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revision 1.84, Thu May 3 12:28:00 2007 UTC revision 1.115, Mon Jan 19 20:50:17 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 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 and write it to the standard output.
492            my $escapedMessage = CGI::escapeHTML($stripped);
493            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
494        } elsif ($Destination =~ m/^>>/) {
495            # Write the trace message to an output file.
496            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
497            # Lock the file.
498            flock TRACING, LOCK_EX;
499            print TRACING "$formatted\n";
500            close TRACING;
501            # If the Tee flag is on, echo it to the standard output.
502            if ($TeeFlag) {
503                print "$formatted\n";
504            }
505        }
506    }
507    
508  would set the default to 2, but trace only to the log file, not to the  =head3 TraceDump
 standard output.  
509    
510  The parameters to this method are as follows.      TraceDump($title, $object);
511    
512  =over 4  Dump an object to the trace log. This method simply calls the C<Dumper>
513    function, but routes the output to the trace log instead of returning it
514    as a string. The output is arranged so that it comes out monospaced when
515    it appears in an HTML trace dump.
516    
517  =item categories  =over 4
518    
519  Reference to a list of tracing category names. These should be names of  =item title
 packages whose internal workings will need to be debugged to get the  
 command working.  
520    
521  =item options  Title to give to the object being dumped.
522    
523  Reference to a hash containing the legal options for the current command mapped  =item object
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
524    
525  =item parmHelp  Reference to a list, hash, or object to dump.
526    
527  A string that vaguely describes the positional parameters. This is used  =back
 if the user specifies the C<-h> option.  
528    
529  =item argv  =cut
530    
531    sub TraceDump {
532        # Get the parameters.
533        my ($title, $object) = @_;
534        # Trace the object.
535        Trace("Object dump for $title:\n" . Dumper($object));
536    }
537    
538    =head3 T
539    
540        my $switch = T($category, $traceLevel);
541    
542        or
543    
544        my $switch = T($traceLevel);
545    
546    Return TRUE if the trace level is at or above a specified value and the specified category
547    is active, else FALSE. If no category is specified, the caller's package name is used.
548    
549    =over 4
550    
551    =item category
552    
553    Category to which the message belongs. If not specified, the caller's package name is
554    used.
555    
556    =item traceLevel
557    
558    Relevant tracing level.
559    
560    =item RETURN
561    
562    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
563    
564    =back
565    
566    =cut
567    
568    sub T {
569        # Declare the return variable.
570        my $retVal = 0;
571        # Only proceed if tracing is turned on.
572        if ($Destination ne "NONE") {
573            # Get the parameters.
574            my ($category, $traceLevel) = @_;
575            if (!defined $traceLevel) {
576                # Here we have no category, so we need to get the calling package.
577                # The calling package is normally the first parameter. If it is
578                # omitted, the first parameter will be the tracelevel. So, the
579                # first thing we do is shift the so-called category into the
580                # $traceLevel variable where it belongs.
581                $traceLevel = $category;
582                my ($package, $fileName, $line) = caller;
583                # If there is no calling package, we default to "main".
584                if (!$package) {
585                    $category = "main";
586                } else {
587                    my @cats = split /::/, $package;
588                    $category = $cats[$#cats];
589                }
590            }
591            # Save the category name and level.
592            $LastCategory = $category;
593            $LastLevel = $traceLevel;
594            # Convert it to lower case before we hash it.
595            $category = lc $category;
596            # Validate the trace level.
597            if (ref $traceLevel) {
598                Confess("Bad trace level.");
599            } elsif (ref $TraceLevel) {
600                Confess("Bad trace config.");
601            }
602            # Make the check. Note that level 0 shows even if the category is turned off.
603            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
604        }
605        # Return the computed result.
606        return $retVal;
607    }
608    
609    =head3 QTrace
610    
611        my $data = QTrace($format);
612    
613    Return the queued trace data in the specified format.
614    
615    =over 4
616    
617    =item format
618    
619    C<html> to format the data as an HTML list, C<text> to format it as straight text.
620    
621    =back
622    
623    =cut
624    
625    sub QTrace {
626        # Get the parameter.
627        my ($format) = @_;
628        # Create the return variable.
629        my $retVal = "";
630        # Only proceed if there is an actual queue.
631        if (@Queue) {
632            # Process according to the format.
633            if ($format =~ m/^HTML$/i) {
634                # Convert the queue into an HTML list.
635                $retVal = "<ul>\n";
636                for my $line (@Queue) {
637                    my $escapedLine = CGI::escapeHTML($line);
638                    $retVal .= "<li>$escapedLine</li>\n";
639                }
640                $retVal .= "</ul>\n";
641            } elsif ($format =~ m/^TEXT$/i) {
642                # Convert the queue into a list of text lines.
643                $retVal = join("\n", @Queue) . "\n";
644            }
645            # Clear the queue.
646            @Queue = ();
647        }
648        # Return the formatted list.
649        return $retVal;
650    }
651    
652    =head3 Confess
653    
654        Confess($message);
655    
656    Trace the call stack and abort the program with the specified message. When used with
657    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
658    So, for example
659    
660        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
661    
662    Will abort the program with a stack trace if the value of C<$recNum> is negative.
663    
664    =over 4
665    
666    =item message
667    
668    Message to include in the trace.
669    
670    =back
671    
672    =cut
673    
674    sub Confess {
675        # Get the parameters.
676        my ($message) = @_;
677        # Set up the category and level.
678        $LastCategory = "(confess)";
679        $LastLevel = 0;
680        # Trace the call stack.
681        Cluck($message);
682        # Abort the program.
683        croak(">>> $message");
684    }
685    
686    =head3 SaveCGI
687    
688        Tracer::SaveCGI($cgi);
689    
690    This method saves the CGI object but does not activate emergency tracing.
691    It is used to allow L</Warn> to work in situations where emergency
692    tracing is contra-indicated (e.g. the wiki).
693    
694    =over 4
695    
696    =item cgi
697    
698    Active CGI query object.
699    
700    =back
701    
702    =cut
703    
704    sub SaveCGI {
705        $SavedCGI = $_[0];
706    }
707    
708    =head3 Warn
709    
710        Warn($message, @options);
711    
712    This method traces an important message. If an RSS feed is configured
713    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
714    then the message will be echoed to the feed. In general, a tracing
715    destination of C<WARN> indicates that the caller is running as a web
716    service in a production environment; however, this is not a requirement.
717    
718    To force warnings into the RSS feed even when the tracing destination
719    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
720    configured automatically when L</StandardSetup> is used.
721    
722    The L</Cluck> method calls this one for its final message. Since
723    L</Confess> calls L</Cluck>, this means that any error which is caught
724    and confessed will put something in the feed. This insures that someone
725    will be alerted relatively quickly when a failure occurs.
726    
727    =over 4
728    
729    =item message
730    
731    Message to be traced.
732    
733    =item options
734    
735    A list containing zero or more options.
736    
737    =back
738    
739    The permissible options are as follows.
740    
741    =over 4
742    
743    =item noStack
744    
745    If specified, then the stack trace is not included in the output.
746    
747    =back
748    
749    =cut
750    
751    sub Warn {
752        # Get the parameters.
753        my $message = shift @_;
754        my %options = map { $_ => 1 } @_;
755        # Save $@;
756        my $savedError = $@;
757        # Trace the message.
758        Trace($message);
759        # This will contain the lock handle. If it's defined, it means we need to unlock.
760        my $lock;
761        # Check for feed forcing.
762        my $forceFeed = exists $Categories{feed};
763        # An error here would be disastrous. Note that if debug mode is specified,
764        # we do this stuff even in a test environment.
765        eval {
766            # Do we need to put this in the RSS feed?
767            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
768                # Probably. We need to check first, however, to see if it's from an
769                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
770                my $key = "127.0.0.1";
771                if (defined $SavedCGI) {
772                    # Get the IP address.
773                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
774                }
775                # Is the IP address in the ignore list?
776                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
777                if (! $found) {
778                    # No. We're good. We now need to compute the date, the link, and the title.
779                    # First, the date, in a very specific format.
780                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
781                        (tz_local_offset() / 30);
782                    # Environment data goes in here. We start with the date.
783                    my $environment = "$date.  ";
784                    # If we need to recap the message (because it's too long to be a title), we'll
785                    # put it in here.
786                    my $recap;
787                    # Copy the message and remove excess space.
788                    my $title = $message;
789                    $title =~ s/\s+/ /gs;
790                    # If it's too long, we have to split it up.
791                    if (length $title > 60) {
792                        # Put the full message in the environment string.
793                        $recap = $title;
794                        # Excerpt it as the title.
795                        $title = substr($title, 0, 50) . "...";
796                    }
797                    # If we have a CGI object, then this is a web error. Otherwise, it's
798                    # command-line.
799                    if (defined $SavedCGI) {
800                        # We're in a web service. The environment is the user's IP, and the link
801                        # is the URL that got us here.
802                        $environment .= "Event Reported at IP address $key process $$.";
803                        my $url = $SavedCGI->self_url();
804                        # We need the user agent string and (if available) the referrer.
805                        # The referrer will be the link.
806                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
807                        if ($ENV{HTTP_REFERER}) {
808                            my $link = $ENV{HTTP_REFERER};
809                            $environment .= " referred from <a href=\"$link\">$link</a>.";
810                        } else {
811                            $environment .= " referrer unknown.";
812                        }
813                        # Close off the sentence with the original link.
814                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
815                    } else {
816                        # No CGI object, so we're a command-line tool. Use the tracing
817                        # key and the PID as the user identifier, and add the command.
818                        my $key = EmergencyKey();
819                        $environment .= "Event Reported by $key process $$.";
820                        if ($CommandLine) {
821                            # We're in a StandardSetup script, so we have the real command line.
822                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
823                        } elsif ($ENV{_}) {
824                            # We're in a BASH script, so the command has been stored in the _ variable.
825                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
826                        }
827                    }
828                    # Build a GUID. We use the current time, the title, and the process ID,
829                    # then digest the result.
830                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
831                    # Finally, the description. This is a stack trace plus various environmental stuff.
832                    # The trace is optional.
833                    my $stackTrace;
834                    if ($options{noStack}) {
835                        $stackTrace = "";
836                    } else {
837                        my @trace = LongMess();
838                        # Only proceed if we got something back.
839                        if (scalar(@trace) > 0) {
840                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
841                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
842                        }
843                    }
844                    # We got the stack trace. Now it's time to put it all together.
845                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
846                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
847                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
848                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
849                    # our <br>s and <pre>s are used to format the description.
850                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
851                    my $description = "$recap$environment  $stackTrace";
852                    # Okay, we have all the pieces. Create a hash of the new event.
853                    my $newItem = { title => $title,
854                                    description => $description,
855                                    category => $LastCategory,
856                                    pubDate => $date,
857                                    guid => $guid,
858                                  };
859                    # We need XML capability for this.
860                    require XML::Simple;
861                    # The RSS document goes in here.
862                    my $rss;
863                    # Get the name of the RSS file. It's in the FIG temporary directory.
864                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
865                    # Open the config file and lock it.
866                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
867                    flock $lock, LOCK_EX;
868                    # Does it exist?
869                    if (-s $fileName) {
870                        # Slurp it in.
871                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
872                    } else {
873                        my $size = -s $fileName;
874                        # Create an empty channel.
875                        $rss = {
876                            channel => {
877                                title => 'NMPDR Warning Feed',
878                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
879                                description => "Important messages regarding the status of the NMPDR.",
880                                generator => "NMPDR Trace Facility",
881                                docs => "http://blogs.law.harvard.edu/tech/rss",
882                                item => []
883                            },
884                        };
885                    }
886                    # Get the channel object.
887                    my $channel = $rss->{channel};
888                    # Update the last-build date.
889                    $channel->{lastBuildDate} = $date;
890                    # Get the item array.
891                    my $items = $channel->{item};
892                    # Insure it has only 100 entries.
893                    while (scalar @{$items} > 100) {
894                        pop @{$items};
895                    }
896                    # Add our new item at the front.
897                    unshift @{$items}, $newItem;
898                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
899                    # the requirements for those.
900                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
901                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
902                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
903                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
904                    # We don't use Open here because we can't afford an error.
905                    if (open XMLOUT, ">$fileName") {
906                        print XMLOUT $xml;
907                        close XMLOUT;
908                    }
909                }
910            }
911        };
912        if ($@) {
913            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
914            # (which is a good thing).
915            my $error = $@;
916            Trace("Feed Error: $error") if T(Feed => 0);
917        }
918        # Be sure to unlock.
919        if ($lock) {
920            flock $lock, LOCK_UN;
921            undef $lock;
922        }
923        # Restore the error message.
924        $@ = $savedError;
925    }
926    
927    
928    
929    
930    =head3 Assert
931    
932        Assert($condition1, $condition2, ... $conditionN);
933    
934    Return TRUE if all the conditions are true. This method can be used in conjunction with
935    the OR operator and the L</Confess> method as a debugging assert.
936    So, for example
937    
938        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
939    
940    Will abort the program with a stack trace if the value of C<$recNum> is negative.
941    
942    =cut
943    sub Assert {
944        my $retVal = 1;
945        LOOP: for my $condition (@_) {
946            if (! $condition) {
947                $retVal = 0;
948                last LOOP;
949            }
950        }
951        return $retVal;
952    }
953    
954    =head3 Cluck
955    
956        Cluck($message);
957    
958    Trace the call stack. Note that for best results, you should qualify the call with a
959    trace condition. For example,
960    
961        Cluck("Starting record parse.") if T(3);
962    
963    will only trace the stack if the trace level for the package is 3 or more.
964    
965    =over 4
966    
967    =item message
968    
969    Message to include in the trace.
970    
971    =back
972    
973    =cut
974    
975    sub Cluck {
976        # Get the parameters.
977        my ($message) = @_;
978        # Trace what's happening.
979        Trace("Stack trace for event: $message");
980        # Get the stack trace.
981        my @trace = LongMess();
982        # Convert the trace to a series of messages.
983        for my $line (@trace) {
984            # Replace the tab at the beginning with spaces.
985            $line =~ s/^\t/    /;
986            # Trace the line.
987            Trace($line);
988        }
989        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
990        Warn($message);
991    }
992    
993    =head3 LongMess
994    
995        my @lines = Tracer::LongMess();
996    
997    Return a stack trace with all tracing methods removed. The return will be in the form of a list
998    of message strings.
999    
1000    =cut
1001    
1002    sub LongMess {
1003        # Declare the return variable.
1004        my @retVal = ();
1005        my $confession = longmess("");
1006        for my $line (split /\s*\n/, $confession) {
1007            unless ($line =~ /Tracer\.pm/) {
1008                # Here we have a line worth keeping. Push it onto the result list.
1009                push @retVal, $line;
1010            }
1011        }
1012        # Return the result.
1013        return @retVal;
1014    }
1015    
1016    =head3 ETracing
1017    
1018        ETracing($parameter);
1019    
1020    Set up emergency tracing. Emergency tracing is tracing that is turned
1021    on automatically for any program that calls this method. The emergency
1022    tracing parameters are stored in a a file identified by a tracing key.
1023    If this method is called with a CGI object, then the tracing key is
1024    taken from a cookie. If it is called with no parameters, then the tracing
1025    key is taken from an environment variable. If it is called with a string,
1026    the tracing key is that string.
1027    
1028    =over 4
1029    
1030    =item parameter
1031    
1032    A parameter from which the tracing key is computed. If it is a scalar,
1033    that scalar is used as the tracing key. If it is a CGI object, the
1034    tracing key is taken from the C<IP> cookie. If it is omitted, the
1035    tracing key is taken from the C<TRACING> environment variable. If it
1036    is a CGI object and emergency tracing is not on, the C<Trace> and
1037    C<TF> parameters will be used to determine the type of tracing.
1038    
1039    =back
1040    
1041    =cut
1042    
1043    sub ETracing {
1044        # Get the parameter.
1045        my ($parameter) = @_;
1046        # Check for CGI mode.
1047        if (defined $parameter && ref $parameter eq 'CGI') {
1048            $SavedCGI = $parameter;
1049        } else {
1050            $SavedCGI = undef;
1051        }
1052        # Default to no tracing except errors.
1053        my ($tracing, $dest) = ("0", "WARN");
1054        # Check for emergency tracing.
1055        my $tkey = EmergencyKey($parameter);
1056        my $emergencyFile = EmergencyFileName($tkey);
1057        if (-e $emergencyFile) {
1058            # We have the file. Read in the data.
1059            my @tracing = GetFile($emergencyFile);
1060            # Pull off the time limit.
1061            my $expire = shift @tracing;
1062            # Convert it to seconds.
1063            $expire *= 3600;
1064            # Check the file data.
1065            my $stat = stat($emergencyFile);
1066            my ($now) = gettimeofday;
1067            if ($now - $stat->mtime > $expire) {
1068                # Delete the expired file.
1069                unlink $emergencyFile;
1070            } else {
1071                # Emergency tracing is on. Pull off the destination and
1072                # the trace level;
1073                $dest = shift @tracing;
1074                my $level = shift @tracing;
1075                # Convert the destination to a real tracing destination.
1076                # temp directory.
1077                $dest = EmergencyTracingDest($tkey, $dest);
1078                # Insure Tracer is specified.
1079                my %moduleHash = map { $_ => 1 } @tracing;
1080                $moduleHash{Tracer} = 1;
1081                # Set the trace parameter.
1082                $tracing = join(" ", $level, sort keys %moduleHash);
1083            }
1084        } elsif (defined $SavedCGI) {
1085            # There's no emergency tracing, but we have a CGI object, so check
1086            # for tracing from the form parameters.
1087            if ($SavedCGI->param('Trace')) {
1088                # Here the user has requested tracing via a form.
1089                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1090                $tracing = $SavedCGI->param('Trace') . " Tracer";
1091            }
1092        }
1093        # Setup the tracing we've determined from all the stuff above.
1094        TSetup($tracing, $dest);
1095        # Check to see if we're a web script.
1096        if (defined $SavedCGI) {
1097            # Yes we are. Trace the form and environment data.
1098            TraceParms($SavedCGI);
1099            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1100            # emitted by the script in its raw form.
1101            if (T(Raw => 3)) {
1102                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1103            }
1104        }
1105    }
1106    
1107    =head3 EmergencyFileName
1108    
1109        my $fileName = Tracer::EmergencyFileName($tkey);
1110    
1111    Return the emergency tracing file name. This is the file that specifies
1112    the tracing information.
1113    
1114    =over 4
1115    
1116    =item tkey
1117    
1118    Tracing key for the current program.
1119    
1120    =item RETURN
1121    
1122    Returns the name of the file to contain the emergency tracing information.
1123    
1124    =back
1125    
1126    =cut
1127    
1128    sub EmergencyFileName {
1129        # Get the parameters.
1130        my ($tkey) = @_;
1131        # Compute the emergency tracing file name.
1132        return "$FIG_Config::temp/Emergency$tkey.txt";
1133    }
1134    
1135    =head3 EmergencyFileTarget
1136    
1137        my $fileName = Tracer::EmergencyFileTarget($tkey);
1138    
1139    Return the emergency tracing target file name. This is the file that receives
1140    the tracing output for file-based tracing.
1141    
1142    =over 4
1143    
1144    =item tkey
1145    
1146    Tracing key for the current program.
1147    
1148    =item RETURN
1149    
1150    Returns the name of the file to contain the trace output.
1151    
1152    =back
1153    
1154    =cut
1155    
1156    sub EmergencyFileTarget {
1157        # Get the parameters.
1158        my ($tkey) = @_;
1159        # Compute the emergency tracing file name.
1160        return "$FIG_Config::temp/trace$tkey.log";
1161    }
1162    
1163    =head3 EmergencyTracingDest
1164    
1165        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1166    
1167    This method converts an emergency tracing destination to a real
1168    tracing destination. The main difference is that if the
1169    destination is C<FILE> or C<APPEND>, we convert it to file
1170    output. If the destination is C<DUAL>, we convert it to file
1171    and standard output.
1172    
1173    =over 4
1174    
1175    =item tkey
1176    
1177    Tracing key for this environment.
1178    
1179    =item myDest
1180    
1181    Destination from the emergency tracing file.
1182    
1183    =item RETURN
1184    
1185    Returns a destination that can be passed into L</TSetup>.
1186    
1187    =back
1188    
1189    =cut
1190    
1191    sub EmergencyTracingDest {
1192        # Get the parameters.
1193        my ($tkey, $myDest) = @_;
1194        # Declare the return variable.
1195        my $retVal = $myDest;
1196        # Process according to the destination value.
1197        if ($myDest eq 'FILE') {
1198            $retVal = ">" . EmergencyFileTarget($tkey);
1199        } elsif ($myDest eq 'APPEND') {
1200            $retVal = ">>" . EmergencyFileTarget($tkey);
1201        } elsif ($myDest eq 'DUAL') {
1202            $retVal = "+>" . EmergencyFileTarget($tkey);
1203        } elsif ($myDest eq 'WARN') {
1204            $retVal = "WARN";
1205        }
1206        # Return the result.
1207        return $retVal;
1208    }
1209    
1210    =head3 Emergency
1211    
1212        Emergency($key, $hours, $dest, $level, @modules);
1213    
1214    Turn on emergency tracing. This method is normally invoked over the web from
1215    a debugging console, but it can also be called by the C<trace.pl> script.
1216    The caller specifies the duration of the emergency in hours, the desired tracing
1217    destination, the trace level, and a list of the trace modules to activate.
1218    For the length of the duration, when a program in an environment with the
1219    specified tracing key active invokes a Sprout CGI script, tracing will be
1220    turned on automatically. See L</TSetup> for more about tracing setup and
1221    L</ETracing> for more about emergency tracing.
1222    
1223    =over 4
1224    
1225    =item tkey
1226    
1227    The tracing key. This is used to identify the control file and the trace file.
1228    
1229    =item hours
1230    
1231    Number of hours to keep emergency tracing alive.
1232    
1233    =item dest
1234    
1235    Tracing destination. If no path information is specified for a file
1236    destination, it is put in the FIG temporary directory.
1237    
1238    =item level
1239    
1240    Tracing level. A higher level means more trace messages.
1241    
1242    =item modules
1243    
1244    A list of the tracing modules to activate.
1245    
1246    =back
1247    
1248    =cut
1249    
1250    sub Emergency {
1251        # Get the parameters.
1252        my ($tkey, $hours, $dest, $level, @modules) = @_;
1253        # Create the emergency file.
1254        my $specFile = EmergencyFileName($tkey);
1255        my $outHandle = Open(undef, ">$specFile");
1256        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1257    }
1258    
1259    =head3 EmergencyKey
1260    
1261        my $tkey = EmergencyKey($parameter);
1262    
1263    Return the Key to be used for emergency tracing. This could be an IP address,
1264     a session ID, or a user name, depending on the environment.
1265    
1266    =over 4
1267    
1268    =item parameter
1269    
1270    Parameter defining the method for finding the tracing key. If it is a scalar,
1271    then it is presumed to be the tracing key itself. If it is a CGI object, then
1272    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1273    taken from the C<TRACING> environment variable.
1274    
1275    =item RETURN
1276    
1277    Returns the key to be used for labels in emergency tracing.
1278    
1279    =back
1280    
1281    =cut
1282    
1283    sub EmergencyKey {
1284        # Get the parameters.
1285        my ($parameter) = @_;
1286        # Declare the return variable.
1287        my $retVal;
1288        # Determine the parameter type.
1289        if (! defined $parameter || defined($ENV{TRACING})) {
1290            # Here we're supposed to check the environment. If that fails, we
1291            # get the effective login ID.
1292            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1293        } else {
1294            my $ptype = ref $parameter;
1295            if ($ptype eq 'CGI') {
1296                # Here we were invoked from a web page. Look for a cookie.
1297                $retVal = $parameter->cookie('IP');
1298            } elsif (! $ptype) {
1299                # Here the key was passed in.
1300                $retVal = $parameter;
1301            }
1302        }
1303        # If no luck finding a key, use the PID.
1304        if (! defined $retVal) {
1305            $retVal = $$;
1306        }
1307        # Return the result.
1308        return $retVal;
1309    }
1310    
1311    
1312    =head3 TraceParms
1313    
1314        Tracer::TraceParms($cgi);
1315    
1316    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1317    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1318    
1319    =over 4
1320    
1321    =item cgi
1322    
1323    CGI query object containing the parameters to trace.
1324    
1325    =back
1326    
1327    =cut
1328    
1329    sub TraceParms {
1330        # Get the parameters.
1331        my ($cgi) = @_;
1332        if (T(CGI => 2)) {
1333            # Here we trace the GET-style URL for the script, but only if it's
1334            # relatively small.
1335            my $url = $cgi->url(-relative => 1, -query => 1);
1336            my $len = length($url);
1337            if ($len < 500) {
1338                Trace("[URL] $url");
1339            } elsif ($len > 2048) {
1340                Trace("[URL] URL is too long to use with GET ($len characters).");
1341            } else {
1342                Trace("[URL] URL length is $len characters.");
1343            }
1344        }
1345        if (T(CGI => 3)) {
1346            # Here we want to trace the parameter data.
1347            my @names = $cgi->param;
1348            for my $parmName (sort @names) {
1349                # Note we skip the Trace parameters, which are for our use only.
1350                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1351                    my @values = $cgi->param($parmName);
1352                    Trace("[CGI] $parmName = " . join(", ", @values));
1353                }
1354            }
1355            # Display the request method.
1356            my $method = $cgi->request_method();
1357            Trace("Method: $method");
1358        }
1359        if (T(CGI => 4)) {
1360            # Here we want the environment data too.
1361            for my $envName (sort keys %ENV) {
1362                Trace("[ENV] $envName = $ENV{$envName}");
1363            }
1364        }
1365    }
1366    
1367    =head3 TraceImages
1368    
1369        Tracer::TraceImages($htmlString);
1370    
1371    Trace information about all of an html document's images. The tracing
1372    will be for type "IMG" at level 3. The image's source string
1373    will be displayed. This is generally either the URL of the image or
1374    raw data for the image itself. If the source is too long, only the first 300
1375    characters will be shown at trace level 3. The entire source will be shown,
1376    however, at trace level 4. This method is not very smart, and might catch
1377    Javascript code, but it is still useful when debugging the arcane
1378    behavior of images in multiple browser environments.
1379    
1380    =over 4
1381    
1382    =item htmlString
1383    
1384    HTML text for an outgoing web page.
1385    
1386    =back
1387    
1388    =cut
1389    
1390    sub TraceImages {
1391        # Only proceed if we're at the proper trace level.
1392        if (T(IMG => 3)) {
1393            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1394            # into a variable called "$htmlString". This is because we expect html strings to be
1395            # long, and don't want to copy them any more than we have to.
1396            Trace(length($_[0]) . " characters in web page.");
1397            # Loop through the HTML, culling image tags.
1398            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1399                # Extract the source string and determine whether or not it's too long.
1400                my $srcString = $1;
1401                my $pos = pos($_[0]) - length($srcString);
1402                my $excess = length($srcString) - 300;
1403                # We'll put the display string in here.
1404                my $srcDisplay = $srcString;
1405                # If it's a data string, split it at the comma.
1406                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1407                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1408                # a long string, however, we only show the first 300 characters.
1409                if ($excess > 0 && ! T(IMG => 4)) {
1410                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1411                }
1412                # Output the trace message.
1413                Trace("Image tag at position $pos:\n$srcDisplay");
1414            }
1415        }
1416    }
1417    
1418    =head2 Command-Line Utility Methods
1419    
1420    =head3 SendSMS
1421    
1422        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1423    
1424    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1425    user name, password, and API ID for the relevant account in the hash reference variable
1426    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1427    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1428    is C<2561022>, then the FIG_Config file must contain
1429    
1430        $phone =  { user => 'BruceTheHumanPet',
1431                    password => 'silly',
1432                    api_id => '2561022' };
1433    
1434    The original purpose of this method was to insure Bruce would be notified immediately when the
1435    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1436    when you call this method.
1437    
1438    The message ID will be returned if successful, and C<undef> if an error occurs.
1439    
1440    =over 4
1441    
1442    =item phoneNumber
1443    
1444    Phone number to receive the message, in international format. A United States phone number
1445    would be prefixed by "1". A British phone number would be prefixed by "44".
1446    
1447    =item msg
1448    
1449    Message to send to the specified phone.
1450    
1451    =item RETURN
1452    
1453    Returns the message ID if successful, and C<undef> if the message could not be sent.
1454    
1455    =back
1456    
1457    =cut
1458    
1459    sub SendSMS {
1460        # Get the parameters.
1461        my ($phoneNumber, $msg) = @_;
1462        # Declare the return variable. If we do not change it, C<undef> will be returned.
1463        my $retVal;
1464        # Only proceed if we have phone support.
1465        if (! defined $FIG_Config::phone) {
1466            Trace("Phone support not present in FIG_Config.") if T(1);
1467        } else {
1468            # Get the phone data.
1469            my $parms = $FIG_Config::phone;
1470            # Get the Clickatell URL.
1471            my $url = "http://api.clickatell.com/http/";
1472            # Create the user agent.
1473            my $ua = LWP::UserAgent->new;
1474            # Request a Clickatell session.
1475            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1476                                         password => $parms->{password},
1477                                         api_id => $parms->{api_id},
1478                                         to => $phoneNumber,
1479                                         text => $msg});
1480            # Check for an error.
1481            if (! $resp->is_success) {
1482                Trace("Alert failed.") if T(1);
1483            } else {
1484                # Get the message ID.
1485                my $rstring = $resp->content;
1486                if ($rstring =~ /^ID:\s+(.*)$/) {
1487                    $retVal = $1;
1488                } else {
1489                    Trace("Phone attempt failed with $rstring") if T(1);
1490                }
1491            }
1492        }
1493        # Return the result.
1494        return $retVal;
1495    }
1496    
1497    =head3 StandardSetup
1498    
1499        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1500    
1501    This method performs standard command-line parsing and tracing setup. The return
1502    values are a hash of the command-line options and a list of the positional
1503    parameters. Tracing is automatically set up and the command-line options are
1504    validated.
1505    
1506    This is a complex method that does a lot of grunt work. The parameters can
1507    be more easily understood, however, once they are examined individually.
1508    
1509    The I<categories> parameter is the most obtuse. It is a reference to a list of
1510    special-purpose tracing categories. Most tracing categories are PERL package
1511    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1512    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1513    
1514        ["Sprout", "SproutLoad", "ERDB"]
1515    
1516    This would cause trace messages in the specified three packages to appear in
1517    the output. There are two special tracing categories that are automatically
1518    handled by this method. In other words, if you used L</TSetup> you would need
1519    to include these categories manually, but if you use this method they are turned
1520    on automatically.
1521    
1522    =over 4
1523    
1524    =item SQL
1525    
1526    Traces SQL commands and activity.
1527    
1528    =item Tracer
1529    
1530    Traces error messages and call stacks.
1531    
1532    =back
1533    
1534    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1535    The trace level is specified using the C<-trace> command-line option. For example,
1536    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1537    all tracing at level 3.
1538    
1539        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1540    
1541    Standard tracing is output to the standard output and echoed to the file
1542    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1543    process ID. You can also specify the C<user> parameter to put a user ID
1544    instead of a process ID in the trace file name. So, for example
1545    
1546    The default trace level is 2. To get all messages, specify a trace level of 4.
1547    For a genome-by-genome update, use 3.
1548    
1549        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1550    
1551    would send the trace output to C<traceBruce.log> in the temporary directory.
1552    
1553    The I<options> parameter is a reference to a hash containing the command-line
1554    options, their default values, and an explanation of what they mean. Command-line
1555    options may be in the form of switches or keywords. In the case of a switch, the
1556    option value is 1 if it is specified and 0 if it is not specified. In the case
1557    of a keyword, the value is separated from the option name by an equal sign. You
1558    can see this last in the command-line example above.
1559    
1560    You can specify a different default trace level by setting C<$options->{trace}>
1561    prior to calling this method.
1562    
1563    An example at this point would help. Consider, for example, the command-line utility
1564    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1565    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1566    the following code.
1567    
1568        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1569                            { safe => [0, "use database transactions"],
1570                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1571                              start => [' ', "start with this genome"],
1572                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1573                            "<command> <transactionDirectory> <IDfile>",
1574                          @ARGV);
1575    
1576    
1577    The call to C<ParseCommand> specifies the default values for the options and
1578    stores the actual options in a hash that is returned as C<$options>. The
1579    positional parameters are returned in C<@parameters>.
1580    
1581    The following is a sample command line for C<TransactFeatures>.
1582    
1583        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1584    
1585    Single and double hyphens are equivalent. So, you could also code the
1586    above command as
1587    
1588        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1589    
1590    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1591    parameters, and would find themselves in I<@parameters> after executing the
1592    above code fragment. The tracing would be set to level 2, and the categories
1593    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1594    and C<DocUtils> was included because it came in within the first parameter
1595    to this method. The I<$options> hash would be
1596    
1597        { trace => 2, sql => 0, safe => 0,
1598          noAlias => 1, start => ' ', tblFiles => 0 }
1599    
1600    Use of C<StandardSetup> in this way provides a simple way of performing
1601    standard tracing setup and command-line parsing. Note that the caller is
1602    not even aware of the command-line switches C<-trace> and C<-sql>, which
1603    are used by this method to control the tracing. If additional tracing features
1604    need to be added in the future, they can be processed by this method without
1605    upsetting the command-line utilities.
1606    
1607    If the C<background> option is specified on the command line, then the
1608    standard and error outputs will be directed to files in the temporary
1609    directory, using the same suffix as the trace file. So, if the command
1610    line specified
1611    
1612        -user=Bruce -background
1613    
1614    then the trace output would go to C<traceBruce.log>, the standard output to
1615    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1616    simplify starting a command in the background.
1617    
1618    The user name is also used as the tracing key for L</Emergency Tracing>.
1619    Specifying a value of C<E> for the trace level causes emergency tracing to
1620    be used instead of custom tracing. If the user name is not specified,
1621    the tracing key is taken from the C<Tracing> environment variable. If there
1622    is no value for that variable, the tracing key will be computed from the active
1623    login ID.
1624    
1625    Since the default situation in StandardSetup is to trace to the standard
1626    output, errors that occur in command-line scripts will not generate
1627    RSS events. To force the events, use the C<warn> option.
1628    
1629        TransactFeatures -background -warn register ../xacts IDs.tbl
1630    
1631    Finally, if the special option C<-help> is specified, the option
1632    names will be traced at level 0 and the program will exit without processing.
1633    This provides a limited help capability. For example, if the user enters
1634    
1635        TransactFeatures -help
1636    
1637    he would see the following output.
1638    
1639        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1640            -trace    tracing level (default E)
1641            -sql      trace SQL commands
1642            -safe     use database transactions
1643            -noAlias  do not expect aliases in CHANGE transactions
1644            -start    start with this genome
1645            -tblFiles output TBL files containing the corrected IDs
1646            -forked   do not erase the trace file before tracing
1647    
1648    The caller has the option of modifying the tracing scheme by placing a value
1649    for C<trace> in the incoming options hash. The default value can be overridden,
1650    or the tracing to the standard output can be turned off by suffixing a minus
1651    sign to the trace level. So, for example,
1652    
1653        { trace => [0, "tracing level (default 0)"],
1654           ...
1655    
1656    would set the default trace level to 0 instead of E, while
1657    
1658        { trace => ["2-", "tracing level (default 2)"],
1659           ...
1660    
1661    would set the default to 2, but trace only to the log file, not to the
1662    standard output.
1663    
1664    The parameters to this method are as follows.
1665    
1666    =over 4
1667    
1668    =item categories
1669    
1670    Reference to a list of tracing category names. These should be names of
1671    packages whose internal workings will need to be debugged to get the
1672    command working.
1673    
1674    =item options
1675    
1676    Reference to a hash containing the legal options for the current command mapped
1677    to their default values and descriptions. The user can override the defaults
1678    by specifying the options as command-line switches prefixed by a hyphen.
1679    Tracing-related options may be added to this hash. If the C<-h> option is
1680    specified on the command line, the option descriptions will be used to
1681    explain the options. To turn off tracing to the standard output, add a
1682    minus sign to the value for C<trace> (see above).
1683    
1684    =item parmHelp
1685    
1686    A string that vaguely describes the positional parameters. This is used
1687    if the user specifies the C<-h> option.
1688    
1689    =item argv
1690    
1691  List of command line parameters, including the option switches, which must  List of command line parameters, including the option switches, which must
1692  precede the positional parameters and be prefixed by a hyphen.  precede the positional parameters and be prefixed by a hyphen.
# Line 577  Line 1707 
1707      my ($categories, $options, $parmHelp, @argv) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1708      # Get the default tracing key.      # Get the default tracing key.
1709      my $tkey = EmergencyKey();      my $tkey = EmergencyKey();
1710        # Save the command line.
1711        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1712      # Add the tracing options.      # Add the tracing options.
1713      if (! exists $options->{trace}) {      if (! exists $options->{trace}) {
1714          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1715        }
1716        if (! exists $options->{forked}) {
1717            $options->{forked} = [0, "keep old trace file"];
1718      }      }
1719      $options->{sql} = [0, "turn on SQL tracing"];      $options->{sql} = [0, "turn on SQL tracing"];
1720      $options->{help} = [0, "display command-line options"];      $options->{help} = [0, "display command-line options"];
1721      $options->{user} = [$tkey, "tracing key"];      $options->{user} = [$tkey, "tracing key"];
1722      $options->{background} = [0, "spool standard and error output"];      $options->{background} = [0, "spool standard and error output"];
1723        $options->{warn} = [0, "send errors to RSS feed"];
1724        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1725      # Create a parsing hash from the options hash. The parsing hash      # Create a parsing hash from the options hash. The parsing hash
1726      # contains the default values rather than the default value      # contains the default values rather than the default value
1727      # and the description. While we're at it, we'll memorize the      # and the description. While we're at it, we'll memorize the
# Line 601  Line 1738 
1738      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1739      # Get the logfile suffix.      # Get the logfile suffix.
1740      my $suffix = $retOptions->{user};      my $suffix = $retOptions->{user};
1741      # Check for background mode.      # We'll put the trace file name in here. We need it later if background
1742      if ($retOptions->{background}) {      # mode is on.
1743          my $outFileName = "$FIG_Config::temp/out$suffix.log";      my $traceFileName;
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
1744      # Now we want to set up tracing. First, we need to know if the user      # Now we want to set up tracing. First, we need to know if the user
1745      # wants emergency tracing.      # wants emergency tracing.
1746      if ($retOptions->{trace} eq 'E') {      if ($retOptions->{trace} eq 'E') {
# Line 618  Line 1751 
1751          if ($retOptions->{sql}) {          if ($retOptions->{sql}) {
1752              push @cats, "SQL";              push @cats, "SQL";
1753          }          }
1754            if ($retOptions->{warn}) {
1755                push @cats, "Feed";
1756            }
1757          # Add the default categories.          # Add the default categories.
1758          push @cats, "Tracer";          push @cats, "Tracer";
1759            # Check for more tracing groups.
1760            if ($retOptions->{moreTracing}) {
1761                push @cats, split /,/, $retOptions->{moreTracing};
1762            }
1763          # Next, we create the category string by joining the categories.          # Next, we create the category string by joining the categories.
1764          my $cats = join(" ", @cats);          my $cats = join(" ", @cats);
1765          # Check to determine whether or not the caller wants to turn off tracing          # Check to determine whether or not the caller wants to turn off tracing
# Line 634  Line 1774 
1774          my $traceMode;          my $traceMode;
1775          # Verify that we can open a file in the FIG temporary directory.          # Verify that we can open a file in the FIG temporary directory.
1776          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1777          if (open TESTTRACE, ">$traceFileName") {          my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1778            if (open TESTTRACE, "$traceFileSpec") {
1779              # Here we can trace to a file.              # Here we can trace to a file.
1780              $traceMode = ">$traceFileName";              $traceMode = ">>$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.  
1781              if ($textOKFlag) {              if ($textOKFlag) {
1782                  $traceMode = "TEXT";                  # Echo to standard output if the text-OK flag is set.
1783              } else {                  $traceMode = "+$traceMode";
1784                  $traceMode = "WARN";              }
1785              }              # Close the test file.
1786          }              close TESTTRACE;
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
             }  
             print "  $name $desc\n";  
         }  
         exit(0);  
     }  
     # Trace the options, if applicable.  
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
     }  
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
 }  
   
 =head3 Setups  
   
 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;  
 }  
   
 =head3 Open  
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
   
 Open a file.  
   
 The I<$fileSpec> is essentially the second argument of the PERL C<open>  
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
   
     Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 would open for output appended to the specified file, and  
   
     Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  
   
 would open a pipe that sorts the records written and removes duplicates. Note  
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
   
     my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 The I<$message> parameter is used if the open fails. If it is set to C<0>, then  
 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.  
   
     Could not open "/usr/spool/news/twitlog"  
   
 Note that the mode characters are automatically cleaned from the file name.  
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
   
     Could not open "/usr/spool/news/twitlog": file not found.  
   
 In some versions of PERL the only error message we get is a number, which  
 corresponds to the C++ C<errno> value.  
   
     Could not open "/usr/spool/news/twitlog": 6.  
   
 =over 4  
   
 =item fileHandle  
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
   
 File name and mode, as per the PERL C<open> function.  
   
 =item message (optional)  
   
 Error message to use if the open fails. If omitted, a standard error message  
 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>.  
   
 =item RETURN  
   
 Returns the name of the file handle assigned to the file, or C<undef> if the  
 open failed.  
   
 =back  
   
 =cut  
   
 sub Open {  
     # Get the parameters.  
     my ($fileHandle, $fileSpec, $message) = @_;  
     # Attempt to open the file.  
     my $rv = open $fileHandle, $fileSpec;  
     # If the open failed, generate an error message.  
     if (! $rv) {  
         # Save the system error message.  
         my $sysMessage = $!;  
         # See if we need a default message.  
         if (!$message) {  
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
         }  
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
     }  
     # Return the file handle.  
     return $fileHandle;  
 }  
   
 =head3 FindNamePart  
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
   
 Returns a three-element list. The first element contains the file name portion of  
 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.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
   
     my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  
   
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
   
 TRUE if a failure to open is okay, else FALSE  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
1787          } else {          } else {
1788              @retVal = readdir $dirHandle;              # Here we can't trace to a file. Complain about this.
1789                warn "Could not open trace file $traceFileName: $!\n";
1790                # We trace to the standard output if it's
1791                # okay, and the error log otherwise.
1792                if ($textOKFlag) {
1793                    $traceMode = "TEXT";
1794                } else {
1795                    $traceMode = "WARN";
1796          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1797      }      }
1798      # Return the result.          # Now set up the tracing.
1799      return @retVal;          TSetup("$traceLevel $cats", $traceMode);
1800  }  }
1801        # Check for background mode.
1802  =head3 SetLevel      if ($retOptions->{background}) {
1803            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1804  C<< Tracer::SetLevel($newLevel); >>          my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1805            # Spool the output.
1806  Modify the trace level. A higher trace level will cause more messages to appear.          open STDOUT, ">$outFileName";
1807            # If we have a trace file, trace the errors to the log. Otherwise,
1808  =over 4          # spool the errors.
1809            if (defined $traceFileName) {
1810  =item newLevel              open STDERR, "| Tracer $traceFileName";
1811            } else {
1812  Proposed new trace level.              open STDERR, ">$errFileName";
   
 =back  
   
 =cut  
   
 sub SetLevel {  
     $TraceLevel = $_[0];  
1813  }  }
1814            # Check for phone support. If we have phone support and a phone number,
1815  =head3 Now          # we want to turn it on.
1816            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1817  C<< my $string = Tracer::Now(); >>              $retOptions->{phone} = $ENV{PHONE};
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     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;  
1818  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1819  }  }
1820        # Check for the "help" option. If it is specified, dump the command-line
1821  =head3 ParseTraceDate      # options and exit the program.
1822        if ($retOptions->{help}) {
1823  C<< my $time = Tracer::ParseTraceDate($dateString); >>          $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1824            print "$1 [options] $parmHelp\n";
1825  Convert a date from the trace file into a PERL timestamp.          for my $key (sort keys %{$options}) {
1826                my $name = Pad($key, $longestName, 0, ' ');
1827  =over 4              my $desc = $options->{$key}->[1];
1828                if ($options->{$key}->[0]) {
1829  =item dateString                  $desc .= " (default " . $options->{$key}->[0] . ")";
   
 The date string from the trace file. The format of the string is determined by the  
 L</Now> method.  
   
 =item RETURN  
   
 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  
 the time string is invalid.  
   
 =back  
   
 =cut  
   
 sub ParseTraceDate {  
     # Get the parameters.  
     my ($dateString) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
1830      }      }
1831      # Return the result.              print "  $name $desc\n";
     return $retVal;  
1832  }  }
1833            exit(0);
1834  =head3 LogErrors      }
1835        # Trace the options, if applicable.
1836  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1837            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1838  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1839        }
1840  =over 4      # Return the parsed parameters.
1841        return ($retOptions, @retParameters);
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1842  }  }
1843    
1844  =head3 ReadOptions  =head3 ReadOptions
1845    
1846  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1847    
1848  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
1849  format  format
# Line 1069  Line 1904 
1904    
1905  =head3 GetOptions  =head3 GetOptions
1906    
1907  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1908    
1909  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
1910  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 1913 
1913    
1914  Consider the following example.  Consider the following example.
1915    
1916  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1917    
1918  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1919  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1921 
1921  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1922  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1923    
1924  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1925    
1926  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1927    
# Line 1130  Line 1965 
1965    
1966  =head3 MergeOptions  =head3 MergeOptions
1967    
1968  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1969    
1970  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
1971  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 1997 
1997      }      }
1998  }  }
1999    
2000  =head3 Trace  =head3 UnparseOptions
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
2001    
2002  C<< my $switch = T($traceLevel); >>      my $optionString = Tracer::UnparseOptions(\%options);
2003    
2004  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
2005  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
2006    produce the same ultimate result when parsed by L</StandardSetup>.
2007    
2008  =over 4  =over 4
2009    
2010  =item category  =item options
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2011    
2012  Relevant tracing level.  Reference to a hash of options to convert into an option string.
2013    
2014  =item RETURN  =item RETURN
2015    
2016  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
2017    parsed by L</StandardSetup>.
2018    
2019  =back  =back
2020    
2021  =cut  =cut
2022    
2023  sub T {  sub UnparseOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2024          # Get the parameters.          # Get the parameters.
2025          my ($category, $traceLevel) = @_;      my ($options) = @_;
2026          if (!defined $traceLevel) {      # The option segments will be put in here.
2027              # Here we have no category, so we need to get the calling package.      my @retVal = ();
2028              # The calling package is normally the first parameter. If it is      # Loop through the options.
2029              # omitted, the first parameter will be the tracelevel. So, the      for my $key (keys %$options) {
2030              # first thing we do is shift the so-called category into the          # Get the option value.
2031              # $traceLevel variable where it belongs.          my $value = $options->{$key};
2032              $traceLevel = $category;          # Only use it if it's nonempty.
2033              my ($package, $fileName, $line) = caller;          if (defined $value && $value ne "") {
2034              # If there is no calling package, we default to "main".              my $segment = "--$key=$value";
2035              if (!$package) {              # Quote it if necessary.
2036                  $category = "main";              if ($segment =~ /[ |<>*]/) {
2037              } else {                  $segment = '"' . $segment . '"';
                 $category = $package;  
             }  
2038          }          }
2039          # Save the category name.              # Add it to the return list.
2040          $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.");  
2041          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2042      }      }
2043      # Return the computed result.      # Return the result.
2044      return $retVal;      return join(" ", @retVal);
2045  }  }
2046    
2047  =head3 ParseCommand  =head3 ParseCommand
2048    
2049  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2050    
2051  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2052  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2053  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2054  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2055    
2056  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2057    
2058  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2059  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2060    
2061  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2062    
2063  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2064    
2065  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2066    
2067  and C<@arguments> will contain  and C<@arguments> will contain
2068    
2069  C<< apple orange rutabaga >>      apple orange rutabaga
2070    
2071  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2072  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 2120 
2120      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2121  }  }
2122    
 =head3 Escape  
2123    
2124  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2125    
2126  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2127  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2128  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2129    
2130        or
2131    
2132        my $fileContents = Tracer::GetFile($fileName);
2133    
2134    Return the entire contents of a file. In list context, line-ends are removed and
2135    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2136    
2137  =over 4  =over 4
2138    
2139  =item realString  =item fileName
2140    
2141  String to escape.  Name of the file to read.
2142    
2143  =item RETURN  =item RETURN
2144    
2145  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2146    In a scalar context, returns the entire file as a string. If an error occurs opening
2147    the file, an empty list will be returned.
2148    
2149  =back  =back
2150    
2151  =cut  =cut
2152    
2153  sub Escape {  sub GetFile {
2154      # Get the parameter.      # Get the parameters.
2155      my ($realString) = @_;      my ($fileName) = @_;
2156      # Initialize the return variable.      # Declare the return variable.
2157      my $retVal = "";      my @retVal = ();
2158      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2159      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2160          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2161          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2162              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2163              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2164              $retVal .= $1;          $lineCount++;
2165              # Strip the processed section off the real string.          $line = Strip($line);
2166              $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;  
2167              }              }
2168        # Close it.
2169        close $handle;
2170        my $actualLines = @retVal;
2171        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2172        # Return the file's contents in the desired format.
2173        if (wantarray) {
2174            return @retVal;
2175          } else {          } else {
2176              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2177      }      }
     # Return the result.  
     return $retVal;  
2178  }  }
2179    
2180  =head3 UnEscape  =head3 PutFile
2181    
2182  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2183    
2184  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2185    
2186  =over 4  =over 4
2187    
2188  =item codedString  =item fileName
2189    
2190  String to un-escape.  Name of the output file.
2191    
2192  =item RETURN  =item lines
2193    
2194  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2195  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2196    modification.
2197    
2198  =back  =back
2199    
2200  =cut  =cut
2201    
2202  sub UnEscape {  sub PutFile {
2203      # Get the parameter.      # Get the parameters.
2204      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2205      # Initialize the return variable.      # Open the output file.
2206      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2207      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2208      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2209          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2210          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2211          # "\<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;  
                 }  
2212              } else {              } else {
2213                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2214                  # transferred unmodified.          my $count = 0;
2215                  $retVal .= $codedString;          for my $line (@{$lines}) {
2216                  $codedString = "";              print $handle "$line\n";
2217              }              $count++;
2218          }          }
2219            Trace("$count lines put to file $fileName.") if T(File => 3);
2220      }      }
2221      # Return the result.      # Close the output file.
2222      return $retVal;      close $handle;
2223  }  }
2224    
2225  =head3 ParseRecord  =head3 ParseRecord
2226    
2227  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2228    
2229  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
2230  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 2269 
2269    
2270  =head3 Merge  =head3 Merge
2271    
2272  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2273    
2274  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2275    
# Line 1567  Line 2315 
2315      return @inputList;      return @inputList;
2316  }  }
2317    
2318  =head3 Percent  =head3 Open
2319    
2320  C<< my $percent = Tracer::Percent($number, $base); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2321    
2322  Returns the percent of the base represented by the given number. If the base  Open a file.
2323  is zero, returns zero.  
2324    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2325    function. The mode is specified using Unix-like shell information. So, for
2326    example,
2327    
2328        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2329    
2330    would open for output appended to the specified file, and
2331    
2332        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2333    
2334    would open a pipe that sorts the records written and removes duplicates. Note
2335    the use of file handle syntax in the Open call. To use anonymous file handles,
2336    code as follows.
2337    
2338        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2339    
2340    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2341    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2342    failed open will throw an exception and the third parameter will be used to construct
2343    an error message. If the parameter is omitted, a standard message is constructed
2344    using the file spec.
2345    
2346        Could not open "/usr/spool/news/twitlog"
2347    
2348    Note that the mode characters are automatically cleaned from the file name.
2349    The actual error message from the file system will be captured and appended to the
2350    message in any case.
2351    
2352        Could not open "/usr/spool/news/twitlog": file not found.
2353    
2354    In some versions of PERL the only error message we get is a number, which
2355    corresponds to the C++ C<errno> value.
2356    
2357        Could not open "/usr/spool/news/twitlog": 6.
2358    
2359  =over 4  =over 4
2360    
2361  =item number  =item fileHandle
2362    
2363  Percent numerator.  File handle. If this parameter is C<undef>, a file handle will be generated
2364    and returned as the value of this method.
2365    
2366  =item base  =item fileSpec
2367    
2368  Percent base.  File name and mode, as per the PERL C<open> function.
2369    
2370    =item message (optional)
2371    
2372    Error message to use if the open fails. If omitted, a standard error message
2373    will be generated. In either case, the error information from the file system
2374    is appended to the message. To specify a conditional open that does not throw
2375    an error if it fails, use C<0>.
2376    
2377  =item RETURN  =item RETURN
2378    
2379  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
2380    open failed.
2381    
2382  =back  =back
2383    
2384  =cut  =cut
2385    
2386  sub Percent {  sub Open {
2387      # Get the parameters.      # Get the parameters.
2388      my ($number, $base) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2389      # Declare the return variable.      # Attempt to open the file.
2390      my $retVal = 0;      my $rv = open $fileHandle, $fileSpec;
2391      # Compute the percent.      # If the open failed, generate an error message.
2392      if ($base != 0) {      if (! $rv) {
2393          $retVal = $number * 100 / $base;          # Save the system error message.
2394            my $sysMessage = $!;
2395            # See if we need a default message.
2396            if (!$message) {
2397                # Clean any obvious mode characters and leading spaces from the
2398                # filename.
2399                my ($fileName) = FindNamePart($fileSpec);
2400                $message = "Could not open \"$fileName\"";
2401            }
2402            # Terminate with an error using the supplied message and the
2403            # error message from the file system.
2404            Confess("$message: $!");
2405        }
2406        # Return the file handle.
2407        return $fileHandle;
2408    }
2409    
2410    =head3 FindNamePart
2411    
2412        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2413    
2414    Extract the portion of a file specification that contains the file name.
2415    
2416    A file specification is the string passed to an C<open> call. It specifies the file
2417    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2418    method assumes that the file name is whatever follows the first angle bracket
2419    sequence.  So, for example, in the following strings the file name is
2420    C</usr/fig/myfile.txt>.
2421    
2422        >>/usr/fig/myfile.txt
2423        </usr/fig/myfile.txt
2424        | sort -u > /usr/fig/myfile.txt
2425    
2426    If the method cannot find a file name using its normal methods, it will return the
2427    whole incoming string.
2428    
2429    =over 4
2430    
2431    =item fileSpec
2432    
2433    File specification string from which the file name is to be extracted.
2434    
2435    =item RETURN
2436    
2437    Returns a three-element list. The first element contains the file name portion of
2438    the specified string, or the whole string if a file name cannot be found via normal
2439    methods. The second element contains the start position of the file name portion and
2440    the third element contains the length.
2441    
2442    =back
2443    
2444    =cut
2445    #: Return Type $;
2446    sub FindNamePart {
2447        # Get the parameters.
2448        my ($fileSpec) = @_;
2449        # Default to the whole input string.
2450        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2451        # Parse out the file name if we can.
2452        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2453            $retVal = $2;
2454            $len = length $retVal;
2455            $pos = (length $fileSpec) - (length $3) - $len;
2456      }      }
2457      # Return the result.      # Return the result.
2458      return $retVal;      return ($retVal, $pos, $len);
2459  }  }
2460    
2461  =head3 GetFile  =head3 OpenDir
2462    
2463  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @files = OpenDir($dirName, $filtered, $flag);
2464    
2465      or  Open a directory and return all the file names. This function essentially performs
2466    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2467    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2468    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2469    filtered out of the return list. If the directory does not open and I<$flag> is not
2470    set, an exception is thrown. So, for example,
2471    
2472  C<< my $fileContents = Tracer::GetFile($fileName); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2473    
2474  Return the entire contents of a file. In list context, line-ends are removed and  is effectively the same as
2475  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2476        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2477        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2478    
2479    Similarly, the following code
2480    
2481        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2482    
2483    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2484    automatically returns an empty list if the directory fails to open.
2485    
2486  =over 4  =over 4
2487    
2488  =item fileName  =item dirName
2489    
2490  Name of the file to read.  Name of the directory to open.
2491    
2492    =item filtered
2493    
2494    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2495    from the list, else FALSE.
2496    
2497  =item RETURN  =item flag
2498    
2499  In a list context, returns the entire file as a list with the line terminators removed.  TRUE if a failure to open is okay, else FALSE
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2500    
2501  =back  =back
2502    
2503  =cut  =cut
2504    #: Return Type @;
2505  sub GetFile {  sub OpenDir {
2506      # Get the parameters.      # Get the parameters.
2507      my ($fileName) = @_;      my ($dirName, $filtered, $flag) = @_;
2508      # Declare the return variable.      # Declare the return variable.
2509      my @retVal = ();      my @retVal = ();
2510      # Open the file for input.      # Open the directory.
2511      my $handle = Open(undef, "<$fileName");      if (opendir(my $dirHandle, $dirName)) {
2512      # Read the whole file into the return variable, stripping off any terminator          # The directory opened successfully. Get the appropriate list according to the
2513      # characters.          # strictures of the filter parameter.
2514      my $lineCount = 0;          if ($filtered) {
2515      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;  
2516      } else {      } else {
2517          return join "\n", @retVal;              @retVal = readdir $dirHandle;
2518            }
2519        } elsif (! $flag) {
2520            # Here the directory would not open and it's considered an error.
2521            Confess("Could not open directory $dirName.");
2522      }      }
2523        # Return the result.
2524        return @retVal;
2525  }  }
2526    
 =head3 PutFile  
2527    
2528  C<< Tracer::PutFile($fileName, \@lines); >>  =head3 Insure
2529    
2530        Insure($dirName, $chmod);
2531    
2532  Write out a file from a list of lines of text.  Insure a directory is present.
2533    
2534  =over 4  =over 4
2535    
2536  =item fileName  =item dirName
2537    
2538  Name of the output file.  Name of the directory to check. If it does not exist, it will be created.
2539    
2540  =item lines  =item chmod (optional)
2541    
2542  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Security privileges to be given to the directory if it is created.
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
2543    
2544  =back  =back
2545    
2546  =cut  =cut
2547    
2548  sub PutFile {  sub Insure {
2549      # Get the parameters.      my ($dirName, $chmod) = @_;
2550      my ($fileName, $lines) = @_;      if (! -d $dirName) {
2551      # Open the output file.          Trace("Creating $dirName directory.") if T(2);
2552      my $handle = Open(undef, ">$fileName");          eval {
2553      # Count the lines written.              mkpath $dirName;
2554      if (ref $lines ne 'ARRAY') {              # If we have permissions specified, set them here.
2555          # Here we have a scalar, so we write it raw.              if (defined($chmod)) {
2556          print $handle $lines;                  chmod $chmod, $dirName;
2557          Trace("Scalar put to file $fileName.") if T(File => 3);              }
2558      } else {          };
2559          # Write the lines one at a time.          if ($@) {
2560          my $count = 0;              Confess("Error creating $dirName: $@");
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
             $count++;  
2561          }          }
         Trace("$count lines put to file $fileName.") if T(File => 3);  
2562      }      }
     # Close the output file.  
     close $handle;  
2563  }  }
2564    
2565  =head3 QTrace  =head3 ChDir
2566    
2567  C<< my $data = QTrace($format); >>      ChDir($dirName);
2568    
2569  Return the queued trace data in the specified format.  Change to the specified directory.
2570    
2571  =over 4  =over 4
2572    
2573  =item format  =item dirName
2574    
2575  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to which we want to change.
2576    
2577  =back  =back
2578    
2579  =cut  =cut
2580    
2581  sub QTrace {  sub ChDir {
2582      # Get the parameter.      my ($dirName) = @_;
2583      my ($format) = @_;      if (! -d $dirName) {
2584      # Create the return variable.          Confess("Cannot change to directory $dirName: no such directory.");
2585      my $retVal = "";      } else {
2586      # Only proceed if there is an actual queue.          Trace("Changing to directory $dirName.") if T(File => 4);
2587      if (@Queue) {          my $okFlag = chdir $dirName;
2588          # Process according to the format.          if (! $okFlag) {
2589          if ($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";  
2590          }          }
         # Clear the queue.  
         @Queue = ();  
2591      }      }
     # Return the formatted list.  
     return $retVal;  
2592  }  }
2593    
2594  =head3 Confess  =head3 SetPermissions
   
 C<< Confess($message); >>  
2595    
2596  Trace the call stack and abort the program with the specified message. When used with      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2597    
2598  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Set the permissions for a directory and all the files and folders inside it.
2599    In addition, the group ownership will be changed to the specified value.
2600    
2601  Will abort the program with a stack trace if the value of C<$recNum> is negative.  This method is more vulnerable than most to permission and compatability
2602    problems, so it does internal error recovery.
2603    
2604  =over 4  =over 4
2605    
2606  =item message  =item dirName
2607    
2608  Message to include in the trace.  Name of the directory to process.
2609    
2610  =back  =item group
2611    
2612  =cut  Name of the group to be assigned.
2613    
2614  sub Confess {  =item mask
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
2615    
2616  =head3 Assert  Permission mask. Bits that are C<1> in this mask will be ORed into the
2617    permission bits of any file or directory that does not already have them
2618    set to 1.
2619    
2620  C<< Assert($condition1, $condition2, ... $conditionN); >>  =item otherMasks
2621    
2622  Return TRUE if all the conditions are true. This method can be used in conjunction with  Map of search patterns to permission masks. If a directory name matches
2623  the OR operator and the L</Confess> method as a debugging assert.  one of the patterns, that directory and all its members and subdirectories
2624  So, for example  will be assigned the new pattern. For example, the following would
2625    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2626    
2627        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2628    
2629  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  The list is ordered, so the following would use 0777 for C<tmp1> and
2630    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2631    
2632  Will abort the program with a stack trace if the value of C<$recNum> is negative.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2633                                                       '^tmp' => 0666);
2634    
2635    Note that the pattern matches are all case-insensitive, and only directory
2636    names are matched, not file names.
2637    
2638    =back
2639    
2640  =cut  =cut
2641  sub Assert {  
2642      my $retVal = 1;  sub SetPermissions {
2643      LOOP: for my $condition (@_) {      # Get the parameters.
2644          if (! $condition) {      my ($dirName, $group, $mask, @otherMasks) = @_;
2645              $retVal = 0;      # Set up for error recovery.
2646              last LOOP;      eval {
2647            # Switch to the specified directory.
2648            ChDir($dirName);
2649            # Get the group ID.
2650            my $gid = getgrnam($group);
2651            # Get the mask for tracing.
2652            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2653            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2654            my $fixCount = 0;
2655            my $lookCount = 0;
2656            # @dirs will be a stack of directories to be processed.
2657            my @dirs = (getcwd());
2658            while (scalar(@dirs) > 0) {
2659                # Get the current directory.
2660                my $dir = pop @dirs;
2661                # Check for a match to one of the specified directory names. To do
2662                # that, we need to pull the individual part of the name off of the
2663                # whole path.
2664                my $simpleName = $dir;
2665                if ($dir =~ m!/([^/]+)$!) {
2666                    $simpleName = $1;
2667                }
2668                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2669                # Search for a match.
2670                my $match = 0;
2671                my $i;
2672                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2673                    my $pattern = $otherMasks[$i];
2674                    if ($simpleName =~ /$pattern/i) {
2675                        $match = 1;
2676                    }
2677                }
2678                # Find out if we have a match. Note we use $i-1 because the loop added 2
2679                # before terminating due to the match.
2680                if ($match && $otherMasks[$i-1] != $mask) {
2681                    # This directory matches one of the incoming patterns, and it's
2682                    # a different mask, so we process it recursively with that mask.
2683                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2684                } else {
2685                    # Here we can process normally. Get all of the non-hidden members.
2686                    my @submems = OpenDir($dir, 1);
2687                    for my $submem (@submems) {
2688                        # Get the full name.
2689                        my $thisMem = "$dir/$submem";
2690                        Trace("Checking member $thisMem.") if T(4);
2691                        $lookCount++;
2692                        if ($lookCount % 1000 == 0) {
2693                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2694                        }
2695                        # Fix the group.
2696                        chown -1, $gid, $thisMem;
2697                        # Insure this member is not a symlink.
2698                        if (! -l $thisMem) {
2699                            # Get its info.
2700                            my $fileInfo = stat $thisMem;
2701                            # Only proceed if we got the info. Otherwise, it's a hard link
2702                            # and we want to skip it anyway.
2703                            if ($fileInfo) {
2704                                my $fileMode = $fileInfo->mode;
2705                                if (($fileMode & $mask) != $mask) {
2706                                    # Fix this member.
2707                                    $fileMode |= $mask;
2708                                    chmod $fileMode, $thisMem;
2709                                    $fixCount++;
2710                                }
2711                                # If it's a subdirectory, stack it.
2712                                if (-d $thisMem) {
2713                                    push @dirs, $thisMem;
2714                                }
2715                            }
2716                        }
2717          }          }
2718      }      }
     return $retVal;  
2719  }  }
2720            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2721  =head3 Cluck      };
2722        # Check for an error.
2723  C<< Cluck($message); >>      if ($@) {
2724            Confess("SetPermissions error: $@");
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Cluck {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
2725      }      }
2726  }  }
2727    
2728  =head3 Min  =head3 GetLine
2729    
2730  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @data = Tracer::GetLine($handle);
2731    
2732  Return the minimum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2733    
2734  =over 4  =over 4
2735    
2736  =item $value1, $value2, ... $valueN  =item handle
2737    
2738  List of numbers to compare.  Open file handle from which to read.
2739    
2740  =item RETURN  =item RETURN
2741    
2742  Returns the lowest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2743    tab-delimited. If we are at the end of the file, then an empty list will be
2744    returned. If an empty line is read, a single list item consisting of a null
2745    string will be returned.
2746    
2747  =back  =back
2748    
2749  =cut  =cut
2750    
2751  sub Min {  sub GetLine {
2752      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2753      my ($retVal, @values) = @_;      my ($handle) = @_;
2754      # Loop through the remaining parameters, looking for the lowest.      # Declare the return variable.
2755      for my $value (@values) {      my @retVal = ();
2756          if ($value < $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2757              $retVal = $value;      # Read from the file.
2758        my $line = <$handle>;
2759        # Only proceed if we found something.
2760        if (defined $line) {
2761            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2762            # upload control and have a nonstandard EOL combination.
2763            $line =~ s/(\r|\n)+$//;
2764            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2765            if (T(File => 4)) {
2766                my $escapedLine = $line;
2767                $escapedLine =~ s/\n/\\n/g;
2768                $escapedLine =~ s/\r/\\r/g;
2769                $escapedLine =~ s/\t/\\t/g;
2770                Trace("Line read: -->$escapedLine<--");
2771          }          }
2772            # If the line is empty, return a single empty string; otherwise, parse
2773            # it into fields.
2774            if ($line eq "") {
2775                push @retVal, "";
2776            } else {
2777                push @retVal, split /\t/,$line;
2778      }      }
2779      # Return the minimum found.      } else {
2780      return $retVal;          # Trace the reason the read failed.
2781            Trace("End of file: $!") if T(File => 3);
2782        }
2783        # Return the result.
2784        return @retVal;
2785  }  }
2786    
2787  =head3 Max  =head3 PutLine
2788    
2789  C<< my $max = Max($value1, $value2, ... $valueN); >>      Tracer::PutLine($handle, \@fields, $eol);
2790    
2791  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
2792    output in tab-separated form, with a trailing new-line.
2793    
2794  =over 4  =over 4
2795    
2796  =item $value1, $value2, ... $valueN  =item handle
2797    
2798  List of numbers to compare.  Output file handle.
2799    
2800  =item RETURN  =item fields
2801    
2802  Returns the highest number in the list.  List of field values.
2803    
2804    =item eol (optional)
2805    
2806    End-of-line character (default is "\n").
2807    
2808  =back  =back
2809    
2810  =cut  =cut
2811    
2812  sub Max {  sub PutLine {
2813      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2814      my ($retVal, @values) = @_;      my ($handle, $fields, $eol) = @_;
2815      # Loop through the remaining parameters, looking for the highest.      # Write the data.
2816      for my $value (@values) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
2817  }  }
2818    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
2819    
2820  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 PrintLine
 is created for the key. Otherwise, the new value is pushed onto the list.  
2821    
2822  =over 4      Tracer::PrintLine($line);
   
 =item hash  
   
 Reference to the target hash.  
2823    
2824  =item key  Print a line of text with a trailing new-line.
2825    
2826  Key for which the value is to be added.  =over 4
2827    
2828  =item value1, value2, ... valueN  =item line
2829    
2830  List of values to add to the key's value list.  Line of text to print.
2831    
2832  =back  =back
2833    
2834  =cut  =cut
2835    
2836  sub AddToListMap {  sub PrintLine {
2837      # Get the parameters.      # Get the parameters.
2838      my ($hash, $key, @values) = @_;      my ($line) = @_;
2839      # Process according to whether or not the key already has a value.      # Print the line.
2840      if (! exists $hash->{$key}) {      print "$line\n";
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
2841  }  }
2842    
 =head3 DebugMode  
2843    
2844  C<< if (Tracer::DebugMode) { ...code... } >>  =head2 Other Useful Methods
2845    
2846    =head3 IDHASH
2847    
2848  Return TRUE if debug mode has been turned on, else abort.      my $hash = SHTargetSearch::IDHASH(@keys);
2849    
2850  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
2851  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.  
2852    
2853  =cut  =cut
2854    
2855  sub DebugMode {  sub IDHASH {
2856      # Declare the return variable.      my %retVal = map { $_ => $_ } @_;
2857      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;  
2858  }  }
2859    
2860  =head3 Strip  =head3 Pluralize
2861    
2862  C<< my $string = Tracer::Strip($line); >>      my $plural = Tracer::Pluralize($word);
2863    
2864  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
2865  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
2866  operating environments.  adds C<es>.
2867    
2868  =over 4  =over 4
2869    
2870  =item line  =item word
2871    
2872  Line of text to be stripped.  Singular word to pluralize.
2873    
2874  =item RETURN  =item RETURN
2875    
2876  The same line of text with all the line-ending characters chopped from the end.  Returns the probable plural form of the word.
2877    
2878  =back  =back
2879    
2880  =cut  =cut
2881    
2882  sub Strip {  sub Pluralize {
2883      # Get a copy of the parameter string.      # Get the parameters.
2884      my ($string) = @_;      my ($word) = @_;
2885      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2886      # Strip the line terminator characters.      my $retVal;
2887      $retVal =~ s/(\r|\n)+$//g;      if ($word =~ /s$/) {
2888            $retVal = $word . 'es';
2889        } else {
2890            $retVal = $word . 's';
2891        }
2892      # Return the result.      # Return the result.
2893      return $retVal;      return $retVal;
2894  }  }
2895    
2896  =head3 Pad  =head3 Numeric
2897    
2898  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $okFlag = Tracer::Numeric($string);
2899    
2900  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
2901  space, and the padding will be on the right side unless specified  if it is not numeric.
 in the third parameter.  
2902    
2903  =over 4  =over 4
2904    
2905  =item string  =item string
2906    
2907  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.  
2908    
2909  =item RETURN  =item RETURN
2910    
2911  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
2912  specified end so that it achieves the desired length.  is not numeric.
2913    
2914  =back  =back
2915    
2916  =cut  =cut
2917    
2918  sub Pad {  sub Numeric {
2919      # Get the parameters.      # Get the parameters.
2920      my ($string, $len, $left, $padChar) = @_;      my ($string) = @_;
2921      # Compute the padding character.      # We'll put the value in here if we succeed.
2922      if (! defined $padChar) {      my $retVal;
2923          $padChar = " ";      # Get a working copy of the string.
2924      }      my $copy = $string;
2925      # Compute the number of spaces needed.      # Trim leading and trailing spaces.
2926      my $needed = $len - length $string;      $copy =~ s/^\s+//;
2927      # Copy the string into the return variable.      $copy =~ s/\s+$//;
2928      my $retVal = $string;      # Check the result.
2929      # Only proceed if padding is needed.      if ($copy =~ /^[+-]?\d+$/) {
2930      if ($needed > 0) {          $retVal = $copy;
2931          # Create the pad string.      } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2932          my $pad = $padChar x $needed;          $retVal = $copy;
2933          # Affix it to the return value.      } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2934          if ($left) {          $retVal = $copy;
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
2935      }      }
2936      # Return the result.      # Return the result.
2937      return $retVal;      return $retVal;
2938  }  }
2939    
 =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`  
2940    
2941  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  
2942    
2943      TICK("./protein.cgi")      my $listValue = Tracer::ParseParm($string);
2944    
2945  it will work correctly in both environments.  Convert a parameter into a list reference. If the parameter is undefined,
2946    an undefined value will be returned. Otherwise, it will be parsed as a
2947    comma-separated list of values.
2948    
2949  =over 4  =over 4
2950    
2951  =item commandString  =item string
2952    
2953  The command string to pass to the system.  Incoming string.
2954    
2955  =item RETURN  =item RETURN
2956    
2957  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
2958    was undefined.
2959    
2960  =back  =back
2961    
2962  =cut  =cut
2963  #: Return Type @;  
2964  sub TICK {  sub ParseParm {
2965      # Get the parameters.      # Get the parameters.
2966      my ($commandString) = @_;      my ($string) = @_;
2967      # Chop off the dot-slash if this is Windows.      # Declare the return variable.
2968      if ($FIG_Config::win_mode) {      my $retVal;
2969          $commandString =~ s!^\./!!;      # Check for data.
2970        if (defined $string) {
2971            # We have some, so split it into a list.
2972            $retVal = [ split /\s*,\s*/, $string];
2973      }      }
2974      # Activate the command and return the result.      # Return the result.
2975      return `$commandString`;      return $retVal;
2976  }  }
2977    
2978  =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  
2979    
2980  Returns a two-element list consisting of a CGI query object and a variable hash for      my $string = Tracer::Now();
 the output page.  
2981    
2982  =back  Return a displayable time stamp containing the local time. Whatever format this
2983    method produces must be parseable by L</ParseDate>.
2984    
2985  =cut  =cut
2986    
2987  sub ScriptSetup {  sub Now {
2988      # Get the parameters.      return DisplayTime(time);
     my ($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, $varHash);  
2989  }  }
2990    
2991  =head3 ETracing  =head3 DisplayTime
2992    
2993  C<< ETracing($parameter); >>      my $string = Tracer::DisplayTime($time);
2994    
2995  Set up emergency tracing. Emergency tracing is tracing that is turned  Convert a time value to a displayable time stamp. Whatever format this
2996  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.  
2997    
2998  =over 4  =over 4
2999    
3000  =item parameter  =item time
3001    
3002  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.
3003  that scalar is used as the tracing key. If it is a CGI object, the  
3004  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item RETURN
3005  tracing key is taken from the C<TRACING> environment variable. If it  
3006  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.  
3007    
3008  =back  =back
3009    
3010  =cut  =cut
3011    
3012  sub ETracing {  sub DisplayTime {
3013      # Get the parameter.      my ($time) = @_;
3014      my ($parameter) = @_;      my $retVal = "(n/a)";
3015      # Check for CGI mode.      if (defined $time) {
3016      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3017      # Default to no tracing except errors.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3018      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";  
         }  
3019      }      }
3020      # 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);  
3021      }      }
3022    
3023    # Pad a number to 2 digits.
3024    sub _p2 {
3025        my ($value) = @_;
3026        $value = "0$value" if ($value < 10);
3027        return $value;
3028  }  }
3029    
3030  =head3 EmergencyFileName  =head3 Escape
3031    
3032  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $codedString = Tracer::Escape($realString);
3033    
3034  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
3035  the tracing information.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3036    result is to reverse the effect of L</UnEscape>.
3037    
3038  =over 4  =over 4
3039    
3040  =item tkey  =item realString
3041    
3042  Tracing key for the current program.  String to escape.
3043    
3044  =item RETURN  =item RETURN
3045    
3046  Returns the name of the file to contain the emergency tracing information.  Escaped equivalent of the real string.
3047    
3048  =back  =back
3049    
3050  =cut  =cut
3051    
3052  sub EmergencyFileName {  sub Escape {
3053      # Get the parameters.      # Get the parameter.
3054      my ($tkey) = @_;      my ($realString) = @_;
3055      # Compute the emergency tracing file name.      # Initialize the return variable.
3056      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal = "";
3057        # Loop through the parameter string, looking for sequences to escape.
3058        while (length $realString > 0) {
3059            # Look for the first sequence to escape.
3060            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3061                # Here we found it. The text preceding the sequence is in $1. The sequence
3062                # itself is in $2. First, move the clear text to the return variable.
3063                $retVal .= $1;
3064                # Strip the processed section off the real string.
3065                $realString = substr $realString, (length $2) + (length $1);
3066                # Get the matched character.
3067                my $char = $2;
3068                # If we have a CR, we are done.
3069                if ($char ne "\r") {
3070                    # It's not a CR, so encode the escape sequence.
3071                    $char =~ tr/\t\n/tn/;
3072                    $retVal .= "\\" . $char;
3073                }
3074            } else {
3075                # Here there are no more escape sequences. The rest of the string is
3076                # transferred unmodified.
3077                $retVal .= $realString;
3078                $realString = "";
3079            }
3080        }
3081        # Return the result.
3082        return $retVal;
3083  }  }
3084    
3085  =head3 EmergencyFileTarget  =head3 UnEscape
3086    
3087  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $realString = Tracer::UnEscape($codedString);
3088    
3089  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
3090  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
3091    be deleted.
3092    
3093  =over 4  =over 4
3094    
3095  =item tkey  =item codedString
3096    
3097  Tracing key for the current program.  String to un-escape.
3098    
3099  =item RETURN  =item RETURN
3100    
3101  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
3102    values.
3103    
3104  =back  =back
3105    
3106  =cut  =cut
3107    
3108  sub EmergencyFileTarget {  sub UnEscape {
3109      # Get the parameters.      # Get the parameter.
3110      my ($tkey) = @_;      my ($codedString) = @_;
3111      # Compute the emergency tracing file name.      # Initialize the return variable.
3112      return "$FIG_Config::temp/trace$tkey.log";      my $retVal = "";
3113        # Only proceed if the incoming string is nonempty.
3114        if (defined $codedString) {
3115            # Loop through the parameter string, looking for escape sequences. We can't do
3116            # translating because it causes problems with the escaped slash. ("\\t" becomes
3117            # "\<tab>" no matter what we do.)
3118            while (length $codedString > 0) {
3119                # Look for the first escape sequence.
3120                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3121                    # Here we found it. The text preceding the sequence is in $1. The sequence
3122                    # itself is in $2. First, move the clear text to the return variable.
3123                    $retVal .= $1;
3124                    $codedString = substr $codedString, (2 + length $1);
3125                    # Get the escape value.
3126                    my $char = $2;
3127                    # If we have a "\r", we are done.
3128                    if ($char ne 'r') {
3129                        # Here it's not an 'r', so we convert it.
3130                        $char =~ tr/\\tn/\\\t\n/;
3131                        $retVal .= $char;
3132                    }
3133                } else {
3134                    # Here there are no more escape sequences. The rest of the string is
3135                    # transferred unmodified.
3136                    $retVal .= $codedString;
3137                    $codedString = "";
3138                }
3139            }
3140        }
3141        # Return the result.
3142        return $retVal;
3143  }  }
3144    
3145  =head3 EmergencyTracingDest  =head3 Percent
3146    
3147  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my $percent = Tracer::Percent($number, $base);
3148    
3149  This method converts an emergency tracing destination to a real  Returns the percent of the base represented by the given number. If the base
3150  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.  
3151    
3152  =over 4  =over 4
3153    
3154  =item tkey  =item number
3155    
3156  Tracing key for this environment.  Percent numerator.
3157    
3158  =item myDest  =item base
3159    
3160  Destination from the emergency tracing file.  Percent base.
3161    
3162  =item RETURN  =item RETURN
3163    
3164  Returns a destination that can be passed into L</TSetup>.  Returns the percentage of the base represented by the numerator.
3165    
3166  =back  =back
3167    
3168  =cut  =cut
3169    
3170  sub EmergencyTracingDest {  sub Percent {
3171      # Get the parameters.      # Get the parameters.
3172      my ($tkey, $myDest) = @_;      my ($number, $base) = @_;
3173      # Declare the return variable.      # Declare the return variable.
3174      my $retVal;      my $retVal = 0;
3175      # Process according to the destination value.      # Compute the percent.
3176      if ($myDest eq 'FILE') {      if ($base != 0) {
3177          $retVal = ">" . EmergencyFileTarget($tkey);          $retVal = $number * 100 / $base;
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
3178      }      }
3179      # Return the result.      # Return the result.
3180      return $retVal;      return $retVal;
3181  }  }
3182    
3183  =head3 Emergency  =head3 In
3184    
3185  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $flag = Tracer::In($value, $min, $max);
3186    
3187  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.  
3188    
3189  =over 4  =cut
3190    
3191  =item tkey  sub In {
3192        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3193    }
3194    
 The tracing key. This is used to identify the control file and the trace file.  
3195    
3196  =item hours  =head3 Constrain
3197    
3198  Number of hours to keep emergency tracing alive.      my $constrained = Constrain($value, $min, $max);
3199    
3200  =item dest  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3201    
3202  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
3203    
3204  =item level  =item value
3205    
3206  Tracing level. A higher level means more trace messages.  Value to constrain.
3207    
3208  =item modules  =item min (optional)
3209    
3210  A list of the tracing modules to activate.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3211    
3212    =item max (optional)
3213    
3214    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3215    
3216    =item RETURN
3217    
3218    Returns the incoming value, constrained according to the other parameters.
3219    
3220  =back  =back
3221    
3222  =cut  =cut
3223    
3224  sub Emergency {  sub Constrain {
3225      # Get the parameters.      # Get the parameters.
3226      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($value, $min, $max) = @_;
3227      # Create the emergency file.      # Declare the return variable.
3228      my $specFile = EmergencyFileName($tkey);      my $retVal = $value;
3229      my $outHandle = Open(undef, ">$specFile");      # Apply the minimum constraint.
3230      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $min && $retVal < $min) {
3231            $retVal = $min;
3232        }
3233        # Apply the maximum constraint.
3234        if (defined $max && $retVal > $max) {
3235            $retVal = $max;
3236        }
3237        # Return the result.
3238        return $retVal;
3239  }  }
3240    
3241  =head3 EmergencyKey  =head3 Min
3242    
3243  C<< my $tkey = EmergencyKey($parameter); >>      my $min = Min($value1, $value2, ... $valueN);
3244    
3245  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.  
3246    
3247  =over 4  =over 4
3248    
3249  =item parameter  =item $value1, $value2, ... $valueN
3250    
3251  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.  
3252    
3253  =item RETURN  =item RETURN
3254    
3255  Returns the key to be used for labels in emergency tracing.  Returns the lowest number in the list.
3256    
3257  =back  =back
3258    
3259  =cut  =cut
3260    
3261  sub EmergencyKey {  sub Min {
3262      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3263      my ($parameter) = @_;      my ($retVal, @values) = @_;
3264      # Declare the return variable.      # Loop through the remaining parameters, looking for the lowest.
3265      my $retVal;      for my $value (@values) {
3266      # Determine the parameter type.          if ($value < $retVal) {
3267      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;  
         }  
3268      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3269      }      }
3270      # Return the result.      # Return the minimum found.
3271      return $retVal;      return $retVal;
3272  }  }
3273    
3274    =head3 Max
3275    
3276  =head3 TraceParms      my $max = Max($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
3277    
3278  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.  
3279    
3280  =over 4  =over 4
3281    
3282  =item cgi  =item $value1, $value2, ... $valueN
3283    
3284  CGI query object containing the parameters to trace.  List of numbers to compare.
3285    
3286    =item RETURN
3287    
3288    Returns the highest number in the list.
3289    
3290  =back  =back
3291    
3292  =cut  =cut
3293    
3294  sub TraceParms {  sub Max {
3295      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3296      my ($cgi) = @_;      my ($retVal, @values) = @_;
3297      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3298          # Here we want to trace the parameter data.      for my $value (@values) {
3299          my @names = $cgi->param;          if ($value > $retVal) {
3300          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}");  
3301          }          }
3302      }      }
3303        # Return the maximum found.
3304        return $retVal;
3305  }  }
3306    
3307  =head3 ScriptFinish  =head3 Strip
3308    
3309  C<< ScriptFinish($webData, $varHash); >>      my $string = Tracer::Strip($line);
3310    
3311  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
3312  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
3313  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.  
3314    
3315  A typical standard script would loook like the following.  =over 4
3316    
3317      BEGIN {  =item line
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3318    
3319      my ($cgi, $varHash) = ScriptSetup();  Line of text to be stripped.
3320      eval {  
3321          # ... get data from $cgi, put it in $varHash ...  =item RETURN
3322      };  
3323      if ($@) {  The same line of text with all the line-ending characters chopped from the end.
3324          Trace("Script Error: $@") if T(0);  
3325    =back
3326    
3327    =cut
3328    
3329    sub Strip {
3330        # Get a copy of the parameter string.
3331        my ($string) = @_;
3332        my $retVal = (defined $string ? $string : "");
3333        # Strip the line terminator characters.
3334        $retVal =~ s/(\r|\n)+$//g;
3335        # Return the result.
3336        return $retVal;
3337      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3338    
3339  The idea here is that even if the script fails, you'll see trace messages and  =head3 Trim
3340  useful output.  
3341        my $string = Tracer::Trim($line);
3342    
3343    Trim all spaces from the beginning and ending of a string.
3344    
3345  =over 4  =over 4
3346    
3347  =item webData  =item line
3348    
3349  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.  
3350    
3351  =item varHash (optional)  =item RETURN
3352    
3353  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.  
3354    
3355  =back  =back
3356    
3357  =cut  =cut
3358    
3359  sub ScriptFinish {  sub Trim {
3360      # Get the parameters.      # Get a copy of the parameter string.
3361      my ($webData, $varHash) = @_;      my ($string) = @_;
3362      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3363      my $outputString;      # Strip the front spaces.
3364      if (defined $varHash) {      $retVal =~ s/^\s+//;
3365          # Here we have a template file. We need to determine the template type.      # Strip the back spaces.
3366          my $template;      $retVal =~ s/\s+$//;
3367          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      # Return the result.
3368              $template = "$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 $outputString;  
3369  }  }
3370    
3371  =head3 Insure  =head3 Pad
3372    
3373  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3374    
3375  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3376    space, and the padding will be on the right side unless specified
3377    in the third parameter.
3378    
3379  =over 4  =over 4
3380    
3381  =item dirName  =item string
3382    
3383  Name of the directory to check. If it does not exist, it will be created.  String to be padded.
3384    
3385  =back  =item len
3386    
3387  =cut  Desired length of the padded string.
3388    
3389  sub Insure {  =item left (optional)
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(File => 2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
3390    
3391  =head3 ChDir  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3392    
3393  C<< ChDir($dirName); >>  =item padChar (optional)
3394    
3395  Change to the specified directory.  Character to use for padding. The default is a space.
3396    
3397  =over 4  =item RETURN
3398    
3399  =item dirName  Returns a copy of the original string with the pad character added to the
3400    specified end so that it achieves the desired length.
3401    
3402    =back
3403    
3404    =cut
3405    
3406    sub Pad {
3407        # Get the parameters.
3408        my ($string, $len, $left, $padChar) = @_;
3409        # Compute the padding character.
3410        if (! defined $padChar) {
3411            $padChar = " ";
3412        }
3413        # Compute the number of spaces needed.
3414        my $needed = $len - length $string;
3415        # Copy the string into the return variable.
3416        my $retVal = $string;
3417        # Only proceed if padding is needed.
3418        if ($needed > 0) {
3419            # Create the pad string.
3420            my $pad = $padChar x $needed;
3421            # Affix it to the return value.
3422            if ($left) {
3423                $retVal = $pad . $retVal;
3424            } else {
3425                $retVal .= $pad;
3426            }
3427        }
3428        # Return the result.
3429        return $retVal;
3430    }
3431    
3432  Name of the directory to which we want to change.  =head3 EOF
3433    
3434  =back  This is a constant that is lexically greater than any useful string.
3435    
3436  =cut  =cut
3437    
3438  sub ChDir {  sub EOF {
3439      my ($dirName) = @_;      return "\xFF\xFF\xFF\xFF\xFF";
     if (! -d $dirName) {  
         Confess("Cannot change to directory $dirName: no such directory.");  
     } else {  
         Trace("Changing to directory $dirName.") if T(File => 4);  
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3440  }  }
3441    
3442  =head3 SendSMS  =head3 TICK
   
 C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  
3443    
3444  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the      my @results = TICK($commandString);
 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  
3445    
3446      $phone =  { user => 'BruceTheHumanPet',  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3447                  password => 'silly',  dot-slash (C<./> will be removed. So, for example, if you were doing
                 api_id => '2561022' };  
3448    
3449  The original purpose of this method was to insure Bruce would be notified immediately when the      `./protein.cgi`
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3450    
3451  The message ID will be returned if successful, and C<undef> if an error occurs.  from inside a CGI script, it would work fine in Unix, but would issue an error message
3452    in Windows complaining that C<'.'> is not a valid command. If instead you code
3453    
3454  =over 4      TICK("./protein.cgi")
3455    
3456  =item phoneNumber  it will work correctly in both environments.
3457    
3458  Phone number to receive the message, in international format. A United States phone number  =over 4
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3459    
3460  =item msg  =item commandString
3461    
3462  Message to send to the specified phone.  The command string to pass to the system.
3463    
3464  =item RETURN  =item RETURN
3465    
3466  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
3467    
3468  =back  =back
3469    
3470  =cut  =cut
3471    #: Return Type @;
3472  sub SendSMS {  sub TICK {
3473      # Get the parameters.      # Get the parameters.
3474      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3475      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3476      my $retVal;      if ($FIG_Config::win_mode) {
3477      # Only proceed if we have phone support.          $commandString =~ s!^\./!!;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
3478      }      }
3479      # Return the result.      # Activate the command and return the result.
3480      return $retVal;      return `$commandString`;
3481  }  }
3482    
3483    
3484  =head3 CommaFormat  =head3 CommaFormat
3485    
3486  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3487    
3488  Insert commas into a number.  Insert commas into a number.
3489    
# Line 2749