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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 ScriptSetup ScriptFinish Insure ChDir);      @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;
29      use FIG_Config;      use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31      use Digest::MD5;      use Digest::MD5;
32      use File::Basename;      use File::Basename;
33      use File::Path;      use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        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 56  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 116  Line 149 
149    
150  =back  =back
151    
152    The format of trace messages is important because some utilities analyze trace files.
153    There are three fields-- the time stamp, the category name, and the text.
154    The time stamp is between square brackets and the category name between angle brackets.
155    After the category name there is a colon (C<:>) followed by the message text.
156    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    =cut
225    
226  =head2 Public Methods  sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 186  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($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() . " 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 208  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 threer 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 FIG  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
328    
329  =item SQL      my $time = Tracer::ParseDate($dateString);
330    
331  Traces SQL commands and activity.  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  =item Tracer  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  Traces error messages and call stacks.  The year must be exactly four digits.
341    
342  =back  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  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  It should be guaranteed that this method will parse the output of the L</Now> function.
 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.  
347    
348      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
349    
350  Standard tracing is output to the standard output and echoed to the file  =over 4
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
351    
352  The default trace level is 2. To get all messages, specify a trace level of 4.  =item dateString
 For a genome-by-genome update, use 3.  
353    
354      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
355    
356  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
357    
358  The I<options> parameter is a reference to a hash containing the command-line  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  options, their default values, and an explanation of what they mean. Command-line  the date string is invalid. A valid date string must contain a month and day.
 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.  
360    
361  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
362    
363  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
364    
365      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
366                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                        @ARGV);                              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    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 $retVal;
412    }
413    
414  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
415    
416  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
417    
418      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
419    
420  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
421    
422      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
423    
424  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
425    
426  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
427    
428      -user=Bruce -background  =cut
429    
430  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
431  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
432  simplify starting a command in the background.      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
438    
439      TransactFeatures -h      Trace($message);
440    
441  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
442    any prior call to B<TSetup>.
443    
444      TransactFeatures [options] command transactionDirectory IDfile  =over 4
         -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  
445    
446  The caller has the option of modifying the tracing scheme by placing a value  =item message
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
447    
448      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
449    
450  would set the default trace level to 0 instead of 2, while  =back
451    
452      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
453    
454  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
455  standard output.      # 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  The parameters to this method are as follows.  =head3 T
504    
505  =over 4      my $switch = T($category, $traceLevel);
506    
507  =item categories      or
508    
509  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
510    
511  =item options  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  Reference to a hash containing the legal options for the current command mapped  =over 4
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
515    
516  =item parmHelp  =item category
517    
518  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
519  if the user specifies the C<-h> option.  used.
520    
521  =item argv  =item traceLevel
522    
523  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
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";
551      # length of the longest option name.              } else {
552                    my @cats = split /::/, $package;
553                    $category = $cats[$#cats];
554                }
555            }
556            # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566            }
567            # Make the check. Note that level 0 shows even if the category is turned off.
568            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569        }
570        # Return the computed result.
571        return $retVal;
572    }
573    
574    =head3 QTrace
575    
576        my $data = QTrace($format);
577    
578    Return the queued trace data in the specified format.
579    
580    =over 4
581    
582    =item format
583    
584    C<html> to format the data as an HTML list, C<text> to format it as straight text.
585    
586    =back
587    
588    =cut
589    
590    sub QTrace {
591        # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615    }
616    
617    =head3 Confess
618    
619        Confess($message);
620    
621    Trace the call stack and abort the program with the specified message. When used with
622    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623    So, for example
624    
625        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627    Will abort the program with a stack trace if the value of C<$recNum> is negative.
628    
629    =over 4
630    
631    =item message
632    
633    Message to include in the trace.
634    
635    =back
636    
637    =cut
638    
639    sub Confess {
640        # Get the parameters.
641        my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663    =head3 Warn
664    
665        Warn($message);
666    
667    This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    The L</Cluck> method calls this one for its final message. Since
674    L</Confess> calls L</Cluck>, this means that any error which is caught
675    and confessed will put something in the feed. This insures that someone
676    will be alerted relatively quickly when a failure occurs.
677    
678    =over 4
679    
680    =item message
681    
682    Message to be traced.
683    
684    =back
685    
686    =cut
687    
688    sub Warn {
689        # Get the parameters.
690        my ($message) = @_;
691        # Trace the message.
692        Trace($message);
693        # An error here would be disastrous. Note, however, that we aren't too worried
694        # about losing events. The error log is always available for the occasions where
695        # we mess up.
696        eval {
697            # Do we need to put this in the RSS feed?
698            if ($FIG_Config::error_feed && $Destination eq 'WARN') {
699                # Yes. We now need to compute the date, the link, and the title.
700                # First, the date, in a very specific format.
701                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
702                    (tz_local_offset() / 30);
703                # We'll put the link and title in here.
704                my ($link, $title);
705                # Environment data goes in here.
706                my $environment;
707                # HTML-escape the message.
708                my $escaped = CGI::escapeHTML($message);
709                # If we have a CGI object, then this is a web error. Otherwise, it's
710                # command-line.
711                if (defined $SavedCGI) {
712                    # We're in a web service. The title is the user's IP, and the link
713                    # is the URL that got us here.
714                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
715                    $title = "Event Reported at IP address $key: $escaped";
716                    $link = $SavedCGI->url(-full => 1, -query => 1);
717                    # We need the user agent string and (if available) the referrer.
718                    $environment = "User Agent $ENV{HTTP_USER_AGENT}";
719                    if ($ENV{HTTP_REFERER}) {
720                        $environment .= " referred from $ENV{HTTP_REFERER}"
721                    }
722                    # Close off the sentence.
723                    $environment .= ". ";
724                } else {
725                    # No CGI object, so we're a command-line tool. Use the tracing
726                    # key and the PID as the user identifier.
727                    my $key = EmergencyKey();
728                    $title = "Event Reported by $key Process $$: $escaped";
729                    # Set the link to the development NMPDR. There is really no good
730                    # choice here.
731                    $link = "http://$FIG_Config::dev_server";
732                    # We need the command
733                    $environment = "Command $ENV{_}.";
734                }
735                # Build a GUID. We use the current time, the title, and the process ID,
736                # then digest the result.
737                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
738                # Finally, the description. This is a stack trace plus various environmental stuff.
739                my @trace = LongMess();
740                my $trace = join "; ", @trace;
741                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
742                # Okay, we have all the pieces. Create a hash of the new event.
743                my $newItem = { title => $title,
744                                description => $description,
745                                link => $link,
746                                category => $LastCategory,
747                                pubDate => $date,
748                                guid => $guid,
749                               };
750                # We need XML capability for this.
751                require XML::Simple;
752                # The RSS document goes in here.
753                my $rss;
754                # Get the name of the RSS file. It's in the FIG temporary directory.
755                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
756                # Does it exist?
757                if (-s $fileName) {
758                    # Slurp it in.
759                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
760                } else {
761                    my $size = -s $fileName;
762                    # Create an empty channel.
763                    $rss = {
764                        channel => {
765                            title => 'NMPDR Warning Feed',
766                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
767                            description => "Important messages regarding the status of the NMPDR.",
768                            generator => "NMPDR Trace Facility",
769                            docs => "http://blogs.law.harvard.edu/tech/rss",
770                            item => []
771                        },
772                    };
773                }
774                # Get the channel object.
775                my $channel = $rss->{channel};
776                # Update the last-build date.
777                $channel->{lastBuildDate} = $date;
778                # Get the item array.
779                my $items = $channel->{item};
780                # Insure it has only 100 entries.
781                while (scalar @{$items} > 100) {
782                    pop @{$items};
783                }
784                # Add our new item at the front.
785                unshift @{$items}, $newItem;
786                # Replace the file.
787                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
788                                              NoEscape => 1);
789                # We don't use Open here because we can't afford an error.
790                if (open XMLOUT, ">$fileName") {
791                    print XMLOUT $xml;
792                    close XMLOUT;
793                }
794            }
795        };
796        # There's no "if ($@)" here, because putting an error message in the log
797        # saying that we missed putting an error message in the feed of messages
798        # in the log is not going to help anybody.
799    }
800    
801    =head3 Assert
802    
803        Assert($condition1, $condition2, ... $conditionN);
804    
805    Return TRUE if all the conditions are true. This method can be used in conjunction with
806    the OR operator and the L</Confess> method as a debugging assert.
807    So, for example
808    
809        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
810    
811    Will abort the program with a stack trace if the value of C<$recNum> is negative.
812    
813    =cut
814    sub Assert {
815        my $retVal = 1;
816        LOOP: for my $condition (@_) {
817            if (! $condition) {
818                $retVal = 0;
819                last LOOP;
820            }
821        }
822        return $retVal;
823    }
824    
825    =head3 Cluck
826    
827        Cluck($message);
828    
829    Trace the call stack. Note that for best results, you should qualify the call with a
830    trace condition. For example,
831    
832        Cluck("Starting record parse.") if T(3);
833    
834    will only trace the stack if the trace level for the package is 3 or more.
835    
836    =over 4
837    
838    =item message
839    
840    Message to include in the trace.
841    
842    =back
843    
844    =cut
845    
846    sub Cluck {
847        # Get the parameters.
848        my ($message) = @_;
849        # Trace what's happening.
850        Trace("Stack trace for event: $message");
851        # Get the stack trace.
852        my @trace = LongMess();
853        # Convert the trace to a series of messages.
854        for my $line (@trace) {
855            # Replace the tab at the beginning with spaces.
856            $line =~ s/^\t/    /;
857            # Trace the line.
858            Trace($line);
859        }
860        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
861        Warn($message);
862    }
863    
864    =head3 LongMess
865    
866        my @lines = Tracer::LongMess();
867    
868    Return a stack trace with all tracing methods removed. The return will be in the form of a list
869    of message strings.
870    
871    =cut
872    
873    sub LongMess {
874        # Declare the return variable.
875        my @retVal = ();
876        my $confession = longmess("");
877        for my $line (split /\s*\n/, $confession) {
878            unless ($line =~ /Tracer\.pm/) {
879                # Here we have a line worth keeping. Push it onto the result list.
880                push @retVal, $line;
881            }
882        }
883        # Return the result.
884        return @retVal;
885    }
886    
887    =head3 ScriptSetup (deprecated)
888    
889        my ($cgi, $varHash) = ScriptSetup($noTrace);
890    
891    Perform standard tracing and debugging setup for scripts. The value returned is
892    the CGI object followed by a pre-built variable hash. At the end of the script,
893    the client should call L</ScriptFinish> to output the web page.
894    
895    This method calls L</ETracing> to configure tracing, which allows the tracing
896    to be configured via the emergency tracing form on the debugging control panel.
897    Tracing will then be turned on automatically for all programs that use the L</ETracing>
898    method, which includes every program that uses this method or L</StandardSetup>.
899    
900    =over 4
901    
902    =item noTrace (optional)
903    
904    If specified, tracing will be suppressed. This is useful if the script wants to set up
905    tracing manually.
906    
907    =item RETURN
908    
909    Returns a two-element list consisting of a CGI query object and a variable hash for
910    the output page.
911    
912    =back
913    
914    =cut
915    
916    sub ScriptSetup {
917        # Get the parameters.
918        my ($noTrace) = @_;
919        # Get the CGI query object.
920        my $cgi = CGI->new();
921        # Set up tracing if it's not suppressed.
922        ETracing($cgi) unless $noTrace;
923        # Create the variable hash.
924        my $varHash = { results => '' };
925        # Return the query object and variable hash.
926        return ($cgi, $varHash);
927    }
928    
929    =head3 ETracing
930    
931        ETracing($parameter);
932    
933    Set up emergency tracing. Emergency tracing is tracing that is turned
934    on automatically for any program that calls this method. The emergency
935    tracing parameters are stored in a a file identified by a tracing key.
936    If this method is called with a CGI object, then the tracing key is
937    taken from a cookie. If it is called with no parameters, then the tracing
938    key is taken from an environment variable. If it is called with a string,
939    the tracing key is that string.
940    
941    =over 4
942    
943    =item parameter
944    
945    A parameter from which the tracing key is computed. If it is a scalar,
946    that scalar is used as the tracing key. If it is a CGI object, the
947    tracing key is taken from the C<IP> cookie. If it is omitted, the
948    tracing key is taken from the C<TRACING> environment variable. If it
949    is a CGI object and emergency tracing is not on, the C<Trace> and
950    C<TF> parameters will be used to determine the type of tracing.
951    
952    =back
953    
954    =cut
955    
956    sub ETracing {
957        # Get the parameter.
958        my ($parameter) = @_;
959        # Check for CGI mode.
960        if (defined $parameter && ref $parameter eq 'CGI') {
961            $SavedCGI = $parameter;
962        } else {
963            $SavedCGI = undef;
964        }
965        # Default to no tracing except errors.
966        my ($tracing, $dest) = ("0", "WARN");
967        # Check for emergency tracing.
968        my $tkey = EmergencyKey($parameter);
969        my $emergencyFile = EmergencyFileName($tkey);
970        if (-e $emergencyFile) {
971            # We have the file. Read in the data.
972            my @tracing = GetFile($emergencyFile);
973            # Pull off the time limit.
974            my $expire = shift @tracing;
975            # Convert it to seconds.
976            $expire *= 3600;
977            # Check the file data.
978            my $stat = stat($emergencyFile);
979            my ($now) = gettimeofday;
980            if ($now - $stat->mtime > $expire) {
981                # Delete the expired file.
982                unlink $emergencyFile;
983            } else {
984                # Emergency tracing is on. Pull off the destination and
985                # the trace level;
986                $dest = shift @tracing;
987                my $level = shift @tracing;
988                # Convert the destination to a real tracing destination.
989                # temp directory.
990                $dest = EmergencyTracingDest($tkey, $dest);
991                # Insure Tracer is specified.
992                my %moduleHash = map { $_ => 1 } @tracing;
993                $moduleHash{Tracer} = 1;
994                # Set the trace parameter.
995                $tracing = join(" ", $level, sort keys %moduleHash);
996            }
997        } elsif (defined $SavedCGI) {
998            # There's no emergency tracing, but we have a CGI object, so check
999            # for tracing from the form parameters.
1000            if ($SavedCGI->param('Trace')) {
1001                # Here the user has requested tracing via a form.
1002                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1003                $tracing = $SavedCGI->param('Trace') . " Tracer";
1004            }
1005        }
1006        # Setup the tracing we've determined from all the stuff above.
1007        TSetup($tracing, $dest);
1008        # Check to see if we're a web script.
1009        if (defined $SavedCGI) {
1010            # Yes we are. Trace the form and environment data.
1011            TraceParms($SavedCGI);
1012            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1013            # emitted by the script in its raw form.
1014            if (T(Raw => 3)) {
1015                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1016            }
1017        }
1018    }
1019    
1020    =head3 EmergencyFileName
1021    
1022        my $fileName = Tracer::EmergencyFileName($tkey);
1023    
1024    Return the emergency tracing file name. This is the file that specifies
1025    the tracing information.
1026    
1027    =over 4
1028    
1029    =item tkey
1030    
1031    Tracing key for the current program.
1032    
1033    =item RETURN
1034    
1035    Returns the name of the file to contain the emergency tracing information.
1036    
1037    =back
1038    
1039    =cut
1040    
1041    sub EmergencyFileName {
1042        # Get the parameters.
1043        my ($tkey) = @_;
1044        # Compute the emergency tracing file name.
1045        return "$FIG_Config::temp/Emergency$tkey.txt";
1046    }
1047    
1048    =head3 EmergencyFileTarget
1049    
1050        my $fileName = Tracer::EmergencyFileTarget($tkey);
1051    
1052    Return the emergency tracing target file name. This is the file that receives
1053    the tracing output for file-based tracing.
1054    
1055    =over 4
1056    
1057    =item tkey
1058    
1059    Tracing key for the current program.
1060    
1061    =item RETURN
1062    
1063    Returns the name of the file to contain the trace output.
1064    
1065    =back
1066    
1067    =cut
1068    
1069    sub EmergencyFileTarget {
1070        # Get the parameters.
1071        my ($tkey) = @_;
1072        # Compute the emergency tracing file name.
1073        return "$FIG_Config::temp/trace$tkey.log";
1074    }
1075    
1076    =head3 EmergencyTracingDest
1077    
1078        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1079    
1080    This method converts an emergency tracing destination to a real
1081    tracing destination. The main difference is that if the
1082    destination is C<FILE> or C<APPEND>, we convert it to file
1083    output. If the destination is C<DUAL>, we convert it to file
1084    and standard output.
1085    
1086    =over 4
1087    
1088    =item tkey
1089    
1090    Tracing key for this environment.
1091    
1092    =item myDest
1093    
1094    Destination from the emergency tracing file.
1095    
1096    =item RETURN
1097    
1098    Returns a destination that can be passed into L</TSetup>.
1099    
1100    =back
1101    
1102    =cut
1103    
1104    sub EmergencyTracingDest {
1105        # Get the parameters.
1106        my ($tkey, $myDest) = @_;
1107        # Declare the return variable.
1108        my $retVal = $myDest;
1109        # Process according to the destination value.
1110        if ($myDest eq 'FILE') {
1111            $retVal = ">" . EmergencyFileTarget($tkey);
1112        } elsif ($myDest eq 'APPEND') {
1113            $retVal = ">>" . EmergencyFileTarget($tkey);
1114        } elsif ($myDest eq 'DUAL') {
1115            $retVal = "+>" . EmergencyFileTarget($tkey);
1116        } elsif ($myDest eq 'WARN') {
1117            $retVal = "WARN";
1118        }
1119        # Return the result.
1120        return $retVal;
1121    }
1122    
1123    =head3 Emergency
1124    
1125        Emergency($key, $hours, $dest, $level, @modules);
1126    
1127    Turn on emergency tracing. This method is normally invoked over the web from
1128    a debugging console, but it can also be called by the C<trace.pl> script.
1129    The caller specifies the duration of the emergency in hours, the desired tracing
1130    destination, the trace level, and a list of the trace modules to activate.
1131    For the length of the duration, when a program in an environment with the
1132    specified tracing key active invokes a Sprout CGI script, tracing will be
1133    turned on automatically. See L</TSetup> for more about tracing setup and
1134    L</ETracing> for more about emergency tracing.
1135    
1136    =over 4
1137    
1138    =item tkey
1139    
1140    The tracing key. This is used to identify the control file and the trace file.
1141    
1142    =item hours
1143    
1144    Number of hours to keep emergency tracing alive.
1145    
1146    =item dest
1147    
1148    Tracing destination. If no path information is specified for a file
1149    destination, it is put in the FIG temporary directory.
1150    
1151    =item level
1152    
1153    Tracing level. A higher level means more trace messages.
1154    
1155    =item modules
1156    
1157    A list of the tracing modules to activate.
1158    
1159    =back
1160    
1161    =cut
1162    
1163    sub Emergency {
1164        # Get the parameters.
1165        my ($tkey, $hours, $dest, $level, @modules) = @_;
1166        # Create the emergency file.
1167        my $specFile = EmergencyFileName($tkey);
1168        my $outHandle = Open(undef, ">$specFile");
1169        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1170    }
1171    
1172    =head3 EmergencyKey
1173    
1174        my $tkey = EmergencyKey($parameter);
1175    
1176    Return the Key to be used for emergency tracing. This could be an IP address,
1177     a session ID, or a user name, depending on the environment.
1178    
1179    =over 4
1180    
1181    =item parameter
1182    
1183    Parameter defining the method for finding the tracing key. If it is a scalar,
1184    then it is presumed to be the tracing key itself. If it is a CGI object, then
1185    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1186    taken from the C<TRACING> environment variable.
1187    
1188    =item RETURN
1189    
1190    Returns the key to be used for labels in emergency tracing.
1191    
1192    =back
1193    
1194    =cut
1195    
1196    sub EmergencyKey {
1197        # Get the parameters.
1198        my ($parameter) = @_;
1199        # Declare the return variable.
1200        my $retVal;
1201        # Determine the parameter type.
1202        if (! defined $parameter) {
1203            # Here we're supposed to check the environment. If that fails, we
1204            # get the effective login ID.
1205            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1206        } else {
1207            my $ptype = ref $parameter;
1208            if ($ptype eq 'CGI') {
1209                # Here we were invoked from a web page. Look for a cookie.
1210                $retVal = $parameter->cookie('IP');
1211            } elsif (! $ptype) {
1212                # Here the key was passed in.
1213                $retVal = $parameter;
1214            }
1215        }
1216        # If no luck finding a key, use the PID.
1217        if (! defined $retVal) {
1218            $retVal = $$;
1219        }
1220        # Return the result.
1221        return $retVal;
1222    }
1223    
1224    
1225    =head3 TraceParms
1226    
1227        Tracer::TraceParms($cgi);
1228    
1229    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1230    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1231    
1232    =over 4
1233    
1234    =item cgi
1235    
1236    CGI query object containing the parameters to trace.
1237    
1238    =back
1239    
1240    =cut
1241    
1242    sub TraceParms {
1243        # Get the parameters.
1244        my ($cgi) = @_;
1245        if (T(CGI => 2)) {
1246            # Here we trace the GET-style URL for the script.
1247            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1248        }
1249        if (T(CGI => 3)) {
1250            # Here we want to trace the parameter data.
1251            my @names = $cgi->param;
1252            for my $parmName (sort @names) {
1253                # Note we skip the Trace parameters, which are for our use only.
1254                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1255                    my @values = $cgi->param($parmName);
1256                    Trace("[CGI] $parmName = " . join(", ", @values));
1257                }
1258            }
1259            # Display the request method.
1260            my $method = $cgi->request_method();
1261            Trace("Method: $method");
1262        }
1263        if (T(CGI => 4)) {
1264            # Here we want the environment data too.
1265            for my $envName (sort keys %ENV) {
1266                Trace("[ENV] $envName = $ENV{$envName}");
1267            }
1268        }
1269    }
1270    
1271    =head3 TraceImages
1272    
1273        Tracer::TraceImages($htmlString);
1274    
1275    Trace information about all of an html document's images. The tracing
1276    will be for type "IMG" at level 3. The image's source string
1277    will be displayed. This is generally either the URL of the image or
1278    raw data for the image itself. If the source is too long, only the first 300
1279    characters will be shown at trace level 3. The entire source will be shown,
1280    however, at trace level 4. This method is not very smart, and might catch
1281    Javascript code, but it is still useful when debugging the arcane
1282    behavior of images in multiple browser environments.
1283    
1284    =over 4
1285    
1286    =item htmlString
1287    
1288    HTML text for an outgoing web page.
1289    
1290    =back
1291    
1292    =cut
1293    
1294    sub TraceImages {
1295        # Only proceed if we're at the proper trace level.
1296        if (T(IMG => 3)) {
1297            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1298            # into a variable called "$htmlString". This is because we expect html strings to be
1299            # long, and don't want to copy them any more than we have to.
1300            Trace(length($_[0]) . " characters in web page.");
1301            # Loop through the HTML, culling image tags.
1302            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1303                # Extract the source string and determine whether or not it's too long.
1304                my $srcString = $1;
1305                my $pos = pos($_[0]) - length($srcString);
1306                my $excess = length($srcString) - 300;
1307                # We'll put the display string in here.
1308                my $srcDisplay = $srcString;
1309                # If it's a data string, split it at the comma.
1310                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1311                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1312                # a long string, however, we only show the first 300 characters.
1313                if ($excess > 0 && ! T(IMG => 4)) {
1314                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1315                }
1316                # Output the trace message.
1317                Trace("Image tag at position $pos:\n$srcDisplay");
1318            }
1319        }
1320    }
1321    
1322    
1323    =head3 ScriptFinish (deprecated)
1324    
1325        ScriptFinish($webData, $varHash);
1326    
1327    Output a web page at the end of a script. Either the string to be output or the
1328    name of a template file can be specified. If the second parameter is omitted,
1329    it is assumed we have a string to be output; otherwise, it is assumed we have the
1330    name of a template file. The template should have the variable C<DebugData>
1331    specified in any form that invokes a standard script. If debugging mode is turned
1332    on, a form field will be put in that allows the user to enter tracing data.
1333    Trace messages will be placed immediately before the terminal C<BODY> tag in
1334    the output, formatted as a list.
1335    
1336    A typical standard script would loook like the following.
1337    
1338        BEGIN {
1339            # Print the HTML header.
1340            print "CONTENT-TYPE: text/html\n\n";
1341        }
1342        use Tracer;
1343        use CGI;
1344        use FIG;
1345        # ... more uses ...
1346    
1347        my ($cgi, $varHash) = ScriptSetup();
1348        eval {
1349            # ... get data from $cgi, put it in $varHash ...
1350        };
1351        if ($@) {
1352            Trace("Script Error: $@") if T(0);
1353        }
1354        ScriptFinish("Html/MyTemplate.html", $varHash);
1355    
1356    The idea here is that even if the script fails, you'll see trace messages and
1357    useful output.
1358    
1359    =over 4
1360    
1361    =item webData
1362    
1363    A string containing either the full web page to be written to the output or the
1364    name of a template file from which the page is to be constructed. If the name
1365    of a template file is specified, then the second parameter must be present;
1366    otherwise, it must be absent.
1367    
1368    =item varHash (optional)
1369    
1370    If specified, then a reference to a hash mapping variable names for a template
1371    to their values. The template file will be read into memory, and variable markers
1372    will be replaced by data in this hash reference.
1373    
1374    =back
1375    
1376    =cut
1377    
1378    sub ScriptFinish {
1379        # Get the parameters.
1380        my ($webData, $varHash) = @_;
1381        # Check for a template file situation.
1382        my $outputString;
1383        if (defined $varHash) {
1384            # Here we have a template file. We need to determine the template type.
1385            my $template;
1386            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1387                $template = "$FIG_Config::template_url/$webData";
1388            } else {
1389                $template = "<<$webData";
1390            }
1391            $outputString = PageBuilder::Build($template, $varHash, "Html");
1392        } else {
1393            # Here the user gave us a raw string.
1394            $outputString = $webData;
1395        }
1396        # Check for trace messages.
1397        if ($Destination ne "NONE" && $TraceLevel > 0) {
1398            # We have trace messages, so we want to put them at the end of the body. This
1399            # is either at the end of the whole string or at the beginning of the BODY
1400            # end-tag.
1401            my $pos = length $outputString;
1402            if ($outputString =~ m#</body>#gi) {
1403                $pos = (pos $outputString) - 7;
1404            }
1405            # If the trace messages were queued, we unroll them. Otherwise, we display the
1406            # destination.
1407            my $traceHtml;
1408            if ($Destination eq "QUEUE") {
1409                $traceHtml = QTrace('Html');
1410            } elsif ($Destination =~ /^>>(.+)$/) {
1411                # Here the tracing output it to a file. We code it as a hyperlink so the user
1412                # can copy the file name into the clipboard easily.
1413                my $actualDest = $1;
1414                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1415            } else {
1416                # Here we have one of the special destinations.
1417                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1418            }
1419            substr $outputString, $pos, 0, $traceHtml;
1420        }
1421        # Write the output string.
1422        print $outputString;
1423    }
1424    
1425    =head2 Command-Line Utility Methods
1426    
1427    =head3 SendSMS
1428    
1429        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1430    
1431    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1432    user name, password, and API ID for the relevant account in the hash reference variable
1433    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1434    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1435    is C<2561022>, then the FIG_Config file must contain
1436    
1437        $phone =  { user => 'BruceTheHumanPet',
1438                    password => 'silly',
1439                    api_id => '2561022' };
1440    
1441    The original purpose of this method was to insure Bruce would be notified immediately when the
1442    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1443    when you call this method.
1444    
1445    The message ID will be returned if successful, and C<undef> if an error occurs.
1446    
1447    =over 4
1448    
1449    =item phoneNumber
1450    
1451    Phone number to receive the message, in international format. A United States phone number
1452    would be prefixed by "1". A British phone number would be prefixed by "44".
1453    
1454    =item msg
1455    
1456    Message to send to the specified phone.
1457    
1458    =item RETURN
1459    
1460    Returns the message ID if successful, and C<undef> if the message could not be sent.
1461    
1462    =back
1463    
1464    =cut
1465    
1466    sub SendSMS {
1467        # Get the parameters.
1468        my ($phoneNumber, $msg) = @_;
1469        # Declare the return variable. If we do not change it, C<undef> will be returned.
1470        my $retVal;
1471        # Only proceed if we have phone support.
1472        if (! defined $FIG_Config::phone) {
1473            Trace("Phone support not present in FIG_Config.") if T(1);
1474        } else {
1475            # Get the phone data.
1476            my $parms = $FIG_Config::phone;
1477            # Get the Clickatell URL.
1478            my $url = "http://api.clickatell.com/http/";
1479            # Create the user agent.
1480            my $ua = LWP::UserAgent->new;
1481            # Request a Clickatell session.
1482            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1483                                         password => $parms->{password},
1484                                         api_id => $parms->{api_id},
1485                                         to => $phoneNumber,
1486                                         text => $msg});
1487            # Check for an error.
1488            if (! $resp->is_success) {
1489                Trace("Alert failed.") if T(1);
1490            } else {
1491                # Get the message ID.
1492                my $rstring = $resp->content;
1493                if ($rstring =~ /^ID:\s+(.*)$/) {
1494                    $retVal = $1;
1495                } else {
1496                    Trace("Phone attempt failed with $rstring") if T(1);
1497                }
1498            }
1499        }
1500        # Return the result.
1501        return $retVal;
1502    }
1503    
1504    =head3 StandardSetup
1505    
1506        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1507    
1508    This method performs standard command-line parsing and tracing setup. The return
1509    values are a hash of the command-line options and a list of the positional
1510    parameters. Tracing is automatically set up and the command-line options are
1511    validated.
1512    
1513    This is a complex method that does a lot of grunt work. The parameters can
1514    be more easily understood, however, once they are examined individually.
1515    
1516    The I<categories> parameter is the most obtuse. It is a reference to a list of
1517    special-purpose tracing categories. Most tracing categories are PERL package
1518    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1519    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1520    
1521        ["Sprout", "SproutLoad", "ERDB"]
1522    
1523    This would cause trace messages in the specified three packages to appear in
1524    the output. There are two special tracing categories that are automatically
1525    handled by this method. In other words, if you used L</TSetup> you would need
1526    to include these categories manually, but if you use this method they are turned
1527    on automatically.
1528    
1529    =over 4
1530    
1531    =item SQL
1532    
1533    Traces SQL commands and activity.
1534    
1535    =item Tracer
1536    
1537    Traces error messages and call stacks.
1538    
1539    =back
1540    
1541    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1542    The trace level is specified using the C<-trace> command-line option. For example,
1543    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1544    all tracing at level 3.
1545    
1546        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1547    
1548    Standard tracing is output to the standard output and echoed to the file
1549    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1550    process ID. You can also specify the C<user> parameter to put a user ID
1551    instead of a process ID in the trace file name. So, for example
1552    
1553    The default trace level is 2. To get all messages, specify a trace level of 4.
1554    For a genome-by-genome update, use 3.
1555    
1556        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1557    
1558    would send the trace output to C<traceBruce.log> in the temporary directory.
1559    
1560    The I<options> parameter is a reference to a hash containing the command-line
1561    options, their default values, and an explanation of what they mean. Command-line
1562    options may be in the form of switches or keywords. In the case of a switch, the
1563    option value is 1 if it is specified and 0 if it is not specified. In the case
1564    of a keyword, the value is separated from the option name by an equal sign. You
1565    can see this last in the command-line example above.
1566    
1567    You can specify a different default trace level by setting C<$options->{trace}>
1568    prior to calling this method.
1569    
1570    An example at this point would help. Consider, for example, the command-line utility
1571    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1572    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1573    the following code.
1574    
1575        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1576                            { safe => [0, "use database transactions"],
1577                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1578                              start => [' ', "start with this genome"],
1579                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1580                            "<command> <transactionDirectory> <IDfile>",
1581                          @ARGV);
1582    
1583    
1584    The call to C<ParseCommand> specifies the default values for the options and
1585    stores the actual options in a hash that is returned as C<$options>. The
1586    positional parameters are returned in C<@parameters>.
1587    
1588    The following is a sample command line for C<TransactFeatures>.
1589    
1590        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1591    
1592    Single and double hyphens are equivalent. So, you could also code the
1593    above command as
1594    
1595        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1596    
1597    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1598    parameters, and would find themselves in I<@parameters> after executing the
1599    above code fragment. The tracing would be set to level 2, and the categories
1600    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1601    and C<DocUtils> was included because it came in within the first parameter
1602    to this method. The I<$options> hash would be
1603    
1604        { trace => 2, sql => 0, safe => 0,
1605          noAlias => 1, start => ' ', tblFiles => 0 }
1606    
1607    Use of C<StandardSetup> in this way provides a simple way of performing
1608    standard tracing setup and command-line parsing. Note that the caller is
1609    not even aware of the command-line switches C<-trace> and C<-sql>, which
1610    are used by this method to control the tracing. If additional tracing features
1611    need to be added in the future, they can be processed by this method without
1612    upsetting the command-line utilities.
1613    
1614    If the C<background> option is specified on the command line, then the
1615    standard and error outputs will be directed to files in the temporary
1616    directory, using the same suffix as the trace file. So, if the command
1617    line specified
1618    
1619        -user=Bruce -background
1620    
1621    then the trace output would go to C<traceBruce.log>, the standard output to
1622    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1623    simplify starting a command in the background.
1624    
1625    The user name is also used as the tracing key for L</Emergency Tracing>.
1626    Specifying a value of C<E> for the trace level causes emergency tracing to
1627    be used instead of custom tracing. If the user name is not specified,
1628    the tracing key is taken from the C<Tracing> environment variable. If there
1629    is no value for that variable, the tracing key will be computed from the PID.
1630    
1631    Finally, if the special option C<-help> is specified, the option
1632    names will be traced at level 0 and the program will exit without processing.
1633    This provides a limited help capability. For example, if the user enters
1634    
1635        TransactFeatures -help
1636    
1637    he would see the following output.
1638    
1639        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1640            -trace    tracing level (default E)
1641            -sql      trace SQL commands
1642            -safe     use database transactions
1643            -noAlias  do not expect aliases in CHANGE transactions
1644            -start    start with this genome
1645            -tblFiles output TBL files containing the corrected IDs
1646    
1647    The caller has the option of modifying the tracing scheme by placing a value
1648    for C<trace> in the incoming options hash. The default value can be overridden,
1649    or the tracing to the standard output can be turned off by suffixing a minus
1650    sign to the trace level. So, for example,
1651    
1652        { trace => [0, "tracing level (default 0)"],
1653           ...
1654    
1655    would set the default trace level to 0 instead of E, while
1656    
1657        { trace => ["2-", "tracing level (default 2)"],
1658           ...
1659    
1660    would set the default to 2, but trace only to the log file, not to the
1661    standard output.
1662    
1663    The parameters to this method are as follows.
1664    
1665    =over 4
1666    
1667    =item categories
1668    
1669    Reference to a list of tracing category names. These should be names of
1670    packages whose internal workings will need to be debugged to get the
1671    command working.
1672    
1673    =item options
1674    
1675    Reference to a hash containing the legal options for the current command mapped
1676    to their default values and descriptions. The user can override the defaults
1677    by specifying the options as command-line switches prefixed by a hyphen.
1678    Tracing-related options may be added to this hash. If the C<-h> option is
1679    specified on the command line, the option descriptions will be used to
1680    explain the options. To turn off tracing to the standard output, add a
1681    minus sign to the value for C<trace> (see above).
1682    
1683    =item parmHelp
1684    
1685    A string that vaguely describes the positional parameters. This is used
1686    if the user specifies the C<-h> option.
1687    
1688    =item argv
1689    
1690    List of command line parameters, including the option switches, which must
1691    precede the positional parameters and be prefixed by a hyphen.
1692    
1693    =item RETURN
1694    
1695    Returns a list. The first element of the list is the reference to a hash that
1696    maps the command-line option switches to their values. These will either be the
1697    default values or overrides specified on the command line. The remaining
1698    elements of the list are the position parameters, in order.
1699    
1700    =back
1701    
1702    =cut
1703    
1704    sub StandardSetup {
1705        # Get the parameters.
1706        my ($categories, $options, $parmHelp, @argv) = @_;
1707        # Get the default tracing key.
1708        my $tkey = EmergencyKey();
1709        # Add the tracing options.
1710        if (! exists $options->{trace}) {
1711            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1712        }
1713        $options->{sql} = [0, "turn on SQL tracing"];
1714        $options->{help} = [0, "display command-line options"];
1715        $options->{user} = [$tkey, "tracing key"];
1716        $options->{background} = [0, "spool standard and error output"];
1717        # Create a parsing hash from the options hash. The parsing hash
1718        # contains the default values rather than the default value
1719        # and the description. While we're at it, we'll memorize the
1720        # length of the longest option name.
1721      my $longestName = 0;      my $longestName = 0;
1722      my %parseOptions = ();      my %parseOptions = ();
1723      for my $key (keys %{$options}) {      for my $key (keys %{$options}) {
1724          if (length $key > $longestName) {          if (length $key > $longestName) {
1725              $longestName = length $key;              $longestName = length $key;
1726          }          }
1727          $parseOptions{$key} = $options->{$key}->[0];          $parseOptions{$key} = $options->{$key}->[0];
1728        }
1729        # Parse the command line.
1730        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1731        # Get the logfile suffix.
1732        my $suffix = $retOptions->{user};
1733        # Check for background mode.
1734        if ($retOptions->{background}) {
1735            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1736            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1737            open STDOUT, ">$outFileName";
1738            open STDERR, ">$errFileName";
1739            # Check for phone support. If we have phone support and a phone number,
1740            # we want to turn it on.
1741            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1742                $retOptions->{phone} = $ENV{PHONE};
1743            }
1744        }
1745        # Now we want to set up tracing. First, we need to know if the user
1746        # wants emergency tracing.
1747        if ($retOptions->{trace} eq 'E') {
1748            ETracing($retOptions->{user});
1749        } else {
1750            # Here the tracing is controlled from the command line.
1751            my @cats = @{$categories};
1752            if ($retOptions->{sql}) {
1753                push @cats, "SQL";
1754            }
1755            # Add the default categories.
1756            push @cats, "Tracer";
1757            # Next, we create the category string by joining the categories.
1758            my $cats = join(" ", @cats);
1759            # Check to determine whether or not the caller wants to turn off tracing
1760            # to the standard output.
1761            my $traceLevel = $retOptions->{trace};
1762            my $textOKFlag = 1;
1763            if ($traceLevel =~ /^(.)-/) {
1764                $traceLevel = $1;
1765                $textOKFlag = 0;
1766            }
1767            # Now we set up the trace mode.
1768            my $traceMode;
1769            # Verify that we can open a file in the FIG temporary directory.
1770            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1771            if (open TESTTRACE, ">$traceFileName") {
1772                # Here we can trace to a file.
1773                $traceMode = ">$traceFileName";
1774                if ($textOKFlag) {
1775                    # Echo to standard output if the text-OK flag is set.
1776                    $traceMode = "+$traceMode";
1777                }
1778                # Close the test file.
1779                close TESTTRACE;
1780            } else {
1781                # Here we can't trace to a file. Complain about this.
1782                warn "Could not open trace file $traceFileName: $!\n";
1783                # We trace to the standard output if it's
1784                # okay, and the error log otherwise.
1785                if ($textOKFlag) {
1786                    $traceMode = "TEXT";
1787                } else {
1788                    $traceMode = "WARN";
1789                }
1790            }
1791            # Now set up the tracing.
1792            TSetup("$traceLevel $cats", $traceMode);
1793        }
1794        # Check for the "help" option. If it is specified, dump the command-line
1795        # options and exit the program.
1796        if ($retOptions->{help}) {
1797            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1798            print "$1 [options] $parmHelp\n";
1799            for my $key (sort keys %{$options}) {
1800                my $name = Pad($key, $longestName, 0, ' ');
1801                my $desc = $options->{$key}->[1];
1802                if ($options->{$key}->[0]) {
1803                    $desc .= " (default " . $options->{$key}->[0] . ")";
1804                }
1805                print "  $name $desc\n";
1806            }
1807            exit(0);
1808        }
1809        # Trace the options, if applicable.
1810        if (T(3)) {
1811            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1812            Trace("Selected options: " . join(", ", sort @parms) . ".");
1813        }
1814        # Return the parsed parameters.
1815        return ($retOptions, @retParameters);
1816    }
1817    
1818    =head3 ReadOptions
1819    
1820        my %options = Tracer::ReadOptions($fileName);
1821    
1822    Read a set of options from a file. Each option is encoded in a line of text that has the
1823    format
1824    
1825    I<optionName>C<=>I<optionValue>C<; >I<comment>
1826    
1827    The option name must consist entirely of letters, digits, and the punctuation characters
1828    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1829    character is a semi-colon will be ignored. The return hash will map each option name to
1830    the corresponding option value.
1831    
1832    =over 4
1833    
1834    =item fileName
1835    
1836    Name of the file containing the option data.
1837    
1838    =item RETURN
1839    
1840    Returns a hash mapping the option names specified in the file to their corresponding option
1841    value.
1842    
1843    =back
1844    
1845    =cut
1846    
1847    sub ReadOptions {
1848        # Get the parameters.
1849        my ($fileName) = @_;
1850        # Open the file.
1851        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1852        # Count the number of records read.
1853        my ($records, $comments) = 0;
1854        # Create the return hash.
1855        my %retVal = ();
1856        # Loop through the file, accumulating key-value pairs.
1857        while (my $line = <CONFIGFILE>) {
1858            # Denote we've read a line.
1859            $records++;
1860            # Determine the line type.
1861            if ($line =~ /^\s*[\n\r]/) {
1862                # A blank line is a comment.
1863                $comments++;
1864            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1865                # Here we have an option assignment.
1866                retVal{$1} = $2;
1867            } elsif ($line =~ /^\s*;/) {
1868                # Here we have a text comment.
1869                $comments++;
1870            } else {
1871                # Here we have an invalid line.
1872                Trace("Invalid option statement in record $records.") if T(0);
1873            }
1874        }
1875        # Return the hash created.
1876        return %retVal;
1877    }
1878    
1879    =head3 GetOptions
1880    
1881        Tracer::GetOptions(\%defaults, \%options);
1882    
1883    Merge a specified set of options into a table of defaults. This method takes two hash references
1884    as input and uses the data from the second to update the first. If the second does not exist,
1885    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1886    exist in the first.
1887    
1888    Consider the following example.
1889    
1890        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1891    
1892    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1893    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1894    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1895    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1896    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1897    
1898        {databaseType => 'Oracle'}
1899    
1900    an error will occur because the B<databaseType> option does not exist.
1901    
1902    =over 4
1903    
1904    =item defaults
1905    
1906    Table of default option values.
1907    
1908    =item options
1909    
1910    Table of overrides, if any.
1911    
1912    =item RETURN
1913    
1914    Returns a reference to the default table passed in as the first parameter.
1915    
1916    =back
1917    
1918    =cut
1919    
1920    sub GetOptions {
1921        # Get the parameters.
1922        my ($defaults, $options) = @_;
1923        # Check for overrides.
1924        if ($options) {
1925            # Loop through the overrides.
1926            while (my ($option, $setting) = each %{$options}) {
1927                # Insure this override exists.
1928                if (!exists $defaults->{$option}) {
1929                    croak "Unrecognized option $option encountered.";
1930                } else {
1931                    # Apply the override.
1932                    $defaults->{$option} = $setting;
1933                }
1934            }
1935        }
1936        # Return the merged table.
1937        return $defaults;
1938    }
1939    
1940    =head3 MergeOptions
1941    
1942        Tracer::MergeOptions(\%table, \%defaults);
1943    
1944    Merge default values into a hash table. This method looks at the key-value pairs in the
1945    second (default) hash, and if a matching key is not found in the first hash, the default
1946    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1947    checking and no return value.
1948    
1949    =over 4
1950    
1951    =item table
1952    
1953    Hash table to be updated with the default values.
1954    
1955    =item defaults
1956    
1957    Default values to be merged into the first hash table if they are not already present.
1958    
1959    =back
1960    
1961    =cut
1962    
1963    sub MergeOptions {
1964        # Get the parameters.
1965        my ($table, $defaults) = @_;
1966        # Loop through the defaults.
1967        while (my ($key, $value) = each %{$defaults}) {
1968            if (!exists $table->{$key}) {
1969                $table->{$key} = $value;
1970            }
1971        }
1972    }
1973    
1974    =head3 ParseCommand
1975    
1976        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1977    
1978    Parse a command line consisting of a list of parameters. The initial parameters may be option
1979    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1980    off and merged into a table of default options. The remainder of the command line is
1981    returned as a list of positional arguments. For example, consider the following invocation.
1982    
1983        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1984    
1985    In this case, the list @words will be treated as a command line and there are two options available,
1986    B<errors> and B<logFile>. If @words has the following format
1987    
1988        -logFile=error.log apple orange rutabaga
1989    
1990    then at the end of the invocation, C<$options> will be
1991    
1992        { errors => 0, logFile => 'error.log' }
1993    
1994    and C<@arguments> will contain
1995    
1996        apple orange rutabaga
1997    
1998    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1999    support for quote characters. Options can be specified with single or double hyphens.
2000    
2001    =over 4
2002    
2003    =item optionTable
2004    
2005    Table of default options.
2006    
2007    =item inputList
2008    
2009    List of words on the command line.
2010    
2011    =item RETURN
2012    
2013    Returns a reference to the option table and a list of the positional arguments.
2014    
2015    =back
2016    
2017    =cut
2018    
2019    sub ParseCommand {
2020        # Get the parameters.
2021        my ($optionTable, @inputList) = @_;
2022        # Process any options in the input list.
2023        my %overrides = ();
2024        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2025            # Get the current option.
2026            my $arg = shift @inputList;
2027            # Pull out the option name.
2028            $arg =~ /^--?([^=]*)/g;
2029            my $name = $1;
2030            # Check for an option value.
2031            if ($arg =~ /\G=(.*)$/g) {
2032                # Here we have a value for the option.
2033                $overrides{$name} = UnEscape($1);
2034            } else {
2035                # Here there is no value, so we use 1.
2036                $overrides{$name} = 1;
2037      }      }
     # 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, ">$errFileName";  
2038      }      }
2039      # Now we want to set up tracing. First, we need to know if SQL is to      # Merge the options into the defaults.
2040      # be traced.      GetOptions($optionTable, \%overrides);
2041      my @cats = @{$categories};      # Translate the remaining parameters.
2042      if ($retOptions->{sql}) {      my @retVal = ();
2043          push @cats, "SQL";      for my $inputParm (@inputList) {
2044            push @retVal, UnEscape($inputParm);
2045      }      }
2046      # Add the default categories.      # Return the results.
2047      push @cats, "Tracer", "FIG";      return ($optionTable, @retVal);
     # 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;  
2048      }      }
2049      # Now we set up the trace mode.  
2050      my $traceMode;  
2051      # Verify that we can open a file in the FIG temporary directory.  =head2 File Utility Methods
2052      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
2053      if (open TESTTRACE, ">$traceFileName") {  =head3 GetFile
2054          # Here we can trace to a file.  
2055          $traceMode = ">$traceFileName";      my @fileContents = Tracer::GetFile($fileName);
2056          if ($textOKFlag) {  
2057              # Echo to standard output if the text-OK flag is set.      or
2058              $traceMode = "+$traceMode";  
2059        my $fileContents = Tracer::GetFile($fileName);
2060    
2061    Return the entire contents of a file. In list context, line-ends are removed and
2062    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2063    
2064    =over 4
2065    
2066    =item fileName
2067    
2068    Name of the file to read.
2069    
2070    =item RETURN
2071    
2072    In a list context, returns the entire file as a list with the line terminators removed.
2073    In a scalar context, returns the entire file as a string. If an error occurs opening
2074    the file, an empty list will be returned.
2075    
2076    =back
2077    
2078    =cut
2079    
2080    sub GetFile {
2081        # Get the parameters.
2082        my ($fileName) = @_;
2083        # Declare the return variable.
2084        my @retVal = ();
2085        # Open the file for input.
2086        my $handle = Open(undef, "<$fileName");
2087        # Read the whole file into the return variable, stripping off any terminator
2088        # characters.
2089        my $lineCount = 0;
2090        while (my $line = <$handle>) {
2091            $lineCount++;
2092            $line = Strip($line);
2093            push @retVal, $line;
2094          }          }
2095          # Close the test file.      # Close it.
2096          close TESTTRACE;      close $handle;
2097      } else {      my $actualLines = @retVal;
2098          # Here we can't trace to a file. We trace to the standard output if it's      Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2099          # okay, and the error log otherwise.      # Return the file's contents in the desired format.
2100          if ($textOKFlag) {      if (wantarray) {
2101              $traceMode = "TEXT";          return @retVal;
2102          } else {          } else {
2103              $traceMode = "WARN";          return join "\n", @retVal;
2104          }          }
2105      }      }
2106      # Now set up the tracing.  
2107      TSetup("$traceLevel $cats", $traceMode);  =head3 PutFile
2108      # Check for the "h" option. If it is specified, dump the command-line  
2109      # options and exit the program.      Tracer::PutFile($fileName, \@lines);
2110      if ($retOptions->{h}) {  
2111          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Write out a file from a list of lines of text.
2112          Trace("$1 [options] $parmHelp") if T(0);  
2113          for my $key (sort keys %{$options}) {  =over 4
2114              my $name = Pad($key, $longestName, 0, ' ');  
2115              my $desc = $options->{$key}->[1];  =item fileName
2116              if ($options->{$key}->[0]) {  
2117                  $desc .= " (default " . $options->{$key}->[0] . ")";  Name of the output file.
2118    
2119    =item lines
2120    
2121    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2122    new-line characters. Alternatively, may be a string, in which case the string will be written without
2123    modification.
2124    
2125    =back
2126    
2127    =cut
2128    
2129    sub PutFile {
2130        # Get the parameters.
2131        my ($fileName, $lines) = @_;
2132        # Open the output file.
2133        my $handle = Open(undef, ">$fileName");
2134        # Count the lines written.
2135        if (ref $lines ne 'ARRAY') {
2136            # Here we have a scalar, so we write it raw.
2137            print $handle $lines;
2138            Trace("Scalar put to file $fileName.") if T(File => 3);
2139        } else {
2140            # Write the lines one at a time.
2141            my $count = 0;
2142            for my $line (@{$lines}) {
2143                print $handle "$line\n";
2144                $count++;
2145              }              }
2146              Trace("  $name $desc") if T(0);          Trace("$count lines put to file $fileName.") if T(File => 3);
2147          }          }
2148          exit(0);      # Close the output file.
2149        close $handle;
2150      }      }
2151      # Return the parsed parameters.  
2152      return ($retOptions, @retParameters);  =head3 ParseRecord
2153    
2154        my @fields = Tracer::ParseRecord($line);
2155    
2156    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2157    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2158    These will automatically be converted.
2159    
2160    =over 4
2161    
2162    =item line
2163    
2164    Line of data containing the tab-delimited fields.
2165    
2166    =item RETURN
2167    
2168    Returns a list of the fields found in the data line.
2169    
2170    =back
2171    
2172    =cut
2173    
2174    sub ParseRecord {
2175        # Get the parameter.
2176        my ($line) = @_;
2177        # Remove the trailing new-line, if any.
2178        chomp $line;
2179        # Split the line read into pieces using the tab character.
2180        my @retVal = split /\t/, $line;
2181        # Trim and fix the escapes in each piece.
2182        for my $value (@retVal) {
2183            # Trim leading whitespace.
2184            $value =~ s/^\s+//;
2185            # Trim trailing whitespace.
2186            $value =~ s/\s+$//;
2187            # Delete the carriage returns.
2188            $value =~ s/\r//g;
2189            # Convert the escapes into their real values.
2190            $value =~ s/\\t/"\t"/ge;
2191            $value =~ s/\\n/"\n"/ge;
2192        }
2193        # Return the result.
2194        return @retVal;
2195  }  }
2196    
2197  =head3 Setups  =head3 Merge
2198    
2199  C<< my $count = Tracer::Setups(); >>      my @mergedList = Tracer::Merge(@inputList);
2200    
2201  Return the number of times L</TSetup> has been called.  Sort a list of strings and remove duplicates.
2202    
2203  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
2204  may want to set up tracing if nobody else has done it before us.  
2205    =item inputList
2206    
2207    List of scalars to sort and merge.
2208    
2209    =item RETURN
2210    
2211    Returns a list containing the same elements sorted in ascending order with duplicates
2212    removed.
2213    
2214    =back
2215    
2216  =cut  =cut
2217    
2218  sub Setups {  sub Merge {
2219      return $SetupCount;      # Get the input list in sort order.
2220        my @inputList = sort @_;
2221        # Only proceed if the list has at least two elements.
2222        if (@inputList > 1) {
2223            # Now we want to move through the list splicing out duplicates.
2224            my $i = 0;
2225            while ($i < @inputList) {
2226                # Get the current entry.
2227                my $thisEntry = $inputList[$i];
2228                # Find out how many elements duplicate the current entry.
2229                my $j = $i + 1;
2230                my $dup1 = $i + 1;
2231                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2232                # If the number is nonzero, splice out the duplicates found.
2233                if ($j > $dup1) {
2234                    splice @inputList, $dup1, $j - $dup1;
2235                }
2236                # Now the element at position $dup1 is different from the element before it
2237                # at position $i. We push $i forward one position and start again.
2238                $i++;
2239            }
2240        }
2241        # Return the merged list.
2242        return @inputList;
2243  }  }
2244    
2245  =head3 Open  =head3 Open
2246    
2247  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2248    
2249  Open a file.  Open a file.
2250    
# Line 605  Line 2336 
2336    
2337  =head3 FindNamePart  =head3 FindNamePart
2338    
2339  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2340    
2341  Extract the portion of a file specification that contains the file name.  Extract the portion of a file specification that contains the file name.
2342    
# Line 656  Line 2387 
2387    
2388  =head3 OpenDir  =head3 OpenDir
2389    
2390  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @files = OpenDir($dirName, $filtered, $flag);
2391    
2392  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
2393  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
# Line 712  Line 2443 
2443          } else {          } else {
2444              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
2445          }          }
2446      } elsif (! $flag) {      } elsif (! $flag) {
2447          # Here the directory would not open and it's considered an error.          # Here the directory would not open and it's considered an error.
2448          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
2449        }
2450        # Return the result.
2451        return @retVal;
2452    }
2453    
2454    
2455    =head3 Insure
2456    
2457        Insure($dirName, $chmod);
2458    
2459    Insure a directory is present.
2460    
2461    =over 4
2462    
2463    =item dirName
2464    
2465    Name of the directory to check. If it does not exist, it will be created.
2466    
2467    =item chmod (optional)
2468    
2469    Security privileges to be given to the directory if it is created.
2470    
2471    =back
2472    
2473    =cut
2474    
2475    sub Insure {
2476        my ($dirName, $chmod) = @_;
2477        if (! -d $dirName) {
2478            Trace("Creating $dirName directory.") if T(2);
2479            eval {
2480                mkpath $dirName;
2481                # If we have permissions specified, set them here.
2482                if (defined($chmod)) {
2483                    chmod $chmod, $dirName;
2484                }
2485            };
2486            if ($@) {
2487                Confess("Error creating $dirName: $@");
2488            }
2489      }      }
     # Return the result.  
     return @retVal;  
2490  }  }
2491    
2492  =head3 SetLevel  =head3 ChDir
2493    
2494  C<< Tracer::SetLevel($newLevel); >>      ChDir($dirName);
2495    
2496  Modify the trace level. A higher trace level will cause more messages to appear.  Change to the specified directory.
2497    
2498  =over 4  =over 4
2499    
2500  =item newLevel  =item dirName
2501    
2502  Proposed new trace level.  Name of the directory to which we want to change.
2503    
2504  =back  =back
2505    
2506  =cut  =cut
2507    
2508  sub SetLevel {  sub ChDir {
2509      $TraceLevel = $_[0];      my ($dirName) = @_;
2510        if (! -d $dirName) {
2511            Confess("Cannot change to directory $dirName: no such directory.");
2512        } else {
2513            Trace("Changing to directory $dirName.") if T(File => 4);
2514            my $okFlag = chdir $dirName;
2515            if (! $okFlag) {
2516                Confess("Error switching to directory $dirName.");
2517  }  }
   
 =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;  
2518  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
2519  }  }
2520    
2521  =head3 LogErrors  =head3 SetPermissions
   
 C<< Tracer::LogErrors($fileName); >>  
2522    
2523  Route the standard error output to a log file.      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
   
 =over 4  
2524    
2525  =item fileName  Set the permissions for a directory and all the files and folders inside it.
2526    In addition, the group ownership will be changed to the specified value.
2527    
2528  Name of the file to receive the error output.  This method is more vulnerable than most to permission and compatability
2529    problems, so it does internal error recovery.
2530    
2531  =back  =over 4
2532    
2533  =cut  =item dirName
2534    
2535  sub LogErrors {  Name of the directory to process.
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
 }  
2536    
2537  =head3 ReadOptions  =item group
2538    
2539  C<< my %options = Tracer::ReadOptions($fileName); >>  Name of the group to be assigned.
2540    
2541  Read a set of options from a file. Each option is encoded in a line of text that has the  =item mask
 format  
2542    
2543  I<optionName>C<=>I<optionValue>C<; >I<comment>  Permission mask. Bits that are C<1> in this mask will be ORed into the
2544    permission bits of any file or directory that does not already have them
2545    set to 1.
2546    
2547  The option name must consist entirely of letters, digits, and the punctuation characters  =item otherMasks
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
2548    
2549  =over 4  Map of search patterns to permission masks. If a directory name matches
2550    one of the patterns, that directory and all its members and subdirectories
2551    will be assigned the new pattern. For example, the following would
2552    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2553    
2554  =item fileName      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2555    
2556  Name of the file containing the option data.  The list is ordered, so the following would use 0777 for C<tmp1> and
2557    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2558    
2559  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2560                                                       '^tmp' => 0666);
2561    
2562  Returns a hash mapping the option names specified in the file to their corresponding option  Note that the pattern matches are all case-insensitive, and only directory
2563  value.  names are matched, not file names.
2564    
2565  =back  =back
2566    
2567  =cut  =cut
2568    
2569  sub ReadOptions {  sub SetPermissions {
2570      # Get the parameters.      # Get the parameters.
2571      my ($fileName) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2572      # Open the file.      # Set up for error recovery.
2573      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      eval {
2574      # Count the number of records read.          # Switch to the specified directory.
2575      my ($records, $comments) = 0;          ChDir($dirName);
2576      # Create the return hash.          # Get the group ID.
2577      my %retVal = ();          my $gid = getgrnam($group);
2578      # Loop through the file, accumulating key-value pairs.          # Get the mask for tracing.
2579      while (my $line = <CONFIGFILE>) {          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2580          # Denote we've read a line.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2581          $records++;          my $fixCount = 0;
2582          # Determine the line type.          my $lookCount = 0;
2583          if ($line =~ /^\s*[\n\r]/) {          # @dirs will be a stack of directories to be processed.
2584              # A blank line is a comment.          my @dirs = (getcwd());
2585              $comments++;          while (scalar(@dirs) > 0) {
2586          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {              # Get the current directory.
2587              # Here we have an option assignment.              my $dir = pop @dirs;
2588              retVal{$1} = $2;              # Check for a match to one of the specified directory names. To do
2589          } elsif ($line =~ /^\s*;/) {              # that, we need to pull the individual part of the name off of the
2590              # Here we have a text comment.              # whole path.
2591              $comments++;              my $simpleName = $dir;
2592                if ($dir =~ m!/([^/]+)$!) {
2593                    $simpleName = $1;
2594                }
2595                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2596                # Search for a match.
2597                my $match = 0;
2598                my $i;
2599                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2600                    my $pattern = $otherMasks[$i];
2601                    if ($simpleName =~ /$pattern/i) {
2602                        $match = 1;
2603                    }
2604                }
2605                # Check for a match. Note we use $i-1 because the loop added 2
2606                # before terminating due to the match.
2607                if ($match && $otherMasks[$i-1] != $mask) {
2608                    # This directory matches one of the incoming patterns, and it's
2609                    # a different mask, so we process it recursively with that mask.
2610                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2611          } else {          } else {
2612              # Here we have an invalid line.                  # Here we can process normally. Get all of the non-hidden members.
2613              Trace("Invalid option statement in record $records.") if T(0);                  my @submems = OpenDir($dir, 1);
2614                    for my $submem (@submems) {
2615                        # Get the full name.
2616                        my $thisMem = "$dir/$submem";
2617                        Trace("Checking member $thisMem.") if T(4);
2618                        $lookCount++;
2619                        if ($lookCount % 1000 == 0) {
2620                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2621                        }
2622                        # Fix the group.
2623                        chown -1, $gid, $thisMem;
2624                        # Insure this member is not a symlink.
2625                        if (! -l $thisMem) {
2626                            # Get its info.
2627                            my $fileInfo = stat $thisMem;
2628                            # Only proceed if we got the info. Otherwise, it's a hard link
2629                            # and we want to skip it anyway.
2630                            if ($fileInfo) {
2631                                my $fileMode = $fileInfo->mode;
2632                                if (($fileMode & $mask) != $mask) {
2633                                    # Fix this member.
2634                                    $fileMode |= $mask;
2635                                    chmod $fileMode, $thisMem;
2636                                    $fixCount++;
2637                                }
2638                                # If it's a subdirectory, stack it.
2639                                if (-d $thisMem) {
2640                                    push @dirs, $thisMem;
2641          }          }
2642      }      }
2643      # Return the hash created.                      }
2644      return %retVal;                  }
2645                }
2646            }
2647            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2648        };
2649        # Check for an error.
2650        if ($@) {
2651            Confess("SetPermissions error: $@");
2652        }
2653  }  }
2654    
2655  =head3 GetOptions  =head3 GetLine
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$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  
2656    
2657  C<< {databaseType => 'Oracle'} >>      my @data = Tracer::GetLine($handle);
2658    
2659  an error will occur because the B<databaseType> option does not exist.  Read a line of data from a tab-delimited file.
2660    
2661  =over 4  =over 4
2662    
2663  =item defaults  =item handle
   
 Table of default option values.  
   
 =item options  
2664    
2665  Table of overrides, if any.  Open file handle from which to read.
2666    
2667  =item RETURN  =item RETURN
2668    
2669  Returns a reference to the default table passed in as the first parameter.  Returns a list of the fields in the record read. The fields are presumed to be
2670    tab-delimited. If we are at the end of the file, then an empty list will be
2671    returned. If an empty line is read, a single list item consisting of a null
2672    string will be returned.
2673    
2674  =back  =back
2675    
2676  =cut  =cut
2677    
2678  sub GetOptions {  sub GetLine {
2679      # Get the parameters.      # Get the parameters.
2680      my ($defaults, $options) = @_;      my ($handle) = @_;
2681      # Check for overrides.      # Declare the return variable.
2682      if ($options) {      my @retVal = ();
2683          # Loop through the overrides.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2684          while (my ($option, $setting) = each %{$options}) {      # Read from the file.
2685              # Insure this override exists.      my $line = <$handle>;
2686              if (!exists $defaults->{$option}) {      # Only proceed if we found something.
2687                  croak "Unrecognized option $option encountered.";      if (defined $line) {
2688            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2689            # upload control and have a nonstandard EOL combination.
2690            $line =~ s/(\r|\n)+$//;
2691            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2692            if (T(File => 4)) {
2693                my $escapedLine = $line;
2694                $escapedLine =~ s/\n/\\n/g;
2695                $escapedLine =~ s/\r/\\r/g;
2696                $escapedLine =~ s/\t/\\t/g;
2697                Trace("Line read: -->$escapedLine<--");
2698            }
2699            # If the line is empty, return a single empty string; otherwise, parse
2700            # it into fields.
2701            if ($line eq "") {
2702                push @retVal, "";
2703              } else {              } else {
2704                  # Apply the override.              push @retVal, split /\t/,$line;
                 $defaults->{$option} = $setting;  
             }  
2705          }          }
2706        } else {
2707            # Trace the reason the read failed.
2708            Trace("End of file: $!") if T(File => 3);
2709      }      }
2710      # Return the merged table.      # Return the result.
2711      return $defaults;      return @retVal;
2712  }  }
2713    
2714  =head3 MergeOptions  =head3 PutLine
2715    
2716  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::PutLine($handle, \@fields, $eol);
2717    
2718  Merge default values into a hash table. This method looks at the key-value pairs in the  Write a line of data to a tab-delimited file. The specified field values will be
2719  second (default) hash, and if a matching key is not found in the first hash, the default  output in tab-separated form, with a trailing new-line.
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
2720    
2721  =over 4  =over 4
2722    
2723  =item table  =item handle
2724    
2725  Hash table to be updated with the default values.  Output file handle.
2726    
2727  =item defaults  =item fields
2728    
2729  Default values to be merged into the first hash table if they are not already present.  List of field values.
2730    
2731    =item eol (optional)
2732    
2733    End-of-line character (default is "\n").
2734    
2735  =back  =back
2736    
2737  =cut  =cut
2738    
2739  sub MergeOptions {  sub PutLine {
2740      # Get the parameters.      # Get the parameters.
2741      my ($table, $defaults) = @_;      my ($handle, $fields, $eol) = @_;
2742      # Loop through the defaults.      # Write the data.
2743      while (my ($key, $value) = each %{$defaults}) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
     }  
2744  }  }
2745    
 =head3 Trace  
2746    
2747  C<< Trace($message); >>  =head3 PrintLine
2748    
2749  Write a trace message to the target location specified in L</TSetup>. If there has not been      Tracer::PrintLine($line);
2750  any prior call to B<TSetup>.  
2751    Print a line of text with a trailing new-line.
2752    
2753  =over 4  =over 4
2754    
2755  =item message  =item line
2756    
2757  Message to write.  Line of text to print.
2758    
2759  =back  =back
2760    
2761  =cut  =cut
2762    
2763  sub Trace {  sub PrintLine {
2764      # Get the parameters.      # Get the parameters.
2765      my ($message) = @_;      my ($line) = @_;
2766      # Get the timestamp.      # Print the line.
2767      my $timeStamp = Now();      print "$line\n";
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
2768  }  }
2769    
 =head3 T  
2770    
2771  C<< my $switch = T($category, $traceLevel); >>  =head2 Other Useful Methods
2772    
2773      or  =head3 ParseParm
2774    
2775  C<< my $switch = T($traceLevel); >>      my $listValue = Tracer::ParseParm($string);
2776    
2777  Return TRUE if the trace level is at or above a specified value and the specified category  Convert a parameter into a list reference. If the parameter is undefined,
2778  is active, else FALSE. If no category is specified, the caller's package name is used.  an undefined value will be returned. Otherwise, it will be parsed as a
2779    comma-separated list of values.
2780    
2781  =over 4  =over 4
2782    
2783  =item category  =item string
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2784    
2785  Relevant tracing level.  Incoming string.
2786    
2787  =item RETURN  =item RETURN
2788    
2789  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a reference to a list of values, or C<undef> if the incoming value
2790    was undefined.
2791    
2792  =back  =back
2793    
2794  =cut  =cut
2795    
2796  sub T {  sub ParseParm {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2797          # Get the parameters.          # Get the parameters.
2798          my ($category, $traceLevel) = @_;      my ($string) = @_;
2799          if (!defined $traceLevel) {      # Declare the return variable.
2800              # Here we have no category, so we need to get the calling package.      my $retVal;
2801              # The calling package is normally the first parameter. If it is      # Check for data.
2802              # omitted, the first parameter will be the tracelevel. So, the      if (defined $string) {
2803              # first thing we do is shift the so-called category into the          # We have some, so split it into a list.
2804              # $traceLevel variable where it belongs.          $retVal = [ split /\s*,\s*/, $string];
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2805      }      }
2806      # Return the computed result.      # Return the result.
2807      return $retVal;      return $retVal;
2808  }  }
   
 =head3 ParseCommand  
   
 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.  
2809    
2810  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =head3 Now
2811    
2812  In this case, the list @words will be treated as a command line. There are two options available,      my $string = Tracer::Now();
 B<errors> and B<logFile>. If @words has the following format  
2813    
2814  C<< -logFile=error.log apple orange rutabaga >>  Return a displayable time stamp containing the local time. Whatever format this
2815    method produces must be parseable by L</ParseDate>.
2816    
2817  then at the end of the invocation, C<$options> will be  =cut
2818    
2819  C<< { errors => 0, logFile => 'error.log' } >>  sub Now {
2820        return DisplayTime(time);
2821    }
2822    
2823  and C<@arguments> will contain  =head3 DisplayTime
2824    
2825  C<< apple orange rutabaga >>      my $string = Tracer::DisplayTime($time);
2826    
2827  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  Convert a time value to a displayable time stamp. Whatever format this
2828  support for quote characters.  method produces must be parseable by L</ParseDate>.
2829    
2830  =over 4  =over 4
2831    
2832  =item optionTable  =item time
   
 Table of default options.  
   
 =item inputList  
2833    
2834  List of words on the command line.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2835    
2836  =item RETURN  =item RETURN
2837    
2838  Returns a reference to the option table and a list of the positional arguments.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2839    
2840  =back  =back
2841    
2842  =cut  =cut
2843    
2844  sub ParseCommand {  sub DisplayTime {
2845      # Get the parameters.      my ($time) = @_;
2846      my ($optionTable, @inputList) = @_;      my $retVal = "(n/a)";
2847      # Process any options in the input list.      if (defined $time) {
2848      my %overrides = ();          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2849      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2850          # Get the current option.                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         my $arg = shift @inputList;  
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
         } else {  
             # Here there is no value, so we use 1.  
             $overrides{$name} = 1;  
         }  
2851      }      }
2852      # Merge the options into the defaults.      return $retVal;
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2853      }      }
2854      # Return the results.  
2855      return ($optionTable, @retVal);  # Pad a number to 2 digits.
2856    sub _p2 {
2857        my ($value) = @_;
2858        $value = "0$value" if ($value < 10);
2859        return $value;
2860  }  }
2861    
2862  =head3 Escape  =head3 Escape
2863    
2864  C<< my $codedString = Tracer::Escape($realString); >>      my $codedString = Tracer::Escape($realString);
2865    
2866  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2867  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2868  result is to reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
2869    
# Line 1195  Line 2916 
2916    
2917  =head3 UnEscape  =head3 UnEscape
2918    
2919  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
2920    
2921  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2922  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
# Line 1253  Line 2974 
2974      return $retVal;      return $retVal;
2975  }  }
2976    
2977  =head3 ParseRecord  =head3 Percent
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
   
 C<< my $fileContents = Tracer::GetFile($fileName); >>  
   
 Return the entire contents of a file. In list context, line-ends are removed and  
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $ok = open INPUTFILE, "<$fileName";  
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
         # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
         while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
             push @retVal, $line;  
         }  
         # Close it.  
         close INPUTFILE;  
         my $actualLines = @retVal;  
     }  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
     }  
 }  
   
 =head3 QTrace  
   
 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  
2978    
2979  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $percent = Tracer::Percent($number, $base);
2980    
2981  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Returns the percent of the base represented by the given number. If the base
2982    is zero, returns zero.
2983    
2984  =over 4  =over 4
2985    
2986  =item message  =item number
   
 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  
2987    
2988  C<< Assert($condition1, $condition2, ... $conditionN); >>  Percent numerator.
2989    
2990  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item base
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2991    
2992  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Percent base.
2993    
2994  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item RETURN
2995    
2996    Returns the percentage of the base represented by the numerator.
2997    
2998    =back
2999    
3000  =cut  =cut
3001  sub Assert {  
3002      my $retVal = 1;  sub Percent {
3003      LOOP: for my $condition (@_) {      # Get the parameters.
3004          if (! $condition) {      my ($number, $base) = @_;
3005              $retVal = 0;      # Declare the return variable.
3006              last LOOP;      my $retVal = 0;
3007          }      # Compute the percent.
3008        if ($base != 0) {
3009            $retVal = $number * 100 / $base;
3010      }      }
3011        # Return the result.
3012      return $retVal;      return $retVal;
3013  }  }
3014    
3015  =head3 Cluck  =head3 Constrain
3016    
3017  C<< Cluck($message); >>      my $constrained = Constrain($value, $min, $max);
3018    
3019  Trace the call stack. Note that for best results, you should qualify the call with a  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 trace condition. For example,  
3020    
3021  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
3022    
3023  will only trace the stack if the trace level for the package is 3 or more.  =item value
3024    
3025  =over 4  Value to constrain.
3026    
3027  =item message  =item min (optional)
3028    
3029  Message to include in the trace.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3030    
3031    =item max (optional)
3032    
3033    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3034    
3035    =item RETURN
3036    
3037    Returns the incoming value, constrained according to the other parameters.
3038    
3039  =back  =back
3040    
3041  =cut  =cut
3042    
3043  sub Cluck {  sub Constrain {
3044      # Get the parameters.      # Get the parameters.
3045      my ($message) = @_;      my ($value, $min, $max) = @_;
3046      # Trace what's happening.      # Declare the return variable.
3047      Trace("Stack trace for event: $message");      my $retVal = $value;
3048      my $confession = longmess($message);      # Apply the minimum constraint.
3049      # Convert the confession to a series of trace messages. Note we skip any      if (defined $min && $retVal < $min) {
3050      # messages relating to calls into Tracer.          $retVal = $min;
3051      for my $line (split /\s*\n/, $confession) {      }
3052          Trace($line) if ($line !~ /Tracer\.pm/);      # Apply the maximum constraint.
3053        if (defined $max && $retVal > $max) {
3054            $retVal = $max;
3055      }      }
3056        # Return the result.
3057        return $retVal;
3058  }  }
3059    
3060  =head3 Min  =head3 Min
3061    
3062  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
3063    
3064  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
3065    
# Line 1571  Line 3092 
3092    
3093  =head3 Max  =head3 Max
3094    
3095  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
3096    
3097  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
3098    
# Line 1602  Line 3123 
3123      return $retVal;      return $retVal;
3124  }  }
3125    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value); >>  
   
 Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  
 is created for the key. Otherwise, the new value is pushed onto the list.  
   
 =over 4  
   
 =item hash  
   
 Reference to the target hash.  
   
 =item key  
   
 Key for which the value is to be added.  
   
 =item value  
   
 Value to add to the key's value list.  
   
 =back  
   
 =cut  
   
 sub AddToListMap {  
     # Get the parameters.  
     my ($hash, $key, $value) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [$value];  
     } else {  
         push @{$hash->{$key}}, $value;  
     }  
 }  
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else output an error  
 page and return FALSE.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error web page will be output directing the  
 user to enter in the correct password.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");  
         print $pageString;  
     }  
     # Return the determination indicator.  
     return $retVal;  
 }  
3126    
3127  =head3 Strip  =head3 Strip
3128    
3129  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::Strip($line);
3130    
3131  Strip all line terminators off a string. This is necessary when dealing with files  Strip all line terminators off a string. This is necessary when dealing with files
3132  that may have been transferred back and forth several times among different  that may have been transferred back and forth several times among different
# Line 1705  Line 3158 
3158    
3159  =head3 Pad  =head3 Pad
3160    
3161  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3162    
3163  Pad a string to a specified length. The pad character will be a  Pad a string to a specified length. The pad character will be a
3164  space, and the padding will be on the right side unless specified  space, and the padding will be on the right side unless specified
# Line 1776  Line 3229 
3229    
3230  =head3 TICK  =head3 TICK
3231    
3232  C<< my @results = TICK($commandString); >>      my @results = TICK($commandString);
3233    
3234  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3235  dot-slash (C<./> will be removed. So, for example, if you were doing  dot-slash (C<./> will be removed. So, for example, if you were doing
# Line 1815  Line 3268 
3268      return `$commandString`;      return `$commandString`;
3269  }  }
3270    
 =head3 ScriptSetup  
3271    
3272  C<< my ($query, $varHash) = ScriptSetup(); >>  =head3 CommaFormat
3273    
3274  Perform standard tracing and debugging setup for scripts. The value returned is      my $formatted = Tracer::CommaFormat($number);
3275  the CGI object followed by a pre-built variable hash.  
3276    Insert commas into a number.
3277    
3278    =over 4
3279    
3280    =item number
3281    
3282    A sequence of digits.
3283    
3284    =item RETURN
3285    
3286    Returns the same digits with commas strategically inserted.
3287    
3288  The C<Trace> query parameter is used to determine whether or not tracing is active and  =back
 which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. At the end of the script, the  
 client should call L</ScriptFinish> to output the web page.  
3289    
3290  =cut  =cut
3291    
3292  sub ScriptSetup {  sub CommaFormat {
3293      # Get the CGI query object.      # Get the parameters.
3294      my $query = CGI->new();      my ($number) = @_;
3295      # Check for tracing. Set it up if the user asked for it.      # Pad the length up to a multiple of three.
3296      if ($query->param('Trace')) {      my $padded = "$number";
3297          # Set up tracing to be queued for display at the bottom of the web page.      $padded = " " . $padded while length($padded) % 3 != 0;
3298          TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3299          # Trace the parameter and environment data.      # cause the delimiters to be included in the output stream. The
3300          if (T(CGI => 3)) {      # GREP removes the empty strings in between the delimiters.
3301              # Here we want to trace the parameter data.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3302              my @names = $query->param;      # Clean out the spaces.
3303              for my $parmName (sort @names) {      $retVal =~ s/ //g;
3304                  # Note we skip "Trace", which is for our use only.      # Return the result.
3305                  if ($parmName ne 'Trace') {      return $retVal;
                     my @values = $query->param($parmName);  
                     Trace("CGI: $parmName = " . join(", ", @values));  
                 }  
             }  
         }  
         if (T(CGI => 4)) {  
             # Here we want the environment data too.  
             for my $envName (sort keys %ENV) {  
                 Trace("ENV: $envName = $ENV{$envName}");  
             }  
3306          }          }
3307    
3308    
3309    =head3 CompareLists
3310    
3311        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3312    
3313    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3314    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3315    The return value contains a list of items that are only in the new list
3316    (inserted) and only in the old list (deleted).
3317    
3318    =over 4
3319    
3320    =item newList
3321    
3322    Reference to a list of new tuples.
3323    
3324    =item oldList
3325    
3326    Reference to a list of old tuples.
3327    
3328    =item keyIndex (optional)
3329    
3330    Index into each tuple of its key field. The default is 0.
3331    
3332    =item RETURN
3333    
3334    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3335    list (inserted) followed by a reference to the list of items that are only in the old
3336    list (deleted).
3337    
3338    =back
3339    
3340    =cut
3341    
3342    sub CompareLists {
3343        # Get the parameters.
3344        my ($newList, $oldList, $keyIndex) = @_;
3345        if (! defined $keyIndex) {
3346            $keyIndex = 0;
3347        }
3348        # Declare the return variables.
3349        my ($inserted, $deleted) = ([], []);
3350        # Loop through the two lists simultaneously.
3351        my ($newI, $oldI) = (0, 0);
3352        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3353        while ($newI < $newN || $oldI < $oldN) {
3354            # Get the current object in each list. Note that if one
3355            # of the lists is past the end, we'll get undef.
3356            my $newItem = $newList->[$newI];
3357            my $oldItem = $oldList->[$oldI];
3358            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3359                # The old item is not in the new list, so mark it deleted.
3360                push @{$deleted}, $oldItem;
3361                $oldI++;
3362            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3363                # The new item is not in the old list, so mark it inserted.
3364                push @{$inserted}, $newItem;
3365                $newI++;
3366      } else {      } else {
3367          # Here tracing is to be turned off. All we allow is errors traced into the              # The item is in both lists, so push forward.
3368          # error log.              $oldI++;
3369          TSetup("0", "WARN");              $newI++;
3370      }      }
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # If we're in DEBUG mode, set up the debug mode data for forms.  
     if (Tracer::DebugMode) {  
         $varHash->{DebugData} = GetFile("Html/DebugFragment.html");  
3371      }      }
3372      # Return the query object and variable hash.      # Return the result.
3373      return ($query, $varHash);      return ($inserted, $deleted);
3374  }  }
3375    
3376  =head3 ScriptFinish  =head3 GenerateURL
3377    
3378  C<< ScriptFinish($webData, $varHash); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3379    
3380  A typical standard script would loook like the following.  Generate a GET-style URL for the specified page with the specified parameter
3381    names and values. The values will be URL-escaped automatically. So, for
3382    example
3383    
3384      BEGIN {      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3385    
3386      my ($query, $varHash) = ScriptSetup();  would return
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3387    
3388  The idea here is that even if the script fails, you'll see trace messages and      form.cgi?type=1;string=%22high%20pass%22%20or%20highway
 useful output.  
3389    
3390  =over 4  =over 4
3391    
3392  =item webData  =item page
3393    
3394  A string containing either the full web page to be written to the output or the  Page URL.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3395    
3396  =item varHash (optional)  =item parameters
3397    
3398  If specified, then a reference to a hash mapping variable names for a template  Hash mapping parameter names to parameter values.
3399  to their values. The template file will be read into memory, and variable markers  
3400  will be replaced by data in this hash reference.  =item RETURN
3401    
3402    Returns a GET-style URL that goes to the specified page and passes in the
3403    specified parameters and values.
3404    
3405  =back  =back
3406    
3407  =cut  =cut
3408    
3409  sub ScriptFinish {  sub GenerateURL {
3410      # Get the parameters.      # Get the parameters.
3411      my ($webData, $varHash) = @_;      my ($page, %parameters) = @_;
3412      # Check for a template file situation.      # Prime the return variable with the page URL.
3413      my $outputString;      my $retVal = $page;
3414      if (defined $varHash) {      # Loop through the parameters, creating parameter elements in a list.
3415          # Here we have a template file. We need to apply the variables to the template.      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3416          $outputString = PageBuilder::Build("<$webData", $varHash, "Html");      # If the list is nonempty, tack it on.
3417      } else {      if (@parmList) {
3418          # Here the user gave us a raw string.          $retVal .= "?" . join(";", @parmList);
         $outputString = $webData;  
3419      }      }
3420      # Check for trace messages.      # Return the result.
3421      if ($Destination eq "QUEUE") {      return $retVal;
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
3422          }          }
3423          substr $outputString, $pos, 0, QTrace('Html');  
3424    =head3 ApplyURL
3425    
3426        Tracer::ApplyURL($table, $target, $url);
3427    
3428    Run through a two-dimensional table (or more accurately, a list of lists), converting the
3429    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3430    URL column will be deleted by this process and the target column will be HTML-escaped.
3431    
3432    This provides a simple way to process the results of a database query into something
3433    displayable by combining a URL with text.
3434    
3435    =over 4
3436    
3437    =item table
3438    
3439    Reference to a list of lists. The elements in the containing list will be updated by
3440    this method.
3441    
3442    =item target
3443    
3444    The index of the column to be converted into HTML.
3445    
3446    =item url
3447    
3448    The index of the column containing the URL. Note that the URL must have a recognizable
3449    C<http:> at the beginning.
3450    
3451    =back
3452    
3453    =cut
3454    
3455    sub ApplyURL {
3456        # Get the parameters.
3457        my ($table, $target, $url) = @_;
3458        # Loop through the table.
3459        for my $row (@{$table}) {
3460            # Apply the URL to the target cell.
3461            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3462            # Delete the URL from the row.
3463            delete $row->[$url];
3464      }      }
     # Write the output string.  
     print $outputString;  
3465  }  }
3466    
3467  =head3 Insure  =head3 CombineURL
3468    
3469  C<< Insure($dirName); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3470    
3471  Insure a directory is present.  This method will convert the specified text into HTML hyperlinked to the specified
3472    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3473    is defined and begins with an C<http:> header.
3474    
3475  =over 4  =over 4
3476    
3477  =item dirName  =item text
3478    
3479  Name of the directory to check. If it does not exist, it will be created.  Text to return. This will be HTML-escaped automatically.
3480    
3481    =item url
3482    
3483    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3484    will be returned without any hyperlinking.
3485    
3486    =item RETURN
3487    
3488    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3489    doesn't look right, the HTML-escaped text will be returned without any further
3490    modification.
3491    
3492  =back  =back
3493    
3494  =cut  =cut
3495    
3496  sub Insure {  sub CombineURL {
3497      my ($dirName) = @_;      # Get the parameters.
3498      if (! -d $dirName) {      my ($text, $url) = @_;
3499          Trace("Creating $dirName directory.") if T(2);      # Declare the return variable.
3500          eval { mkpath $dirName; };      my $retVal = CGI::escapeHTML($text);
3501          if ($@) {      # Verify the URL.
3502              Confess("Error creating $dirName: $@");      if (defined($url) && $url =~ m!http://!i) {
3503          }          # It's good, so we apply it to the text.
3504            $retVal = "<a href=\"$url\">$retVal</a>";
3505      }      }
3506        # Return the result.
3507        return $retVal;
3508  }  }
3509    
3510  =head3 ChDir  =head3 Cmp
3511    
3512  C<< ChDir($dirName); >>      my $cmp = Tracer::Cmp($a, $b);
3513    
3514  Change to the specified directory.  This method performs a universal sort comparison. Each value coming in is
3515    separated into a leading text part and a trailing number part. The text
3516    part is string compared, and if both parts are equal, then the number
3517    parts are compared numerically. A stream of just numbers or a stream of
3518    just strings will sort correctly, and a mixed stream will sort with the
3519    numbers first. Strings with a label and a number will sort in the
3520    expected manner instead of lexically.
3521    
3522  =over 4  =over 4
3523    
3524  =item dirName  =item a
3525    
3526  Name of the directory to which we want to change.  First item to compare.
3527    
3528    =item b
3529    
3530    Second item to compare.
3531    
3532    =item RETURN
3533    
3534    Returns a negative number if the first item should sort first (is less), a positive
3535    number if the first item should sort second (is greater), and a zero if the items are
3536    equal.
3537    
3538  =back  =back
3539    
3540  =cut  =cut
3541    
3542  sub ChDir {  sub Cmp {
3543      my ($dirName) = @_;      # Get the parameters.
3544      if (! -d $dirName) {      my ($a, $b) = @_;
3545          Confess("Cannot change to directory $dirName: no such directory.");      # Declare the return value.
3546        my $retVal;
3547        # Check for nulls.
3548        if (! defined($a)) {
3549            $retVal = (! defined($b) ? 0 : -1);
3550        } elsif (! defined($b)) {
3551            $retVal = 1;
3552      } else {      } else {
3553          Trace("Changing to directory $dirName.") if T(4);          # Here we have two real values. Parse the two strings.
3554          my $okFlag = chdir $dirName;          $a =~ /^(\D*)(\d*)$/;
3555          if (! $okFlag) {          my $aParsed = [$1, $2];
3556              Confess("Error switching to directory $dirName.");          $b =~ /^(\D*)(\d*)$/;
3557            my $bParsed = [$1, $2];
3558            # Compare the string parts.
3559            $retVal = $aParsed->[0] cmp $bParsed->[0];
3560            if (! $retVal) {
3561                $retVal = $aParsed->[1] <=> $bParsed->[1];
3562            }
3563        }
3564        # Return the result.
3565        return $retVal;
3566          }          }
3567    
3568    
3569    =head3 TrackingCode
3570    
3571        my $html = Tracer::TrackingCode();
3572    
3573    Returns the HTML code for doing web page traffic monitoring. If the
3574    current environment is a test system, then it returns a null string;
3575    otherwise, it returns a bunch of javascript containing code for turning
3576    on SiteMeter and Google Analytics.
3577    
3578    =cut
3579    
3580    sub TrackingCode {
3581        # Declare the return variable.
3582        my $retVal = "<!-- tracking off -->";
3583        # Determine if we're in production.
3584        if ($FIG_Config::site_meter) {
3585            $retVal = <<END_HTML
3586            <!-- Site Meter -->
3587            <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3588            </script>
3589            <noscript>
3590            <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3591            <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3592            </noscript>
3593            <!-- Copyright (c)2006 Site Meter -->
3594    END_HTML
3595      }      }
3596        return $retVal;
3597  }  }
3598    
3599    
3600  1;  1;

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