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revision 1.52, Wed Jun 14 01:12:42 2006 UTC revision 1.99, Wed May 7 23:00:16 2008 UTC
# Line 1  Line 1 
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;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 31  Line 32 
32      use File::Basename;      use File::Basename;
33      use File::Path;      use File::Path;
34      use File::stat;      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 58  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 118  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, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 188  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($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 210  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 $longestName = 0;                  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            # Use the category and tracelevel to compute the result.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566            }
567            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
568        }
569        # Return the computed result.
570        return $retVal;
571    }
572    
573    =head3 QTrace
574    
575        my $data = QTrace($format);
576    
577    Return the queued trace data in the specified format.
578    
579    =over 4
580    
581    =item format
582    
583    C<html> to format the data as an HTML list, C<text> to format it as straight text.
584    
585    =back
586    
587    =cut
588    
589    sub QTrace {
590        # Get the parameter.
591        my ($format) = @_;
592        # Create the return variable.
593        my $retVal = "";
594        # Only proceed if there is an actual queue.
595        if (@Queue) {
596            # Process according to the format.
597            if ($format =~ m/^HTML$/i) {
598                # Convert the queue into an HTML list.
599                $retVal = "<ul>\n";
600                for my $line (@Queue) {
601                    my $escapedLine = CGI::escapeHTML($line);
602                    $retVal .= "<li>$escapedLine</li>\n";
603                }
604                $retVal .= "</ul>\n";
605            } elsif ($format =~ m/^TEXT$/i) {
606                # Convert the queue into a list of text lines.
607                $retVal = join("\n", @Queue) . "\n";
608            }
609            # Clear the queue.
610            @Queue = ();
611        }
612        # Return the formatted list.
613        return $retVal;
614    }
615    
616    =head3 Confess
617    
618        Confess($message);
619    
620    Trace the call stack and abort the program with the specified message. When used with
621    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
622    So, for example
623    
624        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
625    
626    Will abort the program with a stack trace if the value of C<$recNum> is negative.
627    
628    =over 4
629    
630    =item message
631    
632    Message to include in the trace.
633    
634    =back
635    
636    =cut
637    
638    sub Confess {
639        # Get the parameters.
640        my ($message) = @_;
641        # Set up the category and level.
642        $LastCategory = "(confess)";
643        $LastLevel = 0;
644        if (! defined($FIG_Config::no_tool_hdr)) {
645            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
646            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
647            # Only proceed if the tool header file is actually present.
648            if (-f $toolHeaderFile) {
649                my $fh;
650                if (open $fh, "<$toolHeaderFile") {
651                    my @lines = <$fh>;
652                    Trace("Tool header has " . scalar(@lines) . " lines.");
653                }
654            }
655        }
656        # Trace the call stack.
657        Cluck($message);
658        # Abort the program.
659        croak(">>> $message");
660    }
661    
662    =head3 Warn
663    
664        Warn($message);
665    
666    This method traces an important message. If an RSS feed is configured
667    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
668    then the message will be echoed to the feed. In general, a tracing
669    destination of C<WARN> indicates that the caller is running as a web
670    service in a production environment; however, this is not a requirement.
671    
672    The L</Cluck> method calls this one for its final message. Since
673    L</Confess> calls L</Cluck>, this means that any error which is caught
674    and confessed will put something in the feed. This insures that someone
675    will be alerted relatively quickly when a failure occurs.
676    
677    =over 4
678    
679    =item message
680    
681    Message to be traced.
682    
683    =back
684    
685    =cut
686    
687    sub Warn {
688        # Get the parameters.
689        my ($message) = @_;
690        # Trace the message.
691        Trace($message);
692        # An error here would be disastrous. Note, however, that we aren't too worried
693        # about losing events. The error log is always available for the occasions where
694        # we mess up.
695        eval {
696            # Do we need to put this in the RSS feed?
697            if ($FIG_Config::error_feed && $Destination eq 'WARN') {
698                # Yes. We now need to compute the date, the link, and the title.
699                # First, the date, in a very specific format.
700                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
701                    (tz_local_offset() / 30);
702                # We'll put the link and title in here.
703                my ($link, $title);
704                # Environment data goes in here.
705                my $environment;
706                # HTML-escape the message.
707                my $escaped = CGI::escapeHTML($message);
708                # If we have a CGI object, then this is a web error. Otherwise, it's
709                # command-line.
710                if (defined $SavedCGI) {
711                    # We're in a web service. The title is the user's IP, and the link
712                    # is the URL that got us here.
713                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
714                    $title = "Event Reported at IP address $key: $escaped";
715                    $link = $SavedCGI->url(-full => 1, -query => 1);
716                    # We need the user agent string.
717                    $environment = "User Agent $ENV{HTTP_USER_AGENT}."
718                } else {
719                    # No CGI object, so we're a command-line tool. Use the tracing
720                    # key and the PID as the user identifier.
721                    my $key = EmergencyKey();
722                    $title = "Event Reported by $key Process $$: $escaped";
723                    # Set the link to the development NMPDR. There is really no good
724                    # choice here.
725                    $link = "http://$FIG_Config::dev_server";
726                    # We need the command
727                    $environment = "Command $ENV{_}.";
728                }
729                # Build a GUID. We use the current time, the title, and the process ID,
730                # then digest the result.
731                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
732                # Finally, the description. This is a stack trace plus various environmental stuff.
733                my @trace = LongMess();
734                my $trace = join "; ", @trace;
735                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
736                # Okay, we have all the pieces. Create a hash of the new event.
737                my $newItem = { title => $title,
738                                description => $description,
739                                link => $link,
740                                category => $LastCategory,
741                                pubDate => $date,
742                                guid => $guid,
743                               };
744                # We need XML capability for this.
745                require XML::Simple;
746                # The RSS document goes in here.
747                my $rss;
748                # Get the name of the RSS file. It's in the FIG temporary directory.
749                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
750                # Does it exist?
751                if (-s $fileName) {
752                    # Slurp it in.
753                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
754                } else {
755                    my $size = -s $fileName;
756                    # Create an empty channel.
757                    $rss = {
758                        channel => {
759                            title => 'NMPDR Warning Feed',
760                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
761                            description => "Important messages regarding the status of the NMPDR.",
762                            generator => "NMPDR Trace Facility",
763                            docs => "http://blogs.law.harvard.edu/tech/rss",
764                            item => []
765                        },
766                    };
767                }
768                # Get the channel object.
769                my $channel = $rss->{channel};
770                # Update the last-build date.
771                $channel->{lastBuildDate} = $date;
772                # Get the item array.
773                my $items = $channel->{item};
774                # Insure it has only 100 entries.
775                while (scalar @{$items} > 100) {
776                    pop @{$items};
777                }
778                # Add our new item at the front.
779                unshift @{$items}, $newItem;
780                # Replace the file.
781                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
782                                              NoEscape => 1);
783                # We don't use Open here because we can't afford an error.
784                if (open XMLOUT, ">$fileName") {
785                    print XMLOUT $xml;
786                    close XMLOUT;
787                }
788            }
789        };
790        # There's no "if ($@)" here, because putting an error message in the log
791        # saying that we missed putting an error message in the feed of messages
792        # in the log is not going to help anybody.
793    }
794    
795    =head3 Assert
796    
797        Assert($condition1, $condition2, ... $conditionN);
798    
799    Return TRUE if all the conditions are true. This method can be used in conjunction with
800    the OR operator and the L</Confess> method as a debugging assert.
801    So, for example
802    
803        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
804    
805    Will abort the program with a stack trace if the value of C<$recNum> is negative.
806    
807    =cut
808    sub Assert {
809        my $retVal = 1;
810        LOOP: for my $condition (@_) {
811            if (! $condition) {
812                $retVal = 0;
813                last LOOP;
814            }
815        }
816        return $retVal;
817    }
818    
819    =head3 Cluck
820    
821        Cluck($message);
822    
823    Trace the call stack. Note that for best results, you should qualify the call with a
824    trace condition. For example,
825    
826        Cluck("Starting record parse.") if T(3);
827    
828    will only trace the stack if the trace level for the package is 3 or more.
829    
830    =over 4
831    
832    =item message
833    
834    Message to include in the trace.
835    
836    =back
837    
838    =cut
839    
840    sub Cluck {
841        # Get the parameters.
842        my ($message) = @_;
843        # Trace what's happening.
844        Trace("Stack trace for event: $message");
845        # Get the stack trace.
846        my @trace = LongMess();
847        # Convert the trace to a series of messages.
848        for my $line (@trace) {
849            # Replace the tab at the beginning with spaces.
850            $line =~ s/^\t/    /;
851            # Trace the line.
852            Trace($line);
853        }
854        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
855        Warn($message);
856    }
857    
858    =head3 LongMess
859    
860        my @lines = Tracer::LongMess();
861    
862    Return a stack trace with all tracing methods removed. The return will be in the form of a list
863    of message strings.
864    
865    =cut
866    
867    sub LongMess {
868        # Declare the return variable.
869        my @retVal = ();
870        my $confession = longmess("");
871        for my $line (split /\s*\n/, $confession) {
872            unless ($line =~ /Tracer\.pm/) {
873                # Here we have a line worth keeping. Push it onto the result list.
874                push @retVal, $line;
875            }
876        }
877        # Return the result.
878        return @retVal;
879    }
880    
881    =head3 ScriptSetup (deprecated)
882    
883        my ($cgi, $varHash) = ScriptSetup($noTrace);
884    
885    Perform standard tracing and debugging setup for scripts. The value returned is
886    the CGI object followed by a pre-built variable hash. At the end of the script,
887    the client should call L</ScriptFinish> to output the web page.
888    
889    This method calls L</ETracing> to configure tracing, which allows the tracing
890    to be configured via the emergency tracing form on the debugging control panel.
891    Tracing will then be turned on automatically for all programs that use the L</ETracing>
892    method, which includes every program that uses this method or L</StandardSetup>.
893    
894    =over 4
895    
896    =item noTrace (optional)
897    
898    If specified, tracing will be suppressed. This is useful if the script wants to set up
899    tracing manually.
900    
901    =item RETURN
902    
903    Returns a two-element list consisting of a CGI query object and a variable hash for
904    the output page.
905    
906    =back
907    
908    =cut
909    
910    sub ScriptSetup {
911        # Get the parameters.
912        my ($noTrace) = @_;
913        # Get the CGI query object.
914        my $cgi = CGI->new();
915        # Set up tracing if it's not suppressed.
916        ETracing($cgi) unless $noTrace;
917        # Create the variable hash.
918        my $varHash = { results => '' };
919        # Return the query object and variable hash.
920        return ($cgi, $varHash);
921    }
922    
923    =head3 ETracing
924    
925        ETracing($parameter);
926    
927    Set up emergency tracing. Emergency tracing is tracing that is turned
928    on automatically for any program that calls this method. The emergency
929    tracing parameters are stored in a a file identified by a tracing key.
930    If this method is called with a CGI object, then the tracing key is
931    taken from a cookie. If it is called with no parameters, then the tracing
932    key is taken from an environment variable. If it is called with a string,
933    the tracing key is that string.
934    
935    =over 4
936    
937    =item parameter
938    
939    A parameter from which the tracing key is computed. If it is a scalar,
940    that scalar is used as the tracing key. If it is a CGI object, the
941    tracing key is taken from the C<IP> cookie. If it is omitted, the
942    tracing key is taken from the C<TRACING> environment variable. If it
943    is a CGI object and emergency tracing is not on, the C<Trace> and
944    C<TF> parameters will be used to determine the type of tracing.
945    
946    =back
947    
948    =cut
949    
950    sub ETracing {
951        # Get the parameter.
952        my ($parameter) = @_;
953        # Check for CGI mode.
954        if (defined $parameter && ref $parameter eq 'CGI') {
955            $SavedCGI = $parameter;
956        } else {
957            $SavedCGI = undef;
958        }
959        # Default to no tracing except errors.
960        my ($tracing, $dest) = ("0", "WARN");
961        # Check for emergency tracing.
962        my $tkey = EmergencyKey($parameter);
963        my $emergencyFile = EmergencyFileName($tkey);
964        if (-e $emergencyFile) {
965            # We have the file. Read in the data.
966            my @tracing = GetFile($emergencyFile);
967            # Pull off the time limit.
968            my $expire = shift @tracing;
969            # Convert it to seconds.
970            $expire *= 3600;
971            # Check the file data.
972            my $stat = stat($emergencyFile);
973            my ($now) = gettimeofday;
974            if ($now - $stat->mtime > $expire) {
975                # Delete the expired file.
976                unlink $emergencyFile;
977            } else {
978                # Emergency tracing is on. Pull off the destination and
979                # the trace level;
980                $dest = shift @tracing;
981                my $level = shift @tracing;
982                # Convert the destination to a real tracing destination.
983                # temp directory.
984                $dest = EmergencyTracingDest($tkey, $dest);
985                # Insure Tracer is specified.
986                my %moduleHash = map { $_ => 1 } @tracing;
987                $moduleHash{Tracer} = 1;
988                # Set the trace parameter.
989                $tracing = join(" ", $level, sort keys %moduleHash);
990            }
991        } elsif (defined $SavedCGI) {
992            # There's no emergency tracing, but we have a CGI object, so check
993            # for tracing from the form parameters.
994            if ($SavedCGI->param('Trace')) {
995                # Here the user has requested tracing via a form.
996                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
997                $tracing = $SavedCGI->param('Trace') . " Tracer";
998            }
999        }
1000        # Setup the tracing we've determined from all the stuff above.
1001        TSetup($tracing, $dest);
1002        # Check to see if we're a web script.
1003        if (defined $SavedCGI) {
1004            # Yes we are. Trace the form and environment data.
1005            TraceParms($SavedCGI);
1006            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1007            # emitted by the script in its raw form.
1008            if (T(Raw => 3)) {
1009                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1010            }
1011        }
1012    }
1013    
1014    =head3 EmergencyFileName
1015    
1016        my $fileName = Tracer::EmergencyFileName($tkey);
1017    
1018    Return the emergency tracing file name. This is the file that specifies
1019    the tracing information.
1020    
1021    =over 4
1022    
1023    =item tkey
1024    
1025    Tracing key for the current program.
1026    
1027    =item RETURN
1028    
1029    Returns the name of the file to contain the emergency tracing information.
1030    
1031    =back
1032    
1033    =cut
1034    
1035    sub EmergencyFileName {
1036        # Get the parameters.
1037        my ($tkey) = @_;
1038        # Compute the emergency tracing file name.
1039        return "$FIG_Config::temp/Emergency$tkey.txt";
1040    }
1041    
1042    =head3 EmergencyFileTarget
1043    
1044        my $fileName = Tracer::EmergencyFileTarget($tkey);
1045    
1046    Return the emergency tracing target file name. This is the file that receives
1047    the tracing output for file-based tracing.
1048    
1049    =over 4
1050    
1051    =item tkey
1052    
1053    Tracing key for the current program.
1054    
1055    =item RETURN
1056    
1057    Returns the name of the file to contain the trace output.
1058    
1059    =back
1060    
1061    =cut
1062    
1063    sub EmergencyFileTarget {
1064        # Get the parameters.
1065        my ($tkey) = @_;
1066        # Compute the emergency tracing file name.
1067        return "$FIG_Config::temp/trace$tkey.log";
1068    }
1069    
1070    =head3 EmergencyTracingDest
1071    
1072        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1073    
1074    This method converts an emergency tracing destination to a real
1075    tracing destination. The main difference is that if the
1076    destination is C<FILE> or C<APPEND>, we convert it to file
1077    output. If the destination is C<DUAL>, we convert it to file
1078    and standard output.
1079    
1080    =over 4
1081    
1082    =item tkey
1083    
1084    Tracing key for this environment.
1085    
1086    =item myDest
1087    
1088    Destination from the emergency tracing file.
1089    
1090    =item RETURN
1091    
1092    Returns a destination that can be passed into L</TSetup>.
1093    
1094    =back
1095    
1096    =cut
1097    
1098    sub EmergencyTracingDest {
1099        # Get the parameters.
1100        my ($tkey, $myDest) = @_;
1101        # Declare the return variable.
1102        my $retVal = $myDest;
1103        # Process according to the destination value.
1104        if ($myDest eq 'FILE') {
1105            $retVal = ">" . EmergencyFileTarget($tkey);
1106        } elsif ($myDest eq 'APPEND') {
1107            $retVal = ">>" . EmergencyFileTarget($tkey);
1108        } elsif ($myDest eq 'DUAL') {
1109            $retVal = "+>" . EmergencyFileTarget($tkey);
1110        } elsif ($myDest eq 'WARN') {
1111            $retVal = "WARN";
1112        }
1113        # Return the result.
1114        return $retVal;
1115    }
1116    
1117    =head3 Emergency
1118    
1119        Emergency($key, $hours, $dest, $level, @modules);
1120    
1121    Turn on emergency tracing. This method is normally invoked over the web from
1122    a debugging console, but it can also be called by the C<trace.pl> script.
1123    The caller specifies the duration of the emergency in hours, the desired tracing
1124    destination, the trace level, and a list of the trace modules to activate.
1125    For the length of the duration, when a program in an environment with the
1126    specified tracing key active invokes a Sprout CGI script, tracing will be
1127    turned on automatically. See L</TSetup> for more about tracing setup and
1128    L</ETracing> for more about emergency tracing.
1129    
1130    =over 4
1131    
1132    =item tkey
1133    
1134    The tracing key. This is used to identify the control file and the trace file.
1135    
1136    =item hours
1137    
1138    Number of hours to keep emergency tracing alive.
1139    
1140    =item dest
1141    
1142    Tracing destination. If no path information is specified for a file
1143    destination, it is put in the FIG temporary directory.
1144    
1145    =item level
1146    
1147    Tracing level. A higher level means more trace messages.
1148    
1149    =item modules
1150    
1151    A list of the tracing modules to activate.
1152    
1153    =back
1154    
1155    =cut
1156    
1157    sub Emergency {
1158        # Get the parameters.
1159        my ($tkey, $hours, $dest, $level, @modules) = @_;
1160        # Create the emergency file.
1161        my $specFile = EmergencyFileName($tkey);
1162        my $outHandle = Open(undef, ">$specFile");
1163        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1164    }
1165    
1166    =head3 EmergencyKey
1167    
1168        my $tkey = EmergencyKey($parameter);
1169    
1170    Return the Key to be used for emergency tracing. This could be an IP address,
1171     a session ID, or a user name, depending on the environment.
1172    
1173    =over 4
1174    
1175    =item parameter
1176    
1177    Parameter defining the method for finding the tracing key. If it is a scalar,
1178    then it is presumed to be the tracing key itself. If it is a CGI object, then
1179    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1180    taken from the C<TRACING> environment variable.
1181    
1182    =item RETURN
1183    
1184    Returns the key to be used for labels in emergency tracing.
1185    
1186    =back
1187    
1188    =cut
1189    
1190    sub EmergencyKey {
1191        # Get the parameters.
1192        my ($parameter) = @_;
1193        # Declare the return variable.
1194        my $retVal;
1195        # Determine the parameter type.
1196        if (! defined $parameter) {
1197            # Here we're supposed to check the environment. If that fails, we
1198            # get the effective login ID.
1199            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1200        } else {
1201            my $ptype = ref $parameter;
1202            if ($ptype eq 'CGI') {
1203                # Here we were invoked from a web page. Look for a cookie.
1204                $retVal = $parameter->cookie('IP');
1205            } elsif (! $ptype) {
1206                # Here the key was passed in.
1207                $retVal = $parameter;
1208            }
1209        }
1210        # If no luck finding a key, use the PID.
1211        if (! defined $retVal) {
1212            $retVal = $$;
1213        }
1214        # Return the result.
1215        return $retVal;
1216    }
1217    
1218    
1219    =head3 TraceParms
1220    
1221        Tracer::TraceParms($cgi);
1222    
1223    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1224    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1225    
1226    =over 4
1227    
1228    =item cgi
1229    
1230    CGI query object containing the parameters to trace.
1231    
1232    =back
1233    
1234    =cut
1235    
1236    sub TraceParms {
1237        # Get the parameters.
1238        my ($cgi) = @_;
1239        if (T(CGI => 2)) {
1240            # Here we trace the GET-style URL for the script.
1241            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1242        }
1243        if (T(CGI => 3)) {
1244            # Here we want to trace the parameter data.
1245            my @names = $cgi->param;
1246            for my $parmName (sort @names) {
1247                # Note we skip the Trace parameters, which are for our use only.
1248                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1249                    my @values = $cgi->param($parmName);
1250                    Trace("[CGI] $parmName = " . join(", ", @values));
1251                }
1252            }
1253            # Display the request method.
1254            my $method = $cgi->request_method();
1255            Trace("Method: $method");
1256        }
1257        if (T(CGI => 4)) {
1258            # Here we want the environment data too.
1259            for my $envName (sort keys %ENV) {
1260                Trace("[ENV] $envName = $ENV{$envName}");
1261            }
1262        }
1263    }
1264    
1265    =head3 TraceImages
1266    
1267        Tracer::TraceImages($htmlString);
1268    
1269    Trace information about all of an html document's images. The tracing
1270    will be for type "IMG" at level 3. The image's source string
1271    will be displayed. This is generally either the URL of the image or
1272    raw data for the image itself. If the source is too long, only the first 300
1273    characters will be shown at trace level 3. The entire source will be shown,
1274    however, at trace level 4. This method is not very smart, and might catch
1275    Javascript code, but it is still useful when debugging the arcane
1276    behavior of images in multiple browser environments.
1277    
1278    =over 4
1279    
1280    =item htmlString
1281    
1282    HTML text for an outgoing web page.
1283    
1284    =back
1285    
1286    =cut
1287    
1288    sub TraceImages {
1289        # Only proceed if we're at the proper trace level.
1290        if (T(IMG => 3)) {
1291            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1292            # into a variable called "$htmlString". This is because we expect html strings to be
1293            # long, and don't want to copy them any more than we have to.
1294            Trace(length($_[0]) . " characters in web page.");
1295            # Loop through the HTML, culling image tags.
1296            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1297                # Extract the source string and determine whether or not it's too long.
1298                my $srcString = $1;
1299                my $pos = pos($_[0]) - length($srcString);
1300                my $excess = length($srcString) - 300;
1301                # We'll put the display string in here.
1302                my $srcDisplay = $srcString;
1303                # If it's a data string, split it at the comma.
1304                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1305                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1306                # a long string, however, we only show the first 300 characters.
1307                if ($excess > 0 && ! T(IMG => 4)) {
1308                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1309                }
1310                # Output the trace message.
1311                Trace("Image tag at position $pos:\n$srcDisplay");
1312            }
1313        }
1314    }
1315    
1316    
1317    =head3 ScriptFinish (deprecated)
1318    
1319        ScriptFinish($webData, $varHash);
1320    
1321    Output a web page at the end of a script. Either the string to be output or the
1322    name of a template file can be specified. If the second parameter is omitted,
1323    it is assumed we have a string to be output; otherwise, it is assumed we have the
1324    name of a template file. The template should have the variable C<DebugData>
1325    specified in any form that invokes a standard script. If debugging mode is turned
1326    on, a form field will be put in that allows the user to enter tracing data.
1327    Trace messages will be placed immediately before the terminal C<BODY> tag in
1328    the output, formatted as a list.
1329    
1330    A typical standard script would loook like the following.
1331    
1332        BEGIN {
1333            # Print the HTML header.
1334            print "CONTENT-TYPE: text/html\n\n";
1335        }
1336        use Tracer;
1337        use CGI;
1338        use FIG;
1339        # ... more uses ...
1340    
1341        my ($cgi, $varHash) = ScriptSetup();
1342        eval {
1343            # ... get data from $cgi, put it in $varHash ...
1344        };
1345        if ($@) {
1346            Trace("Script Error: $@") if T(0);
1347        }
1348        ScriptFinish("Html/MyTemplate.html", $varHash);
1349    
1350    The idea here is that even if the script fails, you'll see trace messages and
1351    useful output.
1352    
1353    =over 4
1354    
1355    =item webData
1356    
1357    A string containing either the full web page to be written to the output or the
1358    name of a template file from which the page is to be constructed. If the name
1359    of a template file is specified, then the second parameter must be present;
1360    otherwise, it must be absent.
1361    
1362    =item varHash (optional)
1363    
1364    If specified, then a reference to a hash mapping variable names for a template
1365    to their values. The template file will be read into memory, and variable markers
1366    will be replaced by data in this hash reference.
1367    
1368    =back
1369    
1370    =cut
1371    
1372    sub ScriptFinish {
1373        # Get the parameters.
1374        my ($webData, $varHash) = @_;
1375        # Check for a template file situation.
1376        my $outputString;
1377        if (defined $varHash) {
1378            # Here we have a template file. We need to determine the template type.
1379            my $template;
1380            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1381                $template = "$FIG_Config::template_url/$webData";
1382            } else {
1383                $template = "<<$webData";
1384            }
1385            $outputString = PageBuilder::Build($template, $varHash, "Html");
1386        } else {
1387            # Here the user gave us a raw string.
1388            $outputString = $webData;
1389        }
1390        # Check for trace messages.
1391        if ($Destination ne "NONE" && $TraceLevel > 0) {
1392            # We have trace messages, so we want to put them at the end of the body. This
1393            # is either at the end of the whole string or at the beginning of the BODY
1394            # end-tag.
1395            my $pos = length $outputString;
1396            if ($outputString =~ m#</body>#gi) {
1397                $pos = (pos $outputString) - 7;
1398            }
1399            # If the trace messages were queued, we unroll them. Otherwise, we display the
1400            # destination.
1401            my $traceHtml;
1402            if ($Destination eq "QUEUE") {
1403                $traceHtml = QTrace('Html');
1404            } elsif ($Destination =~ /^>>(.+)$/) {
1405                # Here the tracing output it to a file. We code it as a hyperlink so the user
1406                # can copy the file name into the clipboard easily.
1407                my $actualDest = $1;
1408                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1409            } else {
1410                # Here we have one of the special destinations.
1411                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1412            }
1413            substr $outputString, $pos, 0, $traceHtml;
1414        }
1415        # Write the output string.
1416        print $outputString;
1417    }
1418    
1419    =head2 Command-Line Utility Methods
1420    
1421    =head3 SendSMS
1422    
1423        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1424    
1425    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1426    user name, password, and API ID for the relevant account in the hash reference variable
1427    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1428    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1429    is C<2561022>, then the FIG_Config file must contain
1430    
1431        $phone =  { user => 'BruceTheHumanPet',
1432                    password => 'silly',
1433                    api_id => '2561022' };
1434    
1435    The original purpose of this method was to insure Bruce would be notified immediately when the
1436    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1437    when you call this method.
1438    
1439    The message ID will be returned if successful, and C<undef> if an error occurs.
1440    
1441    =over 4
1442    
1443    =item phoneNumber
1444    
1445    Phone number to receive the message, in international format. A United States phone number
1446    would be prefixed by "1". A British phone number would be prefixed by "44".
1447    
1448    =item msg
1449    
1450    Message to send to the specified phone.
1451    
1452    =item RETURN
1453    
1454    Returns the message ID if successful, and C<undef> if the message could not be sent.
1455    
1456    =back
1457    
1458    =cut
1459    
1460    sub SendSMS {
1461        # Get the parameters.
1462        my ($phoneNumber, $msg) = @_;
1463        # Declare the return variable. If we do not change it, C<undef> will be returned.
1464        my $retVal;
1465        # Only proceed if we have phone support.
1466        if (! defined $FIG_Config::phone) {
1467            Trace("Phone support not present in FIG_Config.") if T(1);
1468        } else {
1469            # Get the phone data.
1470            my $parms = $FIG_Config::phone;
1471            # Get the Clickatell URL.
1472            my $url = "http://api.clickatell.com/http/";
1473            # Create the user agent.
1474            my $ua = LWP::UserAgent->new;
1475            # Request a Clickatell session.
1476            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1477                                         password => $parms->{password},
1478                                         api_id => $parms->{api_id},
1479                                         to => $phoneNumber,
1480                                         text => $msg});
1481            # Check for an error.
1482            if (! $resp->is_success) {
1483                Trace("Alert failed.") if T(1);
1484            } else {
1485                # Get the message ID.
1486                my $rstring = $resp->content;
1487                if ($rstring =~ /^ID:\s+(.*)$/) {
1488                    $retVal = $1;
1489                } else {
1490                    Trace("Phone attempt failed with $rstring") if T(1);
1491                }
1492            }
1493        }
1494        # Return the result.
1495        return $retVal;
1496    }
1497    
1498    =head3 StandardSetup
1499    
1500        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1501    
1502    This method performs standard command-line parsing and tracing setup. The return
1503    values are a hash of the command-line options and a list of the positional
1504    parameters. Tracing is automatically set up and the command-line options are
1505    validated.
1506    
1507    This is a complex method that does a lot of grunt work. The parameters can
1508    be more easily understood, however, once they are examined individually.
1509    
1510    The I<categories> parameter is the most obtuse. It is a reference to a list of
1511    special-purpose tracing categories. Most tracing categories are PERL package
1512    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1513    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1514    
1515        ["Sprout", "SproutLoad", "ERDB"]
1516    
1517    This would cause trace messages in the specified three packages to appear in
1518    the output. There are two special tracing categories that are automatically
1519    handled by this method. In other words, if you used L</TSetup> you would need
1520    to include these categories manually, but if you use this method they are turned
1521    on automatically.
1522    
1523    =over 4
1524    
1525    =item SQL
1526    
1527    Traces SQL commands and activity.
1528    
1529    =item Tracer
1530    
1531    Traces error messages and call stacks.
1532    
1533    =back
1534    
1535    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1536    The trace level is specified using the C<-trace> command-line option. For example,
1537    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1538    all tracing at level 3.
1539    
1540        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1541    
1542    Standard tracing is output to the standard output and echoed to the file
1543    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1544    process ID. You can also specify the C<user> parameter to put a user ID
1545    instead of a process ID in the trace file name. So, for example
1546    
1547    The default trace level is 2. To get all messages, specify a trace level of 4.
1548    For a genome-by-genome update, use 3.
1549    
1550        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1551    
1552    would send the trace output to C<traceBruce.log> in the temporary directory.
1553    
1554    The I<options> parameter is a reference to a hash containing the command-line
1555    options, their default values, and an explanation of what they mean. Command-line
1556    options may be in the form of switches or keywords. In the case of a switch, the
1557    option value is 1 if it is specified and 0 if it is not specified. In the case
1558    of a keyword, the value is separated from the option name by an equal sign. You
1559    can see this last in the command-line example above.
1560    
1561    You can specify a different default trace level by setting C<$options->{trace}>
1562    prior to calling this method.
1563    
1564    An example at this point would help. Consider, for example, the command-line utility
1565    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1566    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1567    the following code.
1568    
1569        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1570                            { safe => [0, "use database transactions"],
1571                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1572                              start => [' ', "start with this genome"],
1573                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1574                            "<command> <transactionDirectory> <IDfile>",
1575                          @ARGV);
1576    
1577    
1578    The call to C<ParseCommand> specifies the default values for the options and
1579    stores the actual options in a hash that is returned as C<$options>. The
1580    positional parameters are returned in C<@parameters>.
1581    
1582    The following is a sample command line for C<TransactFeatures>.
1583    
1584        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1585    
1586    Single and double hyphens are equivalent. So, you could also code the
1587    above command as
1588    
1589        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1590    
1591    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1592    parameters, and would find themselves in I<@parameters> after executing the
1593    above code fragment. The tracing would be set to level 2, and the categories
1594    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1595    and C<DocUtils> was included because it came in within the first parameter
1596    to this method. The I<$options> hash would be
1597    
1598        { trace => 2, sql => 0, safe => 0,
1599          noAlias => 1, start => ' ', tblFiles => 0 }
1600    
1601    Use of C<StandardSetup> in this way provides a simple way of performing
1602    standard tracing setup and command-line parsing. Note that the caller is
1603    not even aware of the command-line switches C<-trace> and C<-sql>, which
1604    are used by this method to control the tracing. If additional tracing features
1605    need to be added in the future, they can be processed by this method without
1606    upsetting the command-line utilities.
1607    
1608    If the C<background> option is specified on the command line, then the
1609    standard and error outputs will be directed to files in the temporary
1610    directory, using the same suffix as the trace file. So, if the command
1611    line specified
1612    
1613        -user=Bruce -background
1614    
1615    then the trace output would go to C<traceBruce.log>, the standard output to
1616    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1617    simplify starting a command in the background.
1618    
1619    The user name is also used as the tracing key for L</Emergency Tracing>.
1620    Specifying a value of C<E> for the trace level causes emergency tracing to
1621    be used instead of custom tracing. If the user name is not specified,
1622    the tracing key is taken from the C<Tracing> environment variable. If there
1623    is no value for that variable, the tracing key will be computed from the PID.
1624    
1625    Finally, if the special option C<-help> is specified, the option
1626    names will be traced at level 0 and the program will exit without processing.
1627    This provides a limited help capability. For example, if the user enters
1628    
1629        TransactFeatures -help
1630    
1631    he would see the following output.
1632    
1633        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1634            -trace    tracing level (default E)
1635            -sql      trace SQL commands
1636            -safe     use database transactions
1637            -noAlias  do not expect aliases in CHANGE transactions
1638            -start    start with this genome
1639            -tblFiles output TBL files containing the corrected IDs
1640    
1641    The caller has the option of modifying the tracing scheme by placing a value
1642    for C<trace> in the incoming options hash. The default value can be overridden,
1643    or the tracing to the standard output can be turned off by suffixing a minus
1644    sign to the trace level. So, for example,
1645    
1646        { trace => [0, "tracing level (default 0)"],
1647           ...
1648    
1649    would set the default trace level to 0 instead of E, while
1650    
1651        { trace => ["2-", "tracing level (default 2)"],
1652           ...
1653    
1654    would set the default to 2, but trace only to the log file, not to the
1655    standard output.
1656    
1657    The parameters to this method are as follows.
1658    
1659    =over 4
1660    
1661    =item categories
1662    
1663    Reference to a list of tracing category names. These should be names of
1664    packages whose internal workings will need to be debugged to get the
1665    command working.
1666    
1667    =item options
1668    
1669    Reference to a hash containing the legal options for the current command mapped
1670    to their default values and descriptions. The user can override the defaults
1671    by specifying the options as command-line switches prefixed by a hyphen.
1672    Tracing-related options may be added to this hash. If the C<-h> option is
1673    specified on the command line, the option descriptions will be used to
1674    explain the options. To turn off tracing to the standard output, add a
1675    minus sign to the value for C<trace> (see above).
1676    
1677    =item parmHelp
1678    
1679    A string that vaguely describes the positional parameters. This is used
1680    if the user specifies the C<-h> option.
1681    
1682    =item argv
1683    
1684    List of command line parameters, including the option switches, which must
1685    precede the positional parameters and be prefixed by a hyphen.
1686    
1687    =item RETURN
1688    
1689    Returns a list. The first element of the list is the reference to a hash that
1690    maps the command-line option switches to their values. These will either be the
1691    default values or overrides specified on the command line. The remaining
1692    elements of the list are the position parameters, in order.
1693    
1694    =back
1695    
1696    =cut
1697    
1698    sub StandardSetup {
1699        # Get the parameters.
1700        my ($categories, $options, $parmHelp, @argv) = @_;
1701        # Get the default tracing key.
1702        my $tkey = EmergencyKey();
1703        # Add the tracing options.
1704        if (! exists $options->{trace}) {
1705            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1706        }
1707        $options->{sql} = [0, "turn on SQL tracing"];
1708        $options->{help} = [0, "display command-line options"];
1709        $options->{user} = [$tkey, "tracing key"];
1710        $options->{background} = [0, "spool standard and error output"];
1711        # Create a parsing hash from the options hash. The parsing hash
1712        # contains the default values rather than the default value
1713        # and the description. While we're at it, we'll memorize the
1714        # length of the longest option name.
1715        my $longestName = 0;
1716      my %parseOptions = ();      my %parseOptions = ();
1717      for my $key (keys %{$options}) {      for my $key (keys %{$options}) {
1718          if (length $key > $longestName) {          if (length $key > $longestName) {
1719              $longestName = length $key;              $longestName = length $key;
1720          }          }
1721          $parseOptions{$key} = $options->{$key}->[0];          $parseOptions{$key} = $options->{$key}->[0];
1722        }
1723        # Parse the command line.
1724        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1725        # Get the logfile suffix.
1726        my $suffix = $retOptions->{user};
1727        # Check for background mode.
1728        if ($retOptions->{background}) {
1729            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1730            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1731            open STDOUT, ">$outFileName";
1732            open STDERR, ">$errFileName";
1733            # Check for phone support. If we have phone support and a phone number,
1734            # we want to turn it on.
1735            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1736                $retOptions->{phone} = $ENV{PHONE};
1737            }
1738        }
1739        # Now we want to set up tracing. First, we need to know if the user
1740        # wants emergency tracing.
1741        if ($retOptions->{trace} eq 'E') {
1742            ETracing($retOptions->{user});
1743        } else {
1744            # Here the tracing is controlled from the command line.
1745            my @cats = @{$categories};
1746            if ($retOptions->{sql}) {
1747                push @cats, "SQL";
1748            }
1749            # Add the default categories.
1750            push @cats, "Tracer";
1751            # Next, we create the category string by joining the categories.
1752            my $cats = join(" ", @cats);
1753            # Check to determine whether or not the caller wants to turn off tracing
1754            # to the standard output.
1755            my $traceLevel = $retOptions->{trace};
1756            my $textOKFlag = 1;
1757            if ($traceLevel =~ /^(.)-/) {
1758                $traceLevel = $1;
1759                $textOKFlag = 0;
1760            }
1761            # Now we set up the trace mode.
1762            my $traceMode;
1763            # Verify that we can open a file in the FIG temporary directory.
1764            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1765            if (open TESTTRACE, ">$traceFileName") {
1766                # Here we can trace to a file.
1767                $traceMode = ">$traceFileName";
1768                if ($textOKFlag) {
1769                    # Echo to standard output if the text-OK flag is set.
1770                    $traceMode = "+$traceMode";
1771                }
1772                # Close the test file.
1773                close TESTTRACE;
1774            } else {
1775                # Here we can't trace to a file. Complain about this.
1776                warn "Could not open trace file $traceFileName: $!\n";
1777                # We trace to the standard output if it's
1778                # okay, and the error log otherwise.
1779                if ($textOKFlag) {
1780                    $traceMode = "TEXT";
1781                } else {
1782                    $traceMode = "WARN";
1783                }
1784            }
1785            # Now set up the tracing.
1786            TSetup("$traceLevel $cats", $traceMode);
1787        }
1788        # Check for the "help" option. If it is specified, dump the command-line
1789        # options and exit the program.
1790        if ($retOptions->{help}) {
1791            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1792            print "$1 [options] $parmHelp\n";
1793            for my $key (sort keys %{$options}) {
1794                my $name = Pad($key, $longestName, 0, ' ');
1795                my $desc = $options->{$key}->[1];
1796                if ($options->{$key}->[0]) {
1797                    $desc .= " (default " . $options->{$key}->[0] . ")";
1798                }
1799                print "  $name $desc\n";
1800            }
1801            exit(0);
1802        }
1803        # Trace the options, if applicable.
1804        if (T(3)) {
1805            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1806            Trace("Selected options: " . join(", ", sort @parms) . ".");
1807        }
1808        # Return the parsed parameters.
1809        return ($retOptions, @retParameters);
1810    }
1811    
1812    =head3 ReadOptions
1813    
1814        my %options = Tracer::ReadOptions($fileName);
1815    
1816    Read a set of options from a file. Each option is encoded in a line of text that has the
1817    format
1818    
1819    I<optionName>C<=>I<optionValue>C<; >I<comment>
1820    
1821    The option name must consist entirely of letters, digits, and the punctuation characters
1822    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1823    character is a semi-colon will be ignored. The return hash will map each option name to
1824    the corresponding option value.
1825    
1826    =over 4
1827    
1828    =item fileName
1829    
1830    Name of the file containing the option data.
1831    
1832    =item RETURN
1833    
1834    Returns a hash mapping the option names specified in the file to their corresponding option
1835    value.
1836    
1837    =back
1838    
1839    =cut
1840    
1841    sub ReadOptions {
1842        # Get the parameters.
1843        my ($fileName) = @_;
1844        # Open the file.
1845        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1846        # Count the number of records read.
1847        my ($records, $comments) = 0;
1848        # Create the return hash.
1849        my %retVal = ();
1850        # Loop through the file, accumulating key-value pairs.
1851        while (my $line = <CONFIGFILE>) {
1852            # Denote we've read a line.
1853            $records++;
1854            # Determine the line type.
1855            if ($line =~ /^\s*[\n\r]/) {
1856                # A blank line is a comment.
1857                $comments++;
1858            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1859                # Here we have an option assignment.
1860                retVal{$1} = $2;
1861            } elsif ($line =~ /^\s*;/) {
1862                # Here we have a text comment.
1863                $comments++;
1864            } else {
1865                # Here we have an invalid line.
1866                Trace("Invalid option statement in record $records.") if T(0);
1867            }
1868        }
1869        # Return the hash created.
1870        return %retVal;
1871    }
1872    
1873    =head3 GetOptions
1874    
1875        Tracer::GetOptions(\%defaults, \%options);
1876    
1877    Merge a specified set of options into a table of defaults. This method takes two hash references
1878    as input and uses the data from the second to update the first. If the second does not exist,
1879    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1880    exist in the first.
1881    
1882    Consider the following example.
1883    
1884        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1885    
1886    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1887    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1888    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1889    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1890    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1891    
1892        {databaseType => 'Oracle'}
1893    
1894    an error will occur because the B<databaseType> option does not exist.
1895    
1896    =over 4
1897    
1898    =item defaults
1899    
1900    Table of default option values.
1901    
1902    =item options
1903    
1904    Table of overrides, if any.
1905    
1906    =item RETURN
1907    
1908    Returns a reference to the default table passed in as the first parameter.
1909    
1910    =back
1911    
1912    =cut
1913    
1914    sub GetOptions {
1915        # Get the parameters.
1916        my ($defaults, $options) = @_;
1917        # Check for overrides.
1918        if ($options) {
1919            # Loop through the overrides.
1920            while (my ($option, $setting) = each %{$options}) {
1921                # Insure this override exists.
1922                if (!exists $defaults->{$option}) {
1923                    croak "Unrecognized option $option encountered.";
1924                } else {
1925                    # Apply the override.
1926                    $defaults->{$option} = $setting;
1927                }
1928            }
1929        }
1930        # Return the merged table.
1931        return $defaults;
1932    }
1933    
1934    =head3 MergeOptions
1935    
1936        Tracer::MergeOptions(\%table, \%defaults);
1937    
1938    Merge default values into a hash table. This method looks at the key-value pairs in the
1939    second (default) hash, and if a matching key is not found in the first hash, the default
1940    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1941    checking and no return value.
1942    
1943    =over 4
1944    
1945    =item table
1946    
1947    Hash table to be updated with the default values.
1948    
1949    =item defaults
1950    
1951    Default values to be merged into the first hash table if they are not already present.
1952    
1953    =back
1954    
1955    =cut
1956    
1957    sub MergeOptions {
1958        # Get the parameters.
1959        my ($table, $defaults) = @_;
1960        # Loop through the defaults.
1961        while (my ($key, $value) = each %{$defaults}) {
1962            if (!exists $table->{$key}) {
1963                $table->{$key} = $value;
1964            }
1965      }      }
     # Parse the command line.  
     my ($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, ">$errFileName";  
1966      }      }
1967      # Now we want to set up tracing. First, we need to know if SQL is to  
1968      # be traced.  =head3 ParseCommand
1969      my @cats = @{$categories};  
1970      if ($retOptions->{sql}) {      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1971          push @cats, "SQL";  
1972    Parse a command line consisting of a list of parameters. The initial parameters may be option
1973    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1974    off and merged into a table of default options. The remainder of the command line is
1975    returned as a list of positional arguments. For example, consider the following invocation.
1976    
1977        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1978    
1979    In this case, the list @words will be treated as a command line and there are two options available,
1980    B<errors> and B<logFile>. If @words has the following format
1981    
1982        -logFile=error.log apple orange rutabaga
1983    
1984    then at the end of the invocation, C<$options> will be
1985    
1986        { errors => 0, logFile => 'error.log' }
1987    
1988    and C<@arguments> will contain
1989    
1990        apple orange rutabaga
1991    
1992    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1993    support for quote characters. Options can be specified with single or double hyphens.
1994    
1995    =over 4
1996    
1997    =item optionTable
1998    
1999    Table of default options.
2000    
2001    =item inputList
2002    
2003    List of words on the command line.
2004    
2005    =item RETURN
2006    
2007    Returns a reference to the option table and a list of the positional arguments.
2008    
2009    =back
2010    
2011    =cut
2012    
2013    sub ParseCommand {
2014        # Get the parameters.
2015        my ($optionTable, @inputList) = @_;
2016        # Process any options in the input list.
2017        my %overrides = ();
2018        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2019            # Get the current option.
2020            my $arg = shift @inputList;
2021            # Pull out the option name.
2022            $arg =~ /^--?([^=]*)/g;
2023            my $name = $1;
2024            # Check for an option value.
2025            if ($arg =~ /\G=(.*)$/g) {
2026                # Here we have a value for the option.
2027                $overrides{$name} = UnEscape($1);
2028            } else {
2029                # Here there is no value, so we use 1.
2030                $overrides{$name} = 1;
2031      }      }
     # Add the default categories.  
     push @cats, "Tracer", "FIG";  
     # 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;  
2032      }      }
2033      # Now we set up the trace mode.      # Merge the options into the defaults.
2034      my $traceMode;      GetOptions($optionTable, \%overrides);
2035      # Verify that we can open a file in the FIG temporary directory.      # Translate the remaining parameters.
2036      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";      my @retVal = ();
2037      if (open TESTTRACE, ">$traceFileName") {      for my $inputParm (@inputList) {
2038          # Here we can trace to a file.          push @retVal, UnEscape($inputParm);
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
2039          }          }
2040          # Close the test file.      # Return the results.
2041          close TESTTRACE;      return ($optionTable, @retVal);
2042      } else {  }
2043          # Here we can't trace to a file. We trace to the standard output if it's  
2044          # okay, and the error log otherwise.  
2045          if ($textOKFlag) {  =head2 File Utility Methods
2046              $traceMode = "TEXT";  
2047    =head3 GetFile
2048    
2049        my @fileContents = Tracer::GetFile($fileName);
2050    
2051        or
2052    
2053        my $fileContents = Tracer::GetFile($fileName);
2054    
2055    Return the entire contents of a file. In list context, line-ends are removed and
2056    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2057    
2058    =over 4
2059    
2060    =item fileName
2061    
2062    Name of the file to read.
2063    
2064    =item RETURN
2065    
2066    In a list context, returns the entire file as a list with the line terminators removed.
2067    In a scalar context, returns the entire file as a string. If an error occurs opening
2068    the file, an empty list will be returned.
2069    
2070    =back
2071    
2072    =cut
2073    
2074    sub GetFile {
2075        # Get the parameters.
2076        my ($fileName) = @_;
2077        # Declare the return variable.
2078        my @retVal = ();
2079        # Open the file for input.
2080        my $handle = Open(undef, "<$fileName");
2081        # Read the whole file into the return variable, stripping off any terminator
2082        # characters.
2083        my $lineCount = 0;
2084        while (my $line = <$handle>) {
2085            $lineCount++;
2086            $line = Strip($line);
2087            push @retVal, $line;
2088        }
2089        # Close it.
2090        close $handle;
2091        my $actualLines = @retVal;
2092        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2093        # Return the file's contents in the desired format.
2094        if (wantarray) {
2095            return @retVal;
2096          } else {          } else {
2097              $traceMode = "WARN";          return join "\n", @retVal;
2098          }          }
2099      }      }
2100      # Now set up the tracing.  
2101      TSetup("$traceLevel $cats", $traceMode);  =head3 PutFile
2102      # Check for the "h" option. If it is specified, dump the command-line  
2103      # options and exit the program.      Tracer::PutFile($fileName, \@lines);
2104      if ($retOptions->{h}) {  
2105          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Write out a file from a list of lines of text.
2106          Trace("$1 [options] $parmHelp") if T(0);  
2107          for my $key (sort keys %{$options}) {  =over 4
2108              my $name = Pad($key, $longestName, 0, ' ');  
2109              my $desc = $options->{$key}->[1];  =item fileName
2110              if ($options->{$key}->[0]) {  
2111                  $desc .= " (default " . $options->{$key}->[0] . ")";  Name of the output file.
2112    
2113    =item lines
2114    
2115    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2116    new-line characters. Alternatively, may be a string, in which case the string will be written without
2117    modification.
2118    
2119    =back
2120    
2121    =cut
2122    
2123    sub PutFile {
2124        # Get the parameters.
2125        my ($fileName, $lines) = @_;
2126        # Open the output file.
2127        my $handle = Open(undef, ">$fileName");
2128        # Count the lines written.
2129        if (ref $lines ne 'ARRAY') {
2130            # Here we have a scalar, so we write it raw.
2131            print $handle $lines;
2132            Trace("Scalar put to file $fileName.") if T(File => 3);
2133        } else {
2134            # Write the lines one at a time.
2135            my $count = 0;
2136            for my $line (@{$lines}) {
2137                print $handle "$line\n";
2138                $count++;
2139              }              }
2140              Trace("  $name $desc") if T(0);          Trace("$count lines put to file $fileName.") if T(File => 3);
2141          }          }
2142          exit(0);      # Close the output file.
2143        close $handle;
2144      }      }
2145      # Return the parsed parameters.  
2146      return ($retOptions, @retParameters);  =head3 ParseRecord
2147    
2148        my @fields = Tracer::ParseRecord($line);
2149    
2150    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2151    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2152    These will automatically be converted.
2153    
2154    =over 4
2155    
2156    =item line
2157    
2158    Line of data containing the tab-delimited fields.
2159    
2160    =item RETURN
2161    
2162    Returns a list of the fields found in the data line.
2163    
2164    =back
2165    
2166    =cut
2167    
2168    sub ParseRecord {
2169        # Get the parameter.
2170        my ($line) = @_;
2171        # Remove the trailing new-line, if any.
2172        chomp $line;
2173        # Split the line read into pieces using the tab character.
2174        my @retVal = split /\t/, $line;
2175        # Trim and fix the escapes in each piece.
2176        for my $value (@retVal) {
2177            # Trim leading whitespace.
2178            $value =~ s/^\s+//;
2179            # Trim trailing whitespace.
2180            $value =~ s/\s+$//;
2181            # Delete the carriage returns.
2182            $value =~ s/\r//g;
2183            # Convert the escapes into their real values.
2184            $value =~ s/\\t/"\t"/ge;
2185            $value =~ s/\\n/"\n"/ge;
2186        }
2187        # Return the result.
2188        return @retVal;
2189  }  }
2190    
2191  =head3 Setups  =head3 Merge
2192    
2193  C<< my $count = Tracer::Setups(); >>      my @mergedList = Tracer::Merge(@inputList);
2194    
2195  Return the number of times L</TSetup> has been called.  Sort a list of strings and remove duplicates.
2196    
2197  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
2198  may want to set up tracing if nobody else has done it before us.  
2199    =item inputList
2200    
2201    List of scalars to sort and merge.
2202    
2203    =item RETURN
2204    
2205    Returns a list containing the same elements sorted in ascending order with duplicates
2206    removed.
2207    
2208    =back
2209    
2210  =cut  =cut
2211    
2212  sub Setups {  sub Merge {
2213      return $SetupCount;      # Get the input list in sort order.
2214        my @inputList = sort @_;
2215        # Only proceed if the list has at least two elements.
2216        if (@inputList > 1) {
2217            # Now we want to move through the list splicing out duplicates.
2218            my $i = 0;
2219            while ($i < @inputList) {
2220                # Get the current entry.
2221                my $thisEntry = $inputList[$i];
2222                # Find out how many elements duplicate the current entry.
2223                my $j = $i + 1;
2224                my $dup1 = $i + 1;
2225                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2226                # If the number is nonzero, splice out the duplicates found.
2227                if ($j > $dup1) {
2228                    splice @inputList, $dup1, $j - $dup1;
2229                }
2230                # Now the element at position $dup1 is different from the element before it
2231                # at position $i. We push $i forward one position and start again.
2232                $i++;
2233            }
2234        }
2235        # Return the merged list.
2236        return @inputList;
2237  }  }
2238    
2239  =head3 Open  =head3 Open
2240    
2241  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2242    
2243  Open a file.  Open a file.
2244    
# Line 607  Line 2330 
2330    
2331  =head3 FindNamePart  =head3 FindNamePart
2332    
2333  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
   
 Returns a three-element list. The first element contains the file name portion of  
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
   
     my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  
   
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
   
 TRUE if a failure to open is okay, else FALSE  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 SetLevel  
   
 C<< Tracer::SetLevel($newLevel); >>  
   
 Modify the trace level. A higher trace level will cause more messages to appear.  
   
 =over 4  
   
 =item newLevel  
   
 Proposed new trace level.  
   
 =back  
   
 =cut  
   
 sub SetLevel {  
     $TraceLevel = $_[0];  
 }  
   
 =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;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
   
 =head3 LogErrors  
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
 }  
   
 =head3 ReadOptions  
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
   
 I<optionName>C<=>I<optionValue>C<; >I<comment>  
   
 The option name must consist entirely of letters, digits, and the punctuation characters  
 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.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file containing the option data.  
   
 =item RETURN  
   
 Returns a hash mapping the option names specified in the file to their corresponding option  
 value.  
   
 =back  
   
 =cut  
   
 sub ReadOptions {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Open the file.  
     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");  
     # Count the number of records read.  
     my ($records, $comments) = 0;  
     # Create the return hash.  
     my %retVal = ();  
     # Loop through the file, accumulating key-value pairs.  
     while (my $line = <CONFIGFILE>) {  
         # Denote we've read a line.  
         $records++;  
         # Determine the line type.  
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
     }  
     # Return the hash created.  
     return %retVal;  
 }  
   
 =head3 GetOptions  
   
 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  
2334    
2335  C<< {databaseType => 'Oracle'} >>  Extract the portion of a file specification that contains the file name.
2336    
2337  an error will occur because the B<databaseType> option does not exist.  A file specification is the string passed to an C<open> call. It specifies the file
2338    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2339    method assumes that the file name is whatever follows the first angle bracket
2340    sequence.  So, for example, in the following strings the file name is
2341    C</usr/fig/myfile.txt>.
2342    
2343  =over 4      >>/usr/fig/myfile.txt
2344        </usr/fig/myfile.txt
2345        | sort -u > /usr/fig/myfile.txt
2346    
2347  =item defaults  If the method cannot find a file name using its normal methods, it will return the
2348    whole incoming string.
2349    
2350  Table of default option values.  =over 4
2351    
2352  =item options  =item fileSpec
2353    
2354  Table of overrides, if any.  File specification string from which the file name is to be extracted.
2355    
2356  =item RETURN  =item RETURN
2357    
2358  Returns a reference to the default table passed in as the first parameter.  Returns a three-element list. The first element contains the file name portion of
2359    the specified string, or the whole string if a file name cannot be found via normal
2360    methods. The second element contains the start position of the file name portion and
2361    the third element contains the length.
2362    
2363  =back  =back
2364    
2365  =cut  =cut
2366    #: Return Type $;
2367  sub GetOptions {  sub FindNamePart {
2368      # Get the parameters.      # Get the parameters.
2369      my ($defaults, $options) = @_;      my ($fileSpec) = @_;
2370      # Check for overrides.      # Default to the whole input string.
2371      if ($options) {      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2372          # Loop through the overrides.      # Parse out the file name if we can.
2373          while (my ($option, $setting) = each %{$options}) {      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2374              # Insure this override exists.          $retVal = $2;
2375              if (!exists $defaults->{$option}) {          $len = length $retVal;
2376                  croak "Unrecognized option $option encountered.";          $pos = (length $fileSpec) - (length $3) - $len;
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
2377      }      }
2378      # Return the merged table.      # Return the result.
2379      return $defaults;      return ($retVal, $pos, $len);
2380  }  }
2381    
2382  =head3 MergeOptions  =head3 OpenDir
2383    
2384  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my @files = OpenDir($dirName, $filtered, $flag);
2385    
2386  Merge default values into a hash table. This method looks at the key-value pairs in the  Open a directory and return all the file names. This function essentially performs
2387  second (default) hash, and if a matching key is not found in the first hash, the default  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2388  pair is copied in. The process is similar to L</GetOptions>, but there is no error-  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2389  checking and no return value.  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2390    filtered out of the return list. If the directory does not open and I<$flag> is not
2391    set, an exception is thrown. So, for example,
2392    
2393        my @files = OpenDir("/Volumes/fig/contigs", 1);
2394    
2395    is effectively the same as
2396    
2397        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2398        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2399    
2400    Similarly, the following code
2401    
2402        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2403    
2404    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2405    automatically returns an empty list if the directory fails to open.
2406    
2407  =over 4  =over 4
2408    
2409  =item table  =item dirName
2410    
2411  Hash table to be updated with the default values.  Name of the directory to open.
2412    
2413  =item defaults  =item filtered
2414    
2415  Default values to be merged into the first hash table if they are not already present.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2416    from the list, else FALSE.
2417    
2418    =item flag
2419    
2420    TRUE if a failure to open is okay, else FALSE
2421    
2422  =back  =back
2423    
2424  =cut  =cut
2425    #: Return Type @;
2426  sub MergeOptions {  sub OpenDir {
2427      # Get the parameters.      # Get the parameters.
2428      my ($table, $defaults) = @_;      my ($dirName, $filtered, $flag) = @_;
2429      # Loop through the defaults.      # Declare the return variable.
2430      while (my ($key, $value) = each %{$defaults}) {      my @retVal = ();
2431          if (!exists $table->{$key}) {      # Open the directory.
2432              $table->{$key} = $value;      if (opendir(my $dirHandle, $dirName)) {
2433            # The directory opened successfully. Get the appropriate list according to the
2434            # strictures of the filter parameter.
2435            if ($filtered) {
2436                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2437            } else {
2438                @retVal = readdir $dirHandle;
2439          }          }
2440        } elsif (! $flag) {
2441            # Here the directory would not open and it's considered an error.
2442            Confess("Could not open directory $dirName.");
2443      }      }
2444        # Return the result.
2445        return @retVal;
2446  }  }
2447    
 =head3 Trace  
2448    
2449  C<< Trace($message); >>  =head3 Insure
2450    
2451  Write a trace message to the target location specified in L</TSetup>. If there has not been      Insure($dirName, $chmod);
2452  any prior call to B<TSetup>.  
2453    Insure a directory is present.
2454    
2455  =over 4  =over 4
2456    
2457  =item message  =item dirName
2458    
2459  Message to write.  Name of the directory to check. If it does not exist, it will be created.
2460    
2461    =item chmod (optional)
2462    
2463    Security privileges to be given to the directory if it is created.
2464    
2465  =back  =back
2466    
2467  =cut  =cut
2468    
2469  sub Trace {  sub Insure {
2470      # Get the parameters.      my ($dirName, $chmod) = @_;
2471      my ($message) = @_;      if (! -d $dirName) {
2472      # Get the timestamp.          Trace("Creating $dirName directory.") if T(2);
2473      my $timeStamp = Now();          eval {
2474      # Format the message. Note we strip off any line terminators at the end.              mkpath $dirName;
2475      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);              # If we have permissions specified, set them here.
2476      # Process according to the destination.              if (defined($chmod)) {
2477      if ($Destination eq "TEXT") {                  chmod $chmod, $dirName;
2478          # Write the message to the standard output.              }
2479          print "$formatted\n";          };
2480      } elsif ($Destination eq "ERROR") {          if ($@) {
2481          # Write the message to the error output.              Confess("Error creating $dirName: $@");
         print STDERR "$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";  
2482          }          }
2483      }      }
2484  }  }
2485    
2486  =head3 T  =head3 ChDir
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
2487    
2488  C<< my $switch = T($traceLevel); >>      ChDir($dirName);
2489    
2490  Return TRUE if the trace level is at or above a specified value and the specified category  Change to the specified directory.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
2491    
2492  =over 4  =over 4
2493    
2494  =item category  =item dirName
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
2495    
2496  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Name of the directory to which we want to change.
2497    
2498  =back  =back
2499    
2500  =cut  =cut
2501    
2502  sub T {  sub ChDir {
2503      # Declare the return variable.      my ($dirName) = @_;
2504      my $retVal = 0;      if (! -d $dirName) {
2505      # Only proceed if tracing is turned on.          Confess("Cannot change to directory $dirName: no such directory.");
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
2506              } else {              } else {
2507                  $category = $package;          Trace("Changing to directory $dirName.") if T(File => 4);
2508              }          my $okFlag = chdir $dirName;
2509          }          if (! $okFlag) {
2510          # Save the category name.              Confess("Error switching to directory $dirName.");
         $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.");  
2511          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2512      }      }
     # Return the computed result.  
     return $retVal;  
2513  }  }
2514    
2515  =head3 ParseCommand  =head3 SetPermissions
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
2516    
2517  Parse a command line consisting of a list of parameters. The initial parameters may be option      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
2518    
2519  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Set the permissions for a directory and all the files and folders inside it.
2520    In addition, the group ownership will be changed to the specified value.
2521    
2522  In this case, the list @words will be treated as a command line. There are two options available,  This method is more vulnerable than most to permission and compatability
2523  B<errors> and B<logFile>. If @words has the following format  problems, so it does internal error recovery.
2524    
2525  C<< -logFile=error.log apple orange rutabaga >>  =over 4
2526    
2527  then at the end of the invocation, C<$options> will be  =item dirName
2528    
2529  C<< { errors => 0, logFile => 'error.log' } >>  Name of the directory to process.
2530    
2531  and C<@arguments> will contain  =item group
2532    
2533  C<< apple orange rutabaga >>  Name of the group to be assigned.
2534    
2535  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =item mask
 support for quote characters.  
2536    
2537  =over 4  Permission mask. Bits that are C<1> in this mask will be ORed into the
2538    permission bits of any file or directory that does not already have them
2539    set to 1.
2540    
2541  =item optionTable  =item otherMasks
2542    
2543  Table of default options.  Map of search patterns to permission masks. If a directory name matches
2544    one of the patterns, that directory and all its members and subdirectories
2545    will be assigned the new pattern. For example, the following would
2546    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2547    
2548  =item inputList      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2549    
2550  List of words on the command line.  The list is ordered, so the following would use 0777 for C<tmp1> and
2551    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2552    
2553  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2554                                                       '^tmp' => 0666);
2555    
2556  Returns a reference to the option table and a list of the positional arguments.  Note that the pattern matches are all case-insensitive, and only directory
2557    names are matched, not file names.
2558    
2559  =back  =back
2560    
2561  =cut  =cut
2562    
2563  sub ParseCommand {  sub SetPermissions {
2564      # Get the parameters.      # Get the parameters.
2565      my ($optionTable, @inputList) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2566      # Process any options in the input list.      # Set up for error recovery.
2567      my %overrides = ();      eval {
2568      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          # Switch to the specified directory.
2569          # Get the current option.          ChDir($dirName);
2570          my $arg = shift @inputList;          # Get the group ID.
2571          # Pull out the option name.          my $gid = getgrnam($group);
2572          $arg =~ /^-([^=]*)/g;          # Get the mask for tracing.
2573          my $name = $1;          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2574          # Check for an option value.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2575          if ($arg =~ /\G=(.*)$/g) {          my $fixCount = 0;
2576              # Here we have a value for the option.          my $lookCount = 0;
2577              $overrides{$name} = UnEscape($1);          # @dirs will be a stack of directories to be processed.
2578            my @dirs = (getcwd());
2579            while (scalar(@dirs) > 0) {
2580                # Get the current directory.
2581                my $dir = pop @dirs;
2582                # Check for a match to one of the specified directory names. To do
2583                # that, we need to pull the individual part of the name off of the
2584                # whole path.
2585                my $simpleName = $dir;
2586                if ($dir =~ m!/([^/]+)$!) {
2587                    $simpleName = $1;
2588                }
2589                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2590                # Search for a match.
2591                my $match = 0;
2592                my $i;
2593                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2594                    my $pattern = $otherMasks[$i];
2595                    if ($simpleName =~ /$pattern/i) {
2596                        $match = 1;
2597                    }
2598                }
2599                # Check for a match. Note we use $i-1 because the loop added 2
2600                # before terminating due to the match.
2601                if ($match && $otherMasks[$i-1] != $mask) {
2602                    # This directory matches one of the incoming patterns, and it's
2603                    # a different mask, so we process it recursively with that mask.
2604                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2605          } else {          } else {
2606              # Here there is no value, so we use 1.                  # Here we can process normally. Get all of the non-hidden members.
2607              $overrides{$name} = 1;                  my @submems = OpenDir($dir, 1);
2608                    for my $submem (@submems) {
2609                        # Get the full name.
2610                        my $thisMem = "$dir/$submem";
2611                        Trace("Checking member $thisMem.") if T(4);
2612                        $lookCount++;
2613                        if ($lookCount % 1000 == 0) {
2614                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2615          }          }
2616                        # Fix the group.
2617                        chown -1, $gid, $thisMem;
2618                        # Insure this member is not a symlink.
2619                        if (! -l $thisMem) {
2620                            # Get its info.
2621                            my $fileInfo = stat $thisMem;
2622                            # Only proceed if we got the info. Otherwise, it's a hard link
2623                            # and we want to skip it anyway.
2624                            if ($fileInfo) {
2625                                my $fileMode = $fileInfo->mode;
2626                                if (($fileMode & $mask) != $mask) {
2627                                    # Fix this member.
2628                                    $fileMode |= $mask;
2629                                    chmod $fileMode, $thisMem;
2630                                    $fixCount++;
2631      }      }
2632      # Merge the options into the defaults.                              # If it's a subdirectory, stack it.
2633      GetOptions($optionTable, \%overrides);                              if (-d $thisMem) {
2634      # Translate the remaining parameters.                                  push @dirs, $thisMem;
2635      my @retVal = ();                              }
2636      for my $inputParm (@inputList) {                          }
2637          push @retVal, UnEscape($inputParm);                      }
2638                    }
2639                }
2640            }
2641            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2642        };
2643        # Check for an error.
2644        if ($@) {
2645            Confess("SetPermissions error: $@");
2646      }      }
     # Return the results.  
     return ($optionTable, @retVal);  
2647  }  }
2648    
2649  =head3 Escape  =head3 GetLine
2650    
2651  C<< my $codedString = Tracer::Escape($realString); >>      my @data = Tracer::GetLine($handle);
2652    
2653  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Read a line of data from a tab-delimited file.
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
2654    
2655  =over 4  =over 4
2656    
2657  =item realString  =item handle
2658    
2659  String to escape.  Open file handle from which to read.
2660    
2661  =item RETURN  =item RETURN
2662    
2663  Escaped equivalent of the real string.  Returns a list of the fields in the record read. The fields are presumed to be
2664    tab-delimited. If we are at the end of the file, then an empty list will be
2665    returned. If an empty line is read, a single list item consisting of a null
2666    string will be returned.
2667    
2668  =back  =back
2669    
2670  =cut  =cut
2671    
2672  sub Escape {  sub GetLine {
2673      # Get the parameter.      # Get the parameters.
2674      my ($realString) = @_;      my ($handle) = @_;
2675      # Initialize the return variable.      # Declare the return variable.
2676      my $retVal = "";      my @retVal = ();
2677      # Loop through the parameter string, looking for sequences to escape.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2678      while (length $realString > 0) {      # Read from the file.
2679          # Look for the first sequence to escape.      my $line = <$handle>;
2680          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # Only proceed if we found something.
2681              # Here we found it. The text preceding the sequence is in $1. The sequence      if (defined $line) {
2682              # itself is in $2. First, move the clear text to the return variable.          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2683              $retVal .= $1;          # upload control and have a nonstandard EOL combination.
2684              # Strip the processed section off the real string.          $line =~ s/(\r|\n)+$//;
2685              $realString = substr $realString, (length $2) + (length $1);          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2686              # Get the matched character.          if (T(File => 4)) {
2687              my $char = $2;              my $escapedLine = $line;
2688              # If we have a CR, we are done.              $escapedLine =~ s/\n/\\n/g;
2689              if ($char ne "\r") {              $escapedLine =~ s/\r/\\r/g;
2690                  # It's not a CR, so encode the escape sequence.              $escapedLine =~ s/\t/\\t/g;
2691                  $char =~ tr/\t\n/tn/;              Trace("Line read: -->$escapedLine<--");
2692                  $retVal .= "\\" . $char;          }
2693              }          # If the line is empty, return a single empty string; otherwise, parse
2694            # it into fields.
2695            if ($line eq "") {
2696                push @retVal, "";
2697          } else {          } else {
2698              # Here there are no more escape sequences. The rest of the string is              push @retVal, split /\t/,$line;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
2699          }          }
2700        } else {
2701            # Trace the reason the read failed.
2702            Trace("End of file: $!") if T(File => 3);
2703      }      }
2704      # Return the result.      # Return the result.
2705      return $retVal;      return @retVal;
2706  }  }
2707    
2708  =head3 UnEscape  =head3 PutLine
2709    
2710  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutLine($handle, \@fields, $eol);
2711    
2712  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write a line of data to a tab-delimited file. The specified field values will be
2713  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  output in tab-separated form, with a trailing new-line.
 be deleted.  
2714    
2715  =over 4  =over 4
2716    
2717  =item codedString  =item handle
2718    
2719  String to un-escape.  Output file handle.
2720    
2721  =item RETURN  =item fields
2722    
2723  Returns a copy of the original string with the escape sequences converted to their actual  List of field values.
2724  values.  
2725    =item eol (optional)
2726    
2727    End-of-line character (default is "\n").
2728    
2729  =back  =back
2730    
2731  =cut  =cut
2732    
2733  sub UnEscape {  sub PutLine {
2734      # Get the parameter.      # Get the parameters.
2735      my ($codedString) = @_;      my ($handle, $fields, $eol) = @_;
2736      # Initialize the return variable.      # Write the data.
2737      my $retVal = "";      print $handle join("\t", @{$fields}) . ($eol || "\n");
     # Only proceed if the incoming string is nonempty.  
     if (defined $codedString) {  
         # Loop through the parameter string, looking for escape sequences. We can't do  
         # translating because it causes problems with the escaped slash. ("\\t" becomes  
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
2738  }  }
2739    
 =head3 ParseRecord  
2740    
2741  C<< my @fields = Tracer::ParseRecord($line); >>  =head3 PrintLine
2742    
2743  Parse a tab-delimited data line. The data line is split into field values. Embedded tab      Tracer::PrintLine($line);
2744  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
2745  These will automatically be converted.  Print a line of text with a trailing new-line.
2746    
2747  =over 4  =over 4
2748    
2749  =item line  =item line
2750    
2751  Line of data containing the tab-delimited fields.  Line of text to print.
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
2752    
2753  =back  =back
2754    
2755  =cut  =cut
2756    
2757  sub ParseRecord {  sub PrintLine {
2758      # Get the parameter.      # Get the parameters.
2759      my ($line) = @_;      my ($line) = @_;
2760      # Remove the trailing new-line, if any.      # Print the line.
2761      chomp $line;      print "$line\n";
     # 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;  
2762  }  }
2763    
 =head3 Merge  
2764    
2765  C<< my @mergedList = Tracer::Merge(@inputList); >>  =head2 Other Useful Methods
2766    
2767  Sort a list of strings and remove duplicates.  =head3 ParseParm
2768    
2769        my $listValue = Tracer::ParseParm($string);
2770    
2771    Convert a parameter into a list reference. If the parameter is undefined,
2772    an undefined value will be returned. Otherwise, it will be parsed as a
2773    comma-separated list of values.
2774    
2775  =over 4  =over 4
2776    
2777  =item inputList  =item string
2778    
2779  List of scalars to sort and merge.  Incoming string.
2780    
2781  =item RETURN  =item RETURN
2782    
2783  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a reference to a list of values, or C<undef> if the incoming value
2784  removed.  was undefined.
2785    
2786  =back  =back
2787    
2788  =cut  =cut
2789    
2790  sub Merge {  sub ParseParm {
2791      # Get the input list in sort order.      # Get the parameters.
2792      my @inputList = sort @_;      my ($string) = @_;
2793      # Only proceed if the list has at least two elements.      # Declare the return variable.
2794      if (@inputList > 1) {      my $retVal;
2795          # Now we want to move through the list splicing out duplicates.      # Check for data.
2796          my $i = 0;      if (defined $string) {
2797          while ($i < @inputList) {          # We have some, so split it into a list.
2798              # Get the current entry.          $retVal = [ split /\s*,\s*/, $string];
             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++;  
         }  
2799      }      }
2800      # Return the merged list.      # Return the result.
2801      return @inputList;      return $retVal;
2802  }  }
2803    
2804  =head3 GetFile  =head3 Now
2805    
2806  C<< my @fileContents = Tracer::GetFile($fileName); >>      my $string = Tracer::Now();
2807    
2808      or  Return a displayable time stamp containing the local time. Whatever format this
2809    method produces must be parseable by L</ParseDate>.
2810    
2811  C<< my $fileContents = Tracer::GetFile($fileName); >>  =cut
2812    
2813  Return the entire contents of a file. In list context, line-ends are removed and  sub Now {
2814  each line is a list element. In scalar context, line-ends are replaced by C<\n>.      return DisplayTime(time);
2815    }
2816    
2817    =head3 DisplayTime
2818    
2819        my $string = Tracer::DisplayTime($time);
2820    
2821    Convert a time value to a displayable time stamp. Whatever format this
2822    method produces must be parseable by L</ParseDate>.
2823    
2824  =over 4  =over 4
2825    
2826  =item fileName  =item time
2827    
2828  Name of the file to read.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2829    
2830  =item RETURN  =item RETURN
2831    
2832  In a list context, returns the entire file as a list with the line terminators removed.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2833    
2834  =back  =back
2835    
2836  =cut  =cut
2837    
2838  sub GetFile {  sub DisplayTime {
2839      # Get the parameters.      my ($time) = @_;
2840      my ($fileName) = @_;      my $retVal = "(n/a)";
2841      # Declare the return variable.      if (defined $time) {
2842      my @retVal = ();          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2843      # Open the file for input.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2844      my $ok = open INPUTFILE, "<$fileName";                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
     if (!$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;  
2845      }      }
2846      # Return the file's contents in the desired format.      return $retVal;
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2847      }      }
2848    
2849    # Pad a number to 2 digits.
2850    sub _p2 {
2851        my ($value) = @_;
2852        $value = "0$value" if ($value < 10);
2853        return $value;
2854  }  }
2855    
2856  =head3 QTrace  =head3 Escape
2857    
2858  C<< my $data = QTrace($format); >>      my $codedString = Tracer::Escape($realString);
2859    
2860  Return the queued trace data in the specified format.  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2861    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2862    result is to reverse the effect of L</UnEscape>.
2863    
2864  =over 4  =over 4
2865    
2866  =item format  =item realString
2867    
2868  C<html> to format the data as an HTML list, C<text> to format it as straight text.  String to escape.
2869    
2870    =item RETURN
2871    
2872    Escaped equivalent of the real string.
2873    
2874  =back  =back
2875    
2876  =cut  =cut
2877    
2878  sub QTrace {  sub Escape {
2879      # Get the parameter.      # Get the parameter.
2880      my ($format) = @_;      my ($realString) = @_;
2881      # Create the return variable.      # Initialize the return variable.
2882      my $retVal = "";      my $retVal = "";
2883      # Only proceed if there is an actual queue.      # Loop through the parameter string, looking for sequences to escape.
2884      if (@Queue) {      while (length $realString > 0) {
2885          # Process according to the format.          # Look for the first sequence to escape.
2886          if ($format =~ m/^HTML$/i) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2887              # Convert the queue into an HTML list.              # Here we found it. The text preceding the sequence is in $1. The sequence
2888              $retVal = "<ul>\n";              # itself is in $2. First, move the clear text to the return variable.
2889              for my $line (@Queue) {              $retVal .= $1;
2890                  my $escapedLine = CGI::escapeHTML($line);              # Strip the processed section off the real string.
2891                  $retVal .= "<li>$escapedLine</li>\n";              $realString = substr $realString, (length $2) + (length $1);
2892                # Get the matched character.
2893                my $char = $2;
2894                # If we have a CR, we are done.
2895                if ($char ne "\r") {
2896                    # It's not a CR, so encode the escape sequence.
2897                    $char =~ tr/\t\n/tn/;
2898                    $retVal .= "\\" . $char;
2899              }              }
2900              $retVal .= "</ul>\n";          } else {
2901          } elsif ($format =~ m/^TEXT$/i) {              # Here there are no more escape sequences. The rest of the string is
2902              # Convert the queue into a list of text lines.              # transferred unmodified.
2903              $retVal = join("\n", @Queue) . "\n";              $retVal .= $realString;
2904                $realString = "";
2905          }          }
         # Clear the queue.  
         @Queue = ();  
2906      }      }
2907      # Return the formatted list.      # Return the result.
2908      return $retVal;      return $retVal;
2909  }  }
2910    
2911  =head3 Confess  =head3 UnEscape
2912    
2913  C<< Confess($message); >>      my $realString = Tracer::UnEscape($codedString);
2914    
2915  Trace the call stack and abort the program with the specified message. When used with  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2916  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2917  So, for example  be deleted.
2918    
2919  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2920    
2921  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item codedString
2922    
2923  =over 4  String to un-escape.
2924    
2925  =item message  =item RETURN
2926    
2927  Message to include in the trace.  Returns a copy of the original string with the escape sequences converted to their actual
2928    values.
2929    
2930  =back  =back
2931    
2932  =cut  =cut
2933    
2934  sub Confess {  sub UnEscape {
2935      # Get the parameters.      # Get the parameter.
2936      my ($message) = @_;      my ($codedString) = @_;
2937      # Trace the call stack.      # Initialize the return variable.
2938      Cluck($message);      my $retVal = "";
2939      # Abort the program.      # Only proceed if the incoming string is nonempty.
2940      croak(">>> $message");      if (defined $codedString) {
2941            # Loop through the parameter string, looking for escape sequences. We can't do
2942            # translating because it causes problems with the escaped slash. ("\\t" becomes
2943            # "\<tab>" no matter what we do.)
2944            while (length $codedString > 0) {
2945                # Look for the first escape sequence.
2946                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2947                    # Here we found it. The text preceding the sequence is in $1. The sequence
2948                    # itself is in $2. First, move the clear text to the return variable.
2949                    $retVal .= $1;
2950                    $codedString = substr $codedString, (2 + length $1);
2951                    # Get the escape value.
2952                    my $char = $2;
2953                    # If we have a "\r", we are done.
2954                    if ($char ne 'r') {
2955                        # Here it's not an 'r', so we convert it.
2956                        $char =~ tr/\\tn/\\\t\n/;
2957                        $retVal .= $char;
2958                    }
2959                } else {
2960                    # Here there are no more escape sequences. The rest of the string is
2961                    # transferred unmodified.
2962                    $retVal .= $codedString;
2963                    $codedString = "";
2964                }
2965            }
2966        }
2967        # Return the result.
2968        return $retVal;
2969  }  }
2970    
2971  =head3 Assert  =head3 Percent
2972    
2973  C<< Assert($condition1, $condition2, ... $conditionN); >>      my $percent = Tracer::Percent($number, $base);
2974    
2975  Return TRUE if all the conditions are true. This method can be used in conjunction with  Returns the percent of the base represented by the given number. If the base
2976  the OR operator and the L</Confess> method as a debugging assert.  is zero, returns zero.
2977  So, for example  
2978    =over 4
2979    
2980  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =item number
2981    
2982  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Percent numerator.
2983    
2984    =item base
2985    
2986    Percent base.
2987    
2988    =item RETURN
2989    
2990    Returns the percentage of the base represented by the numerator.
2991    
2992    =back
2993    
2994  =cut  =cut
2995  sub Assert {  
2996      my $retVal = 1;  sub Percent {
2997      LOOP: for my $condition (@_) {      # Get the parameters.
2998          if (! $condition) {      my ($number, $base) = @_;
2999              $retVal = 0;      # Declare the return variable.
3000              last LOOP;      my $retVal = 0;
3001          }      # Compute the percent.
3002        if ($base != 0) {
3003            $retVal = $number * 100 / $base;
3004      }      }
3005        # Return the result.
3006      return $retVal;      return $retVal;
3007  }  }
3008    
3009  =head3 Cluck  =head3 Constrain
3010    
3011  C<< Cluck($message); >>      my $constrained = Constrain($value, $min, $max);
3012    
3013  Trace the call stack. Note that for best results, you should qualify the call with a  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 trace condition. For example,  
3014    
3015  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
3016    
3017  will only trace the stack if the trace level for the package is 3 or more.  =item value
3018    
3019  =over 4  Value to constrain.
3020    
3021  =item message  =item min (optional)
3022    
3023  Message to include in the trace.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3024    
3025    =item max (optional)
3026    
3027    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3028    
3029    =item RETURN
3030    
3031    Returns the incoming value, constrained according to the other parameters.
3032    
3033  =back  =back
3034    
3035  =cut  =cut
3036    
3037  sub Cluck {  sub Constrain {
3038      # Get the parameters.      # Get the parameters.
3039      my ($message) = @_;      my ($value, $min, $max) = @_;
3040      # Trace what's happening.      # Declare the return variable.
3041      Trace("Stack trace for event: $message");      my $retVal = $value;
3042      my $confession = longmess($message);      # Apply the minimum constraint.
3043      # Convert the confession to a series of trace messages. Note we skip any      if (defined $min && $retVal < $min) {
3044      # messages relating to calls into Tracer.          $retVal = $min;
3045      for my $line (split /\s*\n/, $confession) {      }
3046          Trace($line) if ($line !~ /Tracer\.pm/);      # Apply the maximum constraint.
3047        if (defined $max && $retVal > $max) {
3048            $retVal = $max;
3049      }      }
3050        # Return the result.
3051        return $retVal;
3052  }  }
3053    
3054  =head3 Min  =head3 Min
3055    
3056  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
3057    
3058  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
3059    
# Line 1573  Line 3086 
3086    
3087  =head3 Max  =head3 Max
3088    
3089  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
3090    
3091  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
3092    
# Line 1604  Line 3117 
3117      return $retVal;      return $retVal;
3118  }  }
3119    
 =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;  
 }  
3120    
3121  =head3 Strip  =head3 Strip
3122    
3123  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::Strip($line);
3124    
3125  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
3126  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 1707  Line 3152 
3152    
3153  =head3 Pad  =head3 Pad
3154    
3155  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3156    
3157  Pad a string to a specified length. The pad character will be a  Pad a string to a specified length. The pad character will be a
3158  space, and the padding will be on the right side unless specified  space, and the padding will be on the right side unless specified
# Line 1778  Line 3223 
3223    
3224  =head3 TICK  =head3 TICK
3225    
3226  C<< my @results = TICK($commandString); >>      my @results = TICK($commandString);
3227    
3228  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3229  dot-slash (C<./> will be removed. So, for example, if you were doing  dot-slash (C<./> will be removed. So, for example, if you were doing
# Line 1817  Line 3262 
3262      return `$commandString`;      return `$commandString`;
3263  }  }
3264    
 =head3 ScriptSetup  
3265    
3266  C<< my ($query, $varHash) = ScriptSetup(); >>  =head3 CommaFormat
3267    
3268        my $formatted = Tracer::CommaFormat($number);
3269    
3270    Insert commas into a number.
3271    
3272    =over 4
3273    
3274    =item number
3275    
3276    A sequence of digits.
3277    
3278  Perform standard tracing and debugging setup for scripts. The value returned is  =item RETURN
3279  the CGI object followed by a pre-built variable hash.  
3280    Returns the same digits with commas strategically inserted.
3281    
3282  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.  
3283    
3284  =cut  =cut
3285    
3286  sub ScriptSetup {  sub CommaFormat {
3287      # Get the CGI query object.      # Get the parameters.
3288      my $query = CGI->new();      my ($number) = @_;
3289      # Check for tracing. Set it up if the user asked for it.      # Pad the length up to a multiple of three.
3290      if ($query->param('Trace')) {      my $padded = "$number";
3291          # Set up tracing to be queued for display at the bottom of the web page.      $padded = " " . $padded while length($padded) % 3 != 0;
3292          TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3293          # Trace the parameter and environment data.      # cause the delimiters to be included in the output stream. The
3294          if (T(CGI => 3)) {      # GREP removes the empty strings in between the delimiters.
3295              # Here we want to trace the parameter data.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3296              my @names = $query->param;      # Clean out the spaces.
3297              for my $parmName (sort @names) {      $retVal =~ s/ //g;
3298                  # Note we skip "Trace", which is for our use only.      # Return the result.
3299                  if ($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}");  
             }  
         }  
     } else {  
         # Here tracing is to be turned off. All we allow is errors traced into the  
         # error log.  
         TSetup("0", "WARN");  
     }  
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # If we're in DEBUG mode, set up the debug mode data for forms.  
     if (Tracer::DebugMode) {  
         $varHash->{DebugData} = GetFile("Html/DebugFragment.html");  
     }  
     # Return the query object and variable hash.  
     return ($query, $varHash);  
3300  }  }
3301    
 =head3 ScriptFinish  
3302    
3303  C<< ScriptFinish($webData, $varHash); >>  =head3 CompareLists
3304    
3305  Output a web page at the end of a script. Either the string to be output or the      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
 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.  
3306    
3307  A typical standard script would loook like the following.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3308    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3309    The return value contains a list of items that are only in the new list
3310    (inserted) and only in the old list (deleted).
3311    
3312      BEGIN {  =over 4
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3313    
3314      my ($query, $varHash) = ScriptSetup();  =item newList
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3315    
3316  The idea here is that even if the script fails, you'll see trace messages and  Reference to a list of new tuples.
 useful output.  
3317    
3318  =over 4  =item oldList
3319    
3320  =item webData  Reference to a list of old tuples.
3321    
3322  A string containing either the full web page to be written to the output or the  =item keyIndex (optional)
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3323    
3324  =item varHash (optional)  Index into each tuple of its key field. The default is 0.
3325    
3326  If specified, then a reference to a hash mapping variable names for a template  =item RETURN
3327  to their values. The template file will be read into memory, and variable markers  
3328  will be replaced by data in this hash reference.  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3329    list (inserted) followed by a reference to the list of items that are only in the old
3330    list (deleted).
3331    
3332  =back  =back
3333    
3334  =cut  =cut
3335    
3336  sub ScriptFinish {  sub CompareLists {
3337      # Get the parameters.      # Get the parameters.
3338      my ($webData, $varHash) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3339      # Check for a template file situation.      if (! defined $keyIndex) {
3340      my $outputString;          $keyIndex = 0;
3341      if (defined $varHash) {      }
3342          # Here we have a template file. We need to apply the variables to the template.      # Declare the return variables.
3343          $outputString = PageBuilder::Build("<$webData", $varHash, "Html");      my ($inserted, $deleted) = ([], []);
3344      } else {      # Loop through the two lists simultaneously.
3345          # Here the user gave us a raw string.      my ($newI, $oldI) = (0, 0);
3346          $outputString = $webData;      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3347      }      while ($newI < $newN || $oldI < $oldN) {
3348      # Check for trace messages.          # Get the current object in each list. Note that if one
3349      if ($Destination eq "QUEUE") {          # of the lists is past the end, we'll get undef.
3350          # We have trace messages, so we want to put them at the end of the body. This          my $newItem = $newList->[$newI];
3351          # is either at the end of the whole string or at the beginning of the BODY          my $oldItem = $oldList->[$oldI];
3352          # end-tag.          if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3353          my $pos = length $outputString;              # The old item is not in the new list, so mark it deleted.
3354          if ($outputString =~ m#</body>#gi) {              push @{$deleted}, $oldItem;
3355              $pos = (pos $outputString) - 7;              $oldI++;
3356            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3357                # The new item is not in the old list, so mark it inserted.
3358                push @{$inserted}, $newItem;
3359                $newI++;
3360            } else {
3361                # The item is in both lists, so push forward.
3362                $oldI++;
3363                $newI++;
3364          }          }
         substr $outputString, $pos, 0, QTrace('Html');  
3365      }      }
3366      # Write the output string.      # Return the result.
3367      print $outputString;      return ($inserted, $deleted);
3368  }  }
3369    
3370  =head3 Insure  =head3 GenerateURL
3371    
3372  C<< Insure($dirName); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3373    
3374  Insure a directory is present.  Generate a GET-style URL for the specified page with the specified parameter
3375    names and values. The values will be URL-escaped automatically. So, for
3376    example
3377    
3378        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3379    
3380    would return
3381    
3382        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3383    
3384  =over 4  =over 4
3385    
3386  =item dirName  =item page
3387    
3388  Name of the directory to check. If it does not exist, it will be created.  Page URL.
3389    
3390    =item parameters
3391    
3392    Hash mapping parameter names to parameter values.
3393    
3394    =item RETURN
3395    
3396    Returns a GET-style URL that goes to the specified page and passes in the
3397    specified parameters and values.
3398    
3399  =back  =back
3400    
3401  =cut  =cut
3402    
3403  sub Insure {  sub GenerateURL {
3404      my ($dirName) = @_;      # Get the parameters.
3405      if (! -d $dirName) {      my ($page, %parameters) = @_;
3406          Trace("Creating $dirName directory.") if T(2);      # Prime the return variable with the page URL.
3407          eval { mkpath $dirName; };      my $retVal = $page;
3408          if ($@) {      # Loop through the parameters, creating parameter elements in a list.
3409              Confess("Error creating $dirName: $@");      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3410          }      # If the list is nonempty, tack it on.
3411        if (@parmList) {
3412            $retVal .= "?" . join(";", @parmList);
3413      }      }
3414        # Return the result.
3415        return $retVal;
3416  }  }
3417    
3418  =head3 ChDir  =head3 ApplyURL
3419    
3420  C<< ChDir($dirName); >>      Tracer::ApplyURL($table, $target, $url);
3421    
3422  Change to the specified directory.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3423    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3424    URL column will be deleted by this process and the target column will be HTML-escaped.
3425    
3426    This provides a simple way to process the results of a database query into something
3427    displayable by combining a URL with text.
3428    
3429  =over 4  =over 4
3430    
3431  =item dirName  =item table
3432    
3433  Name of the directory to which we want to change.  Reference to a list of lists. The elements in the containing list will be updated by
3434    this method.
3435    
3436    =item target
3437    
3438    The index of the column to be converted into HTML.
3439    
3440    =item url
3441    
3442    The index of the column containing the URL. Note that the URL must have a recognizable
3443    C<http:> at the beginning.
3444    
3445  =back  =back
3446    
3447  =cut  =cut
3448    
3449  sub ChDir {  sub ApplyURL {
3450      my ($dirName) = @_;      # Get the parameters.
3451      if (! -d $dirName) {      my ($table, $target, $url) = @_;
3452          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the table.
3453      } else {      for my $row (@{$table}) {
3454          Trace("Changing to directory $dirName.") if T(4);          # Apply the URL to the target cell.
3455          my $okFlag = chdir $dirName;          $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3456          if (! $okFlag) {          # Delete the URL from the row.
3457              Confess("Error switching to directory $dirName.");          delete $row->[$url];
         }  
3458      }      }
3459  }  }
3460    
3461  =head3 SetPermissions  =head3 CombineURL
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
3462    
3463  Set the permissions for a directory and all the files and folders inside it.      my $combinedHtml = Tracer::CombineURL($text, $url);
 In addition, the group ownership will be changed to the specified value.  
3464    
3465  This method is more vulnerable than most to permission and compatability  This method will convert the specified text into HTML hyperlinked to the specified
3466  problems, so it does internal error recovery.  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3467    is defined and begins with an C<http:> header.
3468    
3469  =over 4  =over 4
3470    
3471  =item dirName  =item text
3472    
3473  Name of the directory to process.  Text to return. This will be HTML-escaped automatically.
3474    
3475  =item group  =item url
3476    
3477  Name of the group to be assigned.  A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3478    will be returned without any hyperlinking.
3479    
3480  =item mask  =item RETURN
3481    
3482  Permission mask. Bits that are C<1> in this mask will be ORed into the  Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3483  permission bits of any file or directory that does not already have them  doesn't look right, the HTML-escaped text will be returned without any further
3484  set to 1.  modification.
3485    
3486  =item otherMasks  =back
3487    
3488  Map of search patterns to permission masks. If a directory name matches  =cut
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3489    
3490      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  sub CombineURL {
3491        # Get the parameters.
3492        my ($text, $url) = @_;
3493        # Declare the return variable.
3494        my $retVal = CGI::escapeHTML($text);
3495        # Verify the URL.
3496        if (defined($url) && $url =~ m!http://!i) {
3497            # It's good, so we apply it to the text.
3498            $retVal = "<a href=\"$url\">$retVal</a>";
3499        }
3500        # Return the result.
3501        return $retVal;
3502    }
3503    
3504  The list is ordered, so the following would use 0777 for C<tmp1> and  =head3 Cmp
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3505    
3506      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,      my $cmp = Tracer::Cmp($a, $b);
                                                    '^tmp' => 0666);  
3507    
3508  Note that the pattern matches are all case-insensitive, and only directory  This method performs a universal sort comparison. Each value coming in is
3509  names are matched, not file names.  separated into a leading text part and a trailing number part. The text
3510    part is string compared, and if both parts are equal, then the number
3511    parts are compared numerically. A stream of just numbers or a stream of
3512    just strings will sort correctly, and a mixed stream will sort with the
3513    numbers first. Strings with a label and a number will sort in the
3514    expected manner instead of lexically.
3515    
3516    =over 4
3517    
3518    =item a
3519    
3520    First item to compare.
3521    
3522    =item b
3523    
3524    Second item to compare.
3525    
3526    =item RETURN
3527    
3528    Returns a negative number if the first item should sort first (is less), a positive
3529    number if the first item should sort second (is greater), and a zero if the items are
3530    equal.
3531    
3532  =back  =back
3533    
3534  =cut  =cut
3535    
3536  sub SetPermissions {  sub Cmp {
3537      # Get the parameters.      # Get the parameters.
3538      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($a, $b) = @_;
3539      # Set up for error recovery.      # Declare the return value.
3540      eval {      my $retVal;
3541          # Switch to the specified directory.      # Check for nulls.
3542          ChDir($dirName);      if (! defined($a)) {
3543          # Get the group ID.          $retVal = (! defined($b) ? 0 : -1);
3544          my $gid = getgrnam($group);      } elsif (! defined($b)) {
3545          # Get the mask for tracing.          $retVal = 1;
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/(.+)$!) {  
                 $simpleName = $1;  
             }  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
3546              } else {              } else {
3547                  # Here we can process normally. Get all of the non-hidden members.          # Here we have two real values. Parse the two strings.
3548                  my @submems = OpenDir($dir, 1);          $a =~ /^(\D*)(\d*)$/;
3549                  for my $submem (@submems) {          my $aParsed = [$1, $2];
3550                      # Get the full name.          $b =~ /^(\D*)(\d*)$/;
3551                      my $thisMem = "$dir/$submem";          my $bParsed = [$1, $2];
3552                      Trace("Checking member $thisMem.") if T(4);          # Compare the string parts.
3553                      $lookCount++;          $retVal = $aParsed->[0] cmp $bParsed->[0];