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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.93, Tue Feb 5 02:17:29 2008 UTC
# Line 296  Line 296 
296  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
297  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
298    
299  =head2 Public Methods  =head2 Tracing Methods
300    
301    =head3 Setups
302    
303        my $count = Tracer::Setups();
304    
305    Return the number of times L</TSetup> has been called.
306    
307    This method allows for the creation of conditional tracing setups where, for example, we
308    may want to set up tracing if nobody else has done it before us.
309    
310    =cut
311    
312    sub Setups {
313        return $SetupCount;
314    }
315    
316  =head3 TSetup  =head3 TSetup
317    
318  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
319    
320  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
321  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 372  Line 387 
387      $SetupCount++;      $SetupCount++;
388  }  }
389    
390  =head3 StandardSetup  =head3 SetLevel
   
 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>  
   
 This method performs standard command-line parsing and tracing setup. The return  
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
   
 This is a complex method that does a lot of grunt work. The parameters can  
 be more easily understood, however, once they are examined individually.  
   
 The I<categories> parameter is the most obtuse. It is a reference to a list of  
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
391    
392      ["Sprout", "SproutLoad", "ERDB"]      Tracer::SetLevel($newLevel);
393    
394  This would cause trace messages in the specified three packages to appear in  Modify the trace level. A higher trace level will cause more messages to appear.
 the output. There are two special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
395    
396  =over 4  =over 4
397    
398  =item SQL  =item newLevel
   
 Traces SQL commands and activity.  
   
 =item Tracer  
399    
400  Traces error messages and call stacks.  Proposed new trace level.
401    
402  =back  =back
403    
404  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  =cut
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
   
     TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  
405    
406  Standard tracing is output to the standard output and echoed to the file  sub SetLevel {
407  C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the      $TraceLevel = $_[0];
408  process ID. You can also specify the C<user> parameter to put a user ID  }
 instead of a process ID in the trace file name. So, for example  
409    
410  The default trace level is 2. To get all messages, specify a trace level of 4.  =head3 ParseTraceDate
 For a genome-by-genome update, use 3.  
411    
412      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl      my $time = Tracer::ParseTraceDate($dateString);
413    
414  would send the trace output to C<traceBruce.log> in the temporary directory.  Convert a date from the trace file into a PERL timestamp.
415    
416  The I<options> parameter is a reference to a hash containing the command-line  =over 4
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
417    
418  You can specify a different default trace level by setting C<$options->{trace}>  =item dateString
 prior to calling this method.  
419    
420  An example at this point would help. Consider, for example, the command-line utility  The date string from the trace file. The format of the string is determined by the
421  C<TransactFeatures>. It accepts a list of positional parameters plus the options  L</Now> method.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
422    
423      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =item RETURN
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "<command> <transactionDirectory> <IDfile>",  
                       @ARGV);  
424    
425    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
426    the time string is invalid.
427    
428  The call to C<ParseCommand> specifies the default values for the options and  =back
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
429    
430  The following is a sample command line for C<TransactFeatures>.  =cut
431    
432      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub ParseTraceDate {
433        # Get the parameters.
434        my ($dateString) = @_;
435        # Declare the return variable.
436        my $retVal;
437        # Parse the date.
438        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
439            # Create a time object. Note we need to convert the day, month,
440            # and year to a different base. Years count from 1900, and
441            # the internal month value is relocated to January = 0.
442            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
443        }
444        # Return the result.
445        return $retVal;
446    }
447    
448  Single and double hyphens are equivalent. So, you could also code the  =head3 LogErrors
 above command as  
449    
450      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl      Tracer::LogErrors($fileName);
451    
452  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  Route the standard error output to a log file.
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
453    
454      { trace => 2, sql => 0, safe => 0,  =over 4
       noAlias => 1, start => ' ', tblFiles => 0 }  
455    
456  Use of C<StandardSetup> in this way provides a simple way of performing  =item fileName
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
457    
458  If the C<background> option is specified on the command line, then the  Name of the file to receive the error output.
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
459    
460      -user=Bruce -background  =back
461    
462  then the trace output would go to C<traceBruce.log>, the standard output to  =cut
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
463    
464  The user name is also used as the tracing key for L</Emergency Tracing>.  sub LogErrors {
465  Specifying a value of C<E> for the trace level causes emergency tracing to      # Get the file name.
466  be used instead of custom tracing. If the user name is not specified,      my ($fileName) = @_;
467  the tracing key is taken from the C<Tracing> environment variable. If there      # Open the file as the standard error output.
468  is no value for that variable, the tracing key will be computed from the PID.      open STDERR, '>', $fileName;
469    }
470    
471  Finally, if the special option C<-help> is specified, the option  =head3 Trace
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
472    
473      TransactFeatures -help      Trace($message);
474    
475  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
476    any prior call to B<TSetup>.
477    
478      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =over 4
         -trace    tracing level (default E)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
479    
480  The caller has the option of modifying the tracing scheme by placing a value  =item message
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
481    
482      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
483    
484  would set the default trace level to 0 instead of E, while  =back
485    
486      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
487    
488  would set the default to 2, but trace only to the log file, not to the  sub Trace {
489  standard output.      # Get the parameters.
490        my ($message) = @_;
491        # Get the timestamp.
492        my $timeStamp = Now();
493        # Format the message. Note we strip off any line terminators at the end.
494        my $prefix = "[$timeStamp] <$LastCategory>: ";
495        my $formatted = $prefix . Strip($message);
496        # Process according to the destination.
497        if ($Destination eq "TEXT") {
498            # Write the message to the standard output.
499            print "$formatted\n";
500        } elsif ($Destination eq "ERROR") {
501            # Write the message to the error output.
502            print STDERR "$formatted\n";
503        } elsif ($Destination eq "QUEUE") {
504            # Push the message into the queue.
505            push @Queue, "$formatted";
506        } elsif ($Destination eq "HTML") {
507            # Convert the message to HTML and write it to the standard output.
508            my $escapedMessage = CGI::escapeHTML($message);
509            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
510        } elsif ($Destination eq "WARN") {
511           # Emit the message as a warning.
512           warn $message;
513        } elsif ($Destination =~ m/^>>/) {
514            # Write the trace message to an output file.
515            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
516            print TRACING "$formatted\n";
517            close TRACING;
518            # If the Tee flag is on, echo it to the standard output.
519            if ($TeeFlag) {
520                print "$formatted\n";
521            }
522        }
523    }
524    
525  The parameters to this method are as follows.  =head3 T
526    
527  =over 4      my $switch = T($category, $traceLevel);
528    
529  =item categories      or
530    
531  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
532    
533  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
534    is active, else FALSE. If no category is specified, the caller's package name is used.
535    
536  Reference to a hash containing the legal options for the current command mapped  =over 4
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
537    
538  =item parmHelp  =item category
539    
540  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
541  if the user specifies the C<-h> option.  used.
542    
543  =item argv  =item traceLevel
544    
545  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
546    
547  =item RETURN  =item RETURN
548    
549  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
550    
551  =back  =back
552    
553  =cut  =cut
554    
555  sub StandardSetup {  sub T {
556        # Declare the return variable.
557        my $retVal = 0;
558        # Only proceed if tracing is turned on.
559        if ($Destination ne "NONE") {
560      # Get the parameters.      # 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} = ['2', "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                $traceLevel = $category;
569                my ($package, $fileName, $line) = caller;
570                # If there is no calling package, we default to "main".
571                if (!$package) {
572                    $category = "main";
573                } else {
574                    my @cats = split /::/, $package;
575                    $category = $cats[$#cats];
576      }      }
     $options->{sql} = [0, "turn on SQL tracing"];  
     $options->{help} = [0, "display command-line options"];  
     $options->{user} = [$tkey, "tracing key"];  
     $options->{background} = [0, "spool standard and error output"];  
     # Create a parsing hash from the options hash. The parsing hash  
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
577          }          }
578          $parseOptions{$key} = $options->{$key}->[0];          # Save the category name.
579            $LastCategory = $category;
580            # Convert it to lower case before we hash it.
581            $category = lc $category;
582            # Use the category and tracelevel to compute the result.
583            if (ref $traceLevel) {
584                Confess("Bad trace level.");
585            } elsif (ref $TraceLevel) {
586                Confess("Bad trace config.");
587      }      }
588      # Parse the command line.          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
     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";  
589      }      }
590      # Now we want to set up tracing. First, we need to know if the user      # Return the computed result.
591      # wants emergency tracing.      return $retVal;
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
592          }          }
593          # Add the default categories.  
594          push @cats, "Tracer";  =head3 QTrace
595          # Next, we create the category string by joining the categories.  
596          my $cats = join(" ", @cats);      my $data = QTrace($format);
597          # Check to determine whether or not the caller wants to turn off tracing  
598          # to the standard output.  Return the queued trace data in the specified format.
599          my $traceLevel = $retOptions->{trace};  
600          my $textOKFlag = 1;  =over 4
601          if ($traceLevel =~ /^(.)-/) {  
602              $traceLevel = $1;  =item format
603              $textOKFlag = 0;  
604    C<html> to format the data as an HTML list, C<text> to format it as straight text.
605    
606    =back
607    
608    =cut
609    
610    sub QTrace {
611        # Get the parameter.
612        my ($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          # Now we set up the trace mode.              $retVal .= "</ul>\n";
626          my $traceMode;          } elsif ($format =~ m/^TEXT$/i) {
627          # Verify that we can open a file in the FIG temporary directory.              # Convert the queue into a list of text lines.
628          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";              $retVal = join("\n", @Queue) . "\n";
         if (open TESTTRACE, ">$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";  
629              }              }
630              # Close the test file.          # Clear the queue.
631              close TESTTRACE;          @Queue = ();
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
             } else {  
                 $traceMode = "WARN";  
632              }              }
633        # Return the formatted list.
634        return $retVal;
635          }          }
636          # Now set up the tracing.  
637          TSetup("$traceLevel $cats", $traceMode);  =head3 Confess
638    
639        Confess($message);
640    
641    Trace the call stack and abort the program with the specified message. When used with
642    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
643    So, for example
644    
645        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
646    
647    Will abort the program with a stack trace if the value of C<$recNum> is negative.
648    
649    =over 4
650    
651    =item message
652    
653    Message to include in the trace.
654    
655    =back
656    
657    =cut
658    
659    sub Confess {
660        # Get the parameters.
661        my ($message) = @_;
662        if (! defined($FIG_Config::no_tool_hdr)) {
663            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
664            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
665            # Only proceed if the tool header file is actually present.
666            if (-f $toolHeaderFile) {
667                my @lines = GetFile($toolHeaderFile);
668                Trace("Tool header has " . scalar(@lines) . " lines.");
669      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{help}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
670              }              }
671              print "  $name $desc\n";      # Trace the call stack.
672        Cluck($message);
673        # Abort the program.
674        croak(">>> $message");
675    }
676    
677    =head3 Assert
678    
679        Assert($condition1, $condition2, ... $conditionN);
680    
681    Return TRUE if all the conditions are true. This method can be used in conjunction with
682    the OR operator and the L</Confess> method as a debugging assert.
683    So, for example
684    
685        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
686    
687    Will abort the program with a stack trace if the value of C<$recNum> is negative.
688    
689    =cut
690    sub Assert {
691        my $retVal = 1;
692        LOOP: for my $condition (@_) {
693            if (! $condition) {
694                $retVal = 0;
695                last LOOP;
696            }
697        }
698        return $retVal;
699    }
700    
701    =head3 Cluck
702    
703        Cluck($message);
704    
705    Trace the call stack. Note that for best results, you should qualify the call with a
706    trace condition. For example,
707    
708        Cluck("Starting record parse.") if T(3);
709    
710    will only trace the stack if the trace level for the package is 3 or more.
711    
712    =over 4
713    
714    =item message
715    
716    Message to include in the trace.
717    
718    =back
719    
720    =cut
721    
722    sub Cluck {
723        # Get the parameters.
724        my ($message) = @_;
725        # Trace what's happening.
726        Trace("Stack trace for event: $message");
727        my $confession = longmess($message);
728        # Convert the confession to a series of trace messages. Note we skip any
729        # messages relating to calls into Tracer.
730        for my $line (split /\s*\n/, $confession) {
731            Trace($line) if ($line !~ /Tracer\.pm/);
732        }
733    }
734    
735    =head3 ScriptSetup
736    
737        my ($cgi, $varHash) = ScriptSetup($noTrace);
738    
739    Perform standard tracing and debugging setup for scripts. The value returned is
740    the CGI object followed by a pre-built variable hash. At the end of the script,
741    the client should call L</ScriptFinish> to output the web page.
742    
743    This method calls L</ETracing> to configure tracing, which allows the tracing
744    to be configured via the emergency tracing form on the debugging control panel.
745    Tracing will then be turned on automatically for all programs that use the L</ETracing>
746    method, which includes every program that uses this method or L</StandardSetup>.
747    
748    =over 4
749    
750    =item noTrace (optional)
751    
752    If specified, tracing will be suppressed. This is useful if the script wants to set up
753    tracing manually.
754    
755    =item RETURN
756    
757    Returns a two-element list consisting of a CGI query object and a variable hash for
758    the output page.
759    
760    =back
761    
762    =cut
763    
764    sub ScriptSetup {
765        # Get the parameters.
766        my ($noTrace) = @_;
767        # Get the CGI query object.
768        my $cgi = CGI->new();
769        # Set up tracing if it's not suppressed.
770        ETracing($cgi) unless $noTrace;
771        # Create the variable hash.
772        my $varHash = { results => '' };
773        # Return the query object and variable hash.
774        return ($cgi, $varHash);
775    }
776    
777    =head3 ETracing
778    
779        ETracing($parameter);
780    
781    Set up emergency tracing. Emergency tracing is tracing that is turned
782    on automatically for any program that calls this method. The emergency
783    tracing parameters are stored in a a file identified by a tracing key.
784    If this method is called with a CGI object, then the tracing key is
785    taken from a cookie. If it is called with no parameters, then the tracing
786    key is taken from an environment variable. If it is called with a string,
787    the tracing key is that string.
788    
789    =over 4
790    
791    =item parameter
792    
793    A parameter from which the tracing key is computed. If it is a scalar,
794    that scalar is used as the tracing key. If it is a CGI object, the
795    tracing key is taken from the C<IP> cookie. If it is omitted, the
796    tracing key is taken from the C<TRACING> environment variable. If it
797    is a CGI object and emergency tracing is not on, the C<Trace> and
798    C<TF> parameters will be used to determine the type of tracing.
799    
800    =back
801    
802    =cut
803    
804    sub ETracing {
805        # Get the parameter.
806        my ($parameter) = @_;
807        # Check for CGI mode.
808        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
809        # Default to no tracing except errors.
810        my ($tracing, $dest) = ("0", "WARN");
811        # Check for emergency tracing.
812        my $tkey = EmergencyKey($parameter);
813        my $emergencyFile = EmergencyFileName($tkey);
814        if (-e $emergencyFile) {
815            # We have the file. Read in the data.
816            my @tracing = GetFile($emergencyFile);
817            # Pull off the time limit.
818            my $expire = shift @tracing;
819            # Convert it to seconds.
820            $expire *= 3600;
821            # Check the file data.
822            my $stat = stat($emergencyFile);
823            my ($now) = gettimeofday;
824            if ($now - $stat->mtime > $expire) {
825                # Delete the expired file.
826                unlink $emergencyFile;
827            } else {
828                # Emergency tracing is on. Pull off the destination and
829                # the trace level;
830                $dest = shift @tracing;
831                my $level = shift @tracing;
832                # Convert the destination to a real tracing destination.
833                # temp directory.
834                $dest = EmergencyTracingDest($tkey, $dest);
835                # Insure Tracer is specified.
836                my %moduleHash = map { $_ => 1 } @tracing;
837                $moduleHash{Tracer} = 1;
838                # Set the trace parameter.
839                $tracing = join(" ", $level, sort keys %moduleHash);
840            }
841        } elsif (defined $cgi) {
842            # There's no emergency tracing, but we have a CGI object, so check
843            # for tracing from the form parameters.
844            if ($cgi->param('Trace')) {
845                # Here the user has requested tracing via a form.
846                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
847                $tracing = $cgi->param('Trace') . " Tracer";
848            }
849        }
850        # Setup the tracing we've determined from all the stuff above.
851        TSetup($tracing, $dest);
852        # 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
866    
867    =item tkey
868    
869    Tracing key for the current program.
870    
871    =item RETURN
872    
873    Returns the name of the file to contain the emergency tracing information.
874    
875    =back
876    
877    =cut
878    
879    sub EmergencyFileName {
880        # Get the parameters.
881        my ($tkey) = @_;
882        # Compute the emergency tracing file name.
883        return "$FIG_Config::temp/Emergency$tkey.txt";
884    }
885    
886    =head3 EmergencyFileTarget
887    
888        my $fileName = Tracer::EmergencyFileTarget($tkey);
889    
890    Return the emergency tracing target file name. This is the file that receives
891    the tracing output for file-based tracing.
892    
893    =over 4
894    
895    =item tkey
896    
897    Tracing key for the current program.
898    
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    =head3 EmergencyTracingDest
915    
916        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
917    
918    This method converts an emergency tracing destination to a real
919    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
925    
926    =item tkey
927    
928    Tracing key for this environment.
929    
930    =item myDest
931    
932    Destination from the emergency tracing file.
933    
934    =item RETURN
935    
936    Returns a destination that can be passed into L</TSetup>.
937    
938    =back
939    
940    =cut
941    
942    sub EmergencyTracingDest {
943        # Get the parameters.
944        my ($tkey, $myDest) = @_;
945        # Declare the return variable.
946        my $retVal = $myDest;
947        # Process according to the destination value.
948        if ($myDest eq 'FILE') {
949            $retVal = ">" . EmergencyFileTarget($tkey);
950        } elsif ($myDest eq 'APPEND') {
951            $retVal = ">>" . EmergencyFileTarget($tkey);
952        } elsif ($myDest eq 'DUAL') {
953            $retVal = "+>" . EmergencyFileTarget($tkey);
954        }
955        # Return the result.
956        return $retVal;
957    }
958    
959    =head3 Emergency
960    
961        Emergency($key, $hours, $dest, $level, @modules);
962    
963    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
973    
974    =item tkey
975    
976    The tracing key. This is used to identify the control file and the trace file.
977    
978    =item hours
979    
980    Number of hours to keep emergency tracing alive.
981    
982    =item dest
983    
984    Tracing destination. If no path information is specified for a file
985    destination, it is put in the FIG temporary directory.
986    
987    =item level
988    
989    Tracing level. A higher level means more trace messages.
990    
991    =item modules
992    
993    A list of the tracing modules to activate.
994    
995    =back
996    
997    =cut
998    
999    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 EmergencyKey
1009    
1010        my $tkey = EmergencyKey($parameter);
1011    
1012    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
1016    
1017    =item parameter
1018    
1019    Parameter defining the method for finding the tracing key. If it is a scalar,
1020    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
1025    
1026    Returns the key to be used for labels in emergency tracing.
1027    
1028    =back
1029    
1030    =cut
1031    
1032    sub EmergencyKey {
1033        # Get the parameters.
1034        my ($parameter) = @_;
1035        # Declare the return variable.
1036        my $retVal;
1037        # Determine the parameter type.
1038        if (! defined $parameter) {
1039            # Here we're supposed to check the environment.
1040            $retVal = $ENV{TRACING};
1041        } else {
1042            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          }          }
         exit(0);  
1050      }      }
1051      # Trace the options, if applicable.      # If no luck finding a key, use the PID.
1052      if (T(3)) {      if (! defined $retVal) {
1053          my @parms = grep { $retOptions->{$_} } keys %{$retOptions};          $retVal = $$;
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
1054      }      }
1055      # Return the parsed parameters.      # Return the result.
1056      return ($retOptions, @retParameters);      return $retVal;
1057  }  }
1058    
 =head3 Setups  
1059    
1060  C<< my $count = Tracer::Setups(); >>  =head3 TraceParms
1061    
1062        Tracer::TraceParms($cgi);
1063    
1064  Return the number of times L</TSetup> has been called.  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1065    at level CGI => 4.
1066    
1067  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
1068  may want to set up tracing if nobody else has done it before us.  
1069    =item cgi
1070    
1071    CGI query object containing the parameters to trace.
1072    
1073    =back
1074    
1075  =cut  =cut
1076    
1077  sub Setups {  sub TraceParms {
1078      return $SetupCount;      # Get the parameters.
1079        my ($cgi) = @_;
1080        if (T(CGI => 3)) {
1081            # 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 Open  =head3 ScriptFinish
1103    
1104  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      ScriptFinish($webData, $varHash);
1105    
1106  Open a file.  Output a web page at the end of a script. Either the string to be output or the
1107    name of a template file can be specified. If the second parameter is omitted,
1108    it is assumed we have a string to be output; otherwise, it is assumed we have the
1109    name of a template file. The template should have the variable C<DebugData>
1110    specified in any form that invokes a standard script. If debugging mode is turned
1111    on, a form field will be put in that allows the user to enter tracing data.
1112    Trace messages will be placed immediately before the terminal C<BODY> tag in
1113    the output, formatted as a list.
1114    
1115  The I<$fileSpec> is essentially the second argument of the PERL C<open>  A typical standard script would loook like the following.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
1116    
1117      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");      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  would open for output appended to the specified file, and      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", $varHash);
1134    
1135      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  The idea here is that even if the script fails, you'll see trace messages and
1136    useful output.
1137    
1138  would open a pipe that sorts the records written and removes duplicates. Note  =over 4
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
1139    
1140      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =item webData
1141    
1142  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  A string containing either the full web page to be written to the output or the
1143  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  name of a template file from which the page is to be constructed. If the name
1144  failed open will throw an exception and the third parameter will be used to construct  of a template file is specified, then the second parameter must be present;
1145  an error message. If the parameter is omitted, a standard message is constructed  otherwise, it must be absent.
 using the file spec.  
1146    
1147      Could not open "/usr/spool/news/twitlog"  =item varHash (optional)
1148    
1149  Note that the mode characters are automatically cleaned from the file name.  If specified, then a reference to a hash mapping variable names for a template
1150  The actual error message from the file system will be captured and appended to the  to their values. The template file will be read into memory, and variable markers
1151  message in any case.  will be replaced by data in this hash reference.
1152    
1153      Could not open "/usr/spool/news/twitlog": file not found.  =back
1154    
1155  In some versions of PERL the only error message we get is a number, which  =cut
 corresponds to the C++ C<errno> value.  
1156    
1157      Could not open "/usr/spool/news/twitlog": 6.  sub ScriptFinish {
1158        # Get the parameters.
1159        my ($webData, $varHash) = @_;
1160        # Check for a template file situation.
1161        my $outputString;
1162        if (defined $varHash) {
1163            # Here we have a template file. We need to determine the template type.
1164            my $template;
1165            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1166                $template = "$FIG_Config::template_url/$webData";
1167            } else {
1168                $template = "<<$webData";
1169            }
1170            $outputString = PageBuilder::Build($template, $varHash, "Html");
1171        } else {
1172            # Here the user gave us a raw string.
1173            $outputString = $webData;
1174        }
1175        # Check for trace messages.
1176        if ($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  =over 4  =head2 Command-Line Utility Methods
1205    
1206  =item fileHandle  =head3 SendSMS
1207    
1208  File handle. If this parameter is C<undef>, a file handle will be generated      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
 and returned as the value of this method.  
1209    
1210  =item fileSpec  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1211    user name, password, and API ID for the relevant account in the hash reference variable
1212    I<$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  File name and mode, as per the PERL C<open> function.      $phone =  { user => 'BruceTheHumanPet',
1217                    password => 'silly',
1218                    api_id => '2561022' };
1219    
1220  =item message (optional)  The original purpose of this method was to insure Bruce would be notified immediately when the
1221    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1222    when you call this method.
1223    
1224  Error message to use if the open fails. If omitted, a standard error message  The message ID will be returned if successful, and C<undef> if an error occurs.
1225  will be generated. In either case, the error information from the file system  
1226  is appended to the message. To specify a conditional open that does not throw  =over 4
1227  an error if it fails, use C<0>.  
1228    =item phoneNumber
1229    
1230    Phone number to receive the message, in international format. A United States phone number
1231    would be prefixed by "1". A British phone number would be prefixed by "44".
1232    
1233    =item msg
1234    
1235    Message to send to the specified phone.
1236    
1237  =item RETURN  =item RETURN
1238    
1239  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns the message ID if successful, and C<undef> if the message could not be sent.
 open failed.  
1240    
1241  =back  =back
1242    
1243  =cut  =cut
1244    
1245  sub Open {  sub SendSMS {
1246      # Get the parameters.      # Get the parameters.
1247      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1248      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1249      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1250      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1251      if (! $rv) {      if (! defined $FIG_Config::phone) {
1252          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1253          my $sysMessage = $!;      } else {
1254          # See if we need a default message.          # Get the phone data.
1255          if (!$message) {          my $parms = $FIG_Config::phone;
1256              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1257              # filename.          my $url = "http://api.clickatell.com/http/";
1258              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1259              $message = "Could not open \"$fileName\"";          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 $rstring") if T(1);
1276          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1277      }      }
     # Return the file handle.  
     return $fileHandle;  
1278  }  }
1279        # Return the result.
1280        return $retVal;
1281    }
1282    
1283    =head3 StandardSetup
1284    
1285  =head3 FindNamePart      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1286    
1287  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  This method performs standard command-line parsing and tracing setup. The return
1288    values are a hash of the command-line options and a list of the positional
1289    parameters. Tracing is automatically set up and the command-line options are
1290    validated.
1291    
1292  Extract the portion of a file specification that contains the file name.  This is a complex method that does a lot of grunt work. The parameters can
1293    be more easily understood, however, once they are examined individually.
1294    
1295  A file specification is the string passed to an C<open> call. It specifies the file  The I<categories> parameter is the most obtuse. It is a reference to a list of
1296  mode and name. In a truly complex situation, it can specify a pipe sequence. This  special-purpose tracing categories. Most tracing categories are PERL package
1297  method assumes that the file name is whatever follows the first angle bracket  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1298  sequence.  So, for example, in the following strings the file name is  B<ERDB>, and B<SproutLoad> packages, you would specify the categories
 C</usr/fig/myfile.txt>.  
1299    
1300      >>/usr/fig/myfile.txt      ["Sprout", "SproutLoad", "ERDB"]
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
1301    
1302  If the method cannot find a file name using its normal methods, it will return the  This would cause trace messages in the specified three packages to appear in
1303  whole incoming string.  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 fileSpec  =item SQL
1311    
1312  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1313    
1314  =item RETURN  =item Tracer
1315    
1316  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
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  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1322  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1323      # Get the parameters.  all tracing at level 3.
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
1324    
1325  is effectively the same as      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1326    
1327      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  Standard tracing is output to the standard output and echoed to the file
1328      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  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  Similarly, the following code  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      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1336    
1337  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  would send the trace output to C<traceBruce.log> in the temporary directory.
 automatically returns an empty list if the directory fails to open.  
1338    
1339  =over 4  The I<options> parameter is a reference to a hash containing the command-line
1340    options, their default values, and an explanation of what they mean. Command-line
1341    options may be in the form of switches or keywords. In the case of a switch, the
1342    option value is 1 if it is specified and 0 if it is not specified. In the case
1343    of a keyword, the value is separated from the option name by an equal sign. You
1344    can see this last in the command-line example above.
1345    
1346  =item dirName  You can specify a different default trace level by setting C<$options->{trace}>
1347    prior to calling this method.
1348    
1349  Name of the directory to open.  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  =item filtered      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1355                            { safe => [0, "use database transactions"],
1356                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1357                              start => [' ', "start with this genome"],
1358                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1359                            "<command> <transactionDirectory> <IDfile>",
1360                          @ARGV);
1361    
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
1362    
1363  =item flag  The call to C<ParseCommand> specifies the default values for the options and
1364    stores the actual options in a hash that is returned as C<$options>. The
1365    positional parameters are returned in C<@parameters>.
1366    
1367  TRUE if a failure to open is okay, else FALSE  The following is a sample command line for C<TransactFeatures>.
1368    
1369  =back      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1370    
1371  =cut  Single and double hyphens are equivalent. So, you could also code the
1372  #: Return Type @;  above command as
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1373    
1374  =head3 SetLevel      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1375    
1376  C<< Tracer::SetLevel($newLevel); >>  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  Modify the trace level. A higher trace level will cause more messages to appear.      { trace => 2, sql => 0, safe => 0,
1384          noAlias => 1, start => ' ', tblFiles => 0 }
1385    
1386  =over 4  Use of C<StandardSetup> in this way provides a simple way of performing
1387    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 newLevel  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  Proposed new trace level.      -user=Bruce -background
1399    
1400  =back  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  =cut  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  sub SetLevel {  Finally, if the special option C<-help> is specified, the option
1411      $TraceLevel = $_[0];  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  =head3 Now      TransactFeatures -help
1415    
1416  C<< my $string = Tracer::Now(); >>  he would see the following output.
1417    
1418  Return a displayable time stamp containing the local time.      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1419            -trace    tracing level (default E)
1420            -sql      trace SQL commands
1421            -safe     use database transactions
1422            -noAlias  do not expect aliases in CHANGE transactions
1423            -start    start with this genome
1424            -tblFiles output TBL files containing the corrected IDs
1425    
1426  =cut  The caller has the option of modifying the tracing scheme by placing a value
1427    for C<trace> in the incoming options hash. The default value can be overridden,
1428    or the tracing to the standard output can be turned off by suffixing a minus
1429    sign to the trace level. So, for example,
1430    
1431  sub Now {      { trace => [0, "tracing level (default 0)"],
1432      my ($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 $retVal;  
 }  
1433    
1434  # Pad a number to 2 digits.  would set the default trace level to 0 instead of E, while
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1435    
1436  =head3 ParseTraceDate      { trace => ["2-", "tracing level (default 2)"],
1437           ...
1438    
1439  C<< my $time = Tracer::ParseTraceDate($dateString); >>  would set the default to 2, but trace only to the log file, not to the
1440    standard output.
1441    
1442  Convert a date from the trace file into a PERL timestamp.  The parameters to this method are as follows.
1443    
1444  =over 4  =over 4
1445    
1446  =item dateString  =item categories
   
 The date string from the trace file. The format of the string is determined by the  
 L</Now> method.  
   
 =item RETURN  
   
 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  
 the time string is invalid.  
   
 =back  
1447    
1448  =cut  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  sub ParseTraceDate {  =item options
     # Get the parameters.  
     my ($dateString) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
     }  
     # Return the result.  
     return $retVal;  
 }  
1453    
1454  =head3 LogErrors  Reference to a hash containing the legal options for the current command mapped
1455    to their default values and descriptions. The user can override the defaults
1456    by specifying the options as command-line switches prefixed by a hyphen.
1457    Tracing-related options may be added to this hash. If the C<-h> option is
1458    specified on the command line, the option descriptions will be used to
1459    explain the options. To turn off tracing to the standard output, add a
1460    minus sign to the value for C<trace> (see above).
1461    
1462  C<< Tracer::LogErrors($fileName); >>  =item parmHelp
1463    
1464  Route the standard error output to a log file.  A string that vaguely describes the positional parameters. This is used
1465    if the user specifies the C<-h> option.
1466    
1467  =over 4  =item argv
1468    
1469  =item fileName  List of command line parameters, including the option switches, which must
1470    precede the positional parameters and be prefixed by a hyphen.
1471    
1472  Name of the file to receive the error output.  =item RETURN
1473    
1474    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 LogErrors {  sub StandardSetup {
1484      # Get the file name.      # Get the parameters.
1485      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1486      # Open the file as the standard error output.      # Get the default tracing key.
1487      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1488        # Add the tracing options.
1489        if (! exists $options->{trace}) {
1490            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1491        }
1492        $options->{sql} = [0, "turn on SQL tracing"];
1493        $options->{help} = [0, "display command-line options"];
1494        $options->{user} = [$tkey, "tracing key"];
1495        $options->{background} = [0, "spool standard and error output"];
1496        # Create a parsing hash from the options hash. The parsing hash
1497        # 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($retOptions->{user});
1528        } else {
1529            # Here the tracing is controlled from the command line.
1530            my @cats = @{$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            # Now we set up the trace mode.
1547            my $traceMode;
1548            # Verify that we can open a file in the FIG temporary directory.
1549            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1550            if (open TESTTRACE, ">$traceFileName") {
1551                # 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                # Close the test file.
1558                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 ReadOptions  =head3 ReadOptions
1596    
1597  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1598    
1599  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1600  format  format
# Line 1069  Line 1655 
1655    
1656  =head3 GetOptions  =head3 GetOptions
1657    
1658  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1659    
1660  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1661  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 1078  Line 1664 
1664    
1665  Consider the following example.  Consider the following example.
1666    
1667  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      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  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1670  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1672 
1672  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1673  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1674    
1675  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1676    
1677  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1678    
# Line 1130  Line 1716 
1716    
1717  =head3 MergeOptions  =head3 MergeOptions
1718    
1719  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1720    
1721  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1722  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1149  Line 1735 
1735    
1736  =back  =back
1737    
1738  =cut  =cut
1739    
1740  sub MergeOptions {  sub MergeOptions {
1741      # Get the parameters.      # Get the parameters.
1742      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
1743      # Loop through the defaults.      # Loop through the defaults.
1744      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
1745          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
1746              $table->{$key} = $value;              $table->{$key} = $value;
         }  
     }  
 }  
   
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1747          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1748      }      }
     # Return the computed result.  
     return $retVal;  
1749  }  }
1750    
1751  =head3 ParseCommand  =head3 ParseCommand
1752    
1753  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1754    
1755  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1756  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1757  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1758  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1759    
1760  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1761    
1762  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1763  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1764    
1765  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1766    
1767  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1768    
1769  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1770    
1771  and C<@arguments> will contain  and C<@arguments> will contain
1772    
1773  C<< apple orange rutabaga >>      apple orange rutabaga
1774    
1775  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1776  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 1824 
1824      return ($optionTable, @retVal);      return ($optionTable, @retVal);
1825  }  }
1826    
 =head3 Escape  
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
   
 String to escape.  
   
 =item RETURN  
   
 Escaped equivalent of the real string.  
   
 =back  
   
 =cut  
   
 sub Escape {  
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # Here we found it. The text preceding the sequence is in $1. The sequence  
             # itself is in $2. First, move the clear text to the return variable.  
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 UnEscape  
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
   
 =back  
   
 =cut  
   
 sub UnEscape {  
     # Get the parameter.  
     my ($codedString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Only proceed if the incoming string is nonempty.  
     if (defined $codedString) {  
         # Loop through the parameter string, looking for escape sequences. We can't do  
         # translating because it causes problems with the escaped slash. ("\\t" becomes  
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
1827    
1828  sub Percent {  =head2 File Utility Methods
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
1829    
1830  =head3 GetFile  =head3 GetFile
1831    
1832  C<< my @fileContents = Tracer::GetFile($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 1661  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 1704  Line 1926 
1926      close $handle;      close $handle;
1927  }  }
1928    
1929  =head3 QTrace  =head3 ParseRecord
1930    
1931        my @fields = Tracer::ParseRecord($line);
1932    
1933    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  C<< my $data = QTrace($format); >>  =over 4
1938    
1939  Return the queued trace data in the specified format.  =item line
1940    
1941  =over 4  Line of data containing the tab-delimited fields.
1942    
1943  =item format  =item RETURN
1944    
1945  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Returns a list of the fields found in the data line.
1946    
1947  =back  =back
1948    
1949  =cut  =cut
1950    
1951  sub QTrace {  sub ParseRecord {
1952      # Get the parameter.      # Get the parameter.
1953      my ($format) = @_;      my ($line) = @_;
1954      # Create the return variable.      # Remove the trailing new-line, if any.
1955      my $retVal = "";      chomp $line;
1956      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
1957      if (@Queue) {      my @retVal = split /\t/, $line;
1958          # Process according to the format.      # Trim and fix the escapes in each piece.
1959          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
1960              # Convert the queue into an HTML list.          # Trim leading whitespace.
1961              $retVal = "<ul>\n";          $value =~ s/^\s+//;
1962              for my $line (@Queue) {          # Trim trailing whitespace.
1963                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
1964                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
1965              }          $value =~ s/\r//g;
1966              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
1967          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
1968              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
1969      }      }
1970      # Return the formatted list.      # Return the result.
1971      return $retVal;      return @retVal;
1972  }  }
1973    
1974  =head3 Confess  =head3 Merge
1975    
1976  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
1977    
1978  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
1979    
1980  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
1981    
1982  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
1983    
1984  =over 4  List of scalars to sort and merge.
1985    
1986  =item message  =item RETURN
1987    
1988  Message to include in the trace.  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 Confess {  sub Merge {
1996      # Get the parameters.      # Get the input list in sort order.
1997      my ($message) = @_;      my @inputList = sort @_;
1998      # Trace the call stack.      # Only proceed if the list has at least two elements.
1999      Cluck($message);      if (@inputList > 1) {
2000      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2001      croak(">>> $message");          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 merged list.
2019        return @inputList;
2020  }  }
2021    
2022  =head3 Assert  =head3 Open
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
2023    
2024  Return TRUE if all the conditions are true. This method can be used in conjunction with      my $handle = Open($fileHandle, $fileSpec, $message);
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2025    
2026  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Open a file.
2027    
2028  Will abort the program with a stack trace if the value of C<$recNum> is negative.  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2029    function. The mode is specified using Unix-like shell information. So, for
2030    example,
2031    
2032  =cut      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2033    
2034  =head3 Cluck  would open for output appended to the specified file, and
2035    
2036  C<< Cluck($message); >>      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2037    
2038  Trace the call stack. Note that for best results, you should qualify the call with a  would open a pipe that sorts the records written and removes duplicates. Note
2039  trace condition. For example,  the use of file handle syntax in the Open call. To use anonymous file handles,
2040    code as follows.
2041    
2042  C<< Cluck("Starting record parse.") if T(3); >>      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2043    
2044  will only trace the stack if the trace level for the package is 3 or more.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
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  =over 4      Could not open "/usr/spool/news/twitlog"
2051    
2052  =item message  Note that the mode characters are automatically cleaned from the file name.
2053    The actual error message from the file system will be captured and appended to the
2054    message in any case.
2055    
2056  Message to include in the trace.      Could not open "/usr/spool/news/twitlog": file not found.
2057    
2058  =back  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  =cut      Could not open "/usr/spool/news/twitlog": 6.
2062    
2063  sub Cluck {  =over 4
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
 }  
2064    
2065  =head3 Min  =item fileHandle
2066    
2067  C<< my $min = Min($value1, $value2, ... $valueN); >>  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  Return the minimum argument. The arguments are treated as numbers.  =item fileSpec
2071    
2072  =over 4  File name and mode, as per the PERL C<open> function.
2073    
2074  =item $value1, $value2, ... $valueN  =item message (optional)
2075    
2076  List of numbers to compare.  Error message to use if the open fails. If omitted, a standard error message
2077    will be generated. In either case, the error information from the file system
2078    is appended to the message. To specify a conditional open that does not throw
2079    an error if it fails, use C<0>.
2080    
2081  =item RETURN  =item RETURN
2082    
2083  Returns the lowest number in the list.  Returns the name of the file handle assigned to the file, or C<undef> if the
2084    open failed.
2085    
2086  =back  =back
2087    
2088  =cut  =cut
2089    
2090  sub Min {  sub Open {
2091      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2092      my ($retVal, @values) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2093      # Loop through the remaining parameters, looking for the lowest.      # Attempt to open the file.
2094      for my $value (@values) {      my $rv = open $fileHandle, $fileSpec;
2095          if ($value < $retVal) {      # If the open failed, generate an error message.
2096              $retVal = $value;      if (! $rv) {
2097            # 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 minimum found.      # Return the file handle.
2111      return $retVal;      return $fileHandle;
2112  }  }
2113    
2114  =head3 Max  =head3 FindNamePart
2115    
2116  C<< my $max = Max($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2117    
2118  Return the maximum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2119    
2120    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        >>/usr/fig/myfile.txt
2127        </usr/fig/myfile.txt
2128        | sort -u > /usr/fig/myfile.txt
2129    
2130    If the method cannot find a file name using its normal methods, it will return the
2131    whole incoming string.
2132    
2133  =over 4  =over 4
2134    
2135  =item $value1, $value2, ... $valueN  =item fileSpec
2136    
2137    File specification string from which the file name is to be extracted.
2138    
2139    =item RETURN
2140    
2141    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
2147    
2148    =cut
2149    #: Return Type $;
2150    sub FindNamePart {
2151        # Get the parameters.
2152        my ($fileSpec) = @_;
2153        # Default to the whole input string.
2154        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2155        # Parse out the file name if we can.
2156        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2157            $retVal = $2;
2158            $len = length $retVal;
2159            $pos = (length $fileSpec) - (length $3) - $len;
2160        }
2161        # Return the result.
2162        return ($retVal, $pos, $len);
2163    }
2164    
2165  List of numbers to compare.  =head3 OpenDir
2166    
2167  =item RETURN      my @files = OpenDir($dirName, $filtered, $flag);
2168    
2169  Returns the highest number in the list.  Open a directory and return all the file names. This function essentially performs
2170    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2171    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  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2177    
2178  =cut  is effectively the same as
2179    
2180  sub Max {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2181      # Get the parameters. Note that we prime the return value with the first parameter.      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my ($retVal, @values) = @_;  
     # Loop through the remaining parameters, looking for the highest.  
     for my $value (@values) {  
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
 }  
2182    
2183  =head3 AddToListMap  Similarly, the following code
2184    
2185  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2186    
2187  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2188  is created for the key. Otherwise, the new value is pushed onto the list.  automatically returns an empty list if the directory fails to open.
2189    
2190  =over 4  =over 4
2191    
2192  =item hash  =item dirName
2193    
2194  Reference to the target hash.  Name of the directory to open.
2195    
2196  =item key  =item filtered
2197    
2198  Key for which the value is to be added.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2199    from the list, else FALSE.
2200    
2201  =item value1, value2, ... valueN  =item flag
2202    
2203  List of values to add to the key's value list.  TRUE if a failure to open is okay, else FALSE
2204    
2205  =back  =back
2206    
2207  =cut  =cut
2208    #: Return Type @;
2209  sub AddToListMap {  sub OpenDir {
2210      # Get the parameters.      # Get the parameters.
2211      my ($hash, $key, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2212      # Process according to whether or not the key already has a value.      # Declare the return variable.
2213      if (! exists $hash->{$key}) {      my @retVal = ();
2214          $hash->{$key} = [@values];      # Open the directory.
2215        if (opendir(my $dirHandle, $dirName)) {
2216            # The directory opened successfully. Get the appropriate list according to the
2217            # strictures of the filter parameter.
2218            if ($filtered) {
2219                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2220      } else {      } else {
2221          push @{$hash->{$key}}, @values;              @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 $dirName.");
2226      }      }
2227        # Return the result.
2228        return @retVal;
2229  }  }
2230    
 =head3 DebugMode  
2231    
2232  C<< if (Tracer::DebugMode) { ...code... } >>  =head3 Insure
2233    
2234  Return TRUE if debug mode has been turned on, else abort.      Insure($dirName, $chmod);
2235    
2236  Certain CGI scripts are too dangerous to exist in the production  Insure a directory is present.
2237  environment. This method provides a simple way to prevent them  
2238  from working unless they are explicitly turned on by creating a password  =over 4
2239  cookie via the B<SetPassword> script.  If debugging mode  
2240  is not turned on, an error will occur.  =item dirName
2241    
2242    Name of the directory to check. If it does not exist, it will be created.
2243    
2244    =item chmod (optional)
2245    
2246    Security privileges to be given to the directory if it is created.
2247    
2248    =back
2249    
2250  =cut  =cut
2251    
2252  sub DebugMode {  sub Insure {
2253      # Declare the return variable.      my ($dirName, $chmod) = @_;
2254      my $retVal = 0;      if (! -d $dirName) {
2255      # Check the debug configuration.          Trace("Creating $dirName directory.") if T(2);
2256      my $password = CGI::cookie("DebugMode");          eval {
2257      my $encrypted = Digest::MD5::md5_hex($password);              mkpath $dirName;
2258      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {              # If we have permissions specified, set them here.
2259          $retVal = 1;              if (defined($chmod)) {
2260      } else {                  chmod $chmod, $dirName;
2261          # Here debug mode is off, so we generate an error.              }
2262          Confess("Cannot use this facility without logging in.");          };
2263            if ($@) {
2264                Confess("Error creating $dirName: $@");
2265            }
2266      }      }
     # Return the determination indicator.  
     return $retVal;  
2267  }  }
2268    
2269  =head3 Strip  =head3 ChDir
2270    
2271  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2272    
2273  Strip all line terminators off a string. This is necessary when dealing with files  Change to the specified directory.
 that may have been transferred back and forth several times among different  
 operating environments.  
2274    
2275  =over 4  =over 4
2276    
2277  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2278    
2279  The same line of text with all the line-ending characters chopped from the end.  Name of the directory to which we want to change.
2280    
2281  =back  =back
2282    
2283  =cut  =cut
2284    
2285  sub Strip {  sub ChDir {
2286      # Get a copy of the parameter string.      my ($dirName) = @_;
2287      my ($string) = @_;      if (! -d $dirName) {
2288      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2289      # Strip the line terminator characters.      } else {
2290      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2291      # Return the result.          my $okFlag = chdir $dirName;
2292      return $retVal;          if (! $okFlag) {
2293                Confess("Error switching to directory $dirName.");
2294            }
2295        }
2296  }  }
2297    
2298  =head3 Pad  =head3 SetPermissions
2299    
2300  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2301    
2302  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2303  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2304  in the third parameter.  
2305    This method is more vulnerable than most to permission and compatability
2306    problems, so it does internal error recovery.
2307    
2308  =over 4  =over 4
2309    
2310  =item string  =item dirName
2311    
2312  String to be padded.  Name of the directory to process.
2313    
2314  =item len  =item group
2315    
2316  Desired length of the padded string.  Name of the group to be assigned.
2317    
2318  =item left (optional)  =item mask
2319    
2320  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2321    permission bits of any file or directory that does not already have them
2322    set to 1.
2323    
2324  =item padChar (optional)  =item otherMasks
2325    
2326  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2327    one of the patterns, that directory and all its members and subdirectories
2328    will be assigned the new pattern. For example, the following would
2329    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2330    
2331  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2332    
2333  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2334  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2335    
2336        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2337                                                       '^tmp' => 0666);
2338    
2339    Note that the pattern matches are all case-insensitive, and only directory
2340    names are matched, not file names.
2341    
2342  =back  =back
2343    
2344  =cut  =cut
2345    
2346  sub Pad {  sub SetPermissions {
2347      # Get the parameters.      # Get the parameters.
2348      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2349      # Compute the padding character.      # Set up for error recovery.
2350      if (! defined $padChar) {      eval {
2351          $padChar = " ";          # Switch to the specified directory.
2352            ChDir($dirName);
2353            # Get the group ID.
2354            my $gid = getgrnam($group);
2355            # Get the mask for tracing.
2356            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2357            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2358            my $fixCount = 0;
2359            my $lookCount = 0;
2360            # @dirs will be a stack of directories to be processed.
2361            my @dirs = (getcwd());
2362            while (scalar(@dirs) > 0) {
2363                # Get the current directory.
2364                my $dir = pop @dirs;
2365                # Check for a match to one of the specified directory names. To do
2366                # that, we need to pull the individual part of the name off of the
2367                # whole path.
2368                my $simpleName = $dir;
2369                if ($dir =~ m!/([^/]+)$!) {
2370                    $simpleName = $1;
2371      }      }
2372      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2373      my $needed = $len - length $string;              # Search for a match.
2374      # Copy the string into the return variable.              my $match = 0;
2375      my $retVal = $string;              my $i;
2376      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2377      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2378          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2379          my $pad = $padChar x $needed;                      $match = 1;
2380          # Affix it to the return value.                  }
2381          if ($left) {              }
2382              $retVal = $pad . $retVal;              # 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              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2390                    my @submems = OpenDir($dir, 1);
2391                    for my $submem (@submems) {
2392                        # Get the full name.
2393                        my $thisMem = "$dir/$submem";
2394                        Trace("Checking member $thisMem.") if T(4);
2395                        $lookCount++;
2396                        if ($lookCount % 1000 == 0) {
2397                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2398                        }
2399                        # Fix the group.
2400                        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      }      }
     # Return the result.  
     return $retVal;  
2419  }  }
2420                        }
2421  =head3 EOF                  }
2422                }
2423  This is a constant that is lexically greater than any useful string.          }
2424            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2425  =cut      };
2426        # Check for an error.
2427  sub EOF {      if ($@) {
2428      return "\xFF\xFF\xFF\xFF\xFF";          Confess("SetPermissions error: $@");
2429        }
2430  }  }
2431    
2432  =head3 TICK  =head3 GetLine
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2433    
2434      TICK("./protein.cgi")      my @data = Tracer::GetLine($handle);
2435    
2436  it will work correctly in both environments.  Read a line of data from a tab-delimited file.
2437    
2438  =over 4  =over 4
2439    
2440  =item commandString  =item handle
2441    
2442  The command string to pass to the system.  Open file handle from which to read.
2443    
2444  =item RETURN  =item RETURN
2445    
2446  Returns the standard output from the specified command, as a list.  Returns a list of the fields in the record read. The fields are presumed to be
2447    tab-delimited. If we are at the end of the file, then an empty list will be
2448    returned. If an empty line is read, a single list item consisting of a null
2449    string will be returned.
2450    
2451  =back  =back
2452    
2453  =cut  =cut
2454  #: Return Type @;  
2455  sub TICK {  sub GetLine {
2456      # Get the parameters.      # Get the parameters.
2457      my ($commandString) = @_;      my ($handle) = @_;
2458      # Chop off the dot-slash if this is Windows.      # Declare the return variable.
2459      if ($FIG_Config::win_mode) {      my @retVal = ();
2460          $commandString =~ s!^\./!!;      Trace("File position is " . tell($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      # Activate the command and return the result.          # If the line is empty, return a single empty string; otherwise, parse
2477      return `$commandString`;          # it into fields.
2478            if ($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 ScriptSetup  =head3 PutLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2492    
2493  Perform standard tracing and debugging setup for scripts. The value returned is      Tracer::PutLine($handle, \@fields, $eol);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2494    
2495  This method calls L</ETracing> to configure tracing, which allows the tracing  Write a line of data to a tab-delimited file. The specified field values will be
2496  to be configured via the emergency tracing form on the debugging control panel.  output in tab-separated form, with a trailing new-line.
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2497    
2498  =over 4  =over 4
2499    
2500  =item noTrace (optional)  =item handle
2501    
2502  If specified, tracing will be suppressed. This is useful if the script wants to set up  Output file handle.
 tracing manually.  
2503    
2504  =item RETURN  =item fields
2505    
2506  Returns a two-element list consisting of a CGI query object and a variable hash for  List of field values.
2507  the output page.  
2508    =item eol (optional)
2509    
2510    End-of-line character (default is "\n").
2511    
2512  =back  =back
2513    
2514  =cut  =cut
2515    
2516  sub ScriptSetup {  sub PutLine {
2517      # Get the parameters.      # Get the parameters.
2518      my ($noTrace) = @_;      my ($handle, $fields, $eol) = @_;
2519      # Get the CGI query object.      # Write the data.
2520      my $cgi = CGI->new();      print $handle join("\t", @{$fields}) . ($eol || "\n");
     # Set up tracing if it's not suppressed.  
     ETracing($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
2521  }  }
2522    
 =head3 ETracing  
   
 C<< ETracing($parameter); >>  
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
2523    
 =back  
   
 =cut  
2524    
2525  sub ETracing {  =head2 Other Useful Methods
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
     }  
 }  
2526    
2527  =head3 EmergencyFileName  =head3 ParseParm
2528    
2529  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $listValue = Tracer::ParseParm($string);
2530    
2531  Return the emergency tracing file name. This is the file that specifies  Convert a parameter into a list reference. If the parameter is undefined,
2532  the tracing information.  an undefined value will be returned. Otherwise, it will be parsed as a
2533    comma-separated list of values.
2534    
2535  =over 4  =over 4
2536    
2537  =item tkey  =item string
2538    
2539  Tracing key for the current program.  Incoming string.
2540    
2541  =item RETURN  =item RETURN
2542    
2543  Returns the name of the file to contain the emergency tracing information.  Returns a reference to a list of values, or C<undef> if the incoming value
2544    was undefined.
2545    
2546  =back  =back
2547    
2548  =cut  =cut
2549    
2550  sub EmergencyFileName {  sub ParseParm {
2551      # Get the parameters.      # Get the parameters.
2552      my ($tkey) = @_;      my ($string) = @_;
2553      # Compute the emergency tracing file name.      # Declare the return variable.
2554      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal;
2555        # Check for data.
2556        if (defined $string) {
2557            # We have some, so split it into a list.
2558            $retVal = [ split /\s*,\s*/, $string];
2559        }
2560        # Return the result.
2561        return $retVal;
2562  }  }
2563    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
   
 Return the emergency tracing target file name. This is the file that receives  
 the tracing output for file-based tracing.  
   
 =over 4  
2564    
 =item tkey  
2565    
 Tracing key for the current program.  
2566    
2567  =item RETURN  =head3 Now
2568    
2569  Returns the name of the file to contain the trace output.      my $string = Tracer::Now();
2570    
2571  =back  Return a displayable time stamp containing the local time.
2572    
2573  =cut  =cut
2574    
2575  sub EmergencyFileTarget {  sub Now {
2576      # Get the parameters.      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2577      my ($tkey) = @_;      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2578      # Compute the emergency tracing file name.                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2579      return "$FIG_Config::temp/trace$tkey.log";      return $retVal;
2580    }
2581    
2582    # Pad a number to 2 digits.
2583    sub _p2 {
2584        my ($value) = @_;
2585        $value = "0$value" if ($value < 10);
2586        return $value;
2587  }  }
2588    
2589  =head3 EmergencyTracingDest  =head3 Escape
2590    
2591  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my $codedString = Tracer::Escape($realString);
2592    
2593  This method converts an emergency tracing destination to a real  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2594  tracing destination. The main difference is that if the  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2595  destination is C<FILE> or C<APPEND>, we convert it to file  result is to reverse the effect of L</UnEscape>.
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2596    
2597  =over 4  =over 4
2598    
2599  =item tkey  =item realString
   
 Tracing key for this environment.  
   
 =item myDest  
2600    
2601  Destination from the emergency tracing file.  String to escape.
2602    
2603  =item RETURN  =item RETURN
2604    
2605  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2606    
2607  =back  =back
2608    
2609  =cut  =cut
2610    
2611  sub EmergencyTracingDest {  sub Escape {
2612      # Get the parameters.      # Get the parameter.
2613      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2614      # Declare the return variable.      # Initialize the return variable.
2615      my $retVal = $myDest;      my $retVal = "";
2616      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2617      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2618          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2619      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2620          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2621      } elsif ($myDest eq 'DUAL') {              # itself is in $2. First, move the clear text to the return variable.
2622          $retVal = "+>" . EmergencyFileTarget($tkey);              $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.      # Return the result.
2641      return $retVal;      return $retVal;
2642  }  }
2643    
2644  =head3 Emergency  =head3 UnEscape
2645    
2646  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2647    
2648  Turn on emergency tracing. This method is normally invoked over the web from  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2649  a debugging console, but it can also be called by the C<trace.pl> script.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2650  The caller specifies the duration of the emergency in hours, the desired tracing  be deleted.
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
2651    
2652  =over 4  =over 4
2653    
2654  =item tkey  =item codedString
   
 The tracing key. This is used to identify the control file and the trace file.  
   
 =item hours  
   
 Number of hours to keep emergency tracing alive.  
   
 =item dest  
   
 Tracing destination. If no path information is specified for a file  
 destination, it is put in the FIG temporary directory.  
   
 =item level  
2655    
2656  Tracing level. A higher level means more trace messages.  String to un-escape.
2657    
2658  =item modules  =item RETURN
2659    
2660  A list of the tracing modules to activate.  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 Emergency {  sub UnEscape {
2668      # Get the parameters.      # Get the parameter.
2669      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2670      # Create the emergency file.      # Initialize the return variable.
2671      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2672      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2673      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2674            # Loop through the parameter string, looking for escape sequences. We can't do
2675            # 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 {
2693                    # Here there are no more escape sequences. The rest of the string is
2694                    # transferred unmodified.
2695                    $retVal .= $codedString;
2696                    $codedString = "";
2697                }
2698            }
2699        }
2700        # Return the result.
2701        return $retVal;
2702  }  }
2703    
2704  =head3 EmergencyKey  =head3 Percent
2705    
2706  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
2707    
2708  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
2709   a session ID, or a user name, depending on the environment.  is zero, returns zero.
2710    
2711  =over 4  =over 4
2712    
2713  =item parameter  =item number
2714    
2715  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
2716  then it is presumed to be the tracing key itself. If it is a CGI object, then  
2717  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
2718  taken from the C<TRACING> environment variable.  
2719    Percent base.
2720    
2721  =item RETURN  =item RETURN
2722    
2723  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub EmergencyKey {  sub Percent {
2730      # Get the parameters.      # Get the parameters.
2731      my ($parameter) = @_;      my ($number, $base) = @_;
2732      # Declare the return variable.      # Declare the return variable.
2733      my $retVal;      my $retVal = 0;
2734      # Determine the parameter type.      # Compute the percent.
2735      if (! defined $parameter) {      if ($base != 0) {
2736          # Here we're supposed to check the environment.          $retVal = $number * 100 / $base;
         $retVal = $ENV{TRACING};  
     } else {  
         my $ptype = ref $parameter;  
         if ($ptype eq 'CGI') {  
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2737      }      }
2738      # Return the result.      # Return the result.
2739      return $retVal;      return $retVal;
2740  }  }
2741    
2742    =head3 Min
2743    
2744  =head3 TraceParms      my $min = Min($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
2745    
2746  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Return the minimum argument. The arguments are treated as numbers.
 at level CGI => 4.  
2747    
2748  =over 4  =over 4
2749    
2750  =item cgi  =item $value1, $value2, ... $valueN
2751    
2752  CGI query object containing the parameters to trace.  List of numbers to compare.
2753    
2754    =item RETURN
2755    
2756    Returns the lowest number in the list.
2757    
2758  =back  =back
2759    
2760  =cut  =cut
2761    
2762  sub TraceParms {  sub Min {
2763      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2764      my ($cgi) = @_;      my ($retVal, @values) = @_;
2765      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the lowest.
2766          # Here we want to trace the parameter data.      for my $value (@values) {
2767          my @names = $cgi->param;          if ($value < $retVal) {
2768          for my $parmName (sort @names) {              $retVal = $value;
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
2769  }  }
   
 =head3 ScriptFinish  
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
2770      }      }
2771      use Tracer;      # Return the minimum found.
2772      use CGI;      return $retVal;
     use FIG;  
     # ... more uses ...  
   
     my ($cgi, $varHash) = ScriptSetup();  
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
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";  
2802          }          }
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
2803      }      }
2804      # Check for trace messages.      # Return the maximum found.
2805      if ($Destination ne "NONE" && $TraceLevel > 0) {      return $retVal;
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
2806          }          }
2807          # If the trace messages were queued, we unroll them. Otherwise, we display the  
2808          # destination.  =head3 DebugMode
2809          my $traceHtml;  
2810          if ($Destination eq "QUEUE") {      if (Tracer::DebugMode) { ...code... }
2811              $traceHtml = QTrace('Html');  
2812          } elsif ($Destination =~ /^>>(.+)$/) {  Return TRUE if debug mode has been turned on, else abort.
2813              # Here the tracing output it to a file. We code it as a hyperlink so the user  
2814              # can copy the file name into the clipboard easily.  Certain CGI scripts are too dangerous to exist in the production
2815              my $actualDest = $1;  environment. This method provides a simple way to prevent them
2816              $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  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
2821    
2822    sub DebugMode {
2823        # Declare the return variable.
2824        my $retVal = 0;
2825        # Check the debug configuration.
2826        my $password = CGI::cookie("DebugMode");
2827        my $encrypted = Digest::MD5::md5_hex($password);
2828        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2829            $retVal = 1;
2830          } else {          } else {
2831              # Here we have one of the special destinations.          # Here debug mode is off, so we generate an error.
2832              $traceHtml = "<P>Tracing output type is $Destination.</p>\n";          Confess("Cannot use this facility without logging in.");
         }  
         substr $outputString, $pos, 0, $traceHtml;  
2833      }      }
2834      # Write the output string.      # Return the determination indicator.
2835      print $outputString;      return $retVal;
2836  }  }
2837    
2838  =head3 Insure  =head3 Strip
2839    
2840  C<< Insure($dirName); >>      my $string = Tracer::Strip($line);
2841    
2842  Insure a directory is present.  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 check. If it does not exist, it will be created.  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 Insure {  sub Strip {
2861      my ($dirName) = @_;      # Get a copy of the parameter string.
2862      if (! -d $dirName) {      my ($string) = @_;
2863          Trace("Creating $dirName directory.") if T(File => 2);      my $retVal = (defined $string ? $string : "");
2864          eval { mkpath $dirName; };      # Strip the line terminator characters.
2865          if ($@) {      $retVal =~ s/(\r|\n)+$//g;
2866              Confess("Error creating $dirName: $@");      # Return the result.
2867          }      return $retVal;
     }  
2868  }  }
2869    
2870  =head3 ChDir  =head3 Pad
2871    
2872  C<< ChDir($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2873    
2874  Change to the specified directory.  Pad a string to a specified length. The pad character will be a
2875    space, and the padding will be on the right side unless specified
2876    in the third parameter.
2877    
2878  =over 4  =over 4
2879    
2880  =item dirName  =item string
2881    
2882  Name of the directory to which we want to change.  String to be padded.
2883    
2884    =item len
2885    
2886    Desired length of the padded string.
2887    
2888    =item left (optional)
2889    
2890    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2891    
2892    =item padChar (optional)
2893    
2894    Character to use for padding. The default is a space.
2895    
2896    =item RETURN
2897    
2898    Returns a copy of the original string with the pad character added to the
2899    specified end so that it achieves the desired length.
2900    
2901  =back  =back
2902    
2903  =cut  =cut
2904    
2905  sub ChDir {  sub Pad {
2906      my ($dirName) = @_;      # Get the parameters.
2907      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
2908          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
2909        if (! defined $padChar) {
2910            $padChar = " ";
2911        }
2912        # Compute the number of spaces needed.
2913        my $needed = $len - length $string;
2914        # Copy the string into the return variable.
2915        my $retVal = $string;
2916        # Only proceed if padding is needed.
2917        if ($needed > 0) {
2918            # Create the pad string.
2919            my $pad = $padChar x $needed;
2920            # Affix it to the return value.
2921            if ($left) {
2922                $retVal = $pad . $retVal;
2923      } else {      } else {
2924          Trace("Changing to directory $dirName.") if T(File => 4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
2925          }          }
2926      }      }
2927        # Return the result.
2928        return $retVal;
2929  }  }
2930    
2931  =head3 SendSMS  =head3 EOF
2932    
2933  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
2934    
2935  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
2936    
2937      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
2938                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
2939                  api_id => '2561022' };  }
2940    
2941  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2942    
2943  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
2944    
2945  =over 4  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  =item phoneNumber      `./protein.cgi`
2949    
2950  Phone number to receive the message, in international format. A United States phone number  from inside a CGI script, it would work fine in Unix, but would issue an error message
2951  would be prefixed by "1". A British phone number would be prefixed by "44".  in Windows complaining that C<'.'> is not a valid command. If instead you code
2952    
2953  =item msg      TICK("./protein.cgi")
2954    
2955  Message to send to the specified phone.  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  =item RETURN
2964    
2965  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
2966    
2967  =back  =back
2968    
2969  =cut  =cut
2970    #: Return Type @;
2971  sub SendSMS {  sub TICK {
2972      # Get the parameters.      # Get the parameters.
2973      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
2974      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
2975      my $retVal;      if ($FIG_Config::win_mode) {
2976      # Only proceed if we have phone support.          $commandString =~ s!^\./!!;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
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 2749  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 $keyIndex column.
# Line 2950  Line 3084 
3084      return ($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. We are a bit over-cautious here because the file may be coming in via an  
         # upload control and have a nonstandard EOL combination.  
         $line =~ s/(\r|\n)+$//;  
         # Here we do some fancy tracing to help in debugging complicated EOL marks.  
         if (T(File => 4)) {  
             my $escapedLine = $line;  
             $escapedLine =~ s/\n/\\n/g;  
             $escapedLine =~ s/\r/\\r/g;  
             $escapedLine =~ s/\t/\\t/g;  
             Trace("Line read: -->$escapedLine<--");  
         }  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
     } else {  
         # Trace the reason the read failed.  
         Trace("End of file: $!") if T(File => 3);  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 PutLine  
   
 C<< Tracer::PutLine($handle, \@fields, $eol); >>  
   
 Write a line of data to a tab-delimited file. The specified field values will be  
 output in tab-separated form, with a trailing new-line.  
   
 =over 4  
   
 =item handle  
   
 Output file handle.  
   
 =item fields  
   
 List of field values.  
   
 =item eol (optional)  
   
 End-of-line character (default is "\n").  
   
 =back  
   
 =cut  
   
 sub PutLine {  
     # Get the parameters.  
     my ($handle, $fields, $eol) = @_;  
     # Write the data.  
     print $handle join("\t", @{$fields}) . ($eol || "\n");  
 }  
   
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 3091  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 3134  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 3175  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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