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revision 1.84, Thu May 3 12:28:00 2007 UTC revision 1.118, Thu May 21 18:56:28 2009 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    umask 2;                    # Fix the damn umask so everything is group-writable.
215    
216    =head2 Tracing Methods
217    
218    =head3 Setups
219    
220        my $count = Tracer::Setups();
221    
222    Return the number of times L</TSetup> has been called.
223    
224    This method allows for the creation of conditional tracing setups where, for example, we
225    may want to set up tracing if nobody else has done it before us.
226    
227    =cut
228    
229  =head2 Public Methods  sub Setups {
230        return $SetupCount;
231    }
232    
233  =head3 TSetup  =head3 TSetup
234    
235  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
236    
237  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
238  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 282 
282          }          }
283      }      }
284      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
285      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
287        # the standard output (tee mode).
288      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
289          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
290              $TeeFlag = 1;              $TeeFlag = 1;
291              $target = substr($target, 1);              $target = substr($target, 1);
292          }          }
293          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
294                # We need to initialize the file (which clears it).
295              open TRACEFILE, $target;              open TRACEFILE, $target;
296              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297              close TRACEFILE;              close TRACEFILE;
298                # Set to append mode now that the file has been cleared.
299              $Destination = ">$target";              $Destination = ">$target";
300          } else {          } else {
301              $Destination = $target;              $Destination = $target;
# Line 372  Line 307 
307      $SetupCount++;      $SetupCount++;
308  }  }
309    
310  =head3 StandardSetup  =head3 SetLevel
311    
312  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
313    
314  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.  
315    
316  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.  
317    
318  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  
319    
320      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
321    
322  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.  
323    
324  =over 4  =cut
325    
326  =item SQL  sub SetLevel {
327        $TraceLevel = $_[0];
328    }
329    
330  Traces SQL commands and activity.  =head3 ParseDate
331    
332  =item Tracer      my $time = Tracer::ParseDate($dateString);
333    
334  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
335    and parses it into a number. The string must be vaguely date-like or it will
336    return an undefined value. Our requirement is that a month and day be
337    present and that three pieces of the date string (time of day, month and day,
338    year) be separated by likely delimiters, such as spaces, commas, and such-like.
339    
340  =back  If a time of day is present, it must be in military time with two digits for
341    everything but the hour.
342    
343  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.  
344    
345      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
346    equally innocuous. This means, however, that a sufficiently long sentence with date-like
347    parts in it may be interpreted as a date. Hopefully this will not be a problem.
348    
349  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  
350    
351  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.  
352    
353      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
354    
355  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
356    
357  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.  
358    
359  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
360    
361  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
362  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
363    
364      my ($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);  
365    
366    =cut
367    
368  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
369  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
370  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
371                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
372                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
373                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
374                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
375                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
376                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
377                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
378                                Oct =>  9, October  =>   9, '10' =>  9,
379                                Nov => 10, November =>  10, '11' => 10,
380                                Dec => 11, December =>  11, '12' => 11
381                            };
382    
383  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
384        # Get the parameters.
385        my ($dateString) = @_;
386        # Declare the return variable.
387        my $retVal;
388        # Find the month and day of month. There are two ways that can happen. We check for the
389        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390        # won't be fooled into thinking the month is Sunday.
391        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392            my ($mon, $mday) = (MONTHS->{$1}, $2);
393            # Insist that the month and day are valid.
394            if (defined($mon) && $2 >= 1 && $2 <= 31) {
395                # Find the time.
396                my ($hour, $min, $sec) = (0, 0, 0);
397                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398                    ($hour, $min, $sec) = ($1, $2, $3);
399                }
400                # Find the year.
401                my $year;
402                if ($dateString =~ /\b(\d{4})\b/) {
403                    $year = $1;
404                } else {
405                    # Get the default year, which is this one. Note we must convert it to
406                    # the four-digit value expected by "timelocal".
407                    (undef, undef, undef, undef, undef, $year) = localtime();
408                    $year += 1900;
409                }
410                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411            }
412        }
413        # Return the result.
414        return $retVal;
415    }
416    
417      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
418    
419  Single and double hyphens are equivalent. So, you could also code the      Tracer::LogErrors($fileName);
 above command as  
420    
421      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
422    
423  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<$options> hash would be  
424    
425      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
426    
427  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
428    
429  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
430    
431      -user=Bruce -background  =cut
432    
433  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
434  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
435  simplify starting a command in the background.      my ($fileName) = @_;
436        # Open the file as the standard error output.
437        open STDERR, '>', $fileName;
438    }
439    
440  The user name is also used as the tracing key for L</Emergency Tracing>.  =head3 Trace
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
441    
442  Finally, if the special option C<-help> is specified, the option      Trace($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  
443    
444      TransactFeatures -help  Write a trace message to the target location specified in L</TSetup>. If there has not been
445    any prior call to B<TSetup>.
446    
447  he would see the following output.  =over 4
448    
449      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  
450    
451  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,  
452    
453      { trace => [0, "tracing level (default 0)"],  =back
        ...  
454    
455  would set the default trace level to 0 instead of E, while  =cut
456    
457      { trace => ["2-", "tracing level (default 2)"],  sub Trace {
458         ...      # Get the parameters.
459        my ($message) = @_;
460        # Strip off any line terminators at the end of the message. We will add
461        # new-line stuff ourselves.
462        my $stripped = Strip($message);
463        # Compute the caller information.
464        my ($callPackage, $callFile, $callLine) = caller();
465        my $callFileTitle = basename($callFile);
466        # Check the caller.
467        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468        # Get the timestamp.
469        my $timeStamp = Now();
470        # Build the prefix.
471        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473        # Format the message.
474        my $formatted = "$prefix $stripped";
475        # Process according to the destination.
476        if ($Destination eq "TEXT") {
477            # Write the message to the standard output.
478            print "$formatted\n";
479        } elsif ($Destination eq "ERROR") {
480            # Write the message to the error output. Here, we want our prefix fields.
481            print STDERR "$formatted\n";
482        } elsif ($Destination eq "WARN") {
483            # Emit the message to the standard error output. It is presumed that the
484            # error logger will add its own prefix fields, the notable exception being
485            # the caller info.
486            print STDERR "$callerInfo$stripped\n";
487        } elsif ($Destination eq "QUEUE") {
488            # Push the message into the queue.
489            push @Queue, "$formatted";
490        } elsif ($Destination eq "HTML") {
491            # Convert the message to HTML.
492            my $escapedMessage = CGI::escapeHTML($stripped);
493            # The stuff after the first line feed should be pre-formatted.
494            my @lines = split /\s*\n/, $escapedMessage;
495            # Get the normal portion.
496            my $line1 = shift @lines;
497            print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
498            if (@lines) {
499                print "<pre>" . join("\n", @lines, "<pre>");
500            }
501        } elsif ($Destination =~ m/^>>/) {
502            # Write the trace message to an output file.
503            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
504            # Lock the file.
505            flock TRACING, LOCK_EX;
506            print TRACING "$formatted\n";
507            close TRACING;
508            # If the Tee flag is on, echo it to the standard output.
509            if ($TeeFlag) {
510                print "$formatted\n";
511            }
512        }
513    }
514    
515  would set the default to 2, but trace only to the log file, not to the  =head3 MemTrace
 standard output.  
516    
517  The parameters to this method are as follows.      MemTrace($message);
518    
519    Output a trace message that includes memory size information.
520    
521  =over 4  =over 4
522    
523  =item categories  =item message
524    
525  Reference to a list of tracing category names. These should be names of  Message to display. The message will be followed by a sentence about the memory size.
 packages whose internal workings will need to be debugged to get the  
 command working.  
526    
527  =item options  =back
528    
529  Reference to a hash containing the legal options for the current command mapped  =cut
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
530    
531  =item parmHelp  sub MemTrace {
532        # Get the parameters.
533        my ($message) = @_;
534        my $memory = GetMemorySize();
535        Trace("$message $memory in use.");
536    }
537    
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
538    
539  =item argv  =head3 TraceDump
540    
541        TraceDump($title, $object);
542    
543    Dump an object to the trace log. This method simply calls the C<Dumper>
544    function, but routes the output to the trace log instead of returning it
545    as a string. The output is arranged so that it comes out monospaced when
546    it appears in an HTML trace dump.
547    
548    =over 4
549    
550    =item title
551    
552    Title to give to the object being dumped.
553    
554    =item object
555    
556    Reference to a list, hash, or object to dump.
557    
558    =back
559    
560    =cut
561    
562    sub TraceDump {
563        # Get the parameters.
564        my ($title, $object) = @_;
565        # Trace the object.
566        Trace("Object dump for $title:\n" . Dumper($object));
567    }
568    
569    =head3 T
570    
571        my $switch = T($category, $traceLevel);
572    
573        or
574    
575        my $switch = T($traceLevel);
576    
577    Return TRUE if the trace level is at or above a specified value and the specified category
578    is active, else FALSE. If no category is specified, the caller's package name is used.
579    
580    =over 4
581    
582    =item category
583    
584    Category to which the message belongs. If not specified, the caller's package name is
585    used.
586    
587    =item traceLevel
588    
589    Relevant tracing level.
590    
591    =item RETURN
592    
593    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
594    
595    =back
596    
597    =cut
598    
599    sub T {
600        # Declare the return variable.
601        my $retVal = 0;
602        # Only proceed if tracing is turned on.
603        if ($Destination ne "NONE") {
604            # Get the parameters.
605            my ($category, $traceLevel) = @_;
606            if (!defined $traceLevel) {
607                # Here we have no category, so we need to get the calling package.
608                # The calling package is normally the first parameter. If it is
609                # omitted, the first parameter will be the tracelevel. So, the
610                # first thing we do is shift the so-called category into the
611                # $traceLevel variable where it belongs.
612                $traceLevel = $category;
613                my ($package, $fileName, $line) = caller;
614                # If there is no calling package, we default to "main".
615                if (!$package) {
616                    $category = "main";
617                } else {
618                    my @cats = split /::/, $package;
619                    $category = $cats[$#cats];
620                }
621            }
622            # Save the category name and level.
623            $LastCategory = $category;
624            $LastLevel = $traceLevel;
625            # Convert it to lower case before we hash it.
626            $category = lc $category;
627            # Validate the trace level.
628            if (ref $traceLevel) {
629                Confess("Bad trace level.");
630            } elsif (ref $TraceLevel) {
631                Confess("Bad trace config.");
632            }
633            # Make the check. Note that level 0 shows even if the category is turned off.
634            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
635        }
636        # Return the computed result.
637        return $retVal;
638    }
639    
640    =head3 QTrace
641    
642        my $data = QTrace($format);
643    
644    Return the queued trace data in the specified format.
645    
646    =over 4
647    
648    =item format
649    
650    C<html> to format the data as an HTML list, C<text> to format it as straight text.
651    
652    =back
653    
654    =cut
655    
656    sub QTrace {
657        # Get the parameter.
658        my ($format) = @_;
659        # Create the return variable.
660        my $retVal = "";
661        # Only proceed if there is an actual queue.
662        if (@Queue) {
663            # Process according to the format.
664            if ($format =~ m/^HTML$/i) {
665                # Convert the queue into an HTML list.
666                $retVal = "<ul>\n";
667                for my $line (@Queue) {
668                    my $escapedLine = CGI::escapeHTML($line);
669                    $retVal .= "<li>$escapedLine</li>\n";
670                }
671                $retVal .= "</ul>\n";
672            } elsif ($format =~ m/^TEXT$/i) {
673                # Convert the queue into a list of text lines.
674                $retVal = join("\n", @Queue) . "\n";
675            }
676            # Clear the queue.
677            @Queue = ();
678        }
679        # Return the formatted list.
680        return $retVal;
681    }
682    
683    =head3 Confess
684    
685        Confess($message);
686    
687    Trace the call stack and abort the program with the specified message. When used with
688    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
689    So, for example
690    
691        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
692    
693    Will abort the program with a stack trace if the value of C<$recNum> is negative.
694    
695    =over 4
696    
697    =item message
698    
699    Message to include in the trace.
700    
701    =back
702    
703    =cut
704    
705    sub Confess {
706        # Get the parameters.
707        my ($message) = @_;
708        # Set up the category and level.
709        $LastCategory = "(confess)";
710        $LastLevel = 0;
711        # Trace the call stack.
712        Cluck($message);
713        # Abort the program.
714        croak(">>> $message");
715    }
716    
717    =head3 SaveCGI
718    
719        Tracer::SaveCGI($cgi);
720    
721    This method saves the CGI object but does not activate emergency tracing.
722    It is used to allow L</Warn> to work in situations where emergency
723    tracing is contra-indicated (e.g. the wiki).
724    
725    =over 4
726    
727    =item cgi
728    
729    Active CGI query object.
730    
731    =back
732    
733    =cut
734    
735    sub SaveCGI {
736        $SavedCGI = $_[0];
737    }
738    
739    =head3 Warn
740    
741        Warn($message, @options);
742    
743    This method traces an important message. If an RSS feed is configured
744    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
745    then the message will be echoed to the feed. In general, a tracing
746    destination of C<WARN> indicates that the caller is running as a web
747    service in a production environment; however, this is not a requirement.
748    
749    To force warnings into the RSS feed even when the tracing destination
750    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
751    configured automatically when L</StandardSetup> is used.
752    
753    The L</Cluck> method calls this one for its final message. Since
754    L</Confess> calls L</Cluck>, this means that any error which is caught
755    and confessed will put something in the feed. This insures that someone
756    will be alerted relatively quickly when a failure occurs.
757    
758    =over 4
759    
760    =item message
761    
762    Message to be traced.
763    
764    =item options
765    
766    A list containing zero or more options.
767    
768    =back
769    
770    The permissible options are as follows.
771    
772    =over 4
773    
774    =item noStack
775    
776    If specified, then the stack trace is not included in the output.
777    
778    =back
779    
780    =cut
781    
782    sub Warn {
783        # Get the parameters.
784        my $message = shift @_;
785        my %options = map { $_ => 1 } @_;
786        # Save $@;
787        my $savedError = $@;
788        # Trace the message.
789        Trace($message);
790        # This will contain the lock handle. If it's defined, it means we need to unlock.
791        my $lock;
792        # Check for feed forcing.
793        my $forceFeed = exists $Categories{feed};
794        # An error here would be disastrous. Note that if debug mode is specified,
795        # we do this stuff even in a test environment.
796        eval {
797            # Do we need to put this in the RSS feed?
798            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
799                # Probably. We need to check first, however, to see if it's from an
800                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
801                my $key = "127.0.0.1";
802                if (defined $SavedCGI) {
803                    # Get the IP address.
804                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
805                }
806                # Is the IP address in the ignore list?
807                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
808                if (! $found) {
809                    # No. We're good. We now need to compute the date, the link, and the title.
810                    # First, the date, in a very specific format.
811                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
812                        (tz_local_offset() / 30);
813                    # Environment data goes in here. We start with the date.
814                    my $environment = "$date.  ";
815                    # If we need to recap the message (because it's too long to be a title), we'll
816                    # put it in here.
817                    my $recap;
818                    # Copy the message and remove excess space.
819                    my $title = $message;
820                    $title =~ s/\s+/ /gs;
821                    # If it's too long, we have to split it up.
822                    if (length $title > 60) {
823                        # Put the full message in the environment string.
824                        $recap = $title;
825                        # Excerpt it as the title.
826                        $title = substr($title, 0, 50) . "...";
827                    }
828                    # If we have a CGI object, then this is a web error. Otherwise, it's
829                    # command-line.
830                    if (defined $SavedCGI) {
831                        # We're in a web service. The environment is the user's IP, and the link
832                        # is the URL that got us here.
833                        $environment .= "Event Reported at IP address $key process $$.";
834                        my $url = $SavedCGI->self_url();
835                        # We need the user agent string and (if available) the referrer.
836                        # The referrer will be the link.
837                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
838                        if ($ENV{HTTP_REFERER}) {
839                            my $link = $ENV{HTTP_REFERER};
840                            $environment .= " referred from <a href=\"$link\">$link</a>.";
841                        } else {
842                            $environment .= " referrer unknown.";
843                        }
844                        # Close off the sentence with the original link.
845                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
846                    } else {
847                        # No CGI object, so we're a command-line tool. Use the tracing
848                        # key and the PID as the user identifier, and add the command.
849                        my $key = EmergencyKey();
850                        $environment .= "Event Reported by $key process $$.";
851                        if ($CommandLine) {
852                            # We're in a StandardSetup script, so we have the real command line.
853                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
854                        } elsif ($ENV{_}) {
855                            # We're in a BASH script, so the command has been stored in the _ variable.
856                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
857                        }
858                    }
859                    # Build a GUID. We use the current time, the title, and the process ID,
860                    # then digest the result.
861                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
862                    # Finally, the description. This is a stack trace plus various environmental stuff.
863                    # The trace is optional.
864                    my $stackTrace;
865                    if ($options{noStack}) {
866                        $stackTrace = "";
867                    } else {
868                        my @trace = LongMess();
869                        # Only proceed if we got something back.
870                        if (scalar(@trace) > 0) {
871                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
872                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
873                        }
874                    }
875                    # We got the stack trace. Now it's time to put it all together.
876                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
877                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
878                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
879                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
880                    # our <br>s and <pre>s are used to format the description.
881                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
882                    my $description = "$recap$environment  $stackTrace";
883                    # Okay, we have all the pieces. Create a hash of the new event.
884                    my $newItem = { title => $title,
885                                    description => $description,
886                                    category => $LastCategory,
887                                    pubDate => $date,
888                                    guid => $guid,
889                                  };
890                    # We need XML capability for this.
891                    require XML::Simple;
892                    # The RSS document goes in here.
893                    my $rss;
894                    # Get the name of the RSS file. It's in the FIG temporary directory.
895                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
896                    # Open the config file and lock it.
897                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
898                    flock $lock, LOCK_EX;
899                    # Does it exist?
900                    if (-s $fileName) {
901                        # Slurp it in.
902                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
903                    } else {
904                        my $size = -s $fileName;
905                        # Create an empty channel.
906                        $rss = {
907                            channel => {
908                                title => 'NMPDR Warning Feed',
909                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
910                                description => "Important messages regarding the status of the NMPDR.",
911                                generator => "NMPDR Trace Facility",
912                                docs => "http://blogs.law.harvard.edu/tech/rss",
913                                item => []
914                            },
915                        };
916                    }
917                    # Get the channel object.
918                    my $channel = $rss->{channel};
919                    # Update the last-build date.
920                    $channel->{lastBuildDate} = $date;
921                    # Get the item array.
922                    my $items = $channel->{item};
923                    # Insure it has only 100 entries.
924                    while (scalar @{$items} > 100) {
925                        pop @{$items};
926                    }
927                    # Add our new item at the front.
928                    unshift @{$items}, $newItem;
929                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
930                    # the requirements for those.
931                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
932                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
933                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
934                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
935                    # We don't use Open here because we can't afford an error.
936                    if (open XMLOUT, ">$fileName") {
937                        print XMLOUT $xml;
938                        close XMLOUT;
939                    }
940                }
941            }
942        };
943        if ($@) {
944            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
945            # (which is a good thing).
946            my $error = $@;
947            Trace("Feed Error: $error") if T(Feed => 0);
948        }
949        # Be sure to unlock.
950        if ($lock) {
951            flock $lock, LOCK_UN;
952            undef $lock;
953        }
954        # Restore the error message.
955        $@ = $savedError;
956    }
957    
958    
959    
960    
961    =head3 Assert
962    
963        Assert($condition1, $condition2, ... $conditionN);
964    
965    Return TRUE if all the conditions are true. This method can be used in conjunction with
966    the OR operator and the L</Confess> method as a debugging assert.
967    So, for example
968    
969        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
970    
971    Will abort the program with a stack trace if the value of C<$recNum> is negative.
972    
973    =cut
974    sub Assert {
975        my $retVal = 1;
976        LOOP: for my $condition (@_) {
977            if (! $condition) {
978                $retVal = 0;
979                last LOOP;
980            }
981        }
982        return $retVal;
983    }
984    
985    =head3 Cluck
986    
987        Cluck($message);
988    
989    Trace the call stack. Note that for best results, you should qualify the call with a
990    trace condition. For example,
991    
992        Cluck("Starting record parse.") if T(3);
993    
994    will only trace the stack if the trace level for the package is 3 or more.
995    
996    =over 4
997    
998    =item message
999    
1000    Message to include in the trace.
1001    
1002    =back
1003    
1004    =cut
1005    
1006    sub Cluck {
1007        # Get the parameters.
1008        my ($message) = @_;
1009        # Trace what's happening.
1010        Trace("Stack trace for event: $message");
1011        # Get the stack trace.
1012        my @trace = LongMess();
1013        # Convert the trace to a series of messages.
1014        for my $line (@trace) {
1015            # Replace the tab at the beginning with spaces.
1016            $line =~ s/^\t/    /;
1017            # Trace the line.
1018            Trace($line);
1019        }
1020        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
1021        Warn($message);
1022    }
1023    
1024    =head3 LongMess
1025    
1026        my @lines = Tracer::LongMess();
1027    
1028    Return a stack trace with all tracing methods removed. The return will be in the form of a list
1029    of message strings.
1030    
1031    =cut
1032    
1033    sub LongMess {
1034        # Declare the return variable.
1035        my @retVal = ();
1036        my $confession = longmess("");
1037        for my $line (split /\s*\n/, $confession) {
1038            unless ($line =~ /Tracer\.pm/) {
1039                # Here we have a line worth keeping. Push it onto the result list.
1040                push @retVal, $line;
1041            }
1042        }
1043        # Return the result.
1044        return @retVal;
1045    }
1046    
1047    =head3 ETracing
1048    
1049        ETracing($parameter);
1050    
1051    Set up emergency tracing. Emergency tracing is tracing that is turned
1052    on automatically for any program that calls this method. The emergency
1053    tracing parameters are stored in a a file identified by a tracing key.
1054    If this method is called with a CGI object, then the tracing key is
1055    taken from a cookie. If it is called with no parameters, then the tracing
1056    key is taken from an environment variable. If it is called with a string,
1057    the tracing key is that string.
1058    
1059    =over 4
1060    
1061    =item parameter
1062    
1063    A parameter from which the tracing key is computed. If it is a scalar,
1064    that scalar is used as the tracing key. If it is a CGI object, the
1065    tracing key is taken from the C<IP> cookie. If it is omitted, the
1066    tracing key is taken from the C<TRACING> environment variable. If it
1067    is a CGI object and emergency tracing is not on, the C<Trace> and
1068    C<TF> parameters will be used to determine the type of tracing.
1069    
1070    =back
1071    
1072    =cut
1073    
1074    sub ETracing {
1075        # Get the parameter.
1076        my ($parameter) = @_;
1077        # Check for CGI mode.
1078        if (defined $parameter && ref $parameter eq 'CGI') {
1079            $SavedCGI = $parameter;
1080        } else {
1081            $SavedCGI = undef;
1082        }
1083        # Default to no tracing except errors.
1084        my ($tracing, $dest) = ("0", "WARN");
1085        # Check for emergency tracing.
1086        my $tkey = EmergencyKey($parameter);
1087        my $emergencyFile = EmergencyFileName($tkey);
1088        if (-e $emergencyFile) {
1089            # We have the file. Read in the data.
1090            my @tracing = GetFile($emergencyFile);
1091            # Pull off the time limit.
1092            my $expire = shift @tracing;
1093            # Convert it to seconds.
1094            $expire *= 3600;
1095            # Check the file data.
1096            my $stat = stat($emergencyFile);
1097            my ($now) = gettimeofday;
1098            if ($now - $stat->mtime > $expire) {
1099                # Delete the expired file.
1100                unlink $emergencyFile;
1101            } else {
1102                # Emergency tracing is on. Pull off the destination and
1103                # the trace level;
1104                $dest = shift @tracing;
1105                my $level = shift @tracing;
1106                # Convert the destination to a real tracing destination.
1107                # temp directory.
1108                $dest = EmergencyTracingDest($tkey, $dest);
1109                # Insure Tracer is specified.
1110                my %moduleHash = map { $_ => 1 } @tracing;
1111                $moduleHash{Tracer} = 1;
1112                # Set the trace parameter.
1113                $tracing = join(" ", $level, sort keys %moduleHash);
1114            }
1115        } elsif (defined $SavedCGI) {
1116            # There's no emergency tracing, but we have a CGI object, so check
1117            # for tracing from the form parameters.
1118            if ($SavedCGI->param('Trace')) {
1119                # Here the user has requested tracing via a form.
1120                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1121                $tracing = $SavedCGI->param('Trace') . " Tracer";
1122            }
1123        }
1124        # Setup the tracing we've determined from all the stuff above.
1125        TSetup($tracing, $dest);
1126        # Check to see if we're a web script.
1127        if (defined $SavedCGI) {
1128            # Yes we are. Trace the form and environment data.
1129            TraceParms($SavedCGI);
1130            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1131            # emitted by the script in its raw form.
1132            if (T(Raw => 3)) {
1133                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1134            }
1135        }
1136    }
1137    
1138    =head3 EmergencyFileName
1139    
1140        my $fileName = Tracer::EmergencyFileName($tkey);
1141    
1142    Return the emergency tracing file name. This is the file that specifies
1143    the tracing information.
1144    
1145    =over 4
1146    
1147    =item tkey
1148    
1149    Tracing key for the current program.
1150    
1151    =item RETURN
1152    
1153    Returns the name of the file to contain the emergency tracing information.
1154    
1155    =back
1156    
1157    =cut
1158    
1159    sub EmergencyFileName {
1160        # Get the parameters.
1161        my ($tkey) = @_;
1162        # Compute the emergency tracing file name.
1163        return "$FIG_Config::temp/Emergency$tkey.txt";
1164    }
1165    
1166    =head3 EmergencyFileTarget
1167    
1168        my $fileName = Tracer::EmergencyFileTarget($tkey);
1169    
1170    Return the emergency tracing target file name. This is the file that receives
1171    the tracing output for file-based tracing.
1172    
1173    =over 4
1174    
1175    =item tkey
1176    
1177    Tracing key for the current program.
1178    
1179    =item RETURN
1180    
1181    Returns the name of the file to contain the trace output.
1182    
1183    =back
1184    
1185    =cut
1186    
1187    sub EmergencyFileTarget {
1188        # Get the parameters.
1189        my ($tkey) = @_;
1190        # Compute the emergency tracing file name.
1191        return "$FIG_Config::temp/trace$tkey.log";
1192    }
1193    
1194    =head3 EmergencyTracingDest
1195    
1196        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1197    
1198    This method converts an emergency tracing destination to a real
1199    tracing destination. The main difference is that if the
1200    destination is C<FILE> or C<APPEND>, we convert it to file
1201    output. If the destination is C<DUAL>, we convert it to file
1202    and standard output.
1203    
1204    =over 4
1205    
1206    =item tkey
1207    
1208    Tracing key for this environment.
1209    
1210    =item myDest
1211    
1212    Destination from the emergency tracing file.
1213    
1214    =item RETURN
1215    
1216    Returns a destination that can be passed into L</TSetup>.
1217    
1218    =back
1219    
1220    =cut
1221    
1222    sub EmergencyTracingDest {
1223        # Get the parameters.
1224        my ($tkey, $myDest) = @_;
1225        # Declare the return variable.
1226        my $retVal = $myDest;
1227        # Process according to the destination value.
1228        if ($myDest eq 'FILE') {
1229            $retVal = ">" . EmergencyFileTarget($tkey);
1230        } elsif ($myDest eq 'APPEND') {
1231            $retVal = ">>" . EmergencyFileTarget($tkey);
1232        } elsif ($myDest eq 'DUAL') {
1233            $retVal = "+>" . EmergencyFileTarget($tkey);
1234        } elsif ($myDest eq 'WARN') {
1235            $retVal = "WARN";
1236        }
1237        # Return the result.
1238        return $retVal;
1239    }
1240    
1241    =head3 Emergency
1242    
1243        Emergency($key, $hours, $dest, $level, @modules);
1244    
1245    Turn on emergency tracing. This method is normally invoked over the web from
1246    a debugging console, but it can also be called by the C<trace.pl> script.
1247    The caller specifies the duration of the emergency in hours, the desired tracing
1248    destination, the trace level, and a list of the trace modules to activate.
1249    For the length of the duration, when a program in an environment with the
1250    specified tracing key active invokes a Sprout CGI script, tracing will be
1251    turned on automatically. See L</TSetup> for more about tracing setup and
1252    L</ETracing> for more about emergency tracing.
1253    
1254    =over 4
1255    
1256    =item tkey
1257    
1258    The tracing key. This is used to identify the control file and the trace file.
1259    
1260    =item hours
1261    
1262    Number of hours to keep emergency tracing alive.
1263    
1264    =item dest
1265    
1266    Tracing destination. If no path information is specified for a file
1267    destination, it is put in the FIG temporary directory.
1268    
1269    =item level
1270    
1271    Tracing level. A higher level means more trace messages.
1272    
1273    =item modules
1274    
1275    A list of the tracing modules to activate.
1276    
1277    =back
1278    
1279    =cut
1280    
1281    sub Emergency {
1282        # Get the parameters.
1283        my ($tkey, $hours, $dest, $level, @modules) = @_;
1284        # Create the emergency file.
1285        my $specFile = EmergencyFileName($tkey);
1286        my $outHandle = Open(undef, ">$specFile");
1287        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1288    }
1289    
1290    =head3 EmergencyKey
1291    
1292        my $tkey = EmergencyKey($parameter);
1293    
1294    Return the Key to be used for emergency tracing. This could be an IP address,
1295     a session ID, or a user name, depending on the environment.
1296    
1297    =over 4
1298    
1299    =item parameter
1300    
1301    Parameter defining the method for finding the tracing key. If it is a scalar,
1302    then it is presumed to be the tracing key itself. If it is a CGI object, then
1303    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1304    taken from the C<TRACING> environment variable.
1305    
1306    =item RETURN
1307    
1308    Returns the key to be used for labels in emergency tracing.
1309    
1310    =back
1311    
1312    =cut
1313    
1314    sub EmergencyKey {
1315        # Get the parameters.
1316        my ($parameter) = @_;
1317        # Declare the return variable.
1318        my $retVal;
1319        # Determine the parameter type.
1320        if (! defined $parameter || defined($ENV{TRACING})) {
1321            # Here we're supposed to check the environment. If that fails, we
1322            # get the effective login ID.
1323            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1324        } else {
1325            my $ptype = ref $parameter;
1326            if ($ptype eq 'CGI') {
1327                # Here we were invoked from a web page. Look for a cookie.
1328                $retVal = $parameter->cookie('IP');
1329            } elsif (! $ptype) {
1330                # Here the key was passed in.
1331                $retVal = $parameter;
1332            }
1333        }
1334        # If no luck finding a key, use the PID.
1335        if (! defined $retVal) {
1336            $retVal = $$;
1337        }
1338        # Return the result.
1339        return $retVal;
1340    }
1341    
1342    
1343  List of command line parameters, including the option switches, which must  =head3 TraceParms
 precede the positional parameters and be prefixed by a hyphen.  
1344    
1345  =item RETURN      Tracer::TraceParms($cgi);
1346    
1347  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
1348  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.
1349  default values or overrides specified on the command line. The remaining  
1350  elements of the list are the position parameters, in order.  =over 4
1351    
1352    =item cgi
1353    
1354    CGI query object containing the parameters to trace.
1355    
1356  =back  =back
1357    
1358  =cut  =cut
1359    
1360  sub StandardSetup {  sub TraceParms {
1361      # Get the parameters.      # Get the parameters.
1362      my ($categories, $options, $parmHelp, @argv) = @_;      my ($cgi) = @_;
1363      # Get the default tracing key.      if (T(CGI => 2)) {
1364      my $tkey = EmergencyKey();          # Here we trace the GET-style URL for the script, but only if it's
1365      # Add the tracing options.          # relatively small.
1366      if (! exists $options->{trace}) {          my $url = $cgi->url(-relative => 1, -query => 1);
1367          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];          my $len = length($url);
1368      }          if ($len < 500) {
1369      $options->{sql} = [0, "turn on SQL tracing"];              Trace("[URL] $url");
1370      $options->{help} = [0, "display command-line options"];          } elsif ($len > 2048) {
1371      $options->{user} = [$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";  
1372              } else {              } else {
1373                  $traceMode = "WARN";              Trace("[URL] URL length is $len characters.");
1374              }              }
1375          }          }
1376          # Now set up the tracing.      if (T(CGI => 3)) {
1377          TSetup("$traceLevel $cats", $traceMode);          # Here we want to trace the parameter data.
1378            my @names = $cgi->param;
1379            for my $parmName (sort @names) {
1380                # Note we skip the Trace parameters, which are for our use only.
1381                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1382                    my @values = $cgi->param($parmName);
1383                    Trace("[CGI] $parmName = " . join(", ", @values));
1384      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
1385              }              }
1386              print "  $name $desc\n";          # Display the request method.
1387            my $method = $cgi->request_method();
1388            Trace("Method: $method");
1389          }          }
1390          exit(0);      if (T(CGI => 4)) {
1391            # Here we want the environment data too.
1392            for my $envName (sort keys %ENV) {
1393                Trace("[ENV] $envName = $ENV{$envName}");
1394      }      }
     # Trace the options, if applicable.  
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
1395      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
1396  }  }
1397    
1398  =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 $SetupCount;  
 }  
1399    
1400  =head3 Open      Tracer::TraceImages($htmlString);
1401    
1402  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  Trace information about all of an html document's images. The tracing
1403    will be for type "IMG" at level 3. The image's source string
1404    will be displayed. This is generally either the URL of the image or
1405    raw data for the image itself. If the source is too long, only the first 300
1406    characters will be shown at trace level 3. The entire source will be shown,
1407    however, at trace level 4. This method is not very smart, and might catch
1408    Javascript code, but it is still useful when debugging the arcane
1409    behavior of images in multiple browser environments.
1410    
1411  Open a file.  =over 4
1412    
1413  The I<$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,  
1414    
1415      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  HTML text for an outgoing web page.
1416    
1417  would open for output appended to the specified file, and  =back
1418    
1419      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =cut
1420    
1421  would open a pipe that sorts the records written and removes duplicates. Note  sub TraceImages {
1422  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.
1423  code as follows.      if (T(IMG => 3)) {
1424            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1425            # into a variable called "$htmlString". This is because we expect html strings to be
1426            # long, and don't want to copy them any more than we have to.
1427            Trace(length($_[0]) . " characters in web page.");
1428            # Loop through the HTML, culling image tags.
1429            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1430                # Extract the source string and determine whether or not it's too long.
1431                my $srcString = $1;
1432                my $pos = pos($_[0]) - length($srcString);
1433                my $excess = length($srcString) - 300;
1434                # We'll put the display string in here.
1435                my $srcDisplay = $srcString;
1436                # If it's a data string, split it at the comma.
1437                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1438                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1439                # a long string, however, we only show the first 300 characters.
1440                if ($excess > 0 && ! T(IMG => 4)) {
1441                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1442                }
1443                # Output the trace message.
1444                Trace("Image tag at position $pos:\n$srcDisplay");
1445            }
1446        }
1447    }
1448    
1449      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =head2 Command-Line Utility Methods
1450    
1451  The I<$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.  
1452    
1453      Could not open "/usr/spool/news/twitlog"      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1454    
1455  Note that the mode characters are automatically cleaned from the file name.  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1456  The actual error message from the file system will be captured and appended to the  user name, password, and API ID for the relevant account in the hash reference variable
1457  message in any case.  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1458    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1459    is C<2561022>, then the FIG_Config file must contain
1460    
1461      Could not open "/usr/spool/news/twitlog": file not found.      $phone =  { user => 'BruceTheHumanPet',
1462                    password => 'silly',
1463                    api_id => '2561022' };
1464    
1465  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
1466  corresponds to the C++ C<errno> value.  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1467    when you call this method.
1468    
1469      Could not open "/usr/spool/news/twitlog": 6.  The message ID will be returned if successful, and C<undef> if an error occurs.
1470    
1471  =over 4  =over 4
1472    
1473  =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  
1474    
1475  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
1476    would be prefixed by "1". A British phone number would be prefixed by "44".
1477    
1478  =item message (optional)  =item msg
1479    
1480  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>.  
1481    
1482  =item RETURN  =item RETURN
1483    
1484  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.  
1485    
1486  =back  =back
1487    
1488  =cut  =cut
1489    
1490  sub Open {  sub SendSMS {
1491      # Get the parameters.      # Get the parameters.
1492      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1493      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1494      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1495      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1496      if (! $rv) {      if (! defined $FIG_Config::phone) {
1497          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1498          my $sysMessage = $!;      } else {
1499          # See if we need a default message.          # Get the phone data.
1500          if (!$message) {          my $parms = $FIG_Config::phone;
1501              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1502              # filename.          my $url = "http://api.clickatell.com/http/";
1503              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1504              $message = "Could not open \"$fileName\"";          my $ua = LWP::UserAgent->new;
1505            # Request a Clickatell session.
1506            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1507                                         password => $parms->{password},
1508                                         api_id => $parms->{api_id},
1509                                         to => $phoneNumber,
1510                                         text => $msg});
1511            # Check for an error.
1512            if (! $resp->is_success) {
1513                Trace("Alert failed.") if T(1);
1514            } else {
1515                # Get the message ID.
1516                my $rstring = $resp->content;
1517                if ($rstring =~ /^ID:\s+(.*)$/) {
1518                    $retVal = $1;
1519                } else {
1520                    Trace("Phone attempt failed with $rstring") if T(1);
1521          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1522      }      }
1523      # Return the file handle.      }
1524      return $fileHandle;      # Return the result.
1525        return $retVal;
1526  }  }
1527    
1528  =head3 FindNamePart  =head3 StandardSetup
1529    
1530  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1531    
1532  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1533    values are a hash of the command-line options and a list of the positional
1534    parameters. Tracing is automatically set up and the command-line options are
1535    validated.
1536    
1537  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
1538  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>.  
1539    
1540      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1541      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1542      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1543    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1544    
1545  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1546  whole incoming string.  
1547    This would cause trace messages in the specified three packages to appear in
1548    the output. There are two special tracing categories that are automatically
1549    handled by this method. In other words, if you used L</TSetup> you would need
1550    to include these categories manually, but if you use this method they are turned
1551    on automatically.
1552    
1553  =over 4  =over 4
1554    
1555  =item fileSpec  =item SQL
1556    
1557  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1558    
1559  =item RETURN  =item Tracer
1560    
1561  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.  
1562    
1563  =back  =back
1564    
1565  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1566  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1567  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1568      # Get the parameters.  all tracing at level 3.
     my ($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, $flag); >>  
1569    
1570  Open a directory and return all the file names. This function essentially performs      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
 the functions of an C<opendir> and C<readdir>. If the I<$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,  
1571    
1572      my @files = OpenDir("/Volumes/fig/contigs", 1);  Standard tracing is output to the standard output and echoed to the file
1573    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1574    process ID. You can also specify the C<user> parameter to put a user ID
1575    instead of a process ID in the trace file name. So, for example
1576    
1577  is effectively the same as  The default trace level is 2. To get all messages, specify a trace level of 4.
1578    For a genome-by-genome update, use 3.
1579    
1580      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);  
1581    
1582  Similarly, the following code  would send the trace output to C<traceBruce.log> in the temporary directory.
1583    
1584      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  The I<options> parameter is a reference to a hash containing the command-line
1585    options, their default values, and an explanation of what they mean. Command-line
1586    options may be in the form of switches or keywords. In the case of a switch, the
1587    option value is 1 if it is specified and 0 if it is not specified. In the case
1588    of a keyword, the value is separated from the option name by an equal sign. You
1589    can see this last in the command-line example above.
1590    
1591  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  You can specify a different default trace level by setting C<$options->{trace}>
1592  automatically returns an empty list if the directory fails to open.  prior to calling this method.
1593    
1594  =over 4  An example at this point would help. Consider, for example, the command-line utility
1595    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1596    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1597    the following code.
1598    
1599  =item dirName      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1600                            { safe => [0, "use database transactions"],
1601                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1602                              start => [' ', "start with this genome"],
1603                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1604                            "<command> <transactionDirectory> <IDfile>",
1605                          @ARGV);
1606    
 Name of the directory to open.  
1607    
1608  =item filtered  The call to C<ParseCommand> specifies the default values for the options and
1609    stores the actual options in a hash that is returned as C<$options>. The
1610    positional parameters are returned in C<@parameters>.
1611    
1612  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.  
1613    
1614  =item flag      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1615    
1616  TRUE if a failure to open is okay, else FALSE  Single and double hyphens are equivalent. So, you could also code the
1617    above command as
1618    
1619  =back      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1620    
1621  =cut  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1622  #: Return Type @;  parameters, and would find themselves in I<@parameters> after executing the
1623  sub OpenDir {  above code fragment. The tracing would be set to level 2, and the categories
1624      # Get the parameters.  would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1625      my ($dirName, $filtered, $flag) = @_;  and C<DocUtils> was included because it came in within the first parameter
1626      # Declare the return variable.  to this method. The I<$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 $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1627    
1628  =head3 SetLevel      { trace => 2, sql => 0, safe => 0,
1629          noAlias => 1, start => ' ', tblFiles => 0 }
1630    
1631  C<< Tracer::SetLevel($newLevel); >>  Use of C<StandardSetup> in this way provides a simple way of performing
1632    standard tracing setup and command-line parsing. Note that the caller is
1633    not even aware of the command-line switches C<-trace> and C<-sql>, which
1634    are used by this method to control the tracing. If additional tracing features
1635    need to be added in the future, they can be processed by this method without
1636    upsetting the command-line utilities.
1637    
1638  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
1639    standard and error outputs will be directed to files in the temporary
1640    directory, using the same suffix as the trace file. So, if the command
1641    line specified
1642    
1643  =over 4      -user=Bruce -background
1644    
1645  =item newLevel  then the trace output would go to C<traceBruce.log>, the standard output to
1646    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1647    simplify starting a command in the background.
1648    
1649  Proposed new trace level.  The user name is also used as the tracing key for L</Emergency Tracing>.
1650    Specifying a value of C<E> for the trace level causes emergency tracing to
1651    be used instead of custom tracing. If the user name is not specified,
1652    the tracing key is taken from the C<Tracing> environment variable. If there
1653    is no value for that variable, the tracing key will be computed from the active
1654    login ID.
1655    
1656  =back  Since the default situation in StandardSetup is to trace to the standard
1657    output, errors that occur in command-line scripts will not generate
1658    RSS events. To force the events, use the C<warn> option.
1659    
1660  =cut      TransactFeatures -background -warn register ../xacts IDs.tbl
1661    
1662  sub SetLevel {  Finally, if the special option C<-help> is specified, the option
1663      $TraceLevel = $_[0];  names will be traced at level 0 and the program will exit without processing.
1664  }  This provides a limited help capability. For example, if the user enters
1665    
1666  =head3 Now      TransactFeatures -help
1667    
1668  C<< my $string = Tracer::Now(); >>  he would see the following output.
1669    
1670  Return a displayable time stamp containing the local time.      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1671            -trace    tracing level (default E)
1672            -sql      trace SQL commands
1673            -safe     use database transactions
1674            -noAlias  do not expect aliases in CHANGE transactions
1675            -start    start with this genome
1676            -tblFiles output TBL files containing the corrected IDs
1677            -forked   do not erase the trace file before tracing
1678    
1679  =cut  The caller has the option of modifying the tracing scheme by placing a value
1680    for C<trace> in the incoming options hash. The default value can be overridden,
1681    or the tracing to the standard output can be turned off by suffixing a minus
1682    sign to the trace level. So, for example,
1683    
1684  sub Now {      { trace => [0, "tracing level (default 0)"],
1685      my ($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 $retVal;  
 }  
1686    
1687  # Pad a number to 2 digits.  would set the default trace level to 0 instead of E, while
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1688    
1689  =head3 ParseTraceDate      { trace => ["2-", "tracing level (default 2)"],
1690           ...
1691    
1692  C<< my $time = Tracer::ParseTraceDate($dateString); >>  would set the default to 2, but trace only to the log file, not to the
1693    standard output.
1694    
1695  Convert a date from the trace file into a PERL timestamp.  The parameters to this method are as follows.
1696    
1697  =over 4  =over 4
1698    
1699  =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.  
1700    
1701  =back  Reference to a list of tracing category names. These should be names of
1702    packages whose internal workings will need to be debugged to get the
1703    command working.
1704    
1705  =cut  =item options
1706    
1707  sub ParseTraceDate {  Reference to a hash containing the legal options for the current command mapped
1708      # Get the parameters.  to their default values and descriptions. The user can override the defaults
1709      my ($dateString) = @_;  by specifying the options as command-line switches prefixed by a hyphen.
1710      # Declare the return variable.  Tracing-related options may be added to this hash. If the C<-h> option is
1711      my $retVal;  specified on the command line, the option descriptions will be used to
1712      # Parse the date.  explain the options. To turn off tracing to the standard output, add a
1713      if ($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 $retVal;  
 }  
1714    
1715  =head3 LogErrors  =item parmHelp
1716    
1717  C<< Tracer::LogErrors($fileName); >>  A string that vaguely describes the positional parameters. This is used
1718    if the user specifies the C<-h> option.
1719    
1720  Route the standard error output to a log file.  =item argv
1721    
1722  =over 4  List of command line parameters, including the option switches, which must
1723    precede the positional parameters and be prefixed by a hyphen.
1724    
1725  =item fileName  =item RETURN
1726    
1727  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
1728    maps the command-line option switches to their values. These will either be the
1729    default values or overrides specified on the command line. The remaining
1730    elements of the list are the position parameters, in order.
1731    
1732  =back  =back
1733    
1734  =cut  =cut
1735    
1736  sub LogErrors {  sub StandardSetup {
1737      # Get the file name.      # Get the parameters.
1738      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1739      # Open the file as the standard error output.      # Get the default tracing key.
1740      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1741        # Save the command line.
1742        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1743        # Add the tracing options.
1744        if (! exists $options->{trace}) {
1745            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1746        }
1747        if (! exists $options->{forked}) {
1748            $options->{forked} = [0, "keep old trace file"];
1749        }
1750        $options->{sql} = [0, "turn on SQL tracing"];
1751        $options->{help} = [0, "display command-line options"];
1752        $options->{user} = [$tkey, "tracing key"];
1753        $options->{background} = [0, "spool standard and error output"];
1754        $options->{warn} = [0, "send errors to RSS feed"];
1755        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1756        # Create a parsing hash from the options hash. The parsing hash
1757        # contains the default values rather than the default value
1758        # and the description. While we're at it, we'll memorize the
1759        # length of the longest option name.
1760        my $longestName = 0;
1761        my %parseOptions = ();
1762        for my $key (keys %{$options}) {
1763            if (length $key > $longestName) {
1764                $longestName = length $key;
1765            }
1766            $parseOptions{$key} = $options->{$key}->[0];
1767        }
1768        # Parse the command line.
1769        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1770        # Get the logfile suffix.
1771        my $suffix = $retOptions->{user};
1772        # We'll put the trace file name in here. We need it later if background
1773        # mode is on.
1774        my $traceFileName;
1775        # Now we want to set up tracing. First, we need to know if the user
1776        # wants emergency tracing.
1777        if ($retOptions->{trace} eq 'E') {
1778            ETracing($retOptions->{user});
1779        } else {
1780            # Here the tracing is controlled from the command line.
1781            my @cats = @{$categories};
1782            if ($retOptions->{sql}) {
1783                push @cats, "SQL";
1784            }
1785            if ($retOptions->{warn}) {
1786                push @cats, "Feed";
1787            }
1788            # Add the default categories.
1789            push @cats, "Tracer";
1790            # Check for more tracing groups.
1791            if ($retOptions->{moreTracing}) {
1792                push @cats, split /,/, $retOptions->{moreTracing};
1793            }
1794            # Next, we create the category string by joining the categories.
1795            my $cats = join(" ", @cats);
1796            # Check to determine whether or not the caller wants to turn off tracing
1797            # to the standard output.
1798            my $traceLevel = $retOptions->{trace};
1799            my $textOKFlag = 1;
1800            if ($traceLevel =~ /^(.)-/) {
1801                $traceLevel = $1;
1802                $textOKFlag = 0;
1803            }
1804            # Now we set up the trace mode.
1805            my $traceMode;
1806            # Verify that we can open a file in the FIG temporary directory.
1807            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1808            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1809            if (open TESTTRACE, "$traceFileSpec") {
1810                # Here we can trace to a file.
1811                $traceMode = ">>$traceFileName";
1812                if ($textOKFlag) {
1813                    # Echo to standard output if the text-OK flag is set.
1814                    $traceMode = "+$traceMode";
1815                }
1816                # Close the test file.
1817                close TESTTRACE;
1818            } else {
1819                # Here we can't trace to a file. Complain about this.
1820                warn "Could not open trace file $traceFileName: $!\n";
1821                # We trace to the standard output if it's
1822                # okay, and the error log otherwise.
1823                if ($textOKFlag) {
1824                    $traceMode = "TEXT";
1825                } else {
1826                    $traceMode = "WARN";
1827                }
1828            }
1829            # Now set up the tracing.
1830            TSetup("$traceLevel $cats", $traceMode);
1831        }
1832        # Check for background mode.
1833        if ($retOptions->{background}) {
1834            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1835            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1836            # Spool the output.
1837            open STDOUT, ">$outFileName";
1838            # If we have a trace file, trace the errors to the log. Otherwise,
1839            # spool the errors.
1840            if (defined $traceFileName) {
1841                open STDERR, "| Tracer $traceFileName";
1842            } else {
1843                open STDERR, ">$errFileName";
1844            }
1845            # Check for phone support. If we have phone support and a phone number,
1846            # we want to turn it on.
1847            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1848                $retOptions->{phone} = $ENV{PHONE};
1849            }
1850        }
1851        # Check for the "help" option. If it is specified, dump the command-line
1852        # options and exit the program.
1853        if ($retOptions->{help}) {
1854            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1855            print "$1 [options] $parmHelp\n";
1856            for my $key (sort keys %{$options}) {
1857                my $name = Pad($key, $longestName, 0, ' ');
1858                my $desc = $options->{$key}->[1];
1859                if ($options->{$key}->[0]) {
1860                    $desc .= " (default " . $options->{$key}->[0] . ")";
1861                }
1862                print "  $name $desc\n";
1863            }
1864            exit(0);
1865        }
1866        # Trace the options, if applicable.
1867        if (T(3)) {
1868            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1869            Trace("Selected options: " . join(", ", sort @parms) . ".");
1870        }
1871        # Return the parsed parameters.
1872        return ($retOptions, @retParameters);
1873  }  }
1874    
1875  =head3 ReadOptions  =head3 ReadOptions
1876    
1877  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1878    
1879  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
1880  format  format
# Line 1069  Line 1935 
1935    
1936  =head3 GetOptions  =head3 GetOptions
1937    
1938  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1939    
1940  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
1941  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 1944 
1944    
1945  Consider the following example.  Consider the following example.
1946    
1947  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1948    
1949  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1950  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1952 
1952  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1953  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1954    
1955  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1956    
1957  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1958    
# Line 1130  Line 1996 
1996    
1997  =head3 MergeOptions  =head3 MergeOptions
1998    
1999  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
2000    
2001  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
2002  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 2028 
2028      }      }
2029  }  }
2030    
2031  =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); >>  
2032    
2033      or      my $optionString = Tracer::UnparseOptions(\%options);
   
 C<< my $switch = T($traceLevel); >>  
2034    
2035  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
2036  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
2037    produce the same ultimate result when parsed by L</StandardSetup>.
2038    
2039  =over 4  =over 4
2040    
2041  =item category  =item options
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2042    
2043  Relevant tracing level.  Reference to a hash of options to convert into an option string.
2044    
2045  =item RETURN  =item RETURN
2046    
2047  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
2048    parsed by L</StandardSetup>.
2049    
2050  =back  =back
2051    
2052  =cut  =cut
2053    
2054  sub T {  sub UnparseOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2055          # Get the parameters.          # Get the parameters.
2056          my ($category, $traceLevel) = @_;      my ($options) = @_;
2057          if (!defined $traceLevel) {      # The option segments will be put in here.
2058              # Here we have no category, so we need to get the calling package.      my @retVal = ();
2059              # The calling package is normally the first parameter. If it is      # Loop through the options.
2060              # omitted, the first parameter will be the tracelevel. So, the      for my $key (keys %$options) {
2061              # first thing we do is shift the so-called category into the          # Get the option value.
2062              # $traceLevel variable where it belongs.          my $value = $options->{$key};
2063              $traceLevel = $category;          # Only use it if it's nonempty.
2064              my ($package, $fileName, $line) = caller;          if (defined $value && $value ne "") {
2065              # If there is no calling package, we default to "main".              my $segment = "--$key=$value";
2066              if (!$package) {              # Quote it if necessary.
2067                  $category = "main";              if ($segment =~ /[ |<>*]/) {
2068              } else {                  $segment = '"' . $segment . '"';
                 $category = $package;  
             }  
2069          }          }
2070          # Save the category name.              # Add it to the return list.
2071          $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.");  
2072          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2073      }      }
2074      # Return the computed result.      # Return the result.
2075      return $retVal;      return join(" ", @retVal);
2076  }  }
2077    
2078  =head3 ParseCommand  =head3 ParseCommand
2079    
2080  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2081    
2082  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2083  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2084  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2085  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2086    
2087  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2088    
2089  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2090  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2091    
2092  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2093    
2094  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2095    
2096  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2097    
2098  and C<@arguments> will contain  and C<@arguments> will contain
2099    
2100  C<< apple orange rutabaga >>      apple orange rutabaga
2101    
2102  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2103  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 2151 
2151      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2152  }  }
2153    
 =head3 Escape  
2154    
2155  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2156    
2157  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2158  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2159  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2160    
2161        or
2162    
2163        my $fileContents = Tracer::GetFile($fileName);
2164    
2165    Return the entire contents of a file. In list context, line-ends are removed and
2166    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2167    
2168  =over 4  =over 4
2169    
2170  =item realString  =item fileName
2171    
2172  String to escape.  Name of the file to read.
2173    
2174  =item RETURN  =item RETURN
2175    
2176  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2177    In a scalar context, returns the entire file as a string. If an error occurs opening
2178    the file, an empty list will be returned.
2179    
2180  =back  =back
2181    
2182  =cut  =cut
2183    
2184  sub Escape {  sub GetFile {
2185      # Get the parameter.      # Get the parameters.
2186      my ($realString) = @_;      my ($fileName) = @_;
2187      # Initialize the return variable.      # Declare the return variable.
2188      my $retVal = "";      my @retVal = ();
2189      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2190      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2191          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2192          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2193              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2194              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2195              $retVal .= $1;          $lineCount++;
2196              # Strip the processed section off the real string.          $line = Strip($line);
2197              $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;  
2198              }              }
2199        # Close it.
2200        close $handle;
2201        my $actualLines = @retVal;
2202        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2203        # Return the file's contents in the desired format.
2204        if (wantarray) {
2205            return @retVal;
2206          } else {          } else {
2207              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2208      }      }
     # Return the result.  
     return $retVal;  
2209  }  }
2210    
2211  =head3 UnEscape  =head3 PutFile
2212    
2213  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2214    
2215  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2216    
2217  =over 4  =over 4
2218    
2219  =item codedString  =item fileName
2220    
2221  String to un-escape.  Name of the output file.
2222    
2223  =item RETURN  =item lines
2224    
2225  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2226  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2227    modification.
2228    
2229  =back  =back
2230    
2231  =cut  =cut
2232    
2233  sub UnEscape {  sub PutFile {
2234      # Get the parameter.      # Get the parameters.
2235      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2236      # Initialize the return variable.      # Open the output file.
2237      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2238      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2239      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2240          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2241          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2242          # "\<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;  
                 }  
2243              } else {              } else {
2244                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2245                  # transferred unmodified.          my $count = 0;
2246                  $retVal .= $codedString;          for my $line (@{$lines}) {
2247                  $codedString = "";              print $handle "$line\n";
2248              }              $count++;
2249          }          }
2250            Trace("$count lines put to file $fileName.") if T(File => 3);
2251      }      }
2252      # Return the result.      # Close the output file.
2253      return $retVal;      close $handle;
2254  }  }
2255    
2256  =head3 ParseRecord  =head3 ParseRecord
2257    
2258  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2259    
2260  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
2261  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 2300 
2300    
2301  =head3 Merge  =head3 Merge
2302    
2303  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2304    
2305  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2306    
# Line 1567  Line 2346 
2346      return @inputList;      return @inputList;
2347  }  }
2348    
2349  =head3 Percent  =head3 Open
2350    
2351  C<< my $percent = Tracer::Percent($number, $base); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2352    
2353  Returns the percent of the base represented by the given number. If the base  Open a file.
2354  is zero, returns zero.  
2355    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2356    function. The mode is specified using Unix-like shell information. So, for
2357    example,
2358    
2359        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2360    
2361    would open for output appended to the specified file, and
2362    
2363        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2364    
2365    would open a pipe that sorts the records written and removes duplicates. Note
2366    the use of file handle syntax in the Open call. To use anonymous file handles,
2367    code as follows.
2368    
2369        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2370    
2371    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2372    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2373    failed open will throw an exception and the third parameter will be used to construct
2374    an error message. If the parameter is omitted, a standard message is constructed
2375    using the file spec.
2376    
2377        Could not open "/usr/spool/news/twitlog"
2378    
2379    Note that the mode characters are automatically cleaned from the file name.
2380    The actual error message from the file system will be captured and appended to the
2381    message in any case.
2382    
2383        Could not open "/usr/spool/news/twitlog": file not found.
2384    
2385    In some versions of PERL the only error message we get is a number, which
2386    corresponds to the C++ C<errno> value.
2387    
2388        Could not open "/usr/spool/news/twitlog": 6.
2389    
2390  =over 4  =over 4
2391    
2392  =item number  =item fileHandle
2393    
2394  Percent numerator.  File handle. If this parameter is C<undef>, a file handle will be generated
2395    and returned as the value of this method.
2396    
2397  =item base  =item fileSpec
2398    
2399  Percent base.  File name and mode, as per the PERL C<open> function.
2400    
2401    =item message (optional)
2402    
2403    Error message to use if the open fails. If omitted, a standard error message
2404    will be generated. In either case, the error information from the file system
2405    is appended to the message. To specify a conditional open that does not throw
2406    an error if it fails, use C<0>.
2407    
2408  =item RETURN  =item RETURN
2409    
2410  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
2411    open failed.
2412    
2413  =back  =back
2414    
2415  =cut  =cut
2416    
2417  sub Percent {  sub Open {
2418      # Get the parameters.      # Get the parameters.
2419      my ($number, $base) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2420      # Declare the return variable.      # Attempt to open the file.
2421      my $retVal = 0;      my $rv = open $fileHandle, $fileSpec;
2422      # Compute the percent.      # If the open failed, generate an error message.
2423      if ($base != 0) {      if (! $rv) {
2424          $retVal = $number * 100 / $base;          # Save the system error message.
2425            my $sysMessage = $!;
2426            # See if we need a default message.
2427            if (!$message) {
2428                # Clean any obvious mode characters and leading spaces from the
2429                # filename.
2430                my ($fileName) = FindNamePart($fileSpec);
2431                $message = "Could not open \"$fileName\"";
2432            }
2433            # Terminate with an error using the supplied message and the
2434            # error message from the file system.
2435            Confess("$message: $!");
2436        }
2437        # Return the file handle.
2438        return $fileHandle;
2439    }
2440    
2441    =head3 FindNamePart
2442    
2443        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2444    
2445    Extract the portion of a file specification that contains the file name.
2446    
2447    A file specification is the string passed to an C<open> call. It specifies the file
2448    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2449    method assumes that the file name is whatever follows the first angle bracket
2450    sequence.  So, for example, in the following strings the file name is
2451    C</usr/fig/myfile.txt>.
2452    
2453        >>/usr/fig/myfile.txt
2454        </usr/fig/myfile.txt
2455        | sort -u > /usr/fig/myfile.txt
2456    
2457    If the method cannot find a file name using its normal methods, it will return the
2458    whole incoming string.
2459    
2460    =over 4
2461    
2462    =item fileSpec
2463    
2464    File specification string from which the file name is to be extracted.
2465    
2466    =item RETURN
2467    
2468    Returns a three-element list. The first element contains the file name portion of
2469    the specified string, or the whole string if a file name cannot be found via normal
2470    methods. The second element contains the start position of the file name portion and
2471    the third element contains the length.
2472    
2473    =back
2474    
2475    =cut
2476    #: Return Type $;
2477    sub FindNamePart {
2478        # Get the parameters.
2479        my ($fileSpec) = @_;
2480        # Default to the whole input string.
2481        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2482        # Parse out the file name if we can.
2483        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2484            $retVal = $2;
2485            $len = length $retVal;
2486            $pos = (length $fileSpec) - (length $3) - $len;
2487      }      }
2488      # Return the result.      # Return the result.
2489      return $retVal;      return ($retVal, $pos, $len);
2490  }  }
2491    
2492  =head3 GetFile  =head3 OpenDir
2493    
2494  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @files = OpenDir($dirName, $filtered, $flag);
2495    
2496      or  Open a directory and return all the file names. This function essentially performs
2497    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2498    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2499    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2500    filtered out of the return list. If the directory does not open and I<$flag> is not
2501    set, an exception is thrown. So, for example,
2502    
2503  C<< my $fileContents = Tracer::GetFile($fileName); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2504    
2505  Return the entire contents of a file. In list context, line-ends are removed and  is effectively the same as
2506  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2507        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2508        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2509    
2510    Similarly, the following code
2511    
2512        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2513    
2514    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2515    automatically returns an empty list if the directory fails to open.
2516    
2517  =over 4  =over 4
2518    
2519  =item fileName  =item dirName
2520    
2521    Name of the directory to open.
2522    
2523    =item filtered
2524    
2525  Name of the file to read.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2526    from the list, else FALSE.
2527    
2528  =item RETURN  =item flag
2529    
2530  In a list context, returns the entire file as a list with the line terminators removed.  TRUE if a failure to open is okay, else FALSE
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2531    
2532  =back  =back
2533    
2534  =cut  =cut
2535    #: Return Type @;
2536  sub GetFile {  sub OpenDir {
2537      # Get the parameters.      # Get the parameters.
2538      my ($fileName) = @_;      my ($dirName, $filtered, $flag) = @_;
2539      # Declare the return variable.      # Declare the return variable.
2540      my @retVal = ();      my @retVal = ();
2541      # Open the file for input.      # Open the directory.
2542      my $handle = Open(undef, "<$fileName");      if (opendir(my $dirHandle, $dirName)) {
2543      # Read the whole file into the return variable, stripping off any terminator          # The directory opened successfully. Get the appropriate list according to the
2544      # characters.          # strictures of the filter parameter.
2545      my $lineCount = 0;          if ($filtered) {
2546      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;  
2547      } else {      } else {
2548          return join "\n", @retVal;              @retVal = readdir $dirHandle;
2549      }      }
2550            closedir $dirHandle;
2551        } elsif (! $flag) {
2552            # Here the directory would not open and it's considered an error.
2553            Confess("Could not open directory $dirName.");
2554        }
2555        # Return the result.
2556        return @retVal;
2557  }  }
2558    
 =head3 PutFile  
2559    
2560  C<< Tracer::PutFile($fileName, \@lines); >>  =head3 Insure
2561    
2562        Insure($dirName, $chmod);
2563    
2564  Write out a file from a list of lines of text.  Insure a directory is present.
2565    
2566  =over 4  =over 4
2567    
2568  =item fileName  =item dirName
2569    
2570  Name of the output file.  Name of the directory to check. If it does not exist, it will be created.
2571    
2572  =item lines  =item chmod (optional)
2573    
2574  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Security privileges to be given to the directory if it is created.
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
2575    
2576  =back  =back
2577    
2578  =cut  =cut
2579    
2580  sub PutFile {  sub Insure {
2581      # Get the parameters.      my ($dirName, $chmod) = @_;
2582      my ($fileName, $lines) = @_;      if (! -d $dirName) {
2583      # Open the output file.          Trace("Creating $dirName directory.") if T(2);
2584      my $handle = Open(undef, ">$fileName");          eval {
2585      # Count the lines written.              mkpath $dirName;
2586      if (ref $lines ne 'ARRAY') {              # If we have permissions specified, set them here.
2587          # Here we have a scalar, so we write it raw.              if (defined($chmod)) {
2588          print $handle $lines;                  chmod $chmod, $dirName;
2589          Trace("Scalar put to file $fileName.") if T(File => 3);              }
2590      } else {          };
2591          # Write the lines one at a time.          if ($@) {
2592          my $count = 0;              Confess("Error creating $dirName: $@");
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
             $count++;  
2593          }          }
         Trace("$count lines put to file $fileName.") if T(File => 3);  
2594      }      }
     # Close the output file.  
     close $handle;  
2595  }  }
2596    
2597  =head3 QTrace  =head3 ChDir
2598    
2599  C<< my $data = QTrace($format); >>      ChDir($dirName);
2600    
2601  Return the queued trace data in the specified format.  Change to the specified directory.
2602    
2603  =over 4  =over 4
2604    
2605  =item format  =item dirName
2606    
2607  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to which we want to change.
2608    
2609  =back  =back
2610    
2611  =cut  =cut
2612    
2613  sub QTrace {  sub ChDir {
2614      # Get the parameter.      my ($dirName) = @_;
2615      my ($format) = @_;      if (! -d $dirName) {
2616      # Create the return variable.          Confess("Cannot change to directory $dirName: no such directory.");
2617      my $retVal = "";      } else {
2618      # Only proceed if there is an actual queue.          Trace("Changing to directory $dirName.") if T(File => 4);
2619      if (@Queue) {          my $okFlag = chdir $dirName;
2620          # Process according to the format.          if (! $okFlag) {
2621          if ($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";  
2622          }          }
         # Clear the queue.  
         @Queue = ();  
2623      }      }
     # Return the formatted list.  
     return $retVal;  
2624  }  }
2625    
2626  =head3 Confess  =head3 SetPermissions
   
 C<< Confess($message); >>  
2627    
2628  Trace the call stack and abort the program with the specified message. When used with      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2629    
2630  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Set the permissions for a directory and all the files and folders inside it.
2631    In addition, the group ownership will be changed to the specified value.
2632    
2633  Will abort the program with a stack trace if the value of C<$recNum> is negative.  This method is more vulnerable than most to permission and compatability
2634    problems, so it does internal error recovery.
2635    
2636  =over 4  =over 4
2637    
2638  =item message  =item dirName
2639    
2640  Message to include in the trace.  Name of the directory to process.
2641    
2642  =back  =item group
2643    
2644  =cut  Name of the group to be assigned.
2645    
2646  sub Confess {  =item mask
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
2647    
2648  =head3 Assert  Permission mask. Bits that are C<1> in this mask will be ORed into the
2649    permission bits of any file or directory that does not already have them
2650    set to 1.
2651    
2652  C<< Assert($condition1, $condition2, ... $conditionN); >>  =item otherMasks
2653    
2654  Return TRUE if all the conditions are true. This method can be used in conjunction with  Map of search patterns to permission masks. If a directory name matches
2655  the OR operator and the L</Confess> method as a debugging assert.  one of the patterns, that directory and all its members and subdirectories
2656  So, for example  will be assigned the new pattern. For example, the following would
2657    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2658    
2659  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2660    
2661  Will abort the program with a stack trace if the value of C<$recNum> is negative.  The list is ordered, so the following would use 0777 for C<tmp1> and
2662    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2663    
2664        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2665                                                       '^tmp' => 0666);
2666    
2667    Note that the pattern matches are all case-insensitive, and only directory
2668    names are matched, not file names.
2669    
2670    =back
2671    
2672  =cut  =cut
2673  sub Assert {  
2674      my $retVal = 1;  sub SetPermissions {
2675      LOOP: for my $condition (@_) {      # Get the parameters.
2676          if (! $condition) {      my ($dirName, $group, $mask, @otherMasks) = @_;
2677              $retVal = 0;      # Set up for error recovery.
2678              last LOOP;      eval {
2679            # Switch to the specified directory.
2680            ChDir($dirName);
2681            # Get the group ID.
2682            my $gid = getgrnam($group);
2683            # Get the mask for tracing.
2684            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2685            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2686            my $fixCount = 0;
2687            my $lookCount = 0;
2688            # @dirs will be a stack of directories to be processed.
2689            my @dirs = (getcwd());
2690            while (scalar(@dirs) > 0) {
2691                # Get the current directory.
2692                my $dir = pop @dirs;
2693                # Check for a match to one of the specified directory names. To do
2694                # that, we need to pull the individual part of the name off of the
2695                # whole path.
2696                my $simpleName = $dir;
2697                if ($dir =~ m!/([^/]+)$!) {
2698                    $simpleName = $1;
2699                }
2700                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2701                # Search for a match.
2702                my $match = 0;
2703                my $i;
2704                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2705                    my $pattern = $otherMasks[$i];
2706                    if ($simpleName =~ /$pattern/i) {
2707                        $match = 1;
2708                    }
2709                }
2710                # Find out if we have a match. Note we use $i-1 because the loop added 2
2711                # before terminating due to the match.
2712                if ($match && $otherMasks[$i-1] != $mask) {
2713                    # This directory matches one of the incoming patterns, and it's
2714                    # a different mask, so we process it recursively with that mask.
2715                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2716                } else {
2717                    # Here we can process normally. Get all of the non-hidden members.
2718                    my @submems = OpenDir($dir, 1);
2719                    for my $submem (@submems) {
2720                        # Get the full name.
2721                        my $thisMem = "$dir/$submem";
2722                        Trace("Checking member $thisMem.") if T(4);
2723                        $lookCount++;
2724                        if ($lookCount % 1000 == 0) {
2725                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2726                        }
2727                        # Fix the group.
2728                        chown -1, $gid, $thisMem;
2729                        # Insure this member is not a symlink.
2730                        if (! -l $thisMem) {
2731                            # Get its info.
2732                            my $fileInfo = stat $thisMem;
2733                            # Only proceed if we got the info. Otherwise, it's a hard link
2734                            # and we want to skip it anyway.
2735                            if ($fileInfo) {
2736                                my $fileMode = $fileInfo->mode;
2737                                if (($fileMode & $mask) != $mask) {
2738                                    # Fix this member.
2739                                    $fileMode |= $mask;
2740                                    chmod $fileMode, $thisMem;
2741                                    $fixCount++;
2742                                }
2743                                # If it's a subdirectory, stack it.
2744                                if (-d $thisMem) {
2745                                    push @dirs, $thisMem;
2746                                }
2747          }          }
2748      }      }
     return $retVal;  
2749  }  }
2750                }
2751  =head3 Cluck          }
2752            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2753  C<< Cluck($message); >>      };
2754        # Check for an error.
2755  Trace the call stack. Note that for best results, you should qualify the call with a      if ($@) {
2756  trace condition. For example,          Confess("SetPermissions error: $@");
   
 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/);  
2757      }      }
2758  }  }
2759    
2760  =head3 Min  =head3 GetLine
2761    
2762  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @data = Tracer::GetLine($handle);
2763    
2764  Return the minimum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2765    
2766  =over 4  =over 4
2767    
2768  =item $value1, $value2, ... $valueN  =item handle
2769    
2770  List of numbers to compare.  Open file handle from which to read.
2771    
2772  =item RETURN  =item RETURN
2773    
2774  Returns the lowest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2775    tab-delimited. If we are at the end of the file, then an empty list will be
2776    returned. If an empty line is read, a single list item consisting of a null
2777    string will be returned.
2778    
2779  =back  =back
2780    
2781  =cut  =cut
2782    
2783  sub Min {  sub GetLine {
2784      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2785      my ($retVal, @values) = @_;      my ($handle) = @_;
2786      # Loop through the remaining parameters, looking for the lowest.      # Declare the return variable.
2787      for my $value (@values) {      my @retVal = ();
2788          if ($value < $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2789              $retVal = $value;      # Read from the file.
2790        my $line = <$handle>;
2791        # Only proceed if we found something.
2792        if (defined $line) {
2793            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2794            # upload control and have a nonstandard EOL combination.
2795            $line =~ s/(\r|\n)+$//;
2796            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2797            if (T(File => 4)) {
2798                my $escapedLine = $line;
2799                $escapedLine =~ s/\n/\\n/g;
2800                $escapedLine =~ s/\r/\\r/g;
2801                $escapedLine =~ s/\t/\\t/g;
2802                Trace("Line read: -->$escapedLine<--");
2803            }
2804            # If the line is empty, return a single empty string; otherwise, parse
2805            # it into fields.
2806            if ($line eq "") {
2807                push @retVal, "";
2808            } else {
2809                push @retVal, split /\t/,$line;
2810          }          }
2811        } else {
2812            # Trace the reason the read failed.
2813            Trace("End of file: $!") if T(File => 3);
2814      }      }
2815      # Return the minimum found.      # Return the result.
2816      return $retVal;      return @retVal;
2817  }  }
2818    
2819  =head3 Max  =head3 PutLine
2820    
2821  C<< my $max = Max($value1, $value2, ... $valueN); >>      Tracer::PutLine($handle, \@fields, $eol);
2822    
2823  Return the maximum argument. The arguments are treated as numbers.  Write a line of data to a tab-delimited file. The specified field values will be
2824    output in tab-separated form, with a trailing new-line.
2825    
2826  =over 4  =over 4
2827    
2828  =item $value1, $value2, ... $valueN  =item handle
2829    
2830  List of numbers to compare.  Output file handle.
2831    
2832  =item RETURN  =item fields
2833    
2834  Returns the highest number in the list.  List of field values.
2835    
2836    =item eol (optional)
2837    
2838    End-of-line character (default is "\n").
2839    
2840  =back  =back
2841    
2842  =cut  =cut
2843    
2844  sub Max {  sub PutLine {
2845      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2846      my ($retVal, @values) = @_;      my ($handle, $fields, $eol) = @_;
2847      # Loop through the remaining parameters, looking for the highest.      # Write the data.
2848      for my $value (@values) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
2849  }  }
2850    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
   
 Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  
 is created for the key. Otherwise, the new value is pushed onto the list.  
   
 =over 4  
2851    
2852  =item hash  =head3 PrintLine
2853    
2854  Reference to the target hash.      Tracer::PrintLine($line);
2855    
2856  =item key  Print a line of text with a trailing new-line.
2857    
2858  Key for which the value is to be added.  =over 4
2859    
2860  =item value1, value2, ... valueN  =item line
2861    
2862  List of values to add to the key's value list.  Line of text to print.
2863    
2864  =back  =back
2865    
2866  =cut  =cut
2867    
2868  sub AddToListMap {  sub PrintLine {
2869      # Get the parameters.      # Get the parameters.
2870      my ($hash, $key, @values) = @_;      my ($line) = @_;
2871      # Process according to whether or not the key already has a value.      # Print the line.
2872      if (! exists $hash->{$key}) {      print "$line\n";
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
2873  }  }
2874    
 =head3 DebugMode  
2875    
2876  C<< if (Tracer::DebugMode) { ...code... } >>  =head2 Other Useful Methods
2877    
2878    =head3 IDHASH
2879    
2880  Return TRUE if debug mode has been turned on, else abort.      my $hash = SHTargetSearch::IDHASH(@keys);
2881    
2882  Certain CGI scripts are too dangerous to exist in the production  This is a dinky little method that converts a list of values to a reference
2883  environment. This method provides a simple way to prevent them  to hash of values to labels. The values and labels are the same.
 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.  
2884    
2885  =cut  =cut
2886    
2887  sub DebugMode {  sub IDHASH {
2888      # Declare the return variable.      my %retVal = map { $_ => $_ } @_;
2889      my $retVal = 0;      return \%retVal;
     # 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;  
2890  }  }
2891    
2892  =head3 Strip  =head3 Pluralize
2893    
2894  C<< my $string = Tracer::Strip($line); >>      my $plural = Tracer::Pluralize($word);
2895    
2896  Strip all line terminators off a string. This is necessary when dealing with files  This is a very simple pluralization utility. It adds an C<s> at the end
2897  that may have been transferred back and forth several times among different  of the input word unless it already ends in an C<s>, in which case it
2898  operating environments.  adds C<es>.
2899    
2900  =over 4  =over 4
2901    
2902  =item line  =item word
2903    
2904  Line of text to be stripped.  Singular word to pluralize.
2905    
2906  =item RETURN  =item RETURN
2907    
2908  The same line of text with all the line-ending characters chopped from the end.  Returns the probable plural form of the word.
2909    
2910  =back  =back
2911    
2912  =cut  =cut
2913    
2914  sub Strip {  sub Pluralize {
2915      # Get a copy of the parameter string.      # Get the parameters.
2916      my ($string) = @_;      my ($word) = @_;
2917      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2918      # Strip the line terminator characters.      my $retVal;
2919      $retVal =~ s/(\r|\n)+$//g;      if ($word =~ /s$/) {
2920            $retVal = $word . 'es';
2921        } else {
2922            $retVal = $word . 's';
2923        }
2924      # Return the result.      # Return the result.
2925      return $retVal;      return $retVal;
2926  }  }
2927    
2928  =head3 Pad  =head3 Numeric
2929    
2930  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $okFlag = Tracer::Numeric($string);
2931    
2932  Pad a string to a specified length. The pad character will be a  Return the value of the specified string if it is numeric, or an undefined value
2933  space, and the padding will be on the right side unless specified  if it is not numeric.
 in the third parameter.  
2934    
2935  =over 4  =over 4
2936    
2937  =item string  =item string
2938    
2939  String to be padded.  String to check.
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
   
 Character to use for padding. The default is a space.  
2940    
2941  =item RETURN  =item RETURN
2942    
2943  Returns a copy of the original string with the pad character added to the  Returns the numeric value of the string if successful, or C<undef> if the string
2944  specified end so that it achieves the desired length.  is not numeric.
2945    
2946  =back  =back
2947    
2948  =cut  =cut
2949    
2950  sub Pad {  sub Numeric {
2951      # Get the parameters.      # Get the parameters.
2952      my ($string, $len, $left, $padChar) = @_;      my ($string) = @_;
2953      # Compute the padding character.      # We'll put the value in here if we succeed.
2954      if (! defined $padChar) {      my $retVal;
2955          $padChar = " ";      # Get a working copy of the string.
2956      }      my $copy = $string;
2957      # Compute the number of spaces needed.      # Trim leading and trailing spaces.
2958      my $needed = $len - length $string;      $copy =~ s/^\s+//;
2959      # Copy the string into the return variable.      $copy =~ s/\s+$//;
2960      my $retVal = $string;      # Check the result.
2961      # Only proceed if padding is needed.      if ($copy =~ /^[+-]?\d+$/) {
2962      if ($needed > 0) {          $retVal = $copy;
2963          # Create the pad string.      } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2964          my $pad = $padChar x $needed;          $retVal = $copy;
2965          # Affix it to the return value.      } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2966          if ($left) {          $retVal = $copy;
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
2967      }      }
2968      # Return the result.      # Return the result.
2969      return $retVal;      return $retVal;
2970  }  }
2971    
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
   
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
2972    
2973  from inside a CGI script, it would work fine in Unix, but would issue an error message  =head3 ParseParm
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2974    
2975      TICK("./protein.cgi")      my $listValue = Tracer::ParseParm($string);
2976    
2977  it will work correctly in both environments.  Convert a parameter into a list reference. If the parameter is undefined,
2978    an undefined value will be returned. Otherwise, it will be parsed as a
2979    comma-separated list of values.
2980    
2981  =over 4  =over 4
2982    
2983  =item commandString  =item string
2984    
2985  The command string to pass to the system.  Incoming string.
2986    
2987  =item RETURN  =item RETURN
2988    
2989  Returns the standard output from the specified command, as a list.  Returns a reference to a list of values, or C<undef> if the incoming value
2990    was undefined.
2991    
2992  =back  =back
2993    
2994  =cut  =cut
2995  #: Return Type @;  
2996  sub TICK {  sub ParseParm {
2997      # Get the parameters.      # Get the parameters.
2998      my ($commandString) = @_;      my ($string) = @_;
2999      # Chop off the dot-slash if this is Windows.      # Declare the return variable.
3000      if ($FIG_Config::win_mode) {      my $retVal;
3001          $commandString =~ s!^\./!!;      # Check for data.
3002        if (defined $string) {
3003            # We have some, so split it into a list.
3004            $retVal = [ split /\s*,\s*/, $string];
3005      }      }
3006      # Activate the command and return the result.      # Return the result.
3007      return `$commandString`;      return $retVal;
3008  }  }
3009    
3010  =head3 ScriptSetup  =head3 Now
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
   
 Perform standard tracing and debugging setup for scripts. The value returned is  
 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.  
   
 This method calls L</ETracing> to configure tracing, which allows the tracing  
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
   
 =over 4  
   
 =item noTrace (optional)  
   
 If specified, tracing will be suppressed. This is useful if the script wants to set up  
 tracing manually.  
   
 =item RETURN  
3011    
3012  Returns a two-element list consisting of a CGI query object and a variable hash for      my $string = Tracer::Now();
 the output page.  
3013    
3014  =back  Return a displayable time stamp containing the local time. Whatever format this
3015    method produces must be parseable by L</ParseDate>.
3016    
3017  =cut  =cut
3018    
3019  sub ScriptSetup {  sub Now {
3020      # Get the parameters.      return DisplayTime(time);
     my ($noTrace) = @_;  
     # Get the CGI query object.  
     my $cgi = CGI->new();  
     # Set up tracing if it's not suppressed.  
     ETracing($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
3021  }  }
3022    
3023  =head3 ETracing  =head3 DisplayTime
3024    
3025  C<< ETracing($parameter); >>      my $string = Tracer::DisplayTime($time);
3026    
3027  Set up emergency tracing. Emergency tracing is tracing that is turned  Convert a time value to a displayable time stamp. Whatever format this
3028  on automatically for any program that calls this method. The emergency  method produces must be parseable by L</ParseDate>.
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
3029    
3030  =over 4  =over 4
3031    
3032  =item parameter  =item time
3033    
3034  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.
3035  that scalar is used as the tracing key. If it is a CGI object, the  
3036  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item RETURN
3037  tracing key is taken from the C<TRACING> environment variable. If it  
3038  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.  
3039    
3040  =back  =back
3041    
3042  =cut  =cut
3043    
3044  sub ETracing {  sub DisplayTime {
3045      # Get the parameter.      my ($time) = @_;
3046      my ($parameter) = @_;      my $retVal = "(n/a)";
3047      # Check for CGI mode.      if (defined $time) {
3048      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3049      # Default to no tracing except errors.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3050      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";  
         }  
3051      }      }
3052      # 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);  
3053      }      }
3054    
3055    # Pad a number to 2 digits.
3056    sub _p2 {
3057        my ($value) = @_;
3058        $value = "0$value" if ($value < 10);
3059        return $value;
3060  }  }
3061    
3062  =head3 EmergencyFileName  =head3 Escape
3063    
3064  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $codedString = Tracer::Escape($realString);
3065    
3066  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
3067  the tracing information.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3068    result is to reverse the effect of L</UnEscape>.
3069    
3070  =over 4  =over 4
3071    
3072  =item tkey  =item realString
3073    
3074  Tracing key for the current program.  String to escape.
3075    
3076  =item RETURN  =item RETURN
3077    
3078  Returns the name of the file to contain the emergency tracing information.  Escaped equivalent of the real string.
3079    
3080  =back  =back
3081    
3082  =cut  =cut
3083    
3084  sub EmergencyFileName {  sub Escape {
3085      # Get the parameters.      # Get the parameter.
3086      my ($tkey) = @_;      my ($realString) = @_;
3087      # Compute the emergency tracing file name.      # Initialize the return variable.
3088      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal = "";
3089        # Loop through the parameter string, looking for sequences to escape.
3090        while (length $realString > 0) {
3091            # Look for the first sequence to escape.
3092            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3093                # Here we found it. The text preceding the sequence is in $1. The sequence
3094                # itself is in $2. First, move the clear text to the return variable.
3095                $retVal .= $1;
3096                # Strip the processed section off the real string.
3097                $realString = substr $realString, (length $2) + (length $1);
3098                # Get the matched character.
3099                my $char = $2;
3100                # If we have a CR, we are done.
3101                if ($char ne "\r") {
3102                    # It's not a CR, so encode the escape sequence.
3103                    $char =~ tr/\t\n/tn/;
3104                    $retVal .= "\\" . $char;
3105                }
3106            } else {
3107                # Here there are no more escape sequences. The rest of the string is
3108                # transferred unmodified.
3109                $retVal .= $realString;
3110                $realString = "";
3111            }
3112        }
3113        # Return the result.
3114        return $retVal;
3115  }  }
3116    
3117  =head3 EmergencyFileTarget  =head3 UnEscape
3118    
3119  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $realString = Tracer::UnEscape($codedString);
3120    
3121  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
3122  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
3123    be deleted.
3124    
3125  =over 4  =over 4
3126    
3127  =item tkey  =item codedString
3128    
3129  Tracing key for the current program.  String to un-escape.
3130    
3131  =item RETURN  =item RETURN
3132    
3133  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
3134    values.
3135    
3136  =back  =back
3137    
3138  =cut  =cut
3139    
3140  sub EmergencyFileTarget {  sub UnEscape {
3141      # Get the parameters.      # Get the parameter.
3142      my ($tkey) = @_;      my ($codedString) = @_;
3143      # Compute the emergency tracing file name.      # Initialize the return variable.
3144      return "$FIG_Config::temp/trace$tkey.log";      my $retVal = "";
3145        # Only proceed if the incoming string is nonempty.
3146        if (defined $codedString) {
3147            # Loop through the parameter string, looking for escape sequences. We can't do
3148            # translating because it causes problems with the escaped slash. ("\\t" becomes
3149            # "\<tab>" no matter what we do.)
3150            while (length $codedString > 0) {
3151                # Look for the first escape sequence.
3152                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3153                    # Here we found it. The text preceding the sequence is in $1. The sequence
3154                    # itself is in $2. First, move the clear text to the return variable.
3155                    $retVal .= $1;
3156                    $codedString = substr $codedString, (2 + length $1);
3157                    # Get the escape value.
3158                    my $char = $2;
3159                    # If we have a "\r", we are done.
3160                    if ($char ne 'r') {
3161                        # Here it's not an 'r', so we convert it.
3162                        $char =~ tr/\\tn/\\\t\n/;
3163                        $retVal .= $char;
3164                    }
3165                } else {
3166                    # Here there are no more escape sequences. The rest of the string is
3167                    # transferred unmodified.
3168                    $retVal .= $codedString;
3169                    $codedString = "";
3170                }
3171            }
3172        }
3173        # Return the result.
3174        return $retVal;
3175  }  }
3176    
3177  =head3 EmergencyTracingDest  =head3 Percent
3178    
3179  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my $percent = Tracer::Percent($number, $base);
3180    
3181  This method converts an emergency tracing destination to a real  Returns the percent of the base represented by the given number. If the base
3182  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.  
3183    
3184  =over 4  =over 4
3185    
3186  =item tkey  =item number
3187    
3188  Tracing key for this environment.  Percent numerator.
3189    
3190  =item myDest  =item base
3191    
3192  Destination from the emergency tracing file.  Percent base.
3193    
3194  =item RETURN  =item RETURN
3195    
3196  Returns a destination that can be passed into L</TSetup>.  Returns the percentage of the base represented by the numerator.
3197    
3198  =back  =back
3199    
3200  =cut  =cut
3201    
3202  sub EmergencyTracingDest {  sub Percent {
3203      # Get the parameters.      # Get the parameters.
3204      my ($tkey, $myDest) = @_;      my ($number, $base) = @_;
3205      # Declare the return variable.      # Declare the return variable.
3206      my $retVal;      my $retVal = 0;
3207      # Process according to the destination value.      # Compute the percent.
3208      if ($myDest eq 'FILE') {      if ($base != 0) {
3209          $retVal = ">" . EmergencyFileTarget($tkey);          $retVal = $number * 100 / $base;
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
3210      }      }
3211      # Return the result.      # Return the result.
3212      return $retVal;      return $retVal;
3213  }  }
3214    
3215  =head3 Emergency  =head3 In
3216    
3217  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $flag = Tracer::In($value, $min, $max);
3218    
3219  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.  
3220    
3221  =over 4  =cut
3222    
3223  =item tkey  sub In {
3224        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3225    }
3226    
 The tracing key. This is used to identify the control file and the trace file.  
3227    
3228  =item hours  =head3 Constrain
3229    
3230  Number of hours to keep emergency tracing alive.      my $constrained = Constrain($value, $min, $max);
3231    
3232  =item dest  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3233    
3234  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
3235    
3236  =item level  =item value
3237    
3238  Tracing level. A higher level means more trace messages.  Value to constrain.
3239    
3240  =item modules  =item min (optional)
3241    
3242  A list of the tracing modules to activate.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3243    
3244    =item max (optional)
3245    
3246    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3247    
3248    =item RETURN
3249    
3250    Returns the incoming value, constrained according to the other parameters.
3251    
3252  =back  =back
3253    
3254  =cut  =cut
3255    
3256  sub Emergency {  sub Constrain {
3257      # Get the parameters.      # Get the parameters.
3258      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($value, $min, $max) = @_;
3259      # Create the emergency file.      # Declare the return variable.
3260      my $specFile = EmergencyFileName($tkey);      my $retVal = $value;
3261      my $outHandle = Open(undef, ">$specFile");      # Apply the minimum constraint.
3262      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $min && $retVal < $min) {
3263            $retVal = $min;
3264        }
3265        # Apply the maximum constraint.
3266        if (defined $max && $retVal > $max) {
3267            $retVal = $max;
3268        }
3269        # Return the result.
3270        return $retVal;
3271  }  }
3272    
3273  =head3 EmergencyKey  =head3 Min
3274    
3275  C<< my $tkey = EmergencyKey($parameter); >>      my $min = Min($value1, $value2, ... $valueN);
3276    
3277  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.  
3278    
3279  =over 4  =over 4
3280    
3281  =item parameter  =item $value1, $value2, ... $valueN
3282    
3283  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.  
3284    
3285  =item RETURN  =item RETURN
3286    
3287  Returns the key to be used for labels in emergency tracing.  Returns the lowest number in the list.
3288    
3289  =back  =back
3290    
3291  =cut  =cut
3292    
3293  sub EmergencyKey {  sub Min {
3294      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3295      my ($parameter) = @_;      my ($retVal, @values) = @_;
3296      # Declare the return variable.      # Loop through the remaining parameters, looking for the lowest.
3297      my $retVal;      for my $value (@values) {
3298      # Determine the parameter type.          if ($value < $retVal) {
3299      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;  
         }  
3300      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3301      }      }
3302      # Return the result.      # Return the minimum found.
3303      return $retVal;      return $retVal;
3304  }  }
3305    
3306    =head3 Max
3307    
3308  =head3 TraceParms      my $max = Max($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
3309    
3310  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.  
3311    
3312  =over 4  =over 4
3313    
3314  =item cgi  =item $value1, $value2, ... $valueN
3315    
3316  CGI query object containing the parameters to trace.  List of numbers to compare.
3317    
3318    =item RETURN
3319    
3320    Returns the highest number in the list.
3321    
3322  =back  =back
3323    
3324  =cut  =cut
3325    
3326  sub TraceParms {  sub Max {
3327      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3328      my ($cgi) = @_;      my ($retVal, @values) = @_;
3329      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3330          # Here we want to trace the parameter data.      for my $value (@values) {
3331          my @names = $cgi->param;          if ($value > $retVal) {
3332          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}");  
3333          }          }
3334      }      }
3335        # Return the maximum found.
3336        return $retVal;
3337  }  }
3338    
3339  =head3 ScriptFinish  =head3 Strip
3340    
3341  C<< ScriptFinish($webData, $varHash); >>      my $string = Tracer::Strip($line);
3342    
3343  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
3344  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
3345  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.  
3346    
3347  A typical standard script would loook like the following.  =over 4
3348    
3349      BEGIN {  =item line
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3350    
3351      my ($cgi, $varHash) = ScriptSetup();  Line of text to be stripped.
3352      eval {  
3353          # ... get data from $cgi, put it in $varHash ...  =item RETURN
3354      };  
3355      if ($@) {  The same line of text with all the line-ending characters chopped from the end.
3356          Trace("Script Error: $@") if T(0);  
3357    =back
3358    
3359    =cut
3360    
3361    sub Strip {
3362        # Get a copy of the parameter string.
3363        my ($string) = @_;
3364        my $retVal = (defined $string ? $string : "");
3365        # Strip the line terminator characters.
3366        $retVal =~ s/(\r|\n)+$//g;
3367        # Return the result.
3368        return $retVal;
3369      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3370    
3371  The idea here is that even if the script fails, you'll see trace messages and  =head3 Trim
3372  useful output.  
3373        my $string = Tracer::Trim($line);
3374    
3375    Trim all spaces from the beginning and ending of a string.
3376    
3377  =over 4  =over 4
3378    
3379  =item webData  =item line
3380    
3381  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.  
3382    
3383  =item varHash (optional)  =item RETURN
3384    
3385  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.  
3386    
3387  =back  =back
3388    
3389  =cut  =cut
3390    
3391  sub ScriptFinish {  sub Trim {
3392      # Get the parameters.      # Get a copy of the parameter string.
3393      my ($webData, $varHash) = @_;      my ($string) = @_;
3394      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3395      my $outputString;      # Strip the front spaces.
3396      if (defined $varHash) {      $retVal =~ s/^\s+//;
3397          # Here we have a template file. We need to determine the template type.      # Strip the back spaces.
3398          my $template;      $retVal =~ s/\s+$//;
3399          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      # Return the result.
3400              $template = "$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 $outputString;  
3401  }  }
3402    
3403  =head3 Insure  =head3 Pad
3404    
3405  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3406    
3407  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3408    space, and the padding will be on the right side unless specified
3409    in the third parameter.
3410    
3411  =over 4  =over 4
3412    
3413  =item dirName  =item string
3414    
3415  Name of the directory to check. If it does not exist, it will be created.  String to be padded.
3416    
3417    =item len
3418    
3419    Desired length of the padded string.
3420    
3421    =item left (optional)
3422    
3423    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3424    
3425    =item padChar (optional)
3426    
3427    Character to use for padding. The default is a space.
3428    
3429    =item RETURN
3430    
3431    Returns a copy of the original string with the pad character added to the
3432    specified end so that it achieves the desired length.
3433    
3434  =back  =back
3435    
3436  =cut  =cut
3437    
3438  sub Insure {  sub Pad {
3439      my ($dirName) = @_;      # Get the parameters.
3440      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3441          Trace("Creating $dirName directory.") if T(File => 2);      # Compute the padding character.
3442          eval { mkpath $dirName; };      if (! defined $padChar) {
3443          if ($@) {          $padChar = " ";
3444              Confess("Error creating $dirName: $@");      }
3445        # Compute the number of spaces needed.
3446        my $needed = $len - length $string;
3447        # Copy the string into the return variable.
3448        my $retVal = $string;
3449        # Only proceed if padding is needed.
3450        if ($needed > 0) {
3451            # Create the pad string.
3452            my $pad = $padChar x $needed;
3453            # Affix it to the return value.
3454            if ($left) {
3455                $retVal = $pad . $retVal;
3456            } else {
3457                $retVal .= $pad;
3458          }          }
3459      }      }
3460        # Return the result.
3461        return $retVal;
3462  }  }
3463    
3464  =head3 ChDir  =head3 Quoted
3465    
3466  C<< ChDir($dirName); >>      my $string = Tracer::Quoted($var);
3467    
3468  Change to the specified directory.  Convert the specified value to a string and enclose it in single quotes.
3469    If it's undefined, the string C<undef> in angle brackets will be used
3470    instead.
3471    
3472  =over 4  =over 4
3473    
3474  =item dirName  =item var
3475    
3476  Name of the directory to which we want to change.  Value to quote.
3477    
3478    =item RETURN
3479    
3480    Returns a string enclosed in quotes, or an indication the value is undefined.
3481    
3482  =back  =back
3483    
3484  =cut  =cut
3485    
3486  sub ChDir {  sub Quoted {
3487      my ($dirName) = @_;      # Get the parameters.
3488      if (! -d $dirName) {      my ($var) = @_;
3489          Confess("Cannot change to directory $dirName: no such directory.");      # Declare the return variable.
3490        my $retVal;
3491        # Are we undefined?
3492        if (! defined $var) {
3493            $retVal = "<undef>";
3494      } else {      } else {
3495          Trace("Changing to directory $dirName.") if T(File => 4);          # No, so convert to a string and enclose in quotes.
3496          my $okFlag = chdir $dirName;          $retVal = $var;
3497          if (! $okFlag) {          $retVal =~ s/'/\\'/;
3498              Confess("Error switching to directory $dirName.");          $retVal = "'$retVal'";
         }  
3499      }      }
3500        # Return the result.
3501        return $retVal;
3502  }  }
3503    
3504  =head3 SendSMS  =head3 EOF
3505    
3506  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
3507    
3508  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3509    
3510      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3511                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3512                  api_id => '2561022' };  }
3513    
3514  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3515    
3516  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
3517    
3518  =over 4  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3519    dot-slash (C<./> will be removed. So, for example, if you were doing
3520    
3521  =item phoneNumber      `./protein.cgi`
3522    
3523  Phone number to receive the message, in international format. A United States phone number  from inside a CGI script, it would work fine in Unix, but would issue an error message
3524  would be prefixed by "1". A British phone number would be prefixed by "44".  in Windows complaining that C<'.'> is not a valid command. If instead you code
3525    
3526  =item msg      TICK("./protein.cgi")
3527    
3528  Message to send to the specified phone.  it will work correctly in both environments.
3529    
3530    =over 4
3531    
3532    =item commandString
3533    
3534    The command string to pass to the system.
3535    
3536  =item RETURN  =item RETURN
3537    
3538  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
3539    
3540  =back  =back
3541    
3542  =cut  =cut
3543    #: Return Type @;
3544  sub SendSMS {  sub TICK {
3545      # Get the parameters.      #