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revision 1.84, Thu May 3 12:28:00 2007 UTC revision 1.130, Mon Jun 14 14:36:03 2010 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
     require Exporter;  
     @ISA = ('Exporter');  
     @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);  
     @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);  
21      use strict;      use strict;
22      use Carp qw(longmess croak);      use base qw(Exporter);
23        use vars qw(@EXPORT @EXPORT_OK);
24        @EXPORT = qw(Trace T TSetup QTrace Confess MemTrace Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25        @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26        use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 35  Line 36 
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38      use Time::Local;      use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl qw(:DEFAULT :flock);
42        use Data::Dumper;
43    
44    
45  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
46    
# Line 159  Line 165 
165    
166  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
167  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
170  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
171  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
172  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 189 
189    
190  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
191  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
192  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193  will be configured automatically.  will be configured automatically.
194    
 NOTE: to configure emergency tracing from the command line instead of the Debugging  
 Control Panel (see below), use the C<trace.pl> script.  
   
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
195  =cut  =cut
196    
197  # Declare the configuration variables.  # Declare the configuration variables.
198    
199  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
200  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
201                              # standard output                              # standard output
202  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
203                              # hash of active category names                              # hash of active category names
204    my @LevelNames = qw(error warn notice info detail);
205  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
206                              # messages                              # messages
207  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
208  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
209    my $LastLevel = 0;          # level of the last test call
210  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
211  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
212    my $SavedCGI;               # CGI object passed to ETracing
213    my $CommandLine;            # Command line passed to StandardSetup
214    my $Confessions = 0;        # confession count
215    umask 2;                    # Fix the damn umask so everything is group-writable.
216    
217    =head2 Tracing Methods
218    
219    =head3 Setups
220    
221        my $count = Tracer::Setups();
222    
223    Return the number of times L</TSetup> has been called.
224    
225    This method allows for the creation of conditional tracing setups where, for example, we
226    may want to set up tracing if nobody else has done it before us.
227    
228    =cut
229    
230  =head2 Public Methods  sub Setups {
231        return $SetupCount;
232    }
233    
234  =head3 TSetup  =head3 TSetup
235    
236  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
237    
238  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
239  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 283 
283          }          }
284      }      }
285      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
286      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
287      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
288        # the standard output (tee mode).
289      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
290          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
291              $TeeFlag = 1;              $TeeFlag = 1;
292              $target = substr($target, 1);              $target = substr($target, 1);
293          }          }
294          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
295                # We need to initialize the file (which clears it).
296              open TRACEFILE, $target;              open TRACEFILE, $target;
297              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
298              close TRACEFILE;              close TRACEFILE;
299                # Set to append mode now that the file has been cleared.
300              $Destination = ">$target";              $Destination = ">$target";
301          } else {          } else {
302              $Destination = $target;              $Destination = $target;
# Line 372  Line 308 
308      $SetupCount++;      $SetupCount++;
309  }  }
310    
311  =head3 StandardSetup  =head3 SetLevel
312    
313  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
314    
315  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 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.  
316    
317  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
318    
319  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 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  
320    
321      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
322    
323  This would cause trace messages in the specified three packages to appear in  =back
 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.  
324    
325  =over 4  =cut
326    
327  =item SQL  sub SetLevel {
328        $TraceLevel = $_[0];
329    }
330    
331  Traces SQL commands and activity.  =head3 ParseDate
332    
333  =item Tracer      my $time = Tracer::ParseDate($dateString);
334    
335  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
336    and parses it into a number. The string must be vaguely date-like or it will
337    return an undefined value. Our requirement is that a month and day be
338    present and that three pieces of the date string (time of day, month and day,
339    year) be separated by likely delimiters, such as spaces, commas, and such-like.
340    
341  =back  If a time of day is present, it must be in military time with two digits for
342    everything but the hour.
343    
344  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 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.  
345    
346      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Additional stuff can be in the string. We presume it's time zones or weekdays or something
347    equally innocuous. This means, however, that a sufficiently long sentence with date-like
348    parts in it may be interpreted as a date. Hopefully this will not be a problem.
349    
350  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
351    
352  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
353    
354      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
355    
356  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
357    
358  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 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.  
359    
360  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
361    
362  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
363  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
364    
365      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { 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);  
366    
367    =cut
368    
369  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
370  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
371  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
372                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
373                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
374                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
375                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
376                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
377                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
378                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
379                                Oct =>  9, October  =>   9, '10' =>  9,
380                                Nov => 10, November =>  10, '11' => 10,
381                                Dec => 11, December =>  11, '12' => 11
382                            };
383    
384  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
385        # Get the parameters.
386        my ($dateString) = @_;
387        # Declare the return variable.
388        my $retVal;
389        # Find the month and day of month. There are two ways that can happen. We check for the
390        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
391        # won't be fooled into thinking the month is Sunday.
392        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
393            my ($mon, $mday) = (MONTHS->{$1}, $2);
394            # Insist that the month and day are valid.
395            if (defined($mon) && $2 >= 1 && $2 <= 31) {
396                # Find the time.
397                my ($hour, $min, $sec) = (0, 0, 0);
398                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
399                    ($hour, $min, $sec) = ($1, $2, $3);
400                }
401                # Find the year.
402                my $year;
403                if ($dateString =~ /\b(\d{4})\b/) {
404                    $year = $1;
405                } else {
406                    # Get the default year, which is this one. Note we must convert it to
407                    # the four-digit value expected by "timelocal".
408                    (undef, undef, undef, undef, undef, $year) = localtime();
409                    $year += 1900;
410                }
411                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
412            }
413        }
414        # Return the result.
415        return $retVal;
416    }
417    
418      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
419    
420  Single and double hyphens are equivalent. So, you could also code the      Tracer::LogErrors($fileName);
 above command as  
421    
422      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
423    
424  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 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<$options> hash would be  
425    
426      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
427    
428  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
429    
430  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
431    
432      -user=Bruce -background  =cut
433    
434  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
435  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
436  simplify starting a command in the background.      my ($fileName) = @_;
437        # Open the file as the standard error output.
438        open STDERR, '>', $fileName;
439    }
440    
441  The user name is also used as the tracing key for L</Emergency Tracing>.  =head3 Trace
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
442    
443  Finally, if the special option C<-help> is specified, the option      Trace($message);
 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  
444    
445      TransactFeatures -help  Write a trace message to the target location specified in L</TSetup>. If there has not been
446    any prior call to B<TSetup>.
447    
448  he would see the following output.  =over 4
449    
450      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =item message
         -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  
451    
452  The caller has the option of modifying the tracing scheme by placing a value  Message to write.
 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,  
453    
454      { trace => [0, "tracing level (default 0)"],  =back
        ...  
455    
456  would set the default trace level to 0 instead of E, while  =cut
457    
458      { trace => ["2-", "tracing level (default 2)"],  sub Trace {
459         ...      # Get the parameters.
460        my ($message) = @_;
461        # Strip off any line terminators at the end of the message. We will add
462        # new-line stuff ourselves.
463        my $stripped = Strip($message);
464        # Compute the caller information.
465        my ($callPackage, $callFile, $callLine) = caller();
466        my $callFileTitle = basename($callFile);
467        # Check the caller.
468        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
469        # Get the timestamp.
470        my $timeStamp = Now();
471        # Build the prefix.
472        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
473        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
474        # Format the message.
475        my $formatted = "$prefix $stripped";
476        # Process according to the destination.
477        if ($Destination eq "TEXT") {
478            # Write the message to the standard output.
479            print "$formatted\n";
480        } elsif ($Destination eq "ERROR") {
481            # Write the message to the error output. Here, we want our prefix fields.
482            print STDERR "$formatted\n";
483        } elsif ($Destination eq "WARN") {
484            # Emit the message to the standard error output. It is presumed that the
485            # error logger will add its own prefix fields, the notable exception being
486            # the caller info.
487            print STDERR "$callerInfo$stripped\n";
488        } elsif ($Destination eq "QUEUE") {
489            # Push the message into the queue.
490            push @Queue, "$formatted";
491        } elsif ($Destination eq "HTML") {
492            # Convert the message to HTML.
493            my $escapedMessage = CGI::escapeHTML($stripped);
494            # The stuff after the first line feed should be pre-formatted.
495            my @lines = split /\s*\n/, $escapedMessage;
496            # Get the normal portion.
497            my $line1 = shift @lines;
498            print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
499            if (@lines) {
500                print "<pre>" . join("\n", @lines, "</pre>");
501            }
502        } elsif ($Destination =~ m/^>>/) {
503            # Write the trace message to an output file.
504            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
505            # Lock the file.
506            flock TRACING, LOCK_EX;
507            print TRACING "$formatted\n";
508            close TRACING;
509            # If the Tee flag is on, echo it to the standard output.
510            if ($TeeFlag) {
511                print "$formatted\n";
512            }
513        }
514    }
515    
516  would set the default to 2, but trace only to the log file, not to the  =head3 MemTrace
 standard output.  
517    
518  The parameters to this method are as follows.      MemTrace($message);
519    
520    Output a trace message that includes memory size information.
521    
522  =over 4  =over 4
523    
524  =item categories  =item message
525    
526  Reference to a list of tracing category names. These should be names of  Message to display. The message will be followed by a sentence about the memory size.
 packages whose internal workings will need to be debugged to get the  
 command working.  
527    
528  =item options  =back
529    
530  Reference to a hash containing the legal options for the current command mapped  =cut
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
531    
532  =item parmHelp  sub MemTrace {
533        # Get the parameters.
534        my ($message) = @_;
535        my $memory = GetMemorySize();
536        Trace("$message $memory in use.");
537    }
538    
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
539    
540  =item argv  =head3 TraceDump
541    
542        TraceDump($title, $object);
543    
544    Dump an object to the trace log. This method simply calls the C<Dumper>
545    function, but routes the output to the trace log instead of returning it
546    as a string. The output is arranged so that it comes out monospaced when
547    it appears in an HTML trace dump.
548    
549    =over 4
550    
551    =item title
552    
553    Title to give to the object being dumped.
554    
555    =item object
556    
557    Reference to a list, hash, or object to dump.
558    
559    =back
560    
561    =cut
562    
563    sub TraceDump {
564        # Get the parameters.
565        my ($title, $object) = @_;
566        # Trace the object.
567        Trace("Object dump for $title:\n" . Dumper($object));
568    }
569    
570    =head3 T
571    
572        my $switch = T($category, $traceLevel);
573    
574        or
575    
576        my $switch = T($traceLevel);
577    
578    Return TRUE if the trace level is at or above a specified value and the specified category
579    is active, else FALSE. If no category is specified, the caller's package name is used.
580    
581    =over 4
582    
583    =item category
584    
585    Category to which the message belongs. If not specified, the caller's package name is
586    used.
587    
588    =item traceLevel
589    
590    Relevant tracing level.
591    
592    =item RETURN
593    
594    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
595    
596    =back
597    
598    =cut
599    
600    sub T {
601        # Declare the return variable.
602        my $retVal = 0;
603        # Only proceed if tracing is turned on.
604        if ($Destination ne "NONE") {
605            # Get the parameters.
606            my ($category, $traceLevel) = @_;
607            if (!defined $traceLevel) {
608                # Here we have no category, so we need to get the calling package.
609                # The calling package is normally the first parameter. If it is
610                # omitted, the first parameter will be the tracelevel. So, the
611                # first thing we do is shift the so-called category into the
612                # $traceLevel variable where it belongs.
613                $traceLevel = $category;
614                my ($package, $fileName, $line) = caller;
615                # If there is no calling package, we default to "main".
616                if (!$package) {
617                    $category = "main";
618                } else {
619                    my @cats = split /::/, $package;
620                    $category = $cats[$#cats];
621                }
622            }
623            # Save the category name and level.
624            $LastCategory = $category;
625            $LastLevel = $traceLevel;
626            # Convert it to lower case before we hash it.
627            $category = lc $category;
628            # Validate the trace level.
629            if (ref $traceLevel) {
630                Confess("Bad trace level.");
631            } elsif (ref $TraceLevel) {
632                Confess("Bad trace config.");
633            }
634            # Make the check. Note that level 0 shows even if the category is turned off.
635            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
636        }
637        # Return the computed result.
638        return $retVal;
639    }
640    
641    =head3 QTrace
642    
643        my $data = QTrace($format);
644    
645    Return the queued trace data in the specified format.
646    
647    =over 4
648    
649    =item format
650    
651    C<html> to format the data as an HTML list, C<text> to format it as straight text.
652    
653    =back
654    
655    =cut
656    
657    sub QTrace {
658        # Get the parameter.
659        my ($format) = @_;
660        # Create the return variable.
661        my $retVal = "";
662        # Only proceed if there is an actual queue.
663        if (@Queue) {
664            # Process according to the format.
665            if ($format =~ m/^HTML$/i) {
666                # Convert the queue into an HTML list.
667                $retVal = "<ul>\n";
668                for my $line (@Queue) {
669                    my $escapedLine = CGI::escapeHTML($line);
670                    $retVal .= "<li>$escapedLine</li>\n";
671                }
672                $retVal .= "</ul>\n";
673            } elsif ($format =~ m/^TEXT$/i) {
674                # Convert the queue into a list of text lines.
675                $retVal = join("\n", @Queue) . "\n";
676            }
677            # Clear the queue.
678            @Queue = ();
679        }
680        # Return the formatted list.
681        return $retVal;
682    }
683    
684    =head3 Confess
685    
686        Confess($message);
687    
688    Trace the call stack and abort the program with the specified message. When used with
689    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
690    So, for example
691    
692        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
693    
694    Will abort the program with a stack trace if the value of C<$recNum> is negative.
695    
696    =over 4
697    
698    =item message
699    
700    Message to include in the trace.
701    
702    =back
703    
704    =cut
705    
706    sub Confess {
707        # Get the parameters.
708        my ($message) = @_;
709        # Set up the category and level.
710        $LastCategory = "(confess)";
711        $LastLevel = 0;
712        # Trace the call stack.
713        Cluck($message);
714        # Increment the confession count.
715        $Confessions++;
716        # Abort the program.
717        croak(">>> $message");
718    }
719    
720    =head3 Confessions
721    
722        my $count = Tracer::Confessions();
723    
724    Return the number of calls to L</Confess> by the current task.
725    
726    =cut
727    
728    sub Confessions {
729        return $Confessions;
730    }
731    
732    
733    =head3 SaveCGI
734    
735        Tracer::SaveCGI($cgi);
736    
737    This method saves the CGI object but does not activate emergency tracing.
738    It is used to allow L</Warn> to work in situations where emergency
739    tracing is contra-indicated (e.g. the wiki).
740    
741    =over 4
742    
743    =item cgi
744    
745    Active CGI query object.
746    
747    =back
748    
749    =cut
750    
751    sub SaveCGI {
752        $SavedCGI = $_[0];
753    }
754    
755    =head3 Warn
756    
757        Warn($message, @options);
758    
759    This method traces an important message. If an RSS feed is configured
760    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
761    then the message will be echoed to the feed. In general, a tracing
762    destination of C<WARN> indicates that the caller is running as a web
763    service in a production environment; however, this is not a requirement.
764    
765    To force warnings into the RSS feed even when the tracing destination
766    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
767    configured automatically when L</StandardSetup> is used.
768    
769    The L</Cluck> method calls this one for its final message. Since
770    L</Confess> calls L</Cluck>, this means that any error which is caught
771    and confessed will put something in the feed. This insures that someone
772    will be alerted relatively quickly when a failure occurs.
773    
774    =over 4
775    
776    =item message
777    
778    Message to be traced.
779    
780    =item options
781    
782    A list containing zero or more options.
783    
784    =back
785    
786    The permissible options are as follows.
787    
788    =over 4
789    
790    =item noStack
791    
792    If specified, then the stack trace is not included in the output.
793    
794    =back
795    
796    =cut
797    
798    sub Warn {
799        # Get the parameters.
800        my $message = shift @_;
801        my %options = map { $_ => 1 } @_;
802        # Save $@;
803        my $savedError = $@;
804        # Trace the message.
805        Trace($message);
806        # This will contain the lock handle. If it's defined, it means we need to unlock.
807        my $lock;
808        # Check for feed forcing.
809        my $forceFeed = exists $Categories{feed};
810        # An error here would be disastrous. Note that if debug mode is specified,
811        # we do this stuff even in a test environment.
812        eval {
813            # Do we need to put this in the RSS feed?
814            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
815                # Probably. We need to check first, however, to see if it's from an
816                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
817                my $key = "127.0.0.1";
818                if (defined $SavedCGI) {
819                    # Get the IP address.
820                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
821                }
822                # Is the IP address in the ignore list?
823                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
824                if (! $found) {
825                    # No. We're good. We now need to compute the date, the link, and the title.
826                    # First, the date, in a very specific format.
827                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
828                        (tz_local_offset() / 30);
829                    # Environment data goes in here. We start with the date.
830                    my $environment = "$date.  ";
831                    # If we need to recap the message (because it's too long to be a title), we'll
832                    # put it in here.
833                    my $recap;
834                    # Copy the message and remove excess space.
835                    my $title = $message;
836                    $title =~ s/\s+/ /gs;
837                    # If it's too long, we have to split it up.
838                    if (length $title > 60) {
839                        # Put the full message in the environment string.
840                        $recap = $title;
841                        # Excerpt it as the title.
842                        $title = substr($title, 0, 50) . "...";
843                    }
844                    # If we have a CGI object, then this is a web error. Otherwise, it's
845                    # command-line.
846                    if (defined $SavedCGI) {
847                        # We're in a web service. The environment is the user's IP, and the link
848                        # is the URL that got us here.
849                        $environment .= "Event Reported at IP address $key process $$.";
850                        my $url = $SavedCGI->self_url();
851                        # We need the user agent string and (if available) the referrer.
852                        # The referrer will be the link.
853                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
854                        if ($ENV{HTTP_REFERER}) {
855                            my $link = $ENV{HTTP_REFERER};
856                            $environment .= " referred from <a href=\"$link\">$link</a>.";
857                        } else {
858                            $environment .= " referrer unknown.";
859                        }
860                        # Close off the sentence with the original link.
861                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
862                    } else {
863                        # No CGI object, so we're a command-line tool. Use the tracing
864                        # key and the PID as the user identifier, and add the command.
865                        my $key = EmergencyKey();
866                        $environment .= "Event Reported by $key process $$.";
867                        if ($CommandLine) {
868                            # We're in a StandardSetup script, so we have the real command line.
869                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
870                        } elsif ($ENV{_}) {
871                            # We're in a BASH script, so the command has been stored in the _ variable.
872                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
873                        }
874                    }
875                    # Build a GUID. We use the current time, the title, and the process ID,
876                    # then digest the result.
877                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
878                    # Finally, the description. This is a stack trace plus various environmental stuff.
879                    # The trace is optional.
880                    my $stackTrace;
881                    if ($options{noStack}) {
882                        $stackTrace = "";
883                    } else {
884                        my @trace = LongMess();
885                        # Only proceed if we got something back.
886                        if (scalar(@trace) > 0) {
887                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
888                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
889                        }
890                    }
891                    # We got the stack trace. Now it's time to put it all together.
892                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
893                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
894                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
895                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
896                    # our <br>s and <pre>s are used to format the description.
897                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
898                    my $description = "$recap$environment  $stackTrace";
899                    # Okay, we have all the pieces. Create a hash of the new event.
900                    my $newItem = { title => $title,
901                                    description => $description,
902                                    category => $LastCategory,
903                                    pubDate => $date,
904                                    guid => $guid,
905                                  };
906                    # We need XML capability for this.
907                    require XML::Simple;
908                    # The RSS document goes in here.
909                    my $rss;
910                    # Get the name of the RSS file. It's in the FIG temporary directory.
911                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
912                    # Open the config file and lock it.
913                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
914                    flock $lock, LOCK_EX;
915                    # Does it exist?
916                    if (-s $fileName) {
917                        # Slurp it in.
918                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
919                    } else {
920                        my $size = -s $fileName;
921                        # Create an empty channel.
922                        $rss = {
923                            channel => {
924                                title => 'NMPDR Warning Feed',
925                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
926                                description => "Important messages regarding the status of the NMPDR.",
927                                generator => "NMPDR Trace Facility",
928                                docs => "http://blogs.law.harvard.edu/tech/rss",
929                                item => []
930                            },
931                        };
932                    }
933                    # Get the channel object.
934                    my $channel = $rss->{channel};
935                    # Update the last-build date.
936                    $channel->{lastBuildDate} = $date;
937                    # Get the item array.
938                    my $items = $channel->{item};
939                    # Insure it has only 100 entries.
940                    while (scalar @{$items} > 100) {
941                        pop @{$items};
942                    }
943                    # Add our new item at the front.
944                    unshift @{$items}, $newItem;
945                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
946                    # the requirements for those.
947                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
948                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
949                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
950                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
951                    # We don't use Open here because we can't afford an error.
952                    if (open XMLOUT, ">$fileName") {
953                        print XMLOUT $xml;
954                        close XMLOUT;
955                    }
956                }
957            }
958        };
959        if ($@) {
960            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
961            # (which is a good thing).
962            my $error = $@;
963            Trace("Feed Error: $error") if T(Feed => 0);
964        }
965        # Be sure to unlock.
966        if ($lock) {
967            flock $lock, LOCK_UN;
968            undef $lock;
969        }
970        # Restore the error message.
971        $@ = $savedError;
972    }
973    
974    
975    
976    
977    =head3 Assert
978    
979        Assert($condition1, $condition2, ... $conditionN);
980    
981    Return TRUE if all the conditions are true. This method can be used in conjunction with
982    the OR operator and the L</Confess> method as a debugging assert.
983    So, for example
984    
985        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
986    
987    Will abort the program with a stack trace if the value of C<$recNum> is negative.
988    
989    =cut
990    sub Assert {
991        my $retVal = 1;
992        LOOP: for my $condition (@_) {
993            if (! $condition) {
994                $retVal = 0;
995                last LOOP;
996            }
997        }
998        return $retVal;
999    }
1000    
1001    =head3 Cluck
1002    
1003        Cluck($message);
1004    
1005    Trace the call stack. Note that for best results, you should qualify the call with a
1006    trace condition. For example,
1007    
1008        Cluck("Starting record parse.") if T(3);
1009    
1010    will only trace the stack if the trace level for the package is 3 or more.
1011    
1012    =over 4
1013    
1014    =item message
1015    
1016    Message to include in the trace.
1017    
1018    =back
1019    
1020    =cut
1021    
1022    sub Cluck {
1023        # Get the parameters.
1024        my ($message) = @_;
1025        # Trace what's happening.
1026        Trace("Stack trace for event: $message");
1027        # Get the stack trace.
1028        my @trace = LongMess();
1029        # Convert the trace to a series of messages.
1030        for my $line (@trace) {
1031            # Replace the tab at the beginning with spaces.
1032            $line =~ s/^\t/    /;
1033            # Trace the line.
1034            Trace($line);
1035        }
1036        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
1037        Warn($message);
1038    }
1039    
1040    =head3 LongMess
1041    
1042        my @lines = Tracer::LongMess();
1043    
1044    Return a stack trace with all tracing methods removed. The return will be in the form of a list
1045    of message strings.
1046    
1047    =cut
1048    
1049    sub LongMess {
1050        # Declare the return variable.
1051        my @retVal = ();
1052        my $confession = longmess("");
1053        for my $line (split /\s*\n/, $confession) {
1054            unless ($line =~ /Tracer\.pm/) {
1055                # Here we have a line worth keeping. Push it onto the result list.
1056                push @retVal, $line;
1057            }
1058        }
1059        # Return the result.
1060        return @retVal;
1061    }
1062    
1063    =head3 ETracing
1064    
1065        ETracing($parameter, %options);
1066    
1067    Set up emergency tracing. Emergency tracing is tracing that is turned
1068    on automatically for any program that calls this method. The emergency
1069    tracing parameters are stored in a a file identified by a tracing key.
1070    If this method is called with a CGI object, then the tracing key is
1071    taken from a cookie. If it is called with no parameters, then the tracing
1072    key is taken from an environment variable. If it is called with a string,
1073    the tracing key is that string.
1074    
1075    =over 4
1076    
1077    =item parameter
1078    
1079    A parameter from which the tracing key is computed. If it is a scalar,
1080    that scalar is used as the tracing key. If it is a CGI object, the
1081    tracing key is taken from the C<IP> cookie. If it is omitted, the
1082    tracing key is taken from the C<TRACING> environment variable. If it
1083    is a CGI object and emergency tracing is not on, the C<Trace> and
1084    C<TF> parameters will be used to determine the type of tracing.
1085    
1086    =item options
1087    
1088    Hash of options. The permissible options are given below.
1089    
1090    =over 8
1091    
1092    =item destType
1093    
1094    Emergency tracing destination type to use if no tracing file is found. The
1095    default is C<WARN>.
1096    
1097    =item noParms
1098    
1099    If TRUE, then display of the saved CGI parms is suppressed. The default is FALSE.
1100    
1101    =item level
1102    
1103    The trace level to use if no tracing file is found. The default is C<0>.
1104    
1105    =back
1106    
1107    =back
1108    
1109    =cut
1110    
1111    sub ETracing {
1112        # Get the parameter.
1113        my ($parameter, %options) = @_;
1114        # Check for CGI mode.
1115        if (defined $parameter && ref $parameter eq 'CGI') {
1116            $SavedCGI = $parameter;
1117        } else {
1118            $SavedCGI = undef;
1119        }
1120        # Check for the noParms option.
1121        my $noParms = $options{noParms} || 0;
1122        # Get the default tracing information.
1123        my $tracing = $options{level} || 0;
1124        my $dest = $options{destType} || "WARN";
1125        # Check for emergency tracing.
1126        my $tkey = EmergencyKey($parameter);
1127        my $emergencyFile = EmergencyFileName($tkey);
1128        if (-e $emergencyFile && (my $stat = stat($emergencyFile))) {
1129            # We have the file. Read in the data.
1130            my @tracing = GetFile($emergencyFile);
1131            # Pull off the time limit.
1132            my $expire = shift @tracing;
1133            # Convert it to seconds.
1134            $expire *= 3600;
1135            # Check the file data.
1136            my ($now) = gettimeofday;
1137            if ($now - $stat->mtime <= $expire) {
1138                # Emergency tracing is on. Pull off the destination and
1139                # the trace level;
1140                $dest = shift @tracing;
1141                my $level = shift @tracing;
1142                # Insure Tracer is specified.
1143                my %moduleHash = map { $_ => 1 } @tracing;
1144                $moduleHash{Tracer} = 1;
1145                # Set the trace parameter.
1146                $tracing = join(" ", $level, sort keys %moduleHash);
1147            }
1148        }
1149        # Convert the destination to a real tracing destination.
1150        $dest = EmergencyTracingDest($tkey, $dest);
1151        # Setup the tracing we've determined from all the stuff above.
1152        TSetup($tracing, $dest);
1153        # Check to see if we're a web script.
1154        if (defined $SavedCGI) {
1155            # Yes we are. Trace the form and environment data if it's not suppressed.
1156            if (! $noParms) {
1157                TraceParms($SavedCGI);
1158            }
1159            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1160            # emitted by the script in its raw form.
1161            if (T(Raw => 3)) {
1162                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1163            }
1164        }
1165    }
1166    
1167    =head3 EmergencyFileName
1168    
1169        my $fileName = Tracer::EmergencyFileName($tkey);
1170    
1171    Return the emergency tracing file name. This is the file that specifies
1172    the tracing information.
1173    
1174    =over 4
1175    
1176    =item tkey
1177    
1178    Tracing key for the current program.
1179    
1180    =item RETURN
1181    
1182    Returns the name of the file to contain the emergency tracing information.
1183    
1184    =back
1185    
1186    =cut
1187    
1188    sub EmergencyFileName {
1189        # Get the parameters.
1190        my ($tkey) = @_;
1191        # Compute the emergency tracing file name.
1192        return "$FIG_Config::temp/Emergency$tkey.txt";
1193    }
1194    
1195    =head3 EmergencyFileTarget
1196    
1197        my $fileName = Tracer::EmergencyFileTarget($tkey);
1198    
1199    Return the emergency tracing target file name. This is the file that receives
1200    the tracing output for file-based tracing.
1201    
1202    =over 4
1203    
1204    =item tkey
1205    
1206    Tracing key for the current program.
1207    
1208    =item RETURN
1209    
1210    Returns the name of the file to contain the trace output.
1211    
1212    =back
1213    
1214    =cut
1215    
1216    sub EmergencyFileTarget {
1217        # Get the parameters.
1218        my ($tkey) = @_;
1219        # Compute the emergency tracing file name.
1220        return "$FIG_Config::temp/trace$tkey.log";
1221    }
1222    
1223    =head3 EmergencyTracingDest
1224    
1225        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1226    
1227    This method converts an emergency tracing destination to a real
1228    tracing destination. The main difference is that if the
1229    destination is C<FILE> or C<APPEND>, we convert it to file
1230    output. If the destination is C<DUAL>, we convert it to file
1231    and standard output.
1232    
1233    =over 4
1234    
1235    =item tkey
1236    
1237    Tracing key for this environment.
1238    
1239    =item myDest
1240    
1241    Destination from the emergency tracing file.
1242    
1243    =item RETURN
1244    
1245    Returns a destination that can be passed into L</TSetup>.
1246    
1247    =back
1248    
1249    =cut
1250    
1251    sub EmergencyTracingDest {
1252        # Get the parameters.
1253        my ($tkey, $myDest) = @_;
1254        # Declare the return variable.
1255        my $retVal = $myDest;
1256        # Process according to the destination value.
1257        if ($myDest eq 'FILE') {
1258            $retVal = ">" . EmergencyFileTarget($tkey);
1259        } elsif ($myDest eq 'APPEND') {
1260            $retVal = ">>" . EmergencyFileTarget($tkey);
1261        } elsif ($myDest eq 'DUAL') {
1262            $retVal = "+>" . EmergencyFileTarget($tkey);
1263        } elsif ($myDest eq 'WARN') {
1264            $retVal = "WARN";
1265        }
1266        # Return the result.
1267        return $retVal;
1268    }
1269    
1270    =head3 Emergency
1271    
1272        Emergency($key, $hours, $dest, $level, @modules);
1273    
1274    Turn on emergency tracing. This method is normally invoked over the web from
1275    a debugging console, but it can also be called by the C<trace.pl> script.
1276    The caller specifies the duration of the emergency in hours, the desired tracing
1277    destination, the trace level, and a list of the trace modules to activate.
1278    For the length of the duration, when a program in an environment with the
1279    specified tracing key active invokes a Sprout CGI script, tracing will be
1280    turned on automatically. See L</TSetup> for more about tracing setup and
1281    L</ETracing> for more about emergency tracing.
1282    
1283    =over 4
1284    
1285    =item tkey
1286    
1287    The tracing key. This is used to identify the control file and the trace file.
1288    
1289    =item hours
1290    
1291    Number of hours to keep emergency tracing alive.
1292    
1293    =item dest
1294    
1295    Tracing destination. If no path information is specified for a file
1296    destination, it is put in the FIG temporary directory.
1297    
1298    =item level
1299    
1300    Tracing level. A higher level means more trace messages.
1301    
1302    =item modules
1303    
1304    A list of the tracing modules to activate.
1305    
1306    =back
1307    
1308    =cut
1309    
1310    sub Emergency {
1311        # Get the parameters.
1312        my ($tkey, $hours, $dest, $level, @modules) = @_;
1313        # Create the emergency file.
1314        my $specFile = EmergencyFileName($tkey);
1315        my $outHandle = Open(undef, ">$specFile");
1316        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1317    }
1318    
1319    =head3 EmergencyKey
1320    
1321        my $tkey = EmergencyKey($parameter);
1322    
1323    Return the Key to be used for emergency tracing. This could be an IP address,
1324     a session ID, or a user name, depending on the environment.
1325    
1326    =over 4
1327    
1328    =item parameter
1329    
1330    Parameter defining the method for finding the tracing key. If it is a scalar,
1331    then it is presumed to be the tracing key itself. If it is a CGI object, then
1332    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1333    taken from the C<TRACING> environment variable.
1334    
1335    =item RETURN
1336    
1337    Returns the key to be used for labels in emergency tracing.
1338    
1339    =back
1340    
1341    =cut
1342    
1343    sub EmergencyKey {
1344        # Get the parameters.
1345        my ($parameter) = @_;
1346        # Declare the return variable.
1347        my $retVal;
1348        # Determine the parameter type.
1349        if (! defined $parameter) {
1350            # Here we're supposed to check the environment. If that fails, we
1351            # get the effective login ID.
1352            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1353        } else {
1354            my $ptype = ref $parameter;
1355            if ($ptype eq 'CGI') {
1356                # Here we were invoked from a web page. Look for a cookie.
1357                $retVal = $parameter->cookie('IP');
1358            } elsif (! $ptype) {
1359                # Here the key was passed in.
1360                $retVal = $parameter;
1361            }
1362        }
1363        # If no luck finding a key, use the PID.
1364        if (! defined $retVal) {
1365            $retVal = $$;
1366        }
1367        # Return the result.
1368        return $retVal;
1369    }
1370    
1371    
1372  List of command line parameters, including the option switches, which must  =head3 TraceParms
 precede the positional parameters and be prefixed by a hyphen.  
1373    
1374  =item RETURN      Tracer::TraceParms($cgi);
1375    
1376  Returns a list. The first element of the list is the reference to a hash that  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1377  maps the command-line option switches to their values. These will either be the  at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1378  default values or overrides specified on the command line. The remaining  
1379  elements of the list are the position parameters, in order.  =over 4
1380    
1381    =item cgi
1382    
1383    CGI query object containing the parameters to trace.
1384    
1385  =back  =back
1386    
1387  =cut  =cut
1388    
1389  sub StandardSetup {  sub TraceParms {
1390      # Get the parameters.      # Get the parameters.
1391      my ($categories, $options, $parmHelp, @argv) = @_;      my ($cgi) = @_;
1392      # Get the default tracing key.      if (T(CGI => 2)) {
1393      my $tkey = EmergencyKey();          # Here we trace the GET-style URL for the script, but only if it's
1394      # Add the tracing options.          # relatively small.
1395      if (! exists $options->{trace}) {          my $url = $cgi->url(-relative => 1, -query => 1);
1396          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];          my $len = length($url);
1397      }          if ($len < 500) {
1398      $options->{sql} = [0, "turn on SQL tracing"];              Trace("[URL] $url");
1399      $options->{help} = [0, "display command-line options"];          } elsif ($len > 2048) {
1400      $options->{user} = [$tkey, "tracing key"];              Trace("[URL] URL is too long to use with GET ($len characters).");
     $options->{background} = [0, "spool standard and error output"];  
     # Create a parsing hash from the options hash. The parsing hash  
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($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";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
1401              } else {              } else {
1402                  $traceMode = "WARN";              Trace("[URL] URL length is $len characters.");
1403              }              }
1404          }          }
1405          # Now set up the tracing.      if (T(CGI => 3)) {
1406          TSetup("$traceLevel $cats", $traceMode);          # Here we want to trace the parameter data.
1407            my @names = $cgi->param;
1408            for my $parmName (sort @names) {
1409                # Note we skip the Trace parameters, which are for our use only.
1410                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1411                    my @values = $cgi->param($parmName);
1412                    Trace("[CGI] $parmName = " . join(", ", @values));
1413      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
1414              }              }
1415              print "  $name $desc\n";          # Display the request method.
1416            my $method = $cgi->request_method();
1417            Trace("Method: $method");
1418          }          }
1419          exit(0);      if (T(CGI => 4)) {
1420            # Here we want the environment data too.
1421            for my $envName (sort keys %ENV) {
1422                Trace("[ENV] $envName = $ENV{$envName}");
1423      }      }
     # Trace the options, if applicable.  
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
1424      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
1425  }  }
1426    
1427  =head3 Setups  =head3 TraceImages
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
   
 sub Setups {  
     return $SetupCount;  
 }  
1428    
1429  =head3 Open      Tracer::TraceImages($htmlString);
1430    
1431  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  Trace information about all of an html document's images. The tracing
1432    will be for type "IMG" at level 3. The image's source string
1433    will be displayed. This is generally either the URL of the image or
1434    raw data for the image itself. If the source is too long, only the first 300
1435    characters will be shown at trace level 3. The entire source will be shown,
1436    however, at trace level 4. This method is not very smart, and might catch
1437    Javascript code, but it is still useful when debugging the arcane
1438    behavior of images in multiple browser environments.
1439    
1440  Open a file.  =over 4
1441    
1442  The I<$fileSpec> is essentially the second argument of the PERL C<open>  =item htmlString
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
1443    
1444      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  HTML text for an outgoing web page.
1445    
1446  would open for output appended to the specified file, and  =back
1447    
1448      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =cut
1449    
1450  would open a pipe that sorts the records written and removes duplicates. Note  sub TraceImages {
1451  the use of file handle syntax in the Open call. To use anonymous file handles,      # Only proceed if we're at the proper trace level.
1452  code as follows.      if (T(IMG => 3)) {
1453            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1454            # into a variable called "$htmlString". This is because we expect html strings to be
1455            # long, and don't want to copy them any more than we have to.
1456            Trace(length($_[0]) . " characters in web page.");
1457            # Loop through the HTML, culling image tags.
1458            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1459                # Extract the source string and determine whether or not it's too long.
1460                my $srcString = $1;
1461                my $pos = pos($_[0]) - length($srcString);
1462                my $excess = length($srcString) - 300;
1463                # We'll put the display string in here.
1464                my $srcDisplay = $srcString;
1465                # If it's a data string, split it at the comma.
1466                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1467                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1468                # a long string, however, we only show the first 300 characters.
1469                if ($excess > 0 && ! T(IMG => 4)) {
1470                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1471                }
1472                # Output the trace message.
1473                Trace("Image tag at position $pos:\n$srcDisplay");
1474            }
1475        }
1476    }
1477    
1478      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =head2 Command-Line Utility Methods
1479    
1480  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =head3 SendSMS
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
1481    
1482      Could not open "/usr/spool/news/twitlog"      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1483    
1484  Note that the mode characters are automatically cleaned from the file name.  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1485  The actual error message from the file system will be captured and appended to the  user name, password, and API ID for the relevant account in the hash reference variable
1486  message in any case.  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1487    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1488    is C<2561022>, then the FIG_Config file must contain
1489    
1490      Could not open "/usr/spool/news/twitlog": file not found.      $phone =  { user => 'BruceTheHumanPet',
1491                    password => 'silly',
1492                    api_id => '2561022' };
1493    
1494  In some versions of PERL the only error message we get is a number, which  The original purpose of this method was to insure Bruce would be notified immediately when the
1495  corresponds to the C++ C<errno> value.  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1496    when you call this method.
1497    
1498      Could not open "/usr/spool/news/twitlog": 6.  The message ID will be returned if successful, and C<undef> if an error occurs.
1499    
1500  =over 4  =over 4
1501    
1502  =item fileHandle  =item phoneNumber
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
1503    
1504  File name and mode, as per the PERL C<open> function.  Phone number to receive the message, in international format. A United States phone number
1505    would be prefixed by "1". A British phone number would be prefixed by "44".
1506    
1507  =item message (optional)  =item msg
1508    
1509  Error message to use if the open fails. If omitted, a standard error message  Message to send to the specified phone.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
1510    
1511  =item RETURN  =item RETURN
1512    
1513  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.  
1514    
1515  =back  =back
1516    
1517  =cut  =cut
1518    
1519  sub Open {  sub SendSMS {
1520      # Get the parameters.      # Get the parameters.
1521      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1522      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1523      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1524      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1525      if (! $rv) {      if (! defined $FIG_Config::phone) {
1526          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1527          my $sysMessage = $!;      } else {
1528          # See if we need a default message.          # Get the phone data.
1529          if (!$message) {          my $parms = $FIG_Config::phone;
1530              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1531              # filename.          my $url = "http://api.clickatell.com/http/";
1532              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1533              $message = "Could not open \"$fileName\"";          my $ua = LWP::UserAgent->new;
1534            # Request a Clickatell session.
1535            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1536                                         password => $parms->{password},
1537                                         api_id => $parms->{api_id},
1538                                         to => $phoneNumber,
1539                                         text => $msg});
1540            # Check for an error.
1541            if (! $resp->is_success) {
1542                Trace("Alert failed.") if T(1);
1543            } else {
1544                # Get the message ID.
1545                my $rstring = $resp->content;
1546                if ($rstring =~ /^ID:\s+(.*)$/) {
1547                    $retVal = $1;
1548                } else {
1549                    Trace("Phone attempt failed with $rstring") if T(1);
1550          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1551      }      }
1552      # Return the file handle.      }
1553      return $fileHandle;      # Return the result.
1554        return $retVal;
1555  }  }
1556    
1557  =head3 FindNamePart  =head3 StandardSetup
1558    
1559  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1560    
1561  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1562    values are a hash of the command-line options and a list of the positional
1563    parameters. Tracing is automatically set up and the command-line options are
1564    validated.
1565    
1566  A file specification is the string passed to an C<open> call. It specifies the file  This is a complex method that does a lot of grunt work. The parameters can
1567  mode and name. In a truly complex situation, it can specify a pipe sequence. This  be more easily understood, however, once they are examined individually.
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
1568    
1569      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1570      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1571      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1572    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1573    
1574  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1575  whole incoming string.  
1576    This would cause trace messages in the specified three packages to appear in
1577    the output. There are two special tracing categories that are automatically
1578    handled by this method. In other words, if you used L</TSetup> you would need
1579    to include these categories manually, but if you use this method they are turned
1580    on automatically.
1581    
1582  =over 4  =over 4
1583    
1584  =item fileSpec  =item SQL
1585    
1586  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1587    
1588  =item RETURN  =item Tracer
1589    
1590  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.  
1591    
1592  =back  =back
1593    
1594  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1595  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1596  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1597      # Get the parameters.  all tracing at level 3.
     my ($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, $flag); >>  
1598    
1599  Open a directory and return all the file names. This function essentially performs      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
 the functions of an C<opendir> and C<readdir>. If the I<$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,  
1600    
1601      my @files = OpenDir("/Volumes/fig/contigs", 1);  Standard tracing is output to the standard output and echoed to the file
1602    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1603    process ID. You can also specify the C<user> parameter to put a user ID
1604    instead of a process ID in the trace file name. So, for example
1605    
1606  is effectively the same as  The default trace level is 2. To get all messages, specify a trace level of 4.
1607    For a genome-by-genome update, use 3.
1608    
1609      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
1610    
1611  Similarly, the following code  would send the trace output to C<traceBruce.log> in the temporary directory.
1612    
1613      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  The I<options> parameter is a reference to a hash containing the command-line
1614    options, their default values, and an explanation of what they mean. Command-line
1615    options may be in the form of switches or keywords. In the case of a switch, the
1616    option value is 1 if it is specified and 0 if it is not specified. In the case
1617    of a keyword, the value is separated from the option name by an equal sign. You
1618    can see this last in the command-line example above.
1619    
1620  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  You can specify a different default trace level by setting C<$options->{trace}>
1621  automatically returns an empty list if the directory fails to open.  prior to calling this method.
1622    
1623  =over 4  An example at this point would help. Consider, for example, the command-line utility
1624    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1625    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1626    the following code.
1627    
1628  =item dirName      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1629                            { safe => [0, "use database transactions"],
1630                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1631                              start => [' ', "start with this genome"],
1632                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1633                            "<command> <transactionDirectory> <IDfile>",
1634                          @ARGV);
1635    
 Name of the directory to open.  
1636    
1637  =item filtered  The call to C<ParseCommand> specifies the default values for the options and
1638    stores the actual options in a hash that is returned as C<$options>. The
1639    positional parameters are returned in C<@parameters>.
1640    
1641  TRUE if files whose names begin with a period (C<.>) should be automatically removed  The following is a sample command line for C<TransactFeatures>.
 from the list, else FALSE.  
1642    
1643  =item flag      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1644    
1645  TRUE if a failure to open is okay, else FALSE  Single and double hyphens are equivalent. So, you could also code the
1646    above command as
1647    
1648  =back      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1649    
1650  =cut  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1651  #: Return Type @;  parameters, and would find themselves in I<@parameters> after executing the
1652  sub OpenDir {  above code fragment. The tracing would be set to level 2, and the categories
1653      # Get the parameters.  would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1654      my ($dirName, $filtered, $flag) = @_;  and C<DocUtils> was included because it came in within the first parameter
1655      # Declare the return variable.  to this method. The I<$options> hash would be
     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 $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1656    
1657  =head3 SetLevel      { trace => 2, sql => 0, safe => 0,
1658          noAlias => 1, start => ' ', tblFiles => 0 }
1659    
1660  C<< Tracer::SetLevel($newLevel); >>  Use of C<StandardSetup> in this way provides a simple way of performing
1661    standard tracing setup and command-line parsing. Note that the caller is
1662    not even aware of the command-line switches C<-trace> and C<-sql>, which
1663    are used by this method to control the tracing. If additional tracing features
1664    need to be added in the future, they can be processed by this method without
1665    upsetting the command-line utilities.
1666    
1667  Modify the trace level. A higher trace level will cause more messages to appear.  If the C<background> option is specified on the command line, then the
1668    standard and error outputs will be directed to files in the temporary
1669    directory, using the same suffix as the trace file. So, if the command
1670    line specified
1671    
1672  =over 4      -user=Bruce -background
1673    
1674  =item newLevel  then the trace output would go to C<traceBruce.log>, the standard output to
1675    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1676    simplify starting a command in the background.
1677    
1678  Proposed new trace level.  The user name is also used as the tracing key for L</Emergency Tracing>.
1679    Specifying a value of C<E> for the trace level causes emergency tracing to
1680    be used instead of custom tracing. If the user name is not specified,
1681    the tracing key is taken from the C<Tracing> environment variable. If there
1682    is no value for that variable, the tracing key will be computed from the active
1683    login ID.
1684    
1685  =back  Since the default situation in StandardSetup is to trace to the standard
1686    output, errors that occur in command-line scripts will not generate
1687    RSS events. To force the events, use the C<warn> option.
1688    
1689  =cut      TransactFeatures -background -warn register ../xacts IDs.tbl
1690    
1691  sub SetLevel {  Finally, if the special option C<-help> is specified, the option
1692      $TraceLevel = $_[0];  names will be traced at level 0 and the program will exit without processing.
1693  }  This provides a limited help capability. For example, if the user enters
1694    
1695  =head3 Now      TransactFeatures -help
1696    
1697  C<< my $string = Tracer::Now(); >>  he would see the following output.
1698    
1699  Return a displayable time stamp containing the local time.      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1700            -trace    tracing level (default E)
1701            -sql      trace SQL commands
1702            -safe     use database transactions
1703            -noAlias  do not expect aliases in CHANGE transactions
1704            -start    start with this genome
1705            -tblFiles output TBL files containing the corrected IDs
1706            -forked   do not erase the trace file before tracing
1707    
1708  =cut  The caller has the option of modifying the tracing scheme by placing a value
1709    for C<trace> in the incoming options hash. The default value can be overridden,
1710    or the tracing to the standard output can be turned off by suffixing a minus
1711    sign to the trace level. So, for example,
1712    
1713  sub Now {      { trace => [0, "tracing level (default 0)"],
1714      my ($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 $retVal;  
 }  
1715    
1716  # Pad a number to 2 digits.  would set the default trace level to 0 instead of E, while
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1717    
1718  =head3 ParseTraceDate      { trace => ["2-", "tracing level (default 2)"],
1719           ...
1720    
1721  C<< my $time = Tracer::ParseTraceDate($dateString); >>  would set the default to 2, but trace only to the log file, not to the
1722    standard output.
1723    
1724  Convert a date from the trace file into a PERL timestamp.  The parameters to this method are as follows.
1725    
1726  =over 4  =over 4
1727    
1728  =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.  
1729    
1730  =back  Reference to a list of tracing category names. These should be names of
1731    packages whose internal workings will need to be debugged to get the
1732    command working.
1733    
1734  =cut  =item options
1735    
1736  sub ParseTraceDate {  Reference to a hash containing the legal options for the current command mapped
1737      # Get the parameters.  to their default values and descriptions. The user can override the defaults
1738      my ($dateString) = @_;  by specifying the options as command-line switches prefixed by a hyphen.
1739      # Declare the return variable.  Tracing-related options may be added to this hash. If the C<-h> option is
1740      my $retVal;  specified on the command line, the option descriptions will be used to
1741      # Parse the date.  explain the options. To turn off tracing to the standard output, add a
1742      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  minus sign to the value for C<trace> (see above).
         # 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 $retVal;  
 }  
1743    
1744  =head3 LogErrors  =item parmHelp
1745    
1746  C<< Tracer::LogErrors($fileName); >>  A string that vaguely describes the positional parameters. This is used
1747    if the user specifies the C<-h> option.
1748    
1749  Route the standard error output to a log file.  =item argv
1750    
1751  =over 4  List of command line parameters, including the option switches, which must
1752    precede the positional parameters and be prefixed by a hyphen.
1753    
1754  =item fileName  =item RETURN
1755    
1756  Name of the file to receive the error output.  Returns a list. The first element of the list is the reference to a hash that
1757    maps the command-line option switches to their values. These will either be the
1758    default values or overrides specified on the command line. The remaining
1759    elements of the list are the position parameters, in order.
1760    
1761  =back  =back
1762    
1763  =cut  =cut
1764    
1765  sub LogErrors {  sub StandardSetup {
1766      # Get the file name.      # Get the parameters.
1767      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1768      # Open the file as the standard error output.      # Get the default tracing key.
1769      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1770        # Save the command line.
1771        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1772        # Add the tracing options.
1773        if (! exists $options->{trace}) {
1774            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1775        }
1776        if (! exists $options->{forked}) {
1777            $options->{forked} = [0, "keep old trace file"];
1778        }
1779        $options->{sql} = [0, "turn on SQL tracing"];
1780        $options->{help} = [0, "display command-line options"];
1781        $options->{user} = [$tkey, "tracing key"];
1782        $options->{background} = [0, "spool standard and error output"];
1783        $options->{warn} = [0, "send errors to RSS feed"];
1784        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1785        # Create a parsing hash from the options hash. The parsing hash
1786        # contains the default values rather than the default value
1787        # and the description. While we're at it, we'll memorize the
1788        # length of the longest option name.
1789        my $longestName = 0;
1790        my %parseOptions = ();
1791        for my $key (keys %{$options}) {
1792            if (length $key > $longestName) {
1793                $longestName = length $key;
1794            }
1795            $parseOptions{$key} = $options->{$key}->[0];
1796        }
1797        # Parse the command line.
1798        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1799        # Get the logfile suffix.
1800        my $suffix = $retOptions->{user};
1801        # We'll put the trace file name in here. We need it later if background
1802        # mode is on.
1803        my $traceFileName;
1804        # Now we want to set up tracing. First, we need to know if the user
1805        # wants emergency tracing.
1806        if ($retOptions->{trace} eq 'E') {
1807            ETracing($retOptions->{user});
1808        } else {
1809            # Here the tracing is controlled from the command line.
1810            my @cats = @{$categories};
1811            if ($retOptions->{sql}) {
1812                push @cats, "SQL";
1813            }
1814            if ($retOptions->{warn}) {
1815                push @cats, "Feed";
1816            }
1817            # Add the default categories.
1818            push @cats, "Tracer";
1819            # Check for more tracing groups.
1820            if ($retOptions->{moreTracing}) {
1821                push @cats, split /,/, $retOptions->{moreTracing};
1822            }
1823            # Next, we create the category string by joining the categories.
1824            my $cats = join(" ", @cats);
1825            # Check to determine whether or not the caller wants to turn off tracing
1826            # to the standard output.
1827            my $traceLevel = $retOptions->{trace};
1828            my $textOKFlag = 1;
1829            if ($traceLevel =~ /^(.)-/) {
1830                $traceLevel = $1;
1831                $textOKFlag = 0;
1832            }
1833            # Now we set up the trace mode.
1834            my $traceMode;
1835            # Verify that we can open a file in the FIG temporary directory.
1836            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1837            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1838            if (open TESTTRACE, "$traceFileSpec") {
1839                # Here we can trace to a file.
1840                $traceMode = ">>$traceFileName";
1841                if ($textOKFlag) {
1842                    # Echo to standard output if the text-OK flag is set.
1843                    $traceMode = "+$traceMode";
1844                }
1845                # Close the test file.
1846                close TESTTRACE;
1847            } else {
1848                # Here we can't trace to a file. Complain about this.
1849                warn "Could not open trace file $traceFileName: $!\n";
1850                # We trace to the standard output if it's
1851                # okay, and the error log otherwise.
1852                if ($textOKFlag) {
1853                    $traceMode = "TEXT";
1854                } else {
1855                    $traceMode = "WARN";
1856                }
1857            }
1858            # Now set up the tracing.
1859            TSetup("$traceLevel $cats", $traceMode);
1860        }
1861        # Check for background mode.
1862        if ($retOptions->{background}) {
1863            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1864            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1865            # Spool the output.
1866            open STDOUT, ">$outFileName";
1867            # If we have a trace file, trace the errors to the log. Otherwise,
1868            # spool the errors.
1869            if (defined $traceFileName) {
1870                open STDERR, "| Tracer $traceFileName";
1871            } else {
1872                open STDERR, ">$errFileName";
1873            }
1874            # Check for phone support. If we have phone support and a phone number,
1875            # we want to turn it on.
1876            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1877                $retOptions->{phone} = $ENV{PHONE};
1878            }
1879        }
1880        # Check for the "help" option. If it is specified, dump the command-line
1881        # options and exit the program.
1882        if ($retOptions->{help}) {
1883            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1884            print "$1 [options] $parmHelp\n";
1885            for my $key (sort keys %{$options}) {
1886                my $name = Pad($key, $longestName, 0, ' ');
1887                my $desc = $options->{$key}->[1];
1888                if ($options->{$key}->[0]) {
1889                    $desc .= " (default " . $options->{$key}->[0] . ")";
1890                }
1891                print "  $name $desc\n";
1892            }
1893            exit(0);
1894        }
1895        # Trace the options, if applicable.
1896        if (T(3)) {
1897            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1898            Trace("Selected options: " . join(", ", sort @parms) . ".");
1899        }
1900        # Return the parsed parameters.
1901        return ($retOptions, @retParameters);
1902  }  }
1903    
1904  =head3 ReadOptions  =head3 ReadOptions
1905    
1906  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1907    
1908  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
1909  format  format
# Line 1069  Line 1964 
1964    
1965  =head3 GetOptions  =head3 GetOptions
1966    
1967  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1968    
1969  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
1970  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 1973 
1973    
1974  Consider the following example.  Consider the following example.
1975    
1976  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1977    
1978  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1979  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1981 
1981  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1982  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1983    
1984  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1985    
1986  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1987    
# Line 1130  Line 2025 
2025    
2026  =head3 MergeOptions  =head3 MergeOptions
2027    
2028  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
2029    
2030  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
2031  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 1162  Line 2057 
2057      }      }
2058  }  }
2059    
2060  =head3 Trace  =head3 UnparseOptions
   
 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  
2061    
2062  C<< my $switch = T($traceLevel); >>      my $optionString = Tracer::UnparseOptions(\%options);
2063    
2064  Return TRUE if the trace level is at or above a specified value and the specified category  Convert an option hash into a command-line string. This will not
2065  is active, else FALSE. If no category is specified, the caller's package name is used.  necessarily be the same text that came in, but it will nonetheless
2066    produce the same ultimate result when parsed by L</StandardSetup>.
2067    
2068  =over 4  =over 4
2069    
2070  =item category  =item options
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2071    
2072  Relevant tracing level.  Reference to a hash of options to convert into an option string.
2073    
2074  =item RETURN  =item RETURN
2075    
2076  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a string that will parse to the same set of options when
2077    parsed by L</StandardSetup>.
2078    
2079  =back  =back
2080    
2081  =cut  =cut
2082    
2083  sub T {  sub UnparseOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2084          # Get the parameters.          # Get the parameters.
2085          my ($category, $traceLevel) = @_;      my ($options) = @_;
2086          if (!defined $traceLevel) {      # The option segments will be put in here.
2087              # Here we have no category, so we need to get the calling package.      my @retVal = ();
2088              # The calling package is normally the first parameter. If it is      # Loop through the options.
2089              # omitted, the first parameter will be the tracelevel. So, the      for my $key (keys %$options) {
2090              # first thing we do is shift the so-called category into the          # Get the option value.
2091              # $traceLevel variable where it belongs.          my $value = $options->{$key};
2092              $traceLevel = $category;          # Only use it if it's nonempty.
2093              my ($package, $fileName, $line) = caller;          if (defined $value && $value ne "") {
2094              # If there is no calling package, we default to "main".              my $segment = "--$key=$value";
2095              if (!$package) {              # Quote it if necessary.
2096                  $category = "main";              if ($segment =~ /[ |<>*]/) {
2097              } else {                  $segment = '"' . $segment . '"';
                 $category = $package;  
             }  
2098          }          }
2099          # Save the category name.              # Add it to the return list.
2100          $LastCategory = $category;              push @retVal, $segment;
         # 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.");  
2101          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2102      }      }
2103      # Return the computed result.      # Return the result.
2104      return $retVal;      return join(" ", @retVal);
2105  }  }
2106    
2107  =head3 ParseCommand  =head3 ParseCommand
2108    
2109  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2110    
2111  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2112  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2113  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2114  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2115    
2116  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2117    
2118  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2119  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2120    
2121  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2122    
2123  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2124    
2125  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2126    
2127  and C<@arguments> will contain  and C<@arguments> will contain
2128    
2129  C<< apple orange rutabaga >>      apple orange rutabaga
2130    
2131  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2132  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 2180 
2180      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2181  }  }
2182    
 =head3 Escape  
2183    
2184  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2185    
2186  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2187  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2188  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2189    
2190        or
2191    
2192        my $fileContents = Tracer::GetFile($fileName);
2193    
2194    Return the entire contents of a file. In list context, line-ends are removed and
2195    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2196    
2197  =over 4  =over 4
2198    
2199  =item realString  =item fileName
2200    
2201  String to escape.  Name of the file to read.
2202    
2203  =item RETURN  =item RETURN
2204    
2205  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2206    In a scalar context, returns the entire file as a string. If an error occurs opening
2207    the file, an empty list will be returned.
2208    
2209  =back  =back
2210    
2211  =cut  =cut
2212    
2213  sub Escape {  sub GetFile {
2214      # Get the parameter.      # Get the parameters.
2215      my ($realString) = @_;      my ($fileName) = @_;
2216      # Initialize the return variable.      # Declare the return variable.
2217      my $retVal = "";      my @retVal = ();
2218      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2219      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2220          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2221          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2222              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2223              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2224              $retVal .= $1;          $lineCount++;
2225              # Strip the processed section off the real string.          $line = Strip($line);
2226              $realString = substr $realString, (length $2) + (length $1);          push @retVal, $line;
             # 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;  
2227              }              }
2228        # Close it.
2229        close $handle;
2230        my $actualLines = @retVal;
2231        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2232        # Return the file's contents in the desired format.
2233        if (wantarray) {
2234            return @retVal;
2235          } else {          } else {
2236              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2237      }      }
     # Return the result.  
     return $retVal;  
2238  }  }
2239    
2240  =head3 UnEscape  =head3 PutFile
2241    
2242  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2243    
2244  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2245    
2246  =over 4  =over 4
2247    
2248  =item codedString  =item fileName
2249    
2250  String to un-escape.  Name of the output file.
2251    
2252  =item RETURN  =item lines
2253    
2254  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2255  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2256    modification.
2257    
2258  =back  =back
2259    
2260  =cut  =cut
2261    
2262  sub UnEscape {  sub PutFile {
2263      # Get the parameter.      # Get the parameters.
2264      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2265      # Initialize the return variable.      # Open the output file.
2266      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2267      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2268      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2269          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2270          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2271          # "\<tab>" no matter what we do.)          Trace("Scalar put to file $fileName.") if T(File => 3);
         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;  
                 }  
2272              } else {              } else {
2273                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2274                  # transferred unmodified.          my $count = 0;
2275                  $retVal .= $codedString;          for my $line (@{$lines}) {
2276                  $codedString = "";              print $handle "$line\n";
2277              }              $count++;
2278          }          }
2279            Trace("$count lines put to file $fileName.") if T(File => 3);
2280      }      }
2281      # Return the result.      # Close the output file.
2282      return $retVal;      close $handle;
2283  }  }
2284    
2285  =head3 ParseRecord  =head3 ParseRecord
2286    
2287  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2288    
2289  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2290  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
# Line 1521  Line 2329 
2329    
2330  =head3 Merge  =head3 Merge
2331    
2332  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2333    
2334  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2335    
# Line 1567  Line 2375 
2375      return @inputList;      return @inputList;
2376  }  }
2377    
2378  =head3 Percent  =head3 Open
2379    
2380  C<< my $percent = Tracer::Percent($number, $base); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2381    
2382  Returns the percent of the base represented by the given number. If the base  Open a file.
2383  is zero, returns zero.  
2384    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2385    function. The mode is specified using Unix-like shell information. So, for
2386    example,
2387    
2388        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2389    
2390    would open for output appended to the specified file, and
2391    
2392        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2393    
2394    would open a pipe that sorts the records written and removes duplicates. Note
2395    the use of file handle syntax in the Open call. To use anonymous file handles,
2396    code as follows.
2397    
2398        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2399    
2400    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2401    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2402    failed open will throw an exception and the third parameter will be used to construct
2403    an error message. If the parameter is omitted, a standard message is constructed
2404    using the file spec.
2405    
2406        Could not open "/usr/spool/news/twitlog"
2407    
2408    Note that the mode characters are automatically cleaned from the file name.
2409    The actual error message from the file system will be captured and appended to the
2410    message in any case.
2411    
2412        Could not open "/usr/spool/news/twitlog": file not found.
2413    
2414    In some versions of PERL the only error message we get is a number, which
2415    corresponds to the C++ C<errno> value.
2416    
2417        Could not open "/usr/spool/news/twitlog": 6.
2418    
2419  =over 4  =over 4
2420    
2421  =item number  =item fileHandle
2422    
2423  Percent numerator.  File handle. If this parameter is C<undef>, a file handle will be generated
2424    and returned as the value of this method.
2425    
2426  =item base  =item fileSpec
2427    
2428  Percent base.  File name and mode, as per the PERL C<open> function.
2429    
2430    =item message (optional)
2431    
2432    Error message to use if the open fails. If omitted, a standard error message
2433    will be generated. In either case, the error information from the file system
2434    is appended to the message. To specify a conditional open that does not throw
2435    an error if it fails, use C<0>.
2436    
2437  =item RETURN  =item RETURN
2438    
2439  Returns the percentage of the base represented by the numerator.  Returns the name of the file handle assigned to the file, or C<undef> if the
2440    open failed.
2441    
2442  =back  =back
2443    
2444  =cut  =cut
2445    
2446  sub Percent {  sub Open {
2447      # Get the parameters.      # Get the parameters.
2448      my ($number, $base) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2449      # Declare the return variable.      # Attempt to open the file.
2450      my $retVal = 0;      my $rv = open $fileHandle, $fileSpec;
2451      # Compute the percent.      # If the open failed, generate an error message.
2452      if ($base != 0) {      if (! $rv) {
2453          $retVal = $number * 100 / $base;          # Save the system error message.
2454            my $sysMessage = $!;
2455            # See if we need a default message.
2456            if (!$message) {
2457                # Clean any obvious mode characters and leading spaces from the
2458                # filename.
2459                my ($fileName) = FindNamePart($fileSpec);
2460                $message = "Could not open \"$fileName\"";
2461            }
2462            # Terminate with an error using the supplied message and the
2463            # error message from the file system.
2464            Confess("$message: $!");
2465        }
2466        # Return the file handle.
2467        return $fileHandle;
2468    }
2469    
2470    =head3 FindNamePart
2471    
2472        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2473    
2474    Extract the portion of a file specification that contains the file name.
2475    
2476    A file specification is the string passed to an C<open> call. It specifies the file
2477    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2478    method assumes that the file name is whatever follows the first angle bracket
2479    sequence.  So, for example, in the following strings the file name is
2480    C</usr/fig/myfile.txt>.
2481    
2482        >>/usr/fig/myfile.txt
2483        </usr/fig/myfile.txt
2484        | sort -u > /usr/fig/myfile.txt
2485    
2486    If the method cannot find a file name using its normal methods, it will return the
2487    whole incoming string.
2488    
2489    =over 4
2490    
2491    =item fileSpec
2492    
2493    File specification string from which the file name is to be extracted.
2494    
2495    =item RETURN
2496    
2497    Returns a three-element list. The first element contains the file name portion of
2498    the specified string, or the whole string if a file name cannot be found via normal
2499    methods. The second element contains the start position of the file name portion and
2500    the third element contains the length.
2501    
2502    =back
2503    
2504    =cut
2505    #: Return Type $;
2506    sub FindNamePart {
2507        # Get the parameters.
2508        my ($fileSpec) = @_;
2509        # Default to the whole input string.
2510        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2511        # Parse out the file name if we can.
2512        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2513            $retVal = $2;
2514            $len = length $retVal;
2515            $pos = (length $fileSpec) - (length $3) - $len;
2516      }      }
2517      # Return the result.      # Return the result.
2518      return $retVal;      return ($retVal, $pos, $len);
2519  }  }
2520    
2521  =head3 GetFile  =head3 OpenDir
2522    
2523  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @files = OpenDir($dirName, $filtered, $flag);
2524    
2525      or  Open a directory and return all the file names. This function essentially performs
2526    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2527    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2528    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2529    filtered out of the return list. If the directory does not open and I<$flag> is not
2530    set, an exception is thrown. So, for example,
2531    
2532  C<< my $fileContents = Tracer::GetFile($fileName); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2533    
2534  Return the entire contents of a file. In list context, line-ends are removed and  is effectively the same as
2535  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2536        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2537        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2538    
2539    Similarly, the following code
2540    
2541        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2542    
2543    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2544    automatically returns an empty list if the directory fails to open.
2545    
2546  =over 4  =over 4
2547    
2548  =item fileName  =item dirName
2549    
2550    Name of the directory to open.
2551    
2552    =item filtered
2553    
2554  Name of the file to read.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2555    from the list, else FALSE.
2556    
2557  =item RETURN  =item flag
2558    
2559  In a list context, returns the entire file as a list with the line terminators removed.  TRUE if a failure to open is okay, else FALSE
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2560    
2561  =back  =back
2562    
2563  =cut  =cut
2564    #: Return Type @;
2565  sub GetFile {  sub OpenDir {
2566      # Get the parameters.      # Get the parameters.
2567      my ($fileName) = @_;      my ($dirName, $filtered, $flag) = @_;
2568      # Declare the return variable.      # Declare the return variable.
2569      my @retVal = ();      my @retVal = ();
2570      # Open the file for input.      # Open the directory.
2571      my $handle = Open(undef, "<$fileName");      if (opendir(my $dirHandle, $dirName)) {
2572      # Read the whole file into the return variable, stripping off any terminator          # The directory opened successfully. Get the appropriate list according to the
2573      # characters.          # strictures of the filter parameter.
2574      my $lineCount = 0;          if ($filtered) {
2575      while (my $line = <$handle>) {              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
         $lineCount++;  
         $line = Strip($line);  
         push @retVal, $line;  
     }  
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     Trace("$actualLines lines read from file $fileName.") if T(File => 2);  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
2576      } else {      } else {
2577          return join "\n", @retVal;              @retVal = readdir $dirHandle;
2578            }
2579            closedir $dirHandle;
2580        } elsif (! $flag) {
2581            # Here the directory would not open and it's considered an error.
2582            Confess("Could not open directory $dirName.");
2583      }      }
2584        # Return the result.
2585        return @retVal;
2586  }  }
2587    
 =head3 PutFile  
2588    
2589  C<< Tracer::PutFile($fileName, \@lines); >>  =head3 Insure
2590    
2591        Insure($dirName, $chmod);
2592    
2593  Write out a file from a list of lines of text.  Insure a directory is present.
2594    
2595  =over 4  =over 4
2596    
2597  =item fileName  =item dirName
2598    
2599  Name of the output file.  Name of the directory to check. If it does not exist, it will be created.
2600    
2601  =item lines  =item chmod (optional)
2602    
2603  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Security privileges to be given to the directory if it is created.
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
2604    
2605  =back  =back
2606    
2607  =cut  =cut
2608    
2609  sub PutFile {  sub Insure {
2610      # Get the parameters.      my ($dirName, $chmod) = @_;
2611      my ($fileName, $lines) = @_;      if (! -d $dirName) {
2612      # Open the output file.          Trace("Creating $dirName directory.") if T(2);
2613      my $handle = Open(undef, ">$fileName");          eval {
2614      # Count the lines written.              mkpath $dirName;
2615      if (ref $lines ne 'ARRAY') {              # If we have permissions specified, set them here.
2616          # Here we have a scalar, so we write it raw.              if (defined($chmod)) {
2617          print $handle $lines;                  chmod $chmod, $dirName;
2618          Trace("Scalar put to file $fileName.") if T(File => 3);              }
2619      } else {          };
2620          # Write the lines one at a time.          if ($@) {
2621          my $count = 0;              Confess("Error creating $dirName: $@");
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
             $count++;  
2622          }          }
         Trace("$count lines put to file $fileName.") if T(File => 3);  
2623      }      }
     # Close the output file.  
     close $handle;  
2624  }  }
2625    
2626  =head3 QTrace  =head3 ChDir
2627    
2628  C<< my $data = QTrace($format); >>      ChDir($dirName);
2629    
2630  Return the queued trace data in the specified format.  Change to the specified directory.
2631    
2632  =over 4  =over 4
2633    
2634  =item format  =item dirName
2635    
2636  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to which we want to change.
2637    
2638  =back  =back
2639    
2640  =cut  =cut
2641    
2642  sub QTrace {  sub ChDir {
2643      # Get the parameter.      my ($dirName) = @_;
2644      my ($format) = @_;      if (! -d $dirName) {
2645      # Create the return variable.          Confess("Cannot change to directory $dirName: no such directory.");
2646      my $retVal = "";      } else {
2647      # Only proceed if there is an actual queue.          Trace("Changing to directory $dirName.") if T(File => 4);
2648      if (@Queue) {          my $okFlag = chdir $dirName;
2649          # Process according to the format.          if (! $okFlag) {
2650          if ($format =~ m/^HTML$/i) {              Confess("Error switching to directory $dirName.");
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2651          }          }
         # Clear the queue.  
         @Queue = ();  
2652      }      }
     # Return the formatted list.  
     return $retVal;  
2653  }  }
2654    
2655  =head3 Confess  =head3 SetPermissions
   
 C<< Confess($message); >>  
2656    
2657  Trace the call stack and abort the program with the specified message. When used with      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2658    
2659  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Set the permissions for a directory and all the files and folders inside it.
2660    In addition, the group ownership will be changed to the specified value.
2661    
2662  Will abort the program with a stack trace if the value of C<$recNum> is negative.  This method is more vulnerable than most to permission and compatability
2663    problems, so it does internal error recovery.
2664    
2665  =over 4  =over 4
2666    
2667  =item message  =item dirName
2668    
2669  Message to include in the trace.  Name of the directory to process.
2670    
2671  =back  =item group
2672    
2673  =cut  Name of the group to be assigned.
2674    
2675  sub Confess {  =item mask
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
2676    
2677  =head3 Assert  Permission mask. Bits that are C<1> in this mask will be ORed into the
2678    permission bits of any file or directory that does not already have them
2679    set to 1.
2680    
2681  C<< Assert($condition1, $condition2, ... $conditionN); >>  =item otherMasks
2682    
2683  Return TRUE if all the conditions are true. This method can be used in conjunction with  Map of search patterns to permission masks. If a directory name matches
2684  the OR operator and the L</Confess> method as a debugging assert.  one of the patterns, that directory and all its members and subdirectories
2685  So, for example  will be assigned the new pattern. For example, the following would
2686    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2687    
2688        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2689    
2690  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  The list is ordered, so the following would use 0777 for C<tmp1> and
2691    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2692    
2693  Will abort the program with a stack trace if the value of C<$recNum> is negative.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2694                                                       '^tmp' => 0666);
2695    
2696    Note that the pattern matches are all case-insensitive, and only directory
2697    names are matched, not file names.
2698    
2699    =back
2700    
2701  =cut  =cut
2702  sub Assert {  
2703      my $retVal = 1;  sub SetPermissions {
2704      LOOP: for my $condition (@_) {      # Get the parameters.
2705          if (! $condition) {      my ($dirName, $group, $mask, @otherMasks) = @_;
2706              $retVal = 0;      # Set up for error recovery.
2707              last LOOP;      eval {
2708            # Switch to the specified directory.
2709            ChDir($dirName);
2710            # Get the group ID.
2711            my $gid = getgrnam($group);
2712            # Get the mask for tracing.
2713            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2714            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2715            my $fixCount = 0;
2716            my $lookCount = 0;
2717            # @dirs will be a stack of directories to be processed.
2718            my @dirs = (getcwd());
2719            while (scalar(@dirs) > 0) {
2720                # Get the current directory.
2721                my $dir = pop @dirs;
2722                # Check for a match to one of the specified directory names. To do
2723                # that, we need to pull the individual part of the name off of the
2724                # whole path.
2725                my $simpleName = $dir;
2726                if ($dir =~ m!/([^/]+)$!) {
2727                    $simpleName = $1;
2728                }
2729                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2730                # Search for a match.
2731                my $match = 0;
2732                my $i;
2733                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2734                    my $pattern = $otherMasks[$i];
2735                    if ($simpleName =~ /$pattern/i) {
2736                        $match = 1;
2737                    }
2738                }
2739                # Find out if we have a match. Note we use $i-1 because the loop added 2
2740                # before terminating due to the match.
2741                if ($match && $otherMasks[$i-1] != $mask) {
2742                    # This directory matches one of the incoming patterns, and it's
2743                    # a different mask, so we process it recursively with that mask.
2744                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2745                } else {
2746                    # Here we can process normally. Get all of the non-hidden members.
2747                    my @submems = OpenDir($dir, 1);
2748                    for my $submem (@submems) {
2749                        # Get the full name.
2750                        my $thisMem = "$dir/$submem";
2751                        Trace("Checking member $thisMem.") if T(4);
2752                        $lookCount++;
2753                        if ($lookCount % 1000 == 0) {
2754                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2755                        }
2756                        # Fix the group.
2757                        chown -1, $gid, $thisMem;
2758                        # Insure this member is not a symlink.
2759                        if (! -l $thisMem) {
2760                            # Get its info.
2761                            my $fileInfo = stat $thisMem;
2762                            # Only proceed if we got the info. Otherwise, it's a hard link
2763                            # and we want to skip it anyway.
2764                            if ($fileInfo) {
2765                                my $fileMode = $fileInfo->mode;
2766                                if (($fileMode & $mask) != $mask) {
2767                                    # Fix this member.
2768                                    $fileMode |= $mask;
2769                                    chmod $fileMode, $thisMem;
2770                                    $fixCount++;
2771                                }
2772                                # If it's a subdirectory, stack it.
2773                                if (-d $thisMem) {
2774                                    push @dirs, $thisMem;
2775          }          }
2776      }      }
     return $retVal;  
2777  }  }
   
 =head3 Cluck  
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Cluck {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
2778      }      }
2779  }  }
   
 =head3 Min  
   
 C<< my $min = Min($value1, $value2, ... $valueN); >>  
   
 Return the minimum argument. The arguments are treated as numbers.  
   
 =over 4  
   
 =item $value1, $value2, ... $valueN  
   
 List of numbers to compare.  
   
 =item RETURN  
   
 Returns the lowest number in the list.  
   
 =back  
   
 =cut  
   
 sub Min {  
     # Get the parameters. Note that we prime the return value with the first parameter.  
     my ($retVal, @values) = @_;  
     # Loop through the remaining parameters, looking for the lowest.  
     for my $value (@values) {  
         if ($value < $retVal) {  
             $retVal = $value;  
2780          }          }
2781            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2782        };
2783        # Check for an error.
2784        if ($@) {
2785            Confess("SetPermissions error: $@");
2786      }      }
     # Return the minimum found.  
     return $retVal;  
2787  }  }
2788    
2789  =head3 Max  =head3 GetLine
2790    
2791  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @data = Tracer::GetLine($handle);
2792    
2793  Return the maximum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2794    
2795  =over 4  =over 4
2796    
2797  =item $value1, $value2, ... $valueN  =item handle
2798    
2799  List of numbers to compare.  Open file handle from which to read.
2800    
2801  =item RETURN  =item RETURN
2802    
2803  Returns the highest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2804    tab-delimited. If we are at the end of the file, then an empty list will be
2805    returned. If an empty line is read, a single list item consisting of a null
2806    string will be returned.
2807    
2808  =back  =back
2809    
2810  =cut  =cut
2811    
2812  sub Max {  sub GetLine {
2813      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2814      my ($retVal, @values) = @_;      my ($handle) = @_;
2815      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2816      for my $value (@values) {      my @retVal = ();
2817          if ($value > $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2818              $retVal = $value;      # Read from the file.
2819        my $line = <$handle>;
2820        # Only proceed if we found something.
2821        if (defined $line) {
2822            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2823            # upload control and have a nonstandard EOL combination.
2824            $line =~ s/(\r|\n)+$//;
2825            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2826            if (T(File => 4)) {
2827                my $escapedLine = $line;
2828                $escapedLine =~ s/\n/\\n/g;
2829                $escapedLine =~ s/\r/\\r/g;
2830                $escapedLine =~ s/\t/\\t/g;
2831                Trace("Line read: -->$escapedLine<--");
2832          }          }
2833            # If the line is empty, return a single empty string; otherwise, parse
2834            # it into fields.
2835            if ($line eq "") {
2836                push @retVal, "";
2837            } else {
2838                push @retVal, split /\t/,$line;
2839      }      }
2840      # Return the maximum found.      } else {
2841      return $retVal;          # Trace the reason the read failed.
2842            Trace("End of file: $!") if T(File => 3);
2843        }
2844        # Return the result.
2845        return @retVal;
2846  }  }
2847    
2848  =head3 AddToListMap  =head3 PutLine
2849    
2850  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      Tracer::PutLine($handle, \@fields, $eol);
2851    
2852  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Write a line of data to a tab-delimited file. The specified field values will be
2853  is created for the key. Otherwise, the new value is pushed onto the list.  output in tab-separated form, with a trailing new-line.
2854    
2855  =over 4  =over 4
2856    
2857  =item hash  =item handle
2858    
2859  Reference to the target hash.  Output file handle.
2860    
2861  =item key  =item fields
2862    
2863  Key for which the value is to be added.  List of field values.
2864    
2865  =item value1, value2, ... valueN  =item eol (optional)
2866    
2867  List of values to add to the key's value list.  End-of-line character (default is "\n").
2868    
2869  =back  =back
2870    
2871  =cut  =cut
2872    
2873  sub AddToListMap {  sub PutLine {
2874      # Get the parameters.      # Get the parameters.
2875      my ($hash, $key, @values) = @_;      my ($handle, $fields, $eol) = @_;
2876      # Process according to whether or not the key already has a value.      # Write the data.
2877      if (! exists $hash->{$key}) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
2878  }  }
2879    
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else abort.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error.  
         Confess("Cannot use this facility without logging in.");  
     }  
     # Return the determination indicator.  
     return $retVal;  
 }  
2880    
2881  =head3 Strip  =head3 PrintLine
2882    
2883  C<< my $string = Tracer::Strip($line); >>      Tracer::PrintLine($line);
2884    
2885  Strip all line terminators off a string. This is necessary when dealing with files  Print a line of text with a trailing new-line.
 that may have been transferred back and forth several times among different  
 operating environments.  
2886    
2887  =over 4  =over 4
2888    
2889  =item line  =item line
2890    
2891  Line of text to be stripped.  Line of text to print.
   
 =item RETURN  
   
 The same line of text with all the line-ending characters chopped from the end.  
2892    
2893  =back  =back
2894    
2895  =cut  =cut
2896    
2897  sub Strip {  sub PrintLine {
2898      # Get a copy of the parameter string.      # Get the parameters.
2899      my ($string) = @_;      my ($line) = @_;
2900      my $retVal = (defined $string ? $string : "");      # Print the line.
2901      # Strip the line terminator characters.      print "$line\n";
     $retVal =~ s/(\r|\n)+$//g;  
     # Return the result.  
     return $retVal;  
2902  }  }
2903    
 =head3 Pad  
2904    
2905  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  =head2 Other Useful Methods
2906    
2907  Pad a string to a specified length. The pad character will be a  =head3 IDHASH
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2908    
2909  =over 4      my $hash = SHTargetSearch::IDHASH(@keys);
2910    
2911  =item string  This is a dinky little method that converts a list of values to a reference
2912    to hash of values to labels. The values and labels are the same.
2913    
2914  String to be padded.  =cut
2915    
2916  =item len  sub IDHASH {
2917        my %retVal = map { $_ => $_ } @_;
2918        return \%retVal;
2919    }
2920    
2921  Desired length of the padded string.  =head3 Pluralize
2922    
2923  =item left (optional)      my $plural = Tracer::Pluralize($word);
2924    
2925  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  This is a very simple pluralization utility. It adds an C<s> at the end
2926    of the input word unless it already ends in an C<s>, in which case it
2927    adds C<es>.
2928    
2929  =item padChar (optional)  =over 4
2930    
2931  Character to use for padding. The default is a space.  =item word
2932    
2933    Singular word to pluralize.
2934    
2935  =item RETURN  =item RETURN
2936    
2937  Returns a copy of the original string with the pad character added to the  Returns the probable plural form of the word.
 specified end so that it achieves the desired length.  
2938    
2939  =back  =back
2940    
2941  =cut  =cut
2942    
2943  sub Pad {  sub Pluralize {
2944      # Get the parameters.      # Get the parameters.
2945      my ($string, $len, $left, $padChar) = @_;      my ($word) = @_;
2946      # Compute the padding character.      # Declare the return variable.
2947      if (! defined $padChar) {      my $retVal;
2948          $padChar = " ";      if ($word =~ /s$/) {
2949      }          $retVal = $word . 'es';
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2950          } else {          } else {
2951              $retVal .= $pad;          $retVal = $word . 's';
         }  
2952      }      }
2953      # Return the result.      # Return the result.
2954      return $retVal;      return $retVal;
2955  }  }
2956    
2957  =head3 EOF  =head3 Numeric
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
   
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2958    
2959      TICK("./protein.cgi")      my $okFlag = Tracer::Numeric($string);
2960    
2961  it will work correctly in both environments.  Return the value of the specified string if it is numeric, or an undefined value
2962    if it is not numeric.
2963    
2964  =over 4  =over 4
2965    
2966  =item commandString  =item string
2967    
2968  The command string to pass to the system.  String to check.
2969    
2970  =item RETURN  =item RETURN
2971    
2972  Returns the standard output from the specified command, as a list.  Returns the numeric value of the string if successful, or C<undef> if the string
2973    is not numeric.
2974    
2975  =back  =back
2976    
2977  =cut  =cut
2978  #: Return Type @;  
2979  sub TICK {  sub Numeric {
2980      # Get the parameters.      # Get the parameters.
2981      my ($commandString) = @_;      my ($string) = @_;
2982      # Chop off the dot-slash if this is Windows.      # We'll put the value in here if we succeed.
2983      if ($FIG_Config::win_mode) {      my $retVal;
2984          $commandString =~ s!^\./!!;      # Get a working copy of the string.
2985        my $copy = $string;
2986        # Trim leading and trailing spaces.
2987        $copy =~ s/^\s+//;
2988        $copy =~ s/\s+$//;
2989        # Check the result.
2990        if ($copy =~ /^[+-]?\d+$/) {
2991            $retVal = $copy;
2992        } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2993            $retVal = $copy;
2994        } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2995            $retVal = $copy;
2996      }      }
2997      # Activate the command and return the result.      # Return the result.
2998      return `$commandString`;      return $retVal;
2999  }  }
3000    
 =head3 ScriptSetup  
3001    
3002  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head3 ParseParm
3003    
3004  Perform standard tracing and debugging setup for scripts. The value returned is      my $listValue = Tracer::ParseParm($string);
 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.  
3005    
3006  This method calls L</ETracing> to configure tracing, which allows the tracing  Convert a parameter into a list reference. If the parameter is undefined,
3007  to be configured via the emergency tracing form on the debugging control panel.  an undefined value will be returned. Otherwise, it will be parsed as a
3008  Tracing will then be turned on automatically for all programs that use the L</ETracing>  comma-separated list of values.
 method, which includes every program that uses this method or L</StandardSetup>.  
3009    
3010  =over 4  =over 4
3011    
3012  =item noTrace (optional)  =item string
3013    
3014  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
3015    
3016  =item RETURN  =item RETURN
3017    
3018  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a reference to a list of values, or C<undef> if the incoming value
3019  the output page.  was undefined.
3020    
3021  =back  =back
3022    
3023  =cut  =cut
3024    
3025  sub ScriptSetup {  sub ParseParm {
3026      # Get the parameters.      # Get the parameters.
3027      my ($noTrace) = @_;      my ($string) = @_;
3028      # Get the CGI query object.      # Declare the return variable.
3029      my $cgi = CGI->new();      my $retVal;
3030      # Set up tracing if it's not suppressed.      # Check for data.
3031      ETracing($cgi) unless $noTrace;      if (defined $string) {
3032      # Create the variable hash.          # We have some, so split it into a list.
3033      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
3034      # Return the query object and variable hash.      }
3035      return ($cgi, $varHash);      # Return the result.
3036        return $retVal;
3037  }  }
3038    
3039  =head3 ETracing  =head3 Now
3040    
3041  C<< ETracing($parameter); >>      my $string = Tracer::Now();
3042    
3043  Set up emergency tracing. Emergency tracing is tracing that is turned  Return a displayable time stamp containing the local time. Whatever format this
3044  on automatically for any program that calls this method. The emergency  method produces must be parseable by L</ParseDate>.
3045  tracing parameters are stored in a a file identified by a tracing key.  
3046  If this method is called with a CGI object, then the tracing key is  =cut
3047  taken from a cookie. If it is called with no parameters, then the tracing  
3048  key is taken from an environment variable. If it is called with a string,  sub Now {
3049  the tracing key is that string.      return DisplayTime(time);
3050    }
3051    
3052    =head3 DisplayTime
3053    
3054        my $string = Tracer::DisplayTime($time);
3055    
3056    Convert a time value to a displayable time stamp. Whatever format this
3057    method produces must be parseable by L</ParseDate>.
3058    
3059  =over 4  =over 4
3060    
3061  =item parameter  =item time
3062    
3063  A parameter from which the tracing key is computed. If it is a scalar,  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3064  that scalar is used as the tracing key. If it is a CGI object, the  
3065  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item RETURN
3066  tracing key is taken from the C<TRACING> environment variable. If it  
3067  is a CGI object and emergency tracing is not on, the C<Trace> and  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
 C<TF> parameters will be used to determine the type of tracing.  
3068    
3069  =back  =back
3070    
3071  =cut  =cut
3072    
3073  sub ETracing {  sub DisplayTime {
3074      # Get the parameter.      my ($time) = @_;
3075      my ($parameter) = @_;      my $retVal = "(n/a)";
3076      # Check for CGI mode.      if (defined $time) {
3077      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3078      # Default to no tracing except errors.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3079      my ($tracing, $dest) = ("0", "WARN");                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
     # 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";  
         }  
3080      }      }
3081      # Setup the tracing we've determined from all the stuff above.      return $retVal;
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
3082      }      }
3083    
3084    # Pad a number to 2 digits.
3085    sub _p2 {
3086        my ($value) = @_;
3087        $value = "0$value" if ($value < 10);
3088        return $value;
3089  }  }
3090    
3091  =head3 EmergencyFileName  =head3 Escape
3092    
3093  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $codedString = Tracer::Escape($realString);
3094    
3095  Return the emergency tracing file name. This is the file that specifies  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3096  the tracing information.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3097    result is to reverse the effect of L</UnEscape>.
3098    
3099  =over 4  =over 4
3100    
3101  =item tkey  =item realString
3102    
3103  Tracing key for the current program.  String to escape.
3104    
3105  =item RETURN  =item RETURN
3106    
3107  Returns the name of the file to contain the emergency tracing information.  Escaped equivalent of the real string.
3108    
3109  =back  =back
3110    
3111  =cut  =cut
3112    
3113  sub EmergencyFileName {  sub Escape {
3114      # Get the parameters.      # Get the parameter.
3115      my ($tkey) = @_;      my ($realString) = @_;
3116      # Compute the emergency tracing file name.      # Initialize the return variable.
3117      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal = "";
3118        # Loop through the parameter string, looking for sequences to escape.
3119        while (length $realString > 0) {
3120            # Look for the first sequence to escape.
3121            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3122                # Here we found it. The text preceding the sequence is in $1. The sequence
3123                # itself is in $2. First, move the clear text to the return variable.
3124                $retVal .= $1;
3125                # Strip the processed section off the real string.
3126                $realString = substr $realString, (length $2) + (length $1);
3127                # Get the matched character.
3128                my $char = $2;
3129                # If we have a CR, we are done.
3130                if ($char ne "\r") {
3131                    # It's not a CR, so encode the escape sequence.
3132                    $char =~ tr/\t\n/tn/;
3133                    $retVal .= "\\" . $char;
3134                }
3135            } else {
3136                # Here there are no more escape sequences. The rest of the string is
3137                # transferred unmodified.
3138                $retVal .= $realString;
3139                $realString = "";
3140            }
3141        }
3142        # Return the result.
3143        return $retVal;
3144  }  }
3145    
3146  =head3 EmergencyFileTarget  =head3 UnEscape
3147    
3148  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $realString = Tracer::UnEscape($codedString);
3149    
3150  Return the emergency tracing target file name. This is the file that receives  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3151  the tracing output for file-based tracing.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3152    be deleted.
3153    
3154  =over 4  =over 4
3155    
3156  =item tkey  =item codedString
3157    
3158  Tracing key for the current program.  String to un-escape.
3159    
3160  =item RETURN  =item RETURN
3161    
3162  Returns the name of the file to contain the trace output.  Returns a copy of the original string with the escape sequences converted to their actual
3163    values.
3164    
3165  =back  =back
3166    
3167  =cut  =cut
3168    
3169  sub EmergencyFileTarget {  sub UnEscape {
3170      # Get the parameters.      # Get the parameter.
3171      my ($tkey) = @_;      my ($codedString) = @_;
3172      # Compute the emergency tracing file name.      # Initialize the return variable.
3173      return "$FIG_Config::temp/trace$tkey.log";      my $retVal = "";
3174        # Only proceed if the incoming string is nonempty.
3175        if (defined $codedString) {
3176            # Loop through the parameter string, looking for escape sequences. We can't do
3177            # translating because it causes problems with the escaped slash. ("\\t" becomes
3178            # "\<tab>" no matter what we do.)
3179            while (length $codedString > 0) {
3180                # Look for the first escape sequence.
3181                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3182                    # Here we found it. The text preceding the sequence is in $1. The sequence
3183                    # itself is in $2. First, move the clear text to the return variable.
3184                    $retVal .= $1;
3185                    $codedString = substr $codedString, (2 + length $1);
3186                    # Get the escape value.
3187                    my $char = $2;
3188                    # If we have a "\r", we are done.
3189                    if ($char ne 'r') {
3190                        # Here it's not an 'r', so we convert it.
3191                        $char =~ tr/\\tn/\\\t\n/;
3192                        $retVal .= $char;
3193                    }
3194                } else {
3195                    # Here there are no more escape sequences. The rest of the string is
3196                    # transferred unmodified.
3197                    $retVal .= $codedString;
3198                    $codedString = "";
3199                }
3200            }
3201        }
3202        # Return the result.
3203        return $retVal;
3204  }  }
3205    
3206  =head3 EmergencyTracingDest  =head3 Percent
3207    
3208  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my $percent = Tracer::Percent($number, $base);
3209    
3210  This method converts an emergency tracing destination to a real  Returns the percent of the base represented by the given number. If the base
3211  tracing destination. The main difference is that if the  is zero, returns zero.
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
3212    
3213  =over 4  =over 4
3214    
3215  =item tkey  =item number
3216    
3217  Tracing key for this environment.  Percent numerator.
3218    
3219  =item myDest  =item base
3220    
3221  Destination from the emergency tracing file.  Percent base.
3222    
3223  =item RETURN  =item RETURN
3224    
3225  Returns a destination that can be passed into L</TSetup>.  Returns the percentage of the base represented by the numerator.
3226    
3227  =back  =back
3228    
3229  =cut  =cut
3230    
3231  sub EmergencyTracingDest {  sub Percent {
3232      # Get the parameters.      # Get the parameters.
3233      my ($tkey, $myDest) = @_;      my ($number, $base) = @_;
3234      # Declare the return variable.      # Declare the return variable.
3235      my $retVal;      my $retVal = 0;
3236      # Process according to the destination value.      # Compute the percent.
3237      if ($myDest eq 'FILE') {      if ($base != 0) {
3238          $retVal = ">" . EmergencyFileTarget($tkey);          $retVal = $number * 100 / $base;
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
3239      }      }
3240      # Return the result.      # Return the result.
3241      return $retVal;      return $retVal;
3242  }  }
3243    
3244  =head3 Emergency  =head3 In
3245    
3246  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $flag = Tracer::In($value, $min, $max);
3247    
3248  Turn on emergency tracing. This method is normally invoked over the web from  Return TRUE if the value is between the minimum and the maximum, else FALSE.
 a debugging console, but it can also be called by the C<trace.pl> script.  
 The caller specifies the duration of the emergency in hours, the desired tracing  
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
3249    
3250  =over 4  =cut
3251    
3252  =item tkey  sub In {
3253        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3254    }
3255    
 The tracing key. This is used to identify the control file and the trace file.  
3256    
3257  =item hours  =head3 Constrain
3258    
3259  Number of hours to keep emergency tracing alive.      my $constrained = Constrain($value, $min, $max);
3260    
3261  =item dest  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3262    
3263  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
3264    
3265  =item level  =item value
3266    
3267  Tracing level. A higher level means more trace messages.  Value to constrain.
3268    
3269  =item modules  =item min (optional)
3270    
3271  A list of the tracing modules to activate.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3272    
3273    =item max (optional)
3274    
3275    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3276    
3277    =item RETURN
3278    
3279    Returns the incoming value, constrained according to the other parameters.
3280    
3281  =back  =back
3282    
3283  =cut  =cut
3284    
3285  sub Emergency {  sub Constrain {
3286      # Get the parameters.      # Get the parameters.
3287      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($value, $min, $max) = @_;
3288      # Create the emergency file.      # Declare the return variable.
3289      my $specFile = EmergencyFileName($tkey);      my $retVal = $value;
3290      my $outHandle = Open(undef, ">$specFile");      # Apply the minimum constraint.
3291      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $min && $retVal < $min) {
3292            $retVal = $min;
3293        }
3294        # Apply the maximum constraint.
3295        if (defined $max && $retVal > $max) {
3296            $retVal = $max;
3297        }
3298        # Return the result.
3299        return $retVal;
3300  }  }
3301    
3302  =head3 EmergencyKey  =head3 Min
3303    
3304  C<< my $tkey = EmergencyKey($parameter); >>      my $min = Min($value1, $value2, ... $valueN);
3305    
3306  Return the Key to be used for emergency tracing. This could be an IP address,  Return the minimum argument. The arguments are treated as numbers.
  a session ID, or a user name, depending on the environment.  
3307    
3308  =over 4  =over 4
3309    
3310  =item parameter  =item $value1, $value2, ... $valueN
3311    
3312  Parameter defining the method for finding the tracing key. If it is a scalar,  List of numbers to compare.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
3313    
3314  =item RETURN  =item RETURN
3315    
3316  Returns the key to be used for labels in emergency tracing.  Returns the lowest number in the list.
3317    
3318  =back  =back
3319    
3320  =cut  =cut
3321    
3322  sub EmergencyKey {  sub Min {
3323      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3324      my ($parameter) = @_;      my ($retVal, @values) = @_;
3325      # Declare the return variable.      # Loop through the remaining parameters, looking for the lowest.
3326      my $retVal;      for my $value (@values) {
3327      # Determine the parameter type.          if ($value < $retVal) {
3328      if (! defined $parameter) {              $retVal = $value;
         # Here we're supposed to check the environment.  
         $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;  
         }  
3329      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3330      }      }
3331      # Return the result.      # Return the minimum found.
3332      return $retVal;      return $retVal;
3333  }  }
3334    
3335    =head3 Max
3336    
3337  =head3 TraceParms      my $max = Max($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
3338    
3339  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Return the maximum argument. The arguments are treated as numbers.
 at level CGI => 4.  
3340    
3341  =over 4  =over 4
3342    
3343  =item cgi  =item $value1, $value2, ... $valueN
3344    
3345  CGI query object containing the parameters to trace.  List of numbers to compare.
3346    
3347    =item RETURN
3348    
3349    Returns the highest number in the list.
3350    
3351  =back  =back
3352    
3353  =cut  =cut
3354    
3355  sub TraceParms {  sub Max {
3356      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3357      my ($cgi) = @_;      my ($retVal, @values) = @_;
3358      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3359          # Here we want to trace the parameter data.      for my $value (@values) {
3360          my @names = $cgi->param;          if ($value > $retVal) {
3361          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}");  
3362          }          }
3363      }      }
3364        # Return the maximum found.
3365        return $retVal;
3366  }  }
3367    
3368  =head3 ScriptFinish  =head3 Strip
3369    
3370  C<< ScriptFinish($webData, $varHash); >>      my $string = Tracer::Strip($line);
3371    
3372  Output a web page at the end of a script. Either the string to be output or the  Strip all line terminators off a string. This is necessary when dealing with files
3373  name of a template file can be specified. If the second parameter is omitted,  that may have been transferred back and forth several times among different
3374  it is assumed we have a string to be output; otherwise, it is assumed we have the  operating environments.
 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.  
3375    
3376  A typical standard script would loook like the following.  =over 4
3377    
3378      BEGIN {  =item line
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3379    
3380      my ($cgi, $varHash) = ScriptSetup();  Line of text to be stripped.
3381      eval {  
3382          # ... get data from $cgi, put it in $varHash ...  =item RETURN
3383      };  
3384      if ($@) {  The same line of text with all the line-ending characters chopped from the end.
3385          Trace("Script Error: $@") if T(0);  
3386    =back
3387    
3388    =cut
3389    
3390    sub Strip {
3391        # Get a copy of the parameter string.
3392        my ($string) = @_;
3393        my $retVal = (defined $string ? $string : "");
3394        # Strip the line terminator characters.
3395        $retVal =~ s/(\r|\n)+$//g;
3396        # Return the result.
3397        return $retVal;
3398      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3399    
3400  The idea here is that even if the script fails, you'll see trace messages and  =head3 Trim
3401  useful output.  
3402        my $string = Tracer::Trim($line);
3403    
3404    Trim all spaces from the beginning and ending of a string.
3405    
3406  =over 4  =over 4
3407    
3408  =item webData  =item line
3409    
3410  A string containing either the full web page to be written to the output or the  Line of text to be trimmed.
 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.  
3411    
3412  =item varHash (optional)  =item RETURN
3413    
3414  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all whitespace chopped off either end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3415    
3416  =back  =back
3417    
3418  =cut  =cut
3419    
3420  sub ScriptFinish {  sub Trim {
3421      # Get the parameters.      # Get a copy of the parameter string.
3422      my ($webData, $varHash) = @_;      my ($string) = @_;
3423      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3424      my $outputString;      # Strip the front spaces.
3425      if (defined $varHash) {      $retVal =~ s/^\s+//;
3426          # Here we have a template file. We need to determine the template type.      # Strip the back spaces.
3427          my $template;      $retVal =~ s/\s+$//;
3428          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      # Return the result.
3429              $template = "$FIG_Config::template_url/$webData";      return $retVal;
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
     }  
     # Write the output string.  
     print $outputString;  
3430  }  }
3431    
3432  =head3 Insure  =head3 Pad
3433    
3434  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3435    
3436  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3437    space, and the padding will be on the right side unless specified
3438    in the third parameter.
3439    
3440  =over 4  =over 4
3441    
3442  =item dirName  =item string
3443    
3444  Name of the directory to check. If it does not exist, it will be created.  String to be padded.
3445    
3446    =item len
3447    
3448    Desired length of the padded string.
3449    
3450    =item left (optional)
3451    
3452    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3453    
3454    =item padChar (optional)
3455    
3456    Character to use for padding. The default is a space.
3457    
3458    =item RETURN
3459    
3460    Returns a copy of the original string with the pad character added to the
3461    specified end so that it achieves the desired length.
3462    
3463  =back  =back
3464    
3465  =cut  =cut
3466    
3467  sub Insure {  sub Pad {
3468      my ($dirName) = @_;      # Get the parameters.
3469      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3470          Trace("Creating $dirName directory.") if T(File => 2);      # Compute the padding character.
3471          eval { mkpath $dirName; };      if (! defined $padChar) {
3472          if ($@) {          $padChar = " ";
3473              Confess("Error creating $dirName: $@");      }
3474        # Compute the number of spaces needed.
3475        my $needed = $len - length $string;
3476        # Copy the string into the return variable.
3477        my $retVal = $string;
3478        # Only proceed if padding is needed.
3479        if ($needed > 0) {
3480            # Create the pad string.
3481            my $pad = $padChar x $needed;
3482            # Affix it to the return value.
3483            if ($left) {
3484                $retVal = $pad . $retVal;
3485            } else {
3486                $retVal .= $pad;
3487          }          }
3488      }      }
3489        # Return the result.
3490        return $retVal;
3491  }  }
3492    
3493  =head3 ChDir  =head3 Quoted
3494    
3495  C<< ChDir($dirName); >>      my $string = Tracer::Quoted($var);
3496    
3497  Change to the specified directory.  Convert the specified value to a string and enclose it in single quotes.
3498    If it's undefined, the string C<undef> in angle brackets will be used
3499    instead.
3500    
3501  =over 4  =over 4
3502    
3503  =item dirName  =item var
3504    
3505    Value to quote.
3506    
3507    =item RETURN
3508    
3509  Name of the directory to which we want to change.  Returns a string enclosed in quotes, or an indication the value is undefined.
3510    
3511  =back  =back
3512    
3513  =cut  =cut
3514    
3515  sub ChDir {  sub Quoted {
3516      my ($dirName) = @_;      # Get the parameters.
3517      if (! -d $dirName) {      my ($var) = @_;
3518          Confess("Cannot change to directory $dirName: no such directory.");      # Declare the return variable.
3519        my $retVal;
3520        # Are we undefined?
3521        if (! defined $var) {
3522            $retVal = "<undef>";
3523      } else {      } else {
3524          Trace("Changing to directory $dirName.") if T(File => 4);          # No, so convert to a string and enclose in quotes.
3525          my $okFlag = chdir $dirName;          $retVal = $var;
3526          if (! $okFlag) {          $retVal =~ s/'/\\'/;
3527              Confess("Error switching to directory $dirName.");          $retVal = "'$retVal'";
         }  
3528      }      }
3529        # Return the result.
3530        return $retVal;
3531  }  }
3532    
3533  =head3 SendSMS  =head3 EOF
3534    
3535  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
3536    
3537  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3538    
3539      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3540                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3541                  api_id => '2561022' };  }
3542    
3543  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3544    
3545  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);