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2579        return $retVal;
2580    }
2581    
2582  =item dest  # Pad a number to 2 digits.
2583    sub _p2 {
2584        my ($value) = @_;
2585        $value = "0$value" if ($value < 10);
2586        return $value;
2587    }
2588    
2589  Tracing destination. If no path information is specified for a file  =head3 Escape
 destination, it is put in the FIG temporary directory.  
2590    
2591  =item level      my $codedString = Tracer::Escape($realString);
2592    
2593  Tracing level. A higher level means more trace messages.  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2594    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2595    result is to reverse the effect of L</UnEscape>.
2596    
2597  =item modules  =over 4
2598    
2599  A list of the tracing modules to activate.  =item realString
2600    
2601    String to escape.
2602    
2603    =item RETURN
2604    
2605    Escaped equivalent of the real string.
2606    
2607  =back  =back
2608    
2609  =cut  =cut
2610    
2611  sub Emergency {  sub Escape {
2612      # Get the parameters.      # Get the parameter.
2613      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($realString) = @_;
2614      # Create the emergency file.      # Initialize the return variable.
2615      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2616      my $outHandle = Open(undef, ">$specFile");      # Loop through the parameter string, looking for sequences to escape.
2617      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      while (length $realString > 0) {
2618            # Look for the first sequence to escape.
2619            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2620                # Here we found it. The text preceding the sequence is in $1. The sequence
2621                # itself is in $2. First, move the clear text to the return variable.
2622                $retVal .= $1;
2623                # Strip the processed section off the real string.
2624                $realString = substr $realString, (length $2) + (length $1);
2625                # Get the matched character.
2626                my $char = $2;
2627                # If we have a CR, we are done.
2628                if ($char ne "\r") {
2629                    # It's not a CR, so encode the escape sequence.
2630                    $char =~ tr/\t\n/tn/;
2631                    $retVal .= "\\" . $char;
2632                }
2633            } else {
2634                # Here there are no more escape sequences. The rest of the string is
2635                # transferred unmodified.
2636                $retVal .= $realString;
2637                $realString = "";
2638            }
2639        }
2640        # Return the result.
2641        return $retVal;
2642  }  }
2643    
2644  =head3 EmergencyKey  =head3 UnEscape
2645    
2646  C<< my $tkey = EmergencyKey($parameter); >>      my $realString = Tracer::UnEscape($codedString);
2647    
2648  Return the Key to be used for emergency tracing. This could be an IP address,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2649   a session ID, or a user name, depending on the environment.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2650    be deleted.
2651    
2652  =over 4  =over 4
2653    
2654  =item parameter  =item codedString
2655    
2656  Parameter defining the method for finding the tracing key. If it is a scalar,  String to un-escape.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
2657    
2658  =item RETURN  =item RETURN
2659    
2660  Returns the key to be used for labels in emergency tracing.  Returns a copy of the original string with the escape sequences converted to their actual
2661    values.
2662    
2663  =back  =back
2664    
2665  =cut  =cut
2666    
2667  sub EmergencyKey {  sub UnEscape {
2668      # Get the parameters.      # Get the parameter.
2669      my ($parameter) = @_;      my ($codedString) = @_;
2670      # Declare the return variable.      # Initialize the return variable.
2671      my $retVal;      my $retVal = "";
2672      # Determine the parameter type.      # Only proceed if the incoming string is nonempty.
2673      if (! defined $parameter) {      if (defined $codedString) {
2674          # Here we're supposed to check the environment.          # Loop through the parameter string, looking for escape sequences. We can't do
2675          $retVal = $ENV{TRACING};          # translating because it causes problems with the escaped slash. ("\\t" becomes
2676            # "\<tab>" no matter what we do.)
2677            while (length $codedString > 0) {
2678                # Look for the first escape sequence.
2679                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2680                    # Here we found it. The text preceding the sequence is in $1. The sequence
2681                    # itself is in $2. First, move the clear text to the return variable.
2682                    $retVal .= $1;
2683                    $codedString = substr $codedString, (2 + length $1);
2684                    # Get the escape value.
2685                    my $char = $2;
2686                    # If we have a "\r", we are done.
2687                    if ($char ne 'r') {
2688                        # Here it's not an 'r', so we convert it.
2689                        $char =~ tr/\\tn/\\\t\n/;
2690                        $retVal .= $char;
2691                    }
2692      } else {      } else {
2693          my $ptype = ref $parameter;                  # Here there are no more escape sequences. The rest of the string is
2694          if ($ptype eq 'CGI') {                  # transferred unmodified.
2695              # Here we were invoked from a web page. Look for a cookie.                  $retVal .= $codedString;
2696              $retVal = $parameter->cookie('IP');                  $codedString = "";
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
2697          }          }
2698      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2699      }      }
2700      # Return the result.      # Return the result.
2701      return $retVal;      return $retVal;
2702  }  }
2703    
2704    =head3 Percent
2705    
2706  =head3 TraceParms      my $percent = Tracer::Percent($number, $base);
   
 C<< Tracer::TraceParms($cgi); >>  
2707    
2708  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Returns the percent of the base represented by the given number. If the base
2709  at level CGI => 4.  is zero, returns zero.
2710    
2711  =over 4  =over 4
2712    
2713  =item cgi  =item number
2714    
2715  CGI query object containing the parameters to trace.  Percent numerator.
2716    
2717    =item base
2718    
2719    Percent base.
2720    
2721    =item RETURN
2722    
2723    Returns the percentage of the base represented by the numerator.
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub TraceParms {  sub Percent {
2730      # Get the parameters.      # Get the parameters.
2731      my ($cgi) = @_;      my ($number, $base) = @_;
2732      if (T(CGI => 3)) {      # Declare the return variable.
2733          # Here we want to trace the parameter data.      my $retVal = 0;
2734          my @names = $cgi->param;      # Compute the percent.
2735          for my $parmName (sort @names) {      if ($base != 0) {
2736              # Note we skip the Trace parameters, which are for our use only.          $retVal = $number * 100 / $base;
             if ($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}");  
         }  
2737      }      }
2738        # Return the result.
2739        return $retVal;
2740  }  }
2741    
2742  =head3 ScriptFinish  =head3 Min
2743    
2744  C<< ScriptFinish($webData, $varHash); >>      my $min = Min($value1, $value2, ... $valueN);
2745    
2746  Output a web page at the end of a script. Either the string to be output or the  Return the minimum argument. The arguments are treated as numbers.
 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.  
2747    
2748  A typical standard script would loook like the following.  =over 4
2749    
2750      BEGIN {  =item $value1, $value2, ... $valueN
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2751    
2752      my ($cgi, $varHash) = ScriptSetup();  List of numbers to compare.
2753      eval {  
2754          # ... get data from $cgi, put it in $varHash ...  =item RETURN
2755      };  
2756      if ($@) {  Returns the lowest number in the list.
2757          Trace("Script Error: $@") if T(0);  
2758    =back
2759    
2760    =cut
2761    
2762    sub Min {
2763        # Get the parameters. Note that we prime the return value with the first parameter.
2764        my ($retVal, @values) = @_;
2765        # Loop through the remaining parameters, looking for the lowest.
2766        for my $value (@values) {
2767            if ($value < $retVal) {
2768                $retVal = $value;
2769            }
2770        }
2771        # Return the minimum found.
2772        return $retVal;
2773      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2774    
2775  The idea here is that even if the script fails, you'll see trace messages and  =head3 Max
2776  useful output.  
2777        my $max = Max($value1, $value2, ... $valueN);
2778    
2779    Return the maximum argument. The arguments are treated as numbers.
2780    
2781  =over 4  =over 4
2782    
2783  =item webData  =item $value1, $value2, ... $valueN
2784    
2785  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2786    
2787  =item varHash (optional)  =item RETURN
2788    
2789  If specified, then a reference to a hash mapping variable names for a template  Returns the highest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2790    
2791  =back  =back
2792    
2793  =cut  =cut
2794    
2795  sub ScriptFinish {  sub Max {
2796      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2797      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
2798      # Check for a template file situation.      # Loop through the remaining parameters, looking for the highest.
2799      my $outputString;      for my $value (@values) {
2800      if (defined $varHash) {          if ($value > $retVal) {
2801          # 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";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # 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;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
2802          }          }
         substr $outputString, $pos, 0, $traceHtml;  
2803      }      }
2804      # Write the output string.      # Return the maximum found.
2805      print $outputString;      return $retVal;
2806  }  }
2807    
2808  =head3 Insure  =head3 DebugMode
   
 C<< Insure($dirName); >>  
   
 Insure a directory is present.  
   
 =over 4  
2809    
2810  =item dirName      if (Tracer::DebugMode) { ...code... }
2811    
2812  Name of the directory to check. If it does not exist, it will be created.  Return TRUE if debug mode has been turned on, else abort.
2813    
2814  =back  Certain CGI scripts are too dangerous to exist in the production
2815    environment. This method provides a simple way to prevent them
2816    from working unless they are explicitly turned on by creating a password
2817    cookie via the B<SetPassword> script.  If debugging mode
2818    is not turned on, an error will occur.
2819    
2820  =cut  =cut
2821    
2822  sub Insure {  sub DebugMode {
2823      my ($dirName) = @_;      # Declare the return variable.
2824      if (! -d $dirName) {      my $retVal = 0;
2825          Trace("Creating $dirName directory.") if T(File => 2);      # Check the debug configuration.
2826          eval { mkpath $dirName; };      my $password = CGI::cookie("DebugMode");
2827          if ($@) {      my $encrypted = Digest::MD5::md5_hex($password);
2828              Confess("Error creating $dirName: $@");      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2829          }          $retVal = 1;
2830        } else {
2831            # Here debug mode is off, so we generate an error.
2832            Confess("Cannot use this facility without logging in.");
2833      }      }
2834        # Return the determination indicator.
2835        return $retVal;
2836  }  }
2837    
2838  =head3 ChDir  =head3 Strip
2839    
2840  C<< ChDir($dirName); >>      my $string = Tracer::Strip($line);
2841    
2842  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
2843    that may have been transferred back and forth several times among different
2844    operating environments.
2845    
2846  =over 4  =over 4
2847    
2848  =item dirName  =item line
2849    
2850  Name of the directory to which we want to change.  Line of text to be stripped.
2851    
2852    =item RETURN
2853    
2854    The same line of text with all the line-ending characters chopped from the end.
2855    
2856  =back  =back
2857    
2858  =cut  =cut
2859    
2860  sub ChDir {  sub Strip {
2861      my ($dirName) = @_;      # Get a copy of the parameter string.
2862      if (! -d $dirName) {      my ($string) = @_;
2863          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
2864      } else {      # Strip the line terminator characters.
2865          Trace("Changing to directory $dirName.") if T(File => 4);      $retVal =~ s/(\r|\n)+$//g;
2866          my $okFlag = chdir $dirName;      # Return the result.
2867          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
2868  }  }
2869    
2870  =head3 SendSMS  =head3 Pad
2871    
2872  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2873    
2874  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
2875  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
2876  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 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  
2877    
2878      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
2879    
2880  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2881    
2882  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
2883    
2884  =over 4  =item len
2885    
2886  =item phoneNumber  Desired length of the padded string.
2887    
2888  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
2889    
2890  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2891    
2892  Message to send to the specified phone.  =item padChar (optional)
2893    
2894    Character to use for padding. The default is a space.
2895    
2896  =item RETURN  =item RETURN
2897    
2898  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
2899    specified end so that it achieves the desired length.
2900    
2901  =back  =back
2902    
2903  =cut  =cut
2904    
2905  sub SendSMS {  sub Pad {
2906      # Get the parameters.      # Get the parameters.
2907      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
2908      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
2909      my $retVal;      if (! defined $padChar) {
2910      # Only proceed if we have phone support.          $padChar = " ";
2911      if (! defined $FIG_Config::phone) {      }
2912          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
2913      } else {      my $needed = $len - length $string;
2914          # Get the phone data.      # Copy the string into the return variable.
2915          my $parms = $FIG_Config::phone;      my $retVal = $string;
2916          # Get the Clickatell URL.      # Only proceed if padding is needed.
2917          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
2918          # Create the user agent.          # Create the pad string.
2919          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
2920          # Request a Clickatell session.          # Affix it to the return value.
2921          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
2922                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      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;  
2923              } else {              } else {
2924                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
2925            }
2926              }              }
2927        # Return the result.
2928        return $retVal;
2929    }
2930    
2931    =head3 EOF
2932    
2933    This is a constant that is lexically greater than any useful string.
2934    
2935    =cut
2936    
2937    sub EOF {
2938        return "\xFF\xFF\xFF\xFF\xFF";
2939          }          }
2940    
2941    =head3 TICK
2942    
2943        my @results = TICK($commandString);
2944    
2945    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2946    dot-slash (C<./> will be removed. So, for example, if you were doing
2947    
2948        `./protein.cgi`
2949    
2950    from inside a CGI script, it would work fine in Unix, but would issue an error message
2951    in Windows complaining that C<'.'> is not a valid command. If instead you code
2952    
2953        TICK("./protein.cgi")
2954    
2955    it will work correctly in both environments.
2956    
2957    =over 4
2958    
2959    =item commandString
2960    
2961    The command string to pass to the system.
2962    
2963    =item RETURN
2964    
2965    Returns the standard output from the specified command, as a list.
2966    
2967    =back
2968    
2969    =cut
2970    #: Return Type @;
2971    sub TICK {
2972        # Get the parameters.
2973        my ($commandString) = @_;
2974        # Chop off the dot-slash if this is Windows.
2975        if ($FIG_Config::win_mode) {
2976            $commandString =~ s!^\./!!;
2977      }      }
2978      # Return the result.      # Activate the command and return the result.
2979      return $retVal;      return `$commandString`;
2980  }  }
2981    
2982    
2983  =head3 CommaFormat  =head3 CommaFormat
2984    
2985  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
2986    
2987  Insert commas into a number.  Insert commas into a number.
2988    
# Line 2740  Line 3015 
3015      # Return the result.      # Return the result.
3016      return $retVal;      return $retVal;
3017  }  }
 =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);  
3018    
 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: $@");  
     }  
 }  
3019    
3020  =head3 CompareLists  =head3 CompareLists
3021    
3022  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3023    
3024  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
3025  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2941  Line 3084 
3084      return ($inserted, $deleted);      return ($inserted, $deleted);
3085  }  }
3086    
 =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.  
         chomp $line;  
         Trace("Line read: $line") if T(File => 4);  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($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); >>  
   
 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.  
   
 =back  
   
 =cut  
   
 sub PutLine {  
     # Get the parameters.  
     my ($handle, $fields) = @_;  
     # Write the data.  
     print $handle join("\t", @{$fields}) . "\n";  
 }  
   
3087  =head3 GenerateURL  =head3 GenerateURL
3088    
3089  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3090    
3091  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
3092  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 3070  Line 3134 
3134    
3135  =head3 ApplyURL  =head3 ApplyURL
3136    
3137  C<< Tracer::ApplyURL($table, $target, $url); >>      Tracer::ApplyURL($table, $target, $url);
3138    
3139  Run through a two-dimensional table (or more accurately, a list of lists), converting the  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3140  I<$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 3113  Line 3177 
3177    
3178  =head3 CombineURL  =head3 CombineURL
3179    
3180  C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3181    
3182  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
3183  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 3154  Line 3218 
3218      return $retVal;      return $retVal;
3219  }  }
3220    
3221    =head3 Cmp
3222    
3223        my $cmp = Tracer::Cmp($a, $b);
3224    
3225    This method performs a universal sort comparison. Each value coming in is
3226    separated into a leading text part and a trailing number part. The text
3227    part is string compared, and if both parts are equal, then the number
3228    parts are compared numerically. A stream of just numbers or a stream of
3229    just strings will sort correctly, and a mixed stream will sort with the
3230    numbers first. Strings with a label and a number will sort in the
3231    expected manner instead of lexically.
3232    
3233    =over 4
3234    
3235    =item a
3236    
3237    First item to compare.
3238    
3239    =item b
3240    
3241    Second item to compare.
3242    
3243    =item RETURN
3244    
3245    Returns a negative number if the first item should sort first (is less), a positive
3246    number if the first item should sort second (is greater), and a zero if the items are
3247    equal.
3248    
3249    =back
3250    
3251    =cut
3252    
3253    sub Cmp {
3254        # Get the parameters.
3255        my ($a, $b) = @_;
3256        # Declare the return value.
3257        my $retVal;
3258        # Check for nulls.
3259        if (! defined($a)) {
3260            $retVal = (! defined($b) ? 0 : -1);
3261        } elsif (! defined($b)) {
3262            $retVal = 1;
3263        } else {
3264            # Here we have two real values. Parse the two strings.
3265            $a =~ /^(\D*)(\d*)$/;
3266            my $aParsed = [$1, $2];
3267            $b =~ /^(\D*)(\d*)$/;
3268            my $bParsed = [$1, $2];
3269            # Compare the string parts.
3270            $retVal = $aParsed->[0] cmp $bParsed->[0];
3271            if (! $retVal) {
3272                $retVal = $aParsed->[1] <=> $bParsed->[1];
3273            }
3274        }
3275        # Return the result.
3276        return $retVal;
3277    }
3278    
3279    
3280  1;  1;

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