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revision 1.42, Wed Mar 29 19:41:02 2006 UTC revision 1.128, Wed Dec 16 20:57:35 2009 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
     require Exporter;  
     @ISA = ('Exporter');  
     @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure);  
     @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);  
21      use strict;      use strict;
22      use Carp qw(longmess croak);      use base qw(Exporter);
23        use vars qw(@EXPORT @EXPORT_OK);
24        @EXPORT = qw(Trace T TSetup QTrace Confess MemTrace Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25        @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26        use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28        use Cwd;
29      use FIG_Config;      use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31      use Digest::MD5;      use Digest::MD5;
32      use File::Basename;      use File::Basename;
33      use File::Path;      use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl qw(:DEFAULT :flock);
42        use Data::Dumper;
43    
44    
45  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
46    
47  =head2 Introduction  =head2 Tracing
48    
49  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
50  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.
51  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,
52  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
53  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
54  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
55  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
56  appear. To generate a trace message, use the following syntax.  appear.
57    
58    =head3 Putting Trace Messages in Your Code
59    
60  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
61    
62        Trace($message) if T(errors => 4);
63    
64  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>
65  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
66    
67  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
68    
69  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
70    
# Line 56  Line 72 
72  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
73  active and the trace level is 2 or more.  active and the trace level is 2 or more.
74    
75  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
76    
77    In scripts, where no package name is available, the category defaults to C<main>.
78    
79    =head3 Custom Tracing
80    
81    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
82    the preferred method, but a knowledge of how custom tracing works can make the more modern
83    L</Emergency Tracing> easier to understand.
84    
85  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,
86  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
87  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
88    
89  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
90    
91  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
92  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
93    
94  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
95  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
96  useful in a CGI environment.  useful in a CGI environment.
97    
98  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
99    
100  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
101  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
102  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
103  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
104  it easier to debug page formatting problems.  it easier to debug page formatting problems.
105    
106  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
107    a file at the same time. To trace to a file, specify the filename with an output character in front
108    of it.
109    
110        TSetup('4 SQL', ">$fileName");
111    
112    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
113    bracket.
114    
115        TSetup('3 *', "+>$fileName");
116    
117  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>.
118  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.
119  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
120  being used out in the field.  being used out in the field.
121    
122    =head3 Trace Levels
123    
124  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
125  a suggestion.  a suggestion.
126    
# Line 116  Line 151 
151    
152  =back  =back
153    
154    The format of trace messages is important because some utilities analyze trace files.
155    There are three fields-- the time stamp, the category name, and the text.
156    The time stamp is between square brackets and the category name between angle brackets.
157    After the category name there is a colon (C<:>) followed by the message text.
158    If the square brackets or angle brackets are missing, then the trace management
159    utilities assume that they are encountering a set of pre-formatted lines.
160    
161    Note, however, that this formatting is done automatically by the tracing functions. You
162    only need to know about it if you want to parse a trace file.
163    
164    =head3 Emergency Tracing
165    
166    Sometimes, you need a way for tracing to happen automatically without putting parameters
167    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169    that you specify a tracing key. For command-line tools, the key is
170    taken from the C<TRACING> environment variable. For web services, the key is taken from
171    a cookie. Either way, the key tells the tracing facility who you are, so that you control
172    the tracing in your environment without stepping on other users.
173    
174    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
175    generate one for you.
176    
177    You can activate and de-activate emergency tracing from the debugging control panel, as
178    well as display the trace file itself.
179    
180    To enable emergency tracing in your code, call
181    
182        ETracing($cgi)
183    
184    from a web script and
185    
186        ETracing()
187    
188    from a command-line script.
189    
190    The web script will look for the tracing key in the cookies, and the command-line
191    script will look for it in the C<TRACING> environment variable. If you are
192    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193    will be configured automatically.
194    
195  =cut  =cut
196    
197  # Declare the configuration variables.  # Declare the configuration variables.
198    
199  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
200  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
201                              # standard output                              # standard output
202  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
203                              # hash of active category names                              # hash of active category names
204    my @LevelNames = qw(error warn notice info detail);
205  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
206                              # messages                              # messages
207  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
208  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
209    my $LastLevel = 0;          # level of the last test call
210  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
211  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
212    my $SavedCGI;               # CGI object passed to ETracing
213    my $CommandLine;            # Command line passed to StandardSetup
214    my $Confessions = 0;        # confession count
215    umask 2;                    # Fix the damn umask so everything is group-writable.
216    
217    =head2 Tracing Methods
218    
219    =head3 Setups
220    
221        my $count = Tracer::Setups();
222    
223    Return the number of times L</TSetup> has been called.
224    
225    This method allows for the creation of conditional tracing setups where, for example, we
226    may want to set up tracing if nobody else has done it before us.
227    
228    =cut
229    
230  =head2 Public Methods  sub Setups {
231        return $SetupCount;
232    }
233    
234  =head3 TSetup  =head3 TSetup
235    
236  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
237    
238  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
239  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 186  Line 283 
283          }          }
284      }      }
285      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
286      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
287      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
288        # the standard output (tee mode).
289      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
290          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
291              $TeeFlag = 1;              $TeeFlag = 1;
292              $target = substr($target, 1);              $target = substr($target, 1);
293          }          }
294          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
295                # We need to initialize the file (which clears it).
296              open TRACEFILE, $target;              open TRACEFILE, $target;
297              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
298              close TRACEFILE;              close TRACEFILE;
299                # Set to append mode now that the file has been cleared.
300              $Destination = ">$target";              $Destination = ">$target";
301          } else {          } else {
302              $Destination = $target;              $Destination = $target;
# Line 208  Line 308 
308      $SetupCount++;      $SetupCount++;
309  }  }
310    
311  =head3 StandardSetup  =head3 SetLevel
312    
313  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
314    
315  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.  
316    
317  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.  
318    
319  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  
320    
321      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
322    
323  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.  
324    
325  =over 4  =cut
326    
327  =item FIG  sub SetLevel {
328        $TraceLevel = $_[0];
329    }
330    
331  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
332    
333  =item SQL      my $time = Tracer::ParseDate($dateString);
334    
335  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
336    and parses it into a number. The string must be vaguely date-like or it will
337    return an undefined value. Our requirement is that a month and day be
338    present and that three pieces of the date string (time of day, month and day,
339    year) be separated by likely delimiters, such as spaces, commas, and such-like.
340    
341  =item Tracer  If a time of day is present, it must be in military time with two digits for
342    everything but the hour.
343    
344  Traces error messages and call stacks.  The year must be exactly four digits.
345    
346  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
347    equally innocuous. This means, however, that a sufficiently long sentence with date-like
348    parts in it may be interpreted as a date. Hopefully this will not be a problem.
349    
350  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.  
351    
352      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
353    
354  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  
355    
356  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.  
357    
358      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
359    
360  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
361    
362  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
363  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.  
364    
365  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
366    
367  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
368    
369      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
370                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
371                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
372                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
373                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
374                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
375                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
376                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
377                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
378                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
379                                Oct =>  9, October  =>   9, '10' =>  9,
380                                Nov => 10, November =>  10, '11' => 10,
381                                Dec => 11, December =>  11, '12' => 11
382                            };
383    
384    sub ParseDate {
385        # Get the parameters.
386        my ($dateString) = @_;
387        # Declare the return variable.
388        my $retVal;
389        # Find the month and day of month. There are two ways that can happen. We check for the
390        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
391        # won't be fooled into thinking the month is Sunday.
392        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
393            my ($mon, $mday) = (MONTHS->{$1}, $2);
394            # Insist that the month and day are valid.
395            if (defined($mon) && $2 >= 1 && $2 <= 31) {
396                # Find the time.
397                my ($hour, $min, $sec) = (0, 0, 0);
398                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
399                    ($hour, $min, $sec) = ($1, $2, $3);
400                }
401                # Find the year.
402                my $year;
403                if ($dateString =~ /\b(\d{4})\b/) {
404                    $year = $1;
405                } else {
406                    # Get the default year, which is this one. Note we must convert it to
407                    # the four-digit value expected by "timelocal".
408                    (undef, undef, undef, undef, undef, $year) = localtime();
409                    $year += 1900;
410                }
411                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
412            }
413        }
414        # Return the result.
415        return $retVal;
416    }
417    
418  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
419    
420  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
421    
422      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
423    
424  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
425    
426      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
427    
428  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.  
429    
430  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  
431    
432      -user=Bruce -background  =cut
433    
434  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
435  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
436  simplify starting a command in the background.      my ($fileName) = @_;
437        # Open the file as the standard error output.
438        open STDERR, '>', $fileName;
439    }
440    
441  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
442    
443      TransactFeatures -h      Trace($message);
444    
445  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
446    any prior call to B<TSetup>.
447    
448      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  
449    
450  The parameters to this method are as follows.  =item message
451    
452    Message to write.
453    
454    =back
455    
456    =cut
457    
458    sub Trace {
459        # Get the parameters.
460        my ($message) = @_;
461        # Strip off any line terminators at the end of the message. We will add
462        # new-line stuff ourselves.
463        my $stripped = Strip($message);
464        # Compute the caller information.
465        my ($callPackage, $callFile, $callLine) = caller();
466        my $callFileTitle = basename($callFile);
467        # Check the caller.
468        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
469        # Get the timestamp.
470        my $timeStamp = Now();
471        # Build the prefix.
472        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
473        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
474        # Format the message.
475        my $formatted = "$prefix $stripped";
476        # Process according to the destination.
477        if ($Destination eq "TEXT") {
478            # Write the message to the standard output.
479            print "$formatted\n";
480        } elsif ($Destination eq "ERROR") {
481            # Write the message to the error output. Here, we want our prefix fields.
482            print STDERR "$formatted\n";
483        } elsif ($Destination eq "WARN") {
484            # Emit the message to the standard error output. It is presumed that the
485            # error logger will add its own prefix fields, the notable exception being
486            # the caller info.
487            print STDERR "$callerInfo$stripped\n";
488        } elsif ($Destination eq "QUEUE") {
489            # Push the message into the queue.
490            push @Queue, "$formatted";
491        } elsif ($Destination eq "HTML") {
492            # Convert the message to HTML.
493            my $escapedMessage = CGI::escapeHTML($stripped);
494            # The stuff after the first line feed should be pre-formatted.
495            my @lines = split /\s*\n/, $escapedMessage;
496            # Get the normal portion.
497            my $line1 = shift @lines;
498            print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
499            if (@lines) {
500                print "<pre>" . join("\n", @lines, "</pre>");
501            }
502        } elsif ($Destination =~ m/^>>/) {
503            # Write the trace message to an output file.
504            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
505            # Lock the file.
506            flock TRACING, LOCK_EX;
507            print TRACING "$formatted\n";
508            close TRACING;
509            # If the Tee flag is on, echo it to the standard output.
510            if ($TeeFlag) {
511                print "$formatted\n";
512            }
513        }
514    }
515    
516    =head3 MemTrace
517    
518        MemTrace($message);
519    
520    Output a trace message that includes memory size information.
521    
522  =over 4  =over 4
523    
524  =item categories  =item message
525    
526  Reference to a list of tracing category names. These should be names of  Message to display. The message will be followed by a sentence about the memory size.
 packages whose internal workings will need to be debugged to get the  
 command working.  
527    
528  =item options  =back
529    
530  Reference to a hash containing the legal options for the current command mapped  =cut
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options.  
531    
532  =item parmHelp  sub MemTrace {
533        # Get the parameters.
534        my ($message) = @_;
535        my $memory = GetMemorySize();
536        Trace("$message $memory in use.");
537    }
538    
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
539    
540  =item ARGV  =head3 TraceDump
541    
542  List of command line parameters, including the option switches, which must      TraceDump($title, $object);
 precede the positional parameters and be prefixed by a hyphen.  
543    
544  =item RETURN  Dump an object to the trace log. This method simply calls the C<Dumper>
545    function, but routes the output to the trace log instead of returning it
546    as a string. The output is arranged so that it comes out monospaced when
547    it appears in an HTML trace dump.
548    
549  Returns a list. The first element of the list is the reference to a hash that  =over 4
550  maps the command-line option switches to their values. These will either be the  
551  default values or overrides specified on the command line. The remaining  =item title
552  elements of the list are the position parameters, in order.  
553    Title to give to the object being dumped.
554    
555    =item object
556    
557    Reference to a list, hash, or object to dump.
558    
559  =back  =back
560    
561  =cut  =cut
562    
563  sub StandardSetup {  sub TraceDump {
564      # Get the parameters.      # Get the parameters.
565      my ($categories, $options, $parmHelp, @argv) = @_;      my ($title, $object) = @_;
566      # Add the tracing options.      # Trace the object.
567      if (! exists $options->{trace}) {      Trace("Object dump for $title:\n" . Dumper($object));
         $options->{trace} = [2, "tracing level"];  
     }  
     $options->{sql} = [0, "turn on SQL tracing"];  
     $options->{h} = [0, "display command-line options"];  
     $options->{user} = [$$, "trace log file name suffix"];  
     $options->{background} = [0, "spool standard and error output"];  
     # Create a parsing hash from the options hash. The parsing hash  
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
568      }      }
569      # Parse the command line.  
570      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  =head3 T
571      # Get the logfile suffix.  
572        my $switch = T($category, $traceLevel);
573    
574        or
575    
576        my $switch = T($traceLevel);
577    
578    Return TRUE if the trace level is at or above a specified value and the specified category
579    is active, else FALSE. If no category is specified, the caller's package name is used.
580    
581    =over 4
582    
583    =item category
584    
585    Category to which the message belongs. If not specified, the caller's package name is
586    used.
587    
588    =item traceLevel
589    
590    Relevant tracing level.
591    
592    =item RETURN
593    
594    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
595    
596    =back
597    
598    =cut
599    
600    sub T {
601        # Declare the return variable.
602        my $retVal = 0;
603        # Only proceed if tracing is turned on.
604        if ($Destination ne "NONE") {
605            # Get the parameters.
606            my ($category, $traceLevel) = @_;
607            if (!defined $traceLevel) {
608                # Here we have no category, so we need to get the calling package.
609                # The calling package is normally the first parameter. If it is
610                # omitted, the first parameter will be the tracelevel. So, the
611                # first thing we do is shift the so-called category into the
612                # $traceLevel variable where it belongs.
613                $traceLevel = $category;
614                my ($package, $fileName, $line) = caller;
615                # If there is no calling package, we default to "main".
616                if (!$package) {
617                    $category = "main";
618                } else {
619                    my @cats = split /::/, $package;
620                    $category = $cats[$#cats];
621                }
622            }
623            # Save the category name and level.
624            $LastCategory = $category;
625            $LastLevel = $traceLevel;
626            # Convert it to lower case before we hash it.
627            $category = lc $category;
628            # Validate the trace level.
629            if (ref $traceLevel) {
630                Confess("Bad trace level.");
631            } elsif (ref $TraceLevel) {
632                Confess("Bad trace config.");
633            }
634            # Make the check. Note that level 0 shows even if the category is turned off.
635            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
636        }
637        # Return the computed result.
638        return $retVal;
639    }
640    
641    =head3 QTrace
642    
643        my $data = QTrace($format);
644    
645    Return the queued trace data in the specified format.
646    
647    =over 4
648    
649    =item format
650    
651    C<html> to format the data as an HTML list, C<text> to format it as straight text.
652    
653    =back
654    
655    =cut
656    
657    sub QTrace {
658        # Get the parameter.
659        my ($format) = @_;
660        # Create the return variable.
661        my $retVal = "";
662        # Only proceed if there is an actual queue.
663        if (@Queue) {
664            # Process according to the format.
665            if ($format =~ m/^HTML$/i) {
666                # Convert the queue into an HTML list.
667                $retVal = "<ul>\n";
668                for my $line (@Queue) {
669                    my $escapedLine = CGI::escapeHTML($line);
670                    $retVal .= "<li>$escapedLine</li>\n";
671                }
672                $retVal .= "</ul>\n";
673            } elsif ($format =~ m/^TEXT$/i) {
674                # Convert the queue into a list of text lines.
675                $retVal = join("\n", @Queue) . "\n";
676            }
677            # Clear the queue.
678            @Queue = ();
679        }
680        # Return the formatted list.
681        return $retVal;
682    }
683    
684    =head3 Confess
685    
686        Confess($message);
687    
688    Trace the call stack and abort the program with the specified message. When used with
689    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
690    So, for example
691    
692        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
693    
694    Will abort the program with a stack trace if the value of C<$recNum> is negative.
695    
696    =over 4
697    
698    =item message
699    
700    Message to include in the trace.
701    
702    =back
703    
704    =cut
705    
706    sub Confess {
707        # Get the parameters.
708        my ($message) = @_;
709        # Set up the category and level.
710        $LastCategory = "(confess)";
711        $LastLevel = 0;
712        # Trace the call stack.
713        Cluck($message);
714        # Increment the confession count.
715        $Confessions++;
716        # Abort the program.
717        croak(">>> $message");
718    }
719    
720    =head3 Confessions
721    
722        my $count = Tracer::Confessions();
723    
724    Return the number of calls to L</Confess> by the current task.
725    
726    =cut
727    
728    sub Confessions {
729        return $Confessions;
730    }
731    
732    
733    =head3 SaveCGI
734    
735        Tracer::SaveCGI($cgi);
736    
737    This method saves the CGI object but does not activate emergency tracing.
738    It is used to allow L</Warn> to work in situations where emergency
739    tracing is contra-indicated (e.g. the wiki).
740    
741    =over 4
742    
743    =item cgi
744    
745    Active CGI query object.
746    
747    =back
748    
749    =cut
750    
751    sub SaveCGI {
752        $SavedCGI = $_[0];
753    }
754    
755    =head3 Warn
756    
757        Warn($message, @options);
758    
759    This method traces an important message. If an RSS feed is configured
760    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
761    then the message will be echoed to the feed. In general, a tracing
762    destination of C<WARN> indicates that the caller is running as a web
763    service in a production environment; however, this is not a requirement.
764    
765    To force warnings into the RSS feed even when the tracing destination
766    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
767    configured automatically when L</StandardSetup> is used.
768    
769    The L</Cluck> method calls this one for its final message. Since
770    L</Confess> calls L</Cluck>, this means that any error which is caught
771    and confessed will put something in the feed. This insures that someone
772    will be alerted relatively quickly when a failure occurs.
773    
774    =over 4
775    
776    =item message
777    
778    Message to be traced.
779    
780    =item options
781    
782    A list containing zero or more options.
783    
784    =back
785    
786    The permissible options are as follows.
787    
788    =over 4
789    
790    =item noStack
791    
792    If specified, then the stack trace is not included in the output.
793    
794    =back
795    
796    =cut
797    
798    sub Warn {
799        # Get the parameters.
800        my $message = shift @_;
801        my %options = map { $_ => 1 } @_;
802        # Save $@;
803        my $savedError = $@;
804        # Trace the message.
805        Trace($message);
806        # This will contain the lock handle. If it's defined, it means we need to unlock.
807        my $lock;
808        # Check for feed forcing.
809        my $forceFeed = exists $Categories{feed};
810        # An error here would be disastrous. Note that if debug mode is specified,
811        # we do this stuff even in a test environment.
812        eval {
813            # Do we need to put this in the RSS feed?
814            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
815                # Probably. We need to check first, however, to see if it's from an
816                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
817                my $key = "127.0.0.1";
818                if (defined $SavedCGI) {
819                    # Get the IP address.
820                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
821                }
822                # Is the IP address in the ignore list?
823                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
824                if (! $found) {
825                    # No. We're good. We now need to compute the date, the link, and the title.
826                    # First, the date, in a very specific format.
827                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
828                        (tz_local_offset() / 30);
829                    # Environment data goes in here. We start with the date.
830                    my $environment = "$date.  ";
831                    # If we need to recap the message (because it's too long to be a title), we'll
832                    # put it in here.
833                    my $recap;
834                    # Copy the message and remove excess space.
835                    my $title = $message;
836                    $title =~ s/\s+/ /gs;
837                    # If it's too long, we have to split it up.
838                    if (length $title > 60) {
839                        # Put the full message in the environment string.
840                        $recap = $title;
841                        # Excerpt it as the title.
842                        $title = substr($title, 0, 50) . "...";
843                    }
844                    # If we have a CGI object, then this is a web error. Otherwise, it's
845                    # command-line.
846                    if (defined $SavedCGI) {
847                        # We're in a web service. The environment is the user's IP, and the link
848                        # is the URL that got us here.
849                        $environment .= "Event Reported at IP address $key process $$.";
850                        my $url = $SavedCGI->self_url();
851                        # We need the user agent string and (if available) the referrer.
852                        # The referrer will be the link.
853                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
854                        if ($ENV{HTTP_REFERER}) {
855                            my $link = $ENV{HTTP_REFERER};
856                            $environment .= " referred from <a href=\"$link\">$link</a>.";
857                        } else {
858                            $environment .= " referrer unknown.";
859                        }
860                        # Close off the sentence with the original link.
861                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
862                    } else {
863                        # No CGI object, so we're a command-line tool. Use the tracing
864                        # key and the PID as the user identifier, and add the command.
865                        my $key = EmergencyKey();
866                        $environment .= "Event Reported by $key process $$.";
867                        if ($CommandLine) {
868                            # We're in a StandardSetup script, so we have the real command line.
869                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
870                        } elsif ($ENV{_}) {
871                            # We're in a BASH script, so the command has been stored in the _ variable.
872                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
873                        }
874                    }
875                    # Build a GUID. We use the current time, the title, and the process ID,
876                    # then digest the result.
877                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
878                    # Finally, the description. This is a stack trace plus various environmental stuff.
879                    # The trace is optional.
880                    my $stackTrace;
881                    if ($options{noStack}) {
882                        $stackTrace = "";
883                    } else {
884                        my @trace = LongMess();
885                        # Only proceed if we got something back.
886                        if (scalar(@trace) > 0) {
887                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
888                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
889                        }
890                    }
891                    # We got the stack trace. Now it's time to put it all together.
892                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
893                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
894                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
895                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
896                    # our <br>s and <pre>s are used to format the description.
897                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
898                    my $description = "$recap$environment  $stackTrace";
899                    # Okay, we have all the pieces. Create a hash of the new event.
900                    my $newItem = { title => $title,
901                                    description => $description,
902                                    category => $LastCategory,
903                                    pubDate => $date,
904                                    guid => $guid,
905                                  };
906                    # We need XML capability for this.
907                    require XML::Simple;
908                    # The RSS document goes in here.
909                    my $rss;
910                    # Get the name of the RSS file. It's in the FIG temporary directory.
911                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
912                    # Open the config file and lock it.
913                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
914                    flock $lock, LOCK_EX;
915                    # Does it exist?
916                    if (-s $fileName) {
917                        # Slurp it in.
918                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
919                    } else {
920                        my $size = -s $fileName;
921                        # Create an empty channel.
922                        $rss = {
923                            channel => {
924                                title => 'NMPDR Warning Feed',
925                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
926                                description => "Important messages regarding the status of the NMPDR.",
927                                generator => "NMPDR Trace Facility",
928                                docs => "http://blogs.law.harvard.edu/tech/rss",
929                                item => []
930                            },
931                        };
932                    }
933                    # Get the channel object.
934                    my $channel = $rss->{channel};
935                    # Update the last-build date.
936                    $channel->{lastBuildDate} = $date;
937                    # Get the item array.
938                    my $items = $channel->{item};
939                    # Insure it has only 100 entries.
940                    while (scalar @{$items} > 100) {
941                        pop @{$items};
942                    }
943                    # Add our new item at the front.
944                    unshift @{$items}, $newItem;
945                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
946                    # the requirements for those.
947                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
948                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
949                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
950                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
951                    # We don't use Open here because we can't afford an error.
952                    if (open XMLOUT, ">$fileName") {
953                        print XMLOUT $xml;
954                        close XMLOUT;
955                    }
956                }
957            }
958        };
959        if ($@) {
960            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
961            # (which is a good thing).
962            my $error = $@;
963            Trace("Feed Error: $error") if T(Feed => 0);
964        }
965        # Be sure to unlock.
966        if ($lock) {
967            flock $lock, LOCK_UN;
968            undef $lock;
969        }
970        # Restore the error message.
971        $@ = $savedError;
972    }
973    
974    
975    
976    
977    =head3 Assert
978    
979        Assert($condition1, $condition2, ... $conditionN);
980    
981    Return TRUE if all the conditions are true. This method can be used in conjunction with
982    the OR operator and the L</Confess> method as a debugging assert.
983    So, for example
984    
985        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
986    
987    Will abort the program with a stack trace if the value of C<$recNum> is negative.
988    
989    =cut
990    sub Assert {
991        my $retVal = 1;
992        LOOP: for my $condition (@_) {
993            if (! $condition) {
994                $retVal = 0;
995                last LOOP;
996            }
997        }
998        return $retVal;
999    }
1000    
1001    =head3 Cluck
1002    
1003        Cluck($message);
1004    
1005    Trace the call stack. Note that for best results, you should qualify the call with a
1006    trace condition. For example,
1007    
1008        Cluck("Starting record parse.") if T(3);
1009    
1010    will only trace the stack if the trace level for the package is 3 or more.
1011    
1012    =over 4
1013    
1014    =item message
1015    
1016    Message to include in the trace.
1017    
1018    =back
1019    
1020    =cut
1021    
1022    sub Cluck {
1023        # Get the parameters.
1024        my ($message) = @_;
1025        # Trace what's happening.
1026        Trace("Stack trace for event: $message");
1027        # Get the stack trace.
1028        my @trace = LongMess();
1029        # Convert the trace to a series of messages.
1030        for my $line (@trace) {
1031            # Replace the tab at the beginning with spaces.
1032            $line =~ s/^\t/    /;
1033            # Trace the line.
1034            Trace($line);
1035        }
1036        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
1037        Warn($message);
1038    }
1039    
1040    =head3 LongMess
1041    
1042        my @lines = Tracer::LongMess();
1043    
1044    Return a stack trace with all tracing methods removed. The return will be in the form of a list
1045    of message strings.
1046    
1047    =cut
1048    
1049    sub LongMess {
1050        # Declare the return variable.
1051        my @retVal = ();
1052        my $confession = longmess("");
1053        for my $line (split /\s*\n/, $confession) {
1054            unless ($line =~ /Tracer\.pm/) {
1055                # Here we have a line worth keeping. Push it onto the result list.
1056                push @retVal, $line;
1057            }
1058        }
1059        # Return the result.
1060        return @retVal;
1061    }
1062    
1063    =head3 ETracing
1064    
1065        ETracing($parameter, %options);
1066    
1067    Set up emergency tracing. Emergency tracing is tracing that is turned
1068    on automatically for any program that calls this method. The emergency
1069    tracing parameters are stored in a a file identified by a tracing key.
1070    If this method is called with a CGI object, then the tracing key is
1071    taken from a cookie. If it is called with no parameters, then the tracing
1072    key is taken from an environment variable. If it is called with a string,
1073    the tracing key is that string.
1074    
1075    =over 4
1076    
1077    =item parameter
1078    
1079    A parameter from which the tracing key is computed. If it is a scalar,
1080    that scalar is used as the tracing key. If it is a CGI object, the
1081    tracing key is taken from the C<IP> cookie. If it is omitted, the
1082    tracing key is taken from the C<TRACING> environment variable. If it
1083    is a CGI object and emergency tracing is not on, the C<Trace> and
1084    C<TF> parameters will be used to determine the type of tracing.
1085    
1086    =item options
1087    
1088    Hash of options. The permissible options are given below.
1089    
1090    =over 8
1091    
1092    =item destType
1093    
1094    Emergency tracing destination type to use if no tracing file is found. The
1095    default is C<WARN>.
1096    
1097    =item noParms
1098    
1099    If TRUE, then display of the saved CGI parms is suppressed. The default is FALSE.
1100    
1101    =item level
1102    
1103    The trace level to use if no tracing file is found. The default is C<0>.
1104    
1105    =back
1106    
1107    =cut
1108    
1109    sub ETracing {
1110        # Get the parameter.
1111        my ($parameter, %options) = @_;
1112        # Check for CGI mode.
1113        if (defined $parameter && ref $parameter eq 'CGI') {
1114            $SavedCGI = $parameter;
1115        } else {
1116            $SavedCGI = undef;
1117        }
1118        # Check for the noParms option.
1119        my $noParms = $options{noParms} || 0;
1120        # Get the default tracing information.
1121        my $tracing = $options{level} || 0;
1122        my $dest = $options{destType} || "WARN";
1123        # Check for emergency tracing.
1124        my $tkey = EmergencyKey($parameter);
1125        my $emergencyFile = EmergencyFileName($tkey);
1126        if (-e $emergencyFile) {
1127            # We have the file. Read in the data.
1128            my @tracing = GetFile($emergencyFile);
1129            # Pull off the time limit.
1130            my $expire = shift @tracing;
1131            # Convert it to seconds.
1132            $expire *= 3600;
1133            # Check the file data.
1134            my $stat = stat($emergencyFile);
1135            my ($now) = gettimeofday;
1136            if ($now - $stat->mtime > $expire) {
1137                # Delete the expired file.
1138                unlink $emergencyFile;
1139            } else {
1140                # Emergency tracing is on. Pull off the destination and
1141                # the trace level;
1142                $dest = shift @tracing;
1143                my $level = shift @tracing;
1144                # Insure Tracer is specified.
1145                my %moduleHash = map { $_ => 1 } @tracing;
1146                $moduleHash{Tracer} = 1;
1147                # Set the trace parameter.
1148                $tracing = join(" ", $level, sort keys %moduleHash);
1149            }
1150        }
1151        # Convert the destination to a real tracing destination.
1152        $dest = EmergencyTracingDest($tkey, $dest);
1153        # Setup the tracing we've determined from all the stuff above.
1154        TSetup($tracing, $dest);
1155        # Check to see if we're a web script.
1156        if (defined $SavedCGI) {
1157            # Yes we are. Trace the form and environment data if it's not suppressed.
1158            if (! $noParms) {
1159                TraceParms($SavedCGI);
1160            }
1161            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1162            # emitted by the script in its raw form.
1163            if (T(Raw => 3)) {
1164                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1165            }
1166        }
1167    }
1168    
1169    =head3 EmergencyFileName
1170    
1171        my $fileName = Tracer::EmergencyFileName($tkey);
1172    
1173    Return the emergency tracing file name. This is the file that specifies
1174    the tracing information.
1175    
1176    =over 4
1177    
1178    =item tkey
1179    
1180    Tracing key for the current program.
1181    
1182    =item RETURN
1183    
1184    Returns the name of the file to contain the emergency tracing information.
1185    
1186    =back
1187    
1188    =cut
1189    
1190    sub EmergencyFileName {
1191        # Get the parameters.
1192        my ($tkey) = @_;
1193        # Compute the emergency tracing file name.
1194        return "$FIG_Config::temp/Emergency$tkey.txt";
1195    }
1196    
1197    =head3 EmergencyFileTarget
1198    
1199        my $fileName = Tracer::EmergencyFileTarget($tkey);
1200    
1201    Return the emergency tracing target file name. This is the file that receives
1202    the tracing output for file-based tracing.
1203    
1204    =over 4
1205    
1206    =item tkey
1207    
1208    Tracing key for the current program.
1209    
1210    =item RETURN
1211    
1212    Returns the name of the file to contain the trace output.
1213    
1214    =back
1215    
1216    =cut
1217    
1218    sub EmergencyFileTarget {
1219        # Get the parameters.
1220        my ($tkey) = @_;
1221        # Compute the emergency tracing file name.
1222        return "$FIG_Config::temp/trace$tkey.log";
1223    }
1224    
1225    =head3 EmergencyTracingDest
1226    
1227        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1228    
1229    This method converts an emergency tracing destination to a real
1230    tracing destination. The main difference is that if the
1231    destination is C<FILE> or C<APPEND>, we convert it to file
1232    output. If the destination is C<DUAL>, we convert it to file
1233    and standard output.
1234    
1235    =over 4
1236    
1237    =item tkey
1238    
1239    Tracing key for this environment.
1240    
1241    =item myDest
1242    
1243    Destination from the emergency tracing file.
1244    
1245    =item RETURN
1246    
1247    Returns a destination that can be passed into L</TSetup>.
1248    
1249    =back
1250    
1251    =cut
1252    
1253    sub EmergencyTracingDest {
1254        # Get the parameters.
1255        my ($tkey, $myDest) = @_;
1256        # Declare the return variable.
1257        my $retVal = $myDest;
1258        # Process according to the destination value.
1259        if ($myDest eq 'FILE') {
1260            $retVal = ">" . EmergencyFileTarget($tkey);
1261        } elsif ($myDest eq 'APPEND') {
1262            $retVal = ">>" . EmergencyFileTarget($tkey);
1263        } elsif ($myDest eq 'DUAL') {
1264            $retVal = "+>" . EmergencyFileTarget($tkey);
1265        } elsif ($myDest eq 'WARN') {
1266            $retVal = "WARN";
1267        }
1268        # Return the result.
1269        return $retVal;
1270    }
1271    
1272    =head3 Emergency
1273    
1274        Emergency($key, $hours, $dest, $level, @modules);
1275    
1276    Turn on emergency tracing. This method is normally invoked over the web from
1277    a debugging console, but it can also be called by the C<trace.pl> script.
1278    The caller specifies the duration of the emergency in hours, the desired tracing
1279    destination, the trace level, and a list of the trace modules to activate.
1280    For the length of the duration, when a program in an environment with the
1281    specified tracing key active invokes a Sprout CGI script, tracing will be
1282    turned on automatically. See L</TSetup> for more about tracing setup and
1283    L</ETracing> for more about emergency tracing.
1284    
1285    =over 4
1286    
1287    =item tkey
1288    
1289    The tracing key. This is used to identify the control file and the trace file.
1290    
1291    =item hours
1292    
1293    Number of hours to keep emergency tracing alive.
1294    
1295    =item dest
1296    
1297    Tracing destination. If no path information is specified for a file
1298    destination, it is put in the FIG temporary directory.
1299    
1300    =item level
1301    
1302    Tracing level. A higher level means more trace messages.
1303    
1304    =item modules
1305    
1306    A list of the tracing modules to activate.
1307    
1308    =back
1309    
1310    =cut
1311    
1312    sub Emergency {
1313        # Get the parameters.
1314        my ($tkey, $hours, $dest, $level, @modules) = @_;
1315        # Create the emergency file.
1316        my $specFile = EmergencyFileName($tkey);
1317        my $outHandle = Open(undef, ">$specFile");
1318        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1319    }
1320    
1321    =head3 EmergencyKey
1322    
1323        my $tkey = EmergencyKey($parameter);
1324    
1325    Return the Key to be used for emergency tracing. This could be an IP address,
1326     a session ID, or a user name, depending on the environment.
1327    
1328    =over 4
1329    
1330    =item parameter
1331    
1332    Parameter defining the method for finding the tracing key. If it is a scalar,
1333    then it is presumed to be the tracing key itself. If it is a CGI object, then
1334    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1335    taken from the C<TRACING> environment variable.
1336    
1337    =item RETURN
1338    
1339    Returns the key to be used for labels in emergency tracing.
1340    
1341    =back
1342    
1343    =cut
1344    
1345    sub EmergencyKey {
1346        # Get the parameters.
1347        my ($parameter) = @_;
1348        # Declare the return variable.
1349        my $retVal;
1350        # Determine the parameter type.
1351        if (! defined $parameter) {
1352            # Here we're supposed to check the environment. If that fails, we
1353            # get the effective login ID.
1354            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1355        } else {
1356            my $ptype = ref $parameter;
1357            if ($ptype eq 'CGI') {
1358                # Here we were invoked from a web page. Look for a cookie.
1359                $retVal = $parameter->cookie('IP');
1360            } elsif (! $ptype) {
1361                # Here the key was passed in.
1362                $retVal = $parameter;
1363            }
1364        }
1365        # If no luck finding a key, use the PID.
1366        if (! defined $retVal) {
1367            $retVal = $$;
1368        }
1369        # Return the result.
1370        return $retVal;
1371    }
1372    
1373    
1374    =head3 TraceParms
1375    
1376        Tracer::TraceParms($cgi);
1377    
1378    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1379    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1380    
1381    =over 4
1382    
1383    =item cgi
1384    
1385    CGI query object containing the parameters to trace.
1386    
1387    =back
1388    
1389    =cut
1390    
1391    sub TraceParms {
1392        # Get the parameters.
1393        my ($cgi) = @_;
1394        if (T(CGI => 2)) {
1395            # Here we trace the GET-style URL for the script, but only if it's
1396            # relatively small.
1397            my $url = $cgi->url(-relative => 1, -query => 1);
1398            my $len = length($url);
1399            if ($len < 500) {
1400                Trace("[URL] $url");
1401            } elsif ($len > 2048) {
1402                Trace("[URL] URL is too long to use with GET ($len characters).");
1403            } else {
1404                Trace("[URL] URL length is $len characters.");
1405            }
1406        }
1407        if (T(CGI => 3)) {
1408            # Here we want to trace the parameter data.
1409            my @names = $cgi->param;
1410            for my $parmName (sort @names) {
1411                # Note we skip the Trace parameters, which are for our use only.
1412                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1413                    my @values = $cgi->param($parmName);
1414                    Trace("[CGI] $parmName = " . join(", ", @values));
1415                }
1416            }
1417            # Display the request method.
1418            my $method = $cgi->request_method();
1419            Trace("Method: $method");
1420        }
1421        if (T(CGI => 4)) {
1422            # Here we want the environment data too.
1423            for my $envName (sort keys %ENV) {
1424                Trace("[ENV] $envName = $ENV{$envName}");
1425            }
1426        }
1427    }
1428    
1429    =head3 TraceImages
1430    
1431        Tracer::TraceImages($htmlString);
1432    
1433    Trace information about all of an html document's images. The tracing
1434    will be for type "IMG" at level 3. The image's source string
1435    will be displayed. This is generally either the URL of the image or
1436    raw data for the image itself. If the source is too long, only the first 300
1437    characters will be shown at trace level 3. The entire source will be shown,
1438    however, at trace level 4. This method is not very smart, and might catch
1439    Javascript code, but it is still useful when debugging the arcane
1440    behavior of images in multiple browser environments.
1441    
1442    =over 4
1443    
1444    =item htmlString
1445    
1446    HTML text for an outgoing web page.
1447    
1448    =back
1449    
1450    =cut
1451    
1452    sub TraceImages {
1453        # Only proceed if we're at the proper trace level.
1454        if (T(IMG => 3)) {
1455            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1456            # into a variable called "$htmlString". This is because we expect html strings to be
1457            # long, and don't want to copy them any more than we have to.
1458            Trace(length($_[0]) . " characters in web page.");
1459            # Loop through the HTML, culling image tags.
1460            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1461                # Extract the source string and determine whether or not it's too long.
1462                my $srcString = $1;
1463                my $pos = pos($_[0]) - length($srcString);
1464                my $excess = length($srcString) - 300;
1465                # We'll put the display string in here.
1466                my $srcDisplay = $srcString;
1467                # If it's a data string, split it at the comma.
1468                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1469                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1470                # a long string, however, we only show the first 300 characters.
1471                if ($excess > 0 && ! T(IMG => 4)) {
1472                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1473                }
1474                # Output the trace message.
1475                Trace("Image tag at position $pos:\n$srcDisplay");
1476            }
1477        }
1478    }
1479    
1480    =head2 Command-Line Utility Methods
1481    
1482    =head3 SendSMS
1483    
1484        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1485    
1486    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1487    user name, password, and API ID for the relevant account in the hash reference variable
1488    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1489    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1490    is C<2561022>, then the FIG_Config file must contain
1491    
1492        $phone =  { user => 'BruceTheHumanPet',
1493                    password => 'silly',
1494                    api_id => '2561022' };
1495    
1496    The original purpose of this method was to insure Bruce would be notified immediately when the
1497    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1498    when you call this method.
1499    
1500    The message ID will be returned if successful, and C<undef> if an error occurs.
1501    
1502    =over 4
1503    
1504    =item phoneNumber
1505    
1506    Phone number to receive the message, in international format. A United States phone number
1507    would be prefixed by "1". A British phone number would be prefixed by "44".
1508    
1509    =item msg
1510    
1511    Message to send to the specified phone.
1512    
1513    =item RETURN
1514    
1515    Returns the message ID if successful, and C<undef> if the message could not be sent.
1516    
1517    =back
1518    
1519    =cut
1520    
1521    sub SendSMS {
1522        # Get the parameters.
1523        my ($phoneNumber, $msg) = @_;
1524        # Declare the return variable. If we do not change it, C<undef> will be returned.
1525        my $retVal;
1526        # Only proceed if we have phone support.
1527        if (! defined $FIG_Config::phone) {
1528            Trace("Phone support not present in FIG_Config.") if T(1);
1529        } else {
1530            # Get the phone data.
1531            my $parms = $FIG_Config::phone;
1532            # Get the Clickatell URL.
1533            my $url = "http://api.clickatell.com/http/";
1534            # Create the user agent.
1535            my $ua = LWP::UserAgent->new;
1536            # Request a Clickatell session.
1537            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1538                                         password => $parms->{password},
1539                                         api_id => $parms->{api_id},
1540                                         to => $phoneNumber,
1541                                         text => $msg});
1542            # Check for an error.
1543            if (! $resp->is_success) {
1544                Trace("Alert failed.") if T(1);
1545            } else {
1546                # Get the message ID.
1547                my $rstring = $resp->content;
1548                if ($rstring =~ /^ID:\s+(.*)$/) {
1549                    $retVal = $1;
1550                } else {
1551                    Trace("Phone attempt failed with $rstring") if T(1);
1552                }
1553            }
1554        }
1555        # Return the result.
1556        return $retVal;
1557    }
1558    
1559    =head3 StandardSetup
1560    
1561        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1562    
1563    This method performs standard command-line parsing and tracing setup. The return
1564    values are a hash of the command-line options and a list of the positional
1565    parameters. Tracing is automatically set up and the command-line options are
1566    validated.
1567    
1568    This is a complex method that does a lot of grunt work. The parameters can
1569    be more easily understood, however, once they are examined individually.
1570    
1571    The I<categories> parameter is the most obtuse. It is a reference to a list of
1572    special-purpose tracing categories. Most tracing categories are PERL package
1573    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1574    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1575    
1576        ["Sprout", "SproutLoad", "ERDB"]
1577    
1578    This would cause trace messages in the specified three packages to appear in
1579    the output. There are two special tracing categories that are automatically
1580    handled by this method. In other words, if you used L</TSetup> you would need
1581    to include these categories manually, but if you use this method they are turned
1582    on automatically.
1583    
1584    =over 4
1585    
1586    =item SQL
1587    
1588    Traces SQL commands and activity.
1589    
1590    =item Tracer
1591    
1592    Traces error messages and call stacks.
1593    
1594    =back
1595    
1596    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1597    The trace level is specified using the C<-trace> command-line option. For example,
1598    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1599    all tracing at level 3.
1600    
1601        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1602    
1603    Standard tracing is output to the standard output and echoed to the file
1604    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1605    process ID. You can also specify the C<user> parameter to put a user ID
1606    instead of a process ID in the trace file name. So, for example
1607    
1608    The default trace level is 2. To get all messages, specify a trace level of 4.
1609    For a genome-by-genome update, use 3.
1610    
1611        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1612    
1613    would send the trace output to C<traceBruce.log> in the temporary directory.
1614    
1615    The I<options> parameter is a reference to a hash containing the command-line
1616    options, their default values, and an explanation of what they mean. Command-line
1617    options may be in the form of switches or keywords. In the case of a switch, the
1618    option value is 1 if it is specified and 0 if it is not specified. In the case
1619    of a keyword, the value is separated from the option name by an equal sign. You
1620    can see this last in the command-line example above.
1621    
1622    You can specify a different default trace level by setting C<$options->{trace}>
1623    prior to calling this method.
1624    
1625    An example at this point would help. Consider, for example, the command-line utility
1626    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1627    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1628    the following code.
1629    
1630        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1631                            { safe => [0, "use database transactions"],
1632                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1633                              start => [' ', "start with this genome"],
1634                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1635                            "<command> <transactionDirectory> <IDfile>",
1636                          @ARGV);
1637    
1638    
1639    The call to C<ParseCommand> specifies the default values for the options and
1640    stores the actual options in a hash that is returned as C<$options>. The
1641    positional parameters are returned in C<@parameters>.
1642    
1643    The following is a sample command line for C<TransactFeatures>.
1644    
1645        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1646    
1647    Single and double hyphens are equivalent. So, you could also code the
1648    above command as
1649    
1650        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1651    
1652    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1653    parameters, and would find themselves in I<@parameters> after executing the
1654    above code fragment. The tracing would be set to level 2, and the categories
1655    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1656    and C<DocUtils> was included because it came in within the first parameter
1657    to this method. The I<$options> hash would be
1658    
1659        { trace => 2, sql => 0, safe => 0,
1660          noAlias => 1, start => ' ', tblFiles => 0 }
1661    
1662    Use of C<StandardSetup> in this way provides a simple way of performing
1663    standard tracing setup and command-line parsing. Note that the caller is
1664    not even aware of the command-line switches C<-trace> and C<-sql>, which
1665    are used by this method to control the tracing. If additional tracing features
1666    need to be added in the future, they can be processed by this method without
1667    upsetting the command-line utilities.
1668    
1669    If the C<background> option is specified on the command line, then the
1670    standard and error outputs will be directed to files in the temporary
1671    directory, using the same suffix as the trace file. So, if the command
1672    line specified
1673    
1674        -user=Bruce -background
1675    
1676    then the trace output would go to C<traceBruce.log>, the standard output to
1677    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1678    simplify starting a command in the background.
1679    
1680    The user name is also used as the tracing key for L</Emergency Tracing>.
1681    Specifying a value of C<E> for the trace level causes emergency tracing to
1682    be used instead of custom tracing. If the user name is not specified,
1683    the tracing key is taken from the C<Tracing> environment variable. If there
1684    is no value for that variable, the tracing key will be computed from the active
1685    login ID.
1686    
1687    Since the default situation in StandardSetup is to trace to the standard
1688    output, errors that occur in command-line scripts will not generate
1689    RSS events. To force the events, use the C<warn> option.
1690    
1691        TransactFeatures -background -warn register ../xacts IDs.tbl
1692    
1693    Finally, if the special option C<-help> is specified, the option
1694    names will be traced at level 0 and the program will exit without processing.
1695    This provides a limited help capability. For example, if the user enters
1696    
1697        TransactFeatures -help
1698    
1699    he would see the following output.
1700    
1701        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1702            -trace    tracing level (default E)
1703            -sql      trace SQL commands
1704            -safe     use database transactions
1705            -noAlias  do not expect aliases in CHANGE transactions
1706            -start    start with this genome
1707            -tblFiles output TBL files containing the corrected IDs
1708            -forked   do not erase the trace file before tracing
1709    
1710    The caller has the option of modifying the tracing scheme by placing a value
1711    for C<trace> in the incoming options hash. The default value can be overridden,
1712    or the tracing to the standard output can be turned off by suffixing a minus
1713    sign to the trace level. So, for example,
1714    
1715        { trace => [0, "tracing level (default 0)"],
1716           ...
1717    
1718    would set the default trace level to 0 instead of E, while
1719    
1720        { trace => ["2-", "tracing level (default 2)"],
1721           ...
1722    
1723    would set the default to 2, but trace only to the log file, not to the
1724    standard output.
1725    
1726    The parameters to this method are as follows.
1727    
1728    =over 4
1729    
1730    =item categories
1731    
1732    Reference to a list of tracing category names. These should be names of
1733    packages whose internal workings will need to be debugged to get the
1734    command working.
1735    
1736    =item options
1737    
1738    Reference to a hash containing the legal options for the current command mapped
1739    to their default values and descriptions. The user can override the defaults
1740    by specifying the options as command-line switches prefixed by a hyphen.
1741    Tracing-related options may be added to this hash. If the C<-h> option is
1742    specified on the command line, the option descriptions will be used to
1743    explain the options. To turn off tracing to the standard output, add a
1744    minus sign to the value for C<trace> (see above).
1745    
1746    =item parmHelp
1747    
1748    A string that vaguely describes the positional parameters. This is used
1749    if the user specifies the C<-h> option.
1750    
1751    =item argv
1752    
1753    List of command line parameters, including the option switches, which must
1754    precede the positional parameters and be prefixed by a hyphen.
1755    
1756    =item RETURN
1757    
1758    Returns a list. The first element of the list is the reference to a hash that
1759    maps the command-line option switches to their values. These will either be the
1760    default values or overrides specified on the command line. The remaining
1761    elements of the list are the position parameters, in order.
1762    
1763    =back
1764    
1765    =cut
1766    
1767    sub StandardSetup {
1768        # Get the parameters.
1769        my ($categories, $options, $parmHelp, @argv) = @_;
1770        # Get the default tracing key.
1771        my $tkey = EmergencyKey();
1772        # Save the command line.
1773        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1774        # Add the tracing options.
1775        if (! exists $options->{trace}) {
1776            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1777        }
1778        if (! exists $options->{forked}) {
1779            $options->{forked} = [0, "keep old trace file"];
1780        }
1781        $options->{sql} = [0, "turn on SQL tracing"];
1782        $options->{help} = [0, "display command-line options"];
1783        $options->{user} = [$tkey, "tracing key"];
1784        $options->{background} = [0, "spool standard and error output"];
1785        $options->{warn} = [0, "send errors to RSS feed"];
1786        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1787        # Create a parsing hash from the options hash. The parsing hash
1788        # contains the default values rather than the default value
1789        # and the description. While we're at it, we'll memorize the
1790        # length of the longest option name.
1791        my $longestName = 0;
1792        my %parseOptions = ();
1793        for my $key (keys %{$options}) {
1794            if (length $key > $longestName) {
1795                $longestName = length $key;
1796            }
1797            $parseOptions{$key} = $options->{$key}->[0];
1798        }
1799        # Parse the command line.
1800        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1801        # Get the logfile suffix.
1802      my $suffix = $retOptions->{user};      my $suffix = $retOptions->{user};
1803        # We'll put the trace file name in here. We need it later if background
1804        # mode is on.
1805        my $traceFileName;
1806        # Now we want to set up tracing. First, we need to know if the user
1807        # wants emergency tracing.
1808        if ($retOptions->{trace} eq 'E') {
1809            ETracing($retOptions->{user});
1810        } else {
1811            # Here the tracing is controlled from the command line.
1812            my @cats = @{$categories};
1813            if ($retOptions->{sql}) {
1814                push @cats, "SQL";
1815            }
1816            if ($retOptions->{warn}) {
1817                push @cats, "Feed";
1818            }
1819            # Add the default categories.
1820            push @cats, "Tracer";
1821            # Check for more tracing groups.
1822            if ($retOptions->{moreTracing}) {
1823                push @cats, split /,/, $retOptions->{moreTracing};
1824            }
1825            # Next, we create the category string by joining the categories.
1826            my $cats = join(" ", @cats);
1827            # Check to determine whether or not the caller wants to turn off tracing
1828            # to the standard output.
1829            my $traceLevel = $retOptions->{trace};
1830            my $textOKFlag = 1;
1831            if ($traceLevel =~ /^(.)-/) {
1832                $traceLevel = $1;
1833                $textOKFlag = 0;
1834            }
1835            # Now we set up the trace mode.
1836            my $traceMode;
1837            # Verify that we can open a file in the FIG temporary directory.
1838            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1839            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1840            if (open TESTTRACE, "$traceFileSpec") {
1841                # Here we can trace to a file.
1842                $traceMode = ">>$traceFileName";
1843                if ($textOKFlag) {
1844                    # Echo to standard output if the text-OK flag is set.
1845                    $traceMode = "+$traceMode";
1846                }
1847                # Close the test file.
1848                close TESTTRACE;
1849            } else {
1850                # Here we can't trace to a file. Complain about this.
1851                warn "Could not open trace file $traceFileName: $!\n";
1852                # We trace to the standard output if it's
1853                # okay, and the error log otherwise.
1854                if ($textOKFlag) {
1855                    $traceMode = "TEXT";
1856                } else {
1857                    $traceMode = "WARN";
1858                }
1859            }
1860            # Now set up the tracing.
1861            TSetup("$traceLevel $cats", $traceMode);
1862        }
1863      # Check for background mode.      # Check for background mode.
1864      if ($retOptions->{background}) {      if ($retOptions->{background}) {
1865          my $outFileName = "$FIG_Config::temp/out$suffix.log";          my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1866          my $errFileName = "$FIG_Config::temp/err$suffix.log";          my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1867            # Spool the output.
1868          open STDOUT, ">$outFileName";          open STDOUT, ">$outFileName";
1869            # If we have a trace file, trace the errors to the log. Otherwise,
1870            # spool the errors.
1871            if (defined $traceFileName) {
1872                open STDERR, "| Tracer $traceFileName";
1873            } else {
1874          open STDERR, ">$errFileName";          open STDERR, ">$errFileName";
1875      }      }
1876      # Now we want to set up tracing. First, we need to know if SQL is to          # Check for phone support. If we have phone support and a phone number,
1877      # be traced.          # we want to turn it on.
1878      my @cats = @{$categories};          if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1879      if ($retOptions->{sql}) {              $retOptions->{phone} = $ENV{PHONE};
1880          push @cats, "SQL";          }
1881        }
1882        # Check for the "help" option. If it is specified, dump the command-line
1883        # options and exit the program.
1884        if ($retOptions->{help}) {
1885            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1886            print "$1 [options] $parmHelp\n";
1887            for my $key (sort keys %{$options}) {
1888                my $name = Pad($key, $longestName, 0, ' ');
1889                my $desc = $options->{$key}->[1];
1890                if ($options->{$key}->[0]) {
1891                    $desc .= " (default " . $options->{$key}->[0] . ")";
1892                }
1893                print "  $name $desc\n";
1894            }
1895            exit(0);
1896        }
1897        # Trace the options, if applicable.
1898        if (T(3)) {
1899            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1900            Trace("Selected options: " . join(", ", sort @parms) . ".");
1901        }
1902        # Return the parsed parameters.
1903        return ($retOptions, @retParameters);
1904    }
1905    
1906    =head3 ReadOptions
1907    
1908        my %options = Tracer::ReadOptions($fileName);
1909    
1910    Read a set of options from a file. Each option is encoded in a line of text that has the
1911    format
1912    
1913    I<optionName>C<=>I<optionValue>C<; >I<comment>
1914    
1915    The option name must consist entirely of letters, digits, and the punctuation characters
1916    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1917    character is a semi-colon will be ignored. The return hash will map each option name to
1918    the corresponding option value.
1919    
1920    =over 4
1921    
1922    =item fileName
1923    
1924    Name of the file containing the option data.
1925    
1926    =item RETURN
1927    
1928    Returns a hash mapping the option names specified in the file to their corresponding option
1929    value.
1930    
1931    =back
1932    
1933    =cut
1934    
1935    sub ReadOptions {
1936        # Get the parameters.
1937        my ($fileName) = @_;
1938        # Open the file.
1939        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1940        # Count the number of records read.
1941        my ($records, $comments) = 0;
1942        # Create the return hash.
1943        my %retVal = ();
1944        # Loop through the file, accumulating key-value pairs.
1945        while (my $line = <CONFIGFILE>) {
1946            # Denote we've read a line.
1947            $records++;
1948            # Determine the line type.
1949            if ($line =~ /^\s*[\n\r]/) {
1950                # A blank line is a comment.
1951                $comments++;
1952            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1953                # Here we have an option assignment.
1954                retVal{$1} = $2;
1955            } elsif ($line =~ /^\s*;/) {
1956                # Here we have a text comment.
1957                $comments++;
1958            } else {
1959                # Here we have an invalid line.
1960                Trace("Invalid option statement in record $records.") if T(0);
1961            }
1962        }
1963        # Return the hash created.
1964        return %retVal;
1965    }
1966    
1967    =head3 GetOptions
1968    
1969        Tracer::GetOptions(\%defaults, \%options);
1970    
1971    Merge a specified set of options into a table of defaults. This method takes two hash references
1972    as input and uses the data from the second to update the first. If the second does not exist,
1973    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1974    exist in the first.
1975    
1976    Consider the following example.
1977    
1978        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1979    
1980    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1981    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1982    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1983    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1984    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1985    
1986        {databaseType => 'Oracle'}
1987    
1988    an error will occur because the B<databaseType> option does not exist.
1989    
1990    =over 4
1991    
1992    =item defaults
1993    
1994    Table of default option values.
1995    
1996    =item options
1997    
1998    Table of overrides, if any.
1999    
2000    =item RETURN
2001    
2002    Returns a reference to the default table passed in as the first parameter.
2003    
2004    =back
2005    
2006    =cut
2007    
2008    sub GetOptions {
2009        # Get the parameters.
2010        my ($defaults, $options) = @_;
2011        # Check for overrides.
2012        if ($options) {
2013            # Loop through the overrides.
2014            while (my ($option, $setting) = each %{$options}) {
2015                # Insure this override exists.
2016                if (!exists $defaults->{$option}) {
2017                    croak "Unrecognized option $option encountered.";
2018                } else {
2019                    # Apply the override.
2020                    $defaults->{$option} = $setting;
2021                }
2022            }
2023        }
2024        # Return the merged table.
2025        return $defaults;
2026    }
2027    
2028    =head3 MergeOptions
2029    
2030        Tracer::MergeOptions(\%table, \%defaults);
2031    
2032    Merge default values into a hash table. This method looks at the key-value pairs in the
2033    second (default) hash, and if a matching key is not found in the first hash, the default
2034    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2035    checking and no return value.
2036    
2037    =over 4
2038    
2039    =item table
2040    
2041    Hash table to be updated with the default values.
2042    
2043    =item defaults
2044    
2045    Default values to be merged into the first hash table if they are not already present.
2046    
2047    =back
2048    
2049    =cut
2050    
2051    sub MergeOptions {
2052        # Get the parameters.
2053        my ($table, $defaults) = @_;
2054        # Loop through the defaults.
2055        while (my ($key, $value) = each %{$defaults}) {
2056            if (!exists $table->{$key}) {
2057                $table->{$key} = $value;
2058            }
2059        }
2060    }
2061    
2062    =head3 UnparseOptions
2063    
2064        my $optionString = Tracer::UnparseOptions(\%options);
2065    
2066    Convert an option hash into a command-line string. This will not
2067    necessarily be the same text that came in, but it will nonetheless
2068    produce the same ultimate result when parsed by L</StandardSetup>.
2069    
2070    =over 4
2071    
2072    =item options
2073    
2074    Reference to a hash of options to convert into an option string.
2075    
2076    =item RETURN
2077    
2078    Returns a string that will parse to the same set of options when
2079    parsed by L</StandardSetup>.
2080    
2081    =back
2082    
2083    =cut
2084    
2085    sub UnparseOptions {
2086        # Get the parameters.
2087        my ($options) = @_;
2088        # The option segments will be put in here.
2089        my @retVal = ();
2090        # Loop through the options.
2091        for my $key (keys %$options) {
2092            # Get the option value.
2093            my $value = $options->{$key};
2094            # Only use it if it's nonempty.
2095            if (defined $value && $value ne "") {
2096                my $segment = "--$key=$value";
2097                # Quote it if necessary.
2098                if ($segment =~ /[ |<>*]/) {
2099                    $segment = '"' . $segment . '"';
2100                }
2101                # Add it to the return list.
2102                push @retVal, $segment;
2103            }
2104        }
2105        # Return the result.
2106        return join(" ", @retVal);
2107    }
2108    
2109    =head3 ParseCommand
2110    
2111        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2112    
2113    Parse a command line consisting of a list of parameters. The initial parameters may be option
2114    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2115    off and merged into a table of default options. The remainder of the command line is
2116    returned as a list of positional arguments. For example, consider the following invocation.
2117    
2118        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2119    
2120    In this case, the list @words will be treated as a command line and there are two options available,
2121    B<errors> and B<logFile>. If @words has the following format
2122    
2123        -logFile=error.log apple orange rutabaga
2124    
2125    then at the end of the invocation, C<$options> will be
2126    
2127        { errors => 0, logFile => 'error.log' }
2128    
2129    and C<@arguments> will contain
2130    
2131        apple orange rutabaga
2132    
2133    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2134    support for quote characters. Options can be specified with single or double hyphens.
2135    
2136    =over 4
2137    
2138    =item optionTable
2139    
2140    Table of default options.
2141    
2142    =item inputList
2143    
2144    List of words on the command line.
2145    
2146    =item RETURN
2147    
2148    Returns a reference to the option table and a list of the positional arguments.
2149    
2150    =back
2151    
2152    =cut
2153    
2154    sub ParseCommand {
2155        # Get the parameters.
2156        my ($optionTable, @inputList) = @_;
2157        # Process any options in the input list.
2158        my %overrides = ();
2159        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2160            # Get the current option.
2161            my $arg = shift @inputList;
2162            # Pull out the option name.
2163            $arg =~ /^--?([^=]*)/g;
2164            my $name = $1;
2165            # Check for an option value.
2166            if ($arg =~ /\G=(.*)$/g) {
2167                # Here we have a value for the option.
2168                $overrides{$name} = UnEscape($1);
2169            } else {
2170                # Here there is no value, so we use 1.
2171                $overrides{$name} = 1;
2172            }
2173      }      }
2174      # Add the default categories.      # Merge the options into the defaults.
2175      push @cats, "Tracer", "FIG";      GetOptions($optionTable, \%overrides);
2176      # Next, we create the category string by prefixing the trace level      # Translate the remaining parameters.
2177      # and joining the categories.      my @retVal = ();
2178      my $cats = join(" ", $parseOptions{trace}, @cats);      for my $inputParm (@inputList) {
2179      # Verify that we can open a file in the temporary directory.          push @retVal, UnEscape($inputParm);
     my $traceMode = "TEXT";  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         $traceMode = "+>$traceFileName";  
         close TESTTRACE;  
2180      }      }
2181      # Now set up the tracing.      # Return the results.
2182      TSetup($cats, $traceMode);      return ($optionTable, @retVal);
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         Trace("$1 [options] $parmHelp") if T(0);  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
2183              }              }
2184              Trace("  $name $desc") if T(0);  
2185    
2186    =head2 File Utility Methods
2187    
2188    =head3 GetFile
2189    
2190        my @fileContents = Tracer::GetFile($fileName);
2191    
2192        or
2193    
2194        my $fileContents = Tracer::GetFile($fileName);
2195    
2196    Return the entire contents of a file. In list context, line-ends are removed and
2197    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2198    
2199    =over 4
2200    
2201    =item fileName
2202    
2203    Name of the file to read.
2204    
2205    =item RETURN
2206    
2207    In a list context, returns the entire file as a list with the line terminators removed.
2208    In a scalar context, returns the entire file as a string. If an error occurs opening
2209    the file, an empty list will be returned.
2210    
2211    =back
2212    
2213    =cut
2214    
2215    sub GetFile {
2216        # Get the parameters.
2217        my ($fileName) = @_;
2218        # Declare the return variable.
2219        my @retVal = ();
2220        # Open the file for input.
2221        my $handle = Open(undef, "<$fileName");
2222        # Read the whole file into the return variable, stripping off any terminator
2223        # characters.
2224        my $lineCount = 0;
2225        while (my $line = <$handle>) {
2226            $lineCount++;
2227            $line = Strip($line);
2228            push @retVal, $line;
2229          }          }
2230          exit(0);      # Close it.
2231        close $handle;
2232        my $actualLines = @retVal;
2233        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2234        # Return the file's contents in the desired format.
2235        if (wantarray) {
2236            return @retVal;
2237        } else {
2238            return join "\n", @retVal;
2239      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
2240  }  }
2241    
2242  =head3 Setups  =head3 PutFile
2243    
2244  C<< my $count = Tracer::Setups(); >>      Tracer::PutFile($fileName, \@lines);
2245    
2246  Return the number of times L</TSetup> has been called.  Write out a file from a list of lines of text.
2247    
2248  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
2249  may want to set up tracing if nobody else has done it before us.  
2250    =item fileName
2251    
2252    Name of the output file.
2253    
2254    =item lines
2255    
2256    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2257    new-line characters. Alternatively, may be a string, in which case the string will be written without
2258    modification.
2259    
2260    =back
2261    
2262  =cut  =cut
2263    
2264  sub Setups {  sub PutFile {
2265      return $SetupCount;      # Get the parameters.
2266        my ($fileName, $lines) = @_;
2267        # Open the output file.
2268        my $handle = Open(undef, ">$fileName");
2269        # Count the lines written.
2270        if (ref $lines ne 'ARRAY') {
2271            # Here we have a scalar, so we write it raw.
2272            print $handle $lines;
2273            Trace("Scalar put to file $fileName.") if T(File => 3);
2274        } else {
2275            # Write the lines one at a time.
2276            my $count = 0;
2277            for my $line (@{$lines}) {
2278                print $handle "$line\n";
2279                $count++;
2280            }
2281            Trace("$count lines put to file $fileName.") if T(File => 3);
2282        }
2283        # Close the output file.
2284        close $handle;
2285    }
2286    
2287    =head3 ParseRecord
2288    
2289        my @fields = Tracer::ParseRecord($line);
2290    
2291    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2292    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2293    These will automatically be converted.
2294    
2295    =over 4
2296    
2297    =item line
2298    
2299    Line of data containing the tab-delimited fields.
2300    
2301    =item RETURN
2302    
2303    Returns a list of the fields found in the data line.
2304    
2305    =back
2306    
2307    =cut
2308    
2309    sub ParseRecord {
2310        # Get the parameter.
2311        my ($line) = @_;
2312        # Remove the trailing new-line, if any.
2313        chomp $line;
2314        # Split the line read into pieces using the tab character.
2315        my @retVal = split /\t/, $line;
2316        # Trim and fix the escapes in each piece.
2317        for my $value (@retVal) {
2318            # Trim leading whitespace.
2319            $value =~ s/^\s+//;
2320            # Trim trailing whitespace.
2321            $value =~ s/\s+$//;
2322            # Delete the carriage returns.
2323            $value =~ s/\r//g;
2324            # Convert the escapes into their real values.
2325            $value =~ s/\\t/"\t"/ge;
2326            $value =~ s/\\n/"\n"/ge;
2327        }
2328        # Return the result.
2329        return @retVal;
2330    }
2331    
2332    =head3 Merge
2333    
2334        my @mergedList = Tracer::Merge(@inputList);
2335    
2336    Sort a list of strings and remove duplicates.
2337    
2338    =over 4
2339    
2340    =item inputList
2341    
2342    List of scalars to sort and merge.
2343    
2344    =item RETURN
2345    
2346    Returns a list containing the same elements sorted in ascending order with duplicates
2347    removed.
2348    
2349    =back
2350    
2351    =cut
2352    
2353    sub Merge {
2354        # Get the input list in sort order.
2355        my @inputList = sort @_;
2356        # Only proceed if the list has at least two elements.
2357        if (@inputList > 1) {
2358            # Now we want to move through the list splicing out duplicates.
2359            my $i = 0;
2360            while ($i < @inputList) {
2361                # Get the current entry.
2362                my $thisEntry = $inputList[$i];
2363                # Find out how many elements duplicate the current entry.
2364                my $j = $i + 1;
2365                my $dup1 = $i + 1;
2366                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2367                # If the number is nonzero, splice out the duplicates found.
2368                if ($j > $dup1) {
2369                    splice @inputList, $dup1, $j - $dup1;
2370                }
2371                # Now the element at position $dup1 is different from the element before it
2372                # at position $i. We push $i forward one position and start again.
2373                $i++;
2374            }
2375        }
2376        # Return the merged list.
2377        return @inputList;
2378  }  }
2379    
2380  =head3 Open  =head3 Open
2381    
2382  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2383    
2384  Open a file.  Open a file.
2385    
# Line 566  Line 2471 
2471    
2472  =head3 FindNamePart  =head3 FindNamePart
2473    
2474  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2475    
2476  Extract the portion of a file specification that contains the file name.  Extract the portion of a file specification that contains the file name.
2477    
# Line 617  Line 2522 
2522    
2523  =head3 OpenDir  =head3 OpenDir
2524    
2525  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @files = OpenDir($dirName, $filtered, $flag);
2526    
2527  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
2528  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
# Line 673  Line 2578 
2578          } else {          } else {
2579              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
2580          }          }
2581      } elsif (! $flag) {          closedir $dirHandle;
2582          # Here the directory would not open and it's considered an error.      } elsif (! $flag) {
2583          Confess("Could not open directory $dirName.");          # Here the directory would not open and it's considered an error.
2584            Confess("Could not open directory $dirName.");
2585        }
2586        # Return the result.
2587        return @retVal;
2588    }
2589    
2590    
2591    =head3 Insure
2592    
2593        Insure($dirName, $chmod);
2594    
2595    Insure a directory is present.
2596    
2597    =over 4
2598    
2599    =item dirName
2600    
2601    Name of the directory to check. If it does not exist, it will be created.
2602    
2603    =item chmod (optional)
2604    
2605    Security privileges to be given to the directory if it is created.
2606    
2607    =back
2608    
2609    =cut
2610    
2611    sub Insure {
2612        my ($dirName, $chmod) = @_;
2613        if (! -d $dirName) {
2614            Trace("Creating $dirName directory.") if T(2);
2615            eval {
2616                mkpath $dirName;
2617                # If we have permissions specified, set them here.
2618                if (defined($chmod)) {
2619                    chmod $chmod, $dirName;
2620                }
2621            };
2622            if ($@) {
2623                Confess("Error creating $dirName: $@");
2624            }
2625      }      }
     # Return the result.  
     return @retVal;  
2626  }  }
2627    
2628  =head3 SetLevel  =head3 ChDir
2629    
2630  C<< Tracer::SetLevel($newLevel); >>      ChDir($dirName);
2631    
2632  Modify the trace level. A higher trace level will cause more messages to appear.  Change to the specified directory.
2633    
2634  =over 4  =over 4
2635    
2636  =item newLevel  =item dirName
2637    
2638  Proposed new trace level.  Name of the directory to which we want to change.
2639    
2640  =back  =back
2641    
2642  =cut  =cut
2643    
2644  sub SetLevel {  sub ChDir {
2645      $TraceLevel = $_[0];      my ($dirName) = @_;
2646        if (! -d $dirName) {
2647            Confess("Cannot change to directory $dirName: no such directory.");
2648        } else {
2649            Trace("Changing to directory $dirName.") if T(File => 4);
2650            my $okFlag = chdir $dirName;
2651            if (! $okFlag) {
2652                Confess("Error switching to directory $dirName.");
2653            }
2654        }
2655  }  }
2656    
2657  =head3 Now  =head3 SetPermissions
2658    
2659  C<< my $string = Tracer::Now(); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2660    
2661  Return a displayable time stamp containing the local time.  Set the permissions for a directory and all the files and folders inside it.
2662    In addition, the group ownership will be changed to the specified value.
2663    
2664  =cut  This method is more vulnerable than most to permission and compatability
2665    problems, so it does internal error recovery.
2666    
2667  sub Now {  =over 4
     my ($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 $retVal;  
 }  
2668    
2669  # Pad a number to 2 digits.  =item dirName
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
2670    
2671  =head3 LogErrors  Name of the directory to process.
2672    
2673  C<< Tracer::LogErrors($fileName); >>  =item group
2674    
2675  Route the standard error output to a log file.  Name of the group to be assigned.
2676    
2677  =over 4  =item mask
2678    
2679  =item fileName  Permission mask. Bits that are C<1> in this mask will be ORed into the
2680    permission bits of any file or directory that does not already have them
2681    set to 1.
2682    
2683  Name of the file to receive the error output.  =item otherMasks
2684    
2685    Map of search patterns to permission masks. If a directory name matches
2686    one of the patterns, that directory and all its members and subdirectories
2687    will be assigned the new pattern. For example, the following would
2688    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2689    
2690        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2691    
2692    The list is ordered, so the following would use 0777 for C<tmp1> and
2693    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2694    
2695        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2696                                                       '^tmp' => 0666);
2697    
2698    Note that the pattern matches are all case-insensitive, and only directory
2699    names are matched, not file names.
2700    
2701  =back  =back
2702    
2703  =cut  =cut
2704    
2705  sub LogErrors {  sub SetPermissions {
2706      # Get the file name.      # Get the parameters.
2707      my ($fileName) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2708      # Open the file as the standard error output.      # Set up for error recovery.
2709      open STDERR, '>', $fileName;      eval {
2710            # Switch to the specified directory.
2711            ChDir($dirName);
2712            # Get the group ID.
2713            my $gid = getgrnam($group);
2714            # Get the mask for tracing.
2715            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2716            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2717            my $fixCount = 0;
2718            my $lookCount = 0;
2719            # @dirs will be a stack of directories to be processed.
2720            my @dirs = (getcwd());
2721            while (scalar(@dirs) > 0) {
2722                # Get the current directory.
2723                my $dir = pop @dirs;
2724                # Check for a match to one of the specified directory names. To do
2725                # that, we need to pull the individual part of the name off of the
2726                # whole path.
2727                my $simpleName = $dir;
2728                if ($dir =~ m!/([^/]+)$!) {
2729                    $simpleName = $1;
2730                }
2731                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2732                # Search for a match.
2733                my $match = 0;
2734                my $i;
2735                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2736                    my $pattern = $otherMasks[$i];
2737                    if ($simpleName =~ /$pattern/i) {
2738                        $match = 1;
2739                    }
2740                }
2741                # Find out if we have a match. Note we use $i-1 because the loop added 2
2742                # before terminating due to the match.
2743                if ($match && $otherMasks[$i-1] != $mask) {
2744                    # This directory matches one of the incoming patterns, and it's
2745                    # a different mask, so we process it recursively with that mask.
2746                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2747                } else {
2748                    # Here we can process normally. Get all of the non-hidden members.
2749                    my @submems = OpenDir($dir, 1);
2750                    for my $submem (@submems) {
2751                        # Get the full name.
2752                        my $thisMem = "$dir/$submem";
2753                        Trace("Checking member $thisMem.") if T(4);
2754                        $lookCount++;
2755                        if ($lookCount % 1000 == 0) {
2756                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2757                        }
2758                        # Fix the group.
2759                        chown -1, $gid, $thisMem;
2760                        # Insure this member is not a symlink.
2761                        if (! -l $thisMem) {
2762                            # Get its info.
2763                            my $fileInfo = stat $thisMem;
2764                            # Only proceed if we got the info. Otherwise, it's a hard link
2765                            # and we want to skip it anyway.
2766                            if ($fileInfo) {
2767                                my $fileMode = $fileInfo->mode;
2768                                if (($fileMode & $mask) != $mask) {
2769                                    # Fix this member.
2770                                    $fileMode |= $mask;
2771                                    chmod $fileMode, $thisMem;
2772                                    $fixCount++;
2773                                }
2774                                # If it's a subdirectory, stack it.
2775                                if (-d $thisMem) {
2776                                    push @dirs, $thisMem;
2777                                }
2778                            }
2779                        }
2780                    }
2781                }
2782            }
2783            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2784        };
2785        # Check for an error.
2786        if ($@) {
2787            Confess("SetPermissions error: $@");
2788        }
2789  }  }
2790    
2791  =head3 ReadOptions  =head3 GetLine
   
 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  
2792    
2793  I<optionName>C<=>I<optionValue>C<; >I<comment>      my @data = Tracer::GetLine($handle);
2794    
2795  The option name must consist entirely of letters, digits, and the punctuation characters  Read a line of data from a tab-delimited file.
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
2796    
2797  =over 4  =over 4
2798    
2799  =item fileName  =item handle
2800    
2801  Name of the file containing the option data.  Open file handle from which to read.
2802    
2803  =item RETURN  =item RETURN
2804    
2805  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a list of the fields in the record read. The fields are presumed to be
2806  value.  tab-delimited. If we are at the end of the file, then an empty list will be
2807    returned. If an empty line is read, a single list item consisting of a null
2808    string will be returned.
2809    
2810  =back  =back
2811    
2812  =cut  =cut
2813    
2814  sub ReadOptions {  sub GetLine {
2815      # Get the parameters.      # Get the parameters.
2816      my ($fileName) = @_;      my ($handle) = @_;
2817      # Open the file.      # Declare the return variable.
2818      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my @retVal = ();
2819      # Count the number of records read.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2820      my ($records, $comments) = 0;      # Read from the file.
2821      # Create the return hash.      my $line = <$handle>;
2822      my %retVal = ();      # Only proceed if we found something.
2823      # Loop through the file, accumulating key-value pairs.      if (defined $line) {
2824      while (my $line = <CONFIGFILE>) {          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2825          # Denote we've read a line.          # upload control and have a nonstandard EOL combination.
2826          $records++;          $line =~ s/(\r|\n)+$//;
2827          # Determine the line type.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2828          if ($line =~ /^\s*[\n\r]/) {          if (T(File => 4)) {
2829              # A blank line is a comment.              my $escapedLine = $line;
2830              $comments++;              $escapedLine =~ s/\n/\\n/g;
2831          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {              $escapedLine =~ s/\r/\\r/g;
2832              # Here we have an option assignment.              $escapedLine =~ s/\t/\\t/g;
2833              retVal{$1} = $2;              Trace("Line read: -->$escapedLine<--");
2834          } elsif ($line =~ /^\s*;/) {          }
2835              # Here we have a text comment.          # If the line is empty, return a single empty string; otherwise, parse
2836              $comments++;          # it into fields.
2837            if ($line eq "") {
2838                push @retVal, "";
2839          } else {          } else {
2840              # Here we have an invalid line.              push @retVal, split /\t/,$line;
             Trace("Invalid option statement in record $records.") if T(0);  
2841          }          }
2842        } else {
2843            # Trace the reason the read failed.
2844            Trace("End of file: $!") if T(File => 3);
2845      }      }
2846      # Return the hash created.      # Return the result.
2847      return %retVal;      return @retVal;
2848  }  }
2849    
2850  =head3 GetOptions  =head3 PutLine
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
2851    
2852  C<< {databaseType => 'Oracle'} >>      Tracer::PutLine($handle, \@fields, $eol);
2853    
2854  an error will occur because the B<databaseType> option does not exist.  Write a line of data to a tab-delimited file. The specified field values will be
2855    output in tab-separated form, with a trailing new-line.
2856    
2857  =over 4  =over 4
2858    
2859  =item defaults  =item handle
2860    
2861  Table of default option values.  Output file handle.
2862    
2863  =item options  =item fields
2864    
2865  Table of overrides, if any.  List of field values.
2866    
2867  =item RETURN  =item eol (optional)
2868    
2869  Returns a reference to the default table passed in as the first parameter.  End-of-line character (default is "\n").
2870    
2871  =back  =back
2872    
2873  =cut  =cut
2874    
2875  sub GetOptions {  sub PutLine {
2876      # Get the parameters.      # Get the parameters.
2877      my ($defaults, $options) = @_;      my ($handle, $fields, $eol) = @_;
2878      # Check for overrides.      # Write the data.
2879      if ($options) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         # Loop through the overrides.  
         while (my ($option, $setting) = each %{$options}) {  
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
2880  }  }
2881    
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
2882    
2883  Merge default values into a hash table. This method looks at the key-value pairs in the  =head3 PrintLine
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
2884    
2885  =over 4      Tracer::PrintLine($line);
2886    
2887  =item table  Print a line of text with a trailing new-line.
2888    
2889  Hash table to be updated with the default values.  =over 4
2890    
2891  =item defaults  =item line
2892    
2893  Default values to be merged into the first hash table if they are not already present.  Line of text to print.
2894    
2895  =back  =back
2896    
2897  =cut  =cut
2898    
2899  sub MergeOptions {  sub PrintLine {
2900      # Get the parameters.      # Get the parameters.
2901      my ($table, $defaults) = @_;      my ($line) = @_;
2902      # Loop through the defaults.      # Print the line.
2903      while (my ($key, $value) = each %{$defaults}) {      print "$line\n";
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
2904      }      }
2905    
2906    
2907    =head2 Other Useful Methods
2908    
2909    =head3 IDHASH
2910    
2911        my $hash = SHTargetSearch::IDHASH(@keys);
2912    
2913    This is a dinky little method that converts a list of values to a reference
2914    to hash of values to labels. The values and labels are the same.
2915    
2916    =cut
2917    
2918    sub IDHASH {
2919        my %retVal = map { $_ => $_ } @_;
2920        return \%retVal;
2921  }  }
2922    
2923  =head3 Trace  =head3 Pluralize
2924    
2925  C<< Trace($message); >>      my $plural = Tracer::Pluralize($word);
2926    
2927  Write a trace message to the target location specified in L</TSetup>. If there has not been  This is a very simple pluralization utility. It adds an C<s> at the end
2928  any prior call to B<TSetup>.  of the input word unless it already ends in an C<s>, in which case it
2929    adds C<es>.
2930    
2931  =over 4  =over 4
2932    
2933  =item message  =item word
2934    
2935  Message to write.  Singular word to pluralize.
2936    
2937    =item RETURN
2938    
2939    Returns the probable plural form of the word.
2940    
2941  =back  =back
2942    
2943  =cut  =cut
2944    
2945  sub Trace {  sub Pluralize {
2946      # Get the parameters.      # Get the parameters.
2947      my ($message) = @_;      my ($word) = @_;
2948      # Get the timestamp.      # Declare the return variable.
2949      my $timeStamp = Now();      my $retVal;
2950      # Format the message. Note we strip off any line terminators at the end.      if ($word =~ /s$/) {
2951      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);          $retVal = $word . 'es';
2952      # Process according to the destination.      } else {
2953      if ($Destination eq "TEXT") {          $retVal = $word . 's';
         # Write the message to the standard output.  
         print "$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";  
         }  
2954      }      }
2955        # Return the result.
2956        return $retVal;
2957  }  }
2958    
2959  =head3 T  =head3 Numeric
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
2960    
2961  C<< my $switch = T($traceLevel); >>      my $okFlag = Tracer::Numeric($string);
2962    
2963  Return TRUE if the trace level is at or above a specified value and the specified category  Return the value of the specified string if it is numeric, or an undefined value
2964  is active, else FALSE. If no category is specified, the caller's package name is used.  if it is not numeric.
2965    
2966  =over 4  =over 4
2967    
2968  =item category  =item string
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2969    
2970  Relevant tracing level.  String to check.
2971    
2972  =item RETURN  =item RETURN
2973    
2974  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the numeric value of the string if successful, or C<undef> if the string
2975    is not numeric.
2976    
2977  =back  =back
2978    
2979  =cut  =cut
2980    
2981  sub T {  sub Numeric {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2982          # Get the parameters.          # Get the parameters.
2983          my ($category, $traceLevel) = @_;      my ($string) = @_;
2984          if (!defined $traceLevel) {      # We'll put the value in here if we succeed.
2985              # Here we have no category, so we need to get the calling package.      my $retVal;
2986              # The calling package is normally the first parameter. If it is      # Get a working copy of the string.
2987              # omitted, the first parameter will be the tracelevel. So, the      my $copy = $string;
2988              # first thing we do is shift the so-called category into the      # Trim leading and trailing spaces.
2989              # $traceLevel variable where it belongs.      $copy =~ s/^\s+//;
2990              $traceLevel = $category;      $copy =~ s/\s+$//;
2991              my ($package, $fileName, $line) = caller;      # Check the result.
2992              # If there is no calling package, we default to "main".      if ($copy =~ /^[+-]?\d+$/) {
2993              if (!$package) {          $retVal = $copy;
2994                  $category = "main";      } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2995              } else {          $retVal = $copy;
2996                  $category = $package;      } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2997              }          $retVal = $copy;
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2998      }      }
2999      # Return the computed result.      # Return the result.
3000      return $retVal;      return $retVal;
3001  }  }
3002    
 =head3 ParseCommand  
3003    
3004  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  =head3 ParseParm
3005    
3006  Parse a command line consisting of a list of parameters. The initial parameters may be option      my $listValue = Tracer::ParseParm($string);
 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.  
3007    
3008  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Convert a parameter into a list reference. If the parameter is undefined,
3009    an undefined value will be returned. Otherwise, it will be parsed as a
3010    comma-separated list of values.
3011    
3012  In this case, the list @words will be treated as a command line. There are two options available,  =over 4
 B<errors> and B<logFile>. If @words has the following format  
3013    
3014  C<< -logFile=error.log apple orange rutabaga >>  =item string
3015    
3016  then at the end of the invocation, C<$options> will be  Incoming string.
3017    
3018  C<< { errors => 0, logFile => 'error.log' } >>  =item RETURN
3019    
3020  and C<@arguments> will contain  Returns a reference to a list of values, or C<undef> if the incoming value
3021    was undefined.
3022    
3023  C<< apple orange rutabaga >>  =back
3024    
3025  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =cut
 support for quote characters.  
3026    
3027  =over 4  sub ParseParm {
3028        # Get the parameters.
3029        my ($string) = @_;
3030        # Declare the return variable.
3031        my $retVal;
3032        # Check for data.
3033        if (defined $string) {
3034            # We have some, so split it into a list.
3035            $retVal = [ split /\s*,\s*/, $string];
3036        }
3037        # Return the result.
3038        return $retVal;
3039    }
3040    
3041  =item optionTable  =head3 Now
3042    
3043  Table of default options.      my $string = Tracer::Now();
3044    
3045  =item inputList  Return a displayable time stamp containing the local time. Whatever format this
3046    method produces must be parseable by L</ParseDate>.
3047    
3048  List of words on the command line.  =cut
3049    
3050    sub Now {
3051        return DisplayTime(time);
3052    }
3053    
3054    =head3 DisplayTime
3055    
3056        my $string = Tracer::DisplayTime($time);
3057    
3058    Convert a time value to a displayable time stamp. Whatever format this
3059    method produces must be parseable by L</ParseDate>.
3060    
3061    =over 4
3062    
3063    =item time
3064    
3065    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3066    
3067  =item RETURN  =item RETURN
3068    
3069  Returns a reference to the option table and a list of the positional arguments.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3070    
3071  =back  =back
3072    
3073  =cut  =cut
3074    
3075  sub ParseCommand {  sub DisplayTime {
3076      # Get the parameters.      my ($time) = @_;
3077      my ($optionTable, @inputList) = @_;      my $retVal = "(n/a)";
3078      # Process any options in the input list.      if (defined $time) {
3079      my %overrides = ();          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3080      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3081          # Get the current option.                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         my $arg = shift @inputList;  
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
         } else {  
             # Here there is no value, so we use 1.  
             $overrides{$name} = 1;  
         }  
3082      }      }
3083      # Merge the options into the defaults.      return $retVal;
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
3084      }      }
3085      # Return the results.  
3086      return ($optionTable, @retVal);  # Pad a number to 2 digits.
3087    sub _p2 {
3088        my ($value) = @_;
3089        $value = "0$value" if ($value < 10);
3090        return $value;
3091  }  }
3092    
3093  =head3 Escape  =head3 Escape
3094    
3095  C<< my $codedString = Tracer::Escape($realString); >>      my $codedString = Tracer::Escape($realString);
3096    
3097  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3098  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3099  result is to reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
3100    
# Line 1156  Line 3147 
3147    
3148  =head3 UnEscape  =head3 UnEscape
3149    
3150  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
3151    
3152  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3153  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
# Line 1209  Line 3200 
3200                  $codedString = "";                  $codedString = "";
3201              }              }
3202          }          }
3203      }      }
3204      # Return the result.      # Return the result.
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
   
 C<< my $fileContents = Tracer::GetFile($fileName); >>  
   
 Return the entire contents of a file. In list context, line-ends are removed and  
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $ok = open INPUTFILE, "<$fileName";  
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
         # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
         while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
             push @retVal, $line;  
         }  
         # Close it.  
         close INPUTFILE;  
         my $actualLines = @retVal;  
     }  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
     }  
 }  
   
 =head3 QTrace  
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
3205      return $retVal;      return $retVal;
3206  }  }
3207    
3208  =head3 Confess  =head3 Percent
3209    
3210  C<< Confess($message); >>      my $percent = Tracer::Percent($number, $base);
3211    
3212  Trace the call stack and abort the program with the specified message. When used with  Returns the percent of the base represented by the given number. If the base
3213  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  is zero, returns zero.
 So, for example  
3214    
3215  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
3216    
3217  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item number
3218    
3219  =over 4  Percent numerator.
3220    
3221  =item message  =item base
3222    
3223  Message to include in the trace.  Percent base.
3224    
3225    =item RETURN
3226    
3227    Returns the percentage of the base represented by the numerator.
3228    
3229  =back  =back
3230    
3231  =cut  =cut
3232    
3233  sub Confess {  sub Percent {
3234      # Get the parameters.      # Get the parameters.
3235      my ($message) = @_;      my ($number, $base) = @_;
3236      # Trace the call stack.      # Declare the return variable.
3237      Cluck($message);      my $retVal = 0;
3238      # Abort the program.      # Compute the percent.
3239      croak(">>> $message");      if ($base != 0) {
3240            $retVal = $number * 100 / $base;
3241        }
3242        # Return the result.
3243        return $retVal;
3244  }  }
3245    
3246  =head3 Assert  =head3 In
   
 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  
3247    
3248  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $flag = Tracer::In($value, $min, $max);
3249    
3250  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Return TRUE if the value is between the minimum and the maximum, else FALSE.
3251    
3252  =cut  =cut
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
3253    
3254  =head3 Cluck  sub In {
3255        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3256    }
3257    
 C<< Cluck($message); >>  
3258    
3259  Trace the call stack. Note that for best results, you should qualify the call with a  =head3 Constrain
 trace condition. For example,  
3260    
3261  C<< Cluck("Starting record parse.") if T(3); >>      my $constrained = Constrain($value, $min, $max);
3262    
3263  will only trace the stack if the trace level for the package is 3 or more.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3264    
3265  =over 4  =over 4
3266    
3267  =item message  =item value
3268    
3269  Message to include in the trace.  Value to constrain.
3270    
3271    =item min (optional)
3272    
3273    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3274    
3275    =item max (optional)
3276    
3277    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3278    
3279    =item RETURN
3280    
3281    Returns the incoming value, constrained according to the other parameters.
3282    
3283  =back  =back
3284    
3285  =cut  =cut
3286    
3287  sub Cluck {  sub Constrain {
3288      # Get the parameters.      # Get the parameters.
3289      my ($message) = @_;      my ($value, $min, $max) = @_;
3290      # Trace what's happening.      # Declare the return variable.
3291      Trace("Stack trace for event: $message");      my $retVal = $value;
3292      my $confession = longmess($message);      # Apply the minimum constraint.
3293      # Convert the confession to a series of trace messages. Note we skip any      if (defined $min && $retVal < $min) {
3294      # messages relating to calls into Tracer.          $retVal = $min;
3295      for my $line (split /\s*\n/, $confession) {      }
3296          Trace($line) if ($line !~ /Tracer\.pm/);      # Apply the maximum constraint.
3297        if (defined $max && $retVal > $max) {
3298            $retVal = $max;
3299      }      }
3300        # Return the result.
3301        return $retVal;
3302  }  }
3303    
3304  =head3 Min  =head3 Min
3305    
3306  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
3307    
3308  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
3309    
# Line 1532  Line 3336 
3336    
3337  =head3 Max  =head3 Max
3338    
3339  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
3340    
3341  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
3342    
# Line 1563  Line 3367 
3367      return $retVal;      return $retVal;
3368  }  }
3369    
3370  =head3 AddToListMap  =head3 Strip
3371    
3372  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      my $string = Tracer::Strip($line);
3373    
3374  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Strip all line terminators off a string. This is necessary when dealing with files
3375  is created for the key. Otherwise, the new value is pushed onto the list.  that may have been transferred back and forth several times among different
3376    operating environments.
3377    
3378  =over 4  =over 4
3379    
3380  =item hash  =item line
3381    
3382    Line of text to be stripped.
3383    
3384  Reference to the target hash.  =item RETURN
3385    
3386  =item key  The same line of text with all the line-ending characters chopped from the end.
3387    
3388  Key for which the value is to be added.  =back
3389    
3390  =item value  =cut
3391    
3392    sub Strip {
3393        # Get a copy of the parameter string.
3394        my ($string) = @_;
3395        my $retVal = (defined $string ? $string : "");
3396        # Strip the line terminator characters.
3397        $retVal =~ s/(\r|\n)+$//g;
3398        # Return the result.
3399        return $retVal;
3400    }
3401    
3402    =head3 Trim
3403    
3404        my $string = Tracer::Trim($line);
3405    
3406    Trim all spaces from the beginning and ending of a string.
3407    
3408    =over 4
3409    
3410    =item line
3411    
3412    Line of text to be trimmed.
3413    
3414    =item RETURN
3415    
3416    The same line of text with all whitespace chopped off either end.
3417    
3418    =back
3419    
3420    =cut
3421    
3422    sub Trim {
3423        # Get a copy of the parameter string.
3424        my ($string) = @_;
3425        my $retVal = (defined $string ? $string : "");
3426        # Strip the front spaces.
3427        $retVal =~ s/^\s+//;
3428        # Strip the back spaces.
3429        $retVal =~ s/\s+$//;
3430        # Return the result.
3431        return $retVal;
3432    }
3433    
3434    =head3 Pad
3435    
3436        my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3437    
3438    Pad a string to a specified length. The pad character will be a
3439    space, and the padding will be on the right side unless specified
3440    in the third parameter.
3441    
3442    =over 4
3443    
3444    =item string
3445    
3446    String to be padded.
3447    
3448    =item len
3449    
3450  Value to add to the key's value list.  Desired length of the padded string.
3451    
3452    =item left (optional)
3453    
3454    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3455    
3456    =item padChar (optional)
3457    
3458    Character to use for padding. The default is a space.
3459    
3460    =item RETURN
3461    
3462    Returns a copy of the original string with the pad character added to the
3463    specified end so that it achieves the desired length.
3464    
3465  =back  =back
3466    
3467  =cut  =cut
3468    
3469  sub AddToListMap {  sub Pad {
3470      # Get the parameters.      # Get the parameters.
3471      my ($hash, $key, $value) = @_;      my ($string, $len, $left, $padChar) = @_;
3472      # Process according to whether or not the key already has a value.      # Compute the padding character.
3473      if (! exists $hash->{$key}) {      if (! defined $padChar) {
3474          $hash->{$key} = [$value];          $padChar = " ";
3475        }
3476        # Compute the number of spaces needed.
3477        my $needed = $len - length $string;
3478        # Copy the string into the return variable.
3479        my $retVal = $string;
3480        # Only proceed if padding is needed.
3481        if ($needed > 0) {
3482            # Create the pad string.
3483            my $pad = $padChar x $needed;
3484            # Affix it to the return value.
3485            if ($left) {
3486                $retVal = $pad . $retVal;
3487      } else {      } else {
3488          push @{$hash->{$key}}, $value;              $retVal .= $pad;
3489      }      }
3490  }  }
3491        # Return the result.
3492        return $retVal;
3493    }
3494    
3495    =head3 Quoted
3496    
3497        my $string = Tracer::Quoted($var);
3498    
3499    Convert the specified value to a string and enclose it in single quotes.
3500    If it's undefined, the string C<undef> in angle brackets will be used
3501    instead.
3502    
3503    =over 4
3504    
3505  =head3 DebugMode  =item var
3506    
3507  C<< if (Tracer::DebugMode) { ...code... } >>  Value to quote.
3508    
3509  Return TRUE if debug mode has been turned on, else output an error  =item RETURN
3510  page and return FALSE.  
3511    Returns a string enclosed in quotes, or an indication the value is undefined.
3512    
3513  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.  
3514    
3515  =cut  =cut
3516    
3517  sub DebugMode {  sub Quoted {
3518        # Get the parameters.
3519        my ($var) = @_;
3520      # Declare the return variable.      # Declare the return variable.
3521      my $retVal = 0;      my $retVal;
3522      # Check the debug configuration.      # Are we undefined?
3523      my $password = CGI::cookie("DebugMode");      if (! defined $var) {
3524      my $encrypted = Digest::MD5::md5_hex($password);          $retVal = "<undef>";
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
3525      } else {      } else {
3526          # Here debug mode is off, so we generate an error page.          # No, so convert to a string and enclose in quotes.
3527          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          $retVal = $var;
3528          print $pageString;          $retVal =~ s/'/\\'/;
3529            $retVal = "'$retVal'";
3530      }      }
3531      # Return the determination indicator.      # Return the result.
3532      return $retVal;      return $retVal;
3533  }  }
3534    
3535  =head3 Strip  =head3 EOF
3536    
3537  C<< my $string = Tracer::Strip($line); >>  This is a constant that is lexically greater than any useful string.
3538    
3539  Strip all line terminators off a string. This is necessary when dealing with files  =cut
3540  that may have been transferred back and forth several times among different  
3541  operating environments.  sub EOF {
3542        return "\xFF\xFF\xFF\xFF\xFF";
3543    }
3544    
3545    =head3 TICK
3546    
3547        my @results = TICK($commandString);
3548    
3549    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3550    dot-slash (C<./> will be removed. So, for example, if you were doing
3551    
3552        `./protein.cgi`
3553    
3554    from inside a CGI script, it would work fine in Unix, but would issue an error message
3555    in Windows complaining that C<'.'> is not a valid command. If instead you code
3556    
3557        TICK("./protein.cgi")
3558    
3559    it will work correctly in both environments.
3560    
3561  =over 4  =over 4
3562    
3563  =item line  =item commandString
3564    
3565  Line of text to be stripped.  The command string to pass to the system.
3566    
3567  =item RETURN  =item RETURN
3568    
3569  The same line of text with all the line-ending characters chopped from the end.  Returns the standard output from the specified command, as a list.
3570    
3571  =back  =back
3572    
3573  =cut  =cut
3574    #: Return Type @;
3575    sub TICK {
3576        # Get the parameters.
3577        my ($commandString) = @_;
3578        # Chop off the dot-slash if this is Windows.
3579        if ($FIG_Config::win_mode) {
3580            $commandString =~ s!^\./!!;
3581        }
3582        # Activate the command and return the result.
3583        return `$commandString`;
3584    }
3585    
3586  sub Strip {  
3587      # Get a copy of the parameter string.  =head3 CommaFormat
3588      my ($string) = @_;  
3589      my $retVal = (defined $string ? $string : "");      my $formatted = Tracer::CommaFormat($number);
3590      # Strip the line terminator characters.  
3591      $retVal =~ s/(\r|\n)+$//g;  Insert commas into a number.
3592    
3593    =over 4
3594    
3595    =item number
3596    
3597    A sequence of digits.
3598    
3599    =item RETURN
3600    
3601    Returns the same digits with commas strategically inserted.
3602    
3603    =back
3604    
3605    =cut
3606    
3607    sub CommaFormat {
3608        # Get the parameters.
3609        my ($number) = @_;
3610        # Pad the length up to a multiple of three.
3611        my $padded = "$number";
3612        $padded = " " . $padded while length($padded) % 3 != 0;
3613        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3614        # cause the delimiters to be included in the output stream. The
3615        # GREP removes the empty strings in between the delimiters.
3616        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3617        # Clean out the spaces.
3618        $retVal =~ s/ //g;
3619      # Return the result.      # Return the result.
3620      return $retVal;      return $retVal;
3621  }  }
3622    
 =head3 Pad  
3623    
3624  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  =head3 GetMemorySize
3625    
3626        my $string = Tracer::GetMemorySize();
3627    
3628    Return a memory size string for the current process. The string will be
3629    in comma format, with a size indicator (K, M, G) at the end.
3630    
3631    =cut
3632    
3633    sub GetMemorySize {
3634        # Get the memory size from Unix.
3635        my ($retVal) = `ps h -o vsz $$`;
3636        # Remove the ending new-line.
3637        chomp $retVal;
3638        # Format and return the result.
3639        return CommaFormat($retVal) . "K";
3640    }
3641    
3642    =head3 CompareLists
3643    
3644        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3645    
3646    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3647    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3648    The return value contains a list of items that are only in the new list
3649    (inserted) and only in the old list (deleted).
3650    
3651    =over 4
3652    
3653    =item newList
3654    
3655    Reference to a list of new tuples.
3656    
3657    =item oldList
3658    
3659    Reference to a list of old tuples.
3660    
3661    =item keyIndex (optional)
3662    
3663    Index into each tuple of its key field. The default is 0.
3664    
3665    =item RETURN
3666    
3667    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3668    list (inserted) followed by a reference to the list of items that are only in the old
3669    list (deleted).
3670    
3671    =back
3672    
3673  Pad a string to a specified length. The pad character will be a  =cut
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
3674    
3675  =over 4  sub CompareLists {
3676        # Get the parameters.
3677        my ($newList, $oldList, $keyIndex) = @_;
3678        if (! defined $keyIndex) {
3679            $keyIndex = 0;
3680        }
3681        # Declare the return variables.
3682        my ($inserted, $deleted) = ([], []);
3683        # Loop through the two lists simultaneously.
3684        my ($newI, $oldI) = (0, 0);
3685        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3686        while ($newI < $newN || $oldI < $oldN) {
3687            # Get the current object in each list. Note that if one
3688            # of the lists is past the end, we'll get undef.
3689            my $newItem = $newList->[$newI];
3690            my $oldItem = $oldList->[$oldI];
3691            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3692                # The old item is not in the new list, so mark it deleted.
3693                push @{$deleted}, $oldItem;
3694                $oldI++;
3695            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3696                # The new item is not in the old list, so mark it inserted.
3697                push @{$inserted}, $newItem;
3698                $newI++;
3699            } else {
3700                # The item is in both lists, so push forward.
3701                $oldI++;
3702                $newI++;
3703            }
3704        }
3705        # Return the result.
3706        return ($inserted, $deleted);
3707    }
3708    
3709  =item string  =head3 Cmp
3710    
3711  String to be padded.      my $cmp = Tracer::Cmp($a, $b);
3712    
3713  =item len  This method performs a universal sort comparison. Each value coming in is
3714    separated into a text parts and number parts. The text
3715    part is string compared, and if both parts are equal, then the number
3716    parts are compared numerically. A stream of just numbers or a stream of
3717    just strings will sort correctly, and a mixed stream will sort with the
3718    numbers first. Strings with a label and a number will sort in the
3719    expected manner instead of lexically. Undefined values sort last.
3720    
3721  Desired length of the padded string.  =over 4
3722    
3723  =item left (optional)  =item a
3724    
3725  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  First item to compare.
3726    
3727  =item padChar (optional)  =item b
3728    
3729  Character to use for padding. The default is a space.  Second item to compare.
3730    
3731  =item RETURN  =item RETURN
3732    
3733  Returns a copy of the original string with the pad character added to the  Returns a negative number if the first item should sort first (is less), a positive
3734  specified end so that it achieves the desired length.  number if the first item should sort second (is greater), and a zero if the items are
3735    equal.
3736    
3737  =back  =back
3738    
3739  =cut  =cut
3740    
3741  sub Pad {  sub Cmp {
3742      # Get the parameters.      # Get the parameters.
3743      my ($string, $len, $left, $padChar) = @_;      my ($a, $b) = @_;
3744      # Compute the padding character.      # Declare the return value.
3745      if (! defined $padChar) {      my $retVal;
3746          $padChar = " ";      # Check for nulls.
3747      }      if (! defined($a)) {
3748      # Compute the number of spaces needed.          $retVal = (! defined($b) ? 0 : -1);
3749      my $needed = $len - length $string;      } elsif (! defined($b)) {
3750      # Copy the string into the return variable.          $retVal = 1;
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
3751          } else {          } else {
3752              $retVal .= $pad;          # Here we have two real values. Parse the two strings.
3753            my @aParsed = _Parse($a);
3754            my @bParsed = _Parse($b);
3755            # Loop through the first string.
3756            while (! $retVal && @aParsed) {
3757                # Extract the string parts.
3758                my $aPiece = shift(@aParsed);
3759                my $bPiece = shift(@bParsed) || '';
3760                # Extract the number parts.
3761                my $aNum = shift(@aParsed);
3762                my $bNum = shift(@bParsed) || 0;
3763                # Compare the string parts insensitively.
3764                $retVal = (lc($aPiece) cmp lc($bPiece));
3765                # If they're equal, compare them sensitively.
3766                if (! $retVal) {
3767                    $retVal = ($aPiece cmp $bPiece);
3768                    # If they're STILL equal, compare the number parts.
3769                    if (! $retVal) {
3770                        $retVal = $aNum <=> $bNum;
3771                    }
3772                }
3773          }          }
3774      }      }