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revision 1.52, Wed Jun 14 01:12:42 2006 UTC revision 1.110, Tue Sep 23 21:48:27 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        use Fcntl ':flock';
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
46  =head2 Introduction  =head2 Tracing
47    
48  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
49  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.
50  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,
51  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
52  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
53  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
54  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
55  appear. To generate a trace message, use the following syntax.  appear.
56    
57    =head3 Putting Trace Messages in Your Code
58    
59  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
60    
61        Trace($message) if T(errors => 4);
62    
63  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>
64  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
65    
66  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
67    
68  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
69    
# Line 58  Line 71 
71  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
72  active and the trace level is 2 or more.  active and the trace level is 2 or more.
73    
74  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
75    
76    In scripts, where no package name is available, the category defaults to C<main>.
77    
78    =head3 Custom Tracing
79    
80    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81    the preferred method, but a knowledge of how custom tracing works can make the more modern
82    L</Emergency Tracing> easier to understand.
83    
84  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,
85  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
86  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
87    
88  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
89    
90  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
91  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
92    
93  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
94  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
95  useful in a CGI environment.  useful in a CGI environment.
96    
97  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
98    
99  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
100  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
101  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
102  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
103  it easier to debug page formatting problems.  it easier to debug page formatting problems.
104    
105  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
106    a file at the same time. To trace to a file, specify the filename with an output character in front
107    of it.
108    
109        TSetup('4 SQL', ">$fileName");
110    
111    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112    bracket.
113    
114        TSetup('3 *', "+>$fileName");
115    
116  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>.
117  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.
118  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
119  being used out in the field.  being used out in the field.
120    
121    =head3 Trace Levels
122    
123  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
124  a suggestion.  a suggestion.
125    
# Line 118  Line 150 
150    
151  =back  =back
152    
153    The format of trace messages is important because some utilities analyze trace files.
154    There are three fields-- the time stamp, the category name, and the text.
155    The time stamp is between square brackets and the category name between angle brackets.
156    After the category name there is a colon (C<:>) followed by the message text.
157    If the square brackets or angle brackets are missing, then the trace management
158    utilities assume that they are encountering a set of pre-formatted lines.
159    
160    Note, however, that this formatting is done automatically by the tracing functions. You
161    only need to know about it if you want to parse a trace file.
162    
163    =head3 Emergency Tracing
164    
165    Sometimes, you need a way for tracing to happen automatically without putting parameters
166    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168    that you specify a tracing key. For command-line tools, the key is
169    taken from the C<TRACING> environment variable. For web services, the key is taken from
170    a cookie. Either way, the key tells the tracing facility who you are, so that you control
171    the tracing in your environment without stepping on other users.
172    
173    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
174    generate one for you.
175    
176    You can activate and de-activate emergency tracing from the debugging control panel, as
177    well as display the trace file itself.
178    
179    To enable emergency tracing in your code, call
180    
181        ETracing($cgi)
182    
183    from a web script and
184    
185        ETracing()
186    
187    from a command-line script.
188    
189    The web script will look for the tracing key in the cookies, and the command-line
190    script will look for it in the C<TRACING> environment variable. If you are
191    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192    will be configured automatically.
193    
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199  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
200                              # standard output                              # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                              # hash of active category names                              # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
205                              # messages                              # messages
206  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
207  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
210  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215    =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228  =head2 Public Methods  sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 188  Line 281 
281          }          }
282      }      }
283      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
284      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
288          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
289              $TeeFlag = 1;              $TeeFlag = 1;
290              $target = substr($target, 1);              $target = substr($target, 1);
291          }          }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294              open TRACEFILE, $target;              open TRACEFILE, $target;
295              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296              close TRACEFILE;              close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298              $Destination = ">$target";              $Destination = ">$target";
299          } else {          } else {
300              $Destination = $target;              $Destination = $target;
# Line 210  Line 306 
306      $SetupCount++;      $SetupCount++;
307  }  }
308    
309  =head3 StandardSetup  =head3 SetLevel
310    
311  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
312    
313  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.  
314    
315  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.  
316    
317  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  
318    
319      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
320    
321  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.  
322    
323  =over 4  =cut
324    
325  =item FIG  sub SetLevel {
326        $TraceLevel = $_[0];
327    }
328    
329  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
330    
331  =item SQL      my $time = Tracer::ParseDate($dateString);
332    
333  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
334    and parses it into a number. The string must be vaguely date-like or it will
335    return an undefined value. Our requirement is that a month and day be
336    present and that three pieces of the date string (time of day, month and day,
337    year) be separated by likely delimiters, such as spaces, commas, and such-like.
338    
339  =item Tracer  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  Traces error messages and call stacks.  The year must be exactly four digits.
343    
344  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
345    equally innocuous. This means, however, that a sufficiently long sentence with date-like
346    parts in it may be interpreted as a date. Hopefully this will not be a problem.
347    
348  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.  
349    
350      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
351    
352  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  
353    
354  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.  
355    
356      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
357    
358  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
359    
360  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
361  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.  
362    
363  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
364    
365  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
366    
367      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
368                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377                                Oct =>  9, October  =>   9, '10' =>  9,
378                                Nov => 10, November =>  10, '11' => 10,
379                                Dec => 11, December =>  11, '12' => 11
380                            };
381    
382    sub ParseDate {
383        # Get the parameters.
384        my ($dateString) = @_;
385        # Declare the return variable.
386        my $retVal;
387        # Find the month and day of month. There are two ways that can happen. We check for the
388        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389        # won't be fooled into thinking the month is Sunday.
390        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391            my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                } else {
404                    # Get the default year, which is this one. Note we must convert it to
405                    # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410            }
411        }
412        # Return the result.
413        return $retVal;
414    }
415    
416  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
417    
418  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
419    
420      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
421    
422  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
423    
424      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
425    
426  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.  
427    
428  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  
429    
430      -user=Bruce -background  =cut
431    
432  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
433  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
434  simplify starting a command in the background.      my ($fileName) = @_;
435        # Open the file as the standard error output.
436        open STDERR, '>', $fileName;
437    }
438    
439  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
440    
441      TransactFeatures -h      Trace($message);
442    
443  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
444    any prior call to B<TSetup>.
445    
446      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  
447    
448  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,  
449    
450      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
451    
452  would set the default trace level to 0 instead of 2, while  =back
453    
454      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
455    
456  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
457  standard output.      # Get the parameters.
458        my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467        # Get the timestamp.
468        my $timeStamp = Now();
469        # Build the prefix.
470        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472        # Format the message.
473        my $formatted = "$prefix $stripped";
474        # Process according to the destination.
475        if ($Destination eq "TEXT") {
476            # Write the message to the standard output.
477            print "$formatted\n";
478        } elsif ($Destination eq "ERROR") {
479            # Write the message to the error output. Here, we want our prefix fields.
480            print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486        } elsif ($Destination eq "QUEUE") {
487            # Push the message into the queue.
488            push @Queue, "$formatted";
489        } elsif ($Destination eq "HTML") {
490            # Convert the message to HTML and write it to the standard output.
491            my $escapedMessage = CGI::escapeHTML($stripped);
492            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493        } elsif ($Destination =~ m/^>>/) {
494            # Write the trace message to an output file.
495            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496            print TRACING "$formatted\n";
497            close TRACING;
498            # If the Tee flag is on, echo it to the standard output.
499            if ($TeeFlag) {
500                print "$formatted\n";
501            }
502        }
503    }
504    
505  The parameters to this method are as follows.  =head3 T
506    
507  =over 4      my $switch = T($category, $traceLevel);
508    
509  =item categories      or
510    
511  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.  
512    
513  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
514    is active, else FALSE. If no category is specified, the caller's package name is used.
515    
516  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).  
517    
518  =item parmHelp  =item category
519    
520  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
521  if the user specifies the C<-h> option.  used.
522    
523  =item argv  =item traceLevel
524    
525  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
526    
527  =item RETURN  =item RETURN
528    
529  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.  
530    
531  =back  =back
532    
533  =cut  =cut
534    
535  sub StandardSetup {  sub T {
536        # Declare the return variable.
537        my $retVal = 0;
538        # Only proceed if tracing is turned on.
539        if ($Destination ne "NONE") {
540      # Get the parameters.      # Get the parameters.
541      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
542      # Add the tracing options.          if (!defined $traceLevel) {
543      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
544          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
545      }              # omitted, the first parameter will be the tracelevel. So, the
546      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
547      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
548      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
549      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
550      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
551      # contains the default values rather than the default value              if (!$package) {
552      # and the description. While we're at it, we'll memorize the                  $category = "main";
553      # length of the longest option name.              } else {
554      my $longestName = 0;                  my @cats = split /::/, $package;
555                    $category = $cats[$#cats];
556                }
557            }
558            # Save the category name and level.
559            $LastCategory = $category;
560            $LastLevel = $traceLevel;
561            # Convert it to lower case before we hash it.
562            $category = lc $category;
563            # Validate the trace level.
564            if (ref $traceLevel) {
565                Confess("Bad trace level.");
566            } elsif (ref $TraceLevel) {
567                Confess("Bad trace config.");
568            }
569            # Make the check. Note that level 0 shows even if the category is turned off.
570            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
571        }
572        # Return the computed result.
573        return $retVal;
574    }
575    
576    =head3 QTrace
577    
578        my $data = QTrace($format);
579    
580    Return the queued trace data in the specified format.
581    
582    =over 4
583    
584    =item format
585    
586    C<html> to format the data as an HTML list, C<text> to format it as straight text.
587    
588    =back
589    
590    =cut
591    
592    sub QTrace {
593        # Get the parameter.
594        my ($format) = @_;
595        # Create the return variable.
596        my $retVal = "";
597        # Only proceed if there is an actual queue.
598        if (@Queue) {
599            # Process according to the format.
600            if ($format =~ m/^HTML$/i) {
601                # Convert the queue into an HTML list.
602                $retVal = "<ul>\n";
603                for my $line (@Queue) {
604                    my $escapedLine = CGI::escapeHTML($line);
605                    $retVal .= "<li>$escapedLine</li>\n";
606                }
607                $retVal .= "</ul>\n";
608            } elsif ($format =~ m/^TEXT$/i) {
609                # Convert the queue into a list of text lines.
610                $retVal = join("\n", @Queue) . "\n";
611            }
612            # Clear the queue.
613            @Queue = ();
614        }
615        # Return the formatted list.
616        return $retVal;
617    }
618    
619    =head3 Confess
620    
621        Confess($message);
622    
623    Trace the call stack and abort the program with the specified message. When used with
624    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625    So, for example
626    
627        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628    
629    Will abort the program with a stack trace if the value of C<$recNum> is negative.
630    
631    =over 4
632    
633    =item message
634    
635    Message to include in the trace.
636    
637    =back
638    
639    =cut
640    
641    sub Confess {
642        # Get the parameters.
643        my ($message) = @_;
644        # Set up the category and level.
645        $LastCategory = "(confess)";
646        $LastLevel = 0;
647        if (! defined($FIG_Config::no_tool_hdr)) {
648            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650            # Only proceed if the tool header file is actually present.
651            if (-f $toolHeaderFile) {
652                my $fh;
653                if (open $fh, "<$toolHeaderFile") {
654                    my @lines = <$fh>;
655                    Trace("Tool header has " . scalar(@lines) . " lines.");
656                }
657            }
658        }
659        # Trace the call stack.
660        Cluck($message);
661        # Abort the program.
662        croak(">>> $message");
663    }
664    
665    =head3 SaveCGI
666    
667        Tracer::SaveCGI($cgi);
668    
669    This method saves the CGI object but does not activate emergency tracing.
670    It is used to allow L</Warn> to work in situations where emergency
671    tracing is contra-indicated (e.g. the wiki).
672    
673    =over 4
674    
675    =item cgi
676    
677    Active CGI query object.
678    
679    =back
680    
681    =cut
682    
683    sub SaveCGI {
684        $SavedCGI = $_[0];
685    }
686    
687    =head3 Warn
688    
689        Warn($message, @options);
690    
691    This method traces an important message. If an RSS feed is configured
692    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693    then the message will be echoed to the feed. In general, a tracing
694    destination of C<WARN> indicates that the caller is running as a web
695    service in a production environment; however, this is not a requirement.
696    
697    To force warnings into the RSS feed even when the tracing destination
698    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699    configured automatically when L</StandardSetup> is used.
700    
701    The L</Cluck> method calls this one for its final message. Since
702    L</Confess> calls L</Cluck>, this means that any error which is caught
703    and confessed will put something in the feed. This insures that someone
704    will be alerted relatively quickly when a failure occurs.
705    
706    =over 4
707    
708    =item message
709    
710    Message to be traced.
711    
712    =item options
713    
714    A list containing zero or more options.
715    
716    =back
717    
718    The permissible options are as follows.
719    
720    =over 4
721    
722    =item noStack
723    
724    If specified, then the stack trace is not included in the output.
725    
726    =back
727    
728    =cut
729    
730    sub Warn {
731        # Get the parameters.
732        my $message = shift @_;
733        my %options = map { $_ => 1 } @_;
734        # Save $@;
735        my $savedError = $@;
736        # Trace the message.
737        Trace($message);
738        # This will contain the lock handle. If it's defined, it means we need to unlock.
739        my $lock;
740        # Check for feed forcing.
741        my $forceFeed = exists $Categories{feed};
742        # An error here would be disastrous. Note that if debug mode is specified,
743        # we do this stuff even in a test environment.
744        eval {
745            # Do we need to put this in the RSS feed?
746            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
747                # Probably. We need to check first, however, to see if it's from an
748                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
749                my $key = "127.0.0.1";
750                if (defined $SavedCGI) {
751                    # Get the IP address.
752                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
753                }
754                # Is the IP address in the ignore list?
755                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
756                if (! $found) {
757                    # No. We're good. We now need to compute the date, the link, and the title.
758                    # First, the date, in a very specific format.
759                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
760                        (tz_local_offset() / 30);
761                    # Environment data goes in here. We start with the date.
762                    my $environment = "$date.  ";
763                    # If we need to recap the message (because it's too long to be a title), we'll
764                    # put it in here.
765                    my $recap;
766                    # Copy the message and remove excess space.
767                    my $title = $message;
768                    $title =~ s/\s+/ /gs;
769                    # If it's too long, we have to split it up.
770                    if (length $title > 60) {
771                        # Put the full message in the environment string.
772                        $recap = $title;
773                        # Excerpt it as the title.
774                        $title = substr($title, 0, 50) . "...";
775                    }
776                    # If we have a CGI object, then this is a web error. Otherwise, it's
777                    # command-line.
778                    if (defined $SavedCGI) {
779                        # We're in a web service. The environment is the user's IP, and the link
780                        # is the URL that got us here.
781                        $environment .= "Event Reported at IP address $key process $$.";
782                        my $url = $SavedCGI->self_url();
783                        # We need the user agent string and (if available) the referrer.
784                        # The referrer will be the link.
785                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
786                        if ($ENV{HTTP_REFERER}) {
787                            my $link = $ENV{HTTP_REFERER};
788                            $environment .= " referred from <a href=\"$link\">$link</a>.";
789                        } else {
790                            $environment .= " referrer unknown.";
791                        }
792                        # Close off the sentence with the original link.
793                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
794                    } else {
795                        # No CGI object, so we're a command-line tool. Use the tracing
796                        # key and the PID as the user identifier, and add the command.
797                        my $key = EmergencyKey();
798                        $environment .= "Event Reported by $key process $$.";
799                        if ($CommandLine) {
800                            # We're in a StandardSetup script, so we have the real command line.
801                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
802                        } elsif ($ENV{_}) {
803                            # We're in a BASH script, so the command has been stored in the _ variable.
804                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
805                        }
806                    }
807                    # Build a GUID. We use the current time, the title, and the process ID,
808                    # then digest the result.
809                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
810                    # Finally, the description. This is a stack trace plus various environmental stuff.
811                    # The trace is optional.
812                    my $stackTrace;
813                    if ($options{noStack}) {
814                        $stackTrace = "";
815                    } else {
816                        my @trace = LongMess();
817                        # Only proceed if we got something back.
818                        if (scalar(@trace) > 0) {
819                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
820                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
821                        }
822                    }
823                    # We got the stack trace. Now it's time to put it all together.
824                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
825                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
826                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
827                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
828                    # our <br>s and <pre>s are used to format the description.
829                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
830                    my $description = "$recap$environment  $stackTrace";
831                    # Okay, we have all the pieces. Create a hash of the new event.
832                    my $newItem = { title => $title,
833                                    description => $description,
834                                    category => $LastCategory,
835                                    pubDate => $date,
836                                    guid => $guid,
837                                  };
838                    # We need XML capability for this.
839                    require XML::Simple;
840                    # The RSS document goes in here.
841                    my $rss;
842                    # Get the name of the RSS file. It's in the FIG temporary directory.
843                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
844                    # Open the config file and lock it.
845                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
846                    flock $lock, LOCK_EX;
847                    # Does it exist?
848                    if (-s $fileName) {
849                        # Slurp it in.
850                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
851                    } else {
852                        my $size = -s $fileName;
853                        # Create an empty channel.
854                        $rss = {
855                            channel => {
856                                title => 'NMPDR Warning Feed',
857                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
858                                description => "Important messages regarding the status of the NMPDR.",
859                                generator => "NMPDR Trace Facility",
860                                docs => "http://blogs.law.harvard.edu/tech/rss",
861                                item => []
862                            },
863                        };
864                    }
865                    # Get the channel object.
866                    my $channel = $rss->{channel};
867                    # Update the last-build date.
868                    $channel->{lastBuildDate} = $date;
869                    # Get the item array.
870                    my $items = $channel->{item};
871                    # Insure it has only 100 entries.
872                    while (scalar @{$items} > 100) {
873                        pop @{$items};
874                    }
875                    # Add our new item at the front.
876                    unshift @{$items}, $newItem;
877                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
878                    # the requirements for those.
879                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
880                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
881                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
882                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
883                    # We don't use Open here because we can't afford an error.
884                    if (open XMLOUT, ">$fileName") {
885                        print XMLOUT $xml;
886                        close XMLOUT;
887                    }
888                }
889            }
890        };
891        if ($@) {
892            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
893            # (which is a good thing).
894            my $error = $@;
895            Trace("Feed Error: $error") if T(Feed => 0);
896        }
897        # Be sure to unlock.
898        if ($lock) {
899            flock $lock, LOCK_UN;
900            undef $lock;
901        }
902        # Restore the error message.
903        $@ = $savedError;
904    }
905    
906    
907    
908    
909    =head3 Assert
910    
911        Assert($condition1, $condition2, ... $conditionN);
912    
913    Return TRUE if all the conditions are true. This method can be used in conjunction with
914    the OR operator and the L</Confess> method as a debugging assert.
915    So, for example
916    
917        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
918    
919    Will abort the program with a stack trace if the value of C<$recNum> is negative.
920    
921    =cut
922    sub Assert {
923        my $retVal = 1;
924        LOOP: for my $condition (@_) {
925            if (! $condition) {
926                $retVal = 0;
927                last LOOP;
928            }
929        }
930        return $retVal;
931    }
932    
933    =head3 Cluck
934    
935        Cluck($message);
936    
937    Trace the call stack. Note that for best results, you should qualify the call with a
938    trace condition. For example,
939    
940        Cluck("Starting record parse.") if T(3);
941    
942    will only trace the stack if the trace level for the package is 3 or more.
943    
944    =over 4
945    
946    =item message
947    
948    Message to include in the trace.
949    
950    =back
951    
952    =cut
953    
954    sub Cluck {
955        # Get the parameters.
956        my ($message) = @_;
957        # Trace what's happening.
958        Trace("Stack trace for event: $message");
959        # Get the stack trace.
960        my @trace = LongMess();
961        # Convert the trace to a series of messages.
962        for my $line (@trace) {
963            # Replace the tab at the beginning with spaces.
964            $line =~ s/^\t/    /;
965            # Trace the line.
966            Trace($line);
967        }
968        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
969        Warn($message);
970    }
971    
972    =head3 LongMess
973    
974        my @lines = Tracer::LongMess();
975    
976    Return a stack trace with all tracing methods removed. The return will be in the form of a list
977    of message strings.
978    
979    =cut
980    
981    sub LongMess {
982        # Declare the return variable.
983        my @retVal = ();
984        my $confession = longmess("");
985        for my $line (split /\s*\n/, $confession) {
986            unless ($line =~ /Tracer\.pm/) {
987                # Here we have a line worth keeping. Push it onto the result list.
988                push @retVal, $line;
989            }
990        }
991        # Return the result.
992        return @retVal;
993    }
994    
995    =head3 ETracing
996    
997        ETracing($parameter);
998    
999    Set up emergency tracing. Emergency tracing is tracing that is turned
1000    on automatically for any program that calls this method. The emergency
1001    tracing parameters are stored in a a file identified by a tracing key.
1002    If this method is called with a CGI object, then the tracing key is
1003    taken from a cookie. If it is called with no parameters, then the tracing
1004    key is taken from an environment variable. If it is called with a string,
1005    the tracing key is that string.
1006    
1007    =over 4
1008    
1009    =item parameter
1010    
1011    A parameter from which the tracing key is computed. If it is a scalar,
1012    that scalar is used as the tracing key. If it is a CGI object, the
1013    tracing key is taken from the C<IP> cookie. If it is omitted, the
1014    tracing key is taken from the C<TRACING> environment variable. If it
1015    is a CGI object and emergency tracing is not on, the C<Trace> and
1016    C<TF> parameters will be used to determine the type of tracing.
1017    
1018    =back
1019    
1020    =cut
1021    
1022    sub ETracing {
1023        # Get the parameter.
1024        my ($parameter) = @_;
1025        # Check for CGI mode.
1026        if (defined $parameter && ref $parameter eq 'CGI') {
1027            $SavedCGI = $parameter;
1028        } else {
1029            $SavedCGI = undef;
1030        }
1031        # Default to no tracing except errors.
1032        my ($tracing, $dest) = ("0", "WARN");
1033        # Check for emergency tracing.
1034        my $tkey = EmergencyKey($parameter);
1035        my $emergencyFile = EmergencyFileName($tkey);
1036        if (-e $emergencyFile) {
1037            # We have the file. Read in the data.
1038            my @tracing = GetFile($emergencyFile);
1039            # Pull off the time limit.
1040            my $expire = shift @tracing;
1041            # Convert it to seconds.
1042            $expire *= 3600;
1043            # Check the file data.
1044            my $stat = stat($emergencyFile);
1045            my ($now) = gettimeofday;
1046            if ($now - $stat->mtime > $expire) {
1047                # Delete the expired file.
1048                unlink $emergencyFile;
1049            } else {
1050                # Emergency tracing is on. Pull off the destination and
1051                # the trace level;
1052                $dest = shift @tracing;
1053                my $level = shift @tracing;
1054                # Convert the destination to a real tracing destination.
1055                # temp directory.
1056                $dest = EmergencyTracingDest($tkey, $dest);
1057                # Insure Tracer is specified.
1058                my %moduleHash = map { $_ => 1 } @tracing;
1059                $moduleHash{Tracer} = 1;
1060                # Set the trace parameter.
1061                $tracing = join(" ", $level, sort keys %moduleHash);
1062            }
1063        } elsif (defined $SavedCGI) {
1064            # There's no emergency tracing, but we have a CGI object, so check
1065            # for tracing from the form parameters.
1066            if ($SavedCGI->param('Trace')) {
1067                # Here the user has requested tracing via a form.
1068                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1069                $tracing = $SavedCGI->param('Trace') . " Tracer";
1070            }
1071        }
1072        # Setup the tracing we've determined from all the stuff above.
1073        TSetup($tracing, $dest);
1074        # Check to see if we're a web script.
1075        if (defined $SavedCGI) {
1076            # Yes we are. Trace the form and environment data.
1077            TraceParms($SavedCGI);
1078            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1079            # emitted by the script in its raw form.
1080            if (T(Raw => 3)) {
1081                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1082            }
1083        }
1084    }
1085    
1086    =head3 EmergencyFileName
1087    
1088        my $fileName = Tracer::EmergencyFileName($tkey);
1089    
1090    Return the emergency tracing file name. This is the file that specifies
1091    the tracing information.
1092    
1093    =over 4
1094    
1095    =item tkey
1096    
1097    Tracing key for the current program.
1098    
1099    =item RETURN
1100    
1101    Returns the name of the file to contain the emergency tracing information.
1102    
1103    =back
1104    
1105    =cut
1106    
1107    sub EmergencyFileName {
1108        # Get the parameters.
1109        my ($tkey) = @_;
1110        # Compute the emergency tracing file name.
1111        return "$FIG_Config::temp/Emergency$tkey.txt";
1112    }
1113    
1114    =head3 EmergencyFileTarget
1115    
1116        my $fileName = Tracer::EmergencyFileTarget($tkey);
1117    
1118    Return the emergency tracing target file name. This is the file that receives
1119    the tracing output for file-based tracing.
1120    
1121    =over 4
1122    
1123    =item tkey
1124    
1125    Tracing key for the current program.
1126    
1127    =item RETURN
1128    
1129    Returns the name of the file to contain the trace output.
1130    
1131    =back
1132    
1133    =cut
1134    
1135    sub EmergencyFileTarget {
1136        # Get the parameters.
1137        my ($tkey) = @_;
1138        # Compute the emergency tracing file name.
1139        return "$FIG_Config::temp/trace$tkey.log";
1140    }
1141    
1142    =head3 EmergencyTracingDest
1143    
1144        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1145    
1146    This method converts an emergency tracing destination to a real
1147    tracing destination. The main difference is that if the
1148    destination is C<FILE> or C<APPEND>, we convert it to file
1149    output. If the destination is C<DUAL>, we convert it to file
1150    and standard output.
1151    
1152    =over 4
1153    
1154    =item tkey
1155    
1156    Tracing key for this environment.
1157    
1158    =item myDest
1159    
1160    Destination from the emergency tracing file.
1161    
1162    =item RETURN
1163    
1164    Returns a destination that can be passed into L</TSetup>.
1165    
1166    =back
1167    
1168    =cut
1169    
1170    sub EmergencyTracingDest {
1171        # Get the parameters.
1172        my ($tkey, $myDest) = @_;
1173        # Declare the return variable.
1174        my $retVal = $myDest;
1175        # Process according to the destination value.
1176        if ($myDest eq 'FILE') {
1177            $retVal = ">" . EmergencyFileTarget($tkey);
1178        } elsif ($myDest eq 'APPEND') {
1179            $retVal = ">>" . EmergencyFileTarget($tkey);
1180        } elsif ($myDest eq 'DUAL') {
1181            $retVal = "+>" . EmergencyFileTarget($tkey);
1182        } elsif ($myDest eq 'WARN') {
1183            $retVal = "WARN";
1184        }
1185        # Return the result.
1186        return $retVal;
1187    }
1188    
1189    =head3 Emergency
1190    
1191        Emergency($key, $hours, $dest, $level, @modules);
1192    
1193    Turn on emergency tracing. This method is normally invoked over the web from
1194    a debugging console, but it can also be called by the C<trace.pl> script.
1195    The caller specifies the duration of the emergency in hours, the desired tracing
1196    destination, the trace level, and a list of the trace modules to activate.
1197    For the length of the duration, when a program in an environment with the
1198    specified tracing key active invokes a Sprout CGI script, tracing will be
1199    turned on automatically. See L</TSetup> for more about tracing setup and
1200    L</ETracing> for more about emergency tracing.
1201    
1202    =over 4
1203    
1204    =item tkey
1205    
1206    The tracing key. This is used to identify the control file and the trace file.
1207    
1208    =item hours
1209    
1210    Number of hours to keep emergency tracing alive.
1211    
1212    =item dest
1213    
1214    Tracing destination. If no path information is specified for a file
1215    destination, it is put in the FIG temporary directory.
1216    
1217    =item level
1218    
1219    Tracing level. A higher level means more trace messages.
1220    
1221    =item modules
1222    
1223    A list of the tracing modules to activate.
1224    
1225    =back
1226    
1227    =cut
1228    
1229    sub Emergency {
1230        # Get the parameters.
1231        my ($tkey, $hours, $dest, $level, @modules) = @_;
1232        # Create the emergency file.
1233        my $specFile = EmergencyFileName($tkey);
1234        my $outHandle = Open(undef, ">$specFile");
1235        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1236    }
1237    
1238    =head3 EmergencyKey
1239    
1240        my $tkey = EmergencyKey($parameter);
1241    
1242    Return the Key to be used for emergency tracing. This could be an IP address,
1243     a session ID, or a user name, depending on the environment.
1244    
1245    =over 4
1246    
1247    =item parameter
1248    
1249    Parameter defining the method for finding the tracing key. If it is a scalar,
1250    then it is presumed to be the tracing key itself. If it is a CGI object, then
1251    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1252    taken from the C<TRACING> environment variable.
1253    
1254    =item RETURN
1255    
1256    Returns the key to be used for labels in emergency tracing.
1257    
1258    =back
1259    
1260    =cut
1261    
1262    sub EmergencyKey {
1263        # Get the parameters.
1264        my ($parameter) = @_;
1265        # Declare the return variable.
1266        my $retVal;
1267        # Determine the parameter type.
1268        if (! defined $parameter) {
1269            # Here we're supposed to check the environment. If that fails, we
1270            # get the effective login ID.
1271            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1272        } else {
1273            my $ptype = ref $parameter;
1274            if ($ptype eq 'CGI') {
1275                # Here we were invoked from a web page. Look for a cookie.
1276                $retVal = $parameter->cookie('IP');
1277            } elsif (! $ptype) {
1278                # Here the key was passed in.
1279                $retVal = $parameter;
1280            }
1281        }
1282        # If no luck finding a key, use the PID.
1283        if (! defined $retVal) {
1284            $retVal = $$;
1285        }
1286        # Return the result.
1287        return $retVal;
1288    }
1289    
1290    
1291    =head3 TraceParms
1292    
1293        Tracer::TraceParms($cgi);
1294    
1295    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1296    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1297    
1298    =over 4
1299    
1300    =item cgi
1301    
1302    CGI query object containing the parameters to trace.
1303    
1304    =back
1305    
1306    =cut
1307    
1308    sub TraceParms {
1309        # Get the parameters.
1310        my ($cgi) = @_;
1311        if (T(CGI => 2)) {
1312            # Here we trace the GET-style URL for the script.
1313            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1314        }
1315        if (T(CGI => 3)) {
1316            # Here we want to trace the parameter data.
1317            my @names = $cgi->param;
1318            for my $parmName (sort @names) {
1319                # Note we skip the Trace parameters, which are for our use only.
1320                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1321                    my @values = $cgi->param($parmName);
1322                    Trace("[CGI] $parmName = " . join(", ", @values));
1323                }
1324            }
1325            # Display the request method.
1326            my $method = $cgi->request_method();
1327            Trace("Method: $method");
1328        }
1329        if (T(CGI => 4)) {
1330            # Here we want the environment data too.
1331            for my $envName (sort keys %ENV) {
1332                Trace("[ENV] $envName = $ENV{$envName}");
1333            }
1334        }
1335    }
1336    
1337    =head3 TraceImages
1338    
1339        Tracer::TraceImages($htmlString);
1340    
1341    Trace information about all of an html document's images. The tracing
1342    will be for type "IMG" at level 3. The image's source string
1343    will be displayed. This is generally either the URL of the image or
1344    raw data for the image itself. If the source is too long, only the first 300
1345    characters will be shown at trace level 3. The entire source will be shown,
1346    however, at trace level 4. This method is not very smart, and might catch
1347    Javascript code, but it is still useful when debugging the arcane
1348    behavior of images in multiple browser environments.
1349    
1350    =over 4
1351    
1352    =item htmlString
1353    
1354    HTML text for an outgoing web page.
1355    
1356    =back
1357    
1358    =cut
1359    
1360    sub TraceImages {
1361        # Only proceed if we're at the proper trace level.
1362        if (T(IMG => 3)) {
1363            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1364            # into a variable called "$htmlString". This is because we expect html strings to be
1365            # long, and don't want to copy them any more than we have to.
1366            Trace(length($_[0]) . " characters in web page.");
1367            # Loop through the HTML, culling image tags.
1368            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1369                # Extract the source string and determine whether or not it's too long.
1370                my $srcString = $1;
1371                my $pos = pos($_[0]) - length($srcString);
1372                my $excess = length($srcString) - 300;
1373                # We'll put the display string in here.
1374                my $srcDisplay = $srcString;
1375                # If it's a data string, split it at the comma.
1376                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1377                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1378                # a long string, however, we only show the first 300 characters.
1379                if ($excess > 0 && ! T(IMG => 4)) {
1380                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1381                }
1382                # Output the trace message.
1383                Trace("Image tag at position $pos:\n$srcDisplay");
1384            }
1385        }
1386    }
1387    
1388    =head2 Command-Line Utility Methods
1389    
1390    =head3 SendSMS
1391    
1392        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1393    
1394    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1395    user name, password, and API ID for the relevant account in the hash reference variable
1396    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1397    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1398    is C<2561022>, then the FIG_Config file must contain
1399    
1400        $phone =  { user => 'BruceTheHumanPet',
1401                    password => 'silly',
1402                    api_id => '2561022' };
1403    
1404    The original purpose of this method was to insure Bruce would be notified immediately when the
1405    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1406    when you call this method.
1407    
1408    The message ID will be returned if successful, and C<undef> if an error occurs.
1409    
1410    =over 4
1411    
1412    =item phoneNumber
1413    
1414    Phone number to receive the message, in international format. A United States phone number
1415    would be prefixed by "1". A British phone number would be prefixed by "44".
1416    
1417    =item msg
1418    
1419    Message to send to the specified phone.
1420    
1421    =item RETURN
1422    
1423    Returns the message ID if successful, and C<undef> if the message could not be sent.
1424    
1425    =back
1426    
1427    =cut
1428    
1429    sub SendSMS {
1430        # Get the parameters.
1431        my ($phoneNumber, $msg) = @_;
1432        # Declare the return variable. If we do not change it, C<undef> will be returned.
1433        my $retVal;
1434        # Only proceed if we have phone support.
1435        if (! defined $FIG_Config::phone) {
1436            Trace("Phone support not present in FIG_Config.") if T(1);
1437        } else {
1438            # Get the phone data.
1439            my $parms = $FIG_Config::phone;
1440            # Get the Clickatell URL.
1441            my $url = "http://api.clickatell.com/http/";
1442            # Create the user agent.
1443            my $ua = LWP::UserAgent->new;
1444            # Request a Clickatell session.
1445            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1446                                         password => $parms->{password},
1447                                         api_id => $parms->{api_id},
1448                                         to => $phoneNumber,
1449                                         text => $msg});
1450            # Check for an error.
1451            if (! $resp->is_success) {
1452                Trace("Alert failed.") if T(1);
1453            } else {
1454                # Get the message ID.
1455                my $rstring = $resp->content;
1456                if ($rstring =~ /^ID:\s+(.*)$/) {
1457                    $retVal = $1;
1458                } else {
1459                    Trace("Phone attempt failed with $rstring") if T(1);
1460                }
1461            }
1462        }
1463        # Return the result.
1464        return $retVal;
1465    }
1466    
1467    =head3 StandardSetup
1468    
1469        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1470    
1471    This method performs standard command-line parsing and tracing setup. The return
1472    values are a hash of the command-line options and a list of the positional
1473    parameters. Tracing is automatically set up and the command-line options are
1474    validated.
1475    
1476    This is a complex method that does a lot of grunt work. The parameters can
1477    be more easily understood, however, once they are examined individually.
1478    
1479    The I<categories> parameter is the most obtuse. It is a reference to a list of
1480    special-purpose tracing categories. Most tracing categories are PERL package
1481    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1482    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1483    
1484        ["Sprout", "SproutLoad", "ERDB"]
1485    
1486    This would cause trace messages in the specified three packages to appear in
1487    the output. There are two special tracing categories that are automatically
1488    handled by this method. In other words, if you used L</TSetup> you would need
1489    to include these categories manually, but if you use this method they are turned
1490    on automatically.
1491    
1492    =over 4
1493    
1494    =item SQL
1495    
1496    Traces SQL commands and activity.
1497    
1498    =item Tracer
1499    
1500    Traces error messages and call stacks.
1501    
1502    =back
1503    
1504    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1505    The trace level is specified using the C<-trace> command-line option. For example,
1506    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1507    all tracing at level 3.
1508    
1509        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1510    
1511    Standard tracing is output to the standard output and echoed to the file
1512    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1513    process ID. You can also specify the C<user> parameter to put a user ID
1514    instead of a process ID in the trace file name. So, for example
1515    
1516    The default trace level is 2. To get all messages, specify a trace level of 4.
1517    For a genome-by-genome update, use 3.
1518    
1519        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1520    
1521    would send the trace output to C<traceBruce.log> in the temporary directory.
1522    
1523    The I<options> parameter is a reference to a hash containing the command-line
1524    options, their default values, and an explanation of what they mean. Command-line
1525    options may be in the form of switches or keywords. In the case of a switch, the
1526    option value is 1 if it is specified and 0 if it is not specified. In the case
1527    of a keyword, the value is separated from the option name by an equal sign. You
1528    can see this last in the command-line example above.
1529    
1530    You can specify a different default trace level by setting C<$options->{trace}>
1531    prior to calling this method.
1532    
1533    An example at this point would help. Consider, for example, the command-line utility
1534    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1535    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1536    the following code.
1537    
1538        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1539                            { safe => [0, "use database transactions"],
1540                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1541                              start => [' ', "start with this genome"],
1542                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1543                            "<command> <transactionDirectory> <IDfile>",
1544                          @ARGV);
1545    
1546    
1547    The call to C<ParseCommand> specifies the default values for the options and
1548    stores the actual options in a hash that is returned as C<$options>. The
1549    positional parameters are returned in C<@parameters>.
1550    
1551    The following is a sample command line for C<TransactFeatures>.
1552    
1553        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1554    
1555    Single and double hyphens are equivalent. So, you could also code the
1556    above command as
1557    
1558        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1559    
1560    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1561    parameters, and would find themselves in I<@parameters> after executing the
1562    above code fragment. The tracing would be set to level 2, and the categories
1563    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1564    and C<DocUtils> was included because it came in within the first parameter
1565    to this method. The I<$options> hash would be
1566    
1567        { trace => 2, sql => 0, safe => 0,
1568          noAlias => 1, start => ' ', tblFiles => 0 }
1569    
1570    Use of C<StandardSetup> in this way provides a simple way of performing
1571    standard tracing setup and command-line parsing. Note that the caller is
1572    not even aware of the command-line switches C<-trace> and C<-sql>, which
1573    are used by this method to control the tracing. If additional tracing features
1574    need to be added in the future, they can be processed by this method without
1575    upsetting the command-line utilities.
1576    
1577    If the C<background> option is specified on the command line, then the
1578    standard and error outputs will be directed to files in the temporary
1579    directory, using the same suffix as the trace file. So, if the command
1580    line specified
1581    
1582        -user=Bruce -background
1583    
1584    then the trace output would go to C<traceBruce.log>, the standard output to
1585    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1586    simplify starting a command in the background.
1587    
1588    The user name is also used as the tracing key for L</Emergency Tracing>.
1589    Specifying a value of C<E> for the trace level causes emergency tracing to
1590    be used instead of custom tracing. If the user name is not specified,
1591    the tracing key is taken from the C<Tracing> environment variable. If there
1592    is no value for that variable, the tracing key will be computed from the active
1593    login ID.
1594    
1595    Since the default situation in StandardSetup is to trace to the standard
1596    output, errors that occur in command-line scripts will not generate
1597    RSS events. To force the events, use the C<warn> option.
1598    
1599        TransactFeatures -background -warn register ../xacts IDs.tbl
1600    
1601    Finally, if the special option C<-help> is specified, the option
1602    names will be traced at level 0 and the program will exit without processing.
1603    This provides a limited help capability. For example, if the user enters
1604    
1605        TransactFeatures -help
1606    
1607    he would see the following output.
1608    
1609        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1610            -trace    tracing level (default E)
1611            -sql      trace SQL commands
1612            -safe     use database transactions
1613            -noAlias  do not expect aliases in CHANGE transactions
1614            -start    start with this genome
1615            -tblFiles output TBL files containing the corrected IDs
1616    
1617    The caller has the option of modifying the tracing scheme by placing a value
1618    for C<trace> in the incoming options hash. The default value can be overridden,
1619    or the tracing to the standard output can be turned off by suffixing a minus
1620    sign to the trace level. So, for example,
1621    
1622        { trace => [0, "tracing level (default 0)"],
1623           ...
1624    
1625    would set the default trace level to 0 instead of E, while
1626    
1627        { trace => ["2-", "tracing level (default 2)"],
1628           ...
1629    
1630    would set the default to 2, but trace only to the log file, not to the
1631    standard output.
1632    
1633    The parameters to this method are as follows.
1634    
1635    =over 4
1636    
1637    =item categories
1638    
1639    Reference to a list of tracing category names. These should be names of
1640    packages whose internal workings will need to be debugged to get the
1641    command working.
1642    
1643    =item options
1644    
1645    Reference to a hash containing the legal options for the current command mapped
1646    to their default values and descriptions. The user can override the defaults
1647    by specifying the options as command-line switches prefixed by a hyphen.
1648    Tracing-related options may be added to this hash. If the C<-h> option is
1649    specified on the command line, the option descriptions will be used to
1650    explain the options. To turn off tracing to the standard output, add a
1651    minus sign to the value for C<trace> (see above).
1652    
1653    =item parmHelp
1654    
1655    A string that vaguely describes the positional parameters. This is used
1656    if the user specifies the C<-h> option.
1657    
1658    =item argv
1659    
1660    List of command line parameters, including the option switches, which must
1661    precede the positional parameters and be prefixed by a hyphen.
1662    
1663    =item RETURN
1664    
1665    Returns a list. The first element of the list is the reference to a hash that
1666    maps the command-line option switches to their values. These will either be the
1667    default values or overrides specified on the command line. The remaining
1668    elements of the list are the position parameters, in order.
1669    
1670    =back
1671    
1672    =cut
1673    
1674    sub StandardSetup {
1675        # Get the parameters.
1676        my ($categories, $options, $parmHelp, @argv) = @_;
1677        # Get the default tracing key.
1678        my $tkey = EmergencyKey();
1679        # Save the command line.
1680        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1681        # Add the tracing options.
1682        if (! exists $options->{trace}) {
1683            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1684        }
1685        $options->{sql} = [0, "turn on SQL tracing"];
1686        $options->{help} = [0, "display command-line options"];
1687        $options->{user} = [$tkey, "tracing key"];
1688        $options->{background} = [0, "spool standard and error output"];
1689        $options->{warn} = [0, "send errors to RSS feed"];
1690        # Create a parsing hash from the options hash. The parsing hash
1691        # contains the default values rather than the default value
1692        # and the description. While we're at it, we'll memorize the
1693        # length of the longest option name.
1694        my $longestName = 0;
1695      my %parseOptions = ();      my %parseOptions = ();
1696      for my $key (keys %{$options}) {      for my $key (keys %{$options}) {
1697          if (length $key > $longestName) {          if (length $key > $longestName) {
1698              $longestName = length $key;              $longestName = length $key;
1699          }          }
1700          $parseOptions{$key} = $options->{$key}->[0];          $parseOptions{$key} = $options->{$key}->[0];
1701        }
1702        # Parse the command line.
1703        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1704        # Get the logfile suffix.
1705        my $suffix = $retOptions->{user};
1706        # Check for background mode.
1707        if ($retOptions->{background}) {
1708            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1709            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1710            open STDOUT, ">$outFileName";
1711            open STDERR, ">$errFileName";
1712            # Check for phone support. If we have phone support and a phone number,
1713            # we want to turn it on.
1714            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1715                $retOptions->{phone} = $ENV{PHONE};
1716            }
1717        }
1718        # Now we want to set up tracing. First, we need to know if the user
1719        # wants emergency tracing.
1720        if ($retOptions->{trace} eq 'E') {
1721            ETracing($retOptions->{user});
1722        } else {
1723            # Here the tracing is controlled from the command line.
1724            my @cats = @{$categories};
1725            if ($retOptions->{sql}) {
1726                push @cats, "SQL";
1727            }
1728            if ($retOptions->{warn}) {
1729                push @cats, "Feed";
1730            }
1731            # Add the default categories.
1732            push @cats, "Tracer";
1733            # Next, we create the category string by joining the categories.
1734            my $cats = join(" ", @cats);
1735            # Check to determine whether or not the caller wants to turn off tracing
1736            # to the standard output.
1737            my $traceLevel = $retOptions->{trace};
1738            my $textOKFlag = 1;
1739            if ($traceLevel =~ /^(.)-/) {
1740                $traceLevel = $1;
1741                $textOKFlag = 0;
1742            }
1743            # Now we set up the trace mode.
1744            my $traceMode;
1745            # Verify that we can open a file in the FIG temporary directory.
1746            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1747            if (open TESTTRACE, ">$traceFileName") {
1748                # Here we can trace to a file.
1749                $traceMode = ">$traceFileName";
1750                if ($textOKFlag) {
1751                    # Echo to standard output if the text-OK flag is set.
1752                    $traceMode = "+$traceMode";
1753                }
1754                # Close the test file.
1755                close TESTTRACE;
1756            } else {
1757                # Here we can't trace to a file. Complain about this.
1758                warn "Could not open trace file $traceFileName: $!\n";
1759                # We trace to the standard output if it's
1760                # okay, and the error log otherwise.
1761                if ($textOKFlag) {
1762                    $traceMode = "TEXT";
1763                } else {
1764                    $traceMode = "WARN";
1765                }
1766            }
1767            # Now set up the tracing.
1768            TSetup("$traceLevel $cats", $traceMode);
1769        }
1770        # Check for the "help" option. If it is specified, dump the command-line
1771        # options and exit the program.
1772        if ($retOptions->{help}) {
1773            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1774            print "$1 [options] $parmHelp\n";
1775            for my $key (sort keys %{$options}) {
1776                my $name = Pad($key, $longestName, 0, ' ');
1777                my $desc = $options->{$key}->[1];
1778                if ($options->{$key}->[0]) {
1779                    $desc .= " (default " . $options->{$key}->[0] . ")";
1780                }
1781                print "  $name $desc\n";
1782            }
1783            exit(0);
1784        }
1785        # Trace the options, if applicable.
1786        if (T(3)) {
1787            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1788            Trace("Selected options: " . join(", ", sort @parms) . ".");
1789        }
1790        # Return the parsed parameters.
1791        return ($retOptions, @retParameters);
1792    }
1793    
1794    =head3 ReadOptions
1795    
1796        my %options = Tracer::ReadOptions($fileName);
1797    
1798    Read a set of options from a file. Each option is encoded in a line of text that has the
1799    format
1800    
1801    I<optionName>C<=>I<optionValue>C<; >I<comment>
1802    
1803    The option name must consist entirely of letters, digits, and the punctuation characters
1804    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1805    character is a semi-colon will be ignored. The return hash will map each option name to
1806    the corresponding option value.
1807    
1808    =over 4
1809    
1810    =item fileName
1811    
1812    Name of the file containing the option data.
1813    
1814    =item RETURN
1815    
1816    Returns a hash mapping the option names specified in the file to their corresponding option
1817    value.
1818    
1819    =back
1820    
1821    =cut
1822    
1823    sub ReadOptions {
1824        # Get the parameters.
1825        my ($fileName) = @_;
1826        # Open the file.
1827        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1828        # Count the number of records read.
1829        my ($records, $comments) = 0;
1830        # Create the return hash.
1831        my %retVal = ();
1832        # Loop through the file, accumulating key-value pairs.
1833        while (my $line = <CONFIGFILE>) {
1834            # Denote we've read a line.
1835            $records++;
1836            # Determine the line type.
1837            if ($line =~ /^\s*[\n\r]/) {
1838                # A blank line is a comment.
1839                $comments++;
1840            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1841                # Here we have an option assignment.
1842                retVal{$1} = $2;
1843            } elsif ($line =~ /^\s*;/) {
1844                # Here we have a text comment.
1845                $comments++;
1846            } else {
1847                # Here we have an invalid line.
1848                Trace("Invalid option statement in record $records.") if T(0);
1849            }
1850        }
1851        # Return the hash created.
1852        return %retVal;
1853    }
1854    
1855    =head3 GetOptions
1856    
1857        Tracer::GetOptions(\%defaults, \%options);
1858    
1859    Merge a specified set of options into a table of defaults. This method takes two hash references
1860    as input and uses the data from the second to update the first. If the second does not exist,
1861    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1862    exist in the first.
1863    
1864    Consider the following example.
1865    
1866        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1867    
1868    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1869    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1870    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1871    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1872    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1873    
1874        {databaseType => 'Oracle'}
1875    
1876    an error will occur because the B<databaseType> option does not exist.
1877    
1878    =over 4
1879    
1880    =item defaults
1881    
1882    Table of default option values.
1883    
1884    =item options
1885    
1886    Table of overrides, if any.
1887    
1888    =item RETURN
1889    
1890    Returns a reference to the default table passed in as the first parameter.
1891    
1892    =back
1893    
1894    =cut
1895    
1896    sub GetOptions {
1897        # Get the parameters.
1898        my ($defaults, $options) = @_;
1899        # Check for overrides.
1900        if ($options) {
1901            # Loop through the overrides.
1902            while (my ($option, $setting) = each %{$options}) {
1903                # Insure this override exists.
1904                if (!exists $defaults->{$option}) {
1905                    croak "Unrecognized option $option encountered.";
1906                } else {
1907                    # Apply the override.
1908                    $defaults->{$option} = $setting;
1909                }
1910            }
1911        }
1912        # Return the merged table.
1913        return $defaults;
1914    }
1915    
1916    =head3 MergeOptions
1917    
1918        Tracer::MergeOptions(\%table, \%defaults);
1919    
1920    Merge default values into a hash table. This method looks at the key-value pairs in the
1921    second (default) hash, and if a matching key is not found in the first hash, the default
1922    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1923    checking and no return value.
1924    
1925    =over 4
1926    
1927    =item table
1928    
1929    Hash table to be updated with the default values.
1930    
1931    =item defaults
1932    
1933    Default values to be merged into the first hash table if they are not already present.
1934    
1935    =back
1936    
1937    =cut
1938    
1939    sub MergeOptions {
1940        # Get the parameters.
1941        my ($table, $defaults) = @_;
1942        # Loop through the defaults.
1943        while (my ($key, $value) = each %{$defaults}) {
1944            if (!exists $table->{$key}) {
1945                $table->{$key} = $value;
1946            }
1947      }      }
     # Parse the command line.  
     my ($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, ">$errFileName";  
1948      }      }
1949      # Now we want to set up tracing. First, we need to know if SQL is to  
1950      # be traced.  =head3 ParseCommand
1951      my @cats = @{$categories};  
1952      if ($retOptions->{sql}) {      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1953          push @cats, "SQL";  
1954    Parse a command line consisting of a list of parameters. The initial parameters may be option
1955    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1956    off and merged into a table of default options. The remainder of the command line is
1957    returned as a list of positional arguments. For example, consider the following invocation.
1958    
1959        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1960    
1961    In this case, the list @words will be treated as a command line and there are two options available,
1962    B<errors> and B<logFile>. If @words has the following format
1963    
1964        -logFile=error.log apple orange rutabaga
1965    
1966    then at the end of the invocation, C<$options> will be
1967    
1968        { errors => 0, logFile => 'error.log' }
1969    
1970    and C<@arguments> will contain
1971    
1972        apple orange rutabaga
1973    
1974    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1975    support for quote characters. Options can be specified with single or double hyphens.
1976    
1977    =over 4
1978    
1979    =item optionTable
1980    
1981    Table of default options.
1982    
1983    =item inputList
1984    
1985    List of words on the command line.
1986    
1987    =item RETURN
1988    
1989    Returns a reference to the option table and a list of the positional arguments.
1990    
1991    =back
1992    
1993    =cut
1994    
1995    sub ParseCommand {
1996        # Get the parameters.
1997        my ($optionTable, @inputList) = @_;
1998        # Process any options in the input list.
1999        my %overrides = ();
2000        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2001            # Get the current option.
2002            my $arg = shift @inputList;
2003            # Pull out the option name.
2004            $arg =~ /^--?([^=]*)/g;
2005            my $name = $1;
2006            # Check for an option value.
2007            if ($arg =~ /\G=(.*)$/g) {
2008                # Here we have a value for the option.
2009                $overrides{$name} = UnEscape($1);
2010            } else {
2011                # Here there is no value, so we use 1.
2012                $overrides{$name} = 1;
2013      }      }
     # 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;  
2014      }      }
2015      # Now we set up the trace mode.      # Merge the options into the defaults.
2016      my $traceMode;      GetOptions($optionTable, \%overrides);
2017      # Verify that we can open a file in the FIG temporary directory.      # Translate the remaining parameters.
2018      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";      my @retVal = ();
2019      if (open TESTTRACE, ">$traceFileName") {      for my $inputParm (@inputList) {
2020          # Here we can trace to a file.          push @retVal, UnEscape($inputParm);
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
2021          }          }
2022          # Close the test file.      # Return the results.
2023          close TESTTRACE;      return ($optionTable, @retVal);
2024      } else {  }
2025          # Here we can't trace to a file. We trace to the standard output if it's  
2026          # okay, and the error log otherwise.  
2027          if ($textOKFlag) {  =head2 File Utility Methods
2028              $traceMode = "TEXT";  
2029    =head3 GetFile
2030    
2031        my @fileContents = Tracer::GetFile($fileName);
2032    
2033        or
2034    
2035        my $fileContents = Tracer::GetFile($fileName);
2036    
2037    Return the entire contents of a file. In list context, line-ends are removed and
2038    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2039    
2040    =over 4
2041    
2042    =item fileName
2043    
2044    Name of the file to read.
2045    
2046    =item RETURN
2047    
2048    In a list context, returns the entire file as a list with the line terminators removed.
2049    In a scalar context, returns the entire file as a string. If an error occurs opening
2050    the file, an empty list will be returned.
2051    
2052    =back
2053    
2054    =cut
2055    
2056    sub GetFile {
2057        # Get the parameters.
2058        my ($fileName) = @_;
2059        # Declare the return variable.
2060        my @retVal = ();
2061        # Open the file for input.
2062        my $handle = Open(undef, "<$fileName");
2063        # Read the whole file into the return variable, stripping off any terminator
2064        # characters.
2065        my $lineCount = 0;
2066        while (my $line = <$handle>) {
2067            $lineCount++;
2068            $line = Strip($line);
2069            push @retVal, $line;
2070        }
2071        # Close it.
2072        close $handle;
2073        my $actualLines = @retVal;
2074        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2075        # Return the file's contents in the desired format.
2076        if (wantarray) {
2077            return @retVal;
2078          } else {          } else {
2079              $traceMode = "WARN";          return join "\n", @retVal;
2080          }          }
2081      }      }
2082      # Now set up the tracing.  
2083      TSetup("$traceLevel $cats", $traceMode);  =head3 PutFile
2084      # Check for the "h" option. If it is specified, dump the command-line  
2085      # options and exit the program.      Tracer::PutFile($fileName, \@lines);
2086      if ($retOptions->{h}) {  
2087          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Write out a file from a list of lines of text.
2088          Trace("$1 [options] $parmHelp") if T(0);  
2089          for my $key (sort keys %{$options}) {  =over 4
2090              my $name = Pad($key, $longestName, 0, ' ');  
2091              my $desc = $options->{$key}->[1];  =item fileName
2092              if ($options->{$key}->[0]) {  
2093                  $desc .= " (default " . $options->{$key}->[0] . ")";  Name of the output file.
2094    
2095    =item lines
2096    
2097    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2098    new-line characters. Alternatively, may be a string, in which case the string will be written without
2099    modification.
2100    
2101    =back
2102    
2103    =cut
2104    
2105    sub PutFile {
2106        # Get the parameters.
2107        my ($fileName, $lines) = @_;
2108        # Open the output file.
2109        my $handle = Open(undef, ">$fileName");
2110        # Count the lines written.
2111        if (ref $lines ne 'ARRAY') {
2112            # Here we have a scalar, so we write it raw.
2113            print $handle $lines;
2114            Trace("Scalar put to file $fileName.") if T(File => 3);
2115        } else {
2116            # Write the lines one at a time.
2117            my $count = 0;
2118            for my $line (@{$lines}) {
2119                print $handle "$line\n";
2120                $count++;
2121              }              }
2122              Trace("  $name $desc") if T(0);          Trace("$count lines put to file $fileName.") if T(File => 3);
2123          }          }
2124          exit(0);      # Close the output file.
2125        close $handle;
2126      }      }
2127      # Return the parsed parameters.  
2128      return ($retOptions, @retParameters);  =head3 ParseRecord
2129    
2130        my @fields = Tracer::ParseRecord($line);
2131    
2132    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2133    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2134    These will automatically be converted.
2135    
2136    =over 4
2137    
2138    =item line
2139    
2140    Line of data containing the tab-delimited fields.
2141    
2142    =item RETURN
2143    
2144    Returns a list of the fields found in the data line.
2145    
2146    =back
2147    
2148    =cut
2149    
2150    sub ParseRecord {
2151        # Get the parameter.
2152        my ($line) = @_;
2153        # Remove the trailing new-line, if any.
2154        chomp $line;
2155        # Split the line read into pieces using the tab character.
2156        my @retVal = split /\t/, $line;
2157        # Trim and fix the escapes in each piece.
2158        for my $value (@retVal) {
2159            # Trim leading whitespace.
2160            $value =~ s/^\s+//;
2161            # Trim trailing whitespace.
2162            $value =~ s/\s+$//;
2163            # Delete the carriage returns.
2164            $value =~ s/\r//g;
2165            # Convert the escapes into their real values.
2166            $value =~ s/\\t/"\t"/ge;
2167            $value =~ s/\\n/"\n"/ge;
2168        }
2169        # Return the result.
2170        return @retVal;
2171  }  }
2172    
2173  =head3 Setups  =head3 Merge
2174    
2175        my @mergedList = Tracer::Merge(@inputList);
2176    
2177    Sort a list of strings and remove duplicates.
2178    
2179    =over 4
2180    
2181    =item inputList
2182    
2183    List of scalars to sort and merge.
2184    
2185  C<< my $count = Tracer::Setups(); >>  =item RETURN
2186    
2187  Return the number of times L</TSetup> has been called.  Returns a list containing the same elements sorted in ascending order with duplicates
2188    removed.
2189    
2190  This method allows for the creation of conditional tracing setups where, for example, we  =back
 may want to set up tracing if nobody else has done it before us.  
2191    
2192  =cut  =cut
2193    
2194  sub Setups {  sub Merge {
2195      return $SetupCount;      # Get the input list in sort order.
2196        my @inputList = sort @_;
2197        # Only proceed if the list has at least two elements.
2198        if (@inputList > 1) {
2199            # Now we want to move through the list splicing out duplicates.
2200            my $i = 0;
2201            while ($i < @inputList) {
2202                # Get the current entry.
2203                my $thisEntry = $inputList[$i];
2204                # Find out how many elements duplicate the current entry.
2205                my $j = $i + 1;
2206                my $dup1 = $i + 1;
2207                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2208                # If the number is nonzero, splice out the duplicates found.
2209                if ($j > $dup1) {
2210                    splice @inputList, $dup1, $j - $dup1;
2211                }
2212                # Now the element at position $dup1 is different from the element before it
2213                # at position $i. We push $i forward one position and start again.
2214                $i++;
2215            }
2216        }
2217        # Return the merged list.
2218        return @inputList;
2219  }  }
2220    
2221  =head3 Open  =head3 Open
2222    
2223  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2224    
2225  Open a file.  Open a file.
2226    
# Line 607  Line 2312 
2312    
2313  =head3 FindNamePart  =head3 FindNamePart
2314    
2315  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2316    
2317  Extract the portion of a file specification that contains the file name.  Extract the portion of a file specification that contains the file name.
2318    
# Line 658  Line 2363 
2363    
2364  =head3 OpenDir  =head3 OpenDir
2365    
2366  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @files = OpenDir($dirName, $filtered, $flag);
2367    
2368  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
2369  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
# Line 687  Line 2392 
2392    
2393  Name of the directory to open.  Name of the directory to open.
2394    
2395  =item filtered  =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  
   
 C<< {databaseType => 'Oracle'} >>  
   
 an error will occur because the B<databaseType> option does not exist.  
   
 =over 4  
   
 =item defaults  
   
 Table of default option values.  
   
 =item options  
   
 Table of overrides, if any.  
   
 =item RETURN  
   
 Returns a reference to the default table passed in as the first parameter.  
   
 =back  
   
 =cut  
   
 sub GetOptions {  
     # Get the parameters.  
     my ($defaults, $options) = @_;  
     # Check for overrides.  
     if ($options) {  
         # Loop through the overrides.  
         while (my ($option, $setting) = each %{$options}) {  
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
 }  
   
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
   
 Merge default values into a hash table. This method looks at the key-value pairs in the  
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
   
 =over 4  
   
 =item table  
2396    
2397  Hash table to be updated with the default values.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2398    from the list, else FALSE.
2399    
2400  =item defaults  =item flag
2401    
2402  Default values to be merged into the first hash table if they are not already present.  TRUE if a failure to open is okay, else FALSE
2403    
2404  =back  =back
2405    
2406  =cut  =cut
2407    #: Return Type @;
2408  sub MergeOptions {  sub OpenDir {
2409      # Get the parameters.      # Get the parameters.
2410      my ($table, $defaults) = @_;      my ($dirName, $filtered, $flag) = @_;
2411      # Loop through the defaults.      # Declare the return variable.
2412      while (my ($key, $value) = each %{$defaults}) {      my @retVal = ();
2413          if (!exists $table->{$key}) {      # Open the directory.
2414              $table->{$key} = $value;      if (opendir(my $dirHandle, $dirName)) {
2415            # The directory opened successfully. Get the appropriate list according to the
2416            # strictures of the filter parameter.
2417            if ($filtered) {
2418                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2419            } else {
2420                @retVal = readdir $dirHandle;
2421          }          }
2422        } elsif (! $flag) {
2423            # Here the directory would not open and it's considered an error.
2424            Confess("Could not open directory $dirName.");
2425      }      }
2426        # Return the result.
2427        return @retVal;
2428  }  }
2429    
 =head3 Trace  
2430    
2431  C<< Trace($message); >>  =head3 Insure
2432    
2433        Insure($dirName, $chmod);
2434    
2435  Write a trace message to the target location specified in L</TSetup>. If there has not been  Insure a directory is present.
 any prior call to B<TSetup>.  
2436    
2437  =over 4  =over 4
2438    
2439  =item message  =item dirName
2440    
2441  Message to write.  Name of the directory to check. If it does not exist, it will be created.
2442    
2443    =item chmod (optional)
2444    
2445    Security privileges to be given to the directory if it is created.
2446    
2447  =back  =back
2448    
2449  =cut  =cut
2450    
2451  sub Trace {  sub Insure {
2452      # Get the parameters.      my ($dirName, $chmod) = @_;
2453      my ($message) = @_;      if (! -d $dirName) {
2454      # Get the timestamp.          Trace("Creating $dirName directory.") if T(2);
2455      my $timeStamp = Now();          eval {
2456      # Format the message. Note we strip off any line terminators at the end.              mkpath $dirName;
2457      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);              # If we have permissions specified, set them here.
2458      # Process according to the destination.              if (defined($chmod)) {
2459      if ($Destination eq "TEXT") {                  chmod $chmod, $dirName;
2460          # Write the message to the standard output.              }
2461          print "$formatted\n";          };
2462      } elsif ($Destination eq "ERROR") {          if ($@) {
2463          # 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";  
2464          }          }
2465      }      }
2466  }  }
2467    
2468  =head3 T  =head3 ChDir
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
2469    
2470  C<< my $switch = T($traceLevel); >>      ChDir($dirName);
2471    
2472  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.  
2473    
2474  =over 4  =over 4
2475    
2476  =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  
2477    
2478  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.
2479    
2480  =back  =back
2481    
2482  =cut  =cut
2483    
2484  sub T {  sub ChDir {
2485      # Declare the return variable.      my ($dirName) = @_;
2486      my $retVal = 0;      if (! -d $dirName) {
2487      # 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";  
2488              } else {              } else {
2489                  $category = $package;          Trace("Changing to directory $dirName.") if T(File => 4);
2490              }          my $okFlag = chdir $dirName;
2491          }          if (! $okFlag) {
2492          # 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.");  
2493          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2494      }      }
     # Return the computed result.  
     return $retVal;  
2495  }  }
2496    
2497  =head3 ParseCommand  =head3 SetPermissions
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
2498    
2499  Parse a command line consisting of a list of parameters. The initial parameters may be option      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
2500    
2501  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Set the permissions for a directory and all the files and folders inside it.
2502    In addition, the group ownership will be changed to the specified value.
2503    
2504  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
2505  B<errors> and B<logFile>. If @words has the following format  problems, so it does internal error recovery.
2506    
2507  C<< -logFile=error.log apple orange rutabaga >>  =over 4
2508    
2509  then at the end of the invocation, C<$options> will be  =item dirName
2510    
2511  C<< { errors => 0, logFile => 'error.log' } >>  Name of the directory to process.
2512    
2513  and C<@arguments> will contain  =item group
2514    
2515  C<< apple orange rutabaga >>  Name of the group to be assigned.
2516    
2517  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =item mask
 support for quote characters.  
2518    
2519  =over 4  Permission mask. Bits that are C<1> in this mask will be ORed into the
2520    permission bits of any file or directory that does not already have them
2521    set to 1.
2522    
2523  =item optionTable  =item otherMasks
2524    
2525  Table of default options.  Map of search patterns to permission masks. If a directory name matches
2526    one of the patterns, that directory and all its members and subdirectories
2527    will be assigned the new pattern. For example, the following would
2528    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2529    
2530  =item inputList      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2531    
2532  List of words on the command line.  The list is ordered, so the following would use 0777 for C<tmp1> and
2533    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2534    
2535  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2536                                                       '^tmp' => 0666);
2537    
2538  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
2539    names are matched, not file names.
2540    
2541  =back  =back
2542    
2543  =cut  =cut
2544    
2545  sub ParseCommand {  sub SetPermissions {
2546      # Get the parameters.      # Get the parameters.
2547      my ($optionTable, @inputList) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2548      # Process any options in the input list.      # Set up for error recovery.
2549      my %overrides = ();      eval {
2550      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          # Switch to the specified directory.
2551          # Get the current option.          ChDir($dirName);
2552          my $arg = shift @inputList;          # Get the group ID.
2553          # Pull out the option name.          my $gid = getgrnam($group);
2554          $arg =~ /^-([^=]*)/g;          # Get the mask for tracing.
2555          my $name = $1;          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2556          # Check for an option value.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2557          if ($arg =~ /\G=(.*)$/g) {          my $fixCount = 0;
2558              # Here we have a value for the option.          my $lookCount = 0;
2559              $overrides{$name} = UnEscape($1);          # @dirs will be a stack of directories to be processed.
2560            my @dirs = (getcwd());
2561            while (scalar(@dirs) > 0) {
2562                # Get the current directory.
2563                my $dir = pop @dirs;
2564                # Check for a match to one of the specified directory names. To do
2565                # that, we need to pull the individual part of the name off of the
2566                # whole path.
2567                my $simpleName = $dir;
2568                if ($dir =~ m!/([^/]+)$!) {
2569                    $simpleName = $1;
2570                }
2571                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2572                # Search for a match.
2573                my $match = 0;
2574                my $i;
2575                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2576                    my $pattern = $otherMasks[$i];
2577                    if ($simpleName =~ /$pattern/i) {
2578                        $match = 1;
2579                    }
2580                }
2581                # Find out if we have a match. Note we use $i-1 because the loop added 2
2582                # before terminating due to the match.
2583                if ($match && $otherMasks[$i-1] != $mask) {
2584                    # This directory matches one of the incoming patterns, and it's
2585                    # a different mask, so we process it recursively with that mask.
2586                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2587          } else {          } else {
2588              # Here there is no value, so we use 1.                  # Here we can process normally. Get all of the non-hidden members.
2589              $overrides{$name} = 1;                  my @submems = OpenDir($dir, 1);
2590                    for my $submem (@submems) {
2591                        # Get the full name.
2592                        my $thisMem = "$dir/$submem";
2593                        Trace("Checking member $thisMem.") if T(4);
2594                        $lookCount++;
2595                        if ($lookCount % 1000 == 0) {
2596                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2597                        }
2598                        # Fix the group.
2599                        chown -1, $gid, $thisMem;
2600                        # Insure this member is not a symlink.
2601                        if (! -l $thisMem) {
2602                            # Get its info.
2603                            my $fileInfo = stat $thisMem;
2604                            # Only proceed if we got the info. Otherwise, it's a hard link
2605                            # and we want to skip it anyway.
2606                            if ($fileInfo) {
2607                                my $fileMode = $fileInfo->mode;
2608                                if (($fileMode & $mask) != $mask) {
2609                                    # Fix this member.
2610                                    $fileMode |= $mask;
2611                                    chmod $fileMode, $thisMem;
2612                                    $fixCount++;
2613                                }
2614                                # If it's a subdirectory, stack it.
2615                                if (-d $thisMem) {
2616                                    push @dirs, $thisMem;
2617          }          }
2618      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2619      }      }
2620      # Return the results.                  }
2621      return ($optionTable, @retVal);              }
2622            }
2623            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2624        };
2625        # Check for an error.
2626        if ($@) {
2627            Confess("SetPermissions error: $@");
2628        }
2629  }  }
2630    
2631  =head3 Escape  =head3 GetLine
2632    
2633  C<< my $codedString = Tracer::Escape($realString); >>      my @data = Tracer::GetLine($handle);
2634    
2635  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Read a line of data from a tab-delimited file.
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
2636    
2637  =over 4  =over 4
2638    
2639  =item realString  =item handle
2640    
2641  String to escape.  Open file handle from which to read.
2642    
2643  =item RETURN  =item RETURN
2644    
2645  Escaped equivalent of the real string.  Returns a list of the fields in the record read. The fields are presumed to be
2646    tab-delimited. If we are at the end of the file, then an empty list will be
2647    returned. If an empty line is read, a single list item consisting of a null
2648    string will be returned.
2649    
2650  =back  =back
2651    
2652  =cut  =cut
2653    
2654  sub Escape {  sub GetLine {
2655      # Get the parameter.      # Get the parameters.
2656      my ($realString) = @_;      my ($handle) = @_;
2657      # Initialize the return variable.      # Declare the return variable.
2658      my $retVal = "";      my @retVal = ();
2659      # Loop through the parameter string, looking for sequences to escape.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2660      while (length $realString > 0) {      # Read from the file.
2661          # Look for the first sequence to escape.      my $line = <$handle>;
2662          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # Only proceed if we found something.
2663              # Here we found it. The text preceding the sequence is in $1. The sequence      if (defined $line) {
2664              # 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
2665              $retVal .= $1;          # upload control and have a nonstandard EOL combination.
2666              # Strip the processed section off the real string.          $line =~ s/(\r|\n)+$//;
2667              $realString = substr $realString, (length $2) + (length $1);          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2668              # Get the matched character.          if (T(File => 4)) {
2669              my $char = $2;              my $escapedLine = $line;
2670              # If we have a CR, we are done.              $escapedLine =~ s/\n/\\n/g;
2671              if ($char ne "\r") {              $escapedLine =~ s/\r/\\r/g;
2672                  # It's not a CR, so encode the escape sequence.              $escapedLine =~ s/\t/\\t/g;
2673                  $char =~ tr/\t\n/tn/;              Trace("Line read: -->$escapedLine<--");
2674                  $retVal .= "\\" . $char;          }
2675              }          # If the line is empty, return a single empty string; otherwise, parse
2676            # it into fields.
2677            if ($line eq "") {
2678                push @retVal, "";
2679          } else {          } else {
2680              # Here there are no more escape sequences. The rest of the string is              push @retVal, split /\t/,$line;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
2681          }          }
2682        } else {
2683            # Trace the reason the read failed.
2684            Trace("End of file: $!") if T(File => 3);
2685      }      }
2686      # Return the result.      # Return the result.
2687      return $retVal;      return @retVal;
2688  }  }
2689    
2690  =head3 UnEscape  =head3 PutLine
2691    
2692  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutLine($handle, \@fields, $eol);
2693    
2694  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write a line of data to a tab-delimited file. The specified field values will be
2695  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  output in tab-separated form, with a trailing new-line.
 be deleted.  
2696    
2697  =over 4  =over 4
2698    
2699  =item codedString  =item handle
2700    
2701  String to un-escape.  Output file handle.
2702    
2703  =item RETURN  =item fields
2704    
2705  Returns a copy of the original string with the escape sequences converted to their actual  List of field values.
2706  values.  
2707    =item eol (optional)
2708    
2709    End-of-line character (default is "\n").
2710    
2711  =back  =back
2712    
2713  =cut  =cut
2714    
2715  sub UnEscape {  sub PutLine {
2716      # Get the parameter.      # Get the parameters.
2717      my ($codedString) = @_;      my ($handle, $fields, $eol) = @_;
2718      # Initialize the return variable.      # Write the data.
2719      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 $retVal;  
2720  }  }
2721    
 =head3 ParseRecord  
2722    
2723  C<< my @fields = Tracer::ParseRecord($line); >>  =head3 PrintLine
2724    
2725  Parse a tab-delimited data line. The data line is split into field values. Embedded tab      Tracer::PrintLine($line);
2726  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
2727  These will automatically be converted.  Print a line of text with a trailing new-line.
2728    
2729  =over 4  =over 4
2730    
2731  =item line  =item line
2732    
2733  Line of data containing the tab-delimited fields.  Line of text to print.
2734    
2735    =back
2736    
2737    =cut
2738    
2739    sub PrintLine {
2740        # Get the parameters.
2741        my ($line) = @_;
2742        # Print the line.
2743        print "$line\n";
2744    }
2745    
2746    
2747    =head2 Other Useful Methods
2748    
2749    =head3 ParseParm
2750    
2751        my $listValue = Tracer::ParseParm($string);
2752    
2753    Convert a parameter into a list reference. If the parameter is undefined,
2754    an undefined value will be returned. Otherwise, it will be parsed as a
2755    comma-separated list of values.
2756    
2757    =over 4
2758    
2759    =item string
2760    
2761    Incoming string.
2762    
2763  =item RETURN  =item RETURN
2764    
2765  Returns a list of the fields found in the data line.  Returns a reference to a list of values, or C<undef> if the incoming value
2766    was undefined.
2767    
2768  =back  =back
2769    
2770  =cut  =cut
2771    
2772  sub ParseRecord {  sub ParseParm {
2773      # Get the parameter.      # Get the parameters.
2774      my ($line) = @_;      my ($string) = @_;
2775      # Remove the trailing new-line, if any.      # Declare the return variable.
2776      chomp $line;      my $retVal;
2777      # Split the line read into pieces using the tab character.      # Check for data.
2778      my @retVal = split /\t/, $line;      if (defined $string) {
2779      # Trim and fix the escapes in each piece.          # We have some, so split it into a list.
2780      for my $value (@retVal) {          $retVal = [ split /\s*,\s*/, $string];
         # 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;  
2781      }      }
2782      # Return the result.      # Return the result.
2783      return @retVal;      return $retVal;
2784  }  }
2785    
2786  =head3 Merge  =head3 Now
2787    
2788  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $string = Tracer::Now();
2789    
2790  Sort a list of strings and remove duplicates.  Return a displayable time stamp containing the local time. Whatever format this
2791    method produces must be parseable by L</ParseDate>.
2792    
2793    =cut
2794    
2795    sub Now {
2796        return DisplayTime(time);
2797    }
2798    
2799    =head3 DisplayTime
2800    
2801        my $string = Tracer::DisplayTime($time);
2802    
2803    Convert a time value to a displayable time stamp. Whatever format this
2804    method produces must be parseable by L</ParseDate>.
2805    
2806  =over 4  =over 4
2807    
2808  =item inputList  =item time
2809    
2810  List of scalars to sort and merge.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2811    
2812  =item RETURN  =item RETURN
2813    
2814  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
 removed.  
2815    
2816  =back  =back
2817    
2818  =cut  =cut
2819    
2820  sub Merge {  sub DisplayTime {
2821      # Get the input list in sort order.      my ($time) = @_;
2822      my @inputList = sort @_;      my $retVal = "(n/a)";
2823      # Only proceed if the list has at least two elements.      if (defined $time) {
2824      if (@inputList > 1) {          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2825          # Now we want to move through the list splicing out duplicates.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2826          my $i = 0;                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
2827      }      }
2828      # Return the merged list.      return $retVal;
     return @inputList;  
2829  }  }
2830    
2831  =head3 GetFile  # Pad a number to 2 digits.
2832    sub _p2 {
2833  C<< my @fileContents = Tracer::GetFile($fileName); >>      my ($value) = @_;
2834        $value = "0$value" if ($value < 10);
2835        return $value;
2836    }
2837    
2838      or  =head3 Escape
2839    
2840  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $codedString = Tracer::Escape($realString);
2841    
2842  Return the entire contents of a file. In list context, line-ends are removed and  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2843  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2844    result is to reverse the effect of L</UnEscape>.
2845    
2846  =over 4  =over 4
2847    
2848  =item fileName  =item realString
2849    
2850  Name of the file to read.  String to escape.
2851    
2852  =item RETURN  =item RETURN
2853    
2854  In a list context, returns the entire file as a list with the line terminators removed.  Escaped equivalent of the real string.
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2855    
2856  =back  =back
2857    
2858  =cut  =cut
2859    
2860  sub GetFile {  sub Escape {
2861      # Get the parameters.      # Get the parameter.
2862      my ($fileName) = @_;      my ($realString) = @_;
2863      # Declare the return variable.      # Initialize the return variable.
2864      my @retVal = ();      my $retVal = "";
2865      # Open the file for input.      # Loop through the parameter string, looking for sequences to escape.
2866      my $ok = open INPUTFILE, "<$fileName";      while (length $realString > 0) {
2867      if (!$ok) {          # Look for the first sequence to escape.
2868          # If we had an error, trace it. We will automatically return a null value.          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2869          Trace("Could not open \"$fileName\" for input: $!") if T(0);              # Here we found it. The text preceding the sequence is in $1. The sequence
2870      } else {              # itself is in $2. First, move the clear text to the return variable.
2871          # Read the whole file into the return variable, stripping off any terminator              $retVal .= $1;
2872          # characters.              # Strip the processed section off the real string.
2873          my $lineCount = 0;              $realString = substr $realString, (length $2) + (length $1);
2874          while (my $line = <INPUTFILE>) {              # Get the matched character.
2875              $lineCount++;              my $char = $2;
2876              $line = Strip($line);              # If we have a CR, we are done.
2877              push @retVal, $line;              if ($char ne "\r") {
2878          }                  # It's not a CR, so encode the escape sequence.
2879          # Close it.                  $char =~ tr/\t\n/tn/;
2880          close INPUTFILE;                  $retVal .= "\\" . $char;
         my $actualLines = @retVal;  
2881      }      }
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
2882      } else {      } else {
2883          return join "\n", @retVal;              # Here there are no more escape sequences. The rest of the string is
2884                # transferred unmodified.
2885                $retVal .= $realString;
2886                $realString = "";
2887            }
2888      }      }
2889        # Return the result.
2890        return $retVal;
2891  }  }
2892    
2893  =head3 QTrace  =head3 UnEscape
2894    
2895  C<< my $data = QTrace($format); >>      my $realString = Tracer::UnEscape($codedString);
2896    
2897  Return the queued trace data in the specified format.  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2898    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2899    be deleted.
2900    
2901  =over 4  =over 4
2902    
2903  =item format  =item codedString
2904    
2905  C<html> to format the data as an HTML list, C<text> to format it as straight text.  String to un-escape.
2906    
2907    =item RETURN
2908    
2909    Returns a copy of the original string with the escape sequences converted to their actual
2910    values.
2911    
2912  =back  =back
2913    
2914  =cut  =cut
2915    
2916  sub QTrace {  sub UnEscape {
2917      # Get the parameter.      # Get the parameter.
2918      my ($format) = @_;      my ($codedString) = @_;
2919      # Create the return variable.      # Initialize the return variable.
2920      my $retVal = "";      my $retVal = "";
2921      # Only proceed if there is an actual queue.      # Only proceed if the incoming string is nonempty.
2922      if (@Queue) {      if (defined $codedString) {
2923          # Process according to the format.          # Loop through the parameter string, looking for escape sequences. We can't do
2924          if ($format =~ m/^HTML$/i) {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2925              # Convert the queue into an HTML list.          # "\<tab>" no matter what we do.)
2926              $retVal = "<ul>\n";          while (length $codedString > 0) {
2927              for my $line (@Queue) {              # Look for the first escape sequence.
2928                  my $escapedLine = CGI::escapeHTML($line);              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2929                  $retVal .= "<li>$escapedLine</li>\n";                  # Here we found it. The text preceding the sequence is in $1. The sequence
2930                    # itself is in $2. First, move the clear text to the return variable.
2931                    $retVal .= $1;
2932                    $codedString = substr $codedString, (2 + length $1);
2933                    # Get the escape value.
2934                    my $char = $2;
2935                    # If we have a "\r", we are done.
2936                    if ($char ne 'r') {
2937                        # Here it's not an 'r', so we convert it.
2938                        $char =~ tr/\\tn/\\\t\n/;
2939                        $retVal .= $char;
2940              }              }
2941              $retVal .= "</ul>\n";              } else {
2942          } elsif ($format =~ m/^TEXT$/i) {                  # Here there are no more escape sequences. The rest of the string is
2943              # Convert the queue into a list of text lines.                  # transferred unmodified.
2944              $retVal = join("\n", @Queue) . "\n";                  $retVal .= $codedString;
2945                    $codedString = "";
2946          }          }
         # Clear the queue.  
         @Queue = ();  
2947      }      }
2948      # Return the formatted list.      }
2949        # Return the result.
2950      return $retVal;      return $retVal;
2951  }  }
2952    
2953  =head3 Confess  =head3 Percent
2954    
2955  C<< Confess($message); >>      my $percent = Tracer::Percent($number, $base);
2956    
2957  Trace the call stack and abort the program with the specified message. When used with  Returns the percent of the base represented by the given number. If the base
2958  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  is zero, returns zero.
2959  So, for example  
2960    =over 4
2961    
2962  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =item number
2963    
2964  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Percent numerator.
2965    
2966  =over 4  =item base
2967    
2968  =item message  Percent base.
2969    
2970  Message to include in the trace.  =item RETURN
2971    
2972    Returns the percentage of the base represented by the numerator.
2973    
2974  =back  =back
2975    
2976  =cut  =cut
2977    
2978  sub Confess {  sub Percent {
2979      # Get the parameters.      # Get the parameters.
2980      my ($message) = @_;      my ($number, $base) = @_;
2981      # Trace the call stack.      # Declare the return variable.
2982      Cluck($message);      my $retVal = 0;
2983      # Abort the program.      # Compute the percent.
2984      croak(">>> $message");      if ($base != 0) {
2985            $retVal = $number * 100 / $base;
2986        }
2987        # Return the result.
2988        return $retVal;
2989  }  }
2990    
2991  =head3 Assert  =head3 Constrain
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2992    
2993  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $constrained = Constrain($value, $min, $max);
2994    
2995  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
2996    
2997  =cut  =over 4
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2998    
2999  =head3 Cluck  =item value
3000    
3001  C<< Cluck($message); >>  Value to constrain.
3002    
3003  Trace the call stack. Note that for best results, you should qualify the call with a  =item min (optional)
 trace condition. For example,  
3004    
3005  C<< Cluck("Starting record parse.") if T(3); >>  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3006    
3007  will only trace the stack if the trace level for the package is 3 or more.  =item max (optional)
3008    
3009  =over 4  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3010    
3011  =item message  =item RETURN
3012    
3013  Message to include in the trace.  Returns the incoming value, constrained according to the other parameters.
3014    
3015  =back  =back
3016    
3017  =cut  =cut
3018    
3019  sub Cluck {  sub Constrain {
3020      # Get the parameters.      # Get the parameters.
3021      my ($message) = @_;      my ($value, $min, $max) = @_;
3022      # Trace what's happening.      # Declare the return variable.
3023      Trace("Stack trace for event: $message");      my $retVal = $value;
3024      my $confession = longmess($message);      # Apply the minimum constraint.
3025      # Convert the confession to a series of trace messages. Note we skip any      if (defined $min && $retVal < $min) {
3026      # messages relating to calls into Tracer.          $retVal = $min;
3027      for my $line (split /\s*\n/, $confession) {      }
3028          Trace($line) if ($line !~ /Tracer\.pm/);      # Apply the maximum constraint.
3029        if (defined $max && $retVal > $max) {
3030            $retVal = $max;
3031      }      }
3032        # Return the result.
3033        return $retVal;
3034  }  }
3035    
3036  =head3 Min  =head3 Min
3037    
3038  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
3039    
3040  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
3041    
# Line 1573  Line 3068 
3068    
3069  =head3 Max  =head3 Max
3070    
3071  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
3072    
3073  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
3074    
# Line 1604  Line 3099 
3099      return $retVal;      return $retVal;
3100  }  }
3101    
 =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;  
 }  
   
3102  =head3 Strip  =head3 Strip
3103    
3104  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::Strip($line);
3105    
3106  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
3107  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 3133 
3133    
3134  =head3 Pad  =head3 Pad
3135    
3136  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3137    
3138  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
3139  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 1766  Line 3192 
3192      return $retVal;      return $retVal;
3193  }  }
3194    
3195  =head3 EOF  =head3 EOF
3196    
3197    This is a constant that is lexically greater than any useful string.
3198    
3199    =cut
3200    
3201    sub EOF {
3202        return "\xFF\xFF\xFF\xFF\xFF";
3203    }
3204    
3205    =head3 TICK
3206    
3207        my @results = TICK($commandString);
3208    
3209    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3210    dot-slash (C<./> will be removed. So, for example, if you were doing
3211    
3212        `./protein.cgi`
3213    
3214    from inside a CGI script, it would work fine in Unix, but would issue an error message
3215    in Windows complaining that C<'.'> is not a valid command. If instead you code
3216    
3217        TICK("./protein.cgi")
3218    
3219    it will work correctly in both environments.
3220    
3221    =over 4
3222    
3223    =item commandString
3224    
3225    The command string to pass to the system.
3226    
3227    =item RETURN
3228    
3229    Returns the standard output from the specified command, as a list.
3230    
3231    =back
3232    
3233    =cut
3234    #: Return Type @;
3235    sub TICK {
3236        # Get the parameters.
3237        my ($commandString) = @_;
3238        # Chop off the dot-slash if this is Windows.
3239        if ($FIG_Config::win_mode) {
3240            $commandString =~ s!^\./!!;
3241        }
3242        # Activate the command and return the result.
3243        return `$commandString`;
3244    }
3245    
3246    
3247    =head3 CommaFormat
3248    
3249        my $formatted = Tracer::CommaFormat($number);
3250    
3251    Insert commas into a number.
3252    
3253    =over 4
3254    
3255    =item number
3256    
3257    A sequence of digits.
3258    
3259    =item RETURN
3260    
3261    Returns the same digits with commas strategically inserted.
3262    
3263    =back
3264    
3265    =cut
3266    
3267    sub CommaFormat {
3268        # Get the parameters.
3269        my ($number) = @_;
3270        # Pad the length up to a multiple of three.
3271        my $padded = "$number";
3272        $padded = " " . $padded while length($padded) % 3 != 0;
3273        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3274        # cause the delimiters to be included in the output stream. The
3275        # GREP removes the empty strings in between the delimiters.
3276        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3277        # Clean out the spaces.
3278        $retVal =~ s/ //g;
3279        # Return the result.
3280        return $retVal;
3281    }
3282    
3283    
3284    =head3 CompareLists
3285    
3286        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3287    
3288    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3289    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3290    The return value contains a list of items that are only in the new list
3291    (inserted) and only in the old list (deleted).
3292    
3293    =over 4
3294    
3295    =item newList
3296    
3297    Reference to a list of new tuples.
3298    
3299    =item oldList
3300    
3301    Reference to a list of old tuples.
3302    
3303    =item keyIndex (optional)
3304    
3305    Index into each tuple of its key field. The default is 0.
3306    
3307    =item RETURN
3308    
3309    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3310    list (inserted) followed by a reference to the list of items that are only in the old
3311    list (deleted).
3312    
3313    =back
3314    
3315    =cut
3316    
3317    sub CompareLists {
3318        # Get the parameters.
3319        my ($newList, $oldList, $keyIndex) = @_;
3320        if (! defined $keyIndex) {
3321            $keyIndex = 0;
3322        }
3323        # Declare the return variables.
3324        my ($inserted, $deleted) = ([], []);
3325        # Loop through the two lists simultaneously.
3326        my ($newI, $oldI) = (0, 0);
3327        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3328        while ($newI < $newN || $oldI < $oldN) {
3329            # Get the current object in each list. Note that if one
3330            # of the lists is past the end, we'll get undef.
3331            my $newItem = $newList->[$newI];
3332            my $oldItem = $oldList->[$oldI];
3333            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3334                # The old item is not in the new list, so mark it deleted.
3335                push @{$deleted}, $oldItem;
3336                $oldI++;
3337            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3338                # The new item is not in the old list, so mark it inserted.
3339                push @{$inserted}, $newItem;
3340                $newI++;
3341            } else {
3342                # The item is in both lists, so push forward.
3343                $oldI++;
3344                $newI++;
3345            }
3346        }
3347        # Return the result.
3348        return ($inserted, $deleted);
3349    }
3350    
3351    =head3 Cmp
3352    
3353  This is a constant that is lexically greater than any useful string.      my $cmp = Tracer::Cmp($a, $b);
3354    
3355  =cut  This method performs a universal sort comparison. Each value coming in is
3356    separated into a leading text part and a trailing number part. The text
3357    part is string compared, and if both parts are equal, then the number
3358    parts are compared numerically. A stream of just numbers or a stream of
3359    just strings will sort correctly, and a mixed stream will sort with the
3360    numbers first. Strings with a label and a number will sort in the
3361    expected manner instead of lexically.
3362    
3363  sub EOF {  =over 4
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
3364    
3365  =head3 TICK  =item a
3366    
3367  C<< my @results = TICK($commandString); >>  First item to compare.
3368    
3369  Perform a back-tick operation on a command. If this is a Windows environment, any leading  =item b
 dot-slash (C<./> will be removed. So, for example, if you were doing  
3370    
3371      `./protein.cgi`  Second item to compare.
3372    
3373  from inside a CGI script, it would work fine in Unix, but would issue an error message  =item RETURN
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
3374    
3375      TICK("./protein.cgi")  Returns a negative number if the first item should sort first (is less), a positive
3376    number if the first item should sort second (is greater), and a zero if the items are
3377    equal.
3378    
3379  it will work correctly in both environments.  =back
3380    
3381    =cut
3382    
3383    sub Cmp {
3384        # Get the parameters.
3385        my ($a, $b) = @_;
3386        # Declare the return value.
3387        my $retVal;
3388        # Check for nulls.
3389        if (! defined($a)) {
3390            $retVal = (! defined($b) ? 0 : -1);
3391        } elsif (! defined($b)) {
3392            $retVal = 1;
3393        } else {
3394            # Here we have two real values. Parse the two strings.
3395            $a =~ /^(\D*)(\d*)$/;
3396            my $aParsed = [$1, $2];
3397            $b =~ /^(\D*)(\d*)$/;
3398            my $bParsed = [$1, $2];
3399            # Compare the string parts.
3400            $retVal = $aParsed->[0] cmp $bParsed->[0];
3401            if (! $retVal) {
3402                $retVal = $aParsed->[1] <=> $bParsed->[1];
3403            }
3404        }
3405        # Return the result.
3406        return $retVal;
3407    }
3408    
3409    =head3 ListEQ
3410    
3411        my $flag = Tracer::ListEQ(\@a, \@b);
3412    
3413    Return TRUE if the specified lists contain the same strings in the same
3414    order, else FALSE.
3415    
3416  =over 4  =over 4
3417    
3418  =item commandString  =item a
3419    
3420  The command string to pass to the system.  Reference to the first list.
3421    
3422    =item b
3423    
3424    Reference to the second list.
3425    
3426  =item RETURN  =item RETURN
3427    
3428  Returns the standard output from the specified command, as a list.  Returns TRUE if the two parameters are identical string lists, else FALSE.
3429    
3430  =back  =back
3431    
3432  =cut  =cut
3433  #: Return Type @;  
3434  sub TICK {  sub ListEQ {
3435      # Get the parameters.      # Get the parameters.
3436      my ($commandString) = @_;      my ($a, $b) = @_;
3437      # Chop off the dot-slash if this is Windows.      # Declare the return variable. Start by checking the lengths.
3438      if ($FIG_Config::win_mode) {      my $n = scalar(@$a);
3439          $commandString =~ s!^\./!!;      my $retVal = ($n == scalar(@$b));
3440        # Now compare the list elements.
3441        for (my $i = 0; $retVal && $i < $n; $i++) {
3442            $retVal = ($a->[$i] eq $b->[$i]);
3443      }      }
3444      # Activate the command and return the result.      # Return the result.
3445      return `$commandString`;      return $retVal;
3446  }  }
3447    
3448  =head3 ScriptSetup  =head2 CGI Script Utilities
3449    
3450    =head3 ScriptSetup (deprecated)
3451    
3452  C<< my ($query, $varHash) = ScriptSetup(); >>      my ($cgi, $varHash) = ScriptSetup($noTrace);
3453    
3454  Perform standard tracing and debugging setup for scripts. The value returned is  Perform standard tracing and debugging setup for scripts. The value returned is
3455  the CGI object followed by a pre-built variable hash.  the CGI object followed by a pre-built variable hash. At the end of the script,
3456    the client should call L</ScriptFinish> to output the web page.
3457    
3458  The C<Trace> query parameter is used to determine whether or not tracing is active and  This method calls L</ETracing> to configure tracing, which allows the tracing
3459  which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  to be configured via the emergency tracing form on the debugging control panel.
3460  the C<CGI> trace module will trace parameter and environment information. Parameters are  Tracing will then be turned on automatically for all programs that use the L</ETracing>
3461  traced at level 3 and environment variables at level 4. At the end of the script, the  method, which includes every program that uses this method or L</StandardSetup>.
3462  client should call L</ScriptFinish> to output the web page.  
3463    =over 4
3464    
3465    =item noTrace (optional)
3466    
3467    If specified, tracing will be suppressed. This is useful if the script wants to set up
3468    tracing manually.
3469    
3470    =item RETURN
3471    
3472    Returns a two-element list consisting of a CGI query object and a variable hash for
3473    the output page.
3474    
3475    =back
3476    
3477  =cut  =cut
3478    
3479  sub ScriptSetup {  sub ScriptSetup {
3480        # Get the parameters.
3481        my ($noTrace) = @_;
3482      # Get the CGI query object.      # Get the CGI query object.
3483      my $query = CGI->new();      my $cgi = CGI->new();
3484      # Check for tracing. Set it up if the user asked for it.      # Set up tracing if it's not suppressed.
3485      if ($query->param('Trace')) {      ETracing($cgi) unless $noTrace;
         # Set up tracing to be queued for display at the bottom of the web page.  
         TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");  
         # Trace the parameter and environment data.  
         if (T(CGI => 3)) {  
             # Here we want to trace the parameter data.  
             my @names = $query->param;  
             for my $parmName (sort @names) {  
                 # Note we skip "Trace", which is for our use only.  
                 if ($parmName ne 'Trace') {  
                     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");  
     }  
3486      # Create the variable hash.      # Create the variable hash.
3487      my $varHash = { DebugData => '' };      my $varHash = { results => '' };
     # If we're in DEBUG mode, set up the debug mode data for forms.  
     if (Tracer::DebugMode) {  
         $varHash->{DebugData} = GetFile("Html/DebugFragment.html");  
     }  
3488      # Return the query object and variable hash.      # Return the query object and variable hash.
3489      return ($query, $varHash);      return ($cgi, $varHash);
3490  }  }
3491    
3492  =head3 ScriptFinish  =head3 ScriptFinish (deprecated)
3493    
3494  C<< ScriptFinish($webData, $varHash); >>      ScriptFinish($webData, $varHash);
3495    
3496  Output a web page at the end of a script. Either the string to be output or the  Output a web page at the end of a script. Either the string to be output or the
3497  name of a template file can be specified. If the second parameter is omitted,  name of a template file can be specified. If the second parameter is omitted,
# Line 1896  Line 3513 
3513      use FIG;      use FIG;
3514      # ... more uses ...      # ... more uses ...
3515    
3516      my ($query, $varHash) = ScriptSetup();      my ($cgi, $varHash) = ScriptSetup();
3517      eval {      eval {
3518          # ... get data from $query, put it in $varHash ...          # ... get data from $cgi, put it in $varHash ...
3519      };      };
3520      if ($@) {      if ($@) {
3521          Trace("Script Error: $@") if T(0);          Trace("Script Error: $@") if T(0);
# Line 1933  Line 3550 
3550      # Check for a template file situation.      # Check for a template file situation.
3551      my $outputString;      my $outputString;
3552      if (defined $varHash) {      if (defined $varHash) {
3553          # Here we have a template file. We need to apply the variables to the template.          # Here we have a template file. We need to determine the template type.
3554          $outputString = PageBuilder::Build("<$webData", $varHash, "Html");          my $template;
3555            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3556                $template = "$FIG_Config::template_url/$webData";
3557            } else {
3558                $template = "<<$webData";
3559            }
3560            $outputString = PageBuilder::Build($template, $varHash, "Html");
3561      } else {      } else {
3562          # Here the user gave us a raw string.          # Here the user gave us a raw string.
3563          $outputString = $webData;          $outputString = $webData;
3564      }      }
3565      # Check for trace messages.      # Check for trace messages.
3566      if ($Destination eq "QUEUE") {      if ($Destination ne "NONE" && $TraceLevel > 0) {
3567          # We have trace messages, so we want to put them at the end of the body. This          # We have trace messages, so we want to put them at the end of the body. This
3568          # is either at the end of the whole string or at the beginning of the BODY          # is either at the end of the whole string or at the beginning of the BODY
3569          # end-tag.          # end-tag.
# Line 1948  Line 3571 
3571          if ($outputString =~ m#</body>#gi) {          if ($outputString =~ m#</body>#gi) {
3572              $pos = (pos $outputString) - 7;              $pos = (pos $outputString) - 7;
3573          }          }
3574          substr $outputString, $pos, 0, QTrace('Html');          # If the trace messages were queued, we unroll them. Otherwise, we display the
3575            # destination.
3576            my $traceHtml;
3577            if ($Destination eq "QUEUE") {
3578                $traceHtml = QTrace('Html');
3579            } elsif ($Destination =~ /^>>(.+)$/) {
3580                # Here the tracing output it to a file. We code it as a hyperlink so the user
3581                # can copy the file name into the clipboard easily.
3582                my $actualDest = $1;
3583                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3584            } else {
3585                # Here we have one of the special destinations.
3586                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3587            }
3588            substr $outputString, $pos, 0, $traceHtml;
3589      }      }
3590      # Write the output string.      # Write the output string.
3591      print $outputString;      print $outputString;
3592  }  }
3593    
3594  =head3 Insure  =head3 GenerateURL
3595    
3596  C<< Insure($dirName); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3597    
3598  Insure a directory is present.  Generate a GET-style URL for the specified page with the specified parameter
3599    names and values. The values will be URL-escaped automatically. So, for
3600    example
3601    
3602        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3603    
3604    would return
3605    
3606        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3607    
3608  =over 4  =over 4
3609    
3610  =item dirName  =item page
3611    
3612  Name of the directory to check. If it does not exist, it will be created.  Page URL.
3613    
3614    =item parameters
3615    
3616    Hash mapping parameter names to parameter values.
3617    
3618    =item RETURN
3619    
3620    Returns a GET-style URL that goes to the specified page and passes in the
3621    specified parameters and values.
3622    
3623  =back  =back
3624    
3625  =cut  =cut
3626    
3627  sub Insure {  sub GenerateURL {
3628      my ($dirName) = @_;      # Get the parameters.
3629      if (! -d $dirName) {      my ($page, %parameters) = @_;
3630          Trace("Creating $dirName directory.") if T(2);      # Prime the return variable with the page URL.
3631          eval { mkpath $dirName; };      my $retVal = $page;
3632          if ($@) {      # Loop through the parameters, creating parameter elements in a list.
3633              Confess("Error creating $dirName: $@");      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3634          }      # If the list is nonempty, tack it on.
3635        if (@parmList) {
3636            $retVal .= "?" . join(";", @parmList);
3637      }      }
3638        # Return the result.
3639        return $retVal;
3640  }  }
3641    
3642  =head3 ChDir  =head3 ApplyURL
3643    
3644  C<< ChDir($dirName); >>      Tracer::ApplyURL($table, $target, $url);
3645    
3646  Change to the specified directory.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3647    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3648    URL column will be deleted by this process and the target column will be HTML-escaped.
3649    
3650    This provides a simple way to process the results of a database query into something
3651    displayable by combining a URL with text.
3652    
3653  =over 4  =over 4
3654    
3655  =item dirName  =item table
3656    
3657  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
3658    this method.
3659