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revision 1.48, Thu Jun 8 13:54:49 2006 UTC revision 1.107, Mon Jul 7 19:58:47 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 @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                # Yes. We now need to compute the date, the link, and the title.
748                # First, the date, in a very specific format.
749                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
750                    (tz_local_offset() / 30);
751                # Environment data goes in here. We start with the date.
752                my $environment = "$date.  ";
753                # If we need to recap the message (because it's too long to be a title), we'll
754                # put it in here.
755                my $recap;
756                # Copy the message and remove excess space.
757                my $title = $message;
758                $title =~ s/\s+/ /gs;
759                # If it's too long, we have to split it up.
760                if (length $title > 60) {
761                    # Put the full message in the environment string.
762                    $recap = $title;
763                    # Excerpt it as the title.
764                    $title = substr($title, 0, 50) . "...";
765                }
766                # If we have a CGI object, then this is a web error. Otherwise, it's
767                # command-line.
768                if (defined $SavedCGI) {
769                    # We're in a web service. The environment is the user's IP, and the link
770                    # is the URL that got us here.
771                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
772                    $environment .= "Event Reported at IP address $key process $$.";
773                    my $url = $SavedCGI->self_url();
774                    # We need the user agent string and (if available) the referrer.
775                    # The referrer will be the link.
776                    $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
777                    if ($ENV{HTTP_REFERER}) {
778                        my $link = $ENV{HTTP_REFERER};
779                        $environment .= " referred from <a href=\"$link\">$link</a>.";
780                    } else {
781                        $environment .= " referrer unknown.";
782                    }
783                    # Close off the sentence with the original link.
784                    $environment .= " URL of event is <a href=\"$url\">$url</a>.";
785                } else {
786                    # No CGI object, so we're a command-line tool. Use the tracing
787                    # key and the PID as the user identifier, and add the command.
788                    my $key = EmergencyKey();
789                    $environment .= "Event Reported by $key process $$.";
790                    if ($CommandLine) {
791                        # We're in a StandardSetup script, so we have the real command line.
792                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
793                    } elsif ($ENV{_}) {
794                        # We're in a BASH script, so the command has been stored in the _ variable.
795                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
796                    }
797                }
798                # Build a GUID. We use the current time, the title, and the process ID,
799                # then digest the result.
800                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
801                # Finally, the description. This is a stack trace plus various environmental stuff.
802                # The trace is optional.
803                my $stackTrace;
804                if ($options{noStack}) {
805                    $stackTrace = "";
806                } else {
807                    my @trace = LongMess();
808                    # Only proceed if we got something back.
809                    if (scalar(@trace) > 0) {
810                        $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
811                        $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
812                    }
813                }
814                # We got the stack trace. Now it's time to put it all together.
815                # We have a goofy thing here in that we need to HTML-escape some sections of the description
816                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
817                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
818                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
819                # our <br>s and <pre>s are used to format the description.
820                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
821                my $description = "$recap$environment  $stackTrace";
822                # Okay, we have all the pieces. Create a hash of the new event.
823                my $newItem = { title => $title,
824                                description => $description,
825                                category => $LastCategory,
826                                pubDate => $date,
827                                guid => $guid,
828                              };
829                # We need XML capability for this.
830                require XML::Simple;
831                # The RSS document goes in here.
832                my $rss;
833                # Get the name of the RSS file. It's in the FIG temporary directory.
834                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
835                # Open the config file and lock it.
836                $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
837                flock $lock, LOCK_EX;
838                # Does it exist?
839                if (-s $fileName) {
840                    # Slurp it in.
841                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
842                } else {
843                    my $size = -s $fileName;
844                    # Create an empty channel.
845                    $rss = {
846                        channel => {
847                            title => 'NMPDR Warning Feed',
848                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
849                            description => "Important messages regarding the status of the NMPDR.",
850                            generator => "NMPDR Trace Facility",
851                            docs => "http://blogs.law.harvard.edu/tech/rss",
852                            item => []
853                        },
854                    };
855                }
856                # Get the channel object.
857                my $channel = $rss->{channel};
858                # Update the last-build date.
859                $channel->{lastBuildDate} = $date;
860                # Get the item array.
861                my $items = $channel->{item};
862                # Insure it has only 100 entries.
863                while (scalar @{$items} > 100) {
864                    pop @{$items};
865                }
866                # Add our new item at the front.
867                unshift @{$items}, $newItem;
868                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
869                # the requirements for those.
870                my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
871                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
872                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
873                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
874                # We don't use Open here because we can't afford an error.
875                if (open XMLOUT, ">$fileName") {
876                    print XMLOUT $xml;
877                    close XMLOUT;
878                }
879            }
880        };
881        if ($@) {
882            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
883            # (which is a good thing).
884            my $error = $@;
885            Trace("Feed Error: $error") if T(Feed => 0);
886        }
887        # Be sure to unlock.
888        if ($lock) {
889            flock $lock, LOCK_UN;
890            undef $lock;
891        }
892        # Restore the error message.
893        $@ = $savedError;
894    }
895    
896    
897    
898    
899    =head3 Assert
900    
901        Assert($condition1, $condition2, ... $conditionN);
902    
903    Return TRUE if all the conditions are true. This method can be used in conjunction with
904    the OR operator and the L</Confess> method as a debugging assert.
905    So, for example
906    
907        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
908    
909    Will abort the program with a stack trace if the value of C<$recNum> is negative.
910    
911    =cut
912    sub Assert {
913        my $retVal = 1;
914        LOOP: for my $condition (@_) {
915            if (! $condition) {
916                $retVal = 0;
917                last LOOP;
918            }
919        }
920        return $retVal;
921    }
922    
923    =head3 Cluck
924    
925        Cluck($message);
926    
927    Trace the call stack. Note that for best results, you should qualify the call with a
928    trace condition. For example,
929    
930        Cluck("Starting record parse.") if T(3);
931    
932    will only trace the stack if the trace level for the package is 3 or more.
933    
934    =over 4
935    
936    =item message
937    
938    Message to include in the trace.
939    
940    =back
941    
942    =cut
943    
944    sub Cluck {
945        # Get the parameters.
946        my ($message) = @_;
947        # Trace what's happening.
948        Trace("Stack trace for event: $message");
949        # Get the stack trace.
950        my @trace = LongMess();
951        # Convert the trace to a series of messages.
952        for my $line (@trace) {
953            # Replace the tab at the beginning with spaces.
954            $line =~ s/^\t/    /;
955            # Trace the line.
956            Trace($line);
957        }
958        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
959        Warn($message);
960    }
961    
962    =head3 LongMess
963    
964        my @lines = Tracer::LongMess();
965    
966    Return a stack trace with all tracing methods removed. The return will be in the form of a list
967    of message strings.
968    
969    =cut
970    
971    sub LongMess {
972        # Declare the return variable.
973        my @retVal = ();
974        my $confession = longmess("");
975        for my $line (split /\s*\n/, $confession) {
976            unless ($line =~ /Tracer\.pm/) {
977                # Here we have a line worth keeping. Push it onto the result list.
978                push @retVal, $line;
979            }
980        }
981        # Return the result.
982        return @retVal;
983    }
984    
985    =head3 ETracing
986    
987        ETracing($parameter);
988    
989    Set up emergency tracing. Emergency tracing is tracing that is turned
990    on automatically for any program that calls this method. The emergency
991    tracing parameters are stored in a a file identified by a tracing key.
992    If this method is called with a CGI object, then the tracing key is
993    taken from a cookie. If it is called with no parameters, then the tracing
994    key is taken from an environment variable. If it is called with a string,
995    the tracing key is that string.
996    
997    =over 4
998    
999    =item parameter
1000    
1001    A parameter from which the tracing key is computed. If it is a scalar,
1002    that scalar is used as the tracing key. If it is a CGI object, the
1003    tracing key is taken from the C<IP> cookie. If it is omitted, the
1004    tracing key is taken from the C<TRACING> environment variable. If it
1005    is a CGI object and emergency tracing is not on, the C<Trace> and
1006    C<TF> parameters will be used to determine the type of tracing.
1007    
1008    =back
1009    
1010    =cut
1011    
1012    sub ETracing {
1013        # Get the parameter.
1014        my ($parameter) = @_;
1015        # Check for CGI mode.
1016        if (defined $parameter && ref $parameter eq 'CGI') {
1017            $SavedCGI = $parameter;
1018        } else {
1019            $SavedCGI = undef;
1020        }
1021        # Default to no tracing except errors.
1022        my ($tracing, $dest) = ("0", "WARN");
1023        # Check for emergency tracing.
1024        my $tkey = EmergencyKey($parameter);
1025        my $emergencyFile = EmergencyFileName($tkey);
1026        if (-e $emergencyFile) {
1027            # We have the file. Read in the data.
1028            my @tracing = GetFile($emergencyFile);
1029            # Pull off the time limit.
1030            my $expire = shift @tracing;
1031            # Convert it to seconds.
1032            $expire *= 3600;
1033            # Check the file data.
1034            my $stat = stat($emergencyFile);
1035            my ($now) = gettimeofday;
1036            if ($now - $stat->mtime > $expire) {
1037                # Delete the expired file.
1038                unlink $emergencyFile;
1039            } else {
1040                # Emergency tracing is on. Pull off the destination and
1041                # the trace level;
1042                $dest = shift @tracing;
1043                my $level = shift @tracing;
1044                # Convert the destination to a real tracing destination.
1045                # temp directory.
1046                $dest = EmergencyTracingDest($tkey, $dest);
1047                # Insure Tracer is specified.
1048                my %moduleHash = map { $_ => 1 } @tracing;
1049                $moduleHash{Tracer} = 1;
1050                # Set the trace parameter.
1051                $tracing = join(" ", $level, sort keys %moduleHash);
1052            }
1053        } elsif (defined $SavedCGI) {
1054            # There's no emergency tracing, but we have a CGI object, so check
1055            # for tracing from the form parameters.
1056            if ($SavedCGI->param('Trace')) {
1057                # Here the user has requested tracing via a form.
1058                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1059                $tracing = $SavedCGI->param('Trace') . " Tracer";
1060            }
1061        }
1062        # Setup the tracing we've determined from all the stuff above.
1063        TSetup($tracing, $dest);
1064        # Check to see if we're a web script.
1065        if (defined $SavedCGI) {
1066            # Yes we are. Trace the form and environment data.
1067            TraceParms($SavedCGI);
1068            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1069            # emitted by the script in its raw form.
1070            if (T(Raw => 3)) {
1071                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1072            }
1073        }
1074    }
1075    
1076    =head3 EmergencyFileName
1077    
1078        my $fileName = Tracer::EmergencyFileName($tkey);
1079    
1080    Return the emergency tracing file name. This is the file that specifies
1081    the tracing information.
1082    
1083    =over 4
1084    
1085    =item tkey
1086    
1087    Tracing key for the current program.
1088    
1089    =item RETURN
1090    
1091    Returns the name of the file to contain the emergency tracing information.
1092    
1093    =back
1094    
1095    =cut
1096    
1097    sub EmergencyFileName {
1098        # Get the parameters.
1099        my ($tkey) = @_;
1100        # Compute the emergency tracing file name.
1101        return "$FIG_Config::temp/Emergency$tkey.txt";
1102    }
1103    
1104    =head3 EmergencyFileTarget
1105    
1106        my $fileName = Tracer::EmergencyFileTarget($tkey);
1107    
1108    Return the emergency tracing target file name. This is the file that receives
1109    the tracing output for file-based tracing.
1110    
1111    =over 4
1112    
1113    =item tkey
1114    
1115    Tracing key for the current program.
1116    
1117    =item RETURN
1118    
1119    Returns the name of the file to contain the trace output.
1120    
1121    =back
1122    
1123    =cut
1124    
1125    sub EmergencyFileTarget {
1126        # Get the parameters.
1127        my ($tkey) = @_;
1128        # Compute the emergency tracing file name.
1129        return "$FIG_Config::temp/trace$tkey.log";
1130    }
1131    
1132    =head3 EmergencyTracingDest
1133    
1134        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1135    
1136    This method converts an emergency tracing destination to a real
1137    tracing destination. The main difference is that if the
1138    destination is C<FILE> or C<APPEND>, we convert it to file
1139    output. If the destination is C<DUAL>, we convert it to file
1140    and standard output.
1141    
1142    =over 4
1143    
1144    =item tkey
1145    
1146    Tracing key for this environment.
1147    
1148    =item myDest
1149    
1150    Destination from the emergency tracing file.
1151    
1152    =item RETURN
1153    
1154    Returns a destination that can be passed into L</TSetup>.
1155    
1156    =back
1157    
1158    =cut
1159    
1160    sub EmergencyTracingDest {
1161        # Get the parameters.
1162        my ($tkey, $myDest) = @_;
1163        # Declare the return variable.
1164        my $retVal = $myDest;
1165        # Process according to the destination value.
1166        if ($myDest eq 'FILE') {
1167            $retVal = ">" . EmergencyFileTarget($tkey);
1168        } elsif ($myDest eq 'APPEND') {
1169            $retVal = ">>" . EmergencyFileTarget($tkey);
1170        } elsif ($myDest eq 'DUAL') {
1171            $retVal = "+>" . EmergencyFileTarget($tkey);
1172        } elsif ($myDest eq 'WARN') {
1173            $retVal = "WARN";
1174        }
1175        # Return the result.
1176        return $retVal;
1177    }
1178    
1179    =head3 Emergency
1180    
1181        Emergency($key, $hours, $dest, $level, @modules);
1182    
1183    Turn on emergency tracing. This method is normally invoked over the web from
1184    a debugging console, but it can also be called by the C<trace.pl> script.
1185    The caller specifies the duration of the emergency in hours, the desired tracing
1186    destination, the trace level, and a list of the trace modules to activate.
1187    For the length of the duration, when a program in an environment with the
1188    specified tracing key active invokes a Sprout CGI script, tracing will be
1189    turned on automatically. See L</TSetup> for more about tracing setup and
1190    L</ETracing> for more about emergency tracing.
1191    
1192    =over 4
1193    
1194    =item tkey
1195    
1196    The tracing key. This is used to identify the control file and the trace file.
1197    
1198    =item hours
1199    
1200    Number of hours to keep emergency tracing alive.
1201    
1202    =item dest
1203    
1204    Tracing destination. If no path information is specified for a file
1205    destination, it is put in the FIG temporary directory.
1206    
1207    =item level
1208    
1209    Tracing level. A higher level means more trace messages.
1210    
1211    =item modules
1212    
1213    A list of the tracing modules to activate.
1214    
1215    =back
1216    
1217    =cut
1218    
1219    sub Emergency {
1220        # Get the parameters.
1221        my ($tkey, $hours, $dest, $level, @modules) = @_;
1222        # Create the emergency file.
1223        my $specFile = EmergencyFileName($tkey);
1224        my $outHandle = Open(undef, ">$specFile");
1225        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1226    }
1227    
1228    =head3 EmergencyKey
1229    
1230        my $tkey = EmergencyKey($parameter);
1231    
1232    Return the Key to be used for emergency tracing. This could be an IP address,
1233     a session ID, or a user name, depending on the environment.
1234    
1235    =over 4
1236    
1237    =item parameter
1238    
1239    Parameter defining the method for finding the tracing key. If it is a scalar,
1240    then it is presumed to be the tracing key itself. If it is a CGI object, then
1241    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1242    taken from the C<TRACING> environment variable.
1243    
1244    =item RETURN
1245    
1246    Returns the key to be used for labels in emergency tracing.
1247    
1248    =back
1249    
1250    =cut
1251    
1252    sub EmergencyKey {
1253        # Get the parameters.
1254        my ($parameter) = @_;
1255        # Declare the return variable.
1256        my $retVal;
1257        # Determine the parameter type.
1258        if (! defined $parameter) {
1259            # Here we're supposed to check the environment. If that fails, we
1260            # get the effective login ID.
1261            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1262        } else {
1263            my $ptype = ref $parameter;
1264            if ($ptype eq 'CGI') {
1265                # Here we were invoked from a web page. Look for a cookie.
1266                $retVal = $parameter->cookie('IP');
1267            } elsif (! $ptype) {
1268                # Here the key was passed in.
1269                $retVal = $parameter;
1270            }
1271        }
1272        # If no luck finding a key, use the PID.
1273        if (! defined $retVal) {
1274            $retVal = $$;
1275        }
1276        # Return the result.
1277        return $retVal;
1278    }
1279    
1280    
1281    =head3 TraceParms
1282    
1283        Tracer::TraceParms($cgi);
1284    
1285    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1286    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1287    
1288    =over 4
1289    
1290    =item cgi
1291    
1292    CGI query object containing the parameters to trace.
1293    
1294    =back
1295    
1296    =cut
1297    
1298    sub TraceParms {
1299        # Get the parameters.
1300        my ($cgi) = @_;
1301        if (T(CGI => 2)) {
1302            # Here we trace the GET-style URL for the script.
1303            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1304        }
1305        if (T(CGI => 3)) {
1306            # Here we want to trace the parameter data.
1307            my @names = $cgi->param;
1308            for my $parmName (sort @names) {
1309                # Note we skip the Trace parameters, which are for our use only.
1310                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1311                    my @values = $cgi->param($parmName);
1312                    Trace("[CGI] $parmName = " . join(", ", @values));
1313                }
1314            }
1315            # Display the request method.
1316            my $method = $cgi->request_method();
1317            Trace("Method: $method");
1318        }
1319        if (T(CGI => 4)) {
1320            # Here we want the environment data too.
1321            for my $envName (sort keys %ENV) {
1322                Trace("[ENV] $envName = $ENV{$envName}");
1323            }
1324        }
1325    }
1326    
1327    =head3 TraceImages
1328    
1329        Tracer::TraceImages($htmlString);
1330    
1331    Trace information about all of an html document's images. The tracing
1332    will be for type "IMG" at level 3. The image's source string
1333    will be displayed. This is generally either the URL of the image or
1334    raw data for the image itself. If the source is too long, only the first 300
1335    characters will be shown at trace level 3. The entire source will be shown,
1336    however, at trace level 4. This method is not very smart, and might catch
1337    Javascript code, but it is still useful when debugging the arcane
1338    behavior of images in multiple browser environments.
1339    
1340    =over 4
1341    
1342    =item htmlString
1343    
1344    HTML text for an outgoing web page.
1345    
1346    =back
1347    
1348    =cut
1349    
1350    sub TraceImages {
1351        # Only proceed if we're at the proper trace level.
1352        if (T(IMG => 3)) {
1353            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1354            # into a variable called "$htmlString". This is because we expect html strings to be
1355            # long, and don't want to copy them any more than we have to.
1356            Trace(length($_[0]) . " characters in web page.");
1357            # Loop through the HTML, culling image tags.
1358            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1359                # Extract the source string and determine whether or not it's too long.
1360                my $srcString = $1;
1361                my $pos = pos($_[0]) - length($srcString);
1362                my $excess = length($srcString) - 300;
1363                # We'll put the display string in here.
1364                my $srcDisplay = $srcString;
1365                # If it's a data string, split it at the comma.
1366                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1367                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1368                # a long string, however, we only show the first 300 characters.
1369                if ($excess > 0 && ! T(IMG => 4)) {
1370                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1371                }
1372                # Output the trace message.
1373                Trace("Image tag at position $pos:\n$srcDisplay");
1374            }
1375        }
1376    }
1377    
1378    =head2 Command-Line Utility Methods
1379    
1380    =head3 SendSMS
1381    
1382        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1383    
1384    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1385    user name, password, and API ID for the relevant account in the hash reference variable
1386    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1387    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1388    is C<2561022>, then the FIG_Config file must contain
1389    
1390        $phone =  { user => 'BruceTheHumanPet',
1391                    password => 'silly',
1392                    api_id => '2561022' };
1393    
1394    The original purpose of this method was to insure Bruce would be notified immediately when the
1395    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1396    when you call this method.
1397    
1398    The message ID will be returned if successful, and C<undef> if an error occurs.
1399    
1400    =over 4
1401    
1402    =item phoneNumber
1403    
1404    Phone number to receive the message, in international format. A United States phone number
1405    would be prefixed by "1". A British phone number would be prefixed by "44".
1406    
1407    =item msg
1408    
1409    Message to send to the specified phone.
1410    
1411    =item RETURN
1412    
1413    Returns the message ID if successful, and C<undef> if the message could not be sent.
1414    
1415    =back
1416    
1417    =cut
1418    
1419    sub SendSMS {
1420        # Get the parameters.
1421        my ($phoneNumber, $msg) = @_;
1422        # Declare the return variable. If we do not change it, C<undef> will be returned.
1423        my $retVal;
1424        # Only proceed if we have phone support.
1425        if (! defined $FIG_Config::phone) {
1426            Trace("Phone support not present in FIG_Config.") if T(1);
1427        } else {
1428            # Get the phone data.
1429            my $parms = $FIG_Config::phone;
1430            # Get the Clickatell URL.
1431            my $url = "http://api.clickatell.com/http/";
1432            # Create the user agent.
1433            my $ua = LWP::UserAgent->new;
1434            # Request a Clickatell session.
1435            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1436                                         password => $parms->{password},
1437                                         api_id => $parms->{api_id},
1438                                         to => $phoneNumber,
1439                                         text => $msg});
1440            # Check for an error.
1441            if (! $resp->is_success) {
1442                Trace("Alert failed.") if T(1);
1443            } else {
1444                # Get the message ID.
1445                my $rstring = $resp->content;
1446                if ($rstring =~ /^ID:\s+(.*)$/) {
1447                    $retVal = $1;
1448                } else {
1449                    Trace("Phone attempt failed with $rstring") if T(1);
1450                }
1451            }
1452        }
1453        # Return the result.
1454        return $retVal;
1455    }
1456    
1457    =head3 StandardSetup
1458    
1459        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1460    
1461    This method performs standard command-line parsing and tracing setup. The return
1462    values are a hash of the command-line options and a list of the positional
1463    parameters. Tracing is automatically set up and the command-line options are
1464    validated.
1465    
1466    This is a complex method that does a lot of grunt work. The parameters can
1467    be more easily understood, however, once they are examined individually.
1468    
1469    The I<categories> parameter is the most obtuse. It is a reference to a list of
1470    special-purpose tracing categories. Most tracing categories are PERL package
1471    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1472    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1473    
1474        ["Sprout", "SproutLoad", "ERDB"]
1475    
1476    This would cause trace messages in the specified three packages to appear in
1477    the output. There are two special tracing categories that are automatically
1478    handled by this method. In other words, if you used L</TSetup> you would need
1479    to include these categories manually, but if you use this method they are turned
1480    on automatically.
1481    
1482    =over 4
1483    
1484    =item SQL
1485    
1486    Traces SQL commands and activity.
1487    
1488    =item Tracer
1489    
1490    Traces error messages and call stacks.
1491    
1492    =back
1493    
1494    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1495    The trace level is specified using the C<-trace> command-line option. For example,
1496    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1497    all tracing at level 3.
1498    
1499        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1500    
1501    Standard tracing is output to the standard output and echoed to the file
1502    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1503    process ID. You can also specify the C<user> parameter to put a user ID
1504    instead of a process ID in the trace file name. So, for example
1505    
1506    The default trace level is 2. To get all messages, specify a trace level of 4.
1507    For a genome-by-genome update, use 3.
1508    
1509        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1510    
1511    would send the trace output to C<traceBruce.log> in the temporary directory.
1512    
1513    The I<options> parameter is a reference to a hash containing the command-line
1514    options, their default values, and an explanation of what they mean. Command-line
1515    options may be in the form of switches or keywords. In the case of a switch, the
1516    option value is 1 if it is specified and 0 if it is not specified. In the case
1517    of a keyword, the value is separated from the option name by an equal sign. You
1518    can see this last in the command-line example above.
1519    
1520    You can specify a different default trace level by setting C<$options->{trace}>
1521    prior to calling this method.
1522    
1523    An example at this point would help. Consider, for example, the command-line utility
1524    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1525    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1526    the following code.
1527    
1528        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1529                            { safe => [0, "use database transactions"],
1530                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1531                              start => [' ', "start with this genome"],
1532                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1533                            "<command> <transactionDirectory> <IDfile>",
1534                          @ARGV);
1535    
1536    
1537    The call to C<ParseCommand> specifies the default values for the options and
1538    stores the actual options in a hash that is returned as C<$options>. The
1539    positional parameters are returned in C<@parameters>.
1540    
1541    The following is a sample command line for C<TransactFeatures>.
1542    
1543        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1544    
1545    Single and double hyphens are equivalent. So, you could also code the
1546    above command as
1547    
1548        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1549    
1550    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1551    parameters, and would find themselves in I<@parameters> after executing the
1552    above code fragment. The tracing would be set to level 2, and the categories
1553    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1554    and C<DocUtils> was included because it came in within the first parameter
1555    to this method. The I<$options> hash would be
1556    
1557        { trace => 2, sql => 0, safe => 0,
1558          noAlias => 1, start => ' ', tblFiles => 0 }
1559    
1560    Use of C<StandardSetup> in this way provides a simple way of performing
1561    standard tracing setup and command-line parsing. Note that the caller is
1562    not even aware of the command-line switches C<-trace> and C<-sql>, which
1563    are used by this method to control the tracing. If additional tracing features
1564    need to be added in the future, they can be processed by this method without
1565    upsetting the command-line utilities.
1566    
1567    If the C<background> option is specified on the command line, then the
1568    standard and error outputs will be directed to files in the temporary
1569    directory, using the same suffix as the trace file. So, if the command
1570    line specified
1571    
1572        -user=Bruce -background
1573    
1574    then the trace output would go to C<traceBruce.log>, the standard output to
1575    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1576    simplify starting a command in the background.
1577    
1578    The user name is also used as the tracing key for L</Emergency Tracing>.
1579    Specifying a value of C<E> for the trace level causes emergency tracing to
1580    be used instead of custom tracing. If the user name is not specified,
1581    the tracing key is taken from the C<Tracing> environment variable. If there
1582    is no value for that variable, the tracing key will be computed from the active
1583    login ID.
1584    
1585    Since the default situation in StandardSetup is to trace to the standard
1586    output, errors that occur in command-line scripts will not generate
1587    RSS events. To force the events, use the C<warn> option.
1588    
1589        TransactFeatures -background -warn register ../xacts IDs.tbl
1590    
1591    Finally, if the special option C<-help> is specified, the option
1592    names will be traced at level 0 and the program will exit without processing.
1593    This provides a limited help capability. For example, if the user enters
1594    
1595        TransactFeatures -help
1596    
1597    he would see the following output.
1598    
1599        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1600            -trace    tracing level (default E)
1601            -sql      trace SQL commands
1602            -safe     use database transactions
1603            -noAlias  do not expect aliases in CHANGE transactions
1604            -start    start with this genome
1605            -tblFiles output TBL files containing the corrected IDs
1606    
1607    The caller has the option of modifying the tracing scheme by placing a value
1608    for C<trace> in the incoming options hash. The default value can be overridden,
1609    or the tracing to the standard output can be turned off by suffixing a minus
1610    sign to the trace level. So, for example,
1611    
1612        { trace => [0, "tracing level (default 0)"],
1613           ...
1614    
1615    would set the default trace level to 0 instead of E, while
1616    
1617        { trace => ["2-", "tracing level (default 2)"],
1618           ...
1619    
1620    would set the default to 2, but trace only to the log file, not to the
1621    standard output.
1622    
1623    The parameters to this method are as follows.
1624    
1625    =over 4
1626    
1627    =item categories
1628    
1629    Reference to a list of tracing category names. These should be names of
1630    packages whose internal workings will need to be debugged to get the
1631    command working.
1632    
1633    =item options
1634    
1635    Reference to a hash containing the legal options for the current command mapped
1636    to their default values and descriptions. The user can override the defaults
1637    by specifying the options as command-line switches prefixed by a hyphen.
1638    Tracing-related options may be added to this hash. If the C<-h> option is
1639    specified on the command line, the option descriptions will be used to
1640    explain the options. To turn off tracing to the standard output, add a
1641    minus sign to the value for C<trace> (see above).
1642    
1643    =item parmHelp
1644    
1645    A string that vaguely describes the positional parameters. This is used
1646    if the user specifies the C<-h> option.
1647    
1648    =item argv
1649    
1650    List of command line parameters, including the option switches, which must
1651    precede the positional parameters and be prefixed by a hyphen.
1652    
1653    =item RETURN
1654    
1655    Returns a list. The first element of the list is the reference to a hash that
1656    maps the command-line option switches to their values. These will either be the
1657    default values or overrides specified on the command line. The remaining
1658    elements of the list are the position parameters, in order.
1659    
1660    =back
1661    
1662    =cut
1663    
1664    sub StandardSetup {
1665        # Get the parameters.
1666        my ($categories, $options, $parmHelp, @argv) = @_;
1667        # Get the default tracing key.
1668        my $tkey = EmergencyKey();
1669        # Save the command line.
1670        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1671        # Add the tracing options.
1672        if (! exists $options->{trace}) {
1673            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1674        }
1675        $options->{sql} = [0, "turn on SQL tracing"];
1676        $options->{help} = [0, "display command-line options"];
1677        $options->{user} = [$tkey, "tracing key"];
1678        $options->{background} = [0, "spool standard and error output"];
1679        $options->{warn} = [0, "send errors to RSS feed"];
1680        # Create a parsing hash from the options hash. The parsing hash
1681        # contains the default values rather than the default value
1682        # and the description. While we're at it, we'll memorize the
1683        # length of the longest option name.
1684      my $longestName = 0;      my $longestName = 0;
1685      my %parseOptions = ();      my %parseOptions = ();
1686      for my $key (keys %{$options}) {      for my $key (keys %{$options}) {
1687          if (length $key > $longestName) {          if (length $key > $longestName) {
1688              $longestName = length $key;              $longestName = length $key;
1689          }          }
1690          $parseOptions{$key} = $options->{$key}->[0];          $parseOptions{$key} = $options->{$key}->[0];
1691        }
1692        # Parse the command line.
1693        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1694        # Get the logfile suffix.
1695        my $suffix = $retOptions->{user};
1696        # Check for background mode.
1697        if ($retOptions->{background}) {
1698            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1699            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1700            open STDOUT, ">$outFileName";
1701            open STDERR, ">$errFileName";
1702            # Check for phone support. If we have phone support and a phone number,
1703            # we want to turn it on.
1704            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1705                $retOptions->{phone} = $ENV{PHONE};
1706            }
1707        }
1708        # Now we want to set up tracing. First, we need to know if the user
1709        # wants emergency tracing.
1710        if ($retOptions->{trace} eq 'E') {
1711            ETracing($retOptions->{user});
1712        } else {
1713            # Here the tracing is controlled from the command line.
1714            my @cats = @{$categories};
1715            if ($retOptions->{sql}) {
1716                push @cats, "SQL";
1717            }
1718            if ($retOptions->{warn}) {
1719                push @cats, "Feed";
1720            }
1721            # Add the default categories.
1722            push @cats, "Tracer";
1723            # Next, we create the category string by joining the categories.
1724            my $cats = join(" ", @cats);
1725            # Check to determine whether or not the caller wants to turn off tracing
1726            # to the standard output.
1727            my $traceLevel = $retOptions->{trace};
1728            my $textOKFlag = 1;
1729            if ($traceLevel =~ /^(.)-/) {
1730                $traceLevel = $1;
1731                $textOKFlag = 0;
1732            }
1733            # Now we set up the trace mode.
1734            my $traceMode;
1735            # Verify that we can open a file in the FIG temporary directory.
1736            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1737            if (open TESTTRACE, ">$traceFileName") {
1738                # Here we can trace to a file.
1739                $traceMode = ">$traceFileName";
1740                if ($textOKFlag) {
1741                    # Echo to standard output if the text-OK flag is set.
1742                    $traceMode = "+$traceMode";
1743                }
1744                # Close the test file.
1745                close TESTTRACE;
1746            } else {
1747                # Here we can't trace to a file. Complain about this.
1748                warn "Could not open trace file $traceFileName: $!\n";
1749                # We trace to the standard output if it's
1750                # okay, and the error log otherwise.
1751                if ($textOKFlag) {
1752                    $traceMode = "TEXT";
1753                } else {
1754                    $traceMode = "WARN";
1755                }
1756            }
1757            # Now set up the tracing.
1758            TSetup("$traceLevel $cats", $traceMode);
1759        }
1760        # Check for the "help" option. If it is specified, dump the command-line
1761        # options and exit the program.
1762        if ($retOptions->{help}) {
1763            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1764            print "$1 [options] $parmHelp\n";
1765            for my $key (sort keys %{$options}) {
1766                my $name = Pad($key, $longestName, 0, ' ');
1767                my $desc = $options->{$key}->[1];
1768                if ($options->{$key}->[0]) {
1769                    $desc .= " (default " . $options->{$key}->[0] . ")";
1770                }
1771                print "  $name $desc\n";
1772            }
1773            exit(0);
1774        }
1775        # Trace the options, if applicable.
1776        if (T(3)) {
1777            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1778            Trace("Selected options: " . join(", ", sort @parms) . ".");
1779        }
1780        # Return the parsed parameters.
1781        return ($retOptions, @retParameters);
1782    }
1783    
1784    =head3 ReadOptions
1785    
1786        my %options = Tracer::ReadOptions($fileName);
1787    
1788    Read a set of options from a file. Each option is encoded in a line of text that has the
1789    format
1790    
1791    I<optionName>C<=>I<optionValue>C<; >I<comment>
1792    
1793    The option name must consist entirely of letters, digits, and the punctuation characters
1794    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1795    character is a semi-colon will be ignored. The return hash will map each option name to
1796    the corresponding option value.
1797    
1798    =over 4
1799    
1800    =item fileName
1801    
1802    Name of the file containing the option data.
1803    
1804    =item RETURN
1805    
1806    Returns a hash mapping the option names specified in the file to their corresponding option
1807    value.
1808    
1809    =back
1810    
1811    =cut
1812    
1813    sub ReadOptions {
1814        # Get the parameters.
1815        my ($fileName) = @_;
1816        # Open the file.
1817        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1818        # Count the number of records read.
1819        my ($records, $comments) = 0;
1820        # Create the return hash.
1821        my %retVal = ();
1822        # Loop through the file, accumulating key-value pairs.
1823        while (my $line = <CONFIGFILE>) {
1824            # Denote we've read a line.
1825            $records++;
1826            # Determine the line type.
1827            if ($line =~ /^\s*[\n\r]/) {
1828                # A blank line is a comment.
1829                $comments++;
1830            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1831                # Here we have an option assignment.
1832                retVal{$1} = $2;
1833            } elsif ($line =~ /^\s*;/) {
1834                # Here we have a text comment.
1835                $comments++;
1836            } else {
1837                # Here we have an invalid line.
1838                Trace("Invalid option statement in record $records.") if T(0);
1839            }
1840        }
1841        # Return the hash created.
1842        return %retVal;
1843    }
1844    
1845    =head3 GetOptions
1846    
1847        Tracer::GetOptions(\%defaults, \%options);
1848    
1849    Merge a specified set of options into a table of defaults. This method takes two hash references
1850    as input and uses the data from the second to update the first. If the second does not exist,
1851    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1852    exist in the first.
1853    
1854    Consider the following example.
1855    
1856        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1857    
1858    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1859    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1860    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1861    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1862    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1863    
1864        {databaseType => 'Oracle'}
1865    
1866    an error will occur because the B<databaseType> option does not exist.
1867    
1868    =over 4
1869    
1870    =item defaults
1871    
1872    Table of default option values.
1873    
1874    =item options
1875    
1876    Table of overrides, if any.
1877    
1878    =item RETURN
1879    
1880    Returns a reference to the default table passed in as the first parameter.
1881    
1882    =back
1883    
1884    =cut
1885    
1886    sub GetOptions {
1887        # Get the parameters.
1888        my ($defaults, $options) = @_;
1889        # Check for overrides.
1890        if ($options) {
1891            # Loop through the overrides.
1892            while (my ($option, $setting) = each %{$options}) {
1893                # Insure this override exists.
1894                if (!exists $defaults->{$option}) {
1895                    croak "Unrecognized option $option encountered.";
1896                } else {
1897                    # Apply the override.
1898                    $defaults->{$option} = $setting;
1899                }
1900      }      }
     # Parse the command line.  
     my ($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";  
1901      }      }
1902      # Now we want to set up tracing. First, we need to know if SQL is to      # Return the merged table.
1903      # be traced.      return $defaults;
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
1904      }      }
1905      # Add the default categories.  
1906      push @cats, "Tracer", "FIG";  =head3 MergeOptions
1907      # Next, we create the category string by joining the categories.  
1908      my $cats = join(" ", @cats);      Tracer::MergeOptions(\%table, \%defaults);
1909      # Check to determine whether or not the caller wants to turn off tracing  
1910      # to the standard output.  Merge default values into a hash table. This method looks at the key-value pairs in the
1911      my $traceLevel = $retOptions->{trace};  second (default) hash, and if a matching key is not found in the first hash, the default
1912      my $textOKFlag = 1;  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1913      if ($traceLevel =~ /^(.)-/) {  checking and no return value.
1914          $traceLevel = $1;  
1915          $textOKFlag = 0;  =over 4
1916    
1917    =item table
1918    
1919    Hash table to be updated with the default values.
1920    
1921    =item defaults
1922    
1923    Default values to be merged into the first hash table if they are not already present.
1924    
1925    =back
1926    
1927    =cut
1928    
1929    sub MergeOptions {
1930        # Get the parameters.
1931        my ($table, $defaults) = @_;
1932        # Loop through the defaults.
1933        while (my ($key, $value) = each %{$defaults}) {
1934            if (!exists $table->{$key}) {
1935                $table->{$key} = $value;
1936      }      }
     # Now we set up the trace mode.  
     my $traceMode;  
     # Verify that we can open a file in the FIG temporary directory.  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         # Here we can trace to a file.  
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
1937          }          }
1938          # Close the test file.  }
1939          close TESTTRACE;  
1940    =head3 ParseCommand
1941    
1942        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1943    
1944    Parse a command line consisting of a list of parameters. The initial parameters may be option
1945    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1946    off and merged into a table of default options. The remainder of the command line is
1947    returned as a list of positional arguments. For example, consider the following invocation.
1948    
1949        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1950    
1951    In this case, the list @words will be treated as a command line and there are two options available,
1952    B<errors> and B<logFile>. If @words has the following format
1953    
1954        -logFile=error.log apple orange rutabaga
1955    
1956    then at the end of the invocation, C<$options> will be
1957    
1958        { errors => 0, logFile => 'error.log' }
1959    
1960    and C<@arguments> will contain
1961    
1962        apple orange rutabaga
1963    
1964    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1965    support for quote characters. Options can be specified with single or double hyphens.
1966    
1967    =over 4
1968    
1969    =item optionTable
1970    
1971    Table of default options.
1972    
1973    =item inputList
1974    
1975    List of words on the command line.
1976    
1977    =item RETURN
1978    
1979    Returns a reference to the option table and a list of the positional arguments.
1980    
1981    =back
1982    
1983    =cut
1984    
1985    sub ParseCommand {
1986        # Get the parameters.
1987        my ($optionTable, @inputList) = @_;
1988        # Process any options in the input list.
1989        my %overrides = ();
1990        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1991            # Get the current option.
1992            my $arg = shift @inputList;
1993            # Pull out the option name.
1994            $arg =~ /^--?([^=]*)/g;
1995            my $name = $1;
1996            # Check for an option value.
1997            if ($arg =~ /\G=(.*)$/g) {
1998                # Here we have a value for the option.
1999                $overrides{$name} = UnEscape($1);
2000      } else {      } else {
2001          # Here we can't trace to a file. We trace to the standard output if it's              # Here there is no value, so we use 1.
2002          # okay, and the error log otherwise.              $overrides{$name} = 1;
2003          if ($textOKFlag) {          }
2004              $traceMode = "TEXT";      }
2005        # Merge the options into the defaults.
2006        GetOptions($optionTable, \%overrides);
2007        # Translate the remaining parameters.
2008        my @retVal = ();
2009        for my $inputParm (@inputList) {
2010            push @retVal, UnEscape($inputParm);
2011        }
2012        # Return the results.
2013        return ($optionTable, @retVal);
2014    }
2015    
2016    
2017    =head2 File Utility Methods
2018    
2019    =head3 GetFile
2020    
2021        my @fileContents = Tracer::GetFile($fileName);
2022    
2023        or
2024    
2025        my $fileContents = Tracer::GetFile($fileName);
2026    
2027    Return the entire contents of a file. In list context, line-ends are removed and
2028    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2029    
2030    =over 4
2031    
2032    =item fileName
2033    
2034    Name of the file to read.
2035    
2036    =item RETURN
2037    
2038    In a list context, returns the entire file as a list with the line terminators removed.
2039    In a scalar context, returns the entire file as a string. If an error occurs opening
2040    the file, an empty list will be returned.
2041    
2042    =back
2043    
2044    =cut
2045    
2046    sub GetFile {
2047        # Get the parameters.
2048        my ($fileName) = @_;
2049        # Declare the return variable.
2050        my @retVal = ();
2051        # Open the file for input.
2052        my $handle = Open(undef, "<$fileName");
2053        # Read the whole file into the return variable, stripping off any terminator
2054        # characters.
2055        my $lineCount = 0;
2056        while (my $line = <$handle>) {
2057            $lineCount++;
2058            $line = Strip($line);
2059            push @retVal, $line;
2060        }
2061        # Close it.
2062        close $handle;
2063        my $actualLines = @retVal;
2064        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2065        # Return the file's contents in the desired format.
2066        if (wantarray) {
2067            return @retVal;
2068          } else {          } else {
2069              $traceMode = "WARN";          return join "\n", @retVal;
2070          }          }
2071      }      }
2072      # Now set up the tracing.  
2073      TSetup("$traceLevel $cats", $traceMode);  =head3 PutFile
2074      # Check for the "h" option. If it is specified, dump the command-line  
2075      # options and exit the program.      Tracer::PutFile($fileName, \@lines);
2076      if ($retOptions->{h}) {  
2077          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Write out a file from a list of lines of text.
2078          Trace("$1 [options] $parmHelp") if T(0);  
2079          for my $key (sort keys %{$options}) {  =over 4
2080              my $name = Pad($key, $longestName, 0, ' ');  
2081              my $desc = $options->{$key}->[1];  =item fileName
2082              if ($options->{$key}->[0]) {  
2083                  $desc .= " (default " . $options->{$key}->[0] . ")";  Name of the output file.
2084    
2085    =item lines
2086    
2087    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2088    new-line characters. Alternatively, may be a string, in which case the string will be written without
2089    modification.
2090    
2091    =back
2092    
2093    =cut
2094    
2095    sub PutFile {
2096        # Get the parameters.
2097        my ($fileName, $lines) = @_;
2098        # Open the output file.
2099        my $handle = Open(undef, ">$fileName");
2100        # Count the lines written.
2101        if (ref $lines ne 'ARRAY') {
2102            # Here we have a scalar, so we write it raw.
2103            print $handle $lines;
2104            Trace("Scalar put to file $fileName.") if T(File => 3);
2105        } else {
2106            # Write the lines one at a time.
2107            my $count = 0;
2108            for my $line (@{$lines}) {
2109                print $handle "$line\n";
2110                $count++;
2111              }              }
2112              Trace("  $name $desc") if T(0);          Trace("$count lines put to file $fileName.") if T(File => 3);
2113          }          }
2114          exit(0);      # Close the output file.
2115        close $handle;
2116    }
2117    
2118    =head3 ParseRecord
2119    
2120        my @fields = Tracer::ParseRecord($line);
2121    
2122    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2123    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2124    These will automatically be converted.
2125    
2126    =over 4
2127    
2128    =item line
2129    
2130    Line of data containing the tab-delimited fields.
2131    
2132    =item RETURN
2133    
2134    Returns a list of the fields found in the data line.
2135    
2136    =back
2137    
2138    =cut
2139    
2140    sub ParseRecord {
2141        # Get the parameter.
2142        my ($line) = @_;
2143        # Remove the trailing new-line, if any.
2144        chomp $line;
2145        # Split the line read into pieces using the tab character.
2146        my @retVal = split /\t/, $line;
2147        # Trim and fix the escapes in each piece.
2148        for my $value (@retVal) {
2149            # Trim leading whitespace.
2150            $value =~ s/^\s+//;
2151            # Trim trailing whitespace.
2152            $value =~ s/\s+$//;
2153            # Delete the carriage returns.
2154            $value =~ s/\r//g;
2155            # Convert the escapes into their real values.
2156            $value =~ s/\\t/"\t"/ge;
2157            $value =~ s/\\n/"\n"/ge;
2158      }      }
2159      # Return the parsed parameters.      # Return the result.
2160      return ($retOptions, @retParameters);      return @retVal;
2161  }  }
2162    
2163  =head3 Setups  =head3 Merge
2164    
2165  C<< my $count = Tracer::Setups(); >>      my @mergedList = Tracer::Merge(@inputList);
2166    
2167  Return the number of times L</TSetup> has been called.  Sort a list of strings and remove duplicates.
2168    
2169  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
2170  may want to set up tracing if nobody else has done it before us.  
2171    =item inputList
2172    
2173    List of scalars to sort and merge.
2174    
2175    =item RETURN
2176    
2177    Returns a list containing the same elements sorted in ascending order with duplicates
2178    removed.
2179    
2180    =back
2181    
2182  =cut  =cut
2183    
2184  sub Setups {  sub Merge {
2185      return $SetupCount;      # Get the input list in sort order.
2186        my @inputList = sort @_;
2187        # Only proceed if the list has at least two elements.
2188        if (@inputList > 1) {
2189            # Now we want to move through the list splicing out duplicates.
2190            my $i = 0;
2191            while ($i < @inputList) {
2192                # Get the current entry.
2193                my $thisEntry = $inputList[$i];
2194                # Find out how many elements duplicate the current entry.
2195                my $j = $i + 1;
2196                my $dup1 = $i + 1;
2197                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2198                # If the number is nonzero, splice out the duplicates found.
2199                if ($j > $dup1) {
2200                    splice @inputList, $dup1, $j - $dup1;
2201                }
2202                # Now the element at position $dup1 is different from the element before it
2203                # at position $i. We push $i forward one position and start again.
2204                $i++;
2205            }
2206        }
2207        # Return the merged list.
2208        return @inputList;
2209  }  }
2210    
2211  =head3 Open  =head3 Open
2212    
2213  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2214    
2215  Open a file.  Open a file.
2216    
# Line 607  Line 2302 
2302    
2303  =head3 FindNamePart  =head3 FindNamePart
2304    
2305  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2306    
2307  Extract the portion of a file specification that contains the file name.  Extract the portion of a file specification that contains the file name.
2308    
# Line 618  Line 2313 
2313  C</usr/fig/myfile.txt>.  C</usr/fig/myfile.txt>.
2314    
2315      >>/usr/fig/myfile.txt      >>/usr/fig/myfile.txt
2316      </usr/fig/myfile.txt      </usr/fig/myfile.txt
2317      | sort -u > /usr/fig/myfile.txt      | sort -u > /usr/fig/myfile.txt
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
   
 Returns a three-element list. The first element contains the file name portion of  
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
   
     my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  
   
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
   
 TRUE if a failure to open is okay, else FALSE  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 SetLevel  
   
 C<< Tracer::SetLevel($newLevel); >>  
   
 Modify the trace level. A higher trace level will cause more messages to appear.  
   
 =over 4  
   
 =item newLevel  
   
 Proposed new trace level.  
   
 =back  
   
 =cut  
   
 sub SetLevel {  
     $TraceLevel = $_[0];  
 }  
   
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
   
 =head3 LogErrors  
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
 }  
   
 =head3 ReadOptions  
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
   
 I<optionName>C<=>I<optionValue>C<; >I<comment>  
2318    
2319  The option name must consist entirely of letters, digits, and the punctuation characters  If the method cannot find a file name using its normal methods, it will return the
2320  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  whole incoming string.
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
2321    
2322  =over 4  =over 4
2323    
2324  =item fileName  =item fileSpec
2325    
2326  Name of the file containing the option data.  File specification string from which the file name is to be extracted.
2327    
2328  =item RETURN  =item RETURN
2329    
2330  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a three-element list. The first element contains the file name portion of
2331  value.  the specified string, or the whole string if a file name cannot be found via normal
2332    methods. The second element contains the start position of the file name portion and
2333    the third element contains the length.
2334    
2335  =back  =back
2336    
2337  =cut  =cut
2338    #: Return Type $;
2339  sub ReadOptions {  sub FindNamePart {
2340      # Get the parameters.      # Get the parameters.
2341      my ($fileName) = @_;      my ($fileSpec) = @_;
2342      # Open the file.      # Default to the whole input string.
2343      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2344      # Count the number of records read.      # Parse out the file name if we can.
2345      my ($records, $comments) = 0;      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2346      # Create the return hash.          $retVal = $2;
2347      my %retVal = ();          $len = length $retVal;
2348      # Loop through the file, accumulating key-value pairs.          $pos = (length $fileSpec) - (length $3) - $len;
     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 $records.") if T(0);  
         }  
2349      }      }
2350      # Return the hash created.      # Return the result.
2351      return %retVal;      return ($retVal, $pos, $len);
2352  }  }
2353    
2354  =head3 GetOptions  =head3 OpenDir
2355    
2356  C<< Tracer::GetOptions(\%defaults, \%options); >>      my @files = OpenDir($dirName, $filtered, $flag);
2357    
2358  Merge a specified set of options into a table of defaults. This method takes two hash references  Open a directory and return all the file names. This function essentially performs
2359  as input and uses the data from the second to update the first. If the second does not exist,  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2360  there will be no effect. An error will be thrown if one of the entries in the second hash does not  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2361  exist in the first.  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2362    filtered out of the return list. If the directory does not open and I<$flag> is not
2363    set, an exception is thrown. So, for example,
2364    
2365  Consider the following example.      my @files = OpenDir("/Volumes/fig/contigs", 1);
2366    
2367  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  is effectively the same as
2368    
2369  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2370  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
 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  
2371    
2372  C<< {databaseType => 'Oracle'} >>  Similarly, the following code
2373    
2374  an error will occur because the B<databaseType> option does not exist.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2375    
2376    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2377    automatically returns an empty list if the directory fails to open.
2378    
2379  =over 4  =over 4
2380    
2381  =item defaults  =item dirName
2382    
2383  Table of default option values.  Name of the directory to open.
2384    
2385  =item options  =item filtered
2386    
2387  Table of overrides, if any.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2388    from the list, else FALSE.
2389    
2390  =item RETURN  =item flag
2391    
2392  Returns a reference to the default table passed in as the first parameter.  TRUE if a failure to open is okay, else FALSE
2393    
2394  =back  =back
2395    
2396  =cut  =cut
2397    #: Return Type @;
2398  sub GetOptions {  sub OpenDir {
2399      # Get the parameters.      # Get the parameters.
2400      my ($defaults, $options) = @_;      my ($dirName, $filtered, $flag) = @_;
2401      # Check for overrides.      # Declare the return variable.
2402      if ($options) {      my @retVal = ();
2403          # Loop through the overrides.      # Open the directory.
2404          while (my ($option, $setting) = each %{$options}) {      if (opendir(my $dirHandle, $dirName)) {
2405              # Insure this override exists.          # The directory opened successfully. Get the appropriate list according to the
2406              if (!exists $defaults->{$option}) {          # strictures of the filter parameter.
2407                  croak "Unrecognized option $option encountered.";          if ($filtered) {
2408                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2409              } else {              } else {
2410                  # Apply the override.              @retVal = readdir $dirHandle;
                 $defaults->{$option} = $setting;  
             }  
2411          }          }
2412        } elsif (! $flag) {
2413            # Here the directory would not open and it's considered an error.
2414            Confess("Could not open directory $dirName.");
2415      }      }
2416      # Return the merged table.      # Return the result.
2417      return $defaults;      return @retVal;
2418  }  }
2419    
 =head3 MergeOptions  
2420    
2421  C<< Tracer::MergeOptions(\%table, \%defaults); >>  =head3 Insure
2422    
2423  Merge default values into a hash table. This method looks at the key-value pairs in the      Insure($dirName, $chmod);
2424  second (default) hash, and if a matching key is not found in the first hash, the default  
2425  pair is copied in. The process is similar to L</GetOptions>, but there is no error-  Insure a directory is present.
 checking and no return value.  
2426    
2427  =over 4  =over 4
2428    
2429  =item table  =item dirName
2430    
2431  Hash table to be updated with the default values.  Name of the directory to check. If it does not exist, it will be created.
2432    
2433  =item defaults  =item chmod (optional)
2434    
2435  Default values to be merged into the first hash table if they are not already present.  Security privileges to be given to the directory if it is created.
2436    
2437  =back  =back
2438    
2439  =cut  =cut
2440    
2441  sub MergeOptions {  sub Insure {
2442      # Get the parameters.      my ($dirName, $chmod) = @_;
2443      my ($table, $defaults) = @_;      if (! -d $dirName) {
2444      # Loop through the defaults.          Trace("Creating $dirName directory.") if T(2);
2445      while (my ($key, $value) = each %{$defaults}) {          eval {
2446          if (!exists $table->{$key}) {              mkpath $dirName;
2447              $table->{$key} = $value;              # If we have permissions specified, set them here.
2448          }              if (defined($chmod)) {
2449      }                  chmod $chmod, $dirName;
2450  }  }
2451            };
2452  =head3 Trace          if ($@) {
2453                Confess("Error creating $dirName: $@");
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
2454          }          }
2455      }      }
2456  }  }
2457    
2458  =head3 T  =head3 ChDir
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
2459    
2460  C<< my $switch = T($traceLevel); >>      ChDir($dirName);
2461    
2462  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.  
2463    
2464  =over 4  =over 4
2465    
2466  =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  
2467    
2468  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.
2469    
2470  =back  =back
2471    
2472  =cut  =cut
2473    
2474  sub T {  sub ChDir {
2475      # Declare the return variable.      my ($dirName) = @_;
2476      my $retVal = 0;      if (! -d $dirName) {
2477      # 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";  
2478              } else {              } else {
2479                  $category = $package;          Trace("Changing to directory $dirName.") if T(File => 4);
2480              }          my $okFlag = chdir $dirName;
2481          }          if (! $okFlag) {
2482          # 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.");  
2483          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2484      }      }
     # Return the computed result.  
     return $retVal;  
2485  }  }
2486    
2487  =head3 ParseCommand  =head3 SetPermissions
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
2488    
2489  Parse a command line consisting of a list of parameters. The initial parameters may be option      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
2490    
2491  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Set the permissions for a directory and all the files and folders inside it.
2492    In addition, the group ownership will be changed to the specified value.
2493    
2494  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
2495  B<errors> and B<logFile>. If @words has the following format  problems, so it does internal error recovery.
2496    
2497  C<< -logFile=error.log apple orange rutabaga >>  =over 4
2498    
2499  then at the end of the invocation, C<$options> will be  =item dirName
2500    
2501  C<< { errors => 0, logFile => 'error.log' } >>  Name of the directory to process.
2502    
2503  and C<@arguments> will contain  =item group
2504    
2505  C<< apple orange rutabaga >>  Name of the group to be assigned.
2506    
2507  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =item mask
 support for quote characters.  
2508    
2509  =over 4  Permission mask. Bits that are C<1> in this mask will be ORed into the
2510    permission bits of any file or directory that does not already have them
2511    set to 1.
2512    
2513  =item optionTable  =item otherMasks
2514    
2515  Table of default options.  Map of search patterns to permission masks. If a directory name matches
2516    one of the patterns, that directory and all its members and subdirectories
2517    will be assigned the new pattern. For example, the following would
2518    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2519    
2520  =item inputList      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2521    
2522  List of words on the command line.  The list is ordered, so the following would use 0777 for C<tmp1> and
2523    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2524    
2525  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2526                                                       '^tmp' => 0666);
2527    
2528  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
2529    names are matched, not file names.
2530    
2531  =back  =back
2532    
2533  =cut  =cut
2534    
2535  sub ParseCommand {  sub SetPermissions {
2536      # Get the parameters.      # Get the parameters.
2537      my ($optionTable, @inputList) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2538      # Process any options in the input list.      # Set up for error recovery.
2539      my %overrides = ();      eval {
2540      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          # Switch to the specified directory.
2541          # Get the current option.          ChDir($dirName);
2542          my $arg = shift @inputList;          # Get the group ID.
2543          # Pull out the option name.          my $gid = getgrnam($group);
2544          $arg =~ /^-([^=]*)/g;          # Get the mask for tracing.
2545          my $name = $1;          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2546          # Check for an option value.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2547          if ($arg =~ /\G=(.*)$/g) {          my $fixCount = 0;
2548              # Here we have a value for the option.          my $lookCount = 0;
2549              $overrides{$name} = UnEscape($1);          # @dirs will be a stack of directories to be processed.
2550            my @dirs = (getcwd());
2551            while (scalar(@dirs) > 0) {
2552                # Get the current directory.
2553                my $dir = pop @dirs;
2554                # Check for a match to one of the specified directory names. To do
2555                # that, we need to pull the individual part of the name off of the
2556                # whole path.
2557                my $simpleName = $dir;
2558                if ($dir =~ m!/([^/]+)$!) {
2559                    $simpleName = $1;
2560                }
2561                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2562                # Search for a match.
2563                my $match = 0;
2564                my $i;
2565                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2566                    my $pattern = $otherMasks[$i];
2567                    if ($simpleName =~ /$pattern/i) {
2568                        $match = 1;
2569                    }
2570                }
2571                # Check for a match. Note we use $i-1 because the loop added 2
2572                # before terminating due to the match.
2573                if ($match && $otherMasks[$i-1] != $mask) {
2574                    # This directory matches one of the incoming patterns, and it's
2575                    # a different mask, so we process it recursively with that mask.
2576                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2577          } else {          } else {
2578              # Here there is no value, so we use 1.                  # Here we can process normally. Get all of the non-hidden members.
2579              $overrides{$name} = 1;                  my @submems = OpenDir($dir, 1);
2580                    for my $submem (@submems) {
2581                        # Get the full name.
2582                        my $thisMem = "$dir/$submem";
2583                        Trace("Checking member $thisMem.") if T(4);
2584                        $lookCount++;
2585                        if ($lookCount % 1000 == 0) {
2586                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2587                        }
2588                        # Fix the group.
2589                        chown -1, $gid, $thisMem;
2590                        # Insure this member is not a symlink.
2591                        if (! -l $thisMem) {
2592                            # Get its info.
2593                            my $fileInfo = stat $thisMem;
2594                            # Only proceed if we got the info. Otherwise, it's a hard link
2595                            # and we want to skip it anyway.
2596                            if ($fileInfo) {
2597                                my $fileMode = $fileInfo->mode;
2598                                if (($fileMode & $mask) != $mask) {
2599                                    # Fix this member.
2600                                    $fileMode |= $mask;
2601                                    chmod $fileMode, $thisMem;
2602                                    $fixCount++;
2603          }          }
2604                                # If it's a subdirectory, stack it.
2605                                if (-d $thisMem) {
2606                                    push @dirs, $thisMem;
2607      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2608      }      }
2609      # Return the results.                      }
2610      return ($optionTable, @retVal);                  }
2611                }
2612            }
2613            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2614        };
2615        # Check for an error.
2616        if ($@) {
2617            Confess("SetPermissions error: $@");
2618        }
2619  }  }
2620    
2621  =head3 Escape  =head3 GetLine
2622    
2623  C<< my $codedString = Tracer::Escape($realString); >>      my @data = Tracer::GetLine($handle);
2624    
2625  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Read a line of data from a tab-delimited file.
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
2626    
2627  =over 4  =over 4
2628    
2629  =item realString  =item handle
2630    
2631  String to escape.  Open file handle from which to read.
2632    
2633  =item RETURN  =item RETURN
2634    
2635  Escaped equivalent of the real string.  Returns a list of the fields in the record read. The fields are presumed to be
2636    tab-delimited. If we are at the end of the file, then an empty list will be
2637    returned. If an empty line is read, a single list item consisting of a null
2638    string will be returned.
2639    
2640  =back  =back
2641    
2642  =cut  =cut
2643    
2644  sub Escape {  sub GetLine {
2645      # Get the parameter.      # Get the parameters.
2646      my ($realString) = @_;      my ($handle) = @_;
2647      # Initialize the return variable.      # Declare the return variable.
2648      my $retVal = "";      my @retVal = ();
2649      # Loop through the parameter string, looking for sequences to escape.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2650      while (length $realString > 0) {      # Read from the file.
2651          # Look for the first sequence to escape.      my $line = <$handle>;
2652          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # Only proceed if we found something.
2653              # Here we found it. The text preceding the sequence is in $1. The sequence      if (defined $line) {
2654              # 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
2655              $retVal .= $1;          # upload control and have a nonstandard EOL combination.
2656              # Strip the processed section off the real string.          $line =~ s/(\r|\n)+$//;
2657              $realString = substr $realString, (length $2) + (length $1);          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2658              # Get the matched character.          if (T(File => 4)) {
2659              my $char = $2;              my $escapedLine = $line;
2660              # If we have a CR, we are done.              $escapedLine =~ s/\n/\\n/g;
2661              if ($char ne "\r") {              $escapedLine =~ s/\r/\\r/g;
2662                  # It's not a CR, so encode the escape sequence.              $escapedLine =~ s/\t/\\t/g;
2663                  $char =~ tr/\t\n/tn/;              Trace("Line read: -->$escapedLine<--");
2664                  $retVal .= "\\" . $char;          }
2665              }          # If the line is empty, return a single empty string; otherwise, parse
2666            # it into fields.
2667            if ($line eq "") {
2668                push @retVal, "";
2669          } else {          } else {
2670              # Here there are no more escape sequences. The rest of the string is              push @retVal, split /\t/,$line;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
2671          }          }
2672        } else {
2673            # Trace the reason the read failed.
2674            Trace("End of file: $!") if T(File => 3);
2675      }      }
2676      # Return the result.      # Return the result.
2677      return $retVal;      return @retVal;
2678  }  }
2679    
2680  =head3 UnEscape  =head3 PutLine
2681    
2682  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutLine($handle, \@fields, $eol);
2683    
2684  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write a line of data to a tab-delimited file. The specified field values will be
2685  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  output in tab-separated form, with a trailing new-line.
 be deleted.  
2686    
2687  =over 4  =over 4
2688    
2689  =item codedString  =item handle
2690    
2691  String to un-escape.  Output file handle.
2692    
2693  =item RETURN  =item fields
2694    
2695  Returns a copy of the original string with the escape sequences converted to their actual  List of field values.
2696  values.  
2697    =item eol (optional)
2698    
2699    End-of-line character (default is "\n").
2700    
2701  =back  =back
2702    
2703  =cut  =cut
2704    
2705  sub UnEscape {  sub PutLine {
2706      # Get the parameter.      # Get the parameters.
2707      my ($codedString) = @_;      my ($handle, $fields, $eol) = @_;
2708      # Initialize the return variable.      # Write the data.
2709      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 $retVal;  
2710  }  }
2711    
 =head3 ParseRecord  
2712    
2713  C<< my @fields = Tracer::ParseRecord($line); >>  =head3 PrintLine
2714    
2715  Parse a tab-delimited data line. The data line is split into field values. Embedded tab      Tracer::PrintLine($line);
2716  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
2717  These will automatically be converted.  Print a line of text with a trailing new-line.
2718    
2719  =over 4  =over 4
2720    
2721  =item line  =item line
2722    
2723  Line of data containing the tab-delimited fields.  Line of text to print.
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub ParseRecord {  sub PrintLine {
2730      # Get the parameter.      # Get the parameters.
2731      my ($line) = @_;      my ($line) = @_;
2732      # Remove the trailing new-line, if any.      # Print the line.
2733      chomp $line;      print "$line\n";
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
2734  }  }
2735    
 =head3 Merge  
2736    
2737  C<< my @mergedList = Tracer::Merge(@inputList); >>  =head2 Other Useful Methods
2738    
2739  Sort a list of strings and remove duplicates.  =head3 ParseParm
2740    
2741  =over 4      my $listValue = Tracer::ParseParm($string);
2742    
2743  =item inputList  Convert a parameter into a list reference. If the parameter is undefined,
2744    an undefined value will be returned. Otherwise, it will be parsed as a
2745    comma-separated list of values.
2746    
2747  List of scalars to sort and merge.  =over 4
2748    
2749  =item RETURN  =item string
2750    
2751  Returns a list containing the same elements sorted in ascending order with duplicates  Incoming string.
 removed.  
2752    
2753  =back  =item RETURN
2754    
2755  =cut  Returns a reference to a list of values, or C<undef> if the incoming value
2756    was undefined.
2757    
2758  sub Merge {  =back
2759      # Get the input list in sort order.  
2760      my @inputList = sort @_;  =cut
2761      # Only proceed if the list has at least two elements.  
2762      if (@inputList > 1) {  sub ParseParm {
2763          # Now we want to move through the list splicing out duplicates.      # Get the parameters.
2764          my $i = 0;      my ($string) = @_;
2765          while ($i < @inputList) {      # Declare the return variable.
2766              # Get the current entry.      my $retVal;
2767              my $thisEntry = $inputList[$i];      # Check for data.
2768              # Find out how many elements duplicate the current entry.      if (defined $string) {
2769              my $j = $i + 1;          # We have some, so split it into a list.
2770              my $dup1 = $i + 1;          $retVal = [ split /\s*,\s*/, $string];
             while ($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++;  
         }  
2771      }      }
2772      # Return the merged list.      # Return the result.
2773      return @inputList;      return $retVal;
2774  }  }
2775    
2776  =head3 GetFile  =head3 Now
2777    
2778  C<< my @fileContents = Tracer::GetFile($fileName); >>      my $string = Tracer::Now();
2779    
2780      or  Return a displayable time stamp containing the local time. Whatever format this
2781    method produces must be parseable by L</ParseDate>.
2782    
2783  C<< my $fileContents = Tracer::GetFile($fileName); >>  =cut
2784    
2785  Return the entire contents of a file. In list context, line-ends are removed and  sub Now {
2786  each line is a list element. In scalar context, line-ends are replaced by C<\n>.      return DisplayTime(time);
2787    }
2788    
2789    =head3 DisplayTime
2790    
2791        my $string = Tracer::DisplayTime($time);
2792    
2793    Convert a time value to a displayable time stamp. Whatever format this
2794    method produces must be parseable by L</ParseDate>.
2795    
2796  =over 4  =over 4
2797    
2798  =item fileName  =item time
2799    
2800  Name of the file to read.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2801    
2802  =item RETURN  =item RETURN
2803    
2804  In a list context, returns the entire file as a list with the line terminators removed.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2805    
2806  =back  =back
2807    
2808  =cut  =cut
2809    
2810  sub GetFile {  sub DisplayTime {
2811      # Get the parameters.      my ($time) = @_;
2812      my ($fileName) = @_;      my $retVal = "(n/a)";
2813      # Declare the return variable.      if (defined $time) {
2814      my @retVal = ();          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2815      # Open the file for input.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2816      my $ok = open INPUTFILE, "<$fileName";                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
         # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
         while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
             push @retVal, $line;  
         }  
         # Close it.  
         close INPUTFILE;  
         my $actualLines = @retVal;  
2817      }      }
2818      # Return the file's contents in the desired format.      return $retVal;
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2819      }      }
2820    
2821    # Pad a number to 2 digits.
2822    sub _p2 {
2823        my ($value) = @_;
2824        $value = "0$value" if ($value < 10);
2825        return $value;
2826  }  }
2827    
2828  =head3 QTrace  =head3 Escape
2829    
2830  C<< my $data = QTrace($format); >>      my $codedString = Tracer::Escape($realString);
2831    
2832  Return the queued trace data in the specified format.  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2833    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2834    result is to reverse the effect of L</UnEscape>.
2835    
2836  =over 4  =over 4
2837    
2838  =item format  =item realString
2839    
2840  C<html> to format the data as an HTML list, C<text> to format it as straight text.  String to escape.
2841    
2842    =item RETURN
2843    
2844    Escaped equivalent of the real string.
2845    
2846  =back  =back
2847    
2848  =cut  =cut
2849    
2850  sub QTrace {  sub Escape {
2851      # Get the parameter.      # Get the parameter.
2852      my ($format) = @_;      my ($realString) = @_;
2853      # Create the return variable.      # Initialize the return variable.
2854      my $retVal = "";      my $retVal = "";
2855      # Only proceed if there is an actual queue.      # Loop through the parameter string, looking for sequences to escape.
2856      if (@Queue) {      while (length $realString > 0) {
2857          # Process according to the format.          # Look for the first sequence to escape.
2858          if ($format =~ m/^HTML$/i) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2859              # Convert the queue into an HTML list.              # Here we found it. The text preceding the sequence is in $1. The sequence
2860              $retVal = "<ul>\n";              # itself is in $2. First, move the clear text to the return variable.
2861              for my $line (@Queue) {              $retVal .= $1;
2862                  my $escapedLine = CGI::escapeHTML($line);              # Strip the processed section off the real string.
2863                  $retVal .= "<li>$escapedLine</li>\n";              $realString = substr $realString, (length $2) + (length $1);
2864                # Get the matched character.
2865                my $char = $2;
2866                # If we have a CR, we are done.
2867                if ($char ne "\r") {
2868                    # It's not a CR, so encode the escape sequence.
2869                    $char =~ tr/\t\n/tn/;
2870                    $retVal .= "\\" . $char;
2871              }              }
2872              $retVal .= "</ul>\n";          } else {
2873          } elsif ($format =~ m/^TEXT$/i) {              # Here there are no more escape sequences. The rest of the string is
2874              # Convert the queue into a list of text lines.              # transferred unmodified.
2875              $retVal = join("\n", @Queue) . "\n";              $retVal .= $realString;
2876                $realString = "";
2877          }          }
         # Clear the queue.  
         @Queue = ();  
2878      }      }
2879      # Return the formatted list.      # Return the result.
2880      return $retVal;      return $retVal;
2881  }  }
2882    
2883  =head3 Confess  =head3 UnEscape
2884    
2885  C<< Confess($message); >>      my $realString = Tracer::UnEscape($codedString);
2886    
2887  Trace the call stack and abort the program with the specified message. When used with  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2888  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2889  So, for example  be deleted.
2890    
2891  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2892    
2893  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item codedString
2894    
2895  =over 4  String to un-escape.
2896    
2897  =item message  =item RETURN
2898    
2899  Message to include in the trace.  Returns a copy of the original string with the escape sequences converted to their actual
2900    values.
2901    
2902  =back  =back
2903    
2904  =cut  =cut
2905    
2906  sub Confess {  sub UnEscape {
2907      # Get the parameters.      # Get the parameter.
2908      my ($message) = @_;      my ($codedString) = @_;
2909      # Trace the call stack.      # Initialize the return variable.
2910      Cluck($message);      my $retVal = "";
2911      # Abort the program.      # Only proceed if the incoming string is nonempty.
2912      croak(">>> $message");      if (defined $codedString) {
2913            # Loop through the parameter string, looking for escape sequences. We can't do
2914            # translating because it causes problems with the escaped slash. ("\\t" becomes
2915            # "\<tab>" no matter what we do.)
2916            while (length $codedString > 0) {
2917                # Look for the first escape sequence.
2918                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2919                    # Here we found it. The text preceding the sequence is in $1. The sequence
2920                    # itself is in $2. First, move the clear text to the return variable.
2921                    $retVal .= $1;
2922                    $codedString = substr $codedString, (2 + length $1);
2923                    # Get the escape value.
2924                    my $char = $2;
2925                    # If we have a "\r", we are done.
2926                    if ($char ne 'r') {
2927                        # Here it's not an 'r', so we convert it.
2928                        $char =~ tr/\\tn/\\\t\n/;
2929                        $retVal .= $char;
2930                    }
2931                } else {
2932                    # Here there are no more escape sequences. The rest of the string is
2933                    # transferred unmodified.
2934                    $retVal .= $codedString;
2935                    $codedString = "";
2936  }  }
   
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
2937          }          }
2938      }      }
2939        # Return the result.
2940      return $retVal;      return $retVal;
2941  }  }
2942    
2943  =head3 Cluck  =head3 Percent
2944    
2945  C<< Cluck($message); >>      my $percent = Tracer::Percent($number, $base);
2946    
2947  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the percent of the base represented by the given number. If the base
2948  trace condition. For example,  is zero, returns zero.
2949    
2950  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2951    
2952  will only trace the stack if the trace level for the package is 3 or more.  =item number
2953    
2954  =over 4  Percent numerator.
2955    
2956  =item message  =item base
2957    
2958  Message to include in the trace.  Percent base.
2959    
2960    =item RETURN
2961    
2962    Returns the percentage of the base represented by the numerator.
2963    
2964  =back  =back
2965    
2966  =cut  =cut
2967    
2968  sub Cluck {  sub Percent {
2969      # Get the parameters.      # Get the parameters.
2970      my ($message) = @_;      my ($number, $base) = @_;
2971      # Trace what's happening.      # Declare the return variable.
2972      Trace("Stack trace for event: $message");      my $retVal = 0;
2973      my $confession = longmess($message);      # Compute the percent.
2974      # Convert the confession to a series of trace messages. Note we skip any      if ($base != 0) {
2975      # messages relating to calls into Tracer.          $retVal = $number * 100 / $base;
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
2976      }      }
2977        # Return the result.
2978        return $retVal;
2979  }  }
2980    
2981  =head3 Min  =head3 Constrain
2982    
2983  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $constrained = Constrain($value, $min, $max);
2984    
2985  Return the minimum argument. The arguments are treated as numbers.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
2986    
2987  =over 4  =over 4
2988    
2989  =item $value1, $value2, ... $valueN  =item value
2990    
2991  List of numbers to compare.  Value to constrain.
2992    
2993    =item min (optional)
2994    
2995    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2996    
2997    =item max (optional)
2998    
2999    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3000    
3001  =item RETURN  =item RETURN
3002    
3003  Returns the lowest number in the list.  Returns the incoming value, constrained according to the other parameters.
3004    
3005  =back  =back
3006    
3007  =cut  =cut
3008    
3009  sub Min {  sub Constrain {
3010      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3011      my ($retVal, @values) = @_;      my ($value, $min, $max) = @_;
3012      # Loop through the remaining parameters, looking for the lowest.      # Declare the return variable.
3013      for my $value (@values) {      my $retVal = $value;
3014          if ($value < $retVal) {      # Apply the minimum constraint.
3015              $retVal = $value;      if (defined $min && $retVal < $min) {
3016          }          $retVal = $min;
3017        }
3018        # Apply the maximum constraint.
3019        if (defined $max && $retVal > $max) {
3020            $retVal = $max;
3021      }      }
3022      # Return the minimum found.      # Return the result.
3023      return $retVal;      return $retVal;
3024  }  }
3025    
3026  =head3 Max  =head3 Min
3027    
3028  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
3029    
3030  Return the maximum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
3031    
3032  =over 4  =over 4
3033    
# Line 1585  Line 3037 
3037    
3038  =item RETURN  =item RETURN
3039    
3040  Returns the highest number in the list.  Returns the lowest number in the list.
3041    
3042  =back  =back
3043    
3044  =cut  =cut
3045    
3046  sub Max {  sub Min {
3047      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters. Note that we prime the return value with the first parameter.
3048      my ($retVal, @values) = @_;      my ($retVal, @values) = @_;
3049      # Loop through the remaining parameters, looking for the highest.      # Loop through the remaining parameters, looking for the lowest.
3050      for my $value (@values) {      for my $value (@values) {
3051          if ($value > $retVal) {          if ($value < $retVal) {
3052              $retVal = $value;              $retVal = $value;
3053          }          }
3054      }      }
3055      # Return the maximum found.      # Return the minimum found.
3056      return $retVal;      return $retVal;
3057  }  }
3058    
3059  =head3 AddToListMap  =head3 Max
3060    
3061  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      my $max = Max($value1, $value2, ... $valueN);
3062    
3063  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Return the maximum argument. The arguments are treated as numbers.
 is created for the key. Otherwise, the new value is pushed onto the list.  
3064    
3065  =over 4  =over 4
3066    
3067  =item hash  =item $value1, $value2, ... $valueN
   
 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;  
     }  
 }  
3068    
3069  =head3 DebugMode  List of numbers to compare.
3070    
3071  C<< if (Tracer::DebugMode) { ...code... } >>  =item RETURN
3072    
3073  Return TRUE if debug mode has been turned on, else output an error  Returns the highest number in the list.
 page and return FALSE.  
3074    
3075  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error web page will be output directing the  
 user to enter in the correct password.  
3076    
3077  =cut  =cut
3078    
3079  sub DebugMode {  sub Max {
3080      # Declare the return variable.      # Get the parameters. Note that we prime the return value with the first parameter.
3081      my $retVal = 0;      my ($retVal, @values) = @_;
3082      # Check the debug configuration.      # Loop through the remaining parameters, looking for the highest.
3083      my $password = CGI::cookie("DebugMode");      for my $value (@values) {
3084      my $encrypted = Digest::MD5::md5_hex($password);          if ($value > $retVal) {
3085      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {              $retVal = $value;
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");  
         print $pageString;  
3086      }      }
3087      # Return the determination indicator.      }
3088        # Return the maximum found.
3089      return $retVal;      return $retVal;
3090  }  }
3091    
3092  =head3 Strip  =head3 Strip
3093    
3094  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::Strip($line);
3095    
3096  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
3097  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 3123 
3123    
3124  =head3 Pad  =head3 Pad
3125    
3126  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3127    
3128  Pad a string to a specified length. The pad character will be a  Pad a string to a specified length. The pad character will be a
3129  space, and the padding will be on the right side unless specified  space, and the padding will be on the right side unless specified
# Line 1778  Line 3194 
3194    
3195  =head3 TICK  =head3 TICK
3196    
3197  C<< my @results = TICK($commandString); >>      my @results = TICK($commandString);
3198    
3199  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3200  dot-slash (C<./> will be removed. So, for example, if you were doing  dot-slash (C<./> will be removed. So, for example, if you were doing
# Line 1817  Line 3233 
3233      return `$commandString`;      return `$commandString`;
3234  }  }
3235    
 =head3 ScriptSetup  
3236    
3237  C<< my ($query, $varHash) = ScriptSetup(); >>  =head3 CommaFormat
3238    
3239  Perform standard tracing and debugging setup for scripts. The value returned is      my $formatted = Tracer::CommaFormat($number);
3240  the CGI object followed by a pre-built variable hash.  
3241    Insert commas into a number.
3242    
3243  The C<Trace> query parameter is used to determine whether or not tracing is active and  =over 4
3244  which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  
3245  the C<CGI> trace module will trace parameter and environment information. Parameters are  =item number
3246  traced at level 3 and environment variables at level 4. At the end of the script, the  
3247  client should call L</ScriptFinish> to output the web page.  A sequence of digits.
3248    
3249    =item RETURN
3250    
3251    Returns the same digits with commas strategically inserted.
3252    
3253    =back
3254    
3255  =cut  =cut
3256    
3257  sub ScriptSetup {  sub CommaFormat {
3258      # Get the CGI query object.      # Get the parameters.
3259      my $query = CGI->new();      my ($number) = @_;
3260      # Check for tracing. Set it up if the user asked for it.      # Pad the length up to a multiple of three.
3261      if ($query->param('Trace')) {      my $padded = "$number";
3262          # Set up tracing to be queued for display at the bottom of the web page.      $padded = " " . $padded while length($padded) % 3 != 0;
3263          TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3264          # Trace the parameter and environment data.      # cause the delimiters to be included in the output stream. The
3265          if (T(CGI => 3)) {      # GREP removes the empty strings in between the delimiters.
3266              # Here we want to trace the parameter data.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3267              my @names = $query->param;      # Clean out the spaces.
3268              for my $parmName (sort @names) {      $retVal =~ s/ //g;
3269                  # Note we skip "Trace", which is for our use only.      # Return the result.
3270                  if ($parmName ne 'Trace') {      return $retVal;
                     my @values = $query->param($parmName);  
                     Trace("CGI: $parmName = " . join(", ", @values));  
                 }  
3271              }              }
3272    
3273    
3274    =head3 CompareLists
3275    
3276        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3277    
3278    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3279    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3280    The return value contains a list of items that are only in the new list
3281    (inserted) and only in the old list (deleted).
3282    
3283    =over 4
3284    
3285    =item newList
3286    
3287    Reference to a list of new tuples.
3288    
3289    =item oldList
3290    
3291    Reference to a list of old tuples.
3292    
3293    =item keyIndex (optional)
3294    
3295    Index into each tuple of its key field. The default is 0.
3296    
3297    =item RETURN
3298    
3299    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3300    list (inserted) followed by a reference to the list of items that are only in the old
3301    list (deleted).
3302    
3303    =back
3304    
3305    =cut
3306    
3307    sub CompareLists {
3308        # Get the parameters.
3309        my ($newList, $oldList, $keyIndex) = @_;
3310        if (! defined $keyIndex) {
3311            $keyIndex = 0;
3312        }
3313        # Declare the return variables.
3314        my ($inserted, $deleted) = ([], []);
3315        # Loop through the two lists simultaneously.
3316        my ($newI, $oldI) = (0, 0);
3317        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3318        while ($newI < $newN || $oldI < $oldN) {
3319            # Get the current object in each list. Note that if one
3320            # of the lists is past the end, we'll get undef.
3321            my $newItem = $newList->[$newI];
3322            my $oldItem = $oldList->[$oldI];
3323            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3324                # The old item is not in the new list, so mark it deleted.
3325                push @{$deleted}, $oldItem;
3326                $oldI++;
3327            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3328                # The new item is not in the old list, so mark it inserted.
3329                push @{$inserted}, $newItem;
3330                $newI++;
3331            } else {
3332                # The item is in both lists, so push forward.
3333                $oldI++;
3334                $newI++;
3335          }          }
         if (T(CGI => 4)) {  
             # Here we want the environment data too.  
             for my $envName (sort keys %ENV) {  
                 Trace("ENV: $envName = $ENV{$envName}");  
3336              }              }
3337        # Return the result.
3338        return ($inserted, $deleted);
3339          }          }
3340    
3341    =head3 Cmp
3342    
3343        my $cmp = Tracer::Cmp($a, $b);
3344    
3345    This method performs a universal sort comparison. Each value coming in is
3346    separated into a leading text part and a trailing number part. The text
3347    part is string compared, and if both parts are equal, then the number
3348    parts are compared numerically. A stream of just numbers or a stream of
3349    just strings will sort correctly, and a mixed stream will sort with the
3350    numbers first. Strings with a label and a number will sort in the
3351    expected manner instead of lexically.
3352    
3353    =over 4
3354    
3355    =item a
3356    
3357    First item to compare.
3358    
3359    =item b
3360    
3361    Second item to compare.
3362    
3363    =item RETURN
3364    
3365    Returns a negative number if the first item should sort first (is less), a positive
3366    number if the first item should sort second (is greater), and a zero if the items are
3367    equal.
3368    
3369    =back
3370    
3371    =cut
3372    
3373    sub Cmp {
3374        # Get the parameters.
3375        my ($a, $b) = @_;
3376        # Declare the return value.
3377        my $retVal;
3378        # Check for nulls.
3379        if (! defined($a)) {
3380            $retVal = (! defined($b) ? 0 : -1);
3381        } elsif (! defined($b)) {
3382            $retVal = 1;
3383      } else {      } else {
3384          # Here tracing is to be turned off. All we allow is errors traced into the          # Here we have two real values. Parse the two strings.
3385          # error log.          $a =~ /^(\D*)(\d*)$/;
3386          TSetup("0", "WARN");          my $aParsed = [$1, $2];
3387            $b =~ /^(\D*)(\d*)$/;
3388            my $bParsed = [$1, $2];
3389            # Compare the string parts.
3390            $retVal = $aParsed->[0] cmp $bParsed->[0];
3391            if (! $retVal) {
3392                $retVal = $aParsed->[1] <=> $bParsed->[1];
3393      }      }
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # If we're in DEBUG mode, set up the debug mode data for forms.  
     if (Tracer::DebugMode) {  
         $varHash->{DebugData} = GetFile("Html/DebugFragment.html");  
3394      }      }
3395        # Return the result.
3396        return $retVal;
3397    }
3398    
3399    =head2 CGI Script Utilities
3400    
3401    =head3 ScriptSetup (deprecated)
3402    
3403        my ($cgi, $varHash) = ScriptSetup($noTrace);
3404    
3405    Perform standard tracing and debugging setup for scripts. The value returned is
3406    the CGI object followed by a pre-built variable hash. At the end of the script,
3407    the client should call L</ScriptFinish> to output the web page.
3408    
3409    This method calls L</ETracing> to configure tracing, which allows the tracing
3410    to be configured via the emergency tracing form on the debugging control panel.
3411    Tracing will then be turned on automatically for all programs that use the L</ETracing>
3412    method, which includes every program that uses this method or L</StandardSetup>.
3413    
3414    =over 4
3415    
3416    =item noTrace (optional)
3417    
3418    If specified, tracing will be suppressed. This is useful if the script wants to set up
3419    tracing manually.
3420    
3421    =item RETURN
3422    
3423    Returns a two-element list consisting of a CGI query object and a variable hash for
3424    the output page.
3425    
3426    =back
3427    
3428    =cut
3429    
3430    sub ScriptSetup {
3431        # Get the parameters.
3432        my ($noTrace) = @_;
3433        # Get the CGI query object.
3434        my $cgi = CGI->new();
3435        # Set up tracing if it's not suppressed.
3436        ETracing($cgi) unless $noTrace;
3437        # Create the variable hash.
3438        my $varHash = { results => '' };
3439      # Return the query object and variable hash.      # Return the query object and variable hash.
3440      return ($query, $varHash);      return ($cgi, $varHash);
3441  }  }
3442    
3443  =head3 ScriptFinish  =head3 ScriptFinish (deprecated)
3444    
3445  C<< ScriptFinish($webData, $varHash); >>      ScriptFinish($webData, $varHash);
3446    
3447  Output a web page at the end of a script. Either the string to be output or the  Output a web page at the end of a script. Either the string to be output or the
3448  name of a template file can be specified. If the second parameter is omitted,  name of a template file can be specified. If the second parameter is omitted,
# Line 1896  Line 3464 
3464      use FIG;      use FIG;
3465      # ... more uses ...      # ... more uses ...
3466    
3467      my ($query, $varHash) = ScriptSetup();      my ($cgi, $varHash) = ScriptSetup();
3468      eval {      eval {
3469          # ... get data from $query, put it in $varHash ...          # ... get data from $cgi, put it in $varHash ...
3470      };      };
3471      if ($@) {      if ($@) {
3472          Trace("Script Error: $@") if T(0);          Trace("Script Error: $@") if T(0);
# Line 1933  Line 3501 
3501      # Check for a template file situation.      # Check for a template file situation.
3502      my $outputString;      my $outputString;
3503      if (defined $varHash) {      if (defined $varHash) {
3504          # 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.
3505          $outputString = PageBuilder::Build("<$webData", $varHash, "Html");          my $template;
3506            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3507                $template = "$FIG_Config::template_url/$webData";
3508            } else {
3509                $template = "<<$webData";
3510            }
3511            $outputString = PageBuilder::Build($template, $varHash, "Html");
3512      } else {      } else {
3513          # Here the user gave us a raw string.          # Here the user gave us a raw string.
3514          $outputString = $webData;          $outputString = $webData;
3515      }      }
3516      # Check for trace messages.      # Check for trace messages.
3517      if ($Destination eq "QUEUE") {      if ($Destination ne "NONE" && $TraceLevel > 0) {
3518          # We have trace messages, so we want to put them at the end of the body. This          # We have trace messages, so we want to put them at the end of the body. This
3519          # is either at the end of the whole string or at the beginning of the BODY          # is either at the end of the whole string or at the beginning of the BODY
3520          # end-tag.          # end-tag.
# Line 1948  Line 3522 
3522          if ($outputString =~ m#</body>#gi) {          if ($outputString =~ m#</body>#gi) {
3523              $pos = (pos $outputString) - 7;              $pos = (pos $outputString) - 7;
3524          }          }
3525          substr $outputString, $pos, 0, QTrace('Html');          # If the trace messages were queued, we unroll them. Otherwise, we display the
3526            # destination.
3527            my $traceHtml;
3528            if ($Destination eq "QUEUE") {
3529                $traceHtml = QTrace('Html');
3530            } elsif ($Destination =~ /^>>(.+)$/) {
3531                # Here the tracing output it to a file. We code it as a hyperlink so the user
3532                # can copy the file name into the clipboard easily.
3533                my $actualDest = $1;
3534                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3535            } else {
3536                # Here we have one of the special destinations.
3537                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3538            }
3539            substr $outputString, $pos, 0, $traceHtml;
3540      }      }
3541      # Write the output string.      # Write the output string.
3542      print $outputString;      print $outputString;
3543  }  }
3544    
3545  =head3 Insure  =head3 GenerateURL
3546    
3547  C<< Insure($dirName); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3548    
3549  Insure a directory is present.  Generate a GET-style URL for the specified page with the specified parameter
3550    names and values. The values will be URL-escaped automatically. So, for
3551    example
3552    
3553        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3554    
3555    would return
3556    
3557        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3558    
3559  =over 4  =over 4
3560    
3561  =item dirName  =item page
3562    
3563  Name of the directory to check. If it does not exist, it will be created.  Page URL.
3564    
3565    =item parameters
3566    
3567    Hash mapping parameter names to parameter values.
3568    
3569    =item RETURN
3570    
3571    Returns a GET-style URL that goes to the specified page and passes in the
3572    specified parameters and values.
3573    
3574  =back  =back
3575    
3576  =cut  =cut
3577    
3578  sub Insure {  sub GenerateURL {
3579      my ($dirName) = @_;      # Get the parameters.
3580      if (! -d $dirName) {      my ($page, %parameters) = @_;
3581          Trace("Creating $dirName directory.") if T(2);      # Prime the return variable with the page URL.
3582          eval { mkpath $dirName; };      my $retVal = $page;
3583          if ($@) {      # Loop through the parameters, creating parameter elements in a list.
3584              Confess("Error creating $dirName: $@");      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3585          }      # If the list is nonempty, tack it on.
3586        if (@parmList) {
3587            $retVal .= "?" . join(";", @parmList);
3588      }      }
3589        # Return the result.
3590        return $retVal;
3591  }  }
3592    
3593  =head3 ChDir  =head3 ApplyURL
3594    
3595  C<< ChDir($dirName); >>      Tracer::ApplyURL($table, $target, $url);
3596    
3597  Change to the specified directory.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3598    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3599    URL column will be deleted by this process and the target column will be HTML-escaped.
3600    
3601    This provides a simple way to process the results of a database query into something
3602    displayable by combining a URL with text.
3603    
3604  =over 4  =over 4
3605    
3606  =item dirName  =item table
3607