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revision 1.69, Mon Oct 2 02:59:47 2006 UTC revision 1.99, Wed May 7 23:00:16 2008 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    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyIP ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
45  =head2 Introduction  =head2 Tracing
46    
47  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
48  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
49  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
50  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
51  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
52  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
53  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
54  appear. To generate a trace message, use the following syntax.  appear.
55    
56    =head3 Putting Trace Messages in Your Code
57    
58  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
59    
60        Trace($message) if T(errors => 4);
61    
62  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
63  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
64    
65  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
66    
67  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
68    
# Line 61  Line 70 
70  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
71  active and the trace level is 2 or more.  active and the trace level is 2 or more.
72    
73  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
74    
75    In scripts, where no package name is available, the category defaults to C<main>.
76    
77    =head3 Custom Tracing
78    
79    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80    the preferred method, but a knowledge of how custom tracing works can make the more modern
81    L</Emergency Tracing> easier to understand.
82    
83  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84  of category names, and a set of options. The trace level and list of category names are  a list of category names, and a destination. The trace level and list of category names are
85  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
86    
87  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
88    
89  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
90  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
91    
92  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
93  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
94  useful in a CGI environment.  useful in a CGI environment.
95    
96  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
97    
98  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
99  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
100  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
101  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
102  it easier to debug page formatting problems.  it easier to debug page formatting problems.
103    
104  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
105    a file at the same time. To trace to a file, specify the filename with an output character in front
106    of it.
107    
108        TSetup('4 SQL', ">$fileName");
109    
110    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111    bracket.
112    
113        TSetup('3 *', "+>$fileName");
114    
115  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
116  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
117  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
118  being used out in the field.  being used out in the field.
119    
120    =head3 Trace Levels
121    
122  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
123  a suggestion.  a suggestion.
124    
# Line 122  Line 150 
150  =back  =back
151    
152  The format of trace messages is important because some utilities analyze trace files.  The format of trace messages is important because some utilities analyze trace files.
153  The time stamp is between square brackets, the module name between angle brackets,  There are three fields-- the time stamp, the category name, and the text.
154  a colon (C<:>), and the message text after that. If the square brackets or angle  The time stamp is between square brackets and the category name between angle brackets.
155  brackets are missing, then the trace management utilities assume that they  After the category name there is a colon (C<:>) followed by the message text.
156  are encountering a set of pre-formatted lines.  If the square brackets or angle brackets are missing, then the trace management
157    utilities assume that they are encountering a set of pre-formatted lines.
158    
159    Note, however, that this formatting is done automatically by the tracing functions. You
160    only need to know about it if you want to parse a trace file.
161    
162    =head3 Emergency Tracing
163    
164    Sometimes, you need a way for tracing to happen automatically without putting parameters
165    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167    that you specify a tracing key. For command-line tools, the key is
168    taken from the C<TRACING> environment variable. For web services, the key is taken from
169    a cookie. Either way, the key tells the tracing facility who you are, so that you control
170    the tracing in your environment without stepping on other users.
171    
172    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173    generate one for you.
174    
175    You can activate and de-activate emergency tracing from the debugging control panel, as
176    well as display the trace file itself.
177    
178    To enable emergency tracing in your code, call
179    
180        ETracing($cgi)
181    
182    from a web script and
183    
184        ETracing()
185    
186    from a command-line script.
187    
188    The web script will look for the tracing key in the cookies, and the command-line
189    script will look for it in the C<TRACING> environment variable. If you are
190    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191    will be configured automatically.
192    
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  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
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213    =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224  =head2 Public Methods  =cut
225    
226    sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 197  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 219  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  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.  
312    
313  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.  
314    
315  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  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  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.  
320    
321  =over 4  =cut
322    
323  =item SQL  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Traces SQL commands and activity.  =head3 ParseDate
328    
329  =item Tracer      my $time = Tracer::ParseDate($dateString);
330    
331  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =back  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  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.  
341    
342      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
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  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  
347    
348  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.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
353    
354  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.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
360    
361      my ($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);  
362    
363    =cut
364    
365  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
366  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
415    
416  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
417    
418      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
419    
420  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
421    
422  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
423    
424      -user=Bruce -background  Name of the file to receive the error output.
425    
426  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
427    
428  Finally, if the special option C<-h> is specified, the option names will  =cut
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
429    
430      TransactFeatures -h  sub LogErrors {
431        # Get the file name.
432        my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437  he would see the following output.  =head3 Trace
438    
439      TransactFeatures [options] command transactionDirectory IDfile      Trace($message);
         -trace    tracing level (default 2)  
         -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  
440    
441  The caller has the option of modifying the tracing scheme by placing a value  Write a trace message to the target location specified in L</TSetup>. If there has not been
442  for C<trace> in the incoming options hash. The default value can be overridden,  any prior call to B<TSetup>.
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
443    
444      { trace => [0, "tracing level (default 0)"],  =over 4
        ...  
445    
446  would set the default trace level to 0 instead of 2, while  =item message
447    
448      { trace => ["2-", "tracing level (default 2)"],  Message to write.
        ...  
449    
450  would leave the default at 2, but trace only to the log file, not to the  =back
 standard output.  
451    
452  The parameters to this method are as follows.  =cut
453    
454  =over 4  sub Trace {
455        # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  =item categories  =head3 T
504    
505  Reference to a list of tracing category names. These should be names of      my $switch = T($category, $traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
506    
507  =item options      or
508    
509  Reference to a hash containing the legal options for the current command mapped      my $switch = T($traceLevel);
 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).  
510    
511  =item parmHelp  Return TRUE if the trace level is at or above a specified value and the specified category
512    is active, else FALSE. If no category is specified, the caller's package name is used.
513    
514  A string that vaguely describes the positional parameters. This is used  =over 4
 if the user specifies the C<-h> option.  
515    
516  =item argv  =item category
517    
518  List of command line parameters, including the option switches, which must  Category to which the message belongs. If not specified, the caller's package name is
519  precede the positional parameters and be prefixed by a hyphen.  used.
520    
521    =item traceLevel
522    
523    Relevant tracing level.
524    
525  =item RETURN  =item RETURN
526    
527  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Add the tracing options.          if (!defined $traceLevel) {
541      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
542          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
543      }              # omitted, the first parameter will be the tracelevel. So, the
544      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
545      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
546      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
547      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
548      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
549      # contains the default values rather than the default value              if (!$package) {
550      # and the description. While we're at it, we'll memorize the                  $category = "main";
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if SQL is to  
     # be traced.  
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
     }  
     # Add the default categories.  
     push @cats, "Tracer";  
     # Next, we create the category string by joining the categories.  
     my $cats = join(" ", @cats);  
     # Check to determine whether or not the caller wants to turn off tracing  
     # to the standard output.  
     my $traceLevel = $retOptions->{trace};  
     my $textOKFlag = 1;  
     if ($traceLevel =~ /^(.)-/) {  
         $traceLevel = $1;  
         $textOKFlag = 0;  
     }  
     # Now we set up the trace mode.  
     my $traceMode;  
     # Verify that we can open a file in the FIG temporary directory.  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         # Here we can trace to a file.  
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
         }  
         # Close the test file.  
         close TESTTRACE;  
     } else {  
         # Here we can't trace to a file. We trace to the standard output if it's  
         # okay, and the error log otherwise.  
         if ($textOKFlag) {  
             $traceMode = "TEXT";  
551          } else {          } else {
552              $traceMode = "WARN";                  my @cats = split /::/, $package;
553                    $category = $cats[$#cats];
554          }          }
555      }      }
556      # Now set up the tracing.          # Save the category name and level.
557      TSetup("$traceLevel $cats", $traceMode);          $LastCategory = $category;
558      # Check for the "h" option. If it is specified, dump the command-line          $LastLevel = $traceLevel;
559      # options and exit the program.          # Convert it to lower case before we hash it.
560      if ($retOptions->{h}) {          $category = lc $category;
561          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          # Use the category and tracelevel to compute the result.
562          print "$1 [options] $parmHelp\n";          if (ref $traceLevel) {
563          for my $key (sort keys %{$options}) {              Confess("Bad trace level.");
564              my $name = Pad($key, $longestName, 0, ' ');          } elsif (ref $TraceLevel) {
565              my $desc = $options->{$key}->[1];              Confess("Bad trace config.");
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
             }  
             print "  $name $desc\n";  
566          }          }
567          exit(0);          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
568      }      }
569      # Return the parsed parameters.      # Return the computed result.
570      return ($retOptions, @retParameters);      return $retVal;
571  }  }
572    
573  =head3 Setups  =head3 QTrace
   
 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  
574    
575  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
576    
577  =head3 Open  Return the queued trace data in the specified format.
578    
579  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
580    
581  Open a file.  =item format
582    
583  The I<$fileSpec> is essentially the second argument of the PERL C<open>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
584    
585      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
586    
587  would open for output appended to the specified file, and  =cut
588    
589      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
590        # Get the parameter.
591        my ($format) = @_;
592        # Create the return variable.
593        my $retVal = "";
594        # Only proceed if there is an actual queue.
595        if (@Queue) {
596            # Process according to the format.
597            if ($format =~ m/^HTML$/i) {
598                # Convert the queue into an HTML list.
599                $retVal = "<ul>\n";
600                for my $line (@Queue) {
601                    my $escapedLine = CGI::escapeHTML($line);
602                    $retVal .= "<li>$escapedLine</li>\n";
603                }
604                $retVal .= "</ul>\n";
605            } elsif ($format =~ m/^TEXT$/i) {
606                # Convert the queue into a list of text lines.
607                $retVal = join("\n", @Queue) . "\n";
608            }
609            # Clear the queue.
610            @Queue = ();
611        }
612        # Return the formatted list.
613        return $retVal;
614    }
615    
616  would open a pipe that sorts the records written and removes duplicates. Note  =head3 Confess
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
617    
618      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
619    
620  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
621  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
622  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
623    
624      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
625    
626  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
627    
628      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
629    
630  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
631    
632      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
633    
634  =over 4  =back
635    
636  =item fileHandle  =cut
637    
638  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
639  and returned as the value of this method.      # Get the parameters.
640        my ($message) = @_;
641        # Set up the category and level.
642        $LastCategory = "(confess)";
643        $LastLevel = 0;
644        if (! defined($FIG_Config::no_tool_hdr)) {
645            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
646            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
647            # Only proceed if the tool header file is actually present.
648            if (-f $toolHeaderFile) {
649                my $fh;
650                if (open $fh, "<$toolHeaderFile") {
651                    my @lines = <$fh>;
652                    Trace("Tool header has " . scalar(@lines) . " lines.");
653                }
654            }
655        }
656        # Trace the call stack.
657        Cluck($message);
658        # Abort the program.
659        croak(">>> $message");
660    }
661    
662  =item fileSpec  =head3 Warn
663    
664  File name and mode, as per the PERL C<open> function.      Warn($message);
665    
666  =item message (optional)  This method traces an important message. If an RSS feed is configured
667    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
668    then the message will be echoed to the feed. In general, a tracing
669    destination of C<WARN> indicates that the caller is running as a web
670    service in a production environment; however, this is not a requirement.
671    
672    The L</Cluck> method calls this one for its final message. Since
673    L</Confess> calls L</Cluck>, this means that any error which is caught
674    and confessed will put something in the feed. This insures that someone
675    will be alerted relatively quickly when a failure occurs.
676    
677  Error message to use if the open fails. If omitted, a standard error message  =over 4
 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>.  
678    
679  =item RETURN  =item message
680    
681  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
682    
683  =back  =back
684    
685  =cut  =cut
686    
687  sub Open {  sub Warn {
688      # Get the parameters.      # Get the parameters.
689      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
690      # Attempt to open the file.      # Trace the message.
691      my $rv = open $fileHandle, $fileSpec;      Trace($message);
692      # If the open failed, generate an error message.      # An error here would be disastrous. Note, however, that we aren't too worried
693      if (! $rv) {      # about losing events. The error log is always available for the occasions where
694          # Save the system error message.      # we mess up.
695          my $sysMessage = $!;      eval {
696          # See if we need a default message.          # Do we need to put this in the RSS feed?
697          if (!$message) {          if ($FIG_Config::error_feed && $Destination eq 'WARN') {
698              # Clean any obvious mode characters and leading spaces from the              # Yes. We now need to compute the date, the link, and the title.
699              # filename.              # First, the date, in a very specific format.
700              my ($fileName) = FindNamePart($fileSpec);              my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
701              $message = "Could not open \"$fileName\"";                  (tz_local_offset() / 30);
702                # We'll put the link and title in here.
703                my ($link, $title);
704                # Environment data goes in here.
705                my $environment;
706                # HTML-escape the message.
707                my $escaped = CGI::escapeHTML($message);
708                # If we have a CGI object, then this is a web error. Otherwise, it's
709                # command-line.
710                if (defined $SavedCGI) {
711                    # We're in a web service. The title is the user's IP, and the link
712                    # is the URL that got us here.
713                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
714                    $title = "Event Reported at IP address $key: $escaped";
715                    $link = $SavedCGI->url(-full => 1, -query => 1);
716                    # We need the user agent string.
717                    $environment = "User Agent $ENV{HTTP_USER_AGENT}."
718                } else {
719                    # No CGI object, so we're a command-line tool. Use the tracing
720                    # key and the PID as the user identifier.
721                    my $key = EmergencyKey();
722                    $title = "Event Reported by $key Process $$: $escaped";
723                    # Set the link to the development NMPDR. There is really no good
724                    # choice here.
725                    $link = "http://$FIG_Config::dev_server";
726                    # We need the command
727                    $environment = "Command $ENV{_}.";
728                }
729                # Build a GUID. We use the current time, the title, and the process ID,
730                # then digest the result.
731                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
732                # Finally, the description. This is a stack trace plus various environmental stuff.
733                my @trace = LongMess();
734                my $trace = join "; ", @trace;
735                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
736                # Okay, we have all the pieces. Create a hash of the new event.
737                my $newItem = { title => $title,
738                                description => $description,
739                                link => $link,
740                                category => $LastCategory,
741                                pubDate => $date,
742                                guid => $guid,
743                               };
744                # We need XML capability for this.
745                require XML::Simple;
746                # The RSS document goes in here.
747                my $rss;
748                # Get the name of the RSS file. It's in the FIG temporary directory.
749                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
750                # Does it exist?
751                if (-s $fileName) {
752                    # Slurp it in.
753                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
754                } else {
755                    my $size = -s $fileName;
756                    # Create an empty channel.
757                    $rss = {
758                        channel => {
759                            title => 'NMPDR Warning Feed',
760                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
761                            description => "Important messages regarding the status of the NMPDR.",
762                            generator => "NMPDR Trace Facility",
763                            docs => "http://blogs.law.harvard.edu/tech/rss",
764                            item => []
765                        },
766                    };
767          }          }
768          # Terminate with an error using the supplied message and the              # Get the channel object.
769          # error message from the file system.              my $channel = $rss->{channel};
770          Confess("$message: $!");              # Update the last-build date.
771                $channel->{lastBuildDate} = $date;
772                # Get the item array.
773                my $items = $channel->{item};
774                # Insure it has only 100 entries.
775                while (scalar @{$items} > 100) {
776                    pop @{$items};
777                }
778                # Add our new item at the front.
779                unshift @{$items}, $newItem;
780                # Replace the file.
781                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
782                                              NoEscape => 1);
783                # We don't use Open here because we can't afford an error.
784                if (open XMLOUT, ">$fileName") {
785                    print XMLOUT $xml;
786                    close XMLOUT;
787      }      }
788      # Return the file handle.          }
789      return $fileHandle;      };
790        # There's no "if ($@)" here, because putting an error message in the log
791        # saying that we missed putting an error message in the feed of messages
792        # in the log is not going to help anybody.
793  }  }
794    
795  =head3 FindNamePart  =head3 Assert
796    
797  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      Assert($condition1, $condition2, ... $conditionN);
798    
799  Extract the portion of a file specification that contains the file name.  Return TRUE if all the conditions are true. This method can be used in conjunction with
800    the OR operator and the L</Confess> method as a debugging assert.
801    So, for example
802    
803  A file specification is the string passed to an C<open> call. It specifies the file      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
804    
805      >>/usr/fig/myfile.txt  Will abort the program with a stack trace if the value of C<$recNum> is negative.
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
806    
807  If the method cannot find a file name using its normal methods, it will return the  =cut
808  whole incoming string.  sub Assert {
809        my $retVal = 1;
810        LOOP: for my $condition (@_) {
811            if (! $condition) {
812                $retVal = 0;
813                last LOOP;
814            }
815        }
816        return $retVal;
817    }
818    
819  =over 4  =head3 Cluck
820    
821  =item fileSpec      Cluck($message);
822    
823  File specification string from which the file name is to be extracted.  Trace the call stack. Note that for best results, you should qualify the call with a
824    trace condition. For example,
825    
826  =item RETURN      Cluck("Starting record parse.") if T(3);
827    
828  Returns a three-element list. The first element contains the file name portion of  will only trace the stack if the trace level for the package is 3 or more.
829  the specified string, or the whole string if a file name cannot be found via normal  
830  methods. The second element contains the start position of the file name portion and  =over 4
831  the third element contains the length.  
832    =item message
833    
834    Message to include in the trace.
835    
836  =back  =back
837    
838  =cut  =cut
839  #: Return Type $;  
840  sub FindNamePart {  sub Cluck {
841      # Get the parameters.      # Get the parameters.
842      my ($fileSpec) = @_;      my ($message) = @_;
843      # Default to the whole input string.      # Trace what's happening.
844      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
845      # Parse out the file name if we can.      # Get the stack trace.
846      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
847          $retVal = $2;      # Convert the trace to a series of messages.
848          $len = length $retVal;      for my $line (@trace) {
849          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
850            $line =~ s/^\t/    /;
851            # Trace the line.
852            Trace($line);
853      }      }
854      # Return the result.      # Issue a warning. This displays the event message and inserts it into the RSS error feed.
855      return ($retVal, $pos, $len);      Warn($message);
856  }  }
857    
858  =head3 OpenDir  =head3 LongMess
859    
860  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @lines = Tracer::LongMess();
861    
862  Open a directory and return all the file names. This function essentially performs  Return a stack trace with all tracing methods removed. The return will be in the form of a list
863  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  of message strings.
 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,  
864    
865      my @files = OpenDir("/Volumes/fig/contigs", 1);  =cut
866    
867  is effectively the same as  sub LongMess {
868        # Declare the return variable.
869        my @retVal = ();
870        my $confession = longmess("");
871        for my $line (split /\s*\n/, $confession) {
872            unless ($line =~ /Tracer\.pm/) {
873                # Here we have a line worth keeping. Push it onto the result list.
874                push @retVal, $line;
875            }
876        }
877        # Return the result.
878        return @retVal;
879    }
880    
881      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  =head3 ScriptSetup (deprecated)
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
882    
883  Similarly, the following code      my ($cgi, $varHash) = ScriptSetup($noTrace);
884    
885      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Perform standard tracing and debugging setup for scripts. The value returned is
886    the CGI object followed by a pre-built variable hash. At the end of the script,
887    the client should call L</ScriptFinish> to output the web page.
888    
889  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method calls L</ETracing> to configure tracing, which allows the tracing
890  automatically returns an empty list if the directory fails to open.  to be configured via the emergency tracing form on the debugging control panel.
891    Tracing will then be turned on automatically for all programs that use the L</ETracing>
892    method, which includes every program that uses this method or L</StandardSetup>.
893    
894  =over 4  =over 4
895    
896  =item dirName  =item noTrace (optional)
   
 Name of the directory to open.  
   
 =item filtered  
897    
898  TRUE if files whose names begin with a period (C<.>) should be automatically removed  If specified, tracing will be suppressed. This is useful if the script wants to set up
899  from the list, else FALSE.  tracing manually.
900    
901  =item flag  =item RETURN
902    
903  TRUE if a failure to open is okay, else FALSE  Returns a two-element list consisting of a CGI query object and a variable hash for
904    the output page.
905    
906  =back  =back
907    
908  =cut  =cut
909  #: Return Type @;  
910  sub OpenDir {  sub ScriptSetup {
911      # Get the parameters.      # Get the parameters.
912      my ($dirName, $filtered, $flag) = @_;      my ($noTrace) = @_;
913      # Declare the return variable.      # Get the CGI query object.
914      my @retVal = ();      my $cgi = CGI->new();
915      # Open the directory.      # Set up tracing if it's not suppressed.
916      if (opendir(my $dirHandle, $dirName)) {      ETracing($cgi) unless $noTrace;
917          # The directory opened successfully. Get the appropriate list according to the      # Create the variable hash.
918          # strictures of the filter parameter.      my $varHash = { results => '' };
919          if ($filtered) {      # Return the query object and variable hash.
920              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      return ($cgi, $varHash);
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
921  }  }
922    
923  =head3 SetLevel  =head3 ETracing
924    
925  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
926    
927  Modify the trace level. A higher trace level will cause more messages to appear.  Set up emergency tracing. Emergency tracing is tracing that is turned
928    on automatically for any program that calls this method. The emergency
929    tracing parameters are stored in a a file identified by a tracing key.
930    If this method is called with a CGI object, then the tracing key is
931    taken from a cookie. If it is called with no parameters, then the tracing
932    key is taken from an environment variable. If it is called with a string,
933    the tracing key is that string.
934    
935  =over 4  =over 4
936    
937  =item newLevel  =item parameter
938    
939  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
940    that scalar is used as the tracing key. If it is a CGI object, the
941    tracing key is taken from the C<IP> cookie. If it is omitted, the
942    tracing key is taken from the C<TRACING> environment variable. If it
943    is a CGI object and emergency tracing is not on, the C<Trace> and
944    C<TF> parameters will be used to determine the type of tracing.
945    
946  =back  =back
947    
948  =cut  =cut
949    
950  sub SetLevel {  sub ETracing {
951      $TraceLevel = $_[0];      # Get the parameter.
952        my ($parameter) = @_;
953        # Check for CGI mode.
954        if (defined $parameter && ref $parameter eq 'CGI') {
955            $SavedCGI = $parameter;
956        } else {
957            $SavedCGI = undef;
958        }
959        # Default to no tracing except errors.
960        my ($tracing, $dest) = ("0", "WARN");
961        # Check for emergency tracing.
962        my $tkey = EmergencyKey($parameter);
963        my $emergencyFile = EmergencyFileName($tkey);
964        if (-e $emergencyFile) {
965            # We have the file. Read in the data.
966            my @tracing = GetFile($emergencyFile);
967            # Pull off the time limit.
968            my $expire = shift @tracing;
969            # Convert it to seconds.
970            $expire *= 3600;
971            # Check the file data.
972            my $stat = stat($emergencyFile);
973            my ($now) = gettimeofday;
974            if ($now - $stat->mtime > $expire) {
975                # Delete the expired file.
976                unlink $emergencyFile;
977            } else {
978                # Emergency tracing is on. Pull off the destination and
979                # the trace level;
980                $dest = shift @tracing;
981                my $level = shift @tracing;
982                # Convert the destination to a real tracing destination.
983                # temp directory.
984                $dest = EmergencyTracingDest($tkey, $dest);
985                # Insure Tracer is specified.
986                my %moduleHash = map { $_ => 1 } @tracing;
987                $moduleHash{Tracer} = 1;
988                # Set the trace parameter.
989                $tracing = join(" ", $level, sort keys %moduleHash);
990            }
991        } elsif (defined $SavedCGI) {
992            # There's no emergency tracing, but we have a CGI object, so check
993            # for tracing from the form parameters.
994            if ($SavedCGI->param('Trace')) {
995                # Here the user has requested tracing via a form.
996                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
997                $tracing = $SavedCGI->param('Trace') . " Tracer";
998            }
999        }
1000        # Setup the tracing we've determined from all the stuff above.
1001        TSetup($tracing, $dest);
1002        # Check to see if we're a web script.
1003        if (defined $SavedCGI) {
1004            # Yes we are. Trace the form and environment data.
1005            TraceParms($SavedCGI);
1006            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1007            # emitted by the script in its raw form.
1008            if (T(Raw => 3)) {
1009                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1010  }  }
   
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
   
 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;  
1011  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1012  }  }
1013    
1014  =head3 LogErrors  =head3 EmergencyFileName
1015    
1016  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1017    
1018  Route the standard error output to a log file.  Return the emergency tracing file name. This is the file that specifies
1019    the tracing information.
1020    
1021  =over 4  =over 4
1022    
1023  =item fileName  =item tkey
1024    
1025  Name of the file to receive the error output.  Tracing key for the current program.
1026    
1027    =item RETURN
1028    
1029    Returns the name of the file to contain the emergency tracing information.
1030    
1031  =back  =back
1032    
1033  =cut  =cut
1034    
1035  sub LogErrors {  sub EmergencyFileName {
1036      # Get the file name.      # Get the parameters.
1037      my ($fileName) = @_;      my ($tkey) = @_;
1038      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1039      open STDERR, '>', $fileName;      return "$FIG_Config::temp/Emergency$tkey.txt";
1040  }  }
1041    
1042  =head3 ReadOptions  =head3 EmergencyFileTarget
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1043    
1044  I<optionName>C<=>I<optionValue>C<; >I<comment>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1045    
1046  The option name must consist entirely of letters, digits, and the punctuation characters  Return the emergency tracing target file name. This is the file that receives
1047  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  the tracing output for file-based tracing.
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1048    
1049  =over 4  =over 4
1050    
1051  =item fileName  =item tkey
1052    
1053  Name of the file containing the option data.  Tracing key for the current program.
1054    
1055  =item RETURN  =item RETURN
1056    
1057  Returns a hash mapping the option names specified in the file to their corresponding option  Returns the name of the file to contain the trace output.
 value.  
1058    
1059  =back  =back
1060    
1061  =cut  =cut
1062    
1063  sub ReadOptions {  sub EmergencyFileTarget {
1064      # Get the parameters.      # Get the parameters.
1065      my ($fileName) = @_;      my ($tkey) = @_;
1066      # Open the file.      # Compute the emergency tracing file name.
1067      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      return "$FIG_Config::temp/trace$tkey.log";
     # Count the number of records read.  
     my ($records, $comments) = 0;  
     # Create the return hash.  
     my %retVal = ();  
     # Loop through the file, accumulating key-value pairs.  
     while (my $line = <CONFIGFILE>) {  
         # Denote we've read a line.  
         $records++;  
         # Determine the line type.  
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
     }  
     # Return the hash created.  
     return %retVal;  
1068  }  }
1069    
1070  =head3 GetOptions  =head3 EmergencyTracingDest
1071    
1072  C<< Tracer::GetOptions(\%defaults, \%options); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1073    
1074  Merge a specified set of options into a table of defaults. This method takes two hash references  This method converts an emergency tracing destination to a real
1075  as input and uses the data from the second to update the first. If the second does not exist,  tracing destination. The main difference is that if the
1076  there will be no effect. An error will be thrown if one of the entries in the second hash does not  destination is C<FILE> or C<APPEND>, we convert it to file
1077  exist in the first.  output. If the destination is C<DUAL>, we convert it to file
1078    and standard output.
1079    
1080  Consider the following example.  =over 4
1081    
1082  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =item tkey
1083    
1084  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  Tracing key for this environment.
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1085    
1086  C<< {databaseType => 'Oracle'} >>  =item myDest
1087    
1088  an error will occur because the B<databaseType> option does not exist.  Destination from the emergency tracing file.
1089    
1090  =over 4  =item RETURN
1091    
1092  =item defaults  Returns a destination that can be passed into L</TSetup>.
1093    
1094  Table of default option values.  =back
1095    
1096  =item options  =cut
1097    
1098  Table of overrides, if any.  sub EmergencyTracingDest {
1099        # Get the parameters.
1100        my ($tkey, $myDest) = @_;
1101        # Declare the return variable.
1102        my $retVal = $myDest;
1103        # Process according to the destination value.
1104        if ($myDest eq 'FILE') {
1105            $retVal = ">" . EmergencyFileTarget($tkey);
1106        } elsif ($myDest eq 'APPEND') {
1107            $retVal = ">>" . EmergencyFileTarget($tkey);
1108        } elsif ($myDest eq 'DUAL') {
1109            $retVal = "+>" . EmergencyFileTarget($tkey);
1110        } elsif ($myDest eq 'WARN') {
1111            $retVal = "WARN";
1112        }
1113        # Return the result.
1114        return $retVal;
1115    }
1116    
1117  =item RETURN  =head3 Emergency
1118    
1119  Returns a reference to the default table passed in as the first parameter.      Emergency($key, $hours, $dest, $level, @modules);
1120    
1121    Turn on emergency tracing. This method is normally invoked over the web from
1122    a debugging console, but it can also be called by the C<trace.pl> script.
1123    The caller specifies the duration of the emergency in hours, the desired tracing
1124    destination, the trace level, and a list of the trace modules to activate.
1125    For the length of the duration, when a program in an environment with the
1126    specified tracing key active invokes a Sprout CGI script, tracing will be
1127    turned on automatically. See L</TSetup> for more about tracing setup and
1128    L</ETracing> for more about emergency tracing.
1129    
1130    =over 4
1131    
1132    =item tkey
1133    
1134    The tracing key. This is used to identify the control file and the trace file.
1135    
1136    =item hours
1137    
1138    Number of hours to keep emergency tracing alive.
1139    
1140    =item dest
1141    
1142    Tracing destination. If no path information is specified for a file
1143    destination, it is put in the FIG temporary directory.
1144    
1145    =item level
1146    
1147    Tracing level. A higher level means more trace messages.
1148    
1149    =item modules
1150    
1151    A list of the tracing modules to activate.
1152    
1153  =back  =back
1154    
1155  =cut  =cut
1156    
1157  sub GetOptions {  sub Emergency {
1158      # Get the parameters.      # Get the parameters.
1159      my ($defaults, $options) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
1160      # Check for overrides.      # Create the emergency file.
1161      if ($options) {      my $specFile = EmergencyFileName($tkey);
1162          # Loop through the overrides.      my $outHandle = Open(undef, ">$specFile");
1163          while (my ($option, $setting) = each %{$options}) {      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
1164  }  }
1165    
1166  =head3 MergeOptions  =head3 EmergencyKey
1167    
1168  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $tkey = EmergencyKey($parameter);
1169    
1170  Merge default values into a hash table. This method looks at the key-value pairs in the  Return the Key to be used for emergency tracing. This could be an IP address,
1171  second (default) hash, and if a matching key is not found in the first hash, the default   a session ID, or a user name, depending on the environment.
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1172    
1173  =over 4  =over 4
1174    
1175  =item table  =item parameter
1176    
1177  Hash table to be updated with the default values.  Parameter defining the method for finding the tracing key. If it is a scalar,
1178    then it is presumed to be the tracing key itself. If it is a CGI object, then
1179    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1180    taken from the C<TRACING> environment variable.
1181    
1182  =item defaults  =item RETURN
1183    
1184  Default values to be merged into the first hash table if they are not already present.  Returns the key to be used for labels in emergency tracing.
1185    
1186  =back  =back
1187    
1188  =cut  =cut
1189    
1190  sub MergeOptions {  sub EmergencyKey {
1191      # Get the parameters.      # Get the parameters.
1192      my ($table, $defaults) = @_;      my ($parameter) = @_;
1193      # Loop through the defaults.      # Declare the return variable.
1194      while (my ($key, $value) = each %{$defaults}) {      my $retVal;
1195          if (!exists $table->{$key}) {      # Determine the parameter type.
1196              $table->{$key} = $value;      if (! defined $parameter) {
1197          }          # Here we're supposed to check the environment. If that fails, we
1198            # get the effective login ID.
1199            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1200        } else {
1201            my $ptype = ref $parameter;
1202            if ($ptype eq 'CGI') {
1203                # Here we were invoked from a web page. Look for a cookie.
1204                $retVal = $parameter->cookie('IP');
1205            } elsif (! $ptype) {
1206                # Here the key was passed in.
1207                $retVal = $parameter;
1208            }
1209        }
1210        # If no luck finding a key, use the PID.
1211        if (! defined $retVal) {
1212            $retVal = $$;
1213      }      }
1214        # Return the result.
1215        return $retVal;
1216  }  }
1217    
 =head3 Trace  
1218    
1219  C<< Trace($message); >>  =head3 TraceParms
1220    
1221  Write a trace message to the target location specified in L</TSetup>. If there has not been      Tracer::TraceParms($cgi);
1222  any prior call to B<TSetup>.  
1223    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1224    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1225    
1226  =over 4  =over 4
1227    
1228  =item message  =item cgi
1229    
1230  Message to write.  CGI query object containing the parameters to trace.
1231    
1232  =back  =back
1233    
1234  =cut  =cut
1235    
1236  sub Trace {  sub TraceParms {
1237      # Get the parameters.      # Get the parameters.
1238      my ($message) = @_;      my ($cgi) = @_;
1239      # Get the timestamp.      if (T(CGI => 2)) {
1240      my $timeStamp = Now();          # Here we trace the GET-style URL for the script.
1241      # Format the message. Note we strip off any line terminators at the end.          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1242      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);      }
1243      # Process according to the destination.      if (T(CGI => 3)) {
1244      if ($Destination eq "TEXT") {          # Here we want to trace the parameter data.
1245          # Write the message to the standard output.          my @names = $cgi->param;
1246          print "$formatted\n";          for my $parmName (sort @names) {
1247      } elsif ($Destination eq "ERROR") {              # Note we skip the Trace parameters, which are for our use only.
1248          # Write the message to the error output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1249          print STDERR "$formatted\n";                  my @values = $cgi->param($parmName);
1250      } elsif ($Destination eq "QUEUE") {                  Trace("[CGI] $parmName = " . join(", ", @values));
1251          # Push the message into the queue.              }
1252          push @Queue, "$formatted";          }
1253      } elsif ($Destination eq "HTML") {          # Display the request method.
1254          # Convert the message to HTML and write it to the standard output.          my $method = $cgi->request_method();
1255          my $escapedMessage = CGI::escapeHTML($message);          Trace("Method: $method");
1256          print "<p>$formatted</p>\n";      }
1257      } elsif ($Destination eq "WARN") {      if (T(CGI => 4)) {
1258         # Emit the message as a warning.          # Here we want the environment data too.
1259         warn $message;          for my $envName (sort keys %ENV) {
1260      } elsif ($Destination =~ m/^>>/) {              Trace("[ENV] $envName = $ENV{$envName}");
         # 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";  
1261          }          }
1262      }      }
1263  }  }
1264    
1265  =head3 T  =head3 TraceImages
1266    
1267  C<< my $switch = T($category, $traceLevel); >>      Tracer::TraceImages($htmlString);
1268    
1269      or  Trace information about all of an html document's images. The tracing
1270    will be for type "IMG" at level 3. The image's source string
1271    will be displayed. This is generally either the URL of the image or
1272    raw data for the image itself. If the source is too long, only the first 300
1273    characters will be shown at trace level 3. The entire source will be shown,
1274    however, at trace level 4. This method is not very smart, and might catch
1275    Javascript code, but it is still useful when debugging the arcane
1276    behavior of images in multiple browser environments.
1277    
1278  C<< my $switch = T($traceLevel); >>  =over 4
1279    
1280  Return TRUE if the trace level is at or above a specified value and the specified category  =item htmlString
 is active, else FALSE. If no category is specified, the caller's package name is used.  
1281    
1282  =over 4  HTML text for an outgoing web page.
1283    
1284  =item category  =back
1285    
1286  Category to which the message belongs. If not specified, the caller's package name is  =cut
 used.  
1287    
1288  =item traceLevel  sub TraceImages {
1289        # Only proceed if we're at the proper trace level.
1290        if (T(IMG => 3)) {
1291            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1292            # into a variable called "$htmlString". This is because we expect html strings to be
1293            # long, and don't want to copy them any more than we have to.
1294            Trace(length($_[0]) . " characters in web page.");
1295            # Loop through the HTML, culling image tags.
1296            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1297                # Extract the source string and determine whether or not it's too long.
1298                my $srcString = $1;
1299                my $pos = pos($_[0]) - length($srcString);
1300                my $excess = length($srcString) - 300;
1301                # We'll put the display string in here.
1302                my $srcDisplay = $srcString;
1303                # If it's a data string, split it at the comma.
1304                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1305                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1306                # a long string, however, we only show the first 300 characters.
1307                if ($excess > 0 && ! T(IMG => 4)) {
1308                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1309                }
1310                # Output the trace message.
1311                Trace("Image tag at position $pos:\n$srcDisplay");
1312            }
1313        }
1314    }
1315    
 Relevant tracing level.  
1316    
1317  =item RETURN  =head3 ScriptFinish (deprecated)
1318    
1319  TRUE if a message at the specified trace level would appear in the trace, else FALSE.      ScriptFinish($webData, $varHash);
1320    
1321    Output a web page at the end of a script. Either the string to be output or the
1322    name of a template file can be specified. If the second parameter is omitted,
1323    it is assumed we have a string to be output; otherwise, it is assumed we have the
1324    name of a template file. The template should have the variable C<DebugData>
1325    specified in any form that invokes a standard script. If debugging mode is turned
1326    on, a form field will be put in that allows the user to enter tracing data.
1327    Trace messages will be placed immediately before the terminal C<BODY> tag in
1328    the output, formatted as a list.
1329    
1330    A typical standard script would loook like the following.
1331    
1332        BEGIN {
1333            # Print the HTML header.
1334            print "CONTENT-TYPE: text/html\n\n";
1335        }
1336        use Tracer;
1337        use CGI;
1338        use FIG;
1339        # ... more uses ...
1340    
1341        my ($cgi, $varHash) = ScriptSetup();
1342        eval {
1343            # ... get data from $cgi, put it in $varHash ...
1344        };
1345        if ($@) {
1346            Trace("Script Error: $@") if T(0);
1347        }
1348        ScriptFinish("Html/MyTemplate.html", $varHash);
1349    
1350    The idea here is that even if the script fails, you'll see trace messages and
1351    useful output.
1352    
1353    =over 4
1354    
1355    =item webData
1356    
1357    A string containing either the full web page to be written to the output or the
1358    name of a template file from which the page is to be constructed. If the name
1359    of a template file is specified, then the second parameter must be present;
1360    otherwise, it must be absent.
1361    
1362    =item varHash (optional)
1363    
1364    If specified, then a reference to a hash mapping variable names for a template
1365    to their values. The template file will be read into memory, and variable markers
1366    will be replaced by data in this hash reference.
1367    
1368  =back  =back
1369    
1370  =cut  =cut
1371    
1372  sub T {  sub ScriptFinish {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1373          # Get the parameters.          # Get the parameters.
1374          my ($category, $traceLevel) = @_;      my ($webData, $varHash) = @_;
1375          if (!defined $traceLevel) {      # Check for a template file situation.
1376              # Here we have no category, so we need to get the calling package.      my $outputString;
1377              # The calling package is normally the first parameter. If it is      if (defined $varHash) {
1378              # omitted, the first parameter will be the tracelevel. So, the          # Here we have a template file. We need to determine the template type.
1379              # first thing we do is shift the so-called category into the          my $template;
1380              # $traceLevel variable where it belongs.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1381              $traceLevel = $category;              $template = "$FIG_Config::template_url/$webData";
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
1382              } else {              } else {
1383                  $category = $package;              $template = "<<$webData";
1384              }              }
1385            $outputString = PageBuilder::Build($template, $varHash, "Html");
1386        } else {
1387            # Here the user gave us a raw string.
1388            $outputString = $webData;
1389          }          }
1390          # Save the category name.      # Check for trace messages.
1391          $LastCategory = $category;      if ($Destination ne "NONE" && $TraceLevel > 0) {
1392          # Convert it to lower case before we hash it.          # We have trace messages, so we want to put them at the end of the body. This
1393          $category = lc $category;          # is either at the end of the whole string or at the beginning of the BODY
1394          # Use the category and tracelevel to compute the result.          # end-tag.
1395          if (ref $traceLevel) {          my $pos = length $outputString;
1396              Confess("Bad trace level.");          if ($outputString =~ m#</body>#gi) {
1397          } elsif (ref $TraceLevel) {              $pos = (pos $outputString) - 7;
1398              Confess("Bad trace config.");          }
1399            # If the trace messages were queued, we unroll them. Otherwise, we display the
1400            # destination.
1401            my $traceHtml;
1402            if ($Destination eq "QUEUE") {
1403                $traceHtml = QTrace('Html');
1404            } elsif ($Destination =~ /^>>(.+)$/) {
1405                # Here the tracing output it to a file. We code it as a hyperlink so the user
1406                # can copy the file name into the clipboard easily.
1407                my $actualDest = $1;
1408                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1409            } else {
1410                # Here we have one of the special destinations.
1411                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1412            }
1413            substr $outputString, $pos, 0, $traceHtml;
1414        }
1415        # Write the output string.
1416        print $outputString;
1417    }
1418    
1419    =head2 Command-Line Utility Methods
1420    
1421    =head3 SendSMS
1422    
1423        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1424    
1425    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1426    user name, password, and API ID for the relevant account in the hash reference variable
1427    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1428    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1429    is C<2561022>, then the FIG_Config file must contain
1430    
1431        $phone =  { user => 'BruceTheHumanPet',
1432                    password => 'silly',
1433                    api_id => '2561022' };
1434    
1435    The original purpose of this method was to insure Bruce would be notified immediately when the
1436    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1437    when you call this method.
1438    
1439    The message ID will be returned if successful, and C<undef> if an error occurs.
1440    
1441    =over 4
1442    
1443    =item phoneNumber
1444    
1445    Phone number to receive the message, in international format. A United States phone number
1446    would be prefixed by "1". A British phone number would be prefixed by "44".
1447    
1448    =item msg
1449    
1450    Message to send to the specified phone.
1451    
1452    =item RETURN
1453    
1454    Returns the message ID if successful, and C<undef> if the message could not be sent.
1455    
1456    =back
1457    
1458    =cut
1459    
1460    sub SendSMS {
1461        # Get the parameters.
1462        my ($phoneNumber, $msg) = @_;
1463        # Declare the return variable. If we do not change it, C<undef> will be returned.
1464        my $retVal;
1465        # Only proceed if we have phone support.
1466        if (! defined $FIG_Config::phone) {
1467            Trace("Phone support not present in FIG_Config.") if T(1);
1468        } else {
1469            # Get the phone data.
1470            my $parms = $FIG_Config::phone;
1471            # Get the Clickatell URL.
1472            my $url = "http://api.clickatell.com/http/";
1473            # Create the user agent.
1474            my $ua = LWP::UserAgent->new;
1475            # Request a Clickatell session.
1476            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1477                                         password => $parms->{password},
1478                                         api_id => $parms->{api_id},
1479                                         to => $phoneNumber,
1480                                         text => $msg});
1481            # Check for an error.
1482            if (! $resp->is_success) {
1483                Trace("Alert failed.") if T(1);
1484            } else {
1485                # Get the message ID.
1486                my $rstring = $resp->content;
1487                if ($rstring =~ /^ID:\s+(.*)$/) {
1488                    $retVal = $1;
1489                } else {
1490                    Trace("Phone attempt failed with $rstring") if T(1);
1491                }
1492            }
1493        }
1494        # Return the result.
1495        return $retVal;
1496    }
1497    
1498    =head3 StandardSetup
1499    
1500        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1501    
1502    This method performs standard command-line parsing and tracing setup. The return
1503    values are a hash of the command-line options and a list of the positional
1504    parameters. Tracing is automatically set up and the command-line options are
1505    validated.
1506    
1507    This is a complex method that does a lot of grunt work. The parameters can
1508    be more easily understood, however, once they are examined individually.
1509    
1510    The I<categories> parameter is the most obtuse. It is a reference to a list of
1511    special-purpose tracing categories. Most tracing categories are PERL package
1512    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1513    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1514    
1515        ["Sprout", "SproutLoad", "ERDB"]
1516    
1517    This would cause trace messages in the specified three packages to appear in
1518    the output. There are two special tracing categories that are automatically
1519    handled by this method. In other words, if you used L</TSetup> you would need
1520    to include these categories manually, but if you use this method they are turned
1521    on automatically.
1522    
1523    =over 4
1524    
1525    =item SQL
1526    
1527    Traces SQL commands and activity.
1528    
1529    =item Tracer
1530    
1531    Traces error messages and call stacks.
1532    
1533    =back
1534    
1535    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1536    The trace level is specified using the C<-trace> command-line option. For example,
1537    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1538    all tracing at level 3.
1539    
1540        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1541    
1542    Standard tracing is output to the standard output and echoed to the file
1543    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1544    process ID. You can also specify the C<user> parameter to put a user ID
1545    instead of a process ID in the trace file name. So, for example
1546    
1547    The default trace level is 2. To get all messages, specify a trace level of 4.
1548    For a genome-by-genome update, use 3.
1549    
1550        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1551    
1552    would send the trace output to C<traceBruce.log> in the temporary directory.
1553    
1554    The I<options> parameter is a reference to a hash containing the command-line
1555    options, their default values, and an explanation of what they mean. Command-line
1556    options may be in the form of switches or keywords. In the case of a switch, the
1557    option value is 1 if it is specified and 0 if it is not specified. In the case
1558    of a keyword, the value is separated from the option name by an equal sign. You
1559    can see this last in the command-line example above.
1560    
1561    You can specify a different default trace level by setting C<$options->{trace}>
1562    prior to calling this method.
1563    
1564    An example at this point would help. Consider, for example, the command-line utility
1565    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1566    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1567    the following code.
1568    
1569        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1570                            { safe => [0, "use database transactions"],
1571                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1572                              start => [' ', "start with this genome"],
1573                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1574                            "<command> <transactionDirectory> <IDfile>",
1575                          @ARGV);
1576    
1577    
1578    The call to C<ParseCommand> specifies the default values for the options and
1579    stores the actual options in a hash that is returned as C<$options>. The
1580    positional parameters are returned in C<@parameters>.
1581    
1582    The following is a sample command line for C<TransactFeatures>.
1583    
1584        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1585    
1586    Single and double hyphens are equivalent. So, you could also code the
1587    above command as
1588    
1589        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1590    
1591    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1592    parameters, and would find themselves in I<@parameters> after executing the
1593    above code fragment. The tracing would be set to level 2, and the categories
1594    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1595    and C<DocUtils> was included because it came in within the first parameter
1596    to this method. The I<$options> hash would be
1597    
1598        { trace => 2, sql => 0, safe => 0,
1599          noAlias => 1, start => ' ', tblFiles => 0 }
1600    
1601    Use of C<StandardSetup> in this way provides a simple way of performing
1602    standard tracing setup and command-line parsing. Note that the caller is
1603    not even aware of the command-line switches C<-trace> and C<-sql>, which
1604    are used by this method to control the tracing. If additional tracing features
1605    need to be added in the future, they can be processed by this method without
1606    upsetting the command-line utilities.
1607    
1608    If the C<background> option is specified on the command line, then the
1609    standard and error outputs will be directed to files in the temporary
1610    directory, using the same suffix as the trace file. So, if the command
1611    line specified
1612    
1613        -user=Bruce -background
1614    
1615    then the trace output would go to C<traceBruce.log>, the standard output to
1616    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1617    simplify starting a command in the background.
1618    
1619    The user name is also used as the tracing key for L</Emergency Tracing>.
1620    Specifying a value of C<E> for the trace level causes emergency tracing to
1621    be used instead of custom tracing. If the user name is not specified,
1622    the tracing key is taken from the C<Tracing> environment variable. If there
1623    is no value for that variable, the tracing key will be computed from the PID.
1624    
1625    Finally, if the special option C<-help> is specified, the option
1626    names will be traced at level 0 and the program will exit without processing.
1627    This provides a limited help capability. For example, if the user enters
1628    
1629        TransactFeatures -help
1630    
1631    he would see the following output.
1632    
1633        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1634            -trace    tracing level (default E)
1635            -sql      trace SQL commands
1636            -safe     use database transactions
1637            -noAlias  do not expect aliases in CHANGE transactions
1638            -start    start with this genome
1639            -tblFiles output TBL files containing the corrected IDs
1640    
1641    The caller has the option of modifying the tracing scheme by placing a value
1642    for C<trace> in the incoming options hash. The default value can be overridden,
1643    or the tracing to the standard output can be turned off by suffixing a minus
1644    sign to the trace level. So, for example,
1645    
1646        { trace => [0, "tracing level (default 0)"],
1647           ...
1648    
1649    would set the default trace level to 0 instead of E, while
1650    
1651        { trace => ["2-", "tracing level (default 2)"],
1652           ...
1653    
1654    would set the default to 2, but trace only to the log file, not to the
1655    standard output.
1656    
1657    The parameters to this method are as follows.
1658    
1659    =over 4
1660    
1661    =item categories
1662    
1663    Reference to a list of tracing category names. These should be names of
1664    packages whose internal workings will need to be debugged to get the
1665    command working.
1666    
1667    =item options
1668    
1669    Reference to a hash containing the legal options for the current command mapped
1670    to their default values and descriptions. The user can override the defaults
1671    by specifying the options as command-line switches prefixed by a hyphen.
1672    Tracing-related options may be added to this hash. If the C<-h> option is
1673    specified on the command line, the option descriptions will be used to
1674    explain the options. To turn off tracing to the standard output, add a
1675    minus sign to the value for C<trace> (see above).
1676    
1677    =item parmHelp
1678    
1679    A string that vaguely describes the positional parameters. This is used
1680    if the user specifies the C<-h> option.
1681    
1682    =item argv
1683    
1684    List of command line parameters, including the option switches, which must
1685    precede the positional parameters and be prefixed by a hyphen.
1686    
1687    =item RETURN
1688    
1689    Returns a list. The first element of the list is the reference to a hash that
1690    maps the command-line option switches to their values. These will either be the
1691    default values or overrides specified on the command line. The remaining
1692    elements of the list are the position parameters, in order.
1693    
1694    =back
1695    
1696    =cut
1697    
1698    sub StandardSetup {
1699        # Get the parameters.
1700        my ($categories, $options, $parmHelp, @argv) = @_;
1701        # Get the default tracing key.
1702        my $tkey = EmergencyKey();
1703        # Add the tracing options.
1704        if (! exists $options->{trace}) {
1705            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1706        }
1707        $options->{sql} = [0, "turn on SQL tracing"];
1708        $options->{help} = [0, "display command-line options"];
1709        $options->{user} = [$tkey, "tracing key"];
1710        $options->{background} = [0, "spool standard and error output"];
1711        # Create a parsing hash from the options hash. The parsing hash
1712        # contains the default values rather than the default value
1713        # and the description. While we're at it, we'll memorize the
1714        # length of the longest option name.
1715        my $longestName = 0;
1716        my %parseOptions = ();
1717        for my $key (keys %{$options}) {
1718            if (length $key > $longestName) {
1719                $longestName = length $key;
1720            }
1721            $parseOptions{$key} = $options->{$key}->[0];
1722        }
1723        # Parse the command line.
1724        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1725        # Get the logfile suffix.
1726        my $suffix = $retOptions->{user};
1727        # Check for background mode.
1728        if ($retOptions->{background}) {
1729            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1730            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1731            open STDOUT, ">$outFileName";
1732            open STDERR, ">$errFileName";
1733            # Check for phone support. If we have phone support and a phone number,
1734            # we want to turn it on.
1735            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1736                $retOptions->{phone} = $ENV{PHONE};
1737            }
1738        }
1739        # Now we want to set up tracing. First, we need to know if the user
1740        # wants emergency tracing.
1741        if ($retOptions->{trace} eq 'E') {
1742            ETracing($retOptions->{user});
1743        } else {
1744            # Here the tracing is controlled from the command line.
1745            my @cats = @{$categories};
1746            if ($retOptions->{sql}) {
1747                push @cats, "SQL";
1748            }
1749            # Add the default categories.
1750            push @cats, "Tracer";
1751            # Next, we create the category string by joining the categories.
1752            my $cats = join(" ", @cats);
1753            # Check to determine whether or not the caller wants to turn off tracing
1754            # to the standard output.
1755            my $traceLevel = $retOptions->{trace};
1756            my $textOKFlag = 1;
1757            if ($traceLevel =~ /^(.)-/) {
1758                $traceLevel = $1;
1759                $textOKFlag = 0;
1760            }
1761            # Now we set up the trace mode.
1762            my $traceMode;
1763            # Verify that we can open a file in the FIG temporary directory.
1764            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1765            if (open TESTTRACE, ">$traceFileName") {
1766                # Here we can trace to a file.
1767                $traceMode = ">$traceFileName";
1768                if ($textOKFlag) {
1769                    # Echo to standard output if the text-OK flag is set.
1770                    $traceMode = "+$traceMode";
1771                }
1772                # Close the test file.
1773                close TESTTRACE;
1774            } else {
1775                # Here we can't trace to a file. Complain about this.
1776                warn "Could not open trace file $traceFileName: $!\n";
1777                # We trace to the standard output if it's
1778                # okay, and the error log otherwise.
1779                if ($textOKFlag) {
1780                    $traceMode = "TEXT";
1781                } else {
1782                    $traceMode = "WARN";
1783                }
1784            }
1785            # Now set up the tracing.
1786            TSetup("$traceLevel $cats", $traceMode);
1787        }
1788        # Check for the "help" option. If it is specified, dump the command-line
1789        # options and exit the program.
1790        if ($retOptions->{help}) {
1791            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1792            print "$1 [options] $parmHelp\n";
1793            for my $key (sort keys %{$options}) {
1794                my $name = Pad($key, $longestName, 0, ' ');
1795                my $desc = $options->{$key}->[1];
1796                if ($options->{$key}->[0]) {
1797                    $desc .= " (default " . $options->{$key}->[0] . ")";
1798                }
1799                print "  $name $desc\n";
1800            }
1801            exit(0);
1802          }          }
1803          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));      # Trace the options, if applicable.
1804        if (T(3)) {
1805            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1806            Trace("Selected options: " . join(", ", sort @parms) . ".");
1807      }      }
1808      # Return the computed result.      # Return the parsed parameters.
1809      return $retVal;      return ($retOptions, @retParameters);
1810  }  }
1811    
1812  =head3 ParseCommand  =head3 ReadOptions
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
   
 then at the end of the invocation, C<$options> will be  
1813    
1814  C<< { errors => 0, logFile => 'error.log' } >>      my %options = Tracer::ReadOptions($fileName);
1815    
1816  and C<@arguments> will contain  Read a set of options from a file. Each option is encoded in a line of text that has the
1817    format
1818    
1819  C<< apple orange rutabaga >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1820    
1821  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The option name must consist entirely of letters, digits, and the punctuation characters
1822  support for quote characters.  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1823    character is a semi-colon will be ignored. The return hash will map each option name to
1824    the corresponding option value.
1825    
1826  =over 4  =over 4
1827    
1828  =item optionTable  =item fileName
   
 Table of default options.  
   
 =item inputList  
1829    
1830  List of words on the command line.  Name of the file containing the option data.
1831    
1832  =item RETURN  =item RETURN
1833    
1834  Returns a reference to the option table and a list of the positional arguments.  Returns a hash mapping the option names specified in the file to their corresponding option
1835    value.
1836    
1837  =back  =back
1838    
1839  =cut  =cut
1840    
1841  sub ParseCommand {  sub ReadOptions {
1842      # Get the parameters.      # Get the parameters.
1843      my ($optionTable, @inputList) = @_;      my ($fileName) = @_;
1844      # Process any options in the input list.      # Open the file.
1845      my %overrides = ();      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1846      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Count the number of records read.
1847          # Get the current option.      my ($records, $comments) = 0;
1848          my $arg = shift @inputList;      # Create the return hash.
1849          # Pull out the option name.      my %retVal = ();
1850          $arg =~ /^-([^=]*)/g;      # Loop through the file, accumulating key-value pairs.
1851          my $name = $1;      while (my $line = <CONFIGFILE>) {
1852          # Check for an option value.          # Denote we've read a line.
1853          if ($arg =~ /\G=(.*)$/g) {          $records++;
1854              # Here we have a value for the option.          # Determine the line type.
1855              $overrides{$name} = UnEscape($1);          if ($line =~ /^\s*[\n\r]/) {
1856                # A blank line is a comment.
1857                $comments++;
1858            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1859                # Here we have an option assignment.
1860                retVal{$1} = $2;
1861            } elsif ($line =~ /^\s*;/) {
1862                # Here we have a text comment.
1863                $comments++;
1864          } else {          } else {
1865              # Here there is no value, so we use 1.              # Here we have an invalid line.
1866              $overrides{$name} = 1;              Trace("Invalid option statement in record $records.") if T(0);
         }  
1867      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1868      }      }
1869      # Return the results.      # Return the hash created.
1870      return ($optionTable, @retVal);      return %retVal;
1871  }  }
1872    
1873  =head3 Escape  =head3 GetOptions
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
1874    
1875  String to escape.      Tracer::GetOptions(\%defaults, \%options);
1876    
1877  =item RETURN  Merge a specified set of options into a table of defaults. This method takes two hash references
1878    as input and uses the data from the second to update the first. If the second does not exist,
1879    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1880    exist in the first.
1881    
1882  Escaped equivalent of the real string.  Consider the following example.
1883    
1884  =back      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1885    
1886  =cut  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1887    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1888    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1889    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1890    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1891    
1892  sub Escape {      {databaseType => 'Oracle'}
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # Here we found it. The text preceding the sequence is in $1. The sequence  
             # itself is in $2. First, move the clear text to the return variable.  
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
1893    
1894  =head3 UnEscape  an error will occur because the B<databaseType> option does not exist.
1895    
1896  C<< my $realString = Tracer::UnEscape($codedString); >>  =over 4
1897    
1898  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  =item defaults
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1899    
1900  =over 4  Table of default option values.
1901    
1902  =item codedString  =item options
1903    
1904  String to un-escape.  Table of overrides, if any.
1905    
1906  =item RETURN  =item RETURN
1907    
1908  Returns a copy of the original string with the escape sequences converted to their actual  Returns a reference to the default table passed in as the first parameter.
 values.  
1909    
1910  =back  =back
1911    
1912  =cut  =cut
1913    
1914  sub UnEscape {  sub GetOptions {
1915      # Get the parameter.      # Get the parameters.
1916      my ($codedString) = @_;      my ($defaults, $options) = @_;
1917      # Initialize the return variable.      # Check for overrides.
1918      my $retVal = "";      if ($options) {
1919      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1920      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1921          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1922          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1923          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
1924              } else {              } else {
1925                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1926                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
1927              }              }
1928          }          }
1929      }      }
1930      # Return the result.      # Return the merged table.
1931      return $retVal;      return $defaults;
1932  }  }
1933    
1934  =head3 ParseRecord  =head3 MergeOptions
1935    
1936  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1937    
1938  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Merge default values into a hash table. This method looks at the key-value pairs in the
1939  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  second (default) hash, and if a matching key is not found in the first hash, the default
1940  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1941    checking and no return value.
1942    
1943  =over 4  =over 4
1944    
1945  =item line  =item table
1946    
1947  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
1948    
1949  =item RETURN  =item defaults
1950    
1951  Returns a list of the fields found in the data line.  Default values to be merged into the first hash table if they are not already present.
1952    
1953  =back  =back
1954    
1955  =cut  =cut
1956    
1957  sub ParseRecord {  sub MergeOptions {
1958      # Get the parameter.      # Get the parameters.
1959      my ($line) = @_;      my ($table, $defaults) = @_;
1960      # Remove the trailing new-line, if any.      # Loop through the defaults.
1961      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
1962      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
1963      my @retVal = split /\t/, $line;              $table->{$key} = $value;
1964      # Trim and fix the escapes in each piece.          }
1965      for my $value (@retVal) {      }
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
1966  }  }
1967    
1968  =head3 Merge  =head3 ParseCommand
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
1969    
1970  =item inputList      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1971    
1972  List of scalars to sort and merge.  Parse a command line consisting of a list of parameters. The initial parameters may be option
1973    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1974    off and merged into a table of default options. The remainder of the command line is
1975    returned as a list of positional arguments. For example, consider the following invocation.
1976    
1977  =item RETURN      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1978    
1979  Returns a list containing the same elements sorted in ascending order with duplicates  In this case, the list @words will be treated as a command line and there are two options available,
1980  removed.  B<errors> and B<logFile>. If @words has the following format
1981    
1982  =back      -logFile=error.log apple orange rutabaga
1983    
1984  =cut  then at the end of the invocation, C<$options> will be
1985    
1986  sub Merge {      { errors => 0, logFile => 'error.log' }
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
1987    
1988  =head3 Percent  and C<@arguments> will contain
1989    
1990  C<< my $percent = Tracer::Percent($number, $base); >>      apple orange rutabaga
1991    
1992  Returns the percent of the base represented by the given number. If the base  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1993  is zero, returns zero.  support for quote characters. Options can be specified with single or double hyphens.
1994    
1995  =over 4  =over 4
1996    
1997  =item number  =item optionTable
1998    
1999  Percent numerator.  Table of default options.
2000    
2001  =item base  =item inputList
2002    
2003  Percent base.  List of words on the command line.
2004    
2005  =item RETURN  =item RETURN
2006    
2007  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
2008    
2009  =back  =back
2010    
2011  =cut  =cut
2012    
2013  sub Percent {  sub ParseCommand {
2014      # Get the parameters.      # Get the parameters.
2015      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
2016      # Declare the return variable.      # Process any options in the input list.
2017      my $retVal = 0;      my %overrides = ();
2018      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2019      if ($base != 0) {          # Get the current option.
2020          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
2021            # Pull out the option name.
2022            $arg =~ /^--?([^=]*)/g;
2023            my $name = $1;
2024            # Check for an option value.
2025            if ($arg =~ /\G=(.*)$/g) {
2026                # Here we have a value for the option.
2027                $overrides{$name} = UnEscape($1);
2028            } else {
2029                # Here there is no value, so we use 1.
2030                $overrides{$name} = 1;
2031      }      }
2032      # Return the result.      }
2033      return $retVal;      # Merge the options into the defaults.
2034        GetOptions($optionTable, \%overrides);
2035        # Translate the remaining parameters.
2036        my @retVal = ();
2037        for my $inputParm (@inputList) {
2038            push @retVal, UnEscape($inputParm);
2039        }
2040        # Return the results.
2041        return ($optionTable, @retVal);
2042  }  }
2043    
2044    
2045    =head2 File Utility Methods
2046    
2047  =head3 GetFile  =head3 GetFile
2048    
2049  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2050    
2051      or      or
2052    
2053  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2054    
2055  Return the entire contents of a file. In list context, line-ends are removed and  Return the entire contents of a file. In list context, line-ends are removed and
2056  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1436  Line 2089 
2089      # Close it.      # Close it.
2090      close $handle;      close $handle;
2091      my $actualLines = @retVal;      my $actualLines = @retVal;
2092        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2093      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
2094      if (wantarray) {      if (wantarray) {
2095          return @retVal;          return @retVal;
# Line 1446  Line 2100 
2100    
2101  =head3 PutFile  =head3 PutFile
2102    
2103  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2104    
2105  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2106    
# Line 1471  Line 2125 
2125      my ($fileName, $lines) = @_;      my ($fileName, $lines) = @_;
2126      # Open the output file.      # Open the output file.
2127      my $handle = Open(undef, ">$fileName");      my $handle = Open(undef, ">$fileName");
2128        # Count the lines written.
2129      if (ref $lines ne 'ARRAY') {      if (ref $lines ne 'ARRAY') {
2130          # Here we have a scalar, so we write it raw.          # Here we have a scalar, so we write it raw.
2131          print $handle $lines;          print $handle $lines;
2132            Trace("Scalar put to file $fileName.") if T(File => 3);
2133      } else {      } else {
2134          # Write the lines one at a time.          # Write the lines one at a time.
2135            my $count = 0;
2136          for my $line (@{$lines}) {          for my $line (@{$lines}) {
2137              print $handle "$line\n";              print $handle "$line\n";
2138                $count++;
2139          }          }
2140            Trace("$count lines put to file $fileName.") if T(File => 3);
2141      }      }
2142      # Close the output file.      # Close the output file.
2143      close $handle;      close $handle;
2144  }  }
2145    
2146  =head3 QTrace  =head3 ParseRecord
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
   
 =head3 Confess  
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Confess {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
   
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
   
 =head3 Cluck  
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
   
 =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/);  
     }  
 }  
   
 =head3 Min  
2147    
2148  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @fields = Tracer::ParseRecord($line);
2149    
2150  Return the minimum argument. The arguments are treated as numbers.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2151    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2152    These will automatically be converted.
2153    
2154  =over 4  =over 4
2155    
2156  =item $value1, $value2, ... $valueN  =item line
2157    
2158  List of numbers to compare.  Line of data containing the tab-delimited fields.
2159    
2160  =item RETURN  =item RETURN
2161    
2162  Returns the lowest number in the list.  Returns a list of the fields found in the data line.
2163    
2164  =back  =back
2165    
2166  =cut  =cut
2167    
2168  sub Min {  sub ParseRecord {
2169      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2170      my ($retVal, @values) = @_;      my ($line) = @_;
2171      # Loop through the remaining parameters, looking for the lowest.      # Remove the trailing new-line, if any.
2172      for my $value (@values) {      chomp $line;
2173          if ($value < $retVal) {      # Split the line read into pieces using the tab character.
2174              $retVal = $value;      my @retVal = split /\t/, $line;
2175          }      # Trim and fix the escapes in each piece.
2176        for my $value (@retVal) {
2177            # Trim leading whitespace.
2178            $value =~ s/^\s+//;
2179            # Trim trailing whitespace.
2180            $value =~ s/\s+$//;
2181            # Delete the carriage returns.
2182            $value =~ s/\r//g;
2183            # Convert the escapes into their real values.
2184            $value =~ s/\\t/"\t"/ge;
2185            $value =~ s/\\n/"\n"/ge;
2186      }      }
2187      # Return the minimum found.      # Return the result.
2188      return $retVal;      return @retVal;
2189  }  }
2190    
2191  =head3 Max  =head3 Merge
2192    
2193  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @mergedList = Tracer::Merge(@inputList);
2194    
2195  Return the maximum argument. The arguments are treated as numbers.  Sort a list of strings and remove duplicates.
2196    
2197  =over 4  =over 4
2198    
2199  =item $value1, $value2, ... $valueN  =item inputList
2200    
2201  List of numbers to compare.  List of scalars to sort and merge.
2202    
2203  =item RETURN  =item RETURN
2204    
2205  Returns the highest number in the list.  Returns a list containing the same elements sorted in ascending order with duplicates
2206    removed.
2207    
2208  =back  =back
2209    
2210  =cut  =cut
2211    
2212  sub Max {  sub Merge {
2213      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the input list in sort order.
2214      my ($retVal, @values) = @_;      my @inputList = sort @_;
2215      # Loop through the remaining parameters, looking for the highest.      # Only proceed if the list has at least two elements.
2216      for my $value (@values) {      if (@inputList > 1) {
2217          if ($value > $retVal) {          # Now we want to move through the list splicing out duplicates.
2218              $retVal = $value;          my $i = 0;
2219            while ($i < @inputList) {
2220                # Get the current entry.
2221                my $thisEntry = $inputList[$i];
2222                # Find out how many elements duplicate the current entry.
2223                my $j = $i + 1;
2224                my $dup1 = $i + 1;
2225                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2226                # If the number is nonzero, splice out the duplicates found.
2227                if ($j > $dup1) {
2228                    splice @inputList, $dup1, $j - $dup1;
2229          }          }
2230                # Now the element at position $dup1 is different from the element before it
2231                # at position $i. We push $i forward one position and start again.
2232                $i++;
2233      }      }
2234      # Return the maximum found.      }
2235      return $retVal;      # Return the merged list.
2236        return @inputList;
2237  }  }
2238    
2239  =head3 AddToListMap  =head3 Open
2240    
2241  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2242    
2243  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Open a file.
 is created for the key. Otherwise, the new value is pushed onto the list.  
2244    
2245  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2246    function. The mode is specified using Unix-like shell information. So, for
2247    example,
2248    
2249  =item hash      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2250    
2251  Reference to the target hash.  would open for output appended to the specified file, and
2252    
2253  =item key      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2254    
2255  Key for which the value is to be added.  would open a pipe that sorts the records written and removes duplicates. Note
2256    the use of file handle syntax in the Open call. To use anonymous file handles,
2257    code as follows.
2258    
2259  =item value1, value2, ... valueN      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2260    
2261  List of values to add to the key's value list.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2262    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2263    failed open will throw an exception and the third parameter will be used to construct
2264    an error message. If the parameter is omitted, a standard message is constructed
2265    using the file spec.
2266    
2267  =back      Could not open "/usr/spool/news/twitlog"
2268    
2269  =cut  Note that the mode characters are automatically cleaned from the file name.
2270    The actual error message from the file system will be captured and appended to the
2271    message in any case.
2272    
2273  sub AddToListMap {      Could not open "/usr/spool/news/twitlog": file not found.
2274      # Get the parameters.  
2275      my ($hash, $key, @values) = @_;  In some versions of PERL the only error message we get is a number, which
2276      # Process according to whether or not the key already has a value.  corresponds to the C++ C<errno> value.
2277      if (! exists $hash->{$key}) {  
2278          $hash->{$key} = [@values];      Could not open "/usr/spool/news/twitlog": 6.
2279      } else {  
2280          push @{$hash->{$key}}, @values;  =over 4
     }  
 }  
2281    
2282  =head3 DebugMode  =item fileHandle
2283    
2284    File handle. If this parameter is C<undef>, a file handle will be generated
2285    and returned as the value of this method.
2286    
2287    =item fileSpec
2288    
2289    File name and mode, as per the PERL C<open> function.
2290    
2291  C<< if (Tracer::DebugMode) { ...code... } >>  =item message (optional)
2292    
2293    Error message to use if the open fails. If omitted, a standard error message
2294    will be generated. In either case, the error information from the file system
2295    is appended to the message. To specify a conditional open that does not throw
2296    an error if it fails, use C<0>.
2297    
2298    =item RETURN
2299    
2300  Return TRUE if debug mode has been turned on, else abort.  Returns the name of the file handle assigned to the file, or C<undef> if the
2301    open failed.
2302    
2303  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2304    
2305  =cut  =cut
2306    
2307  sub DebugMode {  sub Open {
2308      # Declare the return variable.      # Get the parameters.
2309      my $retVal = 0;      my ($fileHandle, $fileSpec, $message) = @_;
2310      # Check the debug configuration.      # Attempt to open the file.
2311      my $password = CGI::cookie("DebugMode");      my $rv = open $fileHandle, $fileSpec;
2312      my $encrypted = Digest::MD5::md5_hex($password);      # If the open failed, generate an error message.
2313      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if (! $rv) {
2314          $retVal = 1;          # Save the system error message.
2315      } else {          my $sysMessage = $!;
2316          # Here debug mode is off, so we generate an error.          # See if we need a default message.
2317          Confess("Cannot use this facility without logging in.");          if (!$message) {
2318                # Clean any obvious mode characters and leading spaces from the
2319                # filename.
2320                my ($fileName) = FindNamePart($fileSpec);
2321                $message = "Could not open \"$fileName\"";
2322      }      }
2323      # Return the determination indicator.          # Terminate with an error using the supplied message and the
2324      return $retVal;          # error message from the file system.
2325            Confess("$message: $!");
2326        }
2327        # Return the file handle.
2328        return $fileHandle;
2329  }  }
2330    
2331  =head3 Strip  =head3 FindNamePart
2332    
2333  C<< my $string = Tracer::Strip($line); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2334    
2335  Strip all line terminators off a string. This is necessary when dealing with files  Extract the portion of a file specification that contains the file name.
2336  that may have been transferred back and forth several times among different  
2337  operating environments.  A file specification is the string passed to an C<open> call. It specifies the file
2338    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2339    method assumes that the file name is whatever follows the first angle bracket
2340    sequence.  So, for example, in the following strings the file name is
2341    C</usr/fig/myfile.txt>.
2342    
2343        >>/usr/fig/myfile.txt
2344        </usr/fig/myfile.txt
2345        | sort -u > /usr/fig/myfile.txt
2346    
2347    If the method cannot find a file name using its normal methods, it will return the
2348    whole incoming string.
2349    
2350  =over 4  =over 4
2351    
2352  =item line  =item fileSpec
2353    
2354  Line of text to be stripped.  File specification string from which the file name is to be extracted.
2355    
2356  =item RETURN  =item RETURN
2357    
2358  The same line of text with all the line-ending characters chopped from the end.  Returns a three-element list. The first element contains the file name portion of
2359    the specified string, or the whole string if a file name cannot be found via normal
2360    methods. The second element contains the start position of the file name portion and
2361    the third element contains the length.
2362    
2363  =back  =back
2364    
2365  =cut  =cut
2366    #: Return Type $;
2367  sub Strip {  sub FindNamePart {
2368      # Get a copy of the parameter string.      # Get the parameters.
2369      my ($string) = @_;      my ($fileSpec) = @_;
2370      my $retVal = (defined $string ? $string : "");      # Default to the whole input string.
2371      # Strip the line terminator characters.      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2372      $retVal =~ s/(\r|\n)+$//g;      # Parse out the file name if we can.
2373        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2374            $retVal = $2;
2375            $len = length $retVal;
2376            $pos = (length $fileSpec) - (length $3) - $len;
2377        }
2378      # Return the result.      # Return the result.
2379      return $retVal;      return ($retVal, $pos, $len);
2380  }  }
2381    
2382  =head3 Pad  =head3 OpenDir
2383    
2384  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @files = OpenDir($dirName, $filtered, $flag);
2385    
2386  Pad a string to a specified length. The pad character will be a  Open a directory and return all the file names. This function essentially performs
2387  space, and the padding will be on the right side unless specified  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2388  in the third parameter.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2389    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2390    filtered out of the return list. If the directory does not open and I<$flag> is not
2391    set, an exception is thrown. So, for example,
2392    
2393  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
2394    
2395  =item string  is effectively the same as
2396    
2397  String to be padded.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2398        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2399    
2400  =item len  Similarly, the following code
2401    
2402  Desired length of the padded string.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2403    
2404  =item left (optional)  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2405    automatically returns an empty list if the directory fails to open.
2406    
2407  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =over 4
2408    
2409  =item padChar (optional)  =item dirName
2410    
2411  Character to use for padding. The default is a space.  Name of the directory to open.
2412    
2413  =item RETURN  =item filtered
2414    
2415  Returns a copy of the original string with the pad character added to the  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2416  specified end so that it achieves the desired length.  from the list, else FALSE.
2417    
2418    =item flag
2419    
2420    TRUE if a failure to open is okay, else FALSE
2421    
2422  =back  =back
2423    
2424  =cut  =cut
2425    #: Return Type @;
2426  sub Pad {  sub OpenDir {
2427      # Get the parameters.      # Get the parameters.
2428      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $filtered, $flag) = @_;
2429      # Compute the padding character.      # Declare the return variable.
2430      if (! defined $padChar) {      my @retVal = ();
2431          $padChar = " ";      # Open the directory.
2432      }      if (opendir(my $dirHandle, $dirName)) {
2433      # Compute the number of spaces needed.          # The directory opened successfully. Get the appropriate list according to the
2434      my $needed = $len - length $string;          # strictures of the filter parameter.
2435      # Copy the string into the return variable.          if ($filtered) {
2436      my $retVal = $string;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2437          } else {          } else {
2438              $retVal .= $pad;              @retVal = readdir $dirHandle;
2439          }          }
2440        } elsif (! $flag) {
2441            # Here the directory would not open and it's considered an error.
2442            Confess("Could not open directory $dirName.");
2443      }      }
2444      # Return the result.      # Return the result.
2445      return $retVal;      return @retVal;
2446  }  }
2447    
 =head3 EOF  
2448    
2449  This is a constant that is lexically greater than any useful string.  =head3 Insure
2450    
2451        Insure($dirName, $chmod);
2452    
2453    Insure a directory is present.
2454    
2455  =cut  =over 4
2456    
2457  sub EOF {  =item dirName
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2458    
2459  =head3 TICK  Name of the directory to check. If it does not exist, it will be created.
2460    
2461  C<< my @results = TICK($commandString); >>  =item chmod (optional)
2462    
2463  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Security privileges to be given to the directory if it is created.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2464    
2465      `./protein.cgi`  =back
2466    
2467  from inside a CGI script, it would work fine in Unix, but would issue an error message  =cut
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2468    
2469      TICK("./protein.cgi")  sub Insure {
2470        my ($dirName, $chmod) = @_;
2471        if (! -d $dirName) {
2472            Trace("Creating $dirName directory.") if T(2);
2473            eval {
2474                mkpath $dirName;
2475                # If we have permissions specified, set them here.
2476                if (defined($chmod)) {
2477                    chmod $chmod, $dirName;
2478                }
2479            };
2480            if ($@) {
2481                Confess("Error creating $dirName: $@");
2482            }
2483        }
2484    }
2485    
2486  it will work correctly in both environments.  =head3 ChDir
2487    
2488  =over 4      ChDir($dirName);
2489    
2490  =item commandString  Change to the specified directory.
2491    
2492  The command string to pass to the system.  =over 4
2493    
2494  =item RETURN  =item dirName
2495    
2496  Returns the standard output from the specified command, as a list.  Name of the directory to which we want to change.
2497    
2498  =back  =back
2499    
2500  =cut  =cut
2501  #: Return Type @;  
2502  sub TICK {  sub ChDir {
2503      # Get the parameters.      my ($dirName) = @_;
2504      my ($commandString) = @_;      if (! -d $dirName) {
2505      # Chop off the dot-slash if this is Windows.          Confess("Cannot change to directory $dirName: no such directory.");
2506      if ($FIG_Config::win_mode) {      } else {
2507          $commandString =~ s!^\./!!;          Trace("Changing to directory $dirName.") if T(File => 4);
2508            my $okFlag = chdir $dirName;
2509            if (! $okFlag) {
2510                Confess("Error switching to directory $dirName.");
2511            }
2512      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2513  }  }
2514    
2515  =head3 ScriptSetup  =head3 SetPermissions
2516    
2517  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2518    
2519  Perform standard tracing and debugging setup for scripts. The value returned is  Set the permissions for a directory and all the files and folders inside it.
2520  the CGI object followed by a pre-built variable hash.  In addition, the group ownership will be changed to the specified value.
2521    
2522  The C<Trace> query parameter is used to determine whether or not tracing is active and  This method is more vulnerable than most to permission and compatability
2523  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  problems, so it does internal error recovery.
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
   
 In some situations, it is not practical to invoke tracing via form parameters. For this  
 situation, you can turn on emergency tracing by invoking the L</Emergency> method from  
 a web page. Emergency tracing is detected via a file with the name  
 C<Emergency>I<IPaddr>C<.txt> in the FIG temporary directory, where I<IPaddr> is the  
 IP address of the remote user who wants tracing turned on. The file contains a time  
 limit in hours on the first line, a tracing destination on the second line, a trace  
 level on the third line, and the tracing modules on subsequent lines.  
2524    
2525  =over 4  =over 4
2526    
2527  =item noTrace (optional)  =item dirName
2528    
2529  If specified, tracing will be suppressed. This is useful if the script wants to set up  Name of the directory to process.
 tracing manually.  
2530    
2531  =item RETURN  =item group
2532    
2533  Returns a two-element list consisting of a CGI query object and a variable hash for  Name of the group to be assigned.
2534  the output page.  
2535    =item mask
2536    
2537    Permission mask. Bits that are C<1> in this mask will be ORed into the
2538    permission bits of any file or directory that does not already have them
2539    set to 1.
2540    
2541    =item otherMasks
2542    
2543    Map of search patterns to permission masks. If a directory name matches
2544    one of the patterns, that directory and all its members and subdirectories
2545    will be assigned the new pattern. For example, the following would
2546    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2547    
2548        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2549    
2550    The list is ordered, so the following would use 0777 for C<tmp1> and
2551    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2552    
2553        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2554                                                       '^tmp' => 0666);
2555    
2556    Note that the pattern matches are all case-insensitive, and only directory
2557    names are matched, not file names.
2558    
2559  =back  =back
2560    
2561  =cut  =cut
2562    
2563  sub ScriptSetup {  sub SetPermissions {
2564      # Get the parameters.      # Get the parameters.
2565      my ($noTrace) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2566      # Get the CGI query object.      # Set up for error recovery.
2567      my $cgi = CGI->new();      eval {
2568      # Set up tracing if it's not suppressed.          # Switch to the specified directory.
2569      CGITrace($cgi) unless $noTrace;          ChDir($dirName);
2570      # Create the variable hash.          # Get the group ID.
2571      my $varHash = { results => '' };          my $gid = getgrnam($group);
2572      # Return the query object and variable hash.          # Get the mask for tracing.
2573      return ($cgi, $varHash);          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2574            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2575            my $fixCount = 0;
2576            my $lookCount = 0;
2577            # @dirs will be a stack of directories to be processed.
2578            my @dirs = (getcwd());
2579            while (scalar(@dirs) > 0) {
2580                # Get the current directory.
2581                my $dir = pop @dirs;
2582                # Check for a match to one of the specified directory names. To do
2583                # that, we need to pull the individual part of the name off of the
2584                # whole path.
2585                my $simpleName = $dir;
2586                if ($dir =~ m!/([^/]+)$!) {
2587                    $simpleName = $1;
2588                }
2589                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2590                # Search for a match.
2591                my $match = 0;
2592                my $i;
2593                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2594                    my $pattern = $otherMasks[$i];
2595                    if ($simpleName =~ /$pattern/i) {
2596                        $match = 1;
2597                    }
2598                }
2599                # Check for a match. Note we use $i-1 because the loop added 2
2600                # before terminating due to the match.
2601                if ($match && $otherMasks[$i-1] != $mask) {
2602                    # This directory matches one of the incoming patterns, and it's
2603                    # a different mask, so we process it recursively with that mask.
2604                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2605                } else {
2606                    # Here we can process normally. Get all of the non-hidden members.
2607                    my @submems = OpenDir($dir, 1);
2608                    for my $submem (@submems) {
2609                        # Get the full name.
2610                        my $thisMem = "$dir/$submem";
2611                        Trace("Checking member $thisMem.") if T(4);
2612                        $lookCount++;
2613                        if ($lookCount % 1000 == 0) {
2614                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2615                        }
2616                        # Fix the group.
2617                        chown -1, $gid, $thisMem;
2618                        # Insure this member is not a symlink.
2619                        if (! -l $thisMem) {
2620                            # Get its info.
2621                            my $fileInfo = stat $thisMem;
2622                            # Only proceed if we got the info. Otherwise, it's a hard link
2623                            # and we want to skip it anyway.
2624                            if ($fileInfo) {
2625                                my $fileMode = $fileInfo->mode;
2626                                if (($fileMode & $mask) != $mask) {
2627                                    # Fix this member.
2628                                    $fileMode |= $mask;
2629                                    chmod $fileMode, $thisMem;
2630                                    $fixCount++;
2631                                }
2632                                # If it's a subdirectory, stack it.
2633                                if (-d $thisMem) {
2634                                    push @dirs, $thisMem;
2635                                }
2636                            }
2637                        }
2638                    }
2639                }
2640            }
2641            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2642        };
2643        # Check for an error.
2644        if ($@) {
2645            Confess("SetPermissions error: $@");
2646        }
2647  }  }
2648    
2649  =head3 CGITrace  =head3 GetLine
2650    
2651  C<< Tracer::CGITrace($cgi); >>      my @data = Tracer::GetLine($handle);
2652    
2653  Set up tracing for a CGI script. See L</ScriptSetup> for more information.  Read a line of data from a tab-delimited file.
2654    
2655  =over 4  =over 4
2656    
2657  =item cgi  =item handle
2658    
2659    Open file handle from which to read.
2660    
2661    =item RETURN
2662    
2663  Ths CGI query object for this script.  Returns a list of the fields in the record read. The fields are presumed to be
2664    tab-delimited. If we are at the end of the file, then an empty list will be
2665    returned. If an empty line is read, a single list item consisting of a null
2666    string will be returned.
2667    
2668  =back  =back
2669    
2670  =cut  =cut
2671    
2672  sub CGITrace {  sub GetLine {
2673      # Get the parameters.      # Get the parameters.
2674      my ($cgi) = @_;      my ($handle) = @_;
2675      # Default to no tracing except errors.      # Declare the return variable.
2676      my ($tracing, $dest) = ("0", "WARN");      my @retVal = ();
2677      # Check for emergency tracing.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2678      my $ip = EmergencyIP($cgi);      # Read from the file.
2679      my $emergencyFile = EmergencyFileName($ip);      my $line = <$handle>;
2680      if (-e $emergencyFile) {      # Only proceed if we found something.
2681          # We have the file. Read in the data.      if (defined $line) {
2682          my @tracing = GetFile($emergencyFile);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2683          # Pull off the time limit.          # upload control and have a nonstandard EOL combination.
2684          my $expire = shift @tracing;          $line =~ s/(\r|\n)+$//;
2685          # Convert it to seconds.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2686          $expire *= 3600;          if (T(File => 4)) {
2687          # Check the file data.              my $escapedLine = $line;
2688          my $stat = stat($emergencyFile);              $escapedLine =~ s/\n/\\n/g;
2689          my ($now) = gettimeofday;              $escapedLine =~ s/\r/\\r/g;
2690          if ($now - $stat->mtime > $expire) {              $escapedLine =~ s/\t/\\t/g;
2691              # Delete the expired file.              Trace("Line read: -->$escapedLine<--");
2692              unlink $emergencyFile;          }
2693            # If the line is empty, return a single empty string; otherwise, parse
2694            # it into fields.
2695            if ($line eq "") {
2696                push @retVal, "";
2697          } else {          } else {
2698              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$line;
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($ip, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
             # Make sure the script knows tracing is on.  
             $cgi->param(-name => 'Trace', -value => $tracing);  
             $cgi->param(-name => 'TF', -value => (($dest =~ /^>/) ? 1 : 0));  
2699          }          }
2700      } elsif ($cgi->param('Trace')) {      } else {
2701          # Here the user has requested tracing via a form.          # Trace the reason the read failed.
2702          $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");          Trace("End of file: $!") if T(File => 3);
         $tracing = $cgi->param('Trace') . " Tracer";  
2703      }      }
2704      # Setup the tracing we've determined from all the stuff above.      # Return the result.
2705      TSetup($tracing, $dest);      return @retVal;
     # Trace the parameter and environment data.  
     TraceParms($cgi);  
2706  }  }
2707    
2708  =head3 EmergencyFileName  =head3 PutLine
2709    
2710  C<< my $fileName = Tracer::EmergencyFileName($ip); >>      Tracer::PutLine($handle, \@fields, $eol);
2711    
2712  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2713  the tracing information.  output in tab-separated form, with a trailing new-line.
2714    
2715  =over 4  =over 4
2716    
2717  =item ip  =item handle
2718    
2719    Output file handle.
2720    
2721    =item fields
2722    
2723  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  List of field values.
 method.  
2724    
2725  =item RETURN  =item eol (optional)
2726    
2727  Returns the name of the file to contain the emergency tracing information.  End-of-line character (default is "\n").
2728    
2729  =back  =back
2730    
2731  =cut  =cut
2732    
2733  sub EmergencyFileName {  sub PutLine {
2734      # Get the parameters.      # Get the parameters.
2735      my ($ip) = @_;      my ($handle, $fields, $eol) = @_;
2736      # Compute the emergency tracing file name.      # Write the data.
2737      return "$FIG_Config::temp/Emergency$ip.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2738  }  }
2739    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($ip); >>  
2740    
2741  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2742    
2743  =over 4      Tracer::PrintLine($line);
2744    
2745  =item ip  Print a line of text with a trailing new-line.
2746    
2747  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  =over 4
 method.  
2748    
2749  =item RETURN  =item line
2750    
2751  Returns the name of the file to contain the emergency tracing information.  Line of text to print.
2752    
2753  =back  =back
2754    
2755  =cut  =cut
2756    
2757  sub EmergencyFileTarget {  sub PrintLine {
2758      # Get the parameters.      # Get the parameters.
2759      my ($ip) = @_;      my ($line) = @_;
2760      # Compute the emergency tracing file name.      # Print the line.
2761      return "$FIG_Config::temp/Emergency$ip.log";      print "$line\n";
2762  }  }
2763    
 =head3 EmergencyTracingDest  
2764    
2765  C<< my $dest = Tracer::EmergencyTracingDest($ip, $myDest); >>  =head2 Other Useful Methods
2766    
2767  This method converts an emergency tracing destination to a real  =head3 ParseParm
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2768    
2769  =over 4      my $listValue = Tracer::ParseParm($string);
2770    
2771  =item ip  Convert a parameter into a list reference. If the parameter is undefined,
2772    an undefined value will be returned. Otherwise, it will be parsed as a
2773    comma-separated list of values.
2774    
2775  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  =over 4
 method.  
2776    
2777  =item myDest  =item string
2778    
2779  Destination from the emergency tracing file.  Incoming string.
2780    
2781  =item RETURN  =item RETURN
2782    
2783  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2784    was undefined.
2785    
2786  =back  =back
2787    
2788  =cut  =cut
2789    
2790  sub EmergencyTracingDest {  sub ParseParm {
2791      # Get the parameters.      # Get the parameters.
2792      my ($ip, $myDest) = @_;      my ($string) = @_;
2793      # Declare the return variable.      # Declare the return variable.
2794      my $retVal;      my $retVal;
2795      # Process according to the destination value.      # Check for data.
2796      if ($myDest eq 'FILE') {      if (defined $string) {
2797          $retVal = ">" . EmergencyFileTarget($ip);          # We have some, so split it into a list.
2798      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($ip);  
     } else {  
         $retVal = $myDest;  
2799      }      }
2800      # Return the result.      # Return the result.
2801      return $retVal;      return $retVal;
2802  }  }
2803    
2804  =head3 Emergency  =head3 Now
   
 C<< Emergency($cgi, $hours, $dest, $level, @modules); >>  
2805    
2806  Turn on emergency tracing. This method can only be invoked over the web and is      my $string = Tracer::Now();
 should not be called if debug mode is off. The caller specifies the duration of the  
 emergency in hours, the desired tracing destination, the trace level,  
 and a list of the trace modules to activate. For the duration, when a user  
 from the specified remote web location invokes a Sprout CGI script, tracing  
 will be turned on automatically. See L</TSetup> for more about tracing  
 setup and L</ScriptSetup> for more about emergency tracing.  
2807    
2808  =over 4  Return a displayable time stamp containing the local time. Whatever format this
2809    method produces must be parseable by L</ParseDate>.
2810    
2811  =item cgi  =cut
2812    
2813  A CGI query object.  sub Now {
2814        return DisplayTime(time);
2815    }
2816    
2817  =item hours  =head3 DisplayTime
2818    
2819  Number of hours to keep emergency tracing alive.      my $string = Tracer::DisplayTime($time);
2820    
2821  =item dest  Convert a time value to a displayable time stamp. Whatever format this
2822    method produces must be parseable by L</ParseDate>.
2823    
2824  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2825    
2826  =item level  =item time
2827    
2828  Tracing level. A higher level means more trace messages.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2829    
2830  =item modules  =item RETURN
2831    
2832  A list of the tracing modules to activate.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2833    
2834  =back  =back
2835    
2836  =cut  =cut
2837    
2838  sub Emergency {  sub DisplayTime {
2839      # Get the parameters.      my ($time) = @_;
2840      my ($cgi, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2841      # Get the IP address.      if (defined $time) {
2842      my $ip = EmergencyIP($cgi);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2843      # Create the emergency file.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2844      my $specFile = EmergencyFileName($ip);                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2845      my $outHandle = Open(undef, ">$specFile");      }
2846      print $outHandle join("\n",$hours, $dest, $level, @modules, "");      return $retVal;
2847  }  }
2848    
2849  =head3 EmergencyIP  # Pad a number to 2 digits.
2850    sub _p2 {
2851        my ($value) = @_;
2852        $value = "0$value" if ($value < 10);
2853        return $value;
2854    }
2855    
2856    =head3 Escape
2857    
2858  C<< my $ip = EmergencyIP($cgi); >>      my $codedString = Tracer::Escape($realString);
2859    
2860  Return the IP address to be used for emergency tracing. If at smoe point we need  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2861  to change the way we compute the IP address, or we decide to use something else,  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2862  all we need to do is change this method.  result is to reverse the effect of L</UnEscape>.
2863    
2864  =over 4  =over 4
2865    
2866  =item cgi  =item realString
2867    
2868  CGI query object.  String to escape.
2869    
2870  =item RETURN  =item RETURN
2871    
2872  Returns the IP address to be used for labelling emergency tracing.  Escaped equivalent of the real string.
2873    
2874  =back  =back
2875    
2876  =cut  =cut
2877    
2878  sub EmergencyIP {  sub Escape {
2879      # Get the parameters.      # Get the parameter.
2880      my ($cgi) = @_;      my ($realString) = @_;
2881        # Initialize the return variable.
2882        my $retVal = "";
2883        # Loop through the parameter string, looking for sequences to escape.
2884        while (length $realString > 0) {
2885            # Look for the first sequence to escape.
2886            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2887                # Here we found it. The text preceding the sequence is in $1. The sequence
2888                # itself is in $2. First, move the clear text to the return variable.
2889                $retVal .= $1;
2890                # Strip the processed section off the real string.
2891                $realString = substr $realString, (length $2) + (length $1);
2892                # Get the matched character.
2893                my $char = $2;
2894                # If we have a CR, we are done.
2895                if ($char ne "\r") {
2896                    # It's not a CR, so encode the escape sequence.
2897                    $char =~ tr/\t\n/tn/;
2898                    $retVal .= "\\" . $char;
2899                }
2900            } else {
2901                # Here there are no more escape sequences. The rest of the string is
2902                # transferred unmodified.
2903                $retVal .= $realString;
2904                $realString = "";
2905            }
2906        }
2907      # Return the result.      # Return the result.
2908      return $cgi->remote_addr();      return $retVal;
2909  }  }
2910    
2911    =head3 UnEscape
2912    
2913  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2914    
2915  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2916  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2917    be deleted.
2918    
2919  =over 4  =over 4
2920    
2921  =item cgi  =item codedString
2922    
2923  CGI query object containing the parameters to trace.  String to un-escape.
2924    
2925    =item RETURN
2926    
2927    Returns a copy of the original string with the escape sequences converted to their actual
2928    values.
2929    
2930  =back  =back
2931    
2932  =cut  =cut
2933    
2934  sub TraceParms {  sub UnEscape {
2935      # Get the parameters.      # Get the parameter.
2936      my ($cgi) = @_;      my ($codedString) = @_;
2937      if (T(CGI => 3)) {      # Initialize the return variable.
2938          # Here we want to trace the parameter data.      my $retVal = "";
2939          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2940          for my $parmName (sort @names) {      if (defined $codedString) {
2941              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
2942              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2943                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
2944                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
2945              }              # Look for the first escape sequence.
2946                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2947                    # Here we found it. The text preceding the sequence is in $1. The sequence
2948                    # itself is in $2. First, move the clear text to the return variable.
2949                    $retVal .= $1;
2950                    $codedString = substr $codedString, (2 + length $1);
2951                    # Get the escape value.
2952                    my $char = $2;
2953                    # If we have a "\r", we are done.
2954                    if ($char ne 'r') {
2955                        # Here it's not an 'r', so we convert it.
2956                        $char =~ tr/\\tn/\\\t\n/;
2957                        $retVal .= $char;
2958          }          }
2959          # Display the request method.              } else {
2960          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
2961          Trace("Method: $method");                  # transferred unmodified.
2962                    $retVal .= $codedString;
2963                    $codedString = "";
2964      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
2965          }          }
2966      }      }
2967        # Return the result.
2968        return $retVal;
2969  }  }
2970    
2971  =head3 ScriptFinish  =head3 Percent
2972    
2973  C<< ScriptFinish($webData, $varHash); >>      my $percent = Tracer::Percent($number, $base);
2974    
2975  Output a web page at the end of a script. Either the string to be output or the  Returns the percent of the base represented by the given number. If the base
2976  name of a template file can be specified. If the second parameter is omitted,  is zero, returns zero.
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2977    
2978  A typical standard script would loook like the following.  =over 4
2979    
2980      BEGIN {  =item number
2981          # Print the HTML header.  
2982          print "CONTENT-TYPE: text/html\n\n";  Percent numerator.
2983    
2984    =item base
2985    
2986    Percent base.
2987    
2988    =item RETURN
2989    
2990    Returns the percentage of the base represented by the numerator.
2991    
2992    =back
2993    
2994    =cut
2995    
2996    sub Percent {
2997        # Get the parameters.
2998        my ($number, $base) = @_;
2999        # Declare the return variable.
3000        my $retVal = 0;
3001        # Compute the percent.
3002        if ($base != 0) {
3003            $retVal = $number * 100 / $base;
3004        }
3005        # Return the result.
3006        return $retVal;
3007      }      }
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3008    
3009      my ($cgi, $varHash) = ScriptSetup();  =head3 Constrain
3010      eval {  
3011          # ... get data from $cgi, put it in $varHash ...      my $constrained = Constrain($value, $min, $max);
3012      };  
3013      if ($@) {  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3014          Trace("Script Error: $@") if T(0);  
3015    =over 4
3016    
3017    =item value
3018    
3019    Value to constrain.
3020    
3021    =item min (optional)
3022    
3023    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3024    
3025    =item max (optional)
3026    
3027    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3028    
3029    =item RETURN
3030    
3031    Returns the incoming value, constrained according to the other parameters.
3032    
3033    =back
3034    
3035    =cut
3036    
3037    sub Constrain {
3038        # Get the parameters.
3039        my ($value, $min, $max) = @_;
3040        # Declare the return variable.
3041        my $retVal = $value;
3042        # Apply the minimum constraint.
3043        if (defined $min && $retVal < $min) {
3044            $retVal = $min;
3045        }
3046        # Apply the maximum constraint.
3047        if (defined $max && $retVal > $max) {
3048            $retVal = $max;
3049        }
3050        # Return the result.
3051        return $retVal;
3052      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3053    
3054  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
3055  useful output.  
3056        my $min = Min($value1, $value2, ... $valueN);
3057    
3058    Return the minimum argument. The arguments are treated as numbers.
3059    
3060  =over 4  =over 4
3061    
3062  =item webData  =item $value1, $value2, ... $valueN
3063    
3064  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3065    
3066  =item varHash (optional)  =item RETURN
3067    
3068  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3069    
3070  =back  =back
3071    
3072  =cut  =cut
3073    
3074  sub ScriptFinish {  sub Min {
3075      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3076      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3077      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
3078      my $outputString;      for my $value (@values) {
3079      if (defined $varHash) {          if ($value < $retVal) {
3080          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to <a href=\"$actualDest\">$actualDest</a>.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
3081          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3082      }      }
3083      # Write the output string.      # Return the minimum found.
3084      print $outputString;      return $retVal;
3085  }  }
3086    
3087  =head3 Insure  =head3 Max
3088    
3089  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3090    
3091  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
3092    
3093  =over 4  =over 4
3094    
3095  =item dirName  =item $value1, $value2, ... $valueN
3096    
3097  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3098    
3099    =item RETURN
3100    
3101    Returns the highest number in the list.
3102    
3103  =back  =back
3104    
3105  =cut  =cut
3106    
3107  sub Insure {  sub Max {
3108      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3109      if (! -d $dirName) {      my ($retVal, @values) = @_;
3110          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
3111          eval { mkpath $dirName; };      for my $value (@values) {
3112          if ($@) {          if ($value > $retVal) {
3113              Confess("Error creating $dirName: $@");              $retVal = $value;
3114          }          }
3115      }      }
3116        # Return the maximum found.
3117        return $retVal;
3118  }  }
3119    
 =head3 ChDir  
3120    
3121  C<< ChDir($dirName); >>  =head3 Strip
3122    
3123        my $string = Tracer::Strip($line);
3124    
3125  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
3126    that may have been transferred back and forth several times among different
3127    operating environments.
3128    
3129  =over 4  =over 4
3130    
3131  =item dirName  =item line
3132    
3133  Name of the directory to which we want to change.  Line of text to be stripped.
3134    
3135    =item RETURN
3136    
3137    The same line of text with all the line-ending characters chopped from the end.
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub ChDir {  sub Strip {
3144      my ($dirName) = @_;      # Get a copy of the parameter string.
3145      if (! -d $dirName) {      my ($string) = @_;
3146          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3147      } else {      # Strip the line terminator characters.
3148          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3149          my $okFlag = chdir $dirName;      # Return the result.
3150          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3151  }  }
3152    
3153  =head3 SendSMS  =head3 Pad
3154    
3155  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3156    
3157  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3158  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3159  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3160    
3161      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3162    
3163  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3164    
3165  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3166    
3167  =over 4  =item len
3168    
3169  =item phoneNumber  Desired length of the padded string.
3170    
3171  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3172    
3173  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3174    
3175  Message to send to the specified phone.  =item padChar (optional)
3176    
3177    Character to use for padding. The default is a space.
3178    
3179  =item RETURN  =item RETURN
3180    
3181  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3182    specified end so that it achieves the desired length.
3183    
3184  =back  =back
3185    
3186  =cut  =cut
3187    
3188  sub SendSMS {  sub Pad {
3189      # Get the parameters.      # Get the parameters.
3190      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3191      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3192      my $retVal;      if (! defined $padChar) {
3193      # Only proceed if we have phone support.          $padChar = " ";
3194      if (! defined $FIG_Config::phone) {      }
3195          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
3196      } else {      my $needed = $len - length $string;
3197          # Get the phone data.      # Copy the string into the return variable.
3198          my $parms = $FIG_Config::phone;      my $retVal = $string;
3199          # Get the Clickatell URL.      # Only proceed if padding is needed.
3200          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
3201          # Create the user agent.          # Create the pad string.
3202          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
3203          # Request a Clickatell session.          # Affix it to the return value.
3204          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
3205                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
3206              } else {              } else {
3207                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
3208              }              }
3209          }          }
3210        # Return the result.
3211        return $retVal;
3212    }
3213    
3214    =head3 EOF
3215    
3216    This is a constant that is lexically greater than any useful string.
3217    
3218    =cut
3219    
3220    sub EOF {
3221        return "\xFF\xFF\xFF\xFF\xFF";
3222    }
3223    
3224    =head3 TICK
3225    
3226        my @results = TICK($commandString);
3227    
3228    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3229    dot-slash (C<./> will be removed. So, for example, if you were doing
3230    
3231        `./protein.cgi`
3232    
3233    from inside a CGI script, it would work fine in Unix, but would issue an error message
3234    in Windows complaining that C<'.'> is not a valid command. If instead you code
3235    
3236        TICK("./protein.cgi")
3237    
3238    it will work correctly in both environments.
3239    
3240    =over 4
3241    
3242    =item commandString
3243    
3244    The command string to pass to the system.
3245    
3246    =item RETURN
3247    
3248    Returns the standard output from the specified command, as a list.
3249    
3250    =back
3251    
3252    =cut
3253    #: Return Type @;
3254    sub TICK {
3255        # Get the parameters.
3256        my ($commandString) = @_;
3257        # Chop off the dot-slash if this is Windows.
3258        if ($FIG_Config::win_mode) {
3259            $commandString =~ s!^\./!!;
3260      }      }
3261      # Return the result.      # Activate the command and return the result.
3262      return $retVal;      return `$commandString`;
3263  }  }
3264    
3265    
3266  =head3 CommaFormat  =head3 CommaFormat
3267    
3268  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3269    
3270  Insert commas into a number.  Insert commas into a number.
3271    
# Line 2503  Line 3298 
3298      # Return the result.      # Return the result.
3299      return $retVal;      return $retVal;
3300  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3301    
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.